From 9cf47fb1c8d1d50b602edc61088f61c915f0fefb Mon Sep 17 00:00:00 2001 From: Dan Haraj Date: Tue, 10 Oct 2017 14:41:54 -0400 Subject: [PATCH 001/247] singularity-tools: Only copy into /bin what is specified in contents --- pkgs/build-support/singularity-tools/default.nix | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/pkgs/build-support/singularity-tools/default.nix b/pkgs/build-support/singularity-tools/default.nix index 3c27b9fc1ad9..859e1461c7c7 100644 --- a/pkgs/build-support/singularity-tools/default.nix +++ b/pkgs/build-support/singularity-tools/default.nix @@ -74,7 +74,10 @@ rec { mkdir -p bin nix/store for f in $(cat $layerClosure) ; do cp -ar $f ./$f - for f in $f/bin/* ; do + done + + for c in ${toString contents} ; do + for f in $c/bin/* ; do if [ ! -e bin/$(basename $f) ] ; then ln -s $f bin/ fi From 215c91d79e821834158ed4d69b72c1b39a671fd9 Mon Sep 17 00:00:00 2001 From: Erik Arvstedt Date: Tue, 2 Oct 2018 17:38:06 +0200 Subject: [PATCH 002/247] nixos/initrd: improve descriptions The improved lspci command shows all available ethernet controllers and their kernel modules. Previously, the user had to provide the slot name of a specific device. --- nixos/modules/system/boot/initrd-network.nix | 3 ++- nixos/modules/system/boot/initrd-ssh.nix | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/nixos/modules/system/boot/initrd-network.nix b/nixos/modules/system/boot/initrd-network.nix index 384ae909b701..1bc3f906add4 100644 --- a/nixos/modules/system/boot/initrd-network.nix +++ b/nixos/modules/system/boot/initrd-network.nix @@ -45,7 +45,8 @@ in is acquired using DHCP. You should add the module(s) required for your network card to - boot.initrd.availableKernelModules. lspci -v -s <ethernet controller> + boot.initrd.availableKernelModules. + lspci -v | grep -iA8 'network\|ethernet' will tell you which. ''; }; diff --git a/nixos/modules/system/boot/initrd-ssh.nix b/nixos/modules/system/boot/initrd-ssh.nix index 53e993603e27..2d3e3b05c980 100644 --- a/nixos/modules/system/boot/initrd-ssh.nix +++ b/nixos/modules/system/boot/initrd-ssh.nix @@ -82,6 +82,7 @@ in default = config.users.users.root.openssh.authorizedKeys.keys; description = '' Authorized keys for the root user on initrd. + Note that Dropbear doesn't support OpenSSH's Ed25519 key type. ''; }; From 4ec643b1258537f729af1d9c4f7ef97b69dc2ec7 Mon Sep 17 00:00:00 2001 From: Patrick Hilhorst Date: Sun, 2 Dec 2018 23:42:27 +0100 Subject: [PATCH 003/247] konsole: fix arrow keys (partially?) fixes #29951 --- pkgs/applications/kde/konsole.nix | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/pkgs/applications/kde/konsole.nix b/pkgs/applications/kde/konsole.nix index 2847e312d00a..004fc1c37ae2 100644 --- a/pkgs/applications/kde/konsole.nix +++ b/pkgs/applications/kde/konsole.nix @@ -1,5 +1,5 @@ { - mkDerivation, lib, + mkDerivation, lib, makeWrapper, extra-cmake-modules, kdoctools, kbookmarks, kcompletion, kconfig, kconfigwidgets, kcoreaddons, kguiaddons, ki18n, kiconthemes, kinit, kdelibs4support, kio, knotifications, @@ -18,6 +18,12 @@ mkDerivation { kbookmarks kcompletion kconfig kconfigwidgets kcoreaddons kdelibs4support kguiaddons ki18n kiconthemes kinit kio knotifications knotifyconfig kparts kpty kservice ktextwidgets kwidgetsaddons kwindowsystem kxmlgui qtscript knewstuff + makeWrapper ]; + + postInstall = '' + wrapProgram $out/bin/konsole --prefix XDG_DATA_DIRS ":" $out/share + ''; + propagatedUserEnvPkgs = [ (lib.getBin kinit) ]; } From 691932bba67591a23aa4ad1e844a4cbf4d16eff5 Mon Sep 17 00:00:00 2001 From: Jean-Philippe Braun Date: Wed, 5 Dec 2018 14:56:23 +0100 Subject: [PATCH 004/247] cassandra: add option to configure logging As cassandra start script hardcodes the location of logback configuration to `CASSANDRA_CONF_DIR/logback.xml` there is no way to pass an alternate file via `$JVM_OPTS` for example. Also, without logback configuration DEBUG level is used which is not necessary for standard usage. With this commit a default logback configuration is set with log level INFO. Configuration borrowed from: https://docs.datastax.com/en/cassandra/3.0/cassandra/configuration/configLoggingLevels.html --- .../modules/services/databases/cassandra.nix | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/nixos/modules/services/databases/cassandra.nix b/nixos/modules/services/databases/cassandra.nix index 86e74d5d5ab4..d741ee48c48f 100644 --- a/nixos/modules/services/databases/cassandra.nix +++ b/nixos/modules/services/databases/cassandra.nix @@ -34,11 +34,13 @@ let { name = "cassandra-etc"; cassandraYaml = builtins.toJSON cassandraConfigWithAddresses; cassandraEnvPkg = "${cfg.package}/conf/cassandra-env.sh"; + cassandraLogbackConfig = pkgs.writeText "logback.xml" cfg.logbackConfig; buildCommand = '' mkdir -p "$out" echo "$cassandraYaml" > "$out/cassandra.yaml" ln -s "$cassandraEnvPkg" "$out/cassandra-env.sh" + ln -s "$cassandraLogbackConfig" "$out/logback.xml" ''; }; in { @@ -139,7 +141,27 @@ in { correspond to a single address, IP aliasing is not supported. ''; }; + logbackConfig = mkOption { + type = types.lines; + default = '' + + + + %-5level %date{HH:mm:ss,SSS} %msg%n + + + + + + + + + ''; + description = '' + XML logback configuration for cassandra + ''; + }; extraConfig = mkOption { type = types.attrs; default = {}; From ad0d03283bc3ed23bf4cf7421bf746a4358fc7c0 Mon Sep 17 00:00:00 2001 From: Jim Fowler Date: Fri, 14 Dec 2018 11:04:17 -0500 Subject: [PATCH 005/247] hashcash from http://hashcash.org --- pkgs/tools/security/hashcash/default.nix | 29 ++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 pkgs/tools/security/hashcash/default.nix diff --git a/pkgs/tools/security/hashcash/default.nix b/pkgs/tools/security/hashcash/default.nix new file mode 100644 index 000000000000..5c63845a584a --- /dev/null +++ b/pkgs/tools/security/hashcash/default.nix @@ -0,0 +1,29 @@ +{ stdenv, fetchurl, openssl }: + +stdenv.mkDerivation rec { + name = "hashcash-${version}"; + version = "1.22"; + + buildInputs = [ openssl ]; + + src = fetchurl { + url = "http://www.hashcash.org/source/hashcash-1.22.tgz"; + sha256 = "15kqaimwb2y8wvzpn73021bvay9mz1gqqfc40gk4hj6f84nz34h1"; + }; + + makeFlags = "generic-openssl LIBCRYPTO=-lcrypto"; + + installPhase = '' + mkdir -p $out/bin + mkdir -p $out/share/man/man1 + install -m 0755 hashcash $out/bin + install -m 0755 sha1 $out/bin + install -m 0444 hashcash.1 $out/share/man/man1 + ''; + + meta = with stdenv.lib; { + description = "Hashcash is a proof-of-work algorithm, which has been used as a denial-of-service counter measure technique in a number of systems."; + homepage = http://hashcash.org; + license = licenses.gpl2; + }; +} From bd6cbe256bc8b4ff413473ad78c52ff4c297fff5 Mon Sep 17 00:00:00 2001 From: Jim Fowler Date: Fri, 14 Dec 2018 11:04:49 -0500 Subject: [PATCH 006/247] added hashcash to all packages --- pkgs/top-level/all-packages.nix | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 209a90a16017..aaa48338d32d 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -3233,6 +3233,8 @@ in hardlink = callPackage ../tools/system/hardlink { }; + hashcash = callPackage ../tools/security/hashcash { }; + hashcat = callPackage ../tools/security/hashcat { }; hash_extender = callPackage ../tools/security/hash_extender { }; From fe162a347a7cd521552a7aad1710f341dbfabf21 Mon Sep 17 00:00:00 2001 From: Jim Fowler Date: Fri, 14 Dec 2018 11:10:10 -0500 Subject: [PATCH 007/247] adding myself as a maintainer --- maintainers/maintainer-list.nix | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix index 7a0ff6fe4379..eda5d27391a7 100644 --- a/maintainers/maintainer-list.nix +++ b/maintainers/maintainer-list.nix @@ -2278,6 +2278,11 @@ github = "kirelagin"; name = "Kirill Elagin"; }; + kisonecat = { + email = "kisonecat@gmail.com"; + github = "kisonecat"; + name = "Jim Fowler"; + }; kkallio = { email = "tierpluspluslists@gmail.com"; name = "Karn Kallio"; From e66d3074976c9fe4a377030b547e3c9bf0d0f943 Mon Sep 17 00:00:00 2001 From: Jim Fowler Date: Fri, 14 Dec 2018 11:11:07 -0500 Subject: [PATCH 008/247] hashcash: init at 1.22 --- pkgs/tools/security/hashcash/default.nix | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pkgs/tools/security/hashcash/default.nix b/pkgs/tools/security/hashcash/default.nix index 5c63845a584a..521dcf87a5f3 100644 --- a/pkgs/tools/security/hashcash/default.nix +++ b/pkgs/tools/security/hashcash/default.nix @@ -22,8 +22,9 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - description = "Hashcash is a proof-of-work algorithm, which has been used as a denial-of-service counter measure technique in a number of systems."; + description = "Proof-of-work algorithm used as spam and denial-of-service counter measure"; homepage = http://hashcash.org; license = licenses.gpl2; + maintainers = with maintainers; [ kisonecat ]; }; } From 6206a783d5015463de8e7bc5205bb711d00c49f6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= Date: Fri, 14 Dec 2018 18:07:36 +0000 Subject: [PATCH 009/247] hashcash: simplify installation --- pkgs/tools/security/hashcash/default.nix | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/pkgs/tools/security/hashcash/default.nix b/pkgs/tools/security/hashcash/default.nix index 521dcf87a5f3..337837f3116d 100644 --- a/pkgs/tools/security/hashcash/default.nix +++ b/pkgs/tools/security/hashcash/default.nix @@ -4,21 +4,18 @@ stdenv.mkDerivation rec { name = "hashcash-${version}"; version = "1.22"; - buildInputs = [ openssl ]; + buildInputs = [ openssl ]; src = fetchurl { url = "http://www.hashcash.org/source/hashcash-1.22.tgz"; sha256 = "15kqaimwb2y8wvzpn73021bvay9mz1gqqfc40gk4hj6f84nz34h1"; }; - + makeFlags = "generic-openssl LIBCRYPTO=-lcrypto"; installPhase = '' - mkdir -p $out/bin - mkdir -p $out/share/man/man1 - install -m 0755 hashcash $out/bin - install -m 0755 sha1 $out/bin - install -m 0444 hashcash.1 $out/share/man/man1 + install -D -m 0755 --target $out/bin hashcash sha1 + install -D -m 0444 hashcash.1 $out/share/man/man1/hashcash.1 ''; meta = with stdenv.lib; { From c9a228c20dd76c4e955c230bfaee837aa38ddf59 Mon Sep 17 00:00:00 2001 From: Alex Branham Date: Fri, 21 Dec 2018 14:36:29 -0600 Subject: [PATCH 010/247] ledger: Include info files --- pkgs/applications/office/ledger/default.nix | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/pkgs/applications/office/ledger/default.nix b/pkgs/applications/office/ledger/default.nix index 387a71aa04ee..5c37a38f1d39 100644 --- a/pkgs/applications/office/ledger/default.nix +++ b/pkgs/applications/office/ledger/default.nix @@ -22,7 +22,15 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; - cmakeFlags = [ "-DCMAKE_INSTALL_LIBDIR=lib" (stdenv.lib.optionalString usePython "-DUSE_PYTHON=true") ]; + cmakeFlags = [ + "-DCMAKE_INSTALL_LIBDIR=lib" + "-DBUILD_DOCS:BOOL=ON" + (stdenv.lib.optionalString usePython "-DUSE_PYTHON=true") + ]; + + postBuild = '' + make doc + ''; # Skip byte-compiling of emacs-lisp files because this is currently # broken in ledger... From 78f336b21d1f3b649e54f04cbf6073ef810c6c78 Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Mon, 24 Dec 2018 03:00:14 +0100 Subject: [PATCH 011/247] gitlab: add missing f.truncate() call to update.py script when updating data.json, truncate file after reading and before writing again, or we otherwise might end up with broken json --- pkgs/applications/version-management/gitlab/update.py | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/applications/version-management/gitlab/update.py b/pkgs/applications/version-management/gitlab/update.py index 765f984fba5c..26dc3d39eb1b 100755 --- a/pkgs/applications/version-management/gitlab/update.py +++ b/pkgs/applications/version-management/gitlab/update.py @@ -115,6 +115,7 @@ def _update_data_json(filename: str, repo: GitLabRepo, rev: str, flavour: str): data = json.load(f) data[flavour] = flavour_data f.seek(0) + f.truncate() json.dump(data, f, indent=2) From 7ea6bde0ae961d91634f00d8a2f462a157d634b1 Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Mon, 24 Dec 2018 03:32:18 +0100 Subject: [PATCH 012/247] gitlab-ce: 11.5.5 -> 11.6.0 --- .../version-management/gitlab/data.json | 16 +- .../gitlab/rubyEnv-ce/Gemfile | 61 ++-- .../gitlab/rubyEnv-ce/Gemfile.lock | 258 +++++++------- .../gitlab/rubyEnv-ce/gemset.nix | 315 +++++++++++------- 4 files changed, 377 insertions(+), 273 deletions(-) diff --git a/pkgs/applications/version-management/gitlab/data.json b/pkgs/applications/version-management/gitlab/data.json index 1e0d5de0847e..e7cb8e2b2673 100644 --- a/pkgs/applications/version-management/gitlab/data.json +++ b/pkgs/applications/version-management/gitlab/data.json @@ -1,17 +1,17 @@ { "ce": { - "version": "11.5.5", - "repo_hash": "1dxky06im18s4kxbb33qwm22pkkhgvyjggx31164iy71zcxxj1jr", - "deb_hash": "0wnyfl1bb5wb8kdyarjk9y4ydla84f3alnk3m3zwmdqfg9jsqgb8", - "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ce/packages/debian/stretch/gitlab-ce_11.5.5-ce.0_amd64.deb/download.deb", + "version": "11.6.0", + "repo_hash": "1b3vn1s07c5j6cl9javdlixv3583vx54ag4rlalrj0z35a0zggkd", + "deb_hash": "00lb3c41agcdqrdad77dw361y65kwzrfmjzcplzmpi3ign8wa2h4", + "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ce/packages/debian/stretch/gitlab-ce_11.6.0-ce.0_amd64.deb/download.deb", "owner": "gitlab-org", "repo": "gitlab-ce", - "rev": "v11.5.5", + "rev": "v11.6.0", "passthru": { - "GITALY_SERVER_VERSION": "0.129.0", + "GITALY_SERVER_VERSION": "1.7.1", "GITLAB_PAGES_VERSION": "1.3.1", - "GITLAB_SHELL_VERSION": "8.4.1", - "GITLAB_WORKHORSE_VERSION": "7.1.3" + "GITLAB_SHELL_VERSION": "8.4.3", + "GITLAB_WORKHORSE_VERSION": "7.6.0" } }, "ee": { diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile b/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile index c7efa790cfd8..3d25195f9650 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile @@ -1,13 +1,17 @@ # --- Special code for migrating to Rails 5.0 --- def rails5? - %w[1 true].include?(ENV["RAILS5"]) + !%w[0 false].include?(ENV["RAILS5"]) end gem_versions = {} -gem_versions['activerecord_sane_schema_dumper'] = rails5? ? '1.0' : '0.2' -gem_versions['default_value_for'] = rails5? ? '~> 3.0.5' : '~> 3.0.0' -gem_versions['rails'] = rails5? ? '5.0.7' : '4.2.10' -gem_versions['rails-i18n'] = rails5? ? '~> 5.1' : '~> 4.0.9' +gem_versions['activerecord_sane_schema_dumper'] = rails5? ? '1.0' : '0.2' +gem_versions['rails'] = rails5? ? '5.0.7' : '4.2.11' +gem_versions['rails-i18n'] = rails5? ? '~> 5.1' : '~> 4.0.9' + +# The 2.0.6 version of rack requires monkeypatch to be present in +# `config.ru`. This can be removed once a new update for Rack +# is available that contains https://github.com/rack/rack/pull/1201. +gem_versions['rack'] = rails5? ? '2.0.6' : '1.6.11' # --- The end of special code for migrating to Rails 5.0 --- source 'https://rubygems.org' @@ -15,13 +19,20 @@ source 'https://rubygems.org' gem 'rails', gem_versions['rails'] gem 'rails-deprecated_sanitizer', '~> 1.0.3' +# Improves copy-on-write performance for MRI +gem 'nakayoshi_fork', '~> 0.0.4' + # Responders respond_to and respond_with gem 'responders', '~> 2.0' gem 'sprockets', '~> 3.7.0' # Default values for AR models -gem 'default_value_for', gem_versions['default_value_for'] +if rails5? + gem 'gitlab-default_value_for', '~> 3.1.1', require: 'default_value_for' +else + gem 'default_value_for', '~> 3.0.0' +end # Supported DBs gem 'mysql2', '~> 0.4.10', group: :mysql @@ -71,7 +82,7 @@ gem 'validates_hostname', '~> 1.0.6' gem 'browser', '~> 2.5' # GPG -gem 'gpgme' +gem 'gpgme', '~> 2.0.18' # LDAP Auth # GitLab fork with several improvements to original library. For full list of changes @@ -80,7 +91,7 @@ gem 'gitlab_omniauth-ldap', '~> 2.0.4', require: 'omniauth-ldap' gem 'net-ldap' # API -gem 'grape', '~> 1.1' +gem 'grape', '~> 1.1.0' gem 'grape-entity', '~> 0.7.1' gem 'rack-cors', '~> 1.0.0', require: 'rack/cors' @@ -124,7 +135,7 @@ gem 'seed-fu', '~> 2.3.7' # Markdown and HTML processing gem 'html-pipeline', '~> 2.8' gem 'deckar01-task_list', '2.0.0' -gem 'gitlab-markup', '~> 1.6.4' +gem 'gitlab-markup', '~> 1.6.5' gem 'github-markup', '~> 1.7.0', require: 'github/markup' gem 'redcarpet', '~> 3.4' gem 'commonmarker', '~> 0.17' @@ -133,7 +144,7 @@ gem 'rdoc', '~> 6.0' gem 'org-ruby', '~> 0.9.12' gem 'creole', '~> 0.5.0' gem 'wikicloth', '0.8.1' -gem 'asciidoctor', '~> 1.5.6' +gem 'asciidoctor', '~> 1.5.8' gem 'asciidoctor-plantuml', '0.0.8' gem 'rouge', '~> 3.1' gem 'truncato', '~> 0.7.9' @@ -148,6 +159,8 @@ gem 'icalendar' gem 'diffy', '~> 3.1.0' # Application server +gem 'rack', gem_versions['rack'] + group :unicorn do gem 'unicorn', '~> 5.1.0' gem 'unicorn-worker-killer', '~> 0.4.4' @@ -168,6 +181,7 @@ gem 'acts-as-taggable-on', '~> 5.0' gem 'sidekiq', '~> 5.2.1' gem 'sidekiq-cron', '~> 0.6.0' gem 'redis-namespace', '~> 1.6.0' +gem 'gitlab-sidekiq-fetcher', '~> 0.1.0', require: 'sidekiq-reliable-fetch' # Cron Parser gem 'rufus-scheduler', '~> 3.4' @@ -204,6 +218,9 @@ gem 'redis-rails', '~> 5.0.2' gem 'redis', '~> 3.2' gem 'connection_pool', '~> 2.0' +# Discord integration +gem 'discordrb-webhooks-blackst0ne', '~> 3.3', require: false + # HipChat integration gem 'hipchat', '~> 1.5.0' @@ -220,13 +237,13 @@ gem 'slack-notifier', '~> 1.5.1' gem 'hangouts-chat', '~> 0.0.5' # Asana integration -gem 'asana', '~> 0.6.0' +gem 'asana', '~> 0.8.1' # FogBugz integration gem 'ruby-fogbugz', '~> 0.2.1' # Kubernetes integration -gem 'kubeclient', '~> 3.1.0' +gem 'kubeclient', '~> 4.0.0' # Sanitize user input gem 'sanitize', '~> 4.6' @@ -247,6 +264,9 @@ gem 'ace-rails-ap', '~> 4.1.0' # Detect and convert string character encoding gem 'charlock_holmes', '~> 0.7.5' +# Detect mime content type from content +gem 'mimemagic', '~> 0.3.2' + # Faster blank gem 'fast_blank' @@ -282,7 +302,7 @@ gem 'gettext_i18n_rails', '~> 1.8.0' gem 'gettext_i18n_rails_js', '~> 1.3' gem 'gettext', '~> 3.2.2', require: false, group: :development -gem 'batch-loader', '~> 1.2.1' +gem 'batch-loader', '~> 1.2.2' # Perf bar gem 'peek', '~> 1.0.1' @@ -291,7 +311,6 @@ gem 'peek-mysql2', '~> 1.1.0', group: :mysql gem 'peek-pg', '~> 1.3.0', group: :postgres gem 'peek-rblineprof', '~> 0.2.0' gem 'peek-redis', '~> 1.2.0' -gem 'gitlab-sidekiq-fetcher', require: 'sidekiq-reliable-fetch' # Metrics group :metrics do @@ -311,8 +330,8 @@ group :development do gem 'rblineprof', '~> 0.3.6', platform: :mri, require: false # Better errors handler - gem 'better_errors', '~> 2.1.0' - gem 'binding_of_caller', '~> 0.7.2' + gem 'better_errors', '~> 2.5.0' + gem 'binding_of_caller', '~> 0.8.0' # thin instead webrick gem 'thin', '~> 1.7.0' @@ -339,7 +358,7 @@ group :development, :test do gem 'minitest', '~> 5.7.0' # Generate Fake data - gem 'ffaker', '~> 2.4' + gem 'ffaker', '~> 2.10' gem 'capybara', '~> 2.15' gem 'capybara-screenshot', '~> 1.0.0' @@ -354,14 +373,14 @@ group :development, :test do gem 'rubocop-rspec', '~> 1.22.1' gem 'scss_lint', '~> 0.56.0', require: false - gem 'haml_lint', '~> 0.26.0', require: false + gem 'haml_lint', '~> 0.28.0', require: false gem 'simplecov', '~> 0.14.0', require: false gem 'bundler-audit', '~> 0.5.0', require: false gem 'benchmark-ips', '~> 2.3.0', require: false gem 'license_finder', '~> 5.4', require: false - gem 'knapsack', '~> 1.16' + gem 'knapsack', '~> 1.17' gem 'activerecord_sane_schema_dumper', gem_versions['activerecord_sane_schema_dumper'] @@ -380,7 +399,7 @@ group :test do gem 'rails-controller-testing' if rails5? # Rails5 only gem. gem 'test_after_commit', '~> 1.1' unless rails5? # Remove this gem when migrated to rails 5.0. It's been integrated to rails 5.0. gem 'sham_rack', '~> 1.3.6' - gem 'concurrent-ruby', '~> 1.0.5' + gem 'concurrent-ruby', '~> 1.1' gem 'test-prof', '~> 0.2.5' gem 'rspec_junit_formatter' end @@ -416,7 +435,7 @@ group :ed25519 do end # Gitaly GRPC client -gem 'gitaly-proto', '~> 0.123.0', require: 'gitaly' +gem 'gitaly-proto', '~> 1.3.0', require: 'gitaly' gem 'grpc', '~> 1.15.0' gem 'google-protobuf', '~> 3.6' diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile.lock b/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile.lock index 50e3ddef1e1d..7bc8fdbcb09b 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile.lock +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile.lock @@ -4,41 +4,44 @@ GEM RedCloth (4.3.2) abstract_type (0.0.7) ace-rails-ap (4.1.2) - actionmailer (4.2.10) - actionpack (= 4.2.10) - actionview (= 4.2.10) - activejob (= 4.2.10) + actioncable (5.0.7) + actionpack (= 5.0.7) + nio4r (>= 1.2, < 3.0) + websocket-driver (~> 0.6.1) + actionmailer (5.0.7) + actionpack (= 5.0.7) + actionview (= 5.0.7) + activejob (= 5.0.7) mail (~> 2.5, >= 2.5.4) - rails-dom-testing (~> 1.0, >= 1.0.5) - actionpack (4.2.10) - actionview (= 4.2.10) - activesupport (= 4.2.10) - rack (~> 1.6) - rack-test (~> 0.6.2) - rails-dom-testing (~> 1.0, >= 1.0.5) + rails-dom-testing (~> 2.0) + actionpack (5.0.7) + actionview (= 5.0.7) + activesupport (= 5.0.7) + rack (~> 2.0) + rack-test (~> 0.6.3) + rails-dom-testing (~> 2.0) rails-html-sanitizer (~> 1.0, >= 1.0.2) - actionview (4.2.10) - activesupport (= 4.2.10) + actionview (5.0.7) + activesupport (= 5.0.7) builder (~> 3.1) erubis (~> 2.7.0) - rails-dom-testing (~> 1.0, >= 1.0.5) + rails-dom-testing (~> 2.0) rails-html-sanitizer (~> 1.0, >= 1.0.3) - activejob (4.2.10) - activesupport (= 4.2.10) - globalid (>= 0.3.0) - activemodel (4.2.10) - activesupport (= 4.2.10) - builder (~> 3.1) - activerecord (4.2.10) - activemodel (= 4.2.10) - activesupport (= 4.2.10) - arel (~> 6.0) - activerecord_sane_schema_dumper (0.2) - rails (>= 4, < 5) - activesupport (4.2.10) - i18n (~> 0.7) + activejob (5.0.7) + activesupport (= 5.0.7) + globalid (>= 0.3.6) + activemodel (5.0.7) + activesupport (= 5.0.7) + activerecord (5.0.7) + activemodel (= 5.0.7) + activesupport (= 5.0.7) + arel (~> 7.0) + activerecord_sane_schema_dumper (1.0) + rails (>= 5, < 6) + activesupport (5.0.7) + concurrent-ruby (~> 1.0, >= 1.0.2) + i18n (>= 0.7, < 2) minitest (~> 5.1) - thread_safe (~> 0.3, >= 0.3.4) tzinfo (~> 1.1) acts-as-taggable-on (5.0.0) activerecord (>= 4.2.8) @@ -49,13 +52,13 @@ GEM public_suffix (>= 2.0.2, < 4.0) aes_key_wrap (1.0.1) akismet (2.0.0) - arel (6.0.4) - asana (0.6.0) + arel (7.1.4) + asana (0.8.1) faraday (~> 0.9) faraday_middleware (~> 0.9) faraday_middleware-multi_json (~> 0.0) oauth2 (~> 1.0) - asciidoctor (1.5.6.2) + asciidoctor (1.5.8) asciidoctor-plantuml (0.0.8) asciidoctor (~> 1.5) ast (2.4.0) @@ -70,16 +73,17 @@ GEM thread_safe (~> 0.3, >= 0.3.1) babosa (1.0.2) base32 (0.3.2) - batch-loader (1.2.1) + batch-loader (1.2.2) bcrypt (3.1.12) bcrypt_pbkdf (1.0.0) benchmark-ips (2.3.0) - better_errors (2.1.1) + better_errors (2.5.0) coderay (>= 1.0.0) - erubis (>= 2.6.6) + erubi (>= 1.0.0) rack (>= 0.9.0) bindata (2.4.3) - binding_of_caller (0.7.2) + binding_ninja (0.2.2) + binding_of_caller (0.8.0) debug_inspector (>= 0.0.1) bootsnap (1.3.2) msgpack (~> 1.0) @@ -125,9 +129,9 @@ GEM concord (0.1.5) adamantium (~> 0.2.0) equalizer (~> 0.0.9) - concurrent-ruby (1.0.5) - concurrent-ruby-ext (1.0.5) - concurrent-ruby (= 1.0.5) + concurrent-ruby (1.1.3) + concurrent-ruby-ext (1.1.3) + concurrent-ruby (= 1.1.3) connection_pool (2.2.2) crack (0.4.3) safe_yaml (~> 1.0.0) @@ -137,14 +141,12 @@ GEM addressable daemons (1.2.6) database_cleaner (1.5.3) - debug_inspector (0.0.2) + debug_inspector (0.0.3) debugger-ruby_core_source (1.3.8) deckar01-task_list (2.0.0) html-pipeline declarative (0.0.10) declarative-option (0.1.0) - default_value_for (3.0.2) - activerecord (>= 3.2.0, < 5.1) descendants_tracker (0.0.4) thread_safe (~> 0.3, >= 0.3.1) device_detector (1.0.0) @@ -162,6 +164,8 @@ GEM rotp (~> 2.0) diff-lcs (1.3) diffy (3.1.0) + discordrb-webhooks-blackst0ne (3.3.0) + rest-client (~> 2.0) docile (1.1.5) domain_name (0.5.20180417) unf (>= 0.0.5, < 1.0.0) @@ -178,8 +182,9 @@ GEM mail (~> 2.7) encryptor (3.0.0) equalizer (0.0.11) + erubi (1.7.1) erubis (2.7.0) - escape_utils (1.1.1) + escape_utils (1.2.1) et-orbi (1.0.3) tzinfo eventmachine (1.2.7) @@ -200,7 +205,7 @@ GEM multi_json fast_blank (1.0.0) fast_gettext (1.6.0) - ffaker (2.4.0) + ffaker (2.10.0) ffi (1.9.25) flipper (0.13.0) flipper-active_record (0.13.0) @@ -269,11 +274,13 @@ GEM gettext_i18n_rails (>= 0.7.1) po_to_json (>= 1.0.0) rails (>= 3.2.0) - gitaly-proto (0.123.0) + gitaly-proto (1.3.0) grpc (~> 1.0) github-markup (1.7.0) - gitlab-markup (1.6.4) - gitlab-sidekiq-fetcher (0.3.0) + gitlab-default_value_for (3.1.1) + activerecord (>= 3.2.0, < 6.0) + gitlab-markup (1.6.5) + gitlab-sidekiq-fetcher (0.1.0) sidekiq (~> 5) gitlab-styles (2.4.1) rubocop (~> 0.54.0) @@ -307,8 +314,8 @@ GEM multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (~> 0.7) - gpgme (2.0.13) - mini_portile2 (~> 2.1) + gpgme (2.0.18) + mini_portile2 (~> 2.3) grape (1.1.0) activesupport builder @@ -335,11 +342,11 @@ GEM haml (5.0.4) temple (>= 0.8.0) tilt - haml_lint (0.26.0) + haml_lint (0.28.0) haml (>= 4.0, < 5.1) rainbow rake (>= 10, < 13) - rubocop (>= 0.49.0) + rubocop (>= 0.50.0) sysexits (~> 1.1) hamlit (2.8.8) temple (>= 0.8.0) @@ -361,20 +368,20 @@ GEM html2text (0.2.0) nokogiri (~> 1.6) htmlentities (4.3.4) - http (2.2.2) + http (3.3.0) addressable (~> 2.3) http-cookie (~> 1.0) - http-form_data (~> 1.0.1) + http-form_data (~> 2.0) http_parser.rb (~> 0.6.0) http-cookie (1.0.3) domain_name (~> 0.5) - http-form_data (1.0.3) + http-form_data (2.1.1) http_parser.rb (0.6.0) httparty (0.13.7) json (~> 1.8) multi_xml (>= 0.5.2) httpclient (2.8.3) - i18n (0.9.5) + i18n (1.1.1) concurrent-ruby (~> 1.0) icalendar (2.4.1) ice_nine (0.11.2) @@ -410,10 +417,10 @@ GEM kaminari-core (= 1.0.1) kaminari-core (1.0.1) kgio (2.10.0) - knapsack (1.16.0) + knapsack (1.17.0) rake - kubeclient (3.1.0) - http (~> 2.2.2) + kubeclient (4.0.0) + http (~> 3.0) recursive-open-struct (~> 1.0, >= 1.0.4) rest-client (~> 2.0) launchy (2.4.3) @@ -439,7 +446,7 @@ GEM activesupport (>= 4) railties (>= 4) request_store (~> 1.0) - loofah (2.2.2) + loofah (2.2.3) crass (~> 1.0.2) nokogiri (>= 1.5.9) mail (2.7.0) @@ -448,11 +455,11 @@ GEM memoist (0.16.0) memoizable (0.4.2) thread_safe (~> 0.3, >= 0.3.1) - method_source (0.9.0) - mime-types (3.1) + method_source (0.9.2) + mime-types (3.2.2) mime-types-data (~> 3.2015) - mime-types-data (3.2016.0521) - mimemagic (0.3.0) + mime-types-data (3.2018.0812) + mimemagic (0.3.2) mini_magick (4.8.0) mini_mime (1.0.1) mini_portile2 (2.3.0) @@ -465,10 +472,12 @@ GEM mustermann-grape (1.0.0) mustermann (~> 1.0.0) mysql2 (0.4.10) + nakayoshi_fork (0.0.4) net-ldap (0.16.0) net-ssh (5.0.1) netrc (0.11.0) - nokogiri (1.8.4) + nio4r (2.3.1) + nokogiri (1.8.5) mini_portile2 (~> 2.3.0) nokogumbo (1.5.0) nokogiri @@ -596,7 +605,7 @@ GEM get_process_mem (~> 0.2) puma (>= 2.7, < 4) pyu-ruby-sasl (0.0.3.3) - rack (1.6.10) + rack (2.0.6) rack-accept (0.4.5) rack (>= 0.4) rack-attack (4.4.1) @@ -608,37 +617,42 @@ GEM httpclient (>= 2.4) multi_json (>= 1.3.6) rack (>= 1.1) - rack-protection (2.0.3) + rack-protection (2.0.4) rack rack-proxy (0.6.0) rack rack-test (0.6.3) rack (>= 1.0) - rails (4.2.10) - actionmailer (= 4.2.10) - actionpack (= 4.2.10) - actionview (= 4.2.10) - activejob (= 4.2.10) - activemodel (= 4.2.10) - activerecord (= 4.2.10) - activesupport (= 4.2.10) - bundler (>= 1.3.0, < 2.0) - railties (= 4.2.10) - sprockets-rails + rails (5.0.7) + actioncable (= 5.0.7) + actionmailer (= 5.0.7) + actionpack (= 5.0.7) + actionview (= 5.0.7) + activejob (= 5.0.7) + activemodel (= 5.0.7) + activerecord (= 5.0.7) + activesupport (= 5.0.7) + bundler (>= 1.3.0) + railties (= 5.0.7) + sprockets-rails (>= 2.0.0) + rails-controller-testing (1.0.2) + actionpack (~> 5.x, >= 5.0.1) + actionview (~> 5.x, >= 5.0.1) + activesupport (~> 5.x) rails-deprecated_sanitizer (1.0.3) activesupport (>= 4.2.0.alpha) - rails-dom-testing (1.0.9) - activesupport (>= 4.2.0, < 5.0) - nokogiri (~> 1.6) - rails-deprecated_sanitizer (>= 1.0.1) + rails-dom-testing (2.0.3) + activesupport (>= 4.2.0) + nokogiri (>= 1.6) rails-html-sanitizer (1.0.4) loofah (~> 2.2, >= 2.2.2) - rails-i18n (4.0.9) - i18n (~> 0.7) - railties (~> 4.0) - railties (4.2.10) - actionpack (= 4.2.10) - activesupport (= 4.2.10) + rails-i18n (5.1.1) + i18n (>= 0.7, < 2) + railties (>= 5.0, < 6) + railties (5.0.7) + actionpack (= 5.0.7) + activesupport (= 5.0.7) + method_source rake (>= 0.8.7) thor (>= 0.18.1, < 2.0) rainbow (3.0.0) @@ -676,7 +690,7 @@ GEM redis-actionpack (>= 5.0, < 6) redis-activesupport (>= 5.0, < 6) redis-store (>= 1.2, < 2) - redis-store (1.4.1) + redis-store (1.6.0) redis (>= 2.2, < 5) regexp_parser (0.5.0) representable (3.0.4) @@ -711,8 +725,8 @@ GEM rspec-mocks (3.7.0) diff-lcs (>= 1.2.0, < 2.0) rspec-support (~> 3.7.0) - rspec-parameterized (0.4.0) - binding_of_caller + rspec-parameterized (0.4.1) + binding_ninja (>= 0.2.1) parser proc_to_ast rspec (>= 2.13, < 4) @@ -729,8 +743,7 @@ GEM rspec-core rspec-set (0.1.3) rspec-support (3.7.1) - rspec_junit_formatter (0.2.3) - builder (< 4) + rspec_junit_formatter (0.4.1) rspec-core (>= 2, < 4, != 2.12.0) rspec_profiling (0.0.5) activerecord @@ -756,8 +769,8 @@ GEM ruby-progressbar (1.9.0) ruby-saml (1.7.2) nokogiri (>= 1.5.10) - ruby_parser (3.9.0) - sexp_processor (~> 4.1) + ruby_parser (3.11.0) + sexp_processor (~> 4.9) rubyntlm (0.6.2) rubypants (0.2.0) rubyzip (1.2.2) @@ -794,15 +807,15 @@ GEM selenium-webdriver (3.12.0) childprocess (~> 0.5) rubyzip (~> 1.2) - sentry-raven (2.7.2) + sentry-raven (2.7.4) faraday (>= 0.7.6, < 1.0) settingslogic (2.0.9) - sexp_processor (4.9.0) + sexp_processor (4.11.0) sham_rack (1.3.6) rack shoulda-matchers (3.1.2) activesupport (>= 4.0.0) - sidekiq (5.2.1) + sidekiq (5.2.3) connection_pool (~> 2.2, >= 2.2.2) rack-protection (>= 1.5.0) redis (>= 3.3.5, < 5) @@ -847,8 +860,6 @@ GEM sysexits (1.2.0) temple (0.8.0) test-prof (0.2.5) - test_after_commit (1.1.0) - activerecord (>= 3.2) text (1.3.1) thin (1.7.2) daemons (~> 1.0, >= 1.0.9) @@ -885,7 +896,7 @@ GEM get_process_mem (~> 0) unicorn (>= 4, < 6) uniform_notifier (1.10.0) - unparser (0.2.7) + unparser (0.4.2) abstract_type (~> 0.0.7) adamantium (~> 0.2.0) concord (~> 0.1.5) @@ -911,6 +922,9 @@ GEM hashdiff webpack-rails (0.9.11) railties (>= 3.2.0) + websocket-driver (0.6.5) + websocket-extensions (>= 0.1.0) + websocket-extensions (0.1.3) wikicloth (0.8.1) builder expression_parser @@ -926,22 +940,22 @@ PLATFORMS DEPENDENCIES RedCloth (~> 4.3.2) ace-rails-ap (~> 4.1.0) - activerecord_sane_schema_dumper (= 0.2) + activerecord_sane_schema_dumper (= 1.0) acts-as-taggable-on (~> 5.0) addressable (~> 2.5.2) akismet (~> 2.0) - asana (~> 0.6.0) - asciidoctor (~> 1.5.6) + asana (~> 0.8.1) + asciidoctor (~> 1.5.8) asciidoctor-plantuml (= 0.0.8) attr_encrypted (~> 3.1.0) awesome_print babosa (~> 1.0.2) base32 (~> 0.3.0) - batch-loader (~> 1.2.1) + batch-loader (~> 1.2.2) bcrypt_pbkdf (~> 1.0) benchmark-ips (~> 2.3.0) - better_errors (~> 2.1.0) - binding_of_caller (~> 0.7.2) + better_errors (~> 2.5.0) + binding_of_caller (~> 0.8.0) bootsnap (~> 1.3) bootstrap_form (~> 2.7.0) brakeman (~> 4.2) @@ -955,16 +969,16 @@ DEPENDENCIES chronic (~> 0.10.2) chronic_duration (~> 0.10.6) commonmarker (~> 0.17) - concurrent-ruby (~> 1.0.5) + concurrent-ruby (~> 1.1) connection_pool (~> 2.0) creole (~> 0.5.0) database_cleaner (~> 1.5.0) deckar01-task_list (= 2.0.0) - default_value_for (~> 3.0.0) device_detector devise (~> 4.4) devise-two-factor (~> 3.0.0) diffy (~> 3.1.0) + discordrb-webhooks-blackst0ne (~> 3.3) doorkeeper (~> 4.3) doorkeeper-openid_connect (~> 1.5) ed25519 (~> 1.2) @@ -974,7 +988,7 @@ DEPENDENCIES factory_bot_rails (~> 4.8.2) faraday (~> 0.12) fast_blank - ffaker (~> 2.4) + ffaker (~> 2.10) flipper (~> 0.13.0) flipper-active_record (~> 0.13.0) flipper-active_support_cache_store (~> 0.13.0) @@ -993,24 +1007,25 @@ DEPENDENCIES gettext (~> 3.2.2) gettext_i18n_rails (~> 1.8.0) gettext_i18n_rails_js (~> 1.3) - gitaly-proto (~> 0.123.0) + gitaly-proto (~> 1.3.0) github-markup (~> 1.7.0) - gitlab-markup (~> 1.6.4) - gitlab-sidekiq-fetcher + gitlab-default_value_for (~> 3.1.1) + gitlab-markup (~> 1.6.5) + gitlab-sidekiq-fetcher (~> 0.1.0) gitlab-styles (~> 2.4) gitlab_omniauth-ldap (~> 2.0.4) gon (~> 6.2) google-api-client (~> 0.23) google-protobuf (~> 3.6) - gpgme - grape (~> 1.1) + gpgme (~> 2.0.18) + grape (~> 1.1.0) grape-entity (~> 0.7.1) grape-path-helpers (~> 1.0) grape_logging (~> 1.7) graphiql-rails (~> 1.4.10) graphql (~> 1.8.0) grpc (~> 1.15.0) - haml_lint (~> 0.26.0) + haml_lint (~> 0.28.0) hamlit (~> 2.8.8) hangouts-chat (~> 0.0.5) hashie-forbidden_attributes @@ -1027,8 +1042,8 @@ DEPENDENCIES json-schema (~> 2.8.0) jwt (~> 1.5.6) kaminari (~> 1.0) - knapsack (~> 1.16) - kubeclient (~> 3.1.0) + knapsack (~> 1.17) + kubeclient (~> 4.0.0) letter_opener_web (~> 1.3.0) license_finder (~> 5.4) licensee (~> 8.9) @@ -1036,9 +1051,11 @@ DEPENDENCIES loofah (~> 2.2) mail_room (~> 0.9.1) method_source (~> 0.8) + mimemagic (~> 0.3.2) mini_magick minitest (~> 5.7.0) mysql2 (~> 0.4.10) + nakayoshi_fork (~> 0.0.4) net-ldap net-ssh (~> 5.0) nokogiri (~> 1.8.2) @@ -1073,13 +1090,15 @@ DEPENDENCIES pry-rails (~> 0.3.4) puma (~> 3.12) puma_worker_killer + rack (= 2.0.6) rack-attack (~> 4.4.1) rack-cors (~> 1.0.0) rack-oauth2 (~> 1.2.1) rack-proxy (~> 0.6.0) - rails (= 4.2.10) + rails (= 5.0.7) + rails-controller-testing rails-deprecated_sanitizer (~> 1.0.3) - rails-i18n (~> 4.0.9) + rails-i18n (~> 5.1) rainbow (~> 3.0) raindrops (~> 0.18) rblineprof (~> 0.3.6) @@ -1132,7 +1151,6 @@ DEPENDENCIES state_machines-activerecord (~> 0.5.1) sys-filesystem (~> 1.1.6) test-prof (~> 0.2.5) - test_after_commit (~> 1.1) thin (~> 1.7.0) timecop (~> 0.8.0) toml-rb (~> 1.0.0) diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ce/gemset.nix b/pkgs/applications/version-management/gitlab/rubyEnv-ce/gemset.nix index 9a3944d6feab..fc40ae8cb27c 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ce/gemset.nix +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ce/gemset.nix @@ -15,77 +15,86 @@ }; version = "4.1.2"; }; + actioncable = { + dependencies = ["actionpack" "nio4r" "websocket-driver"]; + source = { + remotes = ["https://rubygems.org"]; + sha256 = "0b2znw81zf11f7kqyks80ha4sb4aiqrs1mia0jnf3xfn5zgx28y0"; + type = "gem"; + }; + version = "5.0.7"; + }; actionmailer = { dependencies = ["actionpack" "actionview" "activejob" "mail" "rails-dom-testing"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1ivyjsapqgn1xfb2p8yqjrg2jldqm5r7hxrjxq6kdr05gk4fsg59"; + sha256 = "0d9f3kwk1z3p6sa9d8vl7yqa689ihm24cy7lp4h6v478dbr156sz"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; actionpack = { dependencies = ["actionview" "activesupport" "rack" "rack-test" "rails-dom-testing" "rails-html-sanitizer"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0l6agrxdaishxjx2zc2x8md95plfp39bfskzgs6v9gsdp2y2arpx"; + sha256 = "15nin3f817dpkjlw94sh4rsvayqy4z6ij7fak82wqdqv5mcd9q08"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; actionview = { dependencies = ["activesupport" "builder" "erubis" "rails-dom-testing" "rails-html-sanitizer"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1jrx2pmkywk70z7n17gw3jrcdw3n03wdzvg45bnq8wxshl1lmbhv"; + sha256 = "12vvq439jjj4byhkvckrk7ap4krrfsbpw54n5xxfwh7fr5y0087b"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; activejob = { dependencies = ["activesupport" "globalid"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "10jsa5pqklcsd2npicqxr5abjlwi53di2brpzgz35k557fkpc1z8"; + sha256 = "1mdqdgwmcx28jznc5mfmqzz42y03mx6i6fs6m4nka0ic61rmp8g8"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; activemodel = { - dependencies = ["activesupport" "builder"]; + dependencies = ["activesupport"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0c4vj9xajxa906bqbcjpni74nya6rh2nbb15gl8xm0vl9zf3ll9v"; + sha256 = "11ycnzi32cd92ylxhqwqfchqk3m7y9z7sfiyf8b7830lzfxv2dgy"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; activerecord = { dependencies = ["activemodel" "activesupport" "arel"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1lws9y4p9c2vnmv3ddfpv8jh6azlddppl3fi31vahaz14ifxjk5s"; + sha256 = "0ri32lhmmd4waphpynwj53ysy9xlhx743lnlsnp8l499kvarqd66"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; activerecord_sane_schema_dumper = { dependencies = ["rails"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "122c7v7lvs0gwckvx2rar07waxnx1vv0lryz322nybb69d8vbhl6"; + sha256 = "16jbf461wjaxyq26si5505wcj46mi23mii9hx4wjpva1zn9hz5m2"; type = "gem"; }; - version = "0.2"; + version = "1.0"; }; activesupport = { - dependencies = ["i18n" "minitest" "thread_safe" "tzinfo"]; + dependencies = ["concurrent-ruby" "i18n" "minitest" "tzinfo"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0s12j8vl8vrxfngkdlz9g8bpz9akq1z42d57mx5r537b2pji8nr7"; + sha256 = "1yx73l984y3ri5ndj37l1dfarcdvbhra7vhz9fcww4za24is95d5"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; acts-as-taggable-on = { dependencies = ["activerecord"]; @@ -133,27 +142,27 @@ arel = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0nfcrdiys6q6ylxiblky9jyssrw2xj96fmxmal7f4f0jj3417vj4"; + sha256 = "0l757dkkaxk5fq3368l79jpyzq9a9driricjamhiwhwvh0h7xcyx"; type = "gem"; }; - version = "6.0.4"; + version = "7.1.4"; }; asana = { dependencies = ["faraday" "faraday_middleware" "faraday_middleware-multi_json" "oauth2"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0bn7f3sc2f02g871jd0y6qdhixn464mflkjchp56x6kcnyqy24z6"; + sha256 = "1h0qiywvjjc9iyzq9nz5iaqyh6qsrix4ip0w86j5c4v5g940z6qx"; type = "gem"; }; - version = "0.6.0"; + version = "0.8.1"; }; asciidoctor = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0zq3az4836nxkc8g5wnnbzmarw7663s1ky6gf8pc04sfpa8n2l3f"; + sha256 = "0qld3a1pbcjvs8lbxp95iz83bfmg5scmnf8q3rklinmdmhzakslx"; type = "gem"; }; - version = "1.5.6.2"; + version = "1.5.8"; }; asciidoctor-plantuml = { dependencies = ["asciidoctor"]; @@ -233,10 +242,10 @@ batch-loader = { source = { remotes = ["https://rubygems.org"]; - sha256 = "1nvmwzn8q6dkp2n8wz47z7gldj3yrj7h6syy0cwrkzi19bfvxba2"; + sha256 = "0pwr2hk9x1qx9i2xpkpjwkdjsmm4kamz5f25wizsaw37zb64apjc"; type = "gem"; }; - version = "1.2.1"; + version = "1.2.2"; }; bcrypt = { source = { @@ -263,13 +272,13 @@ version = "2.3.0"; }; better_errors = { - dependencies = ["coderay" "erubis" "rack"]; + dependencies = ["coderay" "erubi" "rack"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "11csk41yhijqvp0dkky0cjl8kn6blw4jhr8b6v4islfvvayddcxc"; + sha256 = "1pqnxxsqqs7vnqvamk5bzs84dv584g9s0qaf2vqb1v2aj5dabcg7"; type = "gem"; }; - version = "2.1.1"; + version = "2.5.0"; }; bindata = { source = { @@ -279,14 +288,22 @@ }; version = "2.4.3"; }; + binding_ninja = { + source = { + remotes = ["https://rubygems.org"]; + sha256 = "19dk26qyx433ffa6y48511apc2iw71zw4jnlqxhy0wix9dlxr2ri"; + type = "gem"; + }; + version = "0.2.2"; + }; binding_of_caller = { dependencies = ["debug_inspector"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "15jg6dkaq2nzcd602d7ppqbdxw3aji961942w93crs6qw4n6h9yk"; + sha256 = "05syqlks7463zsy1jdfbbdravdhj9hpj5pv2m74blqpv8bq4vv5g"; type = "gem"; }; - version = "0.7.2"; + version = "0.8.0"; }; bootsnap = { dependencies = ["msgpack"]; @@ -478,19 +495,19 @@ concurrent-ruby = { source = { remotes = ["https://rubygems.org"]; - sha256 = "183lszf5gx84kcpb779v6a2y0mx9sssy8dgppng1z9a505nj1qcf"; + sha256 = "18q9skp5pfq4jwbxzmw8q2rn4cpw6mf4561i2hsjcl1nxdag2jvb"; type = "gem"; }; - version = "1.0.5"; + version = "1.1.3"; }; concurrent-ruby-ext = { dependencies = ["concurrent-ruby"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "119l554zi3720d3rk670ldcqhsgmfii28a9z307v4mwdjckdm4gp"; + sha256 = "0h7k4wnvbxv7vzb53kaqxbbyhp3m98g2rgymr6n1l9v0jlzcr1i8"; type = "gem"; }; - version = "1.0.5"; + version = "1.1.3"; }; connection_pool = { source = { @@ -553,10 +570,10 @@ debug_inspector = { source = { remotes = ["https://rubygems.org"]; - sha256 = "109761g00dbrw5q0dfnbqg8blfm699z4jj70l4zrgf9mzn7ii50m"; + sha256 = "0vxr0xa1mfbkfcrn71n7c4f2dj7la5hvphn904vh20j3x4j5lrx0"; type = "gem"; }; - version = "0.0.2"; + version = "0.0.3"; }; debugger-ruby_core_source = { source = { @@ -591,15 +608,6 @@ }; version = "0.1.0"; }; - default_value_for = { - dependencies = ["activerecord"]; - source = { - remotes = ["https://rubygems.org"]; - sha256 = "014482mxjrc227fxv6vff6ccjr9dr0ydz52flxslsa7biq542k73"; - type = "gem"; - }; - version = "3.0.2"; - }; descendants_tracker = { dependencies = ["thread_safe"]; source = { @@ -651,6 +659,15 @@ }; version = "3.1.0"; }; + discordrb-webhooks-blackst0ne = { + dependencies = ["rest-client"]; + source = { + remotes = ["https://rubygems.org"]; + sha256 = "1f0dw6ci5cbrxrvvqw2kqabpzyjisd4hflbi370rpb4cakkzgw39"; + type = "gem"; + }; + version = "3.3.0"; + }; docile = { source = { remotes = ["https://rubygems.org"]; @@ -727,6 +744,14 @@ }; version = "0.0.11"; }; + erubi = { + source = { + remotes = ["https://rubygems.org"]; + sha256 = "0bws86na9k565raiz0kk61yy5pxxp0fmwyzpibdwjkq0xzx8q6q1"; + type = "gem"; + }; + version = "1.7.1"; + }; erubis = { source = { remotes = ["https://rubygems.org"]; @@ -738,10 +763,10 @@ escape_utils = { source = { remotes = ["https://rubygems.org"]; - sha256 = "088r5c2mz2vy2jbbx1xjbi8msnzg631ggli29nhik2spbcp1z6vh"; + sha256 = "0qminivnyzwmqjhrh3b92halwbk0zcl9xn828p5rnap1szl2yag5"; type = "gem"; }; - version = "1.1.1"; + version = "1.2.1"; }; et-orbi = { dependencies = ["tzinfo"]; @@ -848,10 +873,10 @@ ffaker = { source = { remotes = ["https://rubygems.org"]; - sha256 = "1rlfvf2iakphs3krxy1hiywr2jzmrhvhig8n8fw6rcivpz9v52ry"; + sha256 = "01z5lpssjc0n8lm4xrlja0hh8lv4ngzbybjvd4rdkc5x9ddvh8s3"; type = "gem"; }; - version = "2.4.0"; + version = "2.10.0"; }; ffi = { source = { @@ -1060,10 +1085,10 @@ dependencies = ["grpc"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "16b9sdaimhcda401z2s7apf0nz6y0lxs74xhkwlz4jzf6ms44mgg"; + sha256 = "17fg29j089k94ssim9hfzpd5lycvhimbpvz12d73ywrbwz7a7680"; type = "gem"; }; - version = "0.123.0"; + version = "1.3.0"; }; github-markup = { source = { @@ -1073,22 +1098,31 @@ }; version = "1.7.0"; }; + gitlab-default_value_for = { + dependencies = ["activerecord"]; + source = { + remotes = ["https://rubygems.org"]; + sha256 = "0qqjf7nxmwxnkdlrgbnby8wjckaj2s5yna96avgb7fwm0h90f1sn"; + type = "gem"; + }; + version = "3.1.1"; + }; gitlab-markup = { source = { remotes = ["https://rubygems.org"]; - sha256 = "1v6w3z7smmkqnhphb4ghgpqg61vimflqzpszybji0li99f2k1jb6"; + sha256 = "12lzzhbmid4m23pk7d963n3njli2hw7g200arszh75j57bjgs4fy"; type = "gem"; }; - version = "1.6.4"; + version = "1.6.5"; }; gitlab-sidekiq-fetcher = { dependencies = ["sidekiq"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0dvrp4iapwfaakc3qgf7mw05blxzfywpjfr7bhswwflih0pm67l7"; + sha256 = "08bwgagrdryva8vlwiiwfa3v60w9k13nknmjjfadrkn68a4ihk2a"; type = "gem"; }; - version = "0.3.0"; + version = "0.1.0"; }; gitlab-styles = { dependencies = ["rubocop" "rubocop-gitlab-security" "rubocop-rspec"]; @@ -1165,10 +1199,10 @@ dependencies = ["mini_portile2"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1fclgx3pg3sihk9xn3amcf8db0q749dsqkycayn1c8x134zml3gb"; + sha256 = "12fqirxr964mc8jwsfl5nif6q4wcckrmj7w4c9ci4xg9xy2b9v6m"; type = "gem"; }; - version = "2.0.13"; + version = "2.0.18"; }; grape = { dependencies = ["activesupport" "builder" "mustermann-grape" "rack" "rack-accept" "virtus"]; @@ -1245,10 +1279,10 @@ dependencies = ["haml" "rainbow" "rake" "rubocop" "sysexits"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "04illnjl9hsg7wqf8x5s108m5is9aj52g80c6nrgsksyp4vh9ynn"; + sha256 = "125aj0j84nx5gqm42hfx5d8486higlra423ahgfpsdjwbp399rwv"; type = "gem"; }; - version = "0.26.0"; + version = "0.28.0"; }; hamlit = { dependencies = ["temple" "thor" "tilt"]; @@ -1340,10 +1374,10 @@ dependencies = ["addressable" "http-cookie" "http-form_data" "http_parser.rb"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1kcd9qp8vm1rkyp7gfh8j0dbl3zpi97vz2vbhpbcsdsa7l21a59r"; + sha256 = "1jlm5prw437wqpfxcigh88lfap3m7g8mnmj5as7qw6dzqnvrxwmc"; type = "gem"; }; - version = "2.2.2"; + version = "3.3.0"; }; http-cookie = { dependencies = ["domain_name"]; @@ -1357,10 +1391,10 @@ http-form_data = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0j8dwwbfpf8kc0lcsqcgy29lflszd1x4d7kc0f7227892m7r6y0m"; + sha256 = "15lpn604byf7cyxnw949xz4rvpcknqp7a48q73nm630gqxsa76f3"; type = "gem"; }; - version = "1.0.3"; + version = "2.1.1"; }; "http_parser.rb" = { source = { @@ -1391,10 +1425,10 @@ dependencies = ["concurrent-ruby"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "038qvz7kd3cfxk8bvagqhakx68pfbnmghpdkx7573wbf0maqp9a3"; + sha256 = "1gcp1m1p6dpasycfz2sj82ci9ggz7lsskz9c9q6gvfwxrl8y9dx7"; type = "gem"; }; - version = "0.9.5"; + version = "1.1.1"; }; icalendar = { source = { @@ -1536,19 +1570,19 @@ dependencies = ["rake"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1q2y7mb8ii1ncdrlp46l9v2x909gdnjaid2dg5gcicj39hna36di"; + sha256 = "1c69rcwfrdrnx8ddl6k1qxhw9f2dj5x5bbddz435isl2hfr5zh92"; type = "gem"; }; - version = "1.16.0"; + version = "1.17.0"; }; kubeclient = { dependencies = ["http" "recursive-open-struct" "rest-client"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1czzdp9lfsrah2jkaddkqzmphyvnk096zm1ra6jddh626d8d53r4"; + sha256 = "1s250z89nz7vzich3nikc8fs8vgpac38wjv8llm4ldvs4iyc4ypg"; type = "gem"; }; - version = "3.1.0"; + version = "4.0.0"; }; launchy = { dependencies = ["addressable"]; @@ -1616,10 +1650,10 @@ dependencies = ["crass" "nokogiri"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0yjs6wbcj3n06d3xjqpy3qbpx0bfa12h3x2rbpc2k33ldjlkx6zy"; + sha256 = "1ccsid33xjajd0im2xv941aywi58z7ihwkvaf1w2bv89vn5bhsjg"; type = "gem"; }; - version = "2.2.2"; + version = "2.2.3"; }; mail = { dependencies = ["mini_mime"]; @@ -1658,35 +1692,35 @@ method_source = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0xqj21j3vfq4ldia6i2akhn2qd84m0iqcnsl49kfpq3xk6x0dzgn"; + sha256 = "1pviwzvdqd90gn6y7illcdd9adapw8fczml933p5vl739dkvl3lq"; type = "gem"; }; - version = "0.9.0"; + version = "0.9.2"; }; mime-types = { dependencies = ["mime-types-data"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0087z9kbnlqhci7fxh9f6il63hj1k02icq2rs0c6cppmqchr753m"; + sha256 = "0fjxy1jm52ixpnv3vg9ld9pr9f35gy0jp66i1njhqjvmnvq0iwwk"; type = "gem"; }; - version = "3.1"; + version = "3.2.2"; }; mime-types-data = { source = { remotes = ["https://rubygems.org"]; - sha256 = "04my3746hwa4yvbx1ranhfaqkgf6vavi1kyijjnw8w3dy37vqhkm"; + sha256 = "07wvp0aw2gjm4njibb70as6rh5hi1zzri5vky1q6jx95h8l56idc"; type = "gem"; }; - version = "3.2016.0521"; + version = "3.2018.0812"; }; mimemagic = { source = { remotes = ["https://rubygems.org"]; - sha256 = "101lq4bnjs7ywdcicpw3vbz9amg5gbb4va1626fybd2hawgdx8d9"; + sha256 = "00ibc1mhvdfyfyl103xwb45621nwyqxf124cni5hyfhag0fn1c3q"; type = "gem"; }; - version = "0.3.0"; + version = "0.3.2"; }; mini_magick = { source = { @@ -1777,6 +1811,14 @@ }; version = "0.4.10"; }; + nakayoshi_fork = { + source = { + remotes = ["https://rubygems.org"]; + sha256 = "1mj5czi7rxxmfq4v9qjz74lcqypvnjxhxqfs71zhb2rsfa97a6jg"; + type = "gem"; + }; + version = "0.0.4"; + }; net-ldap = { source = { remotes = ["https://rubygems.org"]; @@ -1801,14 +1843,22 @@ }; version = "0.11.0"; }; + nio4r = { + source = { + remotes = ["https://rubygems.org"]; + sha256 = "1a41ca1kpdmrypjp9xbgvckpy8g26zxphkja9vk7j5wl4n8yvlyr"; + type = "gem"; + }; + version = "2.3.1"; + }; nokogiri = { dependencies = ["mini_portile2"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1h9nml9h3m0mpvmh8jfnqvblnz5n5y3mmhgfc38avfmfzdrq9bgc"; + sha256 = "0byyxrazkfm29ypcx5q4syrv126nvjnf7z6bqi01sqkv4llsi4qz"; type = "gem"; }; - version = "1.8.4"; + version = "1.8.5"; }; nokogumbo = { dependencies = ["nokogiri"]; @@ -2250,10 +2300,10 @@ rack = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0in0amn0kwvzmi8h5zg6ijrx5wpsf8h96zrfmnk1kwh2ql4sxs2q"; + sha256 = "1pcgv8dv4vkaczzlix8q3j68capwhk420cddzijwqgi2qb4lm1zm"; type = "gem"; }; - version = "1.6.10"; + version = "2.0.6"; }; rack-accept = { dependencies = ["rack"]; @@ -2294,10 +2344,10 @@ dependencies = ["rack"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1z5598qipilmnf45428jnxi63ykrgvnyywa5ckpr52zv2vpd8jdp"; + sha256 = "0ylx74ravz7nvnyygq0nk3v86qdzrmqxpwpayhppyy50l72rcajq"; type = "gem"; }; - version = "2.0.3"; + version = "2.0.4"; }; rack-proxy = { dependencies = ["rack"]; @@ -2318,13 +2368,22 @@ version = "0.6.3"; }; rails = { - dependencies = ["actionmailer" "actionpack" "actionview" "activejob" "activemodel" "activerecord" "activesupport" "railties" "sprockets-rails"]; + dependencies = ["actioncable" "actionmailer" "actionpack" "actionview" "activejob" "activemodel" "activerecord" "activesupport" "railties" "sprockets-rails"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "15vbdlkmlh470g7msqhmcmhxhi4finv3cjg595x9viafvphnf40l"; + sha256 = "117z277m78cw6bm43dyzxhjmx8awpidmqcjjx99kpj4rgqm5m0bn"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; + }; + rails-controller-testing = { + dependencies = ["actionpack" "actionview" "activesupport"]; + source = { + remotes = ["https://rubygems.org"]; + sha256 = "16kdkk73mhhs73iz3i1i0ryjm84dadiyh817b3nh8acdi490jyhy"; + type = "gem"; + }; + version = "1.0.2"; }; rails-deprecated_sanitizer = { dependencies = ["activesupport"]; @@ -2336,13 +2395,13 @@ version = "1.0.3"; }; rails-dom-testing = { - dependencies = ["activesupport" "nokogiri" "rails-deprecated_sanitizer"]; + dependencies = ["activesupport" "nokogiri"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0wssfqpn00byhvp2372p99mphkcj8qx6pf6646avwr9ifvq0q1x6"; + sha256 = "1lfq2a7kp2x64dzzi5p4cjcbiv62vxh9lyqk2f0rqq3fkzrw8h5i"; type = "gem"; }; - version = "1.0.9"; + version = "2.0.3"; }; rails-html-sanitizer = { dependencies = ["loofah"]; @@ -2357,19 +2416,19 @@ dependencies = ["i18n" "railties"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "17a02f2671pw5r2hl2n3isiz6w9wy2dxq8g52srciyl1xcmvsw01"; + sha256 = "1rqij2ggqz5iq36lbibhnd7pl4qxrvv9kgw9s0c6594vzbbxmhs0"; type = "gem"; }; - version = "4.0.9"; + version = "5.1.1"; }; railties = { - dependencies = ["actionpack" "activesupport" "rake" "thor"]; + dependencies = ["actionpack" "activesupport" "method_source" "rake" "thor"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0snymfqj2cql0gp51i6a44avcirdridc15yggnxjj9raa9f3229p"; + sha256 = "0j6v5ylwgqmxs4pllgip5yxdsivdqs1w00cs8jfqyw5v7pn9b2z0"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; rainbow = { source = { @@ -2536,10 +2595,10 @@ dependencies = ["redis"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "00yh8rhv91vxjlqs4ylic99m9npjxmgib2vjj8hgzk1174y6vcmq"; + sha256 = "1mrcnjgkbmx1zf569mly82agdizqayjvnp2k6055k1iy07in3j8b"; type = "gem"; }; - version = "1.4.1"; + version = "1.6.0"; }; regexp_parser = { source = { @@ -2671,13 +2730,13 @@ version = "3.7.0"; }; rspec-parameterized = { - dependencies = ["binding_of_caller" "parser" "proc_to_ast" "rspec" "unparser"]; + dependencies = ["binding_ninja" "parser" "proc_to_ast" "rspec" "unparser"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0arynbr6cfjhccwc8gy2xf87nybdnncsnmfwknnh8s7d4mj730p0"; + sha256 = "159yw3mb4dab5kr18a97miyyi7dqmyrfjp3aw6r6j9i4xkc4xk3a"; type = "gem"; }; - version = "0.4.0"; + version = "0.4.1"; }; rspec-rails = { dependencies = ["actionpack" "activesupport" "railties" "rspec-core" "rspec-expectations" "rspec-mocks" "rspec-support"]; @@ -2714,13 +2773,13 @@ version = "3.7.1"; }; rspec_junit_formatter = { - dependencies = ["builder" "rspec-core"]; + dependencies = ["rspec-core"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0hphl8iggqh1mpbbv0avf8735x6jgry5wmkqyzgv1zwnimvja1ai"; + sha256 = "1aynmrgnv26pkprrajvp7advb8nbh0x4pkwk6jwq8qmwzarzk21p"; type = "gem"; }; - version = "0.2.3"; + version = "0.4.1"; }; rspec_profiling = { dependencies = ["activerecord" "pg" "rails" "sqlite3"]; @@ -2805,10 +2864,10 @@ dependencies = ["sexp_processor"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "18apbsmmivgc1schfxmkp429aijrwy8psm30dwx5cpmpjf48ir3n"; + sha256 = "0mysmdyxhvyn6dhshfxyw762f9asr3kxw45idvw1bh6np31kk4j1"; type = "gem"; }; - version = "3.9.0"; + version = "3.11.0"; }; rubyntlm = { source = { @@ -2944,10 +3003,10 @@ dependencies = ["faraday"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0yf2gysjw6sy1xcp2jw35z9cp83pwx33lq0qyvaqbs969j4993r4"; + sha256 = "0l0bci35amy7pqv81djyjcx023q4qylmq8a2zbx14zh6ifzib4f4"; type = "gem"; }; - version = "2.7.2"; + version = "2.7.4"; }; settingslogic = { source = { @@ -2960,10 +3019,10 @@ sexp_processor = { source = { remotes = ["https://rubygems.org"]; - sha256 = "1c6kp2qxq550hz7gsxqi37irxn3vynkz7ibgy9hfwqymf6y1jdik"; + sha256 = "1vnmphfrd86694x5k7rxddbhbvv5rqbglsc34kfryy4jqhbzz42c"; type = "gem"; }; - version = "4.9.0"; + version = "4.11.0"; }; sham_rack = { dependencies = ["rack"]; @@ -2987,10 +3046,10 @@ dependencies = ["connection_pool" "rack-protection" "redis"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0s57vl2hwfaga73yiscak2rs7byg1q0z44wa9si9vl92qcmbik2j"; + sha256 = "1zyf9y3rvzizbwh68i2g1lzd40lalrdc4iyjmaa74gnfwsf92i26"; type = "gem"; }; - version = "5.2.1"; + version = "5.2.3"; }; sidekiq-cron = { dependencies = ["rufus-scheduler" "sidekiq"]; @@ -3162,15 +3221,6 @@ }; version = "0.2.5"; }; - test_after_commit = { - dependencies = ["activerecord"]; - source = { - remotes = ["https://rubygems.org"]; - sha256 = "0s8pz00xq28lsa1rfczm83yqwk8wcb5dqw2imlj8gldnsdapcyc2"; - type = "gem"; - }; - version = "1.1.0"; - }; text = { source = { remotes = ["https://rubygems.org"]; @@ -3352,10 +3402,10 @@ dependencies = ["abstract_type" "adamantium" "concord" "diff-lcs" "equalizer" "parser" "procto"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0k2asbk9k5kzq8jidy3frqcmn58i9cvaizn8f6g5xlx1pn70bx1w"; + sha256 = "0w662glqi7hwmfvx0smxckxgc7kw5bsqhqz0pyvalbyv1gc0gs2x"; type = "gem"; }; - version = "0.2.7"; + version = "0.4.2"; }; validates_hostname = { dependencies = ["activerecord" "activesupport"]; @@ -3418,6 +3468,23 @@ }; version = "0.9.11"; }; + websocket-driver = { + dependencies = ["websocket-extensions"]; + source = { + remotes = ["https://rubygems.org"]; + sha256 = "1943442yllhldh9dbp374x2q39cxa49xrm28nb78b7mfbv3y195l"; + type = "gem"; + }; + version = "0.6.5"; + }; + websocket-extensions = { + source = { + remotes = ["https://rubygems.org"]; + sha256 = "034sdr7fd34yag5l6y156rkbhiqgmy395m231dwhlpcswhs6d270"; + type = "gem"; + }; + version = "0.1.3"; + }; wikicloth = { dependencies = ["builder" "expression_parser" "rinku"]; source = { From 4d7ce7a60588ca77d1c9edbaa536cad913e63950 Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Mon, 24 Dec 2018 03:32:43 +0100 Subject: [PATCH 013/247] gitlab-ee: 11.5.5 -> 11.6.0 --- .../version-management/gitlab/data.json | 16 +- .../gitlab/rubyEnv-ee/Gemfile | 61 ++-- .../gitlab/rubyEnv-ee/Gemfile.lock | 258 +++++++------- .../gitlab/rubyEnv-ee/gemset.nix | 315 +++++++++++------- 4 files changed, 377 insertions(+), 273 deletions(-) diff --git a/pkgs/applications/version-management/gitlab/data.json b/pkgs/applications/version-management/gitlab/data.json index e7cb8e2b2673..37925b3be10f 100644 --- a/pkgs/applications/version-management/gitlab/data.json +++ b/pkgs/applications/version-management/gitlab/data.json @@ -15,18 +15,18 @@ } }, "ee": { - "version": "11.5.5", - "repo_hash": "1j5g0x7rxrdb39b12psjirsa3s0lhqgnxh0q3r22cgzgxv0332b8", - "deb_hash": "193s1f7w9lcamqnmrc7c3klmybqqra7yr16x6ay0cznwcdgirisp", - "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ee/packages/debian/stretch/gitlab-ee_11.5.5-ee.0_amd64.deb/download.deb", + "version": "11.6.0", + "repo_hash": "0zaif61qf7y0r7sh3vdmxacvzw8hcgj8xhj69iy0jcxf508wbysh", + "deb_hash": "1ksdnfzfdb2qcvq60dhhxi5iab8bjvddfnjbs6zaw0m0ymdrnsxb", + "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ee/packages/debian/stretch/gitlab-ee_11.6.0-ee.0_amd64.deb/download.deb", "owner": "gitlab-org", "repo": "gitlab-ee", - "rev": "v11.5.5-ee", + "rev": "v11.6.0-ee", "passthru": { - "GITALY_SERVER_VERSION": "0.129.0", + "GITALY_SERVER_VERSION": "1.7.1", "GITLAB_PAGES_VERSION": "1.3.1", - "GITLAB_SHELL_VERSION": "8.4.1", - "GITLAB_WORKHORSE_VERSION": "7.1.3" + "GITLAB_SHELL_VERSION": "8.4.3", + "GITLAB_WORKHORSE_VERSION": "7.6.0" } } } \ No newline at end of file diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile b/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile index fc31db6278df..3e8c5112a39b 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile @@ -1,13 +1,17 @@ # --- Special code for migrating to Rails 5.0 --- def rails5? - %w[1 true].include?(ENV["RAILS5"]) + !%w[0 false].include?(ENV["RAILS5"]) end gem_versions = {} -gem_versions['activerecord_sane_schema_dumper'] = rails5? ? '1.0' : '0.2' -gem_versions['default_value_for'] = rails5? ? '~> 3.0.5' : '~> 3.0.0' -gem_versions['rails'] = rails5? ? '5.0.7' : '4.2.10' -gem_versions['rails-i18n'] = rails5? ? '~> 5.1' : '~> 4.0.9' +gem_versions['activerecord_sane_schema_dumper'] = rails5? ? '1.0' : '0.2' +gem_versions['rails'] = rails5? ? '5.0.7' : '4.2.11' +gem_versions['rails-i18n'] = rails5? ? '~> 5.1' : '~> 4.0.9' + +# The 2.0.6 version of rack requires monkeypatch to be present in +# `config.ru`. This can be removed once a new update for Rack +# is available that contains https://github.com/rack/rack/pull/1201. +gem_versions['rack'] = rails5? ? '2.0.6' : '1.6.11' # --- The end of special code for migrating to Rails 5.0 --- source 'https://rubygems.org' @@ -15,13 +19,20 @@ source 'https://rubygems.org' gem 'rails', gem_versions['rails'] gem 'rails-deprecated_sanitizer', '~> 1.0.3' +# Improves copy-on-write performance for MRI +gem 'nakayoshi_fork', '~> 0.0.4' + # Responders respond_to and respond_with gem 'responders', '~> 2.0' gem 'sprockets', '~> 3.7.0' # Default values for AR models -gem 'default_value_for', gem_versions['default_value_for'] +if rails5? + gem 'gitlab-default_value_for', '~> 3.1.1', require: 'default_value_for' +else + gem 'default_value_for', '~> 3.0.0' +end # Supported DBs gem 'mysql2', '~> 0.4.10', group: :mysql @@ -74,7 +85,7 @@ gem 'validates_hostname', '~> 1.0.6' gem 'browser', '~> 2.5' # GPG -gem 'gpgme' +gem 'gpgme', '~> 2.0.18' # LDAP Auth # GitLab fork with several improvements to original library. For full list of changes @@ -83,7 +94,7 @@ gem 'gitlab_omniauth-ldap', '~> 2.0.4', require: 'omniauth-ldap' gem 'net-ldap' # API -gem 'grape', '~> 1.1' +gem 'grape', '~> 1.1.0' gem 'grape-entity', '~> 0.7.1' gem 'rack-cors', '~> 1.0.0', require: 'rack/cors' @@ -134,7 +145,7 @@ gem 'faraday_middleware-aws-signers-v4' # Markdown and HTML processing gem 'html-pipeline', '~> 2.8' gem 'deckar01-task_list', '2.0.0' -gem 'gitlab-markup', '~> 1.6.4' +gem 'gitlab-markup', '~> 1.6.5' gem 'github-markup', '~> 1.7.0', require: 'github/markup' gem 'redcarpet', '~> 3.4' gem 'commonmarker', '~> 0.17' @@ -143,7 +154,7 @@ gem 'rdoc', '~> 6.0' gem 'org-ruby', '~> 0.9.12' gem 'creole', '~> 0.5.0' gem 'wikicloth', '0.8.1' -gem 'asciidoctor', '~> 1.5.6' +gem 'asciidoctor', '~> 1.5.8' gem 'asciidoctor-plantuml', '0.0.8' gem 'rouge', '~> 3.1' gem 'truncato', '~> 0.7.9' @@ -158,6 +169,8 @@ gem 'icalendar' gem 'diffy', '~> 3.1.0' # Application server +gem 'rack', gem_versions['rack'] + group :unicorn do gem 'unicorn', '~> 5.1.0' gem 'unicorn-worker-killer', '~> 0.4.4' @@ -178,6 +191,7 @@ gem 'acts-as-taggable-on', '~> 5.0' gem 'sidekiq', '~> 5.2.1' gem 'sidekiq-cron', '~> 0.6.0' gem 'redis-namespace', '~> 1.6.0' +gem 'gitlab-sidekiq-fetcher', '~> 0.1.0', require: 'sidekiq-reliable-fetch' # Cron Parser gem 'rufus-scheduler', '~> 3.4' @@ -214,6 +228,9 @@ gem 'redis-rails', '~> 5.0.2' gem 'redis', '~> 3.2' gem 'connection_pool', '~> 2.0' +# Discord integration +gem 'discordrb-webhooks-blackst0ne', '~> 3.3', require: false + # HipChat integration gem 'hipchat', '~> 1.5.0' @@ -230,13 +247,13 @@ gem 'slack-notifier', '~> 1.5.1' gem 'hangouts-chat', '~> 0.0.5' # Asana integration -gem 'asana', '~> 0.6.0' +gem 'asana', '~> 0.8.1' # FogBugz integration gem 'ruby-fogbugz', '~> 0.2.1' # Kubernetes integration -gem 'kubeclient', '~> 3.1.0' +gem 'kubeclient', '~> 4.0.0' # Sanitize user input gem 'sanitize', '~> 4.6' @@ -257,6 +274,9 @@ gem 'ace-rails-ap', '~> 4.1.0' # Detect and convert string character encoding gem 'charlock_holmes', '~> 0.7.5' +# Detect mime content type from content +gem 'mimemagic', '~> 0.3.2' + # Faster blank gem 'fast_blank' @@ -294,7 +314,7 @@ gem 'gettext_i18n_rails', '~> 1.8.0' gem 'gettext_i18n_rails_js', '~> 1.3' gem 'gettext', '~> 3.2.2', require: false, group: :development -gem 'batch-loader', '~> 1.2.1' +gem 'batch-loader', '~> 1.2.2' # Perf bar gem 'peek', '~> 1.0.1' @@ -303,7 +323,6 @@ gem 'peek-mysql2', '~> 1.1.0', group: :mysql gem 'peek-pg', '~> 1.3.0', group: :postgres gem 'peek-rblineprof', '~> 0.2.0' gem 'peek-redis', '~> 1.2.0' -gem 'gitlab-sidekiq-fetcher', require: 'sidekiq-reliable-fetch' # Metrics group :metrics do @@ -323,8 +342,8 @@ group :development do gem 'rblineprof', '~> 0.3.6', platform: :mri, require: false # Better errors handler - gem 'better_errors', '~> 2.1.0' - gem 'binding_of_caller', '~> 0.7.2' + gem 'better_errors', '~> 2.5.0' + gem 'binding_of_caller', '~> 0.8.0' # thin instead webrick gem 'thin', '~> 1.7.0' @@ -351,7 +370,7 @@ group :development, :test do gem 'minitest', '~> 5.7.0' # Generate Fake data - gem 'ffaker', '~> 2.4' + gem 'ffaker', '~> 2.10' gem 'capybara', '~> 2.15' gem 'capybara-screenshot', '~> 1.0.0' @@ -366,14 +385,14 @@ group :development, :test do gem 'rubocop-rspec', '~> 1.22.1' gem 'scss_lint', '~> 0.56.0', require: false - gem 'haml_lint', '~> 0.26.0', require: false + gem 'haml_lint', '~> 0.28.0', require: false gem 'simplecov', '~> 0.14.0', require: false gem 'bundler-audit', '~> 0.5.0', require: false gem 'benchmark-ips', '~> 2.3.0', require: false gem 'license_finder', '~> 5.4', require: false - gem 'knapsack', '~> 1.16' + gem 'knapsack', '~> 1.17' gem 'activerecord_sane_schema_dumper', gem_versions['activerecord_sane_schema_dumper'] @@ -392,7 +411,7 @@ group :test do gem 'rails-controller-testing' if rails5? # Rails5 only gem. gem 'test_after_commit', '~> 1.1' unless rails5? # Remove this gem when migrated to rails 5.0. It's been integrated to rails 5.0. gem 'sham_rack', '~> 1.3.6' - gem 'concurrent-ruby', '~> 1.0.5' + gem 'concurrent-ruby', '~> 1.1' gem 'test-prof', '~> 0.2.5' gem 'rspec_junit_formatter' end @@ -431,7 +450,7 @@ group :ed25519 do end # Gitaly GRPC client -gem 'gitaly-proto', '~> 0.123.0', require: 'gitaly' +gem 'gitaly-proto', '~> 1.3.0', require: 'gitaly' gem 'grpc', '~> 1.15.0' gem 'google-protobuf', '~> 3.6' diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile.lock b/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile.lock index 42b6f0cbc48e..f6ced99bece5 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile.lock +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile.lock @@ -4,41 +4,44 @@ GEM RedCloth (4.3.2) abstract_type (0.0.7) ace-rails-ap (4.1.2) - actionmailer (4.2.10) - actionpack (= 4.2.10) - actionview (= 4.2.10) - activejob (= 4.2.10) + actioncable (5.0.7) + actionpack (= 5.0.7) + nio4r (>= 1.2, < 3.0) + websocket-driver (~> 0.6.1) + actionmailer (5.0.7) + actionpack (= 5.0.7) + actionview (= 5.0.7) + activejob (= 5.0.7) mail (~> 2.5, >= 2.5.4) - rails-dom-testing (~> 1.0, >= 1.0.5) - actionpack (4.2.10) - actionview (= 4.2.10) - activesupport (= 4.2.10) - rack (~> 1.6) - rack-test (~> 0.6.2) - rails-dom-testing (~> 1.0, >= 1.0.5) + rails-dom-testing (~> 2.0) + actionpack (5.0.7) + actionview (= 5.0.7) + activesupport (= 5.0.7) + rack (~> 2.0) + rack-test (~> 0.6.3) + rails-dom-testing (~> 2.0) rails-html-sanitizer (~> 1.0, >= 1.0.2) - actionview (4.2.10) - activesupport (= 4.2.10) + actionview (5.0.7) + activesupport (= 5.0.7) builder (~> 3.1) erubis (~> 2.7.0) - rails-dom-testing (~> 1.0, >= 1.0.5) + rails-dom-testing (~> 2.0) rails-html-sanitizer (~> 1.0, >= 1.0.3) - activejob (4.2.10) - activesupport (= 4.2.10) - globalid (>= 0.3.0) - activemodel (4.2.10) - activesupport (= 4.2.10) - builder (~> 3.1) - activerecord (4.2.10) - activemodel (= 4.2.10) - activesupport (= 4.2.10) - arel (~> 6.0) - activerecord_sane_schema_dumper (0.2) - rails (>= 4, < 5) - activesupport (4.2.10) - i18n (~> 0.7) + activejob (5.0.7) + activesupport (= 5.0.7) + globalid (>= 0.3.6) + activemodel (5.0.7) + activesupport (= 5.0.7) + activerecord (5.0.7) + activemodel (= 5.0.7) + activesupport (= 5.0.7) + arel (~> 7.0) + activerecord_sane_schema_dumper (1.0) + rails (>= 5, < 6) + activesupport (5.0.7) + concurrent-ruby (~> 1.0, >= 1.0.2) + i18n (>= 0.7, < 2) minitest (~> 5.1) - thread_safe (~> 0.3, >= 0.3.4) tzinfo (~> 1.1) acts-as-taggable-on (5.0.0) activerecord (>= 4.2.8) @@ -49,13 +52,13 @@ GEM public_suffix (>= 2.0.2, < 4.0) aes_key_wrap (1.0.1) akismet (2.0.0) - arel (6.0.4) - asana (0.6.0) + arel (7.1.4) + asana (0.8.1) faraday (~> 0.9) faraday_middleware (~> 0.9) faraday_middleware-multi_json (~> 0.0) oauth2 (~> 1.0) - asciidoctor (1.5.6.2) + asciidoctor (1.5.8) asciidoctor-plantuml (0.0.8) asciidoctor (~> 1.5) ast (2.4.0) @@ -78,16 +81,17 @@ GEM thread_safe (~> 0.3, >= 0.3.1) babosa (1.0.2) base32 (0.3.2) - batch-loader (1.2.1) + batch-loader (1.2.2) bcrypt (3.1.12) bcrypt_pbkdf (1.0.0) benchmark-ips (2.3.0) - better_errors (2.1.1) + better_errors (2.5.0) coderay (>= 1.0.0) - erubis (>= 2.6.6) + erubi (>= 1.0.0) rack (>= 0.9.0) bindata (2.4.3) - binding_of_caller (0.7.2) + binding_ninja (0.2.2) + binding_of_caller (0.8.0) debug_inspector (>= 0.0.1) bootsnap (1.3.2) msgpack (~> 1.0) @@ -133,9 +137,9 @@ GEM concord (0.1.5) adamantium (~> 0.2.0) equalizer (~> 0.0.9) - concurrent-ruby (1.0.5) - concurrent-ruby-ext (1.0.5) - concurrent-ruby (= 1.0.5) + concurrent-ruby (1.1.3) + concurrent-ruby-ext (1.1.3) + concurrent-ruby (= 1.1.3) connection_pool (2.2.2) crack (0.4.3) safe_yaml (~> 1.0.0) @@ -145,14 +149,12 @@ GEM addressable daemons (1.2.6) database_cleaner (1.5.3) - debug_inspector (0.0.2) + debug_inspector (0.0.3) debugger-ruby_core_source (1.3.8) deckar01-task_list (2.0.0) html-pipeline declarative (0.0.10) declarative-option (0.1.0) - default_value_for (3.0.2) - activerecord (>= 3.2.0, < 5.1) descendants_tracker (0.0.4) thread_safe (~> 0.3, >= 0.3.1) device_detector (1.0.0) @@ -170,6 +172,8 @@ GEM rotp (~> 2.0) diff-lcs (1.3) diffy (3.1.0) + discordrb-webhooks-blackst0ne (3.3.0) + rest-client (~> 2.0) docile (1.1.5) domain_name (0.5.20180417) unf (>= 0.0.5, < 1.0.0) @@ -199,8 +203,9 @@ GEM mail (~> 2.7) encryptor (3.0.0) equalizer (0.0.11) + erubi (1.7.1) erubis (2.7.0) - escape_utils (1.1.1) + escape_utils (1.2.1) et-orbi (1.0.3) tzinfo eventmachine (1.2.7) @@ -224,7 +229,7 @@ GEM multi_json fast_blank (1.0.0) fast_gettext (1.6.0) - ffaker (2.4.0) + ffaker (2.10.0) ffi (1.9.25) flipper (0.13.0) flipper-active_record (0.13.0) @@ -293,12 +298,14 @@ GEM gettext_i18n_rails (>= 0.7.1) po_to_json (>= 1.0.0) rails (>= 3.2.0) - gitaly-proto (0.123.0) + gitaly-proto (1.3.0) grpc (~> 1.0) github-markup (1.7.0) + gitlab-default_value_for (3.1.1) + activerecord (>= 3.2.0, < 6.0) gitlab-license (1.0.0) - gitlab-markup (1.6.4) - gitlab-sidekiq-fetcher (0.3.0) + gitlab-markup (1.6.5) + gitlab-sidekiq-fetcher (0.1.0) sidekiq (~> 5) gitlab-styles (2.4.1) rubocop (~> 0.54.0) @@ -332,8 +339,8 @@ GEM multi_json (~> 1.11) os (>= 0.9, < 2.0) signet (~> 0.7) - gpgme (2.0.13) - mini_portile2 (~> 2.1) + gpgme (2.0.18) + mini_portile2 (~> 2.3) grape (1.1.0) activesupport builder @@ -362,11 +369,11 @@ GEM haml (5.0.4) temple (>= 0.8.0) tilt - haml_lint (0.26.0) + haml_lint (0.28.0) haml (>= 4.0, < 5.1) rainbow rake (>= 10, < 13) - rubocop (>= 0.49.0) + rubocop (>= 0.50.0) sysexits (~> 1.1) hamlit (2.8.8) temple (>= 0.8.0) @@ -388,20 +395,20 @@ GEM html2text (0.2.0) nokogiri (~> 1.6) htmlentities (4.3.4) - http (2.2.2) + http (3.3.0) addressable (~> 2.3) http-cookie (~> 1.0) - http-form_data (~> 1.0.1) + http-form_data (~> 2.0) http_parser.rb (~> 0.6.0) http-cookie (1.0.3) domain_name (~> 0.5) - http-form_data (1.0.3) + http-form_data (2.1.1) http_parser.rb (0.6.0) httparty (0.13.7) json (~> 1.8) multi_xml (>= 0.5.2) httpclient (2.8.3) - i18n (0.9.5) + i18n (1.1.1) concurrent-ruby (~> 1.0) icalendar (2.4.1) ice_nine (0.11.2) @@ -438,10 +445,10 @@ GEM kaminari-core (= 1.0.1) kaminari-core (1.0.1) kgio (2.10.0) - knapsack (1.16.0) + knapsack (1.17.0) rake - kubeclient (3.1.0) - http (~> 2.2.2) + kubeclient (4.0.0) + http (~> 3.0) recursive-open-struct (~> 1.0, >= 1.0.4) rest-client (~> 2.0) launchy (2.4.3) @@ -467,7 +474,7 @@ GEM activesupport (>= 4) railties (>= 4) request_store (~> 1.0) - loofah (2.2.2) + loofah (2.2.3) crass (~> 1.0.2) nokogiri (>= 1.5.9) mail (2.7.0) @@ -476,11 +483,11 @@ GEM memoist (0.16.0) memoizable (0.4.2) thread_safe (~> 0.3, >= 0.3.1) - method_source (0.9.0) - mime-types (3.1) + method_source (0.9.2) + mime-types (3.2.2) mime-types-data (~> 3.2015) - mime-types-data (3.2016.0521) - mimemagic (0.3.0) + mime-types-data (3.2018.0812) + mimemagic (0.3.2) mini_magick (4.8.0) mini_mime (1.0.1) mini_portile2 (2.3.0) @@ -493,11 +500,13 @@ GEM mustermann-grape (1.0.0) mustermann (~> 1.0.0) mysql2 (0.4.10) + nakayoshi_fork (0.0.4) net-ldap (0.16.0) net-ntp (2.1.3) net-ssh (5.0.1) netrc (0.11.0) - nokogiri (1.8.4) + nio4r (2.3.1) + nokogiri (1.8.5) mini_portile2 (~> 2.3.0) nokogumbo (1.5.0) nokogiri @@ -625,7 +634,7 @@ GEM get_process_mem (~> 0.2) puma (>= 2.7, < 4) pyu-ruby-sasl (0.0.3.3) - rack (1.6.10) + rack (2.0.6) rack-accept (0.4.5) rack (>= 0.4) rack-attack (4.4.1) @@ -637,37 +646,42 @@ GEM httpclient (>= 2.4) multi_json (>= 1.3.6) rack (>= 1.1) - rack-protection (2.0.3) + rack-protection (2.0.4) rack rack-proxy (0.6.0) rack rack-test (0.6.3) rack (>= 1.0) - rails (4.2.10) - actionmailer (= 4.2.10) - actionpack (= 4.2.10) - actionview (= 4.2.10) - activejob (= 4.2.10) - activemodel (= 4.2.10) - activerecord (= 4.2.10) - activesupport (= 4.2.10) - bundler (>= 1.3.0, < 2.0) - railties (= 4.2.10) - sprockets-rails + rails (5.0.7) + actioncable (= 5.0.7) + actionmailer (= 5.0.7) + actionpack (= 5.0.7) + actionview (= 5.0.7) + activejob (= 5.0.7) + activemodel (= 5.0.7) + activerecord (= 5.0.7) + activesupport (= 5.0.7) + bundler (>= 1.3.0) + railties (= 5.0.7) + sprockets-rails (>= 2.0.0) + rails-controller-testing (1.0.2) + actionpack (~> 5.x, >= 5.0.1) + actionview (~> 5.x, >= 5.0.1) + activesupport (~> 5.x) rails-deprecated_sanitizer (1.0.3) activesupport (>= 4.2.0.alpha) - rails-dom-testing (1.0.9) - activesupport (>= 4.2.0, < 5.0) - nokogiri (~> 1.6) - rails-deprecated_sanitizer (>= 1.0.1) + rails-dom-testing (2.0.3) + activesupport (>= 4.2.0) + nokogiri (>= 1.6) rails-html-sanitizer (1.0.4) loofah (~> 2.2, >= 2.2.2) - rails-i18n (4.0.9) - i18n (~> 0.7) - railties (~> 4.0) - railties (4.2.10) - actionpack (= 4.2.10) - activesupport (= 4.2.10) + rails-i18n (5.1.1) + i18n (>= 0.7, < 2) + railties (>= 5.0, < 6) + railties (5.0.7) + actionpack (= 5.0.7) + activesupport (= 5.0.7) + method_source rake (>= 0.8.7) thor (>= 0.18.1, < 2.0) rainbow (3.0.0) @@ -705,7 +719,7 @@ GEM redis-actionpack (>= 5.0, < 6) redis-activesupport (>= 5.0, < 6) redis-store (>= 1.2, < 2) - redis-store (1.4.1) + redis-store (1.6.0) redis (>= 2.2, < 5) regexp_parser (0.5.0) representable (3.0.4) @@ -740,8 +754,8 @@ GEM rspec-mocks (3.7.0) diff-lcs (>= 1.2.0, < 2.0) rspec-support (~> 3.7.0) - rspec-parameterized (0.4.0) - binding_of_caller + rspec-parameterized (0.4.1) + binding_ninja (>= 0.2.1) parser proc_to_ast rspec (>= 2.13, < 4) @@ -758,8 +772,7 @@ GEM rspec-core rspec-set (0.1.3) rspec-support (3.7.1) - rspec_junit_formatter (0.2.3) - builder (< 4) + rspec_junit_formatter (0.4.1) rspec-core (>= 2, < 4, != 2.12.0) rspec_profiling (0.0.5) activerecord @@ -785,8 +798,8 @@ GEM ruby-progressbar (1.9.0) ruby-saml (1.7.2) nokogiri (>= 1.5.10) - ruby_parser (3.9.0) - sexp_processor (~> 4.1) + ruby_parser (3.11.0) + sexp_processor (~> 4.9) rubyntlm (0.6.2) rubypants (0.2.0) rubyzip (1.2.2) @@ -823,15 +836,15 @@ GEM selenium-webdriver (3.12.0) childprocess (~> 0.5) rubyzip (~> 1.2) - sentry-raven (2.7.2) + sentry-raven (2.7.4) faraday (>= 0.7.6, < 1.0) settingslogic (2.0.9) - sexp_processor (4.9.0) + sexp_processor (4.11.0) sham_rack (1.3.6) rack shoulda-matchers (3.1.2) activesupport (>= 4.0.0) - sidekiq (5.2.1) + sidekiq (5.2.3) connection_pool (~> 2.2, >= 2.2.2) rack-protection (>= 1.5.0) redis (>= 3.3.5, < 5) @@ -876,8 +889,6 @@ GEM sysexits (1.2.0) temple (0.8.0) test-prof (0.2.5) - test_after_commit (1.1.0) - activerecord (>= 3.2) text (1.3.1) thin (1.7.2) daemons (~> 1.0, >= 1.0.9) @@ -914,7 +925,7 @@ GEM get_process_mem (~> 0) unicorn (>= 4, < 6) uniform_notifier (1.10.0) - unparser (0.2.7) + unparser (0.4.2) abstract_type (~> 0.0.7) adamantium (~> 0.2.0) concord (~> 0.1.5) @@ -940,6 +951,9 @@ GEM hashdiff webpack-rails (0.9.11) railties (>= 3.2.0) + websocket-driver (0.6.5) + websocket-extensions (>= 0.1.0) + websocket-extensions (0.1.3) wikicloth (0.8.1) builder expression_parser @@ -955,23 +969,23 @@ PLATFORMS DEPENDENCIES RedCloth (~> 4.3.2) ace-rails-ap (~> 4.1.0) - activerecord_sane_schema_dumper (= 0.2) + activerecord_sane_schema_dumper (= 1.0) acts-as-taggable-on (~> 5.0) addressable (~> 2.5.2) akismet (~> 2.0) - asana (~> 0.6.0) - asciidoctor (~> 1.5.6) + asana (~> 0.8.1) + asciidoctor (~> 1.5.8) asciidoctor-plantuml (= 0.0.8) attr_encrypted (~> 3.1.0) awesome_print aws-sdk babosa (~> 1.0.2) base32 (~> 0.3.0) - batch-loader (~> 1.2.1) + batch-loader (~> 1.2.2) bcrypt_pbkdf (~> 1.0) benchmark-ips (~> 2.3.0) - better_errors (~> 2.1.0) - binding_of_caller (~> 0.7.2) + better_errors (~> 2.5.0) + binding_of_caller (~> 0.8.0) bootsnap (~> 1.3) bootstrap_form (~> 2.7.0) brakeman (~> 4.2) @@ -985,16 +999,16 @@ DEPENDENCIES chronic (~> 0.10.2) chronic_duration (~> 0.10.6) commonmarker (~> 0.17) - concurrent-ruby (~> 1.0.5) + concurrent-ruby (~> 1.1) connection_pool (~> 2.0) creole (~> 0.5.0) database_cleaner (~> 1.5.0) deckar01-task_list (= 2.0.0) - default_value_for (~> 3.0.0) device_detector devise (~> 4.4) devise-two-factor (~> 3.0.0) diffy (~> 3.1.0) + discordrb-webhooks-blackst0ne (~> 3.3) doorkeeper (~> 4.3) doorkeeper-openid_connect (~> 1.5) ed25519 (~> 1.2) @@ -1008,7 +1022,7 @@ DEPENDENCIES faraday (~> 0.12) faraday_middleware-aws-signers-v4 fast_blank - ffaker (~> 2.4) + ffaker (~> 2.10) flipper (~> 0.13.0) flipper-active_record (~> 0.13.0) flipper-active_support_cache_store (~> 0.13.0) @@ -1027,18 +1041,19 @@ DEPENDENCIES gettext (~> 3.2.2) gettext_i18n_rails (~> 1.8.0) gettext_i18n_rails_js (~> 1.3) - gitaly-proto (~> 0.123.0) + gitaly-proto (~> 1.3.0) github-markup (~> 1.7.0) + gitlab-default_value_for (~> 3.1.1) gitlab-license (~> 1.0) - gitlab-markup (~> 1.6.4) - gitlab-sidekiq-fetcher + gitlab-markup (~> 1.6.5) + gitlab-sidekiq-fetcher (~> 0.1.0) gitlab-styles (~> 2.4) gitlab_omniauth-ldap (~> 2.0.4) gon (~> 6.2) google-api-client (~> 0.23) google-protobuf (~> 3.6) - gpgme - grape (~> 1.1) + gpgme (~> 2.0.18) + grape (~> 1.1.0) grape-entity (~> 0.7.1) grape-path-helpers (~> 1.0) grape_logging (~> 1.7) @@ -1046,7 +1061,7 @@ DEPENDENCIES graphql (~> 1.8.0) grpc (~> 1.15.0) gssapi - haml_lint (~> 0.26.0) + haml_lint (~> 0.28.0) hamlit (~> 2.8.8) hangouts-chat (~> 0.0.5) hashie-forbidden_attributes @@ -1063,8 +1078,8 @@ DEPENDENCIES json-schema (~> 2.8.0) jwt (~> 1.5.6) kaminari (~> 1.0) - knapsack (~> 1.16) - kubeclient (~> 3.1.0) + knapsack (~> 1.17) + kubeclient (~> 4.0.0) letter_opener_web (~> 1.3.0) license_finder (~> 5.4) licensee (~> 8.9) @@ -1072,9 +1087,11 @@ DEPENDENCIES loofah (~> 2.2) mail_room (~> 0.9.1) method_source (~> 0.8) + mimemagic (~> 0.3.2) mini_magick minitest (~> 5.7.0) mysql2 (~> 0.4.10) + nakayoshi_fork (~> 0.0.4) net-ldap net-ntp net-ssh (~> 5.0) @@ -1110,13 +1127,15 @@ DEPENDENCIES pry-rails (~> 0.3.4) puma (~> 3.12) puma_worker_killer + rack (= 2.0.6) rack-attack (~> 4.4.1) rack-cors (~> 1.0.0) rack-oauth2 (~> 1.2.1) rack-proxy (~> 0.6.0) - rails (= 4.2.10) + rails (= 5.0.7) + rails-controller-testing rails-deprecated_sanitizer (~> 1.0.3) - rails-i18n (~> 4.0.9) + rails-i18n (~> 5.1) rainbow (~> 3.0) raindrops (~> 0.18) rblineprof (~> 0.3.6) @@ -1169,7 +1188,6 @@ DEPENDENCIES state_machines-activerecord (~> 0.5.1) sys-filesystem (~> 1.1.6) test-prof (~> 0.2.5) - test_after_commit (~> 1.1) thin (~> 1.7.0) timecop (~> 0.8.0) toml-rb (~> 1.0.0) diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ee/gemset.nix b/pkgs/applications/version-management/gitlab/rubyEnv-ee/gemset.nix index 460698bbb44a..f85528bb52e7 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ee/gemset.nix +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ee/gemset.nix @@ -15,77 +15,86 @@ }; version = "4.1.2"; }; + actioncable = { + dependencies = ["actionpack" "nio4r" "websocket-driver"]; + source = { + remotes = ["https://rubygems.org"]; + sha256 = "0b2znw81zf11f7kqyks80ha4sb4aiqrs1mia0jnf3xfn5zgx28y0"; + type = "gem"; + }; + version = "5.0.7"; + }; actionmailer = { dependencies = ["actionpack" "actionview" "activejob" "mail" "rails-dom-testing"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1ivyjsapqgn1xfb2p8yqjrg2jldqm5r7hxrjxq6kdr05gk4fsg59"; + sha256 = "0d9f3kwk1z3p6sa9d8vl7yqa689ihm24cy7lp4h6v478dbr156sz"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; actionpack = { dependencies = ["actionview" "activesupport" "rack" "rack-test" "rails-dom-testing" "rails-html-sanitizer"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0l6agrxdaishxjx2zc2x8md95plfp39bfskzgs6v9gsdp2y2arpx"; + sha256 = "15nin3f817dpkjlw94sh4rsvayqy4z6ij7fak82wqdqv5mcd9q08"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; actionview = { dependencies = ["activesupport" "builder" "erubis" "rails-dom-testing" "rails-html-sanitizer"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1jrx2pmkywk70z7n17gw3jrcdw3n03wdzvg45bnq8wxshl1lmbhv"; + sha256 = "12vvq439jjj4byhkvckrk7ap4krrfsbpw54n5xxfwh7fr5y0087b"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; activejob = { dependencies = ["activesupport" "globalid"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "10jsa5pqklcsd2npicqxr5abjlwi53di2brpzgz35k557fkpc1z8"; + sha256 = "1mdqdgwmcx28jznc5mfmqzz42y03mx6i6fs6m4nka0ic61rmp8g8"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; activemodel = { - dependencies = ["activesupport" "builder"]; + dependencies = ["activesupport"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0c4vj9xajxa906bqbcjpni74nya6rh2nbb15gl8xm0vl9zf3ll9v"; + sha256 = "11ycnzi32cd92ylxhqwqfchqk3m7y9z7sfiyf8b7830lzfxv2dgy"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; activerecord = { dependencies = ["activemodel" "activesupport" "arel"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1lws9y4p9c2vnmv3ddfpv8jh6azlddppl3fi31vahaz14ifxjk5s"; + sha256 = "0ri32lhmmd4waphpynwj53ysy9xlhx743lnlsnp8l499kvarqd66"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; activerecord_sane_schema_dumper = { dependencies = ["rails"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "122c7v7lvs0gwckvx2rar07waxnx1vv0lryz322nybb69d8vbhl6"; + sha256 = "16jbf461wjaxyq26si5505wcj46mi23mii9hx4wjpva1zn9hz5m2"; type = "gem"; }; - version = "0.2"; + version = "1.0"; }; activesupport = { - dependencies = ["i18n" "minitest" "thread_safe" "tzinfo"]; + dependencies = ["concurrent-ruby" "i18n" "minitest" "tzinfo"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0s12j8vl8vrxfngkdlz9g8bpz9akq1z42d57mx5r537b2pji8nr7"; + sha256 = "1yx73l984y3ri5ndj37l1dfarcdvbhra7vhz9fcww4za24is95d5"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; acts-as-taggable-on = { dependencies = ["activerecord"]; @@ -133,27 +142,27 @@ arel = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0nfcrdiys6q6ylxiblky9jyssrw2xj96fmxmal7f4f0jj3417vj4"; + sha256 = "0l757dkkaxk5fq3368l79jpyzq9a9driricjamhiwhwvh0h7xcyx"; type = "gem"; }; - version = "6.0.4"; + version = "7.1.4"; }; asana = { dependencies = ["faraday" "faraday_middleware" "faraday_middleware-multi_json" "oauth2"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0bn7f3sc2f02g871jd0y6qdhixn464mflkjchp56x6kcnyqy24z6"; + sha256 = "1h0qiywvjjc9iyzq9nz5iaqyh6qsrix4ip0w86j5c4v5g940z6qx"; type = "gem"; }; - version = "0.6.0"; + version = "0.8.1"; }; asciidoctor = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0zq3az4836nxkc8g5wnnbzmarw7663s1ky6gf8pc04sfpa8n2l3f"; + sha256 = "0qld3a1pbcjvs8lbxp95iz83bfmg5scmnf8q3rklinmdmhzakslx"; type = "gem"; }; - version = "1.5.6.2"; + version = "1.5.8"; }; asciidoctor-plantuml = { dependencies = ["asciidoctor"]; @@ -268,10 +277,10 @@ batch-loader = { source = { remotes = ["https://rubygems.org"]; - sha256 = "1nvmwzn8q6dkp2n8wz47z7gldj3yrj7h6syy0cwrkzi19bfvxba2"; + sha256 = "0pwr2hk9x1qx9i2xpkpjwkdjsmm4kamz5f25wizsaw37zb64apjc"; type = "gem"; }; - version = "1.2.1"; + version = "1.2.2"; }; bcrypt = { source = { @@ -298,13 +307,13 @@ version = "2.3.0"; }; better_errors = { - dependencies = ["coderay" "erubis" "rack"]; + dependencies = ["coderay" "erubi" "rack"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "11csk41yhijqvp0dkky0cjl8kn6blw4jhr8b6v4islfvvayddcxc"; + sha256 = "1pqnxxsqqs7vnqvamk5bzs84dv584g9s0qaf2vqb1v2aj5dabcg7"; type = "gem"; }; - version = "2.1.1"; + version = "2.5.0"; }; bindata = { source = { @@ -314,14 +323,22 @@ }; version = "2.4.3"; }; + binding_ninja = { + source = { + remotes = ["https://rubygems.org"]; + sha256 = "19dk26qyx433ffa6y48511apc2iw71zw4jnlqxhy0wix9dlxr2ri"; + type = "gem"; + }; + version = "0.2.2"; + }; binding_of_caller = { dependencies = ["debug_inspector"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "15jg6dkaq2nzcd602d7ppqbdxw3aji961942w93crs6qw4n6h9yk"; + sha256 = "05syqlks7463zsy1jdfbbdravdhj9hpj5pv2m74blqpv8bq4vv5g"; type = "gem"; }; - version = "0.7.2"; + version = "0.8.0"; }; bootsnap = { dependencies = ["msgpack"]; @@ -513,19 +530,19 @@ concurrent-ruby = { source = { remotes = ["https://rubygems.org"]; - sha256 = "183lszf5gx84kcpb779v6a2y0mx9sssy8dgppng1z9a505nj1qcf"; + sha256 = "18q9skp5pfq4jwbxzmw8q2rn4cpw6mf4561i2hsjcl1nxdag2jvb"; type = "gem"; }; - version = "1.0.5"; + version = "1.1.3"; }; concurrent-ruby-ext = { dependencies = ["concurrent-ruby"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "119l554zi3720d3rk670ldcqhsgmfii28a9z307v4mwdjckdm4gp"; + sha256 = "0h7k4wnvbxv7vzb53kaqxbbyhp3m98g2rgymr6n1l9v0jlzcr1i8"; type = "gem"; }; - version = "1.0.5"; + version = "1.1.3"; }; connection_pool = { source = { @@ -588,10 +605,10 @@ debug_inspector = { source = { remotes = ["https://rubygems.org"]; - sha256 = "109761g00dbrw5q0dfnbqg8blfm699z4jj70l4zrgf9mzn7ii50m"; + sha256 = "0vxr0xa1mfbkfcrn71n7c4f2dj7la5hvphn904vh20j3x4j5lrx0"; type = "gem"; }; - version = "0.0.2"; + version = "0.0.3"; }; debugger-ruby_core_source = { source = { @@ -626,15 +643,6 @@ }; version = "0.1.0"; }; - default_value_for = { - dependencies = ["activerecord"]; - source = { - remotes = ["https://rubygems.org"]; - sha256 = "014482mxjrc227fxv6vff6ccjr9dr0ydz52flxslsa7biq542k73"; - type = "gem"; - }; - version = "3.0.2"; - }; descendants_tracker = { dependencies = ["thread_safe"]; source = { @@ -686,6 +694,15 @@ }; version = "3.1.0"; }; + discordrb-webhooks-blackst0ne = { + dependencies = ["rest-client"]; + source = { + remotes = ["https://rubygems.org"]; + sha256 = "1f0dw6ci5cbrxrvvqw2kqabpzyjisd4hflbi370rpb4cakkzgw39"; + type = "gem"; + }; + version = "3.3.0"; + }; docile = { source = { remotes = ["https://rubygems.org"]; @@ -806,6 +823,14 @@ }; version = "0.0.11"; }; + erubi = { + source = { + remotes = ["https://rubygems.org"]; + sha256 = "0bws86na9k565raiz0kk61yy5pxxp0fmwyzpibdwjkq0xzx8q6q1"; + type = "gem"; + }; + version = "1.7.1"; + }; erubis = { source = { remotes = ["https://rubygems.org"]; @@ -817,10 +842,10 @@ escape_utils = { source = { remotes = ["https://rubygems.org"]; - sha256 = "088r5c2mz2vy2jbbx1xjbi8msnzg631ggli29nhik2spbcp1z6vh"; + sha256 = "0qminivnyzwmqjhrh3b92halwbk0zcl9xn828p5rnap1szl2yag5"; type = "gem"; }; - version = "1.1.1"; + version = "1.2.1"; }; et-orbi = { dependencies = ["tzinfo"]; @@ -936,10 +961,10 @@ ffaker = { source = { remotes = ["https://rubygems.org"]; - sha256 = "1rlfvf2iakphs3krxy1hiywr2jzmrhvhig8n8fw6rcivpz9v52ry"; + sha256 = "01z5lpssjc0n8lm4xrlja0hh8lv4ngzbybjvd4rdkc5x9ddvh8s3"; type = "gem"; }; - version = "2.4.0"; + version = "2.10.0"; }; ffi = { source = { @@ -1148,10 +1173,10 @@ dependencies = ["grpc"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "16b9sdaimhcda401z2s7apf0nz6y0lxs74xhkwlz4jzf6ms44mgg"; + sha256 = "17fg29j089k94ssim9hfzpd5lycvhimbpvz12d73ywrbwz7a7680"; type = "gem"; }; - version = "0.123.0"; + version = "1.3.0"; }; github-markup = { source = { @@ -1161,6 +1186,15 @@ }; version = "1.7.0"; }; + gitlab-default_value_for = { + dependencies = ["activerecord"]; + source = { + remotes = ["https://rubygems.org"]; + sha256 = "0qqjf7nxmwxnkdlrgbnby8wjckaj2s5yna96avgb7fwm0h90f1sn"; + type = "gem"; + }; + version = "3.1.1"; + }; gitlab-license = { source = { remotes = ["https://rubygems.org"]; @@ -1172,19 +1206,19 @@ gitlab-markup = { source = { remotes = ["https://rubygems.org"]; - sha256 = "1v6w3z7smmkqnhphb4ghgpqg61vimflqzpszybji0li99f2k1jb6"; + sha256 = "12lzzhbmid4m23pk7d963n3njli2hw7g200arszh75j57bjgs4fy"; type = "gem"; }; - version = "1.6.4"; + version = "1.6.5"; }; gitlab-sidekiq-fetcher = { dependencies = ["sidekiq"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0dvrp4iapwfaakc3qgf7mw05blxzfywpjfr7bhswwflih0pm67l7"; + sha256 = "08bwgagrdryva8vlwiiwfa3v60w9k13nknmjjfadrkn68a4ihk2a"; type = "gem"; }; - version = "0.3.0"; + version = "0.1.0"; }; gitlab-styles = { dependencies = ["rubocop" "rubocop-gitlab-security" "rubocop-rspec"]; @@ -1261,10 +1295,10 @@ dependencies = ["mini_portile2"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1fclgx3pg3sihk9xn3amcf8db0q749dsqkycayn1c8x134zml3gb"; + sha256 = "12fqirxr964mc8jwsfl5nif6q4wcckrmj7w4c9ci4xg9xy2b9v6m"; type = "gem"; }; - version = "2.0.13"; + version = "2.0.18"; }; grape = { dependencies = ["activesupport" "builder" "mustermann-grape" "rack" "rack-accept" "virtus"]; @@ -1350,10 +1384,10 @@ dependencies = ["haml" "rainbow" "rake" "rubocop" "sysexits"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "04illnjl9hsg7wqf8x5s108m5is9aj52g80c6nrgsksyp4vh9ynn"; + sha256 = "125aj0j84nx5gqm42hfx5d8486higlra423ahgfpsdjwbp399rwv"; type = "gem"; }; - version = "0.26.0"; + version = "0.28.0"; }; hamlit = { dependencies = ["temple" "thor" "tilt"]; @@ -1445,10 +1479,10 @@ dependencies = ["addressable" "http-cookie" "http-form_data" "http_parser.rb"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1kcd9qp8vm1rkyp7gfh8j0dbl3zpi97vz2vbhpbcsdsa7l21a59r"; + sha256 = "1jlm5prw437wqpfxcigh88lfap3m7g8mnmj5as7qw6dzqnvrxwmc"; type = "gem"; }; - version = "2.2.2"; + version = "3.3.0"; }; http-cookie = { dependencies = ["domain_name"]; @@ -1462,10 +1496,10 @@ http-form_data = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0j8dwwbfpf8kc0lcsqcgy29lflszd1x4d7kc0f7227892m7r6y0m"; + sha256 = "15lpn604byf7cyxnw949xz4rvpcknqp7a48q73nm630gqxsa76f3"; type = "gem"; }; - version = "1.0.3"; + version = "2.1.1"; }; "http_parser.rb" = { source = { @@ -1496,10 +1530,10 @@ dependencies = ["concurrent-ruby"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "038qvz7kd3cfxk8bvagqhakx68pfbnmghpdkx7573wbf0maqp9a3"; + sha256 = "1gcp1m1p6dpasycfz2sj82ci9ggz7lsskz9c9q6gvfwxrl8y9dx7"; type = "gem"; }; - version = "0.9.5"; + version = "1.1.1"; }; icalendar = { source = { @@ -1649,19 +1683,19 @@ dependencies = ["rake"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1q2y7mb8ii1ncdrlp46l9v2x909gdnjaid2dg5gcicj39hna36di"; + sha256 = "1c69rcwfrdrnx8ddl6k1qxhw9f2dj5x5bbddz435isl2hfr5zh92"; type = "gem"; }; - version = "1.16.0"; + version = "1.17.0"; }; kubeclient = { dependencies = ["http" "recursive-open-struct" "rest-client"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1czzdp9lfsrah2jkaddkqzmphyvnk096zm1ra6jddh626d8d53r4"; + sha256 = "1s250z89nz7vzich3nikc8fs8vgpac38wjv8llm4ldvs4iyc4ypg"; type = "gem"; }; - version = "3.1.0"; + version = "4.0.0"; }; launchy = { dependencies = ["addressable"]; @@ -1729,10 +1763,10 @@ dependencies = ["crass" "nokogiri"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0yjs6wbcj3n06d3xjqpy3qbpx0bfa12h3x2rbpc2k33ldjlkx6zy"; + sha256 = "1ccsid33xjajd0im2xv941aywi58z7ihwkvaf1w2bv89vn5bhsjg"; type = "gem"; }; - version = "2.2.2"; + version = "2.2.3"; }; mail = { dependencies = ["mini_mime"]; @@ -1771,35 +1805,35 @@ method_source = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0xqj21j3vfq4ldia6i2akhn2qd84m0iqcnsl49kfpq3xk6x0dzgn"; + sha256 = "1pviwzvdqd90gn6y7illcdd9adapw8fczml933p5vl739dkvl3lq"; type = "gem"; }; - version = "0.9.0"; + version = "0.9.2"; }; mime-types = { dependencies = ["mime-types-data"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0087z9kbnlqhci7fxh9f6il63hj1k02icq2rs0c6cppmqchr753m"; + sha256 = "0fjxy1jm52ixpnv3vg9ld9pr9f35gy0jp66i1njhqjvmnvq0iwwk"; type = "gem"; }; - version = "3.1"; + version = "3.2.2"; }; mime-types-data = { source = { remotes = ["https://rubygems.org"]; - sha256 = "04my3746hwa4yvbx1ranhfaqkgf6vavi1kyijjnw8w3dy37vqhkm"; + sha256 = "07wvp0aw2gjm4njibb70as6rh5hi1zzri5vky1q6jx95h8l56idc"; type = "gem"; }; - version = "3.2016.0521"; + version = "3.2018.0812"; }; mimemagic = { source = { remotes = ["https://rubygems.org"]; - sha256 = "101lq4bnjs7ywdcicpw3vbz9amg5gbb4va1626fybd2hawgdx8d9"; + sha256 = "00ibc1mhvdfyfyl103xwb45621nwyqxf124cni5hyfhag0fn1c3q"; type = "gem"; }; - version = "0.3.0"; + version = "0.3.2"; }; mini_magick = { source = { @@ -1890,6 +1924,14 @@ }; version = "0.4.10"; }; + nakayoshi_fork = { + source = { + remotes = ["https://rubygems.org"]; + sha256 = "1mj5czi7rxxmfq4v9qjz74lcqypvnjxhxqfs71zhb2rsfa97a6jg"; + type = "gem"; + }; + version = "0.0.4"; + }; net-ldap = { source = { remotes = ["https://rubygems.org"]; @@ -1922,14 +1964,22 @@ }; version = "0.11.0"; }; + nio4r = { + source = { + remotes = ["https://rubygems.org"]; + sha256 = "1a41ca1kpdmrypjp9xbgvckpy8g26zxphkja9vk7j5wl4n8yvlyr"; + type = "gem"; + }; + version = "2.3.1"; + }; nokogiri = { dependencies = ["mini_portile2"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1h9nml9h3m0mpvmh8jfnqvblnz5n5y3mmhgfc38avfmfzdrq9bgc"; + sha256 = "0byyxrazkfm29ypcx5q4syrv126nvjnf7z6bqi01sqkv4llsi4qz"; type = "gem"; }; - version = "1.8.4"; + version = "1.8.5"; }; nokogumbo = { dependencies = ["nokogiri"]; @@ -2371,10 +2421,10 @@ rack = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0in0amn0kwvzmi8h5zg6ijrx5wpsf8h96zrfmnk1kwh2ql4sxs2q"; + sha256 = "1pcgv8dv4vkaczzlix8q3j68capwhk420cddzijwqgi2qb4lm1zm"; type = "gem"; }; - version = "1.6.10"; + version = "2.0.6"; }; rack-accept = { dependencies = ["rack"]; @@ -2415,10 +2465,10 @@ dependencies = ["rack"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1z5598qipilmnf45428jnxi63ykrgvnyywa5ckpr52zv2vpd8jdp"; + sha256 = "0ylx74ravz7nvnyygq0nk3v86qdzrmqxpwpayhppyy50l72rcajq"; type = "gem"; }; - version = "2.0.3"; + version = "2.0.4"; }; rack-proxy = { dependencies = ["rack"]; @@ -2439,13 +2489,22 @@ version = "0.6.3"; }; rails = { - dependencies = ["actionmailer" "actionpack" "actionview" "activejob" "activemodel" "activerecord" "activesupport" "railties" "sprockets-rails"]; + dependencies = ["actioncable" "actionmailer" "actionpack" "actionview" "activejob" "activemodel" "activerecord" "activesupport" "railties" "sprockets-rails"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "15vbdlkmlh470g7msqhmcmhxhi4finv3cjg595x9viafvphnf40l"; + sha256 = "117z277m78cw6bm43dyzxhjmx8awpidmqcjjx99kpj4rgqm5m0bn"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; + }; + rails-controller-testing = { + dependencies = ["actionpack" "actionview" "activesupport"]; + source = { + remotes = ["https://rubygems.org"]; + sha256 = "16kdkk73mhhs73iz3i1i0ryjm84dadiyh817b3nh8acdi490jyhy"; + type = "gem"; + }; + version = "1.0.2"; }; rails-deprecated_sanitizer = { dependencies = ["activesupport"]; @@ -2457,13 +2516,13 @@ version = "1.0.3"; }; rails-dom-testing = { - dependencies = ["activesupport" "nokogiri" "rails-deprecated_sanitizer"]; + dependencies = ["activesupport" "nokogiri"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0wssfqpn00byhvp2372p99mphkcj8qx6pf6646avwr9ifvq0q1x6"; + sha256 = "1lfq2a7kp2x64dzzi5p4cjcbiv62vxh9lyqk2f0rqq3fkzrw8h5i"; type = "gem"; }; - version = "1.0.9"; + version = "2.0.3"; }; rails-html-sanitizer = { dependencies = ["loofah"]; @@ -2478,19 +2537,19 @@ dependencies = ["i18n" "railties"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "17a02f2671pw5r2hl2n3isiz6w9wy2dxq8g52srciyl1xcmvsw01"; + sha256 = "1rqij2ggqz5iq36lbibhnd7pl4qxrvv9kgw9s0c6594vzbbxmhs0"; type = "gem"; }; - version = "4.0.9"; + version = "5.1.1"; }; railties = { - dependencies = ["actionpack" "activesupport" "rake" "thor"]; + dependencies = ["actionpack" "activesupport" "method_source" "rake" "thor"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0snymfqj2cql0gp51i6a44avcirdridc15yggnxjj9raa9f3229p"; + sha256 = "0j6v5ylwgqmxs4pllgip5yxdsivdqs1w00cs8jfqyw5v7pn9b2z0"; type = "gem"; }; - version = "4.2.10"; + version = "5.0.7"; }; rainbow = { source = { @@ -2657,10 +2716,10 @@ dependencies = ["redis"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "00yh8rhv91vxjlqs4ylic99m9npjxmgib2vjj8hgzk1174y6vcmq"; + sha256 = "1mrcnjgkbmx1zf569mly82agdizqayjvnp2k6055k1iy07in3j8b"; type = "gem"; }; - version = "1.4.1"; + version = "1.6.0"; }; regexp_parser = { source = { @@ -2792,13 +2851,13 @@ version = "3.7.0"; }; rspec-parameterized = { - dependencies = ["binding_of_caller" "parser" "proc_to_ast" "rspec" "unparser"]; + dependencies = ["binding_ninja" "parser" "proc_to_ast" "rspec" "unparser"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0arynbr6cfjhccwc8gy2xf87nybdnncsnmfwknnh8s7d4mj730p0"; + sha256 = "159yw3mb4dab5kr18a97miyyi7dqmyrfjp3aw6r6j9i4xkc4xk3a"; type = "gem"; }; - version = "0.4.0"; + version = "0.4.1"; }; rspec-rails = { dependencies = ["actionpack" "activesupport" "railties" "rspec-core" "rspec-expectations" "rspec-mocks" "rspec-support"]; @@ -2835,13 +2894,13 @@ version = "3.7.1"; }; rspec_junit_formatter = { - dependencies = ["builder" "rspec-core"]; + dependencies = ["rspec-core"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0hphl8iggqh1mpbbv0avf8735x6jgry5wmkqyzgv1zwnimvja1ai"; + sha256 = "1aynmrgnv26pkprrajvp7advb8nbh0x4pkwk6jwq8qmwzarzk21p"; type = "gem"; }; - version = "0.2.3"; + version = "0.4.1"; }; rspec_profiling = { dependencies = ["activerecord" "pg" "rails" "sqlite3"]; @@ -2926,10 +2985,10 @@ dependencies = ["sexp_processor"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "18apbsmmivgc1schfxmkp429aijrwy8psm30dwx5cpmpjf48ir3n"; + sha256 = "0mysmdyxhvyn6dhshfxyw762f9asr3kxw45idvw1bh6np31kk4j1"; type = "gem"; }; - version = "3.9.0"; + version = "3.11.0"; }; rubyntlm = { source = { @@ -3065,10 +3124,10 @@ dependencies = ["faraday"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0yf2gysjw6sy1xcp2jw35z9cp83pwx33lq0qyvaqbs969j4993r4"; + sha256 = "0l0bci35amy7pqv81djyjcx023q4qylmq8a2zbx14zh6ifzib4f4"; type = "gem"; }; - version = "2.7.2"; + version = "2.7.4"; }; settingslogic = { source = { @@ -3081,10 +3140,10 @@ sexp_processor = { source = { remotes = ["https://rubygems.org"]; - sha256 = "1c6kp2qxq550hz7gsxqi37irxn3vynkz7ibgy9hfwqymf6y1jdik"; + sha256 = "1vnmphfrd86694x5k7rxddbhbvv5rqbglsc34kfryy4jqhbzz42c"; type = "gem"; }; - version = "4.9.0"; + version = "4.11.0"; }; sham_rack = { dependencies = ["rack"]; @@ -3108,10 +3167,10 @@ dependencies = ["connection_pool" "rack-protection" "redis"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0s57vl2hwfaga73yiscak2rs7byg1q0z44wa9si9vl92qcmbik2j"; + sha256 = "1zyf9y3rvzizbwh68i2g1lzd40lalrdc4iyjmaa74gnfwsf92i26"; type = "gem"; }; - version = "5.2.1"; + version = "5.2.3"; }; sidekiq-cron = { dependencies = ["rufus-scheduler" "sidekiq"]; @@ -3283,15 +3342,6 @@ }; version = "0.2.5"; }; - test_after_commit = { - dependencies = ["activerecord"]; - source = { - remotes = ["https://rubygems.org"]; - sha256 = "0s8pz00xq28lsa1rfczm83yqwk8wcb5dqw2imlj8gldnsdapcyc2"; - type = "gem"; - }; - version = "1.1.0"; - }; text = { source = { remotes = ["https://rubygems.org"]; @@ -3473,10 +3523,10 @@ dependencies = ["abstract_type" "adamantium" "concord" "diff-lcs" "equalizer" "parser" "procto"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0k2asbk9k5kzq8jidy3frqcmn58i9cvaizn8f6g5xlx1pn70bx1w"; + sha256 = "0w662glqi7hwmfvx0smxckxgc7kw5bsqhqz0pyvalbyv1gc0gs2x"; type = "gem"; }; - version = "0.2.7"; + version = "0.4.2"; }; validates_hostname = { dependencies = ["activerecord" "activesupport"]; @@ -3539,6 +3589,23 @@ }; version = "0.9.11"; }; + websocket-driver = { + dependencies = ["websocket-extensions"]; + source = { + remotes = ["https://rubygems.org"]; + sha256 = "1943442yllhldh9dbp374x2q39cxa49xrm28nb78b7mfbv3y195l"; + type = "gem"; + }; + version = "0.6.5"; + }; + websocket-extensions = { + source = { + remotes = ["https://rubygems.org"]; + sha256 = "034sdr7fd34yag5l6y156rkbhiqgmy395m231dwhlpcswhs6d270"; + type = "gem"; + }; + version = "0.1.3"; + }; wikicloth = { dependencies = ["builder" "expression_parser" "rinku"]; source = { From 97e7cf75fa28f1c25921bf5edc653c7582eda8d1 Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Mon, 24 Dec 2018 03:42:25 +0100 Subject: [PATCH 014/247] gitaly: 0.129.0 -> 1.7.1 --- .../version-management/gitlab/gitaly/Gemfile | 4 +-- .../gitlab/gitaly/Gemfile.lock | 23 ++++++------- .../gitlab/gitaly/default.nix | 4 +-- .../gitlab/gitaly/gemset.nix | 33 ++++++++++--------- 4 files changed, 33 insertions(+), 31 deletions(-) diff --git a/pkgs/applications/version-management/gitlab/gitaly/Gemfile b/pkgs/applications/version-management/gitlab/gitaly/Gemfile index 016f80284da9..81f1864099f3 100644 --- a/pkgs/applications/version-management/gitlab/gitaly/Gemfile +++ b/pkgs/applications/version-management/gitlab/gitaly/Gemfile @@ -5,8 +5,8 @@ gem 'bundler', '>= 1.16.5' gem 'rugged', '~> 0.27' gem 'github-linguist', '~> 6.1', require: 'linguist' -gem 'gitlab-markup', '~> 1.6.4' -gem 'gitaly-proto', '~> 0.123.0', require: 'gitaly' +gem 'gitlab-markup', '~> 1.6.5' +gem 'gitaly-proto', '~> 1.3.0' gem 'activesupport', '~> 5.0.2' gem 'rdoc', '~> 4.2' gem 'gitlab-gollum-lib', '~> 4.2', require: false diff --git a/pkgs/applications/version-management/gitlab/gitaly/Gemfile.lock b/pkgs/applications/version-management/gitlab/gitaly/Gemfile.lock index 0340853524b0..73dab9a33928 100644 --- a/pkgs/applications/version-management/gitlab/gitaly/Gemfile.lock +++ b/pkgs/applications/version-management/gitlab/gitaly/Gemfile.lock @@ -2,9 +2,9 @@ GEM remote: https://rubygems.org/ specs: abstract_type (0.0.7) - activesupport (5.0.6) + activesupport (5.0.7) concurrent-ruby (~> 1.0, >= 1.0.2) - i18n (~> 0.7) + i18n (>= 0.7, < 2) minitest (~> 5.1) tzinfo (~> 1.1) adamantium (0.2.0) @@ -18,7 +18,7 @@ GEM concord (0.1.5) adamantium (~> 0.2.0) equalizer (~> 0.0.9) - concurrent-ruby (1.0.5) + concurrent-ruby (1.1.3) crass (1.0.4) debug_inspector (0.0.3) diff-lcs (1.3) @@ -30,7 +30,7 @@ GEM multipart-post (>= 1.2, < 3) gemojione (3.3.0) json - gitaly-proto (0.123.0) + gitaly-proto (1.3.0) grpc (~> 1.0) github-linguist (6.2.0) charlock_holmes (~> 0.7.6) @@ -54,7 +54,7 @@ GEM diff-lcs (~> 1.1) mime-types (>= 1.16) posix-spawn (~> 0.3) - gitlab-markup (1.6.4) + gitlab-markup (1.6.5) gollum-grit_adapter (1.0.1) gitlab-grit (~> 2.7, >= 2.7.1) google-protobuf (3.6.1) @@ -63,7 +63,8 @@ GEM grpc (1.15.0) google-protobuf (~> 3.1) googleapis-common-protos-types (~> 1.0.0) - i18n (0.8.1) + i18n (1.1.1) + concurrent-ruby (~> 1.0) ice_nine (0.11.2) json (2.1.0) licensee (8.9.2) @@ -74,9 +75,9 @@ GEM mime-types-data (~> 3.2015) mime-types-data (3.2018.0812) mini_portile2 (2.3.0) - minitest (5.9.1) + minitest (5.11.3) multipart-post (2.0.0) - nokogiri (1.8.4) + nokogiri (1.8.5) mini_portile2 (~> 2.3.0) nokogumbo (1.5.0) nokogiri @@ -130,7 +131,7 @@ GEM stringex (2.8.4) thread_safe (0.3.6) timecop (0.9.1) - tzinfo (1.2.2) + tzinfo (1.2.5) thread_safe (~> 0.1) unicode-display_width (1.4.0) unparser (0.2.8) @@ -150,11 +151,11 @@ DEPENDENCIES bundler (>= 1.16.5) factory_bot faraday (~> 0.12) - gitaly-proto (~> 0.123.0) + gitaly-proto (~> 1.3.0) github-linguist (~> 6.1) gitlab-gollum-lib (~> 4.2) gitlab-gollum-rugged_adapter (~> 0.4.4) - gitlab-markup (~> 1.6.4) + gitlab-markup (~> 1.6.5) google-protobuf (~> 3.6) grpc (~> 1.15.0) licensee (~> 8.9.0) diff --git a/pkgs/applications/version-management/gitlab/gitaly/default.nix b/pkgs/applications/version-management/gitlab/gitaly/default.nix index 951dbf0bf25a..19b1d3cab948 100644 --- a/pkgs/applications/version-management/gitlab/gitaly/default.nix +++ b/pkgs/applications/version-management/gitlab/gitaly/default.nix @@ -7,14 +7,14 @@ let gemdir = ./.; }; in buildGoPackage rec { - version = "0.129.0"; + version = "1.7.1"; name = "gitaly-${version}"; src = fetchFromGitLab { owner = "gitlab-org"; repo = "gitaly"; rev = "v${version}"; - sha256 = "0lidqa0w0vy87p5xfmqrfvbyzvl9wj2p918qs2f5rc7shzm38rn6"; + sha256 = "1ravy308b5h9gsbb3ka159f68ghyjkb4bj1ngj7ighb9dd84vlf4"; }; goPackagePath = "gitlab.com/gitlab-org/gitaly"; diff --git a/pkgs/applications/version-management/gitlab/gitaly/gemset.nix b/pkgs/applications/version-management/gitlab/gitaly/gemset.nix index 9bf5601bf634..34c2e5ed036a 100644 --- a/pkgs/applications/version-management/gitlab/gitaly/gemset.nix +++ b/pkgs/applications/version-management/gitlab/gitaly/gemset.nix @@ -11,10 +11,10 @@ dependencies = ["concurrent-ruby" "i18n" "minitest" "tzinfo"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "0g85lqq0smj71g8a2dxb54ajjzw59c9snana4p61knryc83q3yg6"; + sha256 = "1yx73l984y3ri5ndj37l1dfarcdvbhra7vhz9fcww4za24is95d5"; type = "gem"; }; - version = "5.0.6"; + version = "5.0.7"; }; adamantium = { dependencies = ["ice_nine" "memoizable"]; @@ -70,10 +70,10 @@ concurrent-ruby = { source = { remotes = ["https://rubygems.org"]; - sha256 = "183lszf5gx84kcpb779v6a2y0mx9sssy8dgppng1z9a505nj1qcf"; + sha256 = "18q9skp5pfq4jwbxzmw8q2rn4cpw6mf4561i2hsjcl1nxdag2jvb"; type = "gem"; }; - version = "1.0.5"; + version = "1.1.3"; }; crass = { source = { @@ -146,10 +146,10 @@ dependencies = ["grpc"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "16b9sdaimhcda401z2s7apf0nz6y0lxs74xhkwlz4jzf6ms44mgg"; + sha256 = "17fg29j089k94ssim9hfzpd5lycvhimbpvz12d73ywrbwz7a7680"; type = "gem"; }; - version = "0.123.0"; + version = "1.3.0"; }; github-linguist = { dependencies = ["charlock_holmes" "escape_utils" "mime-types" "rugged"]; @@ -198,10 +198,10 @@ gitlab-markup = { source = { remotes = ["https://rubygems.org"]; - sha256 = "1v6w3z7smmkqnhphb4ghgpqg61vimflqzpszybji0li99f2k1jb6"; + sha256 = "12lzzhbmid4m23pk7d963n3njli2hw7g200arszh75j57bjgs4fy"; type = "gem"; }; - version = "1.6.4"; + version = "1.6.5"; }; gollum-grit_adapter = { dependencies = ["gitlab-grit"]; @@ -239,12 +239,13 @@ version = "1.15.0"; }; i18n = { + dependencies = ["concurrent-ruby"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1s6971zmjxszdrp59vybns9gzxpdxzdklakc5lp8nl4fx5kpxkbp"; + sha256 = "1gcp1m1p6dpasycfz2sj82ci9ggz7lsskz9c9q6gvfwxrl8y9dx7"; type = "gem"; }; - version = "0.8.1"; + version = "1.1.1"; }; ice_nine = { source = { @@ -308,10 +309,10 @@ minitest = { source = { remotes = ["https://rubygems.org"]; - sha256 = "0300naf4ilpd9sf0k8si9h9sclkizaschn8bpnri5fqmvm9ybdbq"; + sha256 = "0icglrhghgwdlnzzp4jf76b0mbc71s80njn5afyfjn4wqji8mqbq"; type = "gem"; }; - version = "5.9.1"; + version = "5.11.3"; }; multipart-post = { source = { @@ -325,10 +326,10 @@ dependencies = ["mini_portile2"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1h9nml9h3m0mpvmh8jfnqvblnz5n5y3mmhgfc38avfmfzdrq9bgc"; + sha256 = "0byyxrazkfm29ypcx5q4syrv126nvjnf7z6bqi01sqkv4llsi4qz"; type = "gem"; }; - version = "1.8.4"; + version = "1.8.5"; }; nokogumbo = { dependencies = ["nokogiri"]; @@ -537,10 +538,10 @@ dependencies = ["thread_safe"]; source = { remotes = ["https://rubygems.org"]; - sha256 = "1c01p3kg6xvy1cgjnzdfq45fggbwish8krd0h864jvbpybyx7cgx"; + sha256 = "1fjx9j327xpkkdlxwmkl3a8wqj7i4l4jwlrv3z13mg95z9wl253z"; type = "gem"; }; - version = "1.2.2"; + version = "1.2.5"; }; unicode-display_width = { source = { From ca69c9c2d0b0038d606e455cd242e2abf60dff8c Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Mon, 24 Dec 2018 03:42:53 +0100 Subject: [PATCH 015/247] gitlab-shell: 8.4.1 -> 8.4.3 --- .../version-management/gitlab/gitlab-shell/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/version-management/gitlab/gitlab-shell/default.nix b/pkgs/applications/version-management/gitlab/gitlab-shell/default.nix index c9f21047e5b6..dca9630b04c7 100644 --- a/pkgs/applications/version-management/gitlab/gitlab-shell/default.nix +++ b/pkgs/applications/version-management/gitlab/gitlab-shell/default.nix @@ -1,14 +1,14 @@ { stdenv, ruby, bundler, fetchFromGitLab, go }: stdenv.mkDerivation rec { - version = "8.4.1"; + version = "8.4.3"; name = "gitlab-shell-${version}"; src = fetchFromGitLab { owner = "gitlab-org"; repo = "gitlab-shell"; rev = "v${version}"; - sha256 = "00jzrpdfqgrba2qi5ngc0g07p7gmip7my563hw542gg8l88d27xq"; + sha256 = "0ah039xpff1gmj36rm1ns8lb1k3di49lmnphl54bc45wnj72lw57"; }; buildInputs = [ ruby bundler go ]; From 134a6decae90a94fe3cf90bce267e59f0b954dbc Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Mon, 24 Dec 2018 03:43:04 +0100 Subject: [PATCH 016/247] gitlab-workhorse: 7.1.3 -> 7.6.0 --- .../version-management/gitlab/gitlab-workhorse/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/version-management/gitlab/gitlab-workhorse/default.nix b/pkgs/applications/version-management/gitlab/gitlab-workhorse/default.nix index b0d282e8799c..ea864d700d4c 100644 --- a/pkgs/applications/version-management/gitlab/gitlab-workhorse/default.nix +++ b/pkgs/applications/version-management/gitlab/gitlab-workhorse/default.nix @@ -3,13 +3,13 @@ stdenv.mkDerivation rec { name = "gitlab-workhorse-${version}"; - version = "7.1.3"; + version = "7.6.0"; src = fetchFromGitLab { owner = "gitlab-org"; repo = "gitlab-workhorse"; rev = "v${version}"; - sha256 = "1r75jj0xb4jv5fq2ihxk0vlv43gsk523zx86076mwph1g75gi1nz"; + sha256 = "13wr2az3bp6qnb05505sb5qn0fl2syaclc40dwjcdwwmhaalj2m4"; }; buildInputs = [ git go ]; From 2aafeedd15e33491f637a20baf5b1b3b4fd5b4a3 Mon Sep 17 00:00:00 2001 From: danbst Date: Thu, 27 Dec 2018 15:13:48 +0200 Subject: [PATCH 017/247] squashfs: 4.4dev -> 4.4dev-20180612 This squashfstools release finally has `zstd` support. --- pkgs/tools/filesystems/squashfs/default.nix | 12 +++++++----- .../squashfs/squashfs-tools-4.3-4k-align.patch | 15 ++++++++------- 2 files changed, 15 insertions(+), 12 deletions(-) diff --git a/pkgs/tools/filesystems/squashfs/default.nix b/pkgs/tools/filesystems/squashfs/default.nix index 389a614f54b0..2fd3d52bdf67 100644 --- a/pkgs/tools/filesystems/squashfs/default.nix +++ b/pkgs/tools/filesystems/squashfs/default.nix @@ -1,18 +1,20 @@ { stdenv, fetchFromGitHub, zlib, xz , lz4 ? null , lz4Support ? false +, zstd }: assert lz4Support -> (lz4 != null); stdenv.mkDerivation rec { - name = "squashfs-4.4dev"; + name = "squashfs-${version}"; + version = "4.4dev_20180612"; src = fetchFromGitHub { owner = "plougher"; repo = "squashfs-tools"; - sha256 = "059pa2shdysr3zfmwrhq28s12zbi5nyzbpzyaf5lmspgfh1493ks"; - rev = "9c1db6d13a51a2e009f0027ef336ce03624eac0d"; + sha256 = "1y53z8dkph3khdyhkmkmy0sg9p1n8czv3vj4l324nj8kxyih3l2c"; + rev = "6e242dc95485ada8d1d0b3dd9346c5243d4a517f"; }; patches = [ @@ -28,14 +30,14 @@ stdenv.mkDerivation rec { ./squashfs-tools-4.3-4k-align.patch ] ++ stdenv.lib.optional stdenv.isDarwin ./darwin.patch; - buildInputs = [ zlib xz ] + buildInputs = [ zlib xz zstd ] ++ stdenv.lib.optional lz4Support lz4; preBuild = "cd squashfs-tools"; installFlags = "INSTALL_DIR=\${out}/bin"; - makeFlags = [ "XZ_SUPPORT=1" ] + makeFlags = [ "XZ_SUPPORT=1" "ZSTD_SUPPORT=1" ] ++ stdenv.lib.optional lz4Support "LZ4_SUPPORT=1"; meta = { diff --git a/pkgs/tools/filesystems/squashfs/squashfs-tools-4.3-4k-align.patch b/pkgs/tools/filesystems/squashfs/squashfs-tools-4.3-4k-align.patch index b7c949182e0b..cd4308b489fe 100644 --- a/pkgs/tools/filesystems/squashfs/squashfs-tools-4.3-4k-align.patch +++ b/pkgs/tools/filesystems/squashfs/squashfs-tools-4.3-4k-align.patch @@ -27,11 +27,12 @@ index 8b1376f..683973d 100644 int use_regex = FALSE; int nopad = FALSE; int exit_on_error = FALSE; + static off_t squashfs_start_offset = 0; +int do_4k_align = FALSE; +#define ALIGN_UP(bytes, size) (bytes = (bytes + size - 1) & ~(size - 1)) - + long long global_uid = -1, global_gid = -1; - + @@ -1513,6 +1515,9 @@ void unlock_fragments() * queue at this time. */ @@ -40,7 +41,7 @@ index 8b1376f..683973d 100644 + if(do_4k_align) + ALIGN_UP(bytes, 4096); write_buffer = queue_get(locked_fragment); - frg = write_buffer->block; + frg = write_buffer->block; size = SQUASHFS_COMPRESSED_SIZE_BLOCK(fragment_table[frg].size); @@ -2420,6 +2420,9 @@ compressed_size = SQUASHFS_COMPRESSED_SIZE_BLOCK(c_byte); @@ -55,18 +56,18 @@ index 8b1376f..683973d 100644 @@ -2761,6 +2769,10 @@ int write_file_blocks(squashfs_inode *inode, struct dir_ent *dir_ent, long long sparse = 0; struct file_buffer *fragment_buffer = NULL; - + + // 4k align the start of each file. + if(do_4k_align) + ALIGN_UP(bytes, 4096); + if(pre_duplicate(read_size)) return write_file_blocks_dup(inode, dir_ent, read_buffer, dup); - + @@ -4692,6 +4704,7 @@ void write_filesystem_tables(struct squashfs_super_block *sBlk, int nopad) "compressed", no_fragments ? "no" : noF ? "uncompressed" : "compressed", no_xattrs ? "no" : noX ? "uncompressed" : - "compressed"); + "compressed", noI || noId ? "uncompressed" : "compressed"); + printf("\t4k %saligned\n", do_4k_align ? "" : "un"); printf("\tduplicates are %sremoved\n", duplicate_checking ? "" : "not "); @@ -88,5 +89,5 @@ index 8b1376f..683973d 100644 ERROR("\nFilesystem filter options:\n"); ERROR("-p \tAdd pseudo file " "definition\n"); --- +-- 2.14.1.480.gb18f417b89-goog (previously; hand-patched by charles-dyfis-net) From f1f9543768b83595fa60bce155d377ceff63bca4 Mon Sep 17 00:00:00 2001 From: Sean Haugh Date: Sun, 30 Dec 2018 05:08:15 -0600 Subject: [PATCH 018/247] fuse-overlayfs: init at 0.2 --- .../filesystems/fuse-overlayfs/default.nix | 27 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 29 insertions(+) create mode 100644 pkgs/tools/filesystems/fuse-overlayfs/default.nix diff --git a/pkgs/tools/filesystems/fuse-overlayfs/default.nix b/pkgs/tools/filesystems/fuse-overlayfs/default.nix new file mode 100644 index 000000000000..515fdd4e2608 --- /dev/null +++ b/pkgs/tools/filesystems/fuse-overlayfs/default.nix @@ -0,0 +1,27 @@ +{ pkgs, lib, autoreconfHook, pkgconfig, fuse3 }: + +let + version = "0.2"; +in + pkgs.stdenv.mkDerivation { + name = "fuse-overlayfs-${version}"; + + src = pkgs.fetchFromGitHub { + owner = "containers"; + repo = "fuse-overlayfs"; + rev = "1e2b65baa2f75eea0e4bab90b5ac81dd8471256c"; + sha256 = "0a9ix8rqjs5r28jsriyiv4yq7iilmv69x05kf23s1ihzrvrfkl08"; + }; + + nativeBuildInputs = [ autoreconfHook pkgconfig ]; + buildInputs = [ fuse3 ]; + + meta = with lib; { + homepage = https://github.com/containers/fuse-overlayfs; + description = "FUSE implementation for overlayfs"; + longDescription = "An implementation of overlay+shiftfs in FUSE for rootless containers."; + license = licenses.gpl3; + platforms = platforms.unix; + maintainers = [ maintainers.ma9e ]; + }; + } diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 6aa9f7fe9670..cefe5f0ef22c 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -2813,6 +2813,8 @@ in fuse-7z-ng = callPackage ../tools/filesystems/fuse-7z-ng { }; + fuse-overlayfs = callPackage ../tools/filesystems/fuse-overlayfs {}; + fusee-launcher = callPackage ../development/tools/fusee-launcher { }; fwknop = callPackage ../tools/security/fwknop { }; From 751bdacc9b726bf8e4623a7375e96563ee3614a5 Mon Sep 17 00:00:00 2001 From: aszlig Date: Fri, 4 Jan 2019 01:49:50 +0100 Subject: [PATCH 019/247] nixos/nsd: Don't override bind via nixpkgs.config When generating values for the services.nsd.zones attribute using values from pkgs, we'll run into an infinite recursion because the nsd module has a condition on the top-level definition of nixpkgs.config. While it would work to push the definition a few levels down, it will still only work if we don't use bind tools for generating zones. As far as I could see, Python support for BIND seems to be only needed for the dnssec-* tools, so instead of using nixpkgs.config, we now directly override pkgs.bind instead of globally in nixpkgs. To illustrate the problem with a small test case, instantiating the following Nix expression from the nixpkgs source root will cause the mentioned infinite recursion: (import ./nixos { configuration = { lib, pkgs, ... }: { services.nsd.enable = true; services.nsd.zones = import (pkgs.writeText "foo.nix" '' { "foo.".data = "xyz"; "foo.".dnssec = true; } ''); }; }).vm With this change, generating zones via import-from-derivation is now possible again. Signed-off-by: aszlig Cc: @pngwjpgh --- nixos/modules/services/networking/nsd.nix | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/nixos/modules/services/networking/nsd.nix b/nixos/modules/services/networking/nsd.nix index cde47bf23eae..492845eb4ec7 100644 --- a/nixos/modules/services/networking/nsd.nix +++ b/nixos/modules/services/networking/nsd.nix @@ -437,6 +437,8 @@ let dnssec = length (attrNames dnssecZones) != 0; + dnssecTools = pkgs.bind.override { enablePython = true; }; + signZones = optionalString dnssec '' mkdir -p ${stateDir}/dnssec chown ${username}:${username} ${stateDir}/dnssec @@ -445,8 +447,8 @@ let ${concatStrings (mapAttrsToList signZone dnssecZones)} ''; signZone = name: zone: '' - ${pkgs.bind}/bin/dnssec-keymgr -g ${pkgs.bind}/bin/dnssec-keygen -s ${pkgs.bind}/bin/dnssec-settime -K ${stateDir}/dnssec -c ${policyFile name zone.dnssecPolicy} ${name} - ${pkgs.bind}/bin/dnssec-signzone -S -K ${stateDir}/dnssec -o ${name} -O full -N date ${stateDir}/zones/${name} + ${dnssecTools}/bin/dnssec-keymgr -g ${dnssecTools}/bin/dnssec-keygen -s ${dnssecTools}/bin/dnssec-settime -K ${stateDir}/dnssec -c ${policyFile name zone.dnssecPolicy} ${name} + ${dnssecTools}/bin/dnssec-signzone -S -K ${stateDir}/dnssec -o ${name} -O full -N date ${stateDir}/zones/${name} ${nsdPkg}/sbin/nsd-checkzone ${name} ${stateDir}/zones/${name}.signed && mv -v ${stateDir}/zones/${name}.signed ${stateDir}/zones/${name} ''; policyFile = name: policy: pkgs.writeText "${name}.policy" '' @@ -953,10 +955,6 @@ in ''; }; - nixpkgs.config = mkIf dnssec { - bind.enablePython = true; - }; - systemd.timers."nsd-dnssec" = mkIf dnssec { description = "Automatic DNSSEC key rollover"; From 6446d9eee88e6a708f7d48c69bb0d9001bac9f7a Mon Sep 17 00:00:00 2001 From: aszlig Date: Fri, 4 Jan 2019 01:59:28 +0100 Subject: [PATCH 020/247] nixos/nsd: Improve checking for empty dnssec zones While at it (see previous commit), using attrNames in combination with length is a bit verbose for checking whether the filtered attribute set is empty, so let's just compare it against an empty attribute set. Signed-off-by: aszlig --- nixos/modules/services/networking/nsd.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nixos/modules/services/networking/nsd.nix b/nixos/modules/services/networking/nsd.nix index 492845eb4ec7..8b918dab86dd 100644 --- a/nixos/modules/services/networking/nsd.nix +++ b/nixos/modules/services/networking/nsd.nix @@ -435,7 +435,7 @@ let dnssecZones = (filterAttrs (n: v: if v ? dnssec then v.dnssec else false) zoneConfigs); - dnssec = length (attrNames dnssecZones) != 0; + dnssec = dnssecZones != {}; dnssecTools = pkgs.bind.override { enablePython = true; }; From 9605c575a6d55d3dee28a0bf076e233ba7550c91 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Thu, 3 Jan 2019 19:34:46 -0800 Subject: [PATCH 021/247] clickhouse: 18.14.18 -> 18.16.1 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/clickhouse/versions --- pkgs/servers/clickhouse/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/clickhouse/default.nix b/pkgs/servers/clickhouse/default.nix index bddffc52fd77..90d614553ea8 100644 --- a/pkgs/servers/clickhouse/default.nix +++ b/pkgs/servers/clickhouse/default.nix @@ -6,13 +6,13 @@ stdenv.mkDerivation rec { name = "clickhouse-${version}"; - version = "18.14.18"; + version = "18.16.1"; src = fetchFromGitHub { owner = "yandex"; repo = "ClickHouse"; rev = "v${version}-stable"; - sha256 = "0nivnmlnamcjxwc66ja9fagi5fqzzjsnrrfk32f4g8sxffx2rjy3"; + sha256 = "02slllcan7w3ln4c9yvxc8w0h2vszd7n0wshbn4bra2hb6mrzyp8"; }; nativeBuildInputs = [ cmake libtool ninja ]; From 6edd82d02c8cbda4d6c4a3532af26841a8863f5f Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:49 +0000 Subject: [PATCH 022/247] a2jmidid: fix pthread linkage --- pkgs/applications/audio/a2jmidid/default.nix | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/pkgs/applications/audio/a2jmidid/default.nix b/pkgs/applications/audio/a2jmidid/default.nix index f443aec43ddb..70709ae4ac4c 100644 --- a/pkgs/applications/audio/a2jmidid/default.nix +++ b/pkgs/applications/audio/a2jmidid/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, makeWrapper, pkgconfig, alsaLib, dbus, libjack2 +{ stdenv, fetchurl, fetchpatch, makeWrapper, pkgconfig, alsaLib, dbus, libjack2 , wafHook , python2Packages}: @@ -16,6 +16,17 @@ in stdenv.mkDerivation rec { nativeBuildInputs = [ pkgconfig makeWrapper wafHook ]; buildInputs = [ alsaLib dbus libjack2 python dbus-python ]; + patches = [ + (fetchpatch { + url = https://repo.or.cz/a2jmidid.git/patch/24e3b8e543256ae8fdfb4b75eb9fd775f07c46e2; + sha256 = "1nxrvnhxlgqc9wbxnp1gnpw4wjyzxvymwcg1gh2nqzmssgfykfkc"; + }) + (fetchpatch { + url = https://repo.or.cz/a2jmidid.git/patch/7f82da7eb2f540a94db23331be98d42a58ddc269; + sha256 = "1nab9zf0agbcj5pvhl90pz0cx1d204d4janqflc5ymjhy8jyrsdv"; + }) + ]; + postInstall = '' wrapProgram $out/bin/a2j_control --set PYTHONPATH $PYTHONPATH ''; From 4bdf36d1560d722b13f0a90aeacdc6afe71d9c68 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:49 +0000 Subject: [PATCH 023/247] aegisub: link with pthread explicitly --- pkgs/applications/video/aegisub/default.nix | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/pkgs/applications/video/aegisub/default.nix b/pkgs/applications/video/aegisub/default.nix index 3dd0cc5adc29..d4208aee62e0 100644 --- a/pkgs/applications/video/aegisub/default.nix +++ b/pkgs/applications/video/aegisub/default.nix @@ -48,6 +48,12 @@ stdenv.mkDerivation rec { hardeningDisable = [ "bindnow" "relro" ]; + # this is fixed upstream though not yet in an officially released version, + # should be fine remove on next release (if one ever happens) + NIX_LDFLAGS = [ + "-lpthread" + ]; + postInstall = "ln -s $out/bin/aegisub-* $out/bin/aegisub"; meta = { From e7040637e5ea16a61523b2187f56e1b40d32fec8 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:49 +0000 Subject: [PATCH 024/247] ahoviewer: link with pthread explicitly --- pkgs/applications/graphics/ahoviewer/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/applications/graphics/ahoviewer/default.nix b/pkgs/applications/graphics/ahoviewer/default.nix index 52df41c683cd..6668bc42a8b5 100644 --- a/pkgs/applications/graphics/ahoviewer/default.nix +++ b/pkgs/applications/graphics/ahoviewer/default.nix @@ -29,6 +29,10 @@ stdenv.mkDerivation rec { gst_all_1.gst-plugins-base ] ++ stdenv.lib.optional useUnrar unrar; + NIX_LDFLAGS = [ + "-lpthread" + ]; + postPatch = ''patchShebangs version.sh''; postInstall = '' From 517f2d392ee66f9237c553ef795aff8cf650d32c Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 025/247] airstrike: link with libm explicitly --- pkgs/games/airstrike/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/games/airstrike/default.nix b/pkgs/games/airstrike/default.nix index a0bbd3b1c671..02ea6f688069 100644 --- a/pkgs/games/airstrike/default.nix +++ b/pkgs/games/airstrike/default.nix @@ -11,6 +11,10 @@ stdenv.mkDerivation rec { buildInputs = [ makeWrapper SDL SDL_image ]; + NIX_LDFLAGS = [ + "-lm" + ]; + installPhase = '' ls -l mkdir -p $out/bin From d17273394bcbd8dc9e496877001aacd234c16181 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 026/247] dbus_cplusplus: disable tests They fail to build. --- pkgs/development/libraries/dbus-cplusplus/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/libraries/dbus-cplusplus/default.nix b/pkgs/development/libraries/dbus-cplusplus/default.nix index 6190f6ddc52a..163b0f4be883 100644 --- a/pkgs/development/libraries/dbus-cplusplus/default.nix +++ b/pkgs/development/libraries/dbus-cplusplus/default.nix @@ -34,7 +34,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkgconfig ]; buildInputs = [ dbus glib expat ]; - configureFlags = [ "--disable-ecore" ]; + configureFlags = [ "--disable-ecore" "--disable-tests" ]; meta = with stdenv.lib; { homepage = http://dbus-cplusplus.sourceforge.net; From 6b0d3da79f46a127150f920f089157498a415f24 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 027/247] a52dec: build shared libraries --- pkgs/development/libraries/a52dec/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/development/libraries/a52dec/default.nix b/pkgs/development/libraries/a52dec/default.nix index ef1307c97112..5ff5e609723e 100644 --- a/pkgs/development/libraries/a52dec/default.nix +++ b/pkgs/development/libraries/a52dec/default.nix @@ -8,6 +8,10 @@ stdenv.mkDerivation rec { sha256 = "0czccp4fcpf2ykp16xcrzdfmnircz1ynhls334q374xknd5747d2"; }; + configureFlags = [ + "--enable-shared" + ]; + # fails 1 out of 1 tests with "BAD GLOBAL SYMBOLS" on i686 # which can also be fixed with # hardeningDisable = stdenv.lib.optional stdenv.isi686 "pic"; From 9e551aee94426498dfecbc0e5f26504009667778 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 028/247] artha: fix libgio-2.0 underlinking --- pkgs/applications/misc/artha/default.nix | 8 ++++++-- pkgs/applications/misc/artha/gio-underlink.patch | 13 +++++++++++++ 2 files changed, 19 insertions(+), 2 deletions(-) create mode 100644 pkgs/applications/misc/artha/gio-underlink.patch diff --git a/pkgs/applications/misc/artha/default.nix b/pkgs/applications/misc/artha/default.nix index f69152820e43..202c1669f858 100644 --- a/pkgs/applications/misc/artha/default.nix +++ b/pkgs/applications/misc/artha/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, dbus-glib, gtk2, pkgconfig, wordnet }: +{ stdenv, autoreconfHook, fetchurl, dbus-glib, gtk2, pkgconfig, wordnet }: stdenv.mkDerivation rec { name = "artha-${version}"; @@ -9,9 +9,13 @@ stdenv.mkDerivation rec { sha256 = "0qr4ihl7ma3cq82xi1fpzvf74mm9vsg0j035xvmcp3r6rmw2fycx"; }; - nativeBuildInputs = [ pkgconfig ]; + nativeBuildInputs = [ autoreconfHook pkgconfig ]; buildInputs = [ dbus-glib gtk2 wordnet ]; + patches = [ + ./gio-underlink.patch + ]; + meta = with stdenv.lib; { description = "An offline thesaurus based on WordNet"; homepage = http://artha.sourceforge.net; diff --git a/pkgs/applications/misc/artha/gio-underlink.patch b/pkgs/applications/misc/artha/gio-underlink.patch new file mode 100644 index 000000000000..08d9c4787369 --- /dev/null +++ b/pkgs/applications/misc/artha/gio-underlink.patch @@ -0,0 +1,13 @@ +diff --git a/src/Makefile.am b/src/Makefile.am +index 0236d72..bcc1182 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -38,7 +38,7 @@ artha_LDADD = libwni.a $(WORDNET_LIB) + + if POSIX + AM_CFLAGS += @libdbus_CFLAGS@ +-artha_LDADD += -lX11 -ldbus-1 -ldbus-glib-1 -lgtk-x11-2.0 \ ++artha_LDADD += -lX11 -ldbus-1 -ldbus-glib-1 -lgio-2.0 -lgtk-x11-2.0 \ + -lgdk-x11-2.0 -lgmodule-2.0 -lgobject-2.0 -lglib-2.0 + else + artha_LDADD += @GTK_LIBS@ From 8fe36d7285824606573d286849acc90a3ea874d0 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 029/247] autopanosiftc: fix libm underlinking --- pkgs/applications/graphics/autopanosiftc/default.nix | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/pkgs/applications/graphics/autopanosiftc/default.nix b/pkgs/applications/graphics/autopanosiftc/default.nix index 5fd1810bc284..c64604975ab0 100644 --- a/pkgs/applications/graphics/autopanosiftc/default.nix +++ b/pkgs/applications/graphics/autopanosiftc/default.nix @@ -10,6 +10,13 @@ stdenv.mkDerivation { buildInputs = [ cmake libpng libtiff libjpeg panotools libxml2 ]; + patches = [ + (fetchurl { + url = https://gitweb.gentoo.org/repo/gentoo.git/plain/media-gfx/autopano-sift-C/files/autopano-sift-C-2.5.1-lm.patch; + sha256 = "1bfcr5sps0ip9gl4jprji5jgf9wkczz6d2clsjjlbsy8r3ixi3lv"; + }) + ]; + meta = { homepage = http://hugin.sourceforge.net/; description = "Implementation in C of the autopano-sift algorithm for automatically stitching panoramas"; From ae7557c4cb1d8ef0652da9352c31aad7d90c61fc Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 030/247] avogadro: fix libX11 underlinking --- pkgs/applications/science/chemistry/avogadro/default.nix | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/pkgs/applications/science/chemistry/avogadro/default.nix b/pkgs/applications/science/chemistry/avogadro/default.nix index 78cda9d115ce..a569b82ff59d 100644 --- a/pkgs/applications/science/chemistry/avogadro/default.nix +++ b/pkgs/applications/science/chemistry/avogadro/default.nix @@ -14,6 +14,13 @@ stdenv.mkDerivation rec { NIX_CFLAGS_COMPILE = "-include ${libGLU_combined}/include/GL/glu.h"; + patches = [ + (fetchurl { + url = https://data.gpo.zugaina.org/fusion809/sci-chemistry/avogadro/files/avogadro-1.1.0-xlibs.patch; + sha256 = "1p113v19z3zwr9gxj2k599f8p97a8rwm93pa4amqvd0snn31mw0k"; + }) + ]; + meta = { description = "Molecule editor and visualizer"; maintainers = [ ]; From 0b0430928b7fd12e36239ad6c8e0a5681e0a44fc Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 031/247] bitmeter: fix libm underlinking --- pkgs/applications/audio/bitmeter/default.nix | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/audio/bitmeter/default.nix b/pkgs/applications/audio/bitmeter/default.nix index 5f3229dc157c..fbe2c97042f0 100644 --- a/pkgs/applications/audio/bitmeter/default.nix +++ b/pkgs/applications/audio/bitmeter/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, libjack2, gtk2, pkgconfig }: +{ stdenv, autoreconfHook, fetchurl, libjack2, gtk2, pkgconfig }: stdenv.mkDerivation rec { name = "bitmeter-${version}"; @@ -9,9 +9,16 @@ stdenv.mkDerivation rec { sha256 = "09ck2gxqky701dc1p0ip61rrn16v0pdc7ih2hc2sd63zcw53g2a7"; }; - nativeBuildInputs = [ pkgconfig ]; + nativeBuildInputs = [ autoreconfHook pkgconfig ]; buildInputs = [ libjack2 gtk2 ]; + patches = [ + (fetchurl { + url = https://gitweb.gentoo.org/repo/gentoo.git/plain/media-sound/bitmeter/files/bitmeter-1.2-fix-build-system.patch; + sha256 = "021mz6933iw7mpk6b9cbjr8naj6smbq1hwqjszlyx72qbwrrid7k"; + }) + ]; + meta = with stdenv.lib; { homepage = http://devel.tlrmx.org/audio/bitmeter/; description = "Also known as jack bitscope. Useful to detect denormals"; From 580125f6fc88e39276688e035602cd3674f456a7 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 032/247] box2d: don't build examples They fail to build and aren't included in the output anyway. --- pkgs/development/libraries/box2d/default.nix | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/pkgs/development/libraries/box2d/default.nix b/pkgs/development/libraries/box2d/default.nix index e65980be320e..a6ab33d20f77 100644 --- a/pkgs/development/libraries/box2d/default.nix +++ b/pkgs/development/libraries/box2d/default.nix @@ -17,7 +17,11 @@ stdenv.mkDerivation rec { unzip cmake libGLU_combined freeglut libX11 xproto inputproto libXi ]; - cmakeFlags = [ "-DBOX2D_INSTALL=ON" "-DBOX2D_BUILD_SHARED=ON" ]; + cmakeFlags = [ + "-DBOX2D_INSTALL=ON" + "-DBOX2D_BUILD_SHARED=ON" + "-DBOX2D_BUILD_EXAMPLES=OFF" + ]; prePatch = '' substituteInPlace Box2D/Common/b2Settings.h \ From b137a4c9502d2aa708bb5801f9ad60f688426b2d Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 033/247] buddy: link with libm explicitly --- pkgs/development/libraries/buddy/default.nix | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/development/libraries/buddy/default.nix b/pkgs/development/libraries/buddy/default.nix index a8555a349d08..fb25b0a58108 100644 --- a/pkgs/development/libraries/buddy/default.nix +++ b/pkgs/development/libraries/buddy/default.nix @@ -11,6 +11,9 @@ stdenv.mkDerivation rec { buildInputs = [ bison ]; patches = [ ./gcc-4.3.3-fixes.patch ]; configureFlags = [ "CFLAGS=-O3" "CXXFLAGS=-O3" ]; + NIX_LDFLAGS = [ + "-lm" + ]; doCheck = true; meta = { From e828ad6ad957833dd206deb6af6ddd50709dc8f4 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 034/247] cinepaint: link with lib{m,png} explicitly --- pkgs/applications/graphics/cinepaint/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/applications/graphics/cinepaint/default.nix b/pkgs/applications/graphics/cinepaint/default.nix index 9c736f5ffb57..14c7bb1be61a 100644 --- a/pkgs/applications/graphics/cinepaint/default.nix +++ b/pkgs/applications/graphics/cinepaint/default.nix @@ -26,7 +26,7 @@ in stdenv.mkDerivation rec { nativeBuildInputs = [ cmake pkgconfig ]; - NIX_LDFLAGS = "-llcms -ljpeg -lX11"; + NIX_LDFLAGS = "-lm -llcms -ljpeg -lpng -lX11"; meta = { homepage = http://www.cinepaint.org/; From ef5baf894c0fbb5d7fb1d83ef30ee545e3ce2645 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 035/247] cwiid: link with libbluetooth explicitly --- pkgs/development/libraries/cwiid/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/development/libraries/cwiid/default.nix b/pkgs/development/libraries/cwiid/default.nix index ee646b24c81a..246dd009820c 100644 --- a/pkgs/development/libraries/cwiid/default.nix +++ b/pkgs/development/libraries/cwiid/default.nix @@ -23,6 +23,10 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ autoreconfHook pkgconfig ]; + NIX_LDFLAGS = [ + "-lbluetooth" + ]; + postInstall = '' # Some programs (for example, cabal-install) have problems with the double 0 sed -i -e "s/0.6.00/0.6.0/" $out/lib/pkgconfig/cwiid.pc From 4510ad1807f4644619693d76c89dbda61e3cbeec Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 036/247] dsniff: link with pthreads explicitly --- pkgs/tools/networking/dsniff/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/tools/networking/dsniff/default.nix b/pkgs/tools/networking/dsniff/default.nix index 41acb533a3de..50a3c98af0f7 100644 --- a/pkgs/tools/networking/dsniff/default.nix +++ b/pkgs/tools/networking/dsniff/default.nix @@ -54,7 +54,7 @@ in stdenv.mkDerivation { nativeBuildInputs = [ autoreconfHook ]; buildInputs = [ glib pcap ]; - NIX_CFLAGS_LINK = "-lglib-2.0"; + NIX_CFLAGS_LINK = "-lglib-2.0 -lpthread"; postPatch = '' for patch in debian/patches/*.patch; do patch < $patch From 19d339ce3a16940766ae10597177608186c15c08 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 037/247] eboard: link with libdl explicitly --- pkgs/games/eboard/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/games/eboard/default.nix b/pkgs/games/eboard/default.nix index bed3abccf9b4..206ed02e69ce 100644 --- a/pkgs/games/eboard/default.nix +++ b/pkgs/games/eboard/default.nix @@ -21,6 +21,10 @@ stdenv.mkDerivation { NIX_CFLAGS_COMPILE = [ "-fpermissive" ]; + NIX_LDFLAGS = [ + "-ldl" + ]; + meta = { homepage = http://www.bergo.eng.br/eboard/; description = "Chess interface for Unix-like systems"; From 69981de277684b1f2ab8e8bccead14f0b6187ff1 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 038/247] egoboo: link with libm explicitly --- pkgs/games/egoboo/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/games/egoboo/default.nix b/pkgs/games/egoboo/default.nix index 29ad352c3168..98ab4d27d5f5 100644 --- a/pkgs/games/egoboo/default.nix +++ b/pkgs/games/egoboo/default.nix @@ -44,6 +44,10 @@ stdenv.mkDerivation rec { ''; */ + NIX_LDFLAGS = [ + "-lm" + ]; + meta = { description = "3D dungeon crawling adventure"; From 12c733c292ae04deb1927d628479db71ce84e1be Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 039/247] fileshelter: link with pthreads explicitly --- pkgs/servers/web-apps/fileshelter/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/servers/web-apps/fileshelter/default.nix b/pkgs/servers/web-apps/fileshelter/default.nix index 01fb8c624820..d7510e7d1e03 100644 --- a/pkgs/servers/web-apps/fileshelter/default.nix +++ b/pkgs/servers/web-apps/fileshelter/default.nix @@ -16,6 +16,10 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ autoreconfHook pkgconfig ]; buildInputs = [ libzip boost wt3 libconfig ]; + NIX_LDFLAGS = [ + "-lpthread" + ]; + postInstall = '' ln -s ${wt3}/share/Wt/resources $out/share/fileshelter/docroot/resources ''; From 6910266b0173e5ac8cccc0a5932483596abfa2c2 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 040/247] flatpak: link with pthreads explicitly --- pkgs/development/libraries/flatpak/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/development/libraries/flatpak/default.nix b/pkgs/development/libraries/flatpak/default.nix index 39ff74681690..1b5facbc0d06 100644 --- a/pkgs/development/libraries/flatpak/default.nix +++ b/pkgs/development/libraries/flatpak/default.nix @@ -45,6 +45,10 @@ stdenv.mkDerivation rec { doCheck = false; # TODO: some issues with temporary files + NIX_LDFLAGS = [ + "-lpthread" + ]; + enableParallelBuilding = true; configureFlags = [ From 2fe11f12fb551385875385bf98707316019228f4 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 041/247] gdmap: link with libm explicitly --- pkgs/tools/system/gdmap/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/tools/system/gdmap/default.nix b/pkgs/tools/system/gdmap/default.nix index 72938216b0a4..0c254bb28545 100644 --- a/pkgs/tools/system/gdmap/default.nix +++ b/pkgs/tools/system/gdmap/default.nix @@ -15,6 +15,10 @@ stdenv.mkDerivation rec { hardeningDisable = [ "format" ]; + NIX_LDFLAGS = [ + "-lm" + ]; + meta = with stdenv.lib; { homepage = http://gdmap.sourceforge.net; description = "Recursive rectangle map of disk usage"; From 4477dedfba4ed7f1d396a094513f74e1d4c57c16 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 042/247] gitAndTools.svn-all-fast-export: link with libsvn_fs-1 explicitly --- .../git-and-tools/svn-all-fast-export/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/applications/version-management/git-and-tools/svn-all-fast-export/default.nix b/pkgs/applications/version-management/git-and-tools/svn-all-fast-export/default.nix index 35c6d33d74da..0ee188cc19d0 100644 --- a/pkgs/applications/version-management/git-and-tools/svn-all-fast-export/default.nix +++ b/pkgs/applications/version-management/git-and-tools/svn-all-fast-export/default.nix @@ -22,6 +22,10 @@ stdenv.mkDerivation { "SVN_INCLUDE=${subversion.dev}/include/subversion-1" ]; + NIX_LDFLAGS = [ + "-lsvn_fs-1" + ]; + meta = with stdenv.lib; { homepage = https://github.com/svn-all-fast-export/svn2git; description = "A fast-import based converter for an svn repo to git repos"; From 77b88afa3087d90692485f1ccc38665047409412 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 043/247] globulation2: link with libboost_system explicitly --- pkgs/games/globulation/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/games/globulation/default.nix b/pkgs/games/globulation/default.nix index 0c3b184b4952..a539b79339f9 100644 --- a/pkgs/games/globulation/default.nix +++ b/pkgs/games/globulation/default.nix @@ -41,6 +41,10 @@ stdenv.mkDerivation rec { sconsFlags+=" DATADIR=$out/share/globulation2/glob2" ''; + NIX_LDFLAGS = [ + "-lboost_system" + ]; + meta = with stdenv.lib; { description = "RTS without micromanagement"; maintainers = with maintainers; [ raskin ]; From 3b49822b3d2c5cb58a975dcdf7033021fe18f168 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 044/247] gnujump: link with libm explicitly --- pkgs/games/gnujump/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/games/gnujump/default.nix b/pkgs/games/gnujump/default.nix index ae2cbd818417..d4cbb04f39b8 100644 --- a/pkgs/games/gnujump/default.nix +++ b/pkgs/games/gnujump/default.nix @@ -9,6 +9,10 @@ stdenv.mkDerivation rec { }; buildInputs = [ SDL SDL_image SDL_mixer ]; + NIX_LDFLAGS = [ + "-lm" + ]; + meta = with stdenv.lib; { homepage = "https://jump.gnu.sinusoid.es/"; description = "A clone of the simple yet addictive game Xjump"; From 8c83c4585e0d2430751039680afa165015f7ba24 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 045/247] gnuradio: link with pthreads explicitly --- pkgs/applications/misc/gnuradio/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/applications/misc/gnuradio/default.nix b/pkgs/applications/misc/gnuradio/default.nix index a7c00cceaa72..f9a50313c472 100644 --- a/pkgs/applications/misc/gnuradio/default.nix +++ b/pkgs/applications/misc/gnuradio/default.nix @@ -50,6 +50,10 @@ stdenv.mkDerivation rec { Mako cheetah numpy scipy matplotlib pyqt4 pygtk wxPython pyopengl ]; + NIX_LDFLAGS = [ + "-lpthread" + ]; + enableParallelBuilding = true; postPatch = '' From 12ac71cacafff77df2de985cd9d9dacff68d1971 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 046/247] golden-cheetah: link with libz explicitly --- pkgs/applications/misc/golden-cheetah/default.nix | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/applications/misc/golden-cheetah/default.nix b/pkgs/applications/misc/golden-cheetah/default.nix index 01447281fe76..edf16f806a6b 100644 --- a/pkgs/applications/misc/golden-cheetah/default.nix +++ b/pkgs/applications/misc/golden-cheetah/default.nix @@ -26,6 +26,9 @@ in stdenv.mkDerivation rec { qtconnectivity ]; nativeBuildInputs = [ flex makeWrapper qmake yacc ]; + NIX_LDFLAGS = [ + "-lz" + ]; preConfigure = '' cp src/gcconfig.pri.in src/gcconfig.pri cp qwt/qwtconfig.pri.in qwt/qwtconfig.pri From 71f216b7e68d635dfca2ee0c06316a77e3abb4cc Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 047/247] golly-beta: link with lib{dl,GL} explicitly --- pkgs/applications/science/misc/golly/beta.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/applications/science/misc/golly/beta.nix b/pkgs/applications/science/misc/golly/beta.nix index 83b9c5a04a19..ebc476d3c6d0 100644 --- a/pkgs/applications/science/misc/golly/beta.nix +++ b/pkgs/applications/science/misc/golly/beta.nix @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { makeFlags=[ "AM_LDFLAGS=" ]; - NIX_LDFLAGS="-lpython${python2.majorVersion} -lperl"; + NIX_LDFLAGS="-lpython${python2.majorVersion} -lperl -ldl -lGL"; preConfigure='' export NIX_LDFLAGS="$NIX_LDFLAGS -L$(dirname "$(find ${perl} -name libperl.so)")" export NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE From 418a2d771c26b159faa562a01f01d9ada86c0007 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 048/247] goxel: link with pthreads explicitly --- pkgs/applications/graphics/goxel/default.nix | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/applications/graphics/goxel/default.nix b/pkgs/applications/graphics/goxel/default.nix index 27dd37d1803a..9a2da84cfb91 100644 --- a/pkgs/applications/graphics/goxel/default.nix +++ b/pkgs/applications/graphics/goxel/default.nix @@ -16,6 +16,9 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ scons pkgconfig wrapGAppsHook ]; buildInputs = [ glfw3 gtk3 libpng12 ]; + NIX_LDFLAGS = [ + "-lpthread" + ]; buildPhase = '' make release From 3d94f68c754272538cc9cd523997aa181ed88e1a Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 049/247] gqview: link with libm explicitly --- pkgs/applications/graphics/gqview/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/applications/graphics/gqview/default.nix b/pkgs/applications/graphics/gqview/default.nix index 75140bd005d5..205376b1257c 100644 --- a/pkgs/applications/graphics/gqview/default.nix +++ b/pkgs/applications/graphics/gqview/default.nix @@ -18,6 +18,10 @@ stdenv.mkDerivation { hardeningDisable = [ "format" ]; + NIX_LDFLAGS = [ + "-lm" + ]; + meta = with stdenv.lib; { description = "A fast image viewer"; homepage = http://gqview.sourceforge.net; From 46fad2b3b8edab36967d13e00555e196d9fc2d9d Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 050/247] gtk-server: link with libdl explicitly --- pkgs/development/interpreters/gtk-server/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/development/interpreters/gtk-server/default.nix b/pkgs/development/interpreters/gtk-server/default.nix index ab295dab4443..6f5a5ec0f198 100644 --- a/pkgs/development/interpreters/gtk-server/default.nix +++ b/pkgs/development/interpreters/gtk-server/default.nix @@ -14,6 +14,10 @@ stdenv.mkDerivation rec { configureOptions = [ "--with-gtk2" ]; + NIX_LDFLAGS = [ + "-ldl" + ]; + meta = { description = "gtk-server for interpreted GUI programming"; homepage = http://www.gtk-server.org/; From 0d8bec14f040ddc2bf1db43ec57bca2ad7fb9856 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 051/247] jack_rack: link with pthreads, lib{dl,m} explicitly --- pkgs/applications/audio/jack-rack/default.nix | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pkgs/applications/audio/jack-rack/default.nix b/pkgs/applications/audio/jack-rack/default.nix index d68e67d19dd4..26a717dbd6e4 100644 --- a/pkgs/applications/audio/jack-rack/default.nix +++ b/pkgs/applications/audio/jack-rack/default.nix @@ -7,6 +7,11 @@ stdenv.mkDerivation rec { }; nativeBuildInputs = [ pkgconfig ]; buildInputs = [ libjack2 ladspaH gtk2 alsaLib libxml2 librdf ]; + NIX_LDFLAGS = [ + "-ldl" + "-lm" + "-lpthread" + ]; meta = { description = ''An effects "rack" for the JACK low latency audio API''; From 472c14af6023a2f9b18f8980e2ec60f940526712 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 052/247] k2pdfopt: link with pthreads explicitly --- pkgs/applications/misc/k2pdfopt/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/applications/misc/k2pdfopt/default.nix b/pkgs/applications/misc/k2pdfopt/default.nix index 8f69abd3a987..2a3b2e61fc23 100644 --- a/pkgs/applications/misc/k2pdfopt/default.nix +++ b/pkgs/applications/misc/k2pdfopt/default.nix @@ -104,6 +104,10 @@ stdenv.mkDerivation rec { cmakeFlags = [ "-DCMAKE_C_FLAGS=-I${src}/include_mod" ]; + NIX_LDFLAGS = [ + "-lpthread" + ]; + installPhase = '' install -D -m 755 k2pdfopt $out/bin/k2pdfopt ''; From d02a1bb2ab8c68f5d421f434ed141381bc0c0083 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 053/247] kino: link with lib{avcodec,avutil} explicitly --- pkgs/applications/video/kino/default.nix | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pkgs/applications/video/kino/default.nix b/pkgs/applications/video/kino/default.nix index d6404a82bc34..4ddd84433e88 100644 --- a/pkgs/applications/video/kino/default.nix +++ b/pkgs/applications/video/kino/default.nix @@ -71,6 +71,11 @@ stdenv.mkDerivation { hardeningDisable = [ "format" ]; + NIX_LDFLAGS = [ + "-lavcodec" + "-lavutil" + ]; + patches = [ ./kino-1.3.4-v4l1.patch ./kino-1.3.4-libav-0.7.patch ./kino-1.3.4-libav-0.8.patch ]; #./kino-1.3.4-libavcodec-pkg-config.patch ]; postInstall = " From 46dd3e27d961dd48e68164e1f27fd3af2a001d57 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 054/247] lash: link with pthreads, lib{uuid,m} explicitly --- pkgs/applications/audio/lash/default.nix | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/pkgs/applications/audio/lash/default.nix b/pkgs/applications/audio/lash/default.nix index 9d2950735976..7fb5a01e2c80 100644 --- a/pkgs/applications/audio/lash/default.nix +++ b/pkgs/applications/audio/lash/default.nix @@ -18,6 +18,11 @@ stdenv.mkDerivation rec { buildInputs = [ alsaLib gtk2 libjack2 libxml2 makeWrapper pkgconfig readline ]; propagatedBuildInputs = [ libuuid ]; + NIX_LDFLAGS = [ + "-lm" + "-lpthread" + "-luuid" + ]; postInstall = '' for i in lash_control lash_panel From 3de83a8004c76631ad6fa4831960192b28ace58e Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 055/247] libfakekey: link with libX11 explicitly --- pkgs/development/libraries/libfakekey/default.nix | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/development/libraries/libfakekey/default.nix b/pkgs/development/libraries/libfakekey/default.nix index fa04655341d4..2a8e461d27eb 100644 --- a/pkgs/development/libraries/libfakekey/default.nix +++ b/pkgs/development/libraries/libfakekey/default.nix @@ -11,6 +11,9 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkgconfig ]; buildInputs = [ libX11 libXi libXtst xextproto ]; + NIX_LDFLAGS = [ + "-lX11" + ]; meta = with stdenv.lib; { description = "X virtual keyboard library"; From a830472b0bc7babe6c08392f99d5404697b6f200 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 056/247] libmatchbox: link with libX11 explicitly --- pkgs/development/libraries/libmatchbox/default.nix | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/development/libraries/libmatchbox/default.nix b/pkgs/development/libraries/libmatchbox/default.nix index 798aef8e7da7..8ff02b49e584 100644 --- a/pkgs/development/libraries/libmatchbox/default.nix +++ b/pkgs/development/libraries/libmatchbox/default.nix @@ -6,6 +6,9 @@ stdenv.mkDerivation rec { buildInputs = [ libXft libICE pango libjpeg ]; propagatedBuildInputs = [ libX11 libXext libpng ]; + NIX_LDFLAGS = [ + "-lX11" + ]; src = fetchurl { url = "https://downloads.yoctoproject.org/releases/matchbox/libmatchbox/${version}/libmatchbox-${version}.tar.bz2"; From ff1fc5a19903a7ad92c6698d290ffada1c02e429 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 057/247] multitran.libmtquery: link with libbtree explicitly --- pkgs/tools/text/multitran/libmtquery/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/tools/text/multitran/libmtquery/default.nix b/pkgs/tools/text/multitran/libmtquery/default.nix index 153184bf70f3..8b2032dcaba5 100644 --- a/pkgs/tools/text/multitran/libmtquery/default.nix +++ b/pkgs/tools/text/multitran/libmtquery/default.nix @@ -9,6 +9,10 @@ stdenv.mkDerivation { buildInputs = [ libmtsupport libfacet libbtree multitrandata ]; + NIX_LDFLAGS = [ + "-lbtree" + ]; + patchPhase = '' sed -i -e 's@\$(DESTDIR)/usr@'$out'@' \ -e 's@/usr/include/mt/support@${libmtsupport}/include/mt/support@' \ From a6d2bff76585f0343fc69e40039c5954033bdc83 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 058/247] opendungeons: link with pthreads explicitly --- pkgs/games/opendungeons/default.nix | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/games/opendungeons/default.nix b/pkgs/games/opendungeons/default.nix index 2a162525388f..3c4e85a91e5a 100644 --- a/pkgs/games/opendungeons/default.nix +++ b/pkgs/games/opendungeons/default.nix @@ -15,6 +15,9 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkgconfig ]; buildInputs = [ cmake ogre cegui boost sfml openal ois ]; + NIX_LDFLAGS = [ + "-lpthread" + ]; meta = with stdenv.lib; { description = "An open source, real time strategy game sharing game elements with the Dungeon Keeper series and Evil Genius."; From 86b97b22b6c52bacceafb49e0a329ea2657d76d3 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 059/247] parcellite: link with libgio-2.0 explicitely --- pkgs/tools/misc/parcellite/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/tools/misc/parcellite/default.nix b/pkgs/tools/misc/parcellite/default.nix index 37073daa699d..1e747961499c 100644 --- a/pkgs/tools/misc/parcellite/default.nix +++ b/pkgs/tools/misc/parcellite/default.nix @@ -15,6 +15,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ autoreconfHook intltool pkgconfig wrapGAppsHook ]; buildInputs = [ gtk2 hicolor-icon-theme ]; + NIX_LDFLAGS = [ "-lgio-2.0" ]; preFixup = '' # Need which and xdotool on path to fix auto-pasting. From 90f5c4a810d588165240d1f9e012903f1f79f9b5 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 060/247] pianobooster: link with pthreads, libGL explicitly --- pkgs/applications/audio/pianobooster/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/applications/audio/pianobooster/default.nix b/pkgs/applications/audio/pianobooster/default.nix index d013a26277e8..53afcdd2306a 100644 --- a/pkgs/applications/audio/pianobooster/default.nix +++ b/pkgs/applications/audio/pianobooster/default.nix @@ -17,6 +17,7 @@ stdenv.mkDerivation rec { preConfigure = "cd src"; buildInputs = [ alsaLib cmake makeWrapper libGLU_combined qt4 ]; + NIX_LDFLAGS = [ "-lGL" "-lpthread" ]; postInstall = '' wrapProgram $out/bin/pianobooster \ From 8bc5a019e84910759e13b77a27fc1a5e9dc477a9 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 061/247] pure: link with libLLVMJIT explicitly --- pkgs/development/interpreters/pure/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/development/interpreters/pure/default.nix b/pkgs/development/interpreters/pure/default.nix index c2b120576ea2..188058a73b52 100644 --- a/pkgs/development/interpreters/pure/default.nix +++ b/pkgs/development/interpreters/pure/default.nix @@ -13,6 +13,7 @@ stdenv.mkDerivation rec { buildInputs = [ bison flex makeWrapper ]; propagatedBuildInputs = [ llvm gmp mpfr readline ]; + NIX_LDFLAGS = [ "-lLLVMJIT" ]; postPatch = '' for f in expr.cc matcher.cc printer.cc symtable.cc parserdefs.hh; do From cfdcc387209669a9038f1f30c60ce380b097d07d Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 062/247] qjoypad: link with libX11 explicitly --- pkgs/tools/misc/qjoypad/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/tools/misc/qjoypad/default.nix b/pkgs/tools/misc/qjoypad/default.nix index 6a5e674b698b..4d91c184b0ae 100644 --- a/pkgs/tools/misc/qjoypad/default.nix +++ b/pkgs/tools/misc/qjoypad/default.nix @@ -7,6 +7,7 @@ stdenv.mkDerivation rec { }; nativeBuildInputs = [ pkgconfig ]; buildInputs = [ libX11 libXtst qt4 ]; + NIX_LDFLAGS = [ "-lX11" ]; patchPhase = '' cd src substituteInPlace config --replace /bin/bash /bin/sh From b0f40b4e6026d2312c095ea11e7a65a38de9766e Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 063/247] rox-filer: link with lib{dl,m} explicitly --- pkgs/desktops/rox/rox-filer/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/desktops/rox/rox-filer/default.nix b/pkgs/desktops/rox/rox-filer/default.nix index 65e4463600a9..543e3ca897f1 100644 --- a/pkgs/desktops/rox/rox-filer/default.nix +++ b/pkgs/desktops/rox/rox-filer/default.nix @@ -13,6 +13,7 @@ in stdenv.mkDerivation { nativeBuildInputs = [ pkgconfig ]; buildInputs = [ libxml2 gtk shared-mime-info hicolor-icon-theme libSM ]; + NIX_LDFLAGS = [ "-ldl" "-lm" ]; patches = [ ./rox-filer-2.11-in-source-build.patch From 78ed5680621853e155c6bcd709ba072a4216b393 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:50 +0000 Subject: [PATCH 064/247] skype_call_recorder: link with libvorbis explicitly --- .../instant-messengers/skype-call-recorder/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/applications/networking/instant-messengers/skype-call-recorder/default.nix b/pkgs/applications/networking/instant-messengers/skype-call-recorder/default.nix index 5fcee73c0f90..3ac2b567a8cb 100644 --- a/pkgs/applications/networking/instant-messengers/skype-call-recorder/default.nix +++ b/pkgs/applications/networking/instant-messengers/skype-call-recorder/default.nix @@ -16,6 +16,7 @@ stdenv.mkDerivation { patches = [ ./conference.patch ]; buildInputs = [ cmake lame id3lib libvorbis qt4 libogg ]; + NIX_LDFLAGS = [ "-lvorbis" ]; meta = { homepage = http://atdot.ch/scr/; From a898c8335d10119a1622c4a363cab2a6ae84e044 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:51 +0000 Subject: [PATCH 065/247] sqlitebrowser: link with libQt5PrintSupport explicitly --- pkgs/development/tools/database/sqlitebrowser/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/development/tools/database/sqlitebrowser/default.nix b/pkgs/development/tools/database/sqlitebrowser/default.nix index 1b4a4b7f50b2..929dfc61ba33 100644 --- a/pkgs/development/tools/database/sqlitebrowser/default.nix +++ b/pkgs/development/tools/database/sqlitebrowser/default.nix @@ -16,6 +16,10 @@ mkDerivation rec { nativeBuildInputs = [ cmake antlr qttools ]; + NIX_LDFLAGS = [ + "-lQt5PrintSupport" + ]; + enableParallelBuilding = true; # We have to patch out Test and PrintSupport to make this work with Qt 5.9 From a54cc22d4d20eb51f01c19562b6de5468122c874 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:51 +0000 Subject: [PATCH 066/247] ssmtp: link with libcrypto explicitly --- pkgs/tools/networking/ssmtp/default.nix | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pkgs/tools/networking/ssmtp/default.nix b/pkgs/tools/networking/ssmtp/default.nix index 4c906812f64d..22f60bfcee55 100644 --- a/pkgs/tools/networking/ssmtp/default.nix +++ b/pkgs/tools/networking/ssmtp/default.nix @@ -36,6 +36,8 @@ stdenv.mkDerivation { buildInputs = stdenv.lib.optional tlsSupport openssl; + NIX_LDFLAGS = stdenv.lib.optional tlsSupport [ "-lcrypto" ]; + meta = with stdenv.lib; { platforms = platforms.linux; license = licenses.gpl2; From 19061fb79e126c39c53c7aada9db9ea3b2f811d7 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:51 +0000 Subject: [PATCH 067/247] svnfs: link with libsvn_subr-1 explicitly --- pkgs/tools/filesystems/svnfs/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/tools/filesystems/svnfs/default.nix b/pkgs/tools/filesystems/svnfs/default.nix index 333714182177..ebfb211732e8 100644 --- a/pkgs/tools/filesystems/svnfs/default.nix +++ b/pkgs/tools/filesystems/svnfs/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation { ''; NIX_CFLAGS_COMPILE="-I ${subversion.dev}/include/subversion-1"; - NIX_LDFLAGS="-lsvn_client-1"; + NIX_LDFLAGS="-lsvn_client-1 -lsvn_subr-1"; meta = { description = "FUSE filesystem for accessing Subversion repositories"; From 510b678cb79238f2554dcd499779a4e341f810fb Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:51 +0000 Subject: [PATCH 068/247] tangogps: link with libm explicitly --- pkgs/applications/misc/tangogps/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/applications/misc/tangogps/default.nix b/pkgs/applications/misc/tangogps/default.nix index bde30d9041ae..08bea18d8e9a 100644 --- a/pkgs/applications/misc/tangogps/default.nix +++ b/pkgs/applications/misc/tangogps/default.nix @@ -11,6 +11,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkgconfig ]; buildInputs = [ gettext gtk2 gconf curl libexif sqlite libxml2 ]; + NIX_LDFLAGS = [ "-lm" ]; # bogus includes fail with newer library version postPatch = '' From 1492dcccdaa5ff208bb0c0da47800c5961599a68 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:51 +0000 Subject: [PATCH 069/247] texmacs: link with libz explicitly --- pkgs/applications/editors/texmacs/default.nix | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/pkgs/applications/editors/texmacs/default.nix b/pkgs/applications/editors/texmacs/default.nix index d3d95e5886a5..ac5ac34d2145 100644 --- a/pkgs/applications/editors/texmacs/default.nix +++ b/pkgs/applications/editors/texmacs/default.nix @@ -24,6 +24,7 @@ stdenv.mkDerivation { }; buildInputs = [ guile_1_8 qt4 makeWrapper ghostscriptX freetype ]; + NIX_LDFLAGS = [ "-lz" ]; postInstall = "wrapProgram $out/bin/texmacs --suffix PATH : " + (if ghostscriptX == null then "" else "${ghostscriptX}/bin:") + @@ -33,12 +34,6 @@ stdenv.mkDerivation { inherit (common) postPatch; - postFixup = '' - bin="$out/libexec/TeXmacs/bin/texmacs.bin" - rpath=$(patchelf --print-rpath "$bin") - patchelf --set-rpath "$rpath:${zlib.out}/lib" "$bin" - ''; - meta = common.meta // { maintainers = [ stdenv.lib.maintainers.roconnor ]; platforms = stdenv.lib.platforms.gnu ++ stdenv.lib.platforms.linux; # arbitrary choice From 89bcdd1184c8f996b6f9a7d76f8fe8a3815f2df2 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:51 +0000 Subject: [PATCH 070/247] timemachine: link with libm explicitly --- pkgs/applications/audio/timemachine/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/applications/audio/timemachine/default.nix b/pkgs/applications/audio/timemachine/default.nix index 8837566b13d0..643f50752985 100644 --- a/pkgs/applications/audio/timemachine/default.nix +++ b/pkgs/applications/audio/timemachine/default.nix @@ -19,6 +19,10 @@ stdenv.mkDerivation rec { preConfigure = "./autogen.sh"; + NIX_LDFLAGS = [ + "-lm" + ]; + meta = { description = "JACK audio recorder"; homepage = http://plugin.org.uk/timemachine/; From bf61e100d7c9f10d02370a68dcbda71e8606958f Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:51 +0000 Subject: [PATCH 071/247] xautoclick: use c++ compiler for linkage --- pkgs/applications/misc/xautoclick/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/applications/misc/xautoclick/default.nix b/pkgs/applications/misc/xautoclick/default.nix index 045354da3d60..bf3d9b737a9e 100644 --- a/pkgs/applications/misc/xautoclick/default.nix +++ b/pkgs/applications/misc/xautoclick/default.nix @@ -21,6 +21,7 @@ stdenv.mkDerivation rec { mkdir .bin ln -s ${qt4}/bin/moc .bin/moc-qt4 addToSearchPath PATH .bin + sed -i -e "s@LD=\$_cc@LD=\$_cxx@" configure ''; meta = with stdenv.lib; { From eb411132703a7e92097df0ae98a74adbed0397f1 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:51 +0000 Subject: [PATCH 072/247] qshowdiff: build with a c++ compiler --- pkgs/tools/text/qshowdiff/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/tools/text/qshowdiff/default.nix b/pkgs/tools/text/qshowdiff/default.nix index 761a498bcfb6..e3970c059027 100644 --- a/pkgs/tools/text/qshowdiff/default.nix +++ b/pkgs/tools/text/qshowdiff/default.nix @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { configurePhase = '' mkdir -p $out/{bin,man/man1} - makeFlags="PREFIX=$out" + makeFlags="PREFIX=$out CC=$CXX" ''; meta = { From 2e5cb0cb5b6dd9994cc15892b053ae3d59fc1900 Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:51 +0000 Subject: [PATCH 073/247] offrss: use c++ compiler for linkage --- pkgs/applications/networking/offrss/default.nix | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/pkgs/applications/networking/offrss/default.nix b/pkgs/applications/networking/offrss/default.nix index d499916c7b6c..d91bfbae501d 100644 --- a/pkgs/applications/networking/offrss/default.nix +++ b/pkgs/applications/networking/offrss/default.nix @@ -12,7 +12,10 @@ stdenv.mkDerivation { ++ stdenv.lib.optional (stdenv.hostPlatform == stdenv.buildPlatform) podofo ++ stdenv.lib.optional (!stdenv.isLinux) libiconv; - configurePhase = stdenv.lib.optionalString (!stdenv.isLinux) '' + configurePhase = '' + substituteInPlace Makefile \ + --replace '$(CC) $(CFLAGS) $(LDFLAGS)' '$(CXX) $(CFLAGS) $(LDFLAGS)' + '' + stdenv.lib.optionalString (!stdenv.isLinux) '' sed 's/#EXTRA/EXTRA/' -i Makefile '' + stdenv.lib.optionalString (stdenv.hostPlatform != stdenv.buildPlatform) '' sed 's/^PDF/#PDF/' -i Makefile From ac1122f264ea99f091ab413586cd739690a7ca1f Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Fri, 4 Jan 2019 19:33:51 +0000 Subject: [PATCH 074/247] pythonPackages.sipsimple: use c compiler for linkage --- pkgs/development/python-modules/sipsimple/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/development/python-modules/sipsimple/default.nix b/pkgs/development/python-modules/sipsimple/default.nix index 1df36dcf5d0a..bf76166d73b4 100644 --- a/pkgs/development/python-modules/sipsimple/default.nix +++ b/pkgs/development/python-modules/sipsimple/default.nix @@ -25,6 +25,7 @@ buildPythonPackage rec { preConfigure = '' chmod +x ./deps/pjsip/configure ./deps/pjsip/aconfigure + export LD=$CC ''; nativeBuildInputs = [ pkgs.pkgconfig ]; From 0a2c8cc1dbda287bdeb9c47b53f87f881f2f9710 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= Date: Sat, 5 Jan 2019 13:55:27 +0100 Subject: [PATCH 075/247] nixos/systemd-udev-settle: don't restart on upgrades The idea is that we only need this target during boot, however there is no point on restarting it on every upgrade. This hopefully fixes #21954 --- nixos/modules/system/boot/systemd.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/nixos/modules/system/boot/systemd.nix b/nixos/modules/system/boot/systemd.nix index d1029bb57982..860268ab23a6 100644 --- a/nixos/modules/system/boot/systemd.nix +++ b/nixos/modules/system/boot/systemd.nix @@ -898,6 +898,7 @@ in systemd.services.systemd-remount-fs.restartIfChanged = false; systemd.services.systemd-update-utmp.restartIfChanged = false; systemd.services.systemd-user-sessions.restartIfChanged = false; # Restart kills all active sessions. + systemd.services.systemd-udev-settle.restartIfChanged = false; # Causes long delays in nixos-rebuild # Restarting systemd-logind breaks X11 # - upstream commit: https://cgit.freedesktop.org/xorg/xserver/commit/?id=dc48bd653c7e101 # - systemd announcement: https://github.com/systemd/systemd/blob/22043e4317ecd2bc7834b48a6d364de76bb26d91/NEWS#L103-L112 From 256ae3ab4821280931e17fb28131d0b1ea7c9170 Mon Sep 17 00:00:00 2001 From: Markus Kowalewski Date: Sat, 5 Jan 2019 19:52:55 +0100 Subject: [PATCH 076/247] uhd: 3.12.0.0 -> 3.13.0.1 --- pkgs/development/tools/misc/uhd/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/development/tools/misc/uhd/default.nix b/pkgs/development/tools/misc/uhd/default.nix index 0730ef1fb09c..484e8787d50a 100644 --- a/pkgs/development/tools/misc/uhd/default.nix +++ b/pkgs/development/tools/misc/uhd/default.nix @@ -12,12 +12,12 @@ let # UHD seems to use three different version number styles: x.y.z, xxx_yyy_zzz # and xxx.yyy.zzz. Hrmpf... style keeps changing - version = "3.12.0.0"; + version = "3.13.0.1"; # Firmware images are downloaded (pre-built) from the respective release on Github uhdImagesSrc = fetchurl { url = "https://github.com/EttusResearch/uhd/releases/download/${uhdVer}/uhd-images_${version}.tar.xz"; - sha256 = "1glf2qay4asajbl92fy432idqk0sj5h603najr8sgkbdyyyr933p"; + sha256 = "0y9i93z188ch0hdlkvv0k9m0k7vns7rbxaqsnk35xnlqlxxgqdvj"; }; in stdenv.mkDerivation { @@ -27,7 +27,7 @@ in stdenv.mkDerivation { owner = "EttusResearch"; repo = "uhd"; rev = "${uhdVer}"; - sha256 = "0m7vw7dmvn7d01kkzphayzi0bk50m5v9a17rpnxhn0bqhw282ksv"; + sha256 = "0si49qk96zhpanmcrzlr3igc5s1y30x4p0z973q60dx9fhqsbb6k"; }; enableParallelBuilding = true; From fada7041a0cb7c92fa48a4094a7d8b32d8a96b90 Mon Sep 17 00:00:00 2001 From: Luke Sandell Date: Sat, 5 Jan 2019 09:16:52 -0600 Subject: [PATCH 077/247] wsjtx: 1.9.1 -> 2.0.0 Old version of FT8 protocol was obsoleted on 2019-01-01. --- pkgs/applications/misc/wsjtx/default.nix | 13 ++++++++----- pkgs/applications/misc/wsjtx/super.patch | 12 ++++++++++++ pkgs/applications/misc/wsjtx/wsjtx.patch | 12 ++++++------ 3 files changed, 26 insertions(+), 11 deletions(-) create mode 100644 pkgs/applications/misc/wsjtx/super.patch diff --git a/pkgs/applications/misc/wsjtx/default.nix b/pkgs/applications/misc/wsjtx/default.nix index fd6be8f59201..930515b93825 100644 --- a/pkgs/applications/misc/wsjtx/default.nix +++ b/pkgs/applications/misc/wsjtx/default.nix @@ -4,12 +4,12 @@ stdenv.mkDerivation rec { name = "wsjtx-${version}"; - version = "1.9.1"; + version = "2.0.0"; - # This is a composite source tarball containing both wsjtx and a hamlib fork + # This is a "superbuild" tarball containing both wsjtx and a hamlib fork src = fetchurl { - url = "http://physics.princeton.edu/pulsar/K1JT/wsjtx-${version}.tgz"; - sha256 = "143r17fri08mwz28g17wcfxy60h3xgfk46mln5lmdr9k6355aqqc"; + url = "http://physics.princeton.edu/pulsar/k1jt/wsjtx-${version}.tgz"; + sha256 = "66434f69f256742da1fe057ec51e4464cab2614f0bfb1a310c04a385b77bd014"; }; # Hamlib builds with autotools, wsjtx builds with cmake @@ -20,7 +20,10 @@ stdenv.mkDerivation rec { ]; buildInputs = [ fftw fftwFloat libusb1 qtbase qtmultimedia qtserialport ]; - # Composite build has its own patch step after it extracts the inner archives + # Remove Git dependency from superbuild since sources are included + patches = [ ./super.patch ]; + + # Superbuild has its own patch step after it extracts the inner archives postPatch = "cp ${./wsjtx.patch} wsjtx.patch"; meta = with stdenv.lib; { diff --git a/pkgs/applications/misc/wsjtx/super.patch b/pkgs/applications/misc/wsjtx/super.patch new file mode 100644 index 000000000000..d903171ffc5a --- /dev/null +++ b/pkgs/applications/misc/wsjtx/super.patch @@ -0,0 +1,12 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 3bf97a4..2c9dce5 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -23,7 +23,6 @@ source tarball." ) + # + # Find_library (USB_LIBRARY NAMES libusb.a usb) + Find_program (PATCH_EXECUTABLE patch REQUIRED) +-Find_package (Git REQUIRED) + + # + # extra C flags to minimize hamlib excutable sizes diff --git a/pkgs/applications/misc/wsjtx/wsjtx.patch b/pkgs/applications/misc/wsjtx/wsjtx.patch index a5bd7ec3e196..e92b420e58a4 100644 --- a/pkgs/applications/misc/wsjtx/wsjtx.patch +++ b/pkgs/applications/misc/wsjtx/wsjtx.patch @@ -1,11 +1,11 @@ -Index: wsjtx/CMakeLists.txt -=================================================================== ---- wsjtx/CMakeLists.txt (revision 8382) -+++ wsjtx/CMakeLists.txt (working copy) -@@ -866,6 +866,7 @@ - find_package (Qt5Widgets 5 REQUIRED) +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 3e7e816b..e7dbb14a 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -860,6 +860,7 @@ find_package (Qt5Widgets 5 REQUIRED) find_package (Qt5Multimedia 5 REQUIRED) find_package (Qt5PrintSupport 5 REQUIRED) + find_package (Qt5Sql 5 REQUIRED) +find_package (Qt5SerialPort 5 REQUIRED) if (WIN32) From 83ba7beb1a13545c42da18a1cbaa286c623b293e Mon Sep 17 00:00:00 2001 From: Andrew Dunham Date: Sat, 5 Jan 2019 23:23:54 -0500 Subject: [PATCH 078/247] uriparser: 0.9.0 -> 0.9.1 --- pkgs/development/libraries/uriparser/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/uriparser/default.nix b/pkgs/development/libraries/uriparser/default.nix index ac9f67e1e129..a4f99b942eae 100644 --- a/pkgs/development/libraries/uriparser/default.nix +++ b/pkgs/development/libraries/uriparser/default.nix @@ -2,12 +2,12 @@ stdenv.mkDerivation rec { name = "uriparser-${version}"; - version = "0.9.0"; + version = "0.9.1"; # Release tarball differs from source tarball src = fetchurl { url = "https://github.com/uriparser/uriparser/releases/download/${name}/${name}.tar.bz2"; - sha256 = "0b2yagxzhq9ghpszci6a9xlqg0yl7vq9j5r8dwbar3nszqsfnrzc"; + sha256 = "1gisi7h8hd6mswbiaaa3s25bnb77xf37pzrmjy63rcdpwcyqy93m"; }; nativeBuildInputs = [ pkgconfig doxygen graphviz ]; From ee9bc405b9a231ca88ee13cc2da91f9080cb12ec Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Sat, 5 Jan 2019 13:51:05 +0100 Subject: [PATCH 079/247] neovim-qt: wrap in separate derivation This makes it possible to swap out the (wrapped) neovim without recompiling neovim-qt. In particular, the user can use `neovim.override` to configure their neovim and then use that same configuration for neovim-qt, without having to give up binary caching. --- pkgs/applications/editors/neovim/qt.nix | 116 +++++++++++++----------- 1 file changed, 64 insertions(+), 52 deletions(-) diff --git a/pkgs/applications/editors/neovim/qt.nix b/pkgs/applications/editors/neovim/qt.nix index 315a51256f28..d562557ae005 100644 --- a/pkgs/applications/editors/neovim/qt.nix +++ b/pkgs/applications/editors/neovim/qt.nix @@ -1,62 +1,74 @@ { stdenv, fetchFromGitHub, cmake, doxygen, makeWrapper , msgpack, neovim, pythonPackages, qtbase }: -stdenv.mkDerivation rec { - name = "neovim-qt-${version}"; - version = "0.2.11"; +let + unwrapped = stdenv.mkDerivation rec { + pname = "neovim-qt-unwrapped"; + version = "0.2.11"; - src = fetchFromGitHub { - owner = "equalsraf"; - repo = "neovim-qt"; - rev = "v${version}"; - sha256 = "0pc1adxc89p2rdvb6nxyqr9sjzqz9zw2dg7a4ardxsl3a8jga1wh"; + src = fetchFromGitHub { + owner = "equalsraf"; + repo = "neovim-qt"; + rev = "v${version}"; + sha256 = "0pc1adxc89p2rdvb6nxyqr9sjzqz9zw2dg7a4ardxsl3a8jga1wh"; + }; + + cmakeFlags = [ + "-DUSE_SYSTEM_MSGPACK=1" + ]; + + buildInputs = [ + neovim.unwrapped # only used to generate help tags at build time + qtbase + ] ++ (with pythonPackages; [ + jinja2 python msgpack + ]); + + nativeBuildInputs = [ cmake doxygen makeWrapper ]; + + enableParallelBuilding = true; + + preCheck = '' + # The GUI tests require a running X server, disable them + sed -i ../test/CMakeLists.txt \ + -e '/^add_xtest_gui/d' + ''; + + doCheck = true; + + meta = with stdenv.lib; { + description = "Neovim client library and GUI, in Qt5"; + license = licenses.isc; + maintainers = with maintainers; [ peterhoeg ]; + inherit (neovim.meta) platforms; + inherit version; + }; }; +in + stdenv.mkDerivation { + pname = "neovim-qt"; + version = unwrapped.version; + buildCommand = if stdenv.isDarwin then '' + mkdir -p $out/Applications + cp -r ${unwrapped}/bin/nvim-qt.app $out/Applications - cmakeFlags = [ - "-DUSE_SYSTEM_MSGPACK=1" - ]; + chmod -R a+w "$out/Applications/nvim-qt.app/Contents/MacOS" + wrapProgram "$out/Applications/nvim-qt.app/Contents/MacOS/nvim-qt" \ + --prefix PATH : "${neovim}/bin" + '' else '' + makeWrapper '${unwrapped}/bin/nvim-qt' "$out/bin/nvim-qt" \ + --prefix PATH : "${neovim}/bin" + ''; - buildInputs = with pythonPackages; [ - neovim qtbase msgpack - ] ++ (with pythonPackages; [ - jinja2 msgpack python - ]); + preferLocalBuild = true; - nativeBuildInputs = [ cmake doxygen makeWrapper ]; + nativeBuildInputs = [ + makeWrapper + ]; - enableParallelBuilding = true; + passthru = { + inherit unwrapped; + }; - preConfigure = '' - # we rip out a number of tests that fail in the build env - # the GUI tests will never work but the others should - they did before neovim 0.2.0 - # was released - sed -i test/CMakeLists.txt \ - -e '/^add_xtest_gui/d' \ - -e '/tst_neovimobject/d' \ - -e '/tst_neovimconnector/d' \ - -e '/tst_callallmethods/d' \ - -e '/tst_encoding/d' - ''; - - doCheck = true; - - postInstall = if stdenv.isDarwin then '' - mkdir -p $out/Applications - mv $out/bin/nvim-qt.app $out/Applications - rmdir $out/bin || : - - wrapProgram "$out/Applications/nvim-qt.app/Contents/MacOS/nvim-qt" \ - --prefix PATH : "${neovim}/bin" - '' else '' - wrapProgram "$out/bin/nvim-qt" \ - --prefix PATH : "${neovim}/bin" - ''; - - meta = with stdenv.lib; { - description = "Neovim client library and GUI, in Qt5"; - license = licenses.isc; - maintainers = with maintainers; [ peterhoeg ]; - inherit (neovim.meta) platforms; - inherit version; - }; -} + inherit (unwrapped) meta; + } From c52c4a00a28ce89562b00e77ba66f32393b079a3 Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Sat, 5 Jan 2019 13:58:00 +0100 Subject: [PATCH 080/247] doc: add neovim-qt configuration --- doc/languages-frameworks/vim.section.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/doc/languages-frameworks/vim.section.md b/doc/languages-frameworks/vim.section.md index 6ed60028ae20..e4c486a0e52e 100644 --- a/doc/languages-frameworks/vim.section.md +++ b/doc/languages-frameworks/vim.section.md @@ -46,6 +46,21 @@ neovim.override { } ``` +If you want to use `neovim-qt` as a graphical editor, you can configure it by overriding neovim in an overlay +or passing it an overridden neovimn: + +``` +neovim-qt.override { + neovim = neovim.override { + configure = { + customRC = '' + # your custom configuration + ''; + }; + }; +} +``` + ## Managing plugins with Vim packages To store you plugins in Vim packages (the native vim plugin manager, see `:help packages`) the following example can be used: From d94cbd418820a2a9c28b91de1efc427489038278 Mon Sep 17 00:00:00 2001 From: Kirill Elagin Date: Sun, 6 Jan 2019 12:58:27 +0300 Subject: [PATCH 081/247] lighttpd: Disable WebDAV by default MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * It is disabled by default in lighttpd itself * Darwin doesn’t seem to have a function in libuiid that it needs --- pkgs/servers/http/lighttpd/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/servers/http/lighttpd/default.nix b/pkgs/servers/http/lighttpd/default.nix index cdebbf739e6a..13bf0f518c5a 100644 --- a/pkgs/servers/http/lighttpd/default.nix +++ b/pkgs/servers/http/lighttpd/default.nix @@ -2,7 +2,7 @@ , openssl, enableMagnet ? false, lua5_1 ? null , enableMysql ? false, mysql ? null , enableLdap ? false, openldap ? null -, enableWebDAV ? true, sqlite ? null, libuuid ? null +, enableWebDAV ? false, sqlite ? null, libuuid ? null , perl }: From bd141e9af10f2705ef03054758903b98e771eb47 Mon Sep 17 00:00:00 2001 From: Kirill Elagin Date: Sun, 6 Jan 2019 13:03:49 +0300 Subject: [PATCH 082/247] lighttpd: Hide attr dependency behind an option * Unbreak darwin * It was unused anyway, as it is disabled by default * Now there is an feature-argument to enable it --- pkgs/servers/http/lighttpd/default.nix | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/pkgs/servers/http/lighttpd/default.nix b/pkgs/servers/http/lighttpd/default.nix index 13bf0f518c5a..4023265b49bb 100644 --- a/pkgs/servers/http/lighttpd/default.nix +++ b/pkgs/servers/http/lighttpd/default.nix @@ -1,8 +1,9 @@ -{ stdenv, fetchurl, pkgconfig, pcre, libxml2, zlib, attr, bzip2, which, file +{ stdenv, fetchurl, pkgconfig, pcre, libxml2, zlib, bzip2, which, file , openssl, enableMagnet ? false, lua5_1 ? null , enableMysql ? false, mysql ? null , enableLdap ? false, openldap ? null , enableWebDAV ? false, sqlite ? null, libuuid ? null +, enableExtendedAttrs ? false, attr ? null , perl }: @@ -11,6 +12,7 @@ assert enableMysql -> mysql != null; assert enableLdap -> openldap != null; assert enableWebDAV -> sqlite != null; assert enableWebDAV -> libuuid != null; +assert enableExtendedAttrs -> attr != null; stdenv.mkDerivation rec { name = "lighttpd-1.4.52"; @@ -25,7 +27,7 @@ stdenv.mkDerivation rec { ''; nativeBuildInputs = [ pkgconfig ]; - buildInputs = [ pcre libxml2 zlib attr bzip2 which file openssl ] + buildInputs = [ pcre libxml2 zlib bzip2 which file openssl ] ++ stdenv.lib.optional enableMagnet lua5_1 ++ stdenv.lib.optional enableMysql mysql.connector-c ++ stdenv.lib.optional enableLdap openldap @@ -37,7 +39,8 @@ stdenv.mkDerivation rec { ++ stdenv.lib.optional enableMysql "--with-mysql" ++ stdenv.lib.optional enableLdap "--with-ldap" ++ stdenv.lib.optional enableWebDAV "--with-webdav-props" - ++ stdenv.lib.optional enableWebDAV "--with-webdav-locks"; + ++ stdenv.lib.optional enableWebDAV "--with-webdav-locks" + ++ stdenv.lib.optional enableExtendedAttrs "--with-attr"; preConfigure = '' sed -i "s:/usr/bin/file:${file}/bin/file:g" configure @@ -59,7 +62,7 @@ stdenv.mkDerivation rec { description = "Lightweight high-performance web server"; homepage = http://www.lighttpd.net/; license = stdenv.lib.licenses.bsd3; - platforms = platforms.linux; + platforms = platforms.linux ++ platforms.darwin; maintainers = [ maintainers.bjornfor ]; }; } From a162a562bd78a7d3587347fab5b8c6cfdc48b248 Mon Sep 17 00:00:00 2001 From: Kirill Elagin Date: Sun, 6 Jan 2019 13:05:30 +0300 Subject: [PATCH 083/247] lighttpd: Enable tests They seem to pass now, so why not. --- pkgs/servers/http/lighttpd/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/servers/http/lighttpd/default.nix b/pkgs/servers/http/lighttpd/default.nix index 4023265b49bb..a7e9c1447f1c 100644 --- a/pkgs/servers/http/lighttpd/default.nix +++ b/pkgs/servers/http/lighttpd/default.nix @@ -47,7 +47,7 @@ stdenv.mkDerivation rec { ''; checkInputs = [ perl ]; - doCheck = false; # fails 2 tests + doCheck = true; postInstall = '' mkdir -p "$out/share/lighttpd/doc/config" From 68c3097b9666fe036bb1574bd475175125a97518 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vladim=C3=ADr=20=C4=8Cun=C3=A1t?= Date: Sat, 5 Jan 2019 15:44:12 +0100 Subject: [PATCH 084/247] rtkit: link with librt explicitly --- pkgs/os-specific/linux/rtkit/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/os-specific/linux/rtkit/default.nix b/pkgs/os-specific/linux/rtkit/default.nix index 059b09449619..78bcd925aea0 100644 --- a/pkgs/os-specific/linux/rtkit/default.nix +++ b/pkgs/os-specific/linux/rtkit/default.nix @@ -34,6 +34,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkgconfig ]; buildInputs = [ dbus libcap ]; + NIX_LDFLAGS = [ "-lrt" ]; meta = with stdenv.lib; { homepage = http://0pointer.de/blog/projects/rtkit; From 981b504ecddd981488578494304d141849697dba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vladim=C3=ADr=20=C4=8Cun=C3=A1t?= Date: Sun, 6 Jan 2019 12:13:19 +0100 Subject: [PATCH 085/247] gst_all_1.gst-plugins-ugly: link with libm explicitly --- pkgs/development/libraries/gstreamer/ugly/default.nix | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pkgs/development/libraries/gstreamer/ugly/default.nix b/pkgs/development/libraries/gstreamer/ugly/default.nix index 6bc2ea8af896..0cdfd1f4a7b6 100644 --- a/pkgs/development/libraries/gstreamer/ugly/default.nix +++ b/pkgs/development/libraries/gstreamer/ugly/default.nix @@ -39,4 +39,6 @@ stdenv.mkDerivation rec { libintl ] ++ lib.optionals stdenv.isDarwin (with darwin.apple_sdk.frameworks; [ IOKit CoreFoundation DiskArbitration ]); + + NIX_LDFLAGS = [ "-lm" ]; } From 9211bcc7eaf9a0ba25e55eae6a5dad8bab3029ab Mon Sep 17 00:00:00 2001 From: pukkamustard Date: Thu, 3 Jan 2019 23:58:36 +0100 Subject: [PATCH 086/247] ocamlPackages: Use lib.makeScope --- pkgs/top-level/ocaml-packages.nix | 38 +++++++++++++------------------ 1 file changed, 16 insertions(+), 22 deletions(-) diff --git a/pkgs/top-level/ocaml-packages.nix b/pkgs/top-level/ocaml-packages.nix index c670db817728..a80aec268b9a 100644 --- a/pkgs/top-level/ocaml-packages.nix +++ b/pkgs/top-level/ocaml-packages.nix @@ -1,16 +1,13 @@ -{ lib, callPackage, newScope, pkgs, config }: +{ lib, newScope, pkgs, config }: let inherit (pkgs.stdenv.hostPlatform) system; - mkOcamlPackages = ocaml: overrides: - let - packageSet = self: - with self; let inherit (self) callPackage; in - let ocamlPackages = - { - callPackage = newScope self; + liftJaneStreet = self: super: super.janeStreet // super; + mkOcamlPackages = ocaml: + (lib.makeScope newScope (self: with self; + { inherit ocaml; # Libs @@ -1062,29 +1059,26 @@ let camlp5 = callPackage ../development/tools/ocaml/camlp5 { legacy = true; }; }; - }; - in (ocamlPackages.janeStreet // ocamlPackages); - in lib.fix' (lib.extends overrides packageSet); -in rec + })).overrideScope' liftJaneStreet; + +in let inherit (pkgs) callPackage; in rec { - inherit mkOcamlPackages; + ocamlPackages_4_00_1 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.00.1.nix { }); - ocamlPackages_4_00_1 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.00.1.nix { }) (self: super: { }); + ocamlPackages_4_01_0 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.01.0.nix { }); - ocamlPackages_4_01_0 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.01.0.nix { }) (self: super: { }); + ocamlPackages_4_02 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.02.nix { }); - ocamlPackages_4_02 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.02.nix { }) (self: super: { }); + ocamlPackages_4_03 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.03.nix { }); - ocamlPackages_4_03 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.03.nix { }) (self: super: { }); + ocamlPackages_4_04 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.04.nix { }); - ocamlPackages_4_04 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.04.nix { }) (self: super: { }); + ocamlPackages_4_05 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.05.nix { }); - ocamlPackages_4_05 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.05.nix { }) (self: super: { }); + ocamlPackages_4_06 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.06.nix { }); - ocamlPackages_4_06 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.06.nix { }) (self: super: { }); - - ocamlPackages_4_07 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.07.nix { }) (self: super: { }); + ocamlPackages_4_07 = mkOcamlPackages (callPackage ../development/compilers/ocaml/4.07.nix { }); ocamlPackages_latest = ocamlPackages_4_07; From b3d8aa2677e8adf0fa6a779695e87d4ad091fd2f Mon Sep 17 00:00:00 2001 From: Mario Rodas Date: Wed, 2 Jan 2019 23:46:25 -0500 Subject: [PATCH 087/247] 1password: 0.5.4 -> 0.5.5 --- pkgs/applications/misc/1password/default.nix | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/pkgs/applications/misc/1password/default.nix b/pkgs/applications/misc/1password/default.nix index a25d40e29bd0..6de7c3daed19 100644 --- a/pkgs/applications/misc/1password/default.nix +++ b/pkgs/applications/misc/1password/default.nix @@ -1,25 +1,25 @@ { stdenv, fetchzip }: stdenv.mkDerivation rec { - name = "1password-${version}"; - version = "0.5.4"; + pname = "1password"; + version = "0.5.5"; src = if stdenv.hostPlatform.system == "i686-linux" then fetchzip { url = "https://cache.agilebits.com/dist/1P/op/pkg/v${version}/op_linux_386_v${version}.zip"; - sha256 = "0wni2hk5b1qfr24vi24jiprpi08k3qgaw9lqp61k41a1sjp3izv0"; + sha256 = "14qx69fq1a3h93h167nhwp6gxka8r34295p82kim9grijrx5zz5f"; stripRoot = false; } else if stdenv.hostPlatform.system == "x86_64-linux" then fetchzip { url = "https://cache.agilebits.com/dist/1P/op/pkg/v${version}/op_linux_amd64_v${version}.zip"; - sha256 = "169d5fl3cfw3xrlpm9nlmwbnp0xgh0la9qybzf8ragp0020nlyih"; + sha256 = "1jh1sk07k3whbr0rvc4kf221wskcdbk0zpxaj49qbwq1d89cjnpg"; stripRoot = false; } else if stdenv.hostPlatform.system == "x86_64-darwin" then fetchzip { url = "https://cache.agilebits.com/dist/1P/op/pkg/v${version}/op_darwin_amd64_v${version}.zip"; - sha256 = "1scikv7v33kzg9rqsrz97yklxaskvif84br13zg8annm43k5vlma"; + sha256 = "1s6gw2qwsbhj4z9nrwrxs776y45ingpfp9533qz0gc1pk7ia99js"; stripRoot = false; } else throw "Architecture not supported"; From 39c30a33c182764a26dba00f56fa4e3982a1c979 Mon Sep 17 00:00:00 2001 From: Joachim Fasting Date: Sun, 6 Jan 2019 13:17:38 +0100 Subject: [PATCH 088/247] nixos/tests/hardened: test loading out-of-tree-modules --- nixos/tests/hardened.nix | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/nixos/tests/hardened.nix b/nixos/tests/hardened.nix index 683f56c45af4..07bd10963bab 100644 --- a/nixos/tests/hardened.nix +++ b/nixos/tests/hardened.nix @@ -5,7 +5,7 @@ import ./make-test.nix ({ pkgs, ...} : { }; machine = - { lib, pkgs, ... }: + { lib, pkgs, config, ... }: with lib; { users.users.alice = { isNormalUser = true; extraGroups = [ "proc" ]; }; users.users.sybil = { isNormalUser = true; group = "wheel"; }; @@ -22,12 +22,19 @@ import ./make-test.nix ({ pkgs, ...} : { options = [ "noauto" ]; }; }; + boot.extraModulePackages = [ config.boot.kernelPackages.wireguard ]; + boot.kernelModules = [ "wireguard" ]; }; testScript = '' $machine->waitForUnit("multi-user.target"); + # Test loading out-of-tree modules + subtest "extra-module-packages", sub { + $machine->succeed("grep -Fq wireguard /proc/modules"); + }; + # Test hidepid subtest "hidepid", sub { $machine->succeed("grep -Fq hidepid=2 /proc/mounts"); From cf58744a166d7edc4db2b4b7a590350db3245d10 Mon Sep 17 00:00:00 2001 From: Matt McHenry Date: Sat, 5 Jan 2019 17:23:20 -0500 Subject: [PATCH 089/247] client-ip-echo: 0.1.0.3 -> 0.1.0.4 --- pkgs/servers/misc/client-ip-echo/client-ip-echo.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/servers/misc/client-ip-echo/client-ip-echo.nix b/pkgs/servers/misc/client-ip-echo/client-ip-echo.nix index 1f5c6a20843a..ec1f82507ce1 100644 --- a/pkgs/servers/misc/client-ip-echo/client-ip-echo.nix +++ b/pkgs/servers/misc/client-ip-echo/client-ip-echo.nix @@ -1,12 +1,12 @@ { mkDerivation, fetchFromGitHub, base, bytestring, network, stdenv }: mkDerivation { pname = "client-ip-echo"; - version = "0.1.0.3"; + version = "0.1.0.4"; src = fetchFromGitHub { owner = "jerith666"; repo = "client-ip-echo"; - rev = "8d1a79d94a962b3266c1db51200913c2295d8922"; - sha256 = "1g1s7i68n3906m3yjfygw96j64n8nh88lmf77blnz0xzrq4y3bgf"; + rev = "58d1bc627c21008236afb1af4c09ba8153c95dad"; + sha256 = "153fab87qq080a819bqbdan925045icqwxldwj3ps40w2ssn7a53"; }; isLibrary = false; isExecutable = true; From e6538caa481606f208ee2f3ac0a907549236cfc5 Mon Sep 17 00:00:00 2001 From: Joachim Fasting Date: Sun, 6 Jan 2019 14:04:41 +0100 Subject: [PATCH 090/247] nixos/tests: re-enable hardened test Has been okay since 62623b60d5fed91ac676d6f4a70a12570090d513 --- nixos/tests/all-tests.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nixos/tests/all-tests.nix b/nixos/tests/all-tests.nix index 38fa9ffad3cd..7bd7df9b177f 100644 --- a/nixos/tests/all-tests.nix +++ b/nixos/tests/all-tests.nix @@ -92,7 +92,7 @@ in hadoop.yarn = handleTestOn [ "x86_64-linux" ] ./hadoop/yarn.nix {}; handbrake = handleTestOn ["x86_64-linux"] ./handbrake.nix {}; haproxy = handleTest ./haproxy.nix {}; - #hardened = handleTest ./hardened.nix {}; # broken due useSandbox = true + hardened = handleTest ./hardened.nix {}; hibernate = handleTest ./hibernate.nix {}; hitch = handleTest ./hitch {}; hocker-fetchdocker = handleTest ./hocker-fetchdocker {}; From 4bb0a719cf8f6b89ec89cd902a511a7e043d9a0d Mon Sep 17 00:00:00 2001 From: Joachim Fasting Date: Sun, 6 Jan 2019 14:05:51 +0100 Subject: [PATCH 091/247] openafs: fix build against linux_hardened See https://hydra.nixos.org/build/86750041 and https://hydra.nixos.org/build/86749971 --- pkgs/servers/openafs/1.6/module.nix | 3 +++ pkgs/servers/openafs/1.8/module.nix | 3 +++ 2 files changed, 6 insertions(+) diff --git a/pkgs/servers/openafs/1.6/module.nix b/pkgs/servers/openafs/1.6/module.nix index c133161cf576..374046cfdb61 100644 --- a/pkgs/servers/openafs/1.6/module.nix +++ b/pkgs/servers/openafs/1.6/module.nix @@ -15,6 +15,9 @@ in stdenv.mkDerivation rec { hardeningDisable = [ "pic" ]; + # The RANDSTRUCT gcc plugin rewrites structs using designated initializers + NIX_CFLAGS_COMPILE = [ "-Wno-error=designated-init" ]; + configureFlags = [ "--with-linux-kernel-build=${kernelBuildDir}" "--sysconfdir=/etc" diff --git a/pkgs/servers/openafs/1.8/module.nix b/pkgs/servers/openafs/1.8/module.nix index 958fcd578c2b..c60b96f1693e 100644 --- a/pkgs/servers/openafs/1.8/module.nix +++ b/pkgs/servers/openafs/1.8/module.nix @@ -18,6 +18,9 @@ in stdenv.mkDerivation rec { hardeningDisable = [ "pic" ]; + # The RANDSTRUCT gcc plugin rewrites structs using designated initializers + NIX_CFLAGS_COMPILE = [ "-Wno-error=designated-init" ]; + configureFlags = [ "--with-linux-kernel-build=${kernelBuildDir}" "--sysconfdir=/etc" From c6b8312f21484f5948413ac4e80747cb41fa8c43 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vladim=C3=ADr=20=C4=8Cun=C3=A1t?= Date: Sun, 6 Jan 2019 14:26:03 +0100 Subject: [PATCH 092/247] bird2: fixup build after 7bb24a65e I didn't look whether bird2 cross-compiles, but the patch wouldn't apply. --- pkgs/servers/bird/default.nix | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/pkgs/servers/bird/default.nix b/pkgs/servers/bird/default.nix index 94579e1bdb16..7e0bf298b029 100644 --- a/pkgs/servers/bird/default.nix +++ b/pkgs/servers/bird/default.nix @@ -18,12 +18,14 @@ let patches = [ (./. + "/dont-create-sysconfdir-${builtins.substring 0 1 version}.patch") + ] + ++ optional (lib.versionOlder version "2") # https://github.com/BIRD/bird/pull/4 (fetchpatch { url = "https://github.com/BIRD/bird/commit/fca9ab48e3823c734886f47156a92f6b804c16e9.patch"; sha256 = "1pnndc3n56lqqcy74ln0w5kn3i9rbzsm2dqiyp1qw7j33dpkln1b"; }) - ]; + ; CPP="${stdenv.cc.targetPrefix}cpp -E"; From ca531efae8d44921c423998c73787f5473bd1078 Mon Sep 17 00:00:00 2001 From: Edmund Wu Date: Sun, 6 Jan 2019 08:30:57 -0500 Subject: [PATCH 093/247] feh: include prove for tests --- pkgs/applications/graphics/feh/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/applications/graphics/feh/default.nix b/pkgs/applications/graphics/feh/default.nix index a1ef5fcb4b6f..02e6a10295e9 100644 --- a/pkgs/applications/graphics/feh/default.nix +++ b/pkgs/applications/graphics/feh/default.nix @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { install -D -m 644 man/*.1 $out/share/man/man1 ''; - checkInputs = [ perlPackages.TestCommand ]; + checkInputs = [ perlPackages.perl perlPackages.TestCommand ]; preCheck = '' export PERL5LIB="${perlPackages.TestCommand}/${perlPackages.perl.libPrefix}" ''; From 13c58d89dd40ce39946454a23c76f54f3062496d Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Sun, 6 Jan 2019 14:33:53 +0100 Subject: [PATCH 094/247] gcr: fix evaluation error --- pkgs/top-level/all-packages.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 6815da9c3fe5..e23e92703dcb 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -9818,7 +9818,7 @@ in gcab = callPackage ../development/libraries/gcab { }; - gcr = callPackages ../development/libraries/gcr { }; + gcr = callPackage ../development/libraries/gcr { }; gdome2 = callPackage ../development/libraries/gdome2 { inherit (gnome2) gtkdoc; From 747531a46e444ab66bdf33d73097abe3bdda7349 Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Sun, 6 Jan 2019 14:34:15 +0100 Subject: [PATCH 095/247] gsound: fix evaluation error --- pkgs/top-level/all-packages.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index e23e92703dcb..3064cb38b08e 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -10120,7 +10120,7 @@ in gsoap = callPackage ../development/libraries/gsoap { }; - gsound = callPackages ../development/libraries/gsound { }; + gsound = callPackage ../development/libraries/gsound { }; gss = callPackage ../development/libraries/gss { }; From 711db1b0cd6d8a4726232ec1446feb5a1ccad73f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vladim=C3=ADr=20=C4=8Cun=C3=A1t?= Date: Sun, 6 Jan 2019 14:52:11 +0100 Subject: [PATCH 096/247] postfix: fix linking error after #51770; issue #53001 --- pkgs/servers/mail/postfix/default.nix | 2 ++ 1 file changed, 2 insertions(+) diff --git a/pkgs/servers/mail/postfix/default.nix b/pkgs/servers/mail/postfix/default.nix index 019cc1b1948c..a418e2af4685 100644 --- a/pkgs/servers/mail/postfix/default.nix +++ b/pkgs/servers/mail/postfix/default.nix @@ -79,6 +79,8 @@ in stdenv.mkDerivation rec { make makefiles CCARGS='${ccargs}' AUXLIBS='${auxlibs}' ''; + NIX_LDFLAGS = lib.optional withLDAP "-llber"; + installTargets = [ "non-interactive-package" ]; installFlags = [ "install_root=installdir" ]; From 9ee8cf517713135cfe395a56fd59d107fda0103b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vladim=C3=ADr=20=C4=8Cun=C3=A1t?= Date: Sun, 6 Jan 2019 14:59:03 +0100 Subject: [PATCH 097/247] linuxPackages.nvidia_x11*: unmaintain I now no longer use an nvidia card commonly, so it would be harder for me to test at least a bit. And I'm overcommited anyway. Hopefully someone else can be found. --- pkgs/os-specific/linux/nvidia-x11/generic.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/os-specific/linux/nvidia-x11/generic.nix b/pkgs/os-specific/linux/nvidia-x11/generic.nix index be378d66caf9..906e59eb1c1f 100644 --- a/pkgs/os-specific/linux/nvidia-x11/generic.nix +++ b/pkgs/os-specific/linux/nvidia-x11/generic.nix @@ -90,7 +90,7 @@ let description = "X.org driver and kernel module for NVIDIA graphics cards"; license = licenses.unfreeRedistributable; platforms = [ "i686-linux" "x86_64-linux" ]; - maintainers = [ maintainers.vcunat ]; + maintainers = [ ]; priority = 4; # resolves collision with xorg-server's "lib/xorg/modules/extensions/libglx.so" inherit broken; }; From 5b201a8e98e50e25f284860d7e84ebc7b93a6d34 Mon Sep 17 00:00:00 2001 From: Artur Kireev Date: Sun, 6 Jan 2019 20:37:53 +0500 Subject: [PATCH 098/247] ksh: init at 93v --- pkgs/shells/ksh/default.nix | 34 +++++++++++++++++++++++++++++++++ pkgs/top-level/all-packages.nix | 4 +++- 2 files changed, 37 insertions(+), 1 deletion(-) create mode 100644 pkgs/shells/ksh/default.nix diff --git a/pkgs/shells/ksh/default.nix b/pkgs/shells/ksh/default.nix new file mode 100644 index 000000000000..05335a1eb68c --- /dev/null +++ b/pkgs/shells/ksh/default.nix @@ -0,0 +1,34 @@ +{ stdenv, meson, ninja, fetchFromGitHub, which, python }: + +stdenv.mkDerivation rec { + name = "ksh-${version}"; + version = "93v"; + + src = fetchFromGitHub { + owner = "att"; + repo = "ast"; + rev = "b8d88244ae87857e7bbd6da230ffbbc51165df70"; + sha256 = "12kf14n8vz36hnsy3wp6lnyv1841p7hcq25y1d78w532dil69lx9"; + }; + + nativeBuildInputs = [ meson ninja which python ]; + + meta = with stdenv.lib; { + description = "KornShell Command And Programming Language"; + longDescription = '' + The KornShell language was designed and developed by David G. Korn at + AT&T Bell Laboratories. It is an interactive command language that + provides access to the UNIX system and to many other systems, on the + many different computers and workstations on which it is implemented. + ''; + homepage = https://github.com/att/ast; + license = licenses.cpl10; + maintainers = with maintainers; [ ]; + platforms = platforms.all; + }; + + passthru = { + shellPath = "/bin/ksh"; + }; +} + diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 3064cb38b08e..adf85fa0a6ec 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -6521,7 +6521,9 @@ in fish-foreign-env = callPackage ../shells/fish/fish-foreign-env { }; ion = callPackage ../shells/ion { }; - + + ksh = callPackage ../shells/ksh { }; + mksh = callPackage ../shells/mksh { }; oh = callPackage ../shells/oh { }; From dda2cdfe938a6bfdb64690d548d15baeb4719ed6 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Sun, 6 Jan 2019 08:27:18 -0800 Subject: [PATCH 099/247] wavemon: 0.8.2 -> 0.9.0 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/wavemon/versions --- pkgs/tools/networking/wavemon/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/networking/wavemon/default.nix b/pkgs/tools/networking/wavemon/default.nix index a4c707442345..fefff8573816 100644 --- a/pkgs/tools/networking/wavemon/default.nix +++ b/pkgs/tools/networking/wavemon/default.nix @@ -1,7 +1,7 @@ { stdenv, fetchFromGitHub, ncurses, libnl, pkgconfig }: stdenv.mkDerivation rec { - version = "0.8.2"; + version = "0.9.0"; baseName = "wavemon"; name = "${baseName}-${version}"; @@ -12,7 +12,7 @@ stdenv.mkDerivation rec { owner = "uoaerg"; repo = "wavemon"; rev = "v${version}"; - sha256 = "0rqpp7rhl9rlwnihsapaiy62v33h45fm3d0ia2nhdjw7fwkwcqvs"; + sha256 = "07cid0h3mcyr74nnrzzf8k5n1p9a4y3wij43jbiaqmkpxilcc1i6"; }; meta = with stdenv.lib; { From 9d2c9157d77c2f183c1c5cee37dd625bf55183d7 Mon Sep 17 00:00:00 2001 From: Falco Peijnenburg Date: Fri, 4 Jan 2019 12:01:18 +0100 Subject: [PATCH 100/247] nixos/apache-httpd/wordpress: copy plugins and themes instead of symlinking Symlinking works for most plugins and themes, but Avada, for instance, fails to understand the symlink, causing its file path stripping to fail. This results in requests that look like: https://example.com/wp-content//nix/store/...plugin/path/some-file.js Since hard linking directories is not allowed, copying is the next best thing. --- .../services/web-servers/apache-httpd/wordpress.nix | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nixos/modules/services/web-servers/apache-httpd/wordpress.nix b/nixos/modules/services/web-servers/apache-httpd/wordpress.nix index c810b914e258..c68bfd25f6a8 100644 --- a/nixos/modules/services/web-servers/apache-httpd/wordpress.nix +++ b/nixos/modules/services/web-servers/apache-httpd/wordpress.nix @@ -85,10 +85,10 @@ let # remove bundled themes(s) coming with wordpress rm -Rf $out/wp-content/themes/* - # symlink additional theme(s) - ${concatMapStrings (theme: "ln -s ${theme} $out/wp-content/themes/${theme.name}\n") config.themes} - # symlink additional plugin(s) - ${concatMapStrings (plugin: "ln -s ${plugin} $out/wp-content/plugins/${plugin.name}\n") (config.plugins) } + # copy additional theme(s) + ${concatMapStrings (theme: "cp -r ${theme} $out/wp-content/themes/${theme.name}\n") config.themes} + # copy additional plugin(s) + ${concatMapStrings (plugin: "cp -r ${plugin} $out/wp-content/plugins/${plugin.name}\n") (config.plugins) } # symlink additional translation(s) mkdir -p $out/wp-content/languages From e4e695548c126297ccef27af62a65a9bb8d099fd Mon Sep 17 00:00:00 2001 From: Orivej Desh Date: Sun, 6 Jan 2019 04:16:10 +0000 Subject: [PATCH 101/247] clickhouse: link to libLLVM rather than to individual LLVM libs The clickhouse program links to LLVM and to the clickhouse library, that also links to LLVM. When the library is shared but LLVM is static, LLVM gets linked into the program twice (once via the library and once directly), which causes this error when running clickhouse: : CommandLine Error: Option 'x86-use-base-pointer' registered more than once! LLVM ERROR: inconsistency in registered CommandLine options A common LLVM installation provides static component libraries and a shared libLLVM. Linking to libLLVM when libclickhouse is shared solves this issue. Upstream pull request: https://github.com/yandex/ClickHouse/pull/3989 --- pkgs/servers/clickhouse/default.nix | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/pkgs/servers/clickhouse/default.nix b/pkgs/servers/clickhouse/default.nix index 90d614553ea8..3272065efbef 100644 --- a/pkgs/servers/clickhouse/default.nix +++ b/pkgs/servers/clickhouse/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, libtool +{ stdenv, fetchFromGitHub, fetchpatch, cmake, libtool , boost, capnproto, cctz, clang-unwrapped, double-conversion, gperftools, icu , libcpuid, libxml2, lld, llvm, lz4 , mysql, openssl, poco, re2, rdkafka , readline, sparsehash, unixODBC, zstd, ninja, jemalloc @@ -28,10 +28,16 @@ stdenv.mkDerivation rec { "-DUSE_STATIC_LIBRARIES=OFF" "-DUSE_INTERNAL_SSL_LIBRARY=False" ]; - hardeningDisable = [ "format" ]; - patchPhase = '' - patchShebangs . + patches = [ + (fetchpatch { + url = "https://github.com/yandex/ClickHouse/commit/afbcdf2f00a04e747c5279414cf4691f29bb5cc2.patch"; + sha256 = "17y891q0dp179w3jv32h74pbfwyzgnz4dxxwv73vzdwvys4i8c8z"; + }) + ]; + + postPatch = '' + patchShebangs copy_headers.sh ''; postInstall = '' @@ -43,6 +49,8 @@ stdenv.mkDerivation rec { --replace "/var/log/clickhouse-server/clickhouse-server.err.log" "1" ''; + hardeningDisable = [ "format" ]; + meta = with stdenv.lib; { homepage = https://clickhouse.yandex/; description = "Column-oriented database management system"; From a2ffb3fcd8422e046ab88d79cfcbcffbe583ec1f Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Sun, 6 Jan 2019 19:10:47 +0100 Subject: [PATCH 102/247] python.pkgs.r2pipe: init at 1.2.0 (#53504) --- .../python-modules/r2pipe/default.nix | 51 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 53 insertions(+) create mode 100644 pkgs/development/python-modules/r2pipe/default.nix diff --git a/pkgs/development/python-modules/r2pipe/default.nix b/pkgs/development/python-modules/r2pipe/default.nix new file mode 100644 index 000000000000..354f2743e984 --- /dev/null +++ b/pkgs/development/python-modules/r2pipe/default.nix @@ -0,0 +1,51 @@ +{ stdenv +, lib +, python +, buildPythonPackage +, fetchPypi +, radare2 +, coreutils +}: + +buildPythonPackage rec { + pname = "r2pipe"; + version = "1.2.0"; + + postPatch = let + r2lib = "${lib.getOutput "lib" radare2}/lib"; + libr_core = "${r2lib}/libr_core${stdenv.hostPlatform.extensions.sharedLibrary}"; + in + '' + # Fix find_library, can be removed after + # https://github.com/NixOS/nixpkgs/issues/7307 is resolved. + substituteInPlace r2pipe/native.py --replace "find_library('r_core')" "'${libr_core}'" + + # Fix the default r2 executable + substituteInPlace r2pipe/open_sync.py --replace "r2e = 'radare2'" "r2e = '${radare2}/bin/radare2'" + substituteInPlace r2pipe/open_base.py --replace 'which("radare2")' "'${radare2}/bin/radare2'" + ''; + + src = fetchPypi { + inherit pname version; + sha256 = "1qs3xqmi9alahsgr8akzw06ia4c3554dz8pran1h7z5llk262nj4"; + }; + + # Tiny sanity check to make sure r2pipe finds radare2 (since r2pipe doesn't + # provide its own tests): + # Analyze ls with the fastest analysis and do nothing with the result. + postCheck = '' + ${python.interpreter} < Date: Sun, 6 Jan 2019 20:11:35 +0100 Subject: [PATCH 103/247] scons: Add version 3.0.2 "SCons release 3.0.2 now available from the download page at SourceForge. This release should be used instead of 3.0.1. This release fixes several issues. This release supports Python versions 2.7.* as well as 3.5+." [0] Details can be found in the changelog [1]. I'll update the default after running additional tests. [0]: https://scons.org/scons-302-is-available.html [1]: https://raw.githubusercontent.com/SConsProject/scons/rel_3.0.2/src/CHANGES.txt --- pkgs/development/tools/build-managers/scons/default.nix | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/pkgs/development/tools/build-managers/scons/default.nix b/pkgs/development/tools/build-managers/scons/default.nix index 3bd31523412a..1374d5b6dde5 100644 --- a/pkgs/development/tools/build-managers/scons/default.nix +++ b/pkgs/development/tools/build-managers/scons/default.nix @@ -15,4 +15,8 @@ in { version = "3.0.1"; sha256 = "0wzid419mlwqw9llrg8gsx4nkzhqy16m4m40r0xnh6cwscw5wir4"; }; + scons_3_0_2 = mkScons { + version = "3.0.2"; + sha256 = "00fyvb2rrixj9h6f2sqr6z8q677anc61qcn9ydxgm99f9j7wzbyh"; + }; } From a684ae6e53d3dd7e946c917acbea771a49778b29 Mon Sep 17 00:00:00 2001 From: Michael Weiss Date: Sun, 6 Jan 2019 20:19:54 +0100 Subject: [PATCH 104/247] scons: Remove version 3.0.0 --- pkgs/development/tools/build-managers/scons/default.nix | 4 ---- 1 file changed, 4 deletions(-) diff --git a/pkgs/development/tools/build-managers/scons/default.nix b/pkgs/development/tools/build-managers/scons/default.nix index 1374d5b6dde5..21893545c9a3 100644 --- a/pkgs/development/tools/build-managers/scons/default.nix +++ b/pkgs/development/tools/build-managers/scons/default.nix @@ -7,10 +7,6 @@ in { version = "2.5.1"; sha256 = "1wji1z9jdkhnmm99apx6fhld9cs52rr56aigniyrcsmlwy52298b"; }; - scons_3_0_0 = mkScons { - version = "3.0.0"; - sha256 = "05jjykllk4icnq6gfrkgkbc4ggxm7983q6r33mrhpilqbd02ylqg"; - }; scons_3_0_1 = mkScons { version = "3.0.1"; sha256 = "0wzid419mlwqw9llrg8gsx4nkzhqy16m4m40r0xnh6cwscw5wir4"; From b4ed953bb2f7486173ebc062296a1c2a04933b34 Mon Sep 17 00:00:00 2001 From: Roman Volosatovs Date: Sun, 6 Jan 2019 21:49:16 +0100 Subject: [PATCH 105/247] neovim: 0.3.2 -> 0.3.3 --- pkgs/applications/editors/neovim/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/editors/neovim/default.nix b/pkgs/applications/editors/neovim/default.nix index 99c3c62663c9..1bc7f1688ea8 100644 --- a/pkgs/applications/editors/neovim/default.nix +++ b/pkgs/applications/editors/neovim/default.nix @@ -11,13 +11,13 @@ let neovim = stdenv.mkDerivation rec { name = "neovim-unwrapped-${version}"; - version = "0.3.2"; + version = "0.3.3"; src = fetchFromGitHub { owner = "neovim"; repo = "neovim"; rev = "v${version}"; - sha256 = "0gniick8jbra1xz5nmg9jyxr7dsnbh9n9bcbp7fq3acb2qnrd22y"; + sha256 = "0jf39br0c7kkvmc8b5n9b3lgy9cmf5sv1gghzafc8qk54bqymy2f"; }; enableParallelBuilding = true; From a339eec2f56fe4e6b90d335feaf82427e1a32926 Mon Sep 17 00:00:00 2001 From: Jorge Acereda Date: Sun, 6 Jan 2019 22:56:29 +0100 Subject: [PATCH 106/247] futhark: remove obsolete non-hackage package --- .../development/compilers/futhark/default.nix | 55 ------------------- .../haskell-modules/non-hackage-packages.nix | 3 - 2 files changed, 58 deletions(-) delete mode 100644 pkgs/development/compilers/futhark/default.nix diff --git a/pkgs/development/compilers/futhark/default.nix b/pkgs/development/compilers/futhark/default.nix deleted file mode 100644 index 890be3431c3a..000000000000 --- a/pkgs/development/compilers/futhark/default.nix +++ /dev/null @@ -1,55 +0,0 @@ -# Generated using `cabal2nix --hpack .`, then replace src -{ mkDerivation, alex, array, base, bifunctors, binary, blaze-html -, bytestring, containers, data-binary-ieee754, directory -, directory-tree, dlist, extra, file-embed, filepath, gitrev, happy -, haskeline, hpack, HUnit, json, language-c-quote, mainland-pretty -, markdown, mtl, neat-interpolation, parallel, parsec, process -, process-extras, QuickCheck, random, raw-strings-qq, regex-tdfa -, srcloc, stdenv, template-haskell, temporary, test-framework -, test-framework-hunit, test-framework-quickcheck2, text -, th-lift-instances, transformers, vector, vector-binary-instances -, zlib, fetchFromGitHub -}: -mkDerivation { - pname = "futhark"; - version = "0.6.2"; - src = fetchFromGitHub { - owner = "diku-dk"; - repo = "futhark"; - rev = "v0.6.2"; - sha256 = "0yj7n01swpvqblybdnks3mjf0mzf1gdg2b2cpxdpxnrjw5j0pnq2"; - }; - isLibrary = true; - isExecutable = true; - libraryHaskellDepends = [ - array base bifunctors binary blaze-html bytestring containers - data-binary-ieee754 directory directory-tree dlist extra file-embed - filepath gitrev language-c-quote mainland-pretty markdown mtl - neat-interpolation parallel parsec process raw-strings-qq - regex-tdfa srcloc template-haskell text th-lift-instances - transformers vector vector-binary-instances zlib - ]; - libraryToolDepends = [ alex happy hpack ]; - executableHaskellDepends = [ - array base bifunctors binary blaze-html bytestring containers - data-binary-ieee754 directory directory-tree dlist extra file-embed - filepath gitrev haskeline json language-c-quote mainland-pretty - markdown mtl neat-interpolation parallel parsec process - process-extras random raw-strings-qq regex-tdfa srcloc - template-haskell temporary text th-lift-instances transformers - vector vector-binary-instances zlib - ]; - testHaskellDepends = [ - array base bifunctors binary blaze-html bytestring containers - data-binary-ieee754 directory directory-tree dlist extra file-embed - filepath gitrev HUnit language-c-quote mainland-pretty markdown mtl - neat-interpolation parallel parsec process QuickCheck - raw-strings-qq regex-tdfa srcloc template-haskell test-framework - test-framework-hunit test-framework-quickcheck2 text - th-lift-instances transformers vector vector-binary-instances zlib - ]; - preConfigure = "hpack"; - homepage = "https://futhark-lang.org"; - description = "An optimising compiler for a functional, array-oriented language"; - license = stdenv.lib.licenses.isc; -} diff --git a/pkgs/development/haskell-modules/non-hackage-packages.nix b/pkgs/development/haskell-modules/non-hackage-packages.nix index 68fcbdb79a5d..b7b057f2dc20 100644 --- a/pkgs/development/haskell-modules/non-hackage-packages.nix +++ b/pkgs/development/haskell-modules/non-hackage-packages.nix @@ -12,7 +12,4 @@ self: super: { # https://github.com/channable/vaultenv/issues/1 vaultenv = self.callPackage ../tools/haskell/vaultenv { }; - - # https://github.com/diku-dk/futhark/issues/614 - futhark = self.callPackage ../compilers/futhark { }; } From 2118e66fc310297e9a8ebe0cfb25fe7583206477 Mon Sep 17 00:00:00 2001 From: Jorge Acereda Date: Sun, 6 Jan 2019 22:56:50 +0100 Subject: [PATCH 107/247] futhark: fix darwin build --- pkgs/development/haskell-modules/configuration-nix.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/haskell-modules/configuration-nix.nix b/pkgs/development/haskell-modules/configuration-nix.nix index 62f2782e8f77..37c1d2ce6534 100644 --- a/pkgs/development/haskell-modules/configuration-nix.nix +++ b/pkgs/development/haskell-modules/configuration-nix.nix @@ -532,7 +532,7 @@ self: super: builtins.intersectAttrs super { # The test-suite requires a running PostgreSQL server. Frames-beam = dontCheck super.Frames-beam; - futhark = with pkgs; + futhark = if pkgs.stdenv.isDarwin then super.futhark else with pkgs; let path = stdenv.lib.makeBinPath [ gcc ]; in overrideCabal (addBuildTool super.futhark makeWrapper) (_drv: { postInstall = '' From 445c73afeda0bbbe4ba067b1013e03a881c883f7 Mon Sep 17 00:00:00 2001 From: buffet Date: Mon, 7 Jan 2019 00:10:46 +0100 Subject: [PATCH 108/247] maintainer-list: countingsort -> buffet --- maintainers/maintainer-list.nix | 10 +++++----- pkgs/tools/package-management/bunny/default.nix | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix index f72d02bcbfde..62e18e48c155 100644 --- a/maintainers/maintainer-list.nix +++ b/maintainers/maintainer-list.nix @@ -669,6 +669,11 @@ github = "bstrik"; name = "Berno Strik"; }; + buffet = { + email = "niclas@countingsort.com"; + github = "buffet"; + name = "Niclas Meyer"; + }; bugworm = { email = "bugworm@zoho.com"; github = "bugworm"; @@ -927,11 +932,6 @@ github = "couchemar"; name = "Andrey Pavlov"; }; - countingsort = { - email = "niclas@countingsort.com"; - github = "countingsort"; - name = "Niclas Meyer"; - }; cpages = { email = "page@ruiec.cat"; github = "cpages"; diff --git a/pkgs/tools/package-management/bunny/default.nix b/pkgs/tools/package-management/bunny/default.nix index cb99e5af055b..0f45084f3c05 100644 --- a/pkgs/tools/package-management/bunny/default.nix +++ b/pkgs/tools/package-management/bunny/default.nix @@ -20,6 +20,6 @@ stdenv.mkDerivation rec { homepage = https://gitlab.com/tim241/bunny; license = licenses.gpl3; platforms = platforms.all; - maintainers = with maintainers; [ countingsort ]; + maintainers = with maintainers; [ buffet ]; }; } From 1c1fd0935b6a9f94df2639659a32aa0d83e781cf Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Sun, 6 Jan 2019 15:12:50 -0800 Subject: [PATCH 109/247] simpleitk: 1.1.0 -> 1.2.0 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/simpleitk/versions --- pkgs/development/libraries/simpleitk/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/simpleitk/default.nix b/pkgs/development/libraries/simpleitk/default.nix index 1c17124a2bbb..90dfe8ebfab8 100644 --- a/pkgs/development/libraries/simpleitk/default.nix +++ b/pkgs/development/libraries/simpleitk/default.nix @@ -2,12 +2,12 @@ stdenv.mkDerivation rec { pname = "simpleitk"; - version = "1.1.0"; + version = "1.2.0"; name = "${pname}-${version}"; src = fetchurl { url = "https://sourceforge.net/projects/${pname}/files/SimpleITK/${version}/Source/SimpleITK-${version}.tar.gz"; - sha256 = "01y8s73mw4yabqir2f8qp5zc1c0y6szi18rr4zwgsxz62g4drzgm"; + sha256 = "10lxsr0144li6bmfgs646cvczczqkgmvvs3ndds66q8lg9zwbnky"; }; nativeBuildInputs = [ cmake git swig ]; From 721486626a46dd7913755ae50a8128fd585b6e2c Mon Sep 17 00:00:00 2001 From: Jack Kelly Date: Sat, 5 Jan 2019 11:00:26 +1100 Subject: [PATCH 110/247] edbrowse: Fix compilation against newer libcurl --- pkgs/applications/editors/edbrowse/default.nix | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/editors/edbrowse/default.nix b/pkgs/applications/editors/edbrowse/default.nix index 28775e48e1a7..0b6e28434f56 100644 --- a/pkgs/applications/editors/edbrowse/default.nix +++ b/pkgs/applications/editors/edbrowse/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, duktape, curl, pcre, readline, openssl, perl, html-tidy }: +{ stdenv, fetchFromGitHub, fetchpatch, duktape, curl, pcre, readline, openssl, perl, html-tidy }: stdenv.mkDerivation rec { name = "edbrowse-${version}"; @@ -6,7 +6,15 @@ stdenv.mkDerivation rec { buildInputs = [ curl pcre readline openssl duktape perl html-tidy ]; - patchPhase = '' + patches = [ + # Fix build against recent libcurl + (fetchpatch { + url = https://github.com/CMB/edbrowse/commit/5d2b9e21fdf019f461ebe62738d615428d5db963.diff; + sha256 = "167q8n0syj3iv6lxrbpv4kvb63j4byj4qxrxayy08bah3pss3gky"; + }) + ]; + + postPatch = '' for i in ./tools/*.pl do substituteInPlace $i --replace "/usr/bin/perl" "${perl}/bin/perl" From b5b80afa5b681b787615fd49b15bdbed80b325b6 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Sun, 6 Jan 2019 12:35:07 -0800 Subject: [PATCH 111/247] trilium: 0.26.1 -> 0.27.3 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/trilium/versions --- pkgs/applications/office/trilium/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/office/trilium/default.nix b/pkgs/applications/office/trilium/default.nix index c274ef0440d7..df93f00dfa26 100644 --- a/pkgs/applications/office/trilium/default.nix +++ b/pkgs/applications/office/trilium/default.nix @@ -13,11 +13,11 @@ let in stdenv.mkDerivation rec { name = "trilium-${version}"; - version = "0.26.1"; + version = "0.27.3"; src = fetchurl { url = "https://github.com/zadam/trilium/releases/download/v${version}/trilium-linux-x64-${version}.7z"; - sha256 = "184b0b0s8q32h1mpkrin8x1q0kjvard7r7xqrclziwwxg4khp3cz"; + sha256 = "07r4gwf4l76x1m6xlvrfad075kmmpdr4n6vd36vrxsf475rhlmsp"; }; nativeBuildInputs = [ From 96ea9e8917aa9598c72bcbfb9032759fc9829267 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Sun, 6 Jan 2019 12:01:04 -0800 Subject: [PATCH 112/247] sshguard: 2.3.0 -> 2.3.1 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/sshguard/versions --- pkgs/tools/security/sshguard/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/security/sshguard/default.nix b/pkgs/tools/security/sshguard/default.nix index 4bbb943ee937..4774e5cef139 100644 --- a/pkgs/tools/security/sshguard/default.nix +++ b/pkgs/tools/security/sshguard/default.nix @@ -1,12 +1,12 @@ { stdenv, fetchurl, autoreconfHook, yacc, flex}: stdenv.mkDerivation rec { - version = "2.3.0"; + version = "2.3.1"; name = "sshguard-${version}"; src = fetchurl { url = "mirror://sourceforge/sshguard/${name}.tar.gz"; - sha256 = "0s501hdgnjvhqblvvxda6rmaapw1dd81d6w9lbjm4rn2lf3kzdfl"; + sha256 = "18i0kmjvym9xym3ysg5kap0298nzcprar9y96k54p3zpdpi5b43n"; }; doCheck = true; From ed630cbe2b3033ec2da35e831bef28de6a7e535d Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Sun, 6 Jan 2019 10:07:38 -0800 Subject: [PATCH 113/247] toot: 0.19.0 -> 0.20.0 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/toot/versions --- pkgs/applications/misc/toot/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/misc/toot/default.nix b/pkgs/applications/misc/toot/default.nix index cb3146d4c0dd..c6ee75088902 100644 --- a/pkgs/applications/misc/toot/default.nix +++ b/pkgs/applications/misc/toot/default.nix @@ -1,14 +1,14 @@ { stdenv, fetchFromGitHub, python3Packages }: python3Packages.buildPythonApplication rec { - version = "0.19.0"; + version = "0.20.0"; name = "toot-${version}"; src = fetchFromGitHub { owner = "ihabunek"; repo = "toot"; rev = "${version}"; - sha256 = "1z0r6yqi522d5jbpd0w3prd33l067jb1jhfnxf6hkzhnx1wddjsa"; + sha256 = "0s5i6fjip5kvvyb59yndi2rhgn962lr0g9b0pi5w2aqnv1mwjbfh"; }; checkInputs = with python3Packages; [ pytest ]; From 16cef9de77b6cea686f6ac695630dc4723e64a23 Mon Sep 17 00:00:00 2001 From: Will Dietz Date: Sat, 5 Jan 2019 00:42:37 -0600 Subject: [PATCH 114/247] otter-browser: 0.9.99.3 -> 1.0.01 --- pkgs/applications/networking/browsers/otter/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/networking/browsers/otter/default.nix b/pkgs/applications/networking/browsers/otter/default.nix index 321980757b9b..5b9ddfc8e714 100644 --- a/pkgs/applications/networking/browsers/otter/default.nix +++ b/pkgs/applications/networking/browsers/otter/default.nix @@ -1,7 +1,7 @@ { stdenv, cmake, fetchFromGitHub , qtbase, qtmultimedia, qtwebengine -, version ? "0.9.99.3" -, sourceSha ? "0dkismjs3daz5afx6s5arwvynsw5qpvv2rqbzvmpihn6khnhap55" +, version ? "1.0.01" +, sourceSha ? "1jw8bj3lcqngr0mqwvz1gf47qjxbwiyda7x4sm96a6ckga7pcwyb" }: stdenv.mkDerivation { name = "otter-browser-${version}"; From 8e05911ccb73c28b3040cd0a1ef240e655a1e83c Mon Sep 17 00:00:00 2001 From: worldofpeace Date: Sun, 6 Jan 2019 19:16:39 -0500 Subject: [PATCH 115/247] otter-browser: add homepage --- pkgs/applications/networking/browsers/otter/default.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/applications/networking/browsers/otter/default.nix b/pkgs/applications/networking/browsers/otter/default.nix index 5b9ddfc8e714..9a47e18fad12 100644 --- a/pkgs/applications/networking/browsers/otter/default.nix +++ b/pkgs/applications/networking/browsers/otter/default.nix @@ -18,6 +18,7 @@ stdenv.mkDerivation { buildInputs = [ qtbase qtmultimedia qtwebengine ]; meta = with stdenv.lib; { + homepage = https://otter-browser.org; license = licenses.gpl3Plus; description = "Browser aiming to recreate the best aspects of the classic Opera (12.x) UI using Qt5"; maintainers = with maintainers; [ lheckemann ]; From 23da4c67c8de90df289a596e2f7537ff3e0bcea6 Mon Sep 17 00:00:00 2001 From: Mario Rodas Date: Sat, 5 Jan 2019 22:40:08 -0500 Subject: [PATCH 116/247] clair: init at 2.0.7 --- pkgs/tools/admin/clair/default.nix | 29 +++++++++++++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 31 insertions(+) create mode 100644 pkgs/tools/admin/clair/default.nix diff --git a/pkgs/tools/admin/clair/default.nix b/pkgs/tools/admin/clair/default.nix new file mode 100644 index 000000000000..8f521ed36d09 --- /dev/null +++ b/pkgs/tools/admin/clair/default.nix @@ -0,0 +1,29 @@ +{ lib, buildGoPackage, fetchFromGitHub, makeWrapper, rpm, xz }: + +buildGoPackage rec { + pname = "clair"; + version = "2.0.7"; + + goPackagePath = "github.com/coreos/clair"; + + src = fetchFromGitHub { + owner = "coreos"; + repo = "clair"; + rev = "v${version}"; + sha256 = "0n4pxdw71hd1rxzgf422fvycpjkrxxnvcidys0hpjy7gs88zjz5x"; + }; + + nativeBuildInputs = [ makeWrapper ]; + + postInstall = '' + wrapProgram $bin/bin/clair \ + --prefix PATH : "${lib.makeBinPath [ rpm xz ]}" + ''; + + meta = with lib; { + description = "Vulnerability Static Analysis for Containers"; + homepage = https://github.com/coreos/clair; + license = licenses.asl20; + maintainers = [ maintainers.marsam ]; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index adf85fa0a6ec..842b8183d1c4 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -685,6 +685,8 @@ in bunny = callPackage ../tools/package-management/bunny { }; + clair = callPackage ../tools/admin/clair { }; + cloud-sql-proxy = callPackage ../tools/misc/cloud-sql-proxy { }; container-linux-config-transpiler = callPackage ../development/tools/container-linux-config-transpiler { }; From 67b8195774797dea6a657b8a1a66625cbe073c52 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Sun, 6 Jan 2019 19:10:46 -0800 Subject: [PATCH 117/247] qtbitcointrader: 1.40.30 -> 1.40.40 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/qtbitcointrader/versions --- pkgs/applications/misc/qtbitcointrader/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/misc/qtbitcointrader/default.nix b/pkgs/applications/misc/qtbitcointrader/default.nix index 444c72602d35..9ad9f4fe15a7 100644 --- a/pkgs/applications/misc/qtbitcointrader/default.nix +++ b/pkgs/applications/misc/qtbitcointrader/default.nix @@ -1,14 +1,14 @@ { stdenv, fetchzip, qt5 }: let - version = "1.40.30"; + version = "1.40.40"; in stdenv.mkDerivation { name = "qtbitcointrader-${version}"; src = fetchzip { url = "https://github.com/JulyIGHOR/QtBitcoinTrader/archive/v${version}.tar.gz"; - sha256 = "0xbgdmwb8d3lrddcnx2amfsknd3g408f5gy5mdydcm3vqqfi9a0c"; + sha256 = "10gxxkmn7w2hbmznpx6ybbbvlvh640nyzya1yfn162vzbjg14jdi"; }; buildInputs = [ qt5.qtbase qt5.qtmultimedia qt5.qtscript ]; From 09ff7707ae0b275f18e151cc8bd70448bafa6f46 Mon Sep 17 00:00:00 2001 From: Matthew Bauer Date: Sun, 6 Jan 2019 22:11:38 -0600 Subject: [PATCH 118/247] llvm3.{8,9}: use old CMAKE_INSTALL_NAME_DIR value adcf4aa5241f8dc37195d9bcbce27a80b913a512 broke these two. The old way seems to work and might still avoid the original lldb issues. --- pkgs/development/compilers/llvm/3.8/llvm.nix | 2 +- pkgs/development/compilers/llvm/3.9/llvm.nix | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/compilers/llvm/3.8/llvm.nix b/pkgs/development/compilers/llvm/3.8/llvm.nix index fcb4214a1de8..ca6723172d7a 100644 --- a/pkgs/development/compilers/llvm/3.8/llvm.nix +++ b/pkgs/development/compilers/llvm/3.8/llvm.nix @@ -49,7 +49,7 @@ in stdenv.mkDerivation rec { sed -i 's/os_trace(\(.*\)");$/printf(\1\\n");/g' ./projects/compiler-rt/lib/sanitizer_common/sanitizer_mac.cc substituteInPlace CMakeLists.txt \ - --replace 'set(_install_name_dir INSTALL_NAME_DIR "@rpath")' "set(_install_name_dir)" \ + --replace 'set(CMAKE_INSTALL_NAME_DIR "@rpath")' "set(CMAKE_INSTALL_NAME_DIR "$out/lib")" \ --replace 'set(CMAKE_INSTALL_RPATH "@executable_path/../lib")' "" '' + '' diff --git a/pkgs/development/compilers/llvm/3.9/llvm.nix b/pkgs/development/compilers/llvm/3.9/llvm.nix index 00c56e49e374..678ec759425d 100644 --- a/pkgs/development/compilers/llvm/3.9/llvm.nix +++ b/pkgs/development/compilers/llvm/3.9/llvm.nix @@ -82,7 +82,7 @@ in stdenv.mkDerivation rec { --replace 'set(COMPILER_RT_HAS_TSAN TRUE)' 'set(COMPILER_RT_HAS_TSAN FALSE)' substituteInPlace CMakeLists.txt \ - --replace 'set(_install_name_dir INSTALL_NAME_DIR "@rpath")' "set(_install_name_dir)" \ + --replace 'set(CMAKE_INSTALL_NAME_DIR "@rpath")' "set(CMAKE_INSTALL_NAME_DIR "$lib/lib")" \ --replace 'set(CMAKE_INSTALL_RPATH "@executable_path/../lib")' "" '' # Patch llvm-config to return correct library path based on --link-{shared,static}. From 2bbec30c2e8a639da4a93038e002dff5d3a421c7 Mon Sep 17 00:00:00 2001 From: Matthew Bauer Date: Sun, 6 Jan 2019 22:13:11 -0600 Subject: [PATCH 119/247] darwin.diskdev_cmds: fix build with dsymutil MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit xcbuild doesn’t handle dsymutil correctly. fuser.pl does not contain debug symbols, but xcbuild doesn’t handle this like xcodebuild does. So, just disable the debug information. We probably should do this in more places using xcbuild, but it requires some arbitrary patching. --- .../darwin/apple-source-releases/diskdev_cmds/default.nix | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/pkgs/os-specific/darwin/apple-source-releases/diskdev_cmds/default.nix b/pkgs/os-specific/darwin/apple-source-releases/diskdev_cmds/default.nix index 0f46e50de3a0..08c7a883502d 100644 --- a/pkgs/os-specific/darwin/apple-source-releases/diskdev_cmds/default.nix +++ b/pkgs/os-specific/darwin/apple-source-releases/diskdev_cmds/default.nix @@ -18,14 +18,16 @@ appleDerivation { cp xnu-*/bsd/i386/disklabel.h i386 cp -r xnu-*/bsd/sys System cp -r Libc-*/uuid System + substituteInPlace diskdev_cmds.xcodeproj/project.pbxproj \ + --replace 'DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";' "" ''; installPhase = '' install -D Products/Release/libdisk.a $out/lib/libdisk.a rm Products/Release/libdisk.a for f in Products/Release/*; do if [ -f $f ]; then - install -D $file $out/bin/$(basename $f) - done + install -D $f $out/bin/$(basename $f) + fi done ''; From d02bb3c1978f96259a98efcb0f280b973c756cd0 Mon Sep 17 00:00:00 2001 From: Matthew Bauer Date: Sun, 6 Jan 2019 22:15:43 -0600 Subject: [PATCH 120/247] darwin.make-bootstrap-tools: remove dsymutil This hopefully is not needed for the bootstrap tools. Needs more testing. --- pkgs/stdenv/darwin/make-bootstrap-tools.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/stdenv/darwin/make-bootstrap-tools.nix b/pkgs/stdenv/darwin/make-bootstrap-tools.nix index eee3b1ce0759..670215a735d7 100644 --- a/pkgs/stdenv/darwin/make-bootstrap-tools.nix +++ b/pkgs/stdenv/darwin/make-bootstrap-tools.nix @@ -98,7 +98,7 @@ in rec { cp -d ${xz.out}/lib/liblzma*.* $out/lib # Copy binutils. - for i in as ld ar ranlib nm strip otool install_name_tool dsymutil lipo; do + for i in as ld ar ranlib nm strip otool install_name_tool lipo; do cp ${cctools_}/bin/$i $out/bin done From ed6148726b9e9b2f6edf38e889dc39c28648dda4 Mon Sep 17 00:00:00 2001 From: Matthew Bauer Date: Sun, 6 Jan 2019 22:31:21 -0600 Subject: [PATCH 121/247] darwin: fix more *_cmds derivation Doh --- .../darwin/apple-source-releases/adv_cmds/xcode.nix | 3 ++- .../darwin/apple-source-releases/file_cmds/default.nix | 4 ++-- .../darwin/apple-source-releases/network_cmds/default.nix | 2 +- pkgs/os-specific/darwin/insert_dylib/default.nix | 3 +-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/pkgs/os-specific/darwin/apple-source-releases/adv_cmds/xcode.nix b/pkgs/os-specific/darwin/apple-source-releases/adv_cmds/xcode.nix index 7b1492799ddb..45912041a24c 100644 --- a/pkgs/os-specific/darwin/apple-source-releases/adv_cmds/xcode.nix +++ b/pkgs/os-specific/darwin/apple-source-releases/adv_cmds/xcode.nix @@ -16,7 +16,8 @@ appleDerivation { substituteInPlace adv_cmds.xcodeproj/project.pbxproj \ --replace "FD201DC214369B4200906237 /* pkill.c in Sources */," "" \ --replace "FDF278D60FC6204E00D7A3C6 /* locale.cc in Sources */," "" \ - --replace '/usr/lib/libtermcap.dylib' 'libncurses.dylib' + --replace '/usr/lib/libtermcap.dylib' 'libncurses.dylib' \ + --replace 'DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";' "" ''; buildPhase = '' diff --git a/pkgs/os-specific/darwin/apple-source-releases/file_cmds/default.nix b/pkgs/os-specific/darwin/apple-source-releases/file_cmds/default.nix index c23205253221..2f5e4f542d7e 100644 --- a/pkgs/os-specific/darwin/apple-source-releases/file_cmds/default.nix +++ b/pkgs/os-specific/darwin/apple-source-releases/file_cmds/default.nix @@ -21,8 +21,8 @@ appleDerivation rec { installPhase = '' for f in Products/Release/*; do if [ -f $f ]; then - install -D $file $out/bin/$(basename $f) - done + install -D $f $out/bin/$(basename $f) + fi done for n in 1; do diff --git a/pkgs/os-specific/darwin/apple-source-releases/network_cmds/default.nix b/pkgs/os-specific/darwin/apple-source-releases/network_cmds/default.nix index 8e69cb4bfa7e..feee054c2ac8 100644 --- a/pkgs/os-specific/darwin/apple-source-releases/network_cmds/default.nix +++ b/pkgs/os-specific/darwin/apple-source-releases/network_cmds/default.nix @@ -22,7 +22,7 @@ appleDerivation rec { installPhase = '' for f in Products/Release/*; do if [ -f $f ]; then - install -D $file $out/bin/$(basename $f) + install -D $f $out/bin/$(basename $f) fi done diff --git a/pkgs/os-specific/darwin/insert_dylib/default.nix b/pkgs/os-specific/darwin/insert_dylib/default.nix index 510c7154f2bc..0ab6a4157075 100644 --- a/pkgs/os-specific/darwin/insert_dylib/default.nix +++ b/pkgs/os-specific/darwin/insert_dylib/default.nix @@ -11,9 +11,8 @@ stdenv.mkDerivation nativeBuildInputs = [ xcbuildHook ]; installPhase = '' - prog=$(find . -type f -name insert_dylib) mkdir -p $out/bin - install -m755 $prog $out/bin + install -m755 Products/Release/insert_dylib $out/bin ''; meta.platforms = stdenv.lib.platforms.darwin; } From 4976bc2fe261d2304711e7ffda62170b21ebdf5d Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Sat, 5 Jan 2019 02:30:41 +0100 Subject: [PATCH 122/247] hackage-packages.nix: automatic Haskell package set update This update was generated by hackage2nix v2.13-1-gda47f40 from Hackage revision https://github.com/commercialhaskell/all-cabal-hashes/commit/7f0cb0143c351efb24bcb8fb5531ea6e5578bcfd. --- .../haskell-modules/hackage-packages.nix | 678 ++++++++++++++---- 1 file changed, 545 insertions(+), 133 deletions(-) diff --git a/pkgs/development/haskell-modules/hackage-packages.nix b/pkgs/development/haskell-modules/hackage-packages.nix index b48dad3b1cb9..d6796741eb49 100644 --- a/pkgs/development/haskell-modules/hackage-packages.nix +++ b/pkgs/development/haskell-modules/hackage-packages.nix @@ -18372,6 +18372,8 @@ self: { pname = "TypeCompose"; version = "0.9.14"; sha256 = "0msss17lrya6y5xfvxl41xsqs6yr09iw6m1px4xlwin72xwly0sn"; + revision = "1"; + editedCabalFile = "1pxg6az5vkl0zvs3zdvvvnhxqawd9fkkd44jmzzzyyibppgni6x4"; libraryHaskellDepends = [ base base-orphans ]; description = "Type composition classes & instances"; license = stdenv.lib.licenses.bsd3; @@ -21560,8 +21562,8 @@ self: { pname = "adjunctions"; version = "4.4"; sha256 = "1sbal7cbhm12crfnfhkk322jnzgx7lhw3jzq0p463bipagsjwz2h"; - revision = "1"; - editedCabalFile = "0582nnn3fab63nd7ng8smk2c8j7pciiyzfj1na34wqid2hs675as"; + revision = "2"; + editedCabalFile = "1yfsjx7dqikg3hvld7i91xfsg5lawmr5980lvfd794sybmgxsf17"; libraryHaskellDepends = [ array base comonad containers contravariant distributive free mtl profunctors semigroupoids semigroups tagged transformers @@ -21750,6 +21752,8 @@ self: { pname = "aeson"; version = "1.4.2.0"; sha256 = "1l4b675nxddim3v30kd7zr3vmrs7i1m81rh8h9bfbm9k9a0p3kkm"; + revision = "1"; + editedCabalFile = "067y82gq86740j2zj4y6v7z9b5860ncg2g9lfnrpsnb9jqm7arl1"; libraryHaskellDepends = [ attoparsec base base-compat bytestring containers deepseq dlist ghc-prim hashable primitive scientific tagged template-haskell text @@ -23270,6 +23274,8 @@ self: { pname = "algebra"; version = "4.3.1"; sha256 = "090jaipyx5pcav2wqcqzds51fwx49l4c9cpp9nnk16bgkf92z615"; + revision = "1"; + editedCabalFile = "1lxxbbibsf1lkm6fv0svfvfbr0dg16jwcm18hcmfgwypzxqdrbdz"; libraryHaskellDepends = [ adjunctions array base containers distributive mtl nats semigroupoids semigroups tagged transformers void @@ -34504,14 +34510,16 @@ self: { }) {}; "bencoding" = callPackage - ({ mkDerivation, AttoBencode, attoparsec, base, bencode, bytestring - , containers, criterion, deepseq, ghc-prim, hspec, integer-gmp, mtl - , pretty, QuickCheck, text + ({ mkDerivation, attoparsec, base, bencode, bytestring, containers + , criterion, deepseq, ghc-prim, hspec, integer-gmp, mtl, pretty + , QuickCheck, text }: mkDerivation { pname = "bencoding"; - version = "0.4.4.0"; - sha256 = "088w5r0yz81b3iid3bc61lvm4d9f361kv2gq9jz7sbm43fkraxpp"; + version = "0.4.5.1"; + sha256 = "1q2xpcskpj3hk3vkk09flrnbyss1aq5yqngkxwm7qrcly2798pxa"; + revision = "1"; + editedCabalFile = "17yr0lcpsm482as9qcl44padm2ahz51al4izfq2z1p1jizih4mxv"; libraryHaskellDepends = [ attoparsec base bytestring deepseq ghc-prim integer-gmp mtl pretty text @@ -34520,8 +34528,7 @@ self: { attoparsec base bytestring containers ghc-prim hspec QuickCheck ]; benchmarkHaskellDepends = [ - AttoBencode attoparsec base bencode bytestring criterion deepseq - ghc-prim + attoparsec base bencode bytestring criterion deepseq ghc-prim ]; description = "A library for encoding and decoding of BEncode data"; license = stdenv.lib.licenses.bsd3; @@ -40022,6 +40029,8 @@ self: { pname = "bsparse"; version = "0.0.5"; sha256 = "12wn8jlqkb9d9vpdbwc3m288cgnr15cq4wv5fxlp7f10p3y42l2a"; + revision = "1"; + editedCabalFile = "0vlcwcgmlk4ghwhiyy4234driyvq5ap5g587nmf23fh8b54g7j3q"; libraryHaskellDepends = [ base bytestring ]; description = "A simple unassuming parser for bytestring"; license = stdenv.lib.licenses.bsd3; @@ -40811,6 +40820,8 @@ self: { pname = "byteset"; version = "0.1.1.0"; sha256 = "18dg863wbbjh95yial4gy6vi5spwygp0l7dfx6bj00lz4xdrqj8k"; + revision = "1"; + editedCabalFile = "1lgxxxrmw4g32pa861n6qbfpzwv14wfjrlp4hv5zd9hygy6v6q2p"; libraryHaskellDepends = [ base binary ]; description = "Set of bytes"; license = stdenv.lib.licenses.bsd3; @@ -45937,6 +45948,30 @@ self: { hydraPlatforms = stdenv.lib.platforms.none; }) {}; + "chiasma" = callPackage + ({ mkDerivation, base, bytestring, data-default-class, directory + , either, filepath, free, HTF, lens, mtl, parsec, posix-pty + , process, resourcet, split, transformers, typed-process, unix + , unliftio + }: + mkDerivation { + pname = "chiasma"; + version = "0.1.0.0"; + sha256 = "140p3qrrdh3im5qj43swl9cvljgyc39zy7ci5048j42h8x9q7glg"; + libraryHaskellDepends = [ + base bytestring data-default-class directory either filepath free + lens mtl parsec posix-pty process resourcet split transformers + typed-process unix unliftio + ]; + testHaskellDepends = [ + base bytestring data-default-class directory either filepath free + HTF lens mtl parsec posix-pty process resourcet split transformers + typed-process unix unliftio + ]; + description = "tmux api"; + license = stdenv.lib.licenses.mit; + }) {}; + "chimera" = callPackage ({ mkDerivation, base, gauge, ghc-prim, QuickCheck, tasty , tasty-hunit, tasty-quickcheck, tasty-smallcheck, vector @@ -47290,29 +47325,29 @@ self: { "classify-frog" = callPackage ({ mkDerivation, array, audacity, base, bifunctors, Cabal, carray - , concurrent-split, containers, deepseq, explicit-exception, fft - , filemanip, gnuplot, hmatrix, hmm-hmatrix, lazy-csv, llvm-extra - , llvm-tf, non-empty, numeric-prelude, optparse-applicative - , parallel, pathtype, pooled-io, semigroups, soxlib - , storable-record, storablevector, storablevector-carray + , comfort-array, concurrent-split, containers, deepseq + , explicit-exception, fft, filemanip, gnuplot, hmm-lapack, lapack + , lazy-csv, llvm-extra, llvm-tf, non-empty, numeric-prelude + , optparse-applicative, parallel, pathtype, pooled-io, semigroups + , soxlib, storable-record, storablevector, storablevector-carray , synthesizer-core, synthesizer-llvm, tagchup, text, time , transformers, utility-ht, xml-basic }: mkDerivation { pname = "classify-frog"; - version = "0.2.3"; - sha256 = "1fhiia335snb14nkvn3sglv0z7mkc7y5vj6jsaa8v9l72fwacz9a"; + version = "0.2.4.1"; + sha256 = "1jw61n54g65s9chqmp58ikngzmrabg8s90ghsqvm2hjg8hbx4h7p"; isLibrary = false; isExecutable = true; enableSeparateDataOutput = true; executableHaskellDepends = [ - array audacity base bifunctors Cabal carray concurrent-split - containers deepseq explicit-exception fft filemanip gnuplot hmatrix - hmm-hmatrix lazy-csv llvm-extra llvm-tf non-empty numeric-prelude - optparse-applicative parallel pathtype pooled-io semigroups soxlib - storable-record storablevector storablevector-carray - synthesizer-core synthesizer-llvm tagchup text time transformers - utility-ht xml-basic + array audacity base bifunctors Cabal carray comfort-array + concurrent-split containers deepseq explicit-exception fft + filemanip gnuplot hmm-lapack lapack lazy-csv llvm-extra llvm-tf + non-empty numeric-prelude optparse-applicative parallel pathtype + pooled-io semigroups soxlib storable-record storablevector + storablevector-carray synthesizer-core synthesizer-llvm tagchup + text time transformers utility-ht xml-basic ]; description = "Classify sounds produced by Xenopus laevis"; license = stdenv.lib.licenses.bsd3; @@ -47804,20 +47839,18 @@ self: { }) {}; "cli" = callPackage - ({ mkDerivation, base, directory, mtl, QuickCheck, tasty - , tasty-quickcheck, terminfo, transformers - }: + ({ mkDerivation, base, basement, foundation }: mkDerivation { pname = "cli"; - version = "0.1.2"; - sha256 = "1jsavqpjnwmfipvyv4wnxv5qkw295nvvzbnkbaxqv67b4py322jq"; + version = "0.2.0"; + sha256 = "04hfcpbk1w2iyy9y78hr0klrffczkd9ni892a34gmc65qc1nwil8"; revision = "1"; - editedCabalFile = "19q9vp287yg068ilfjd2qp3nkly31s3jshg7yanv9j0dar5gp17a"; - libraryHaskellDepends = [ base mtl terminfo transformers ]; - testHaskellDepends = [ - base directory QuickCheck tasty tasty-quickcheck transformers - ]; - description = "Command Line Interface"; + editedCabalFile = "0nl0f952rsywalnfsahd6cjbmrn568mmbcpnd7xcy1xgnkajxk42"; + isLibrary = true; + isExecutable = true; + libraryHaskellDepends = [ base basement foundation ]; + executableHaskellDepends = [ base basement foundation ]; + description = "CLI"; license = stdenv.lib.licenses.bsd3; hydraPlatforms = stdenv.lib.platforms.none; }) {}; @@ -50003,16 +50036,16 @@ self: { }) {}; "comfort-array" = callPackage - ({ mkDerivation, base, guarded-allocation, primitive, QuickCheck - , storable-record, transformers, utility-ht + ({ mkDerivation, base, deepseq, guarded-allocation, non-empty + , primitive, QuickCheck, storable-record, transformers, utility-ht }: mkDerivation { pname = "comfort-array"; - version = "0.1.2"; - sha256 = "1rc8gfgjid10wajjk5pp1vmm8wc2apr5qcr2w41pwk25m554iyz1"; + version = "0.2"; + sha256 = "0h8qn36ivxd2bc7cmqgyfa54jlwcfwr3rwpfp02p0yxqb4q03z45"; libraryHaskellDepends = [ - base guarded-allocation primitive QuickCheck storable-record - transformers utility-ht + base deepseq guarded-allocation non-empty primitive QuickCheck + storable-record transformers utility-ht ]; testHaskellDepends = [ base QuickCheck ]; description = "Arrays where the index type is a function of the shape type"; @@ -50900,6 +50933,8 @@ self: { pname = "compressed"; version = "3.11"; sha256 = "0gfxmfyzgpa176igsby50jpfhpfvd078d7nyvwwg2cjx8hpvyyyp"; + revision = "1"; + editedCabalFile = "0h3kfr2kdn74vk0mam5mwk6phclrcm79khd8yz2pp8j9zv1v8q3r"; libraryHaskellDepends = [ base comonad containers fingertree hashable keys pointed reducers semigroupoids semigroups unordered-containers @@ -62434,7 +62469,7 @@ self: { license = stdenv.lib.licenses.bsd3; }) {}; - "dhall_1_20_0" = callPackage + "dhall_1_20_1" = callPackage ({ mkDerivation, aeson, aeson-pretty, ansi-terminal, base , bytestring, case-insensitive, cborg, cborg-json, containers , contravariant, criterion, cryptonite, deepseq, Diff, directory @@ -62448,8 +62483,8 @@ self: { }: mkDerivation { pname = "dhall"; - version = "1.20.0"; - sha256 = "0hygghwx2dzci56x24md64b12p8mmx1spq012301ipkkbvk64a36"; + version = "1.20.1"; + sha256 = "1p5whphy666q0h22yq3jb4aipb5bkqp45bp86m7dp12ljksfhxz0"; isLibrary = true; isExecutable = true; libraryHaskellDepends = [ @@ -67351,6 +67386,22 @@ self: { license = stdenv.lib.licenses.bsd3; }) {}; + "dualizer" = callPackage + ({ mkDerivation, base, bifunctors, comonad, containers, lens + , template-haskell, transformers + }: + mkDerivation { + pname = "dualizer"; + version = "0.1.0.1"; + sha256 = "022wiqvy2lxfc9zqibrd3av994r6hi9pkqi3b3m53h6zaphpnwl7"; + libraryHaskellDepends = [ + base bifunctors comonad containers lens template-haskell + transformers + ]; + description = "Automatically generate dual constructions"; + license = "AGPL"; + }) {}; + "dublincore-xml-conduit" = callPackage ({ mkDerivation, base, bytestring, conduit, conduit-combinators , data-default, QuickCheck, quickcheck-instances, resourcet @@ -73425,22 +73476,26 @@ self: { "expresso" = callPackage ({ mkDerivation, base, containers, directory, filepath, hashable - , haskeline, mtl, parsec, tasty, tasty-hunit, text - , unordered-containers, wl-pprint + , haskeline, mtl, parsec, tasty, tasty-hunit, template-haskell + , terminfo, text, unordered-containers, wl-pprint }: mkDerivation { pname = "expresso"; - version = "0.1.0.2"; - sha256 = "19qg0nwvmh0apn2fmffsmhrwcw9kd5c3fp118shkr12xdab9x23k"; + version = "0.1.1.0"; + sha256 = "1c0mibbgwdxz36qr02nc31mpg6d3l9mgjfqwy174ib2kv3wndivh"; isLibrary = true; isExecutable = true; libraryHaskellDepends = [ base containers directory filepath hashable haskeline mtl parsec - text unordered-containers wl-pprint + template-haskell terminfo text unordered-containers wl-pprint + ]; + executableHaskellDepends = [ + base containers directory filepath hashable haskeline mtl parsec + terminfo text unordered-containers wl-pprint ]; testHaskellDepends = [ base containers directory filepath hashable haskeline mtl parsec - tasty tasty-hunit text unordered-containers wl-pprint + tasty tasty-hunit terminfo text unordered-containers wl-pprint ]; description = "A simple expressions language based on row types"; license = stdenv.lib.licenses.bsd3; @@ -76623,6 +76678,21 @@ self: { license = stdenv.lib.licenses.bsd3; }) {}; + "fixed-length_0_2_1" = callPackage + ({ mkDerivation, base, non-empty, storable-record, tfp, utility-ht + }: + mkDerivation { + pname = "fixed-length"; + version = "0.2.1"; + sha256 = "0jabfv9ga94maw35a7xdw5lwi55d7z92nn2zs2c8z3jk0a4bcld1"; + libraryHaskellDepends = [ + base non-empty storable-record tfp utility-ht + ]; + description = "Lists with statically known length based on non-empty package"; + license = stdenv.lib.licenses.bsd3; + hydraPlatforms = stdenv.lib.platforms.none; + }) {}; + "fixed-list" = callPackage ({ mkDerivation, base }: mkDerivation { @@ -81058,8 +81128,8 @@ self: { }: mkDerivation { pname = "futhark"; - version = "0.7.4"; - sha256 = "1qjcza0i0y6qalyim5kclz3x4lj667d4d4y2amk3sn4qbgaibajs"; + version = "0.8.1"; + sha256 = "18qha0bai5zf4shcz2a6lixkhx6mk395njm81ds2zcp1iilwgih2"; isLibrary = true; isExecutable = true; libraryHaskellDepends = [ @@ -82263,18 +82333,20 @@ self: { license = stdenv.lib.licenses.mit; }) {}; - "generic-data_0_4_0_0" = callPackage + "generic-data_0_5_0_0" = callPackage ({ mkDerivation, base, base-orphans, contravariant, generic-lens - , show-combinators, tasty, tasty-hunit + , one-liner, show-combinators, tasty, tasty-hunit }: mkDerivation { pname = "generic-data"; - version = "0.4.0.0"; - sha256 = "01x5f1xi1yvi2d5pym5jchgrl3ya2cbx6npa7c8rf206n414sq23"; + version = "0.5.0.0"; + sha256 = "1hy43a1f5y1ymszilz908sl7an7hj7sz7yzchhxh83ki2sf0ya7s"; libraryHaskellDepends = [ base base-orphans contravariant show-combinators ]; - testHaskellDepends = [ base generic-lens tasty tasty-hunit ]; + testHaskellDepends = [ + base generic-lens one-liner tasty tasty-hunit + ]; description = "Utilities for GHC.Generics"; license = stdenv.lib.licenses.mit; hydraPlatforms = stdenv.lib.platforms.none; @@ -96730,6 +96802,8 @@ self: { pname = "happstack-util"; version = "6.0.3"; sha256 = "0hqssd5wzir6rxn46q8r3hdp3nl7v5m7w322j39120xpg2bhiphh"; + revision = "1"; + editedCabalFile = "00j8h4r2dy3wj56487zh2g4ghj2jf0wj09cbxd7iswpapzwq6f1f"; isLibrary = true; isExecutable = true; libraryHaskellDepends = [ @@ -102191,6 +102265,8 @@ self: { pname = "haxr"; version = "3000.11.2"; sha256 = "0iwbdvywily6ma1a1v9l4kflvm8d8234zhvyb9imx7g7grns1kgb"; + revision = "1"; + editedCabalFile = "1l0xrffx8xy023g89xijmm7vnaci5hsshpm1rvdchb0nbvq08cnr"; libraryHaskellDepends = [ array base base-compat base64-bytestring blaze-builder bytestring HaXml HsOpenSSL http-streams http-types io-streams mtl mtl-compat @@ -108180,6 +108256,26 @@ self: { hydraPlatforms = stdenv.lib.platforms.none; }) {}; + "hmm-lapack" = callPackage + ({ mkDerivation, base, boxes, comfort-array, containers, deepseq + , explicit-exception, fixed-length, lapack, lazy-csv, netlib-ffi + , non-empty, prelude-compat, QuickCheck, random, semigroups, tfp + , transformers, utility-ht + }: + mkDerivation { + pname = "hmm-lapack"; + version = "0.3.0.1"; + sha256 = "150aqwg7n9i5hsdlxxbsynaxn3shgnx20drax16z5785rz0bbrjx"; + libraryHaskellDepends = [ + base boxes comfort-array containers deepseq explicit-exception + fixed-length lapack lazy-csv netlib-ffi non-empty prelude-compat + QuickCheck random semigroups tfp transformers utility-ht + ]; + testHaskellDepends = [ base QuickCheck ]; + description = "Hidden Markov Models using LAPACK primitives"; + license = stdenv.lib.licenses.bsd3; + }) {}; + "hmp3" = callPackage ({ mkDerivation, array, base, binary, bytestring, containers , directory, mersenne-random, ncurses, old-time, pcre-light @@ -110396,8 +110492,8 @@ self: { }: mkDerivation { pname = "hpio"; - version = "0.9.0.6"; - sha256 = "07443kb6w1kwcg78j8jaffb5pblv9si7bvsmlg4dbm32m4wd66xx"; + version = "0.9.0.7"; + sha256 = "1l08b668bl9gwbrzkhljg73aizv640gcc7smiafhgrnk2bsl7q2p"; isLibrary = true; isExecutable = true; libraryHaskellDepends = [ @@ -113113,6 +113209,30 @@ self: { license = stdenv.lib.licenses.mit; }) {inherit (pkgs) lua5_3;}; + "hslua_1_0_2" = callPackage + ({ mkDerivation, base, bytestring, containers, criterion, deepseq + , exceptions, fail, lua5_3, mtl, QuickCheck, quickcheck-instances + , tasty, tasty-hunit, tasty-quickcheck, text + }: + mkDerivation { + pname = "hslua"; + version = "1.0.2"; + sha256 = "0w2gcp66ny3crxip0gn86abz8psz2z14nx2z2wna0s8p0n8v5agx"; + configureFlags = [ "-fsystem-lua" "-f-use-pkgconfig" ]; + libraryHaskellDepends = [ + base bytestring containers exceptions fail mtl text + ]; + librarySystemDepends = [ lua5_3 ]; + testHaskellDepends = [ + base bytestring containers exceptions fail mtl QuickCheck + quickcheck-instances tasty tasty-hunit tasty-quickcheck text + ]; + benchmarkHaskellDepends = [ base bytestring criterion deepseq ]; + description = "Bindings to Lua, an embeddable scripting language"; + license = stdenv.lib.licenses.mit; + hydraPlatforms = stdenv.lib.platforms.none; + }) {inherit (pkgs) lua5_3;}; + "hslua-aeson" = callPackage ({ mkDerivation, aeson, base, bytestring, hashable, hslua, hspec , HUnit, ieee754, QuickCheck, quickcheck-instances, scientific @@ -117622,23 +117742,22 @@ self: { }) {}; "hw-dsv" = callPackage - ({ mkDerivation, base, bits-extra, bytestring, c2hs, cassava - , criterion, deepseq, directory, ghc-prim, hedgehog, hspec, hw-bits + ({ mkDerivation, base, bits-extra, bytestring, cassava, criterion + , deepseq, directory, ghc-prim, hedgehog, hspec, hw-bits , hw-hspec-hedgehog, hw-prim, hw-rankselect, hw-rankselect-base , hw-simd, lens, mmap, optparse-applicative, resourcet, text , vector, weigh }: mkDerivation { pname = "hw-dsv"; - version = "0.3.2"; - sha256 = "14xkyvqggax9vx46kvsg3w0h7pnsfsbwbd5jbr95p5nw8yrsa8pg"; + version = "0.3.3"; + sha256 = "008za7xcqnmkypbv9s1bkzrzap2h11vagpjqyqfymvanzwj1bv2h"; isLibrary = true; isExecutable = true; libraryHaskellDepends = [ base bits-extra bytestring deepseq ghc-prim hw-bits hw-prim hw-rankselect hw-rankselect-base hw-simd vector ]; - libraryToolDepends = [ c2hs ]; executableHaskellDepends = [ base bits-extra bytestring deepseq ghc-prim hedgehog hw-bits hw-prim hw-rankselect hw-rankselect-base hw-simd lens @@ -122720,8 +122839,8 @@ self: { }: mkDerivation { pname = "intero"; - version = "0.1.35"; - sha256 = "1vja9hfgisvkyv3qd69lswwxjmkddvd2ijag6jxc0w2bq25v452h"; + version = "0.1.37"; + sha256 = "15vpmqdadc179cnzzc6rp86mwc2bak4g260jz7mkv7m5hzm5d846"; isLibrary = false; isExecutable = true; enableSeparateDataOutput = true; @@ -127384,6 +127503,8 @@ self: { pname = "jwt"; version = "0.9.0"; sha256 = "1glkaahp3jq744s61y0ja5fdggwac9p1dwia4c19k1ld6qhd5395"; + revision = "1"; + editedCabalFile = "1vpd4pq8mh4dha7i2pfv4iqpw411yachzkf7p9rnfyicipj53pw2"; libraryHaskellDepends = [ aeson base bytestring containers cryptonite http-types memory network-uri scientific semigroups text time unordered-containers @@ -127951,8 +128072,8 @@ self: { }: mkDerivation { pname = "katip-syslog"; - version = "0.1.1.0"; - sha256 = "0q566wxbm8h97zmsayy0s93kjxfbxfxqljacmsz8213pfivxq4aa"; + version = "0.1.2.0"; + sha256 = "0ff6zxl2jddwgkzyg9lli843lww06j75x7r8bg55grph34pf13p5"; libraryHaskellDepends = [ aeson base bytestring hsyslog katip string-conv text ]; @@ -131521,17 +131642,26 @@ self: { }) {}; "lapack" = callPackage - ({ mkDerivation, base, blas-ffi, comfort-array, lapack-ffi - , netlib-ffi, non-empty, transformers, utility-ht + ({ mkDerivation, base, blas-ffi, boxes, ChasingBottoms + , comfort-array, deepseq, fixed-length, guarded-allocation + , lapack-ffi, lazyio, netlib-ffi, non-empty, QuickCheck, semigroups + , tfp, transformers, utility-ht }: mkDerivation { pname = "lapack"; - version = "0.1"; - sha256 = "195v3jpz5n5vksa8svqng1kwc629ds2kd1p55f6npz2q2j6k8lac"; + version = "0.2"; + sha256 = "173yjhf2drabx13rw7kzs6wp40pg2r5yibr7psgdyidx7543svvy"; + isLibrary = true; + isExecutable = true; libraryHaskellDepends = [ - base blas-ffi comfort-array lapack-ffi netlib-ffi non-empty + base blas-ffi boxes comfort-array deepseq fixed-length + guarded-allocation lapack-ffi lazyio netlib-ffi non-empty tfp transformers utility-ht ]; + testHaskellDepends = [ + base ChasingBottoms comfort-array netlib-ffi non-empty QuickCheck + semigroups tfp transformers utility-ht + ]; description = "Numerical Linear Algebra using LAPACK"; license = stdenv.lib.licenses.bsd3; hydraPlatforms = stdenv.lib.platforms.none; @@ -140611,6 +140741,23 @@ self: { license = stdenv.lib.licenses.bsd3; }) {}; + "massiv-io_0_1_5_0" = callPackage + ({ mkDerivation, base, bytestring, data-default, deepseq, directory + , filepath, JuicyPixels, massiv, netpbm, process, vector + }: + mkDerivation { + pname = "massiv-io"; + version = "0.1.5.0"; + sha256 = "1vgq6rdmnh3v2rgch9k46sw9jfwhfpngxxl4cz0w1pjsjq7sp2fw"; + libraryHaskellDepends = [ + base bytestring data-default deepseq directory filepath JuicyPixels + massiv netpbm process vector + ]; + description = "Import/export of Image files into massiv Arrays"; + license = stdenv.lib.licenses.bsd3; + hydraPlatforms = stdenv.lib.platforms.none; + }) {}; + "master-plan" = callPackage ({ mkDerivation, base, diagrams, diagrams-lib, diagrams-rasterific , hspec, megaparsec, mtl, optparse-applicative, QuickCheck @@ -141759,24 +141906,27 @@ self: { }) {}; "mediawiki2latex" = callPackage - ({ mkDerivation, array, base, blaze-html, bytestring, containers - , directory, directory-tree, file-embed, filepath, happstack-server - , highlighting-kate, HTTP, http-conduit, hxt, hxt-http, mtl - , network, parsec, process, split, temporary, text, transformers - , url, utf8-string, utility-ht + ({ mkDerivation, array, base, blaze-html, blaze-markup, bytestring + , containers, deepseq, directory, directory-tree, file-embed + , filepath, happstack-server, hashable, highlighting-kate, HTTP + , http-client, http-conduit, http-types, hxt, hxt-http, mtl + , network, network-uri, parsec, process, split, strict, temporary + , text, time, transformers, url, utf8-string, utility-ht + , zip-archive }: mkDerivation { pname = "mediawiki2latex"; - version = "7.9.0.1"; - sha256 = "0q708hh5280k5hknf1mh3nza7qvpszplcis90y0i78a2jd0x2r3w"; + version = "7.33"; + sha256 = "1a8k0yh8j9si4aj8xpwlssmp31qgc7g53pds1hdi2mfi8clxmah7"; isLibrary = false; isExecutable = true; executableHaskellDepends = [ - array base blaze-html bytestring containers directory - directory-tree file-embed filepath happstack-server - highlighting-kate HTTP http-conduit hxt hxt-http mtl network parsec - process split temporary text transformers url utf8-string - utility-ht + array base blaze-html blaze-markup bytestring containers deepseq + directory directory-tree file-embed filepath happstack-server + hashable highlighting-kate HTTP http-client http-conduit http-types + hxt hxt-http mtl network network-uri parsec process split strict + temporary text time transformers url utf8-string utility-ht + zip-archive ]; description = "Convert MediaWiki text to LaTeX"; license = "GPL"; @@ -143447,8 +143597,8 @@ self: { }: mkDerivation { pname = "milena"; - version = "0.5.2.3"; - sha256 = "0s3bxj6d3p0fng08da9y2qb8cl967lqhsqplhcwmaj3aai72rj5w"; + version = "0.5.2.4"; + sha256 = "104mvrjf5dk3afqvqc6p1p8ww6dqc1ygi59pgc4yk2zzzllbiczz"; libraryHaskellDepends = [ base bytestring cereal containers digest lens lifted-base monad-control mtl murmur-hash network random resource-pool @@ -146840,8 +146990,8 @@ self: { ({ mkDerivation }: mkDerivation { pname = "morphisms"; - version = "0.1.0"; - sha256 = "0mgkpasj9jd4fhmxcxaij8jkcvp57q8xymf2wvldpwcgi05602az"; + version = "0.1.1"; + sha256 = "0waj252x6xpxaph50l248r0xf44xzfsz6jpmza5mwi9qf1br6dws"; description = "It's all about functions"; license = stdenv.lib.licenses.mit; }) {}; @@ -148613,6 +148763,8 @@ self: { pname = "music-parts"; version = "1.9.0"; sha256 = "1kiz968kcwcyczxg5gl40c7bwgkn86l7qi0ak8p68bm4rmsw9id4"; + revision = "1"; + editedCabalFile = "03w6wqxrz00gr6wbk6id3bf0yyqvcy1jpqwjl26bxc0vn3r2jizz"; enableSeparateDataOutput = true; libraryHaskellDepends = [ adjunctions aeson base bytestring cassava containers data-default @@ -150806,6 +150958,34 @@ self: { broken = true; }) {ghc-binary = null;}; + "net-mqtt" = callPackage + ({ mkDerivation, async, attoparsec, base, binary, bytestring + , conduit, conduit-extra, containers, HUnit, network-conduit-tls + , QuickCheck, stm, tasty, tasty-hunit, tasty-quickcheck, text + }: + mkDerivation { + pname = "net-mqtt"; + version = "0.1.0.0"; + sha256 = "0gh2c83n0dc0f9878kmac94l074c9rd24yyrsid2s52qqv1j953j"; + isLibrary = true; + isExecutable = true; + libraryHaskellDepends = [ + async attoparsec base binary bytestring conduit conduit-extra + containers network-conduit-tls stm text + ]; + executableHaskellDepends = [ + async attoparsec base binary bytestring conduit conduit-extra + containers network-conduit-tls stm text + ]; + testHaskellDepends = [ + async attoparsec base binary bytestring conduit conduit-extra + containers HUnit network-conduit-tls QuickCheck stm tasty + tasty-hunit tasty-quickcheck text + ]; + description = "An MQTT Protocol Implementation"; + license = stdenv.lib.licenses.bsd3; + }) {}; + "net-spider" = callPackage ({ mkDerivation, aeson, base, containers, data-interval, doctest , doctest-discover, extended-reals, greskell, greskell-websocket @@ -150926,6 +151106,22 @@ self: { license = stdenv.lib.licenses.bsd3; }) {}; + "netlib-ffi_0_1_1" = callPackage + ({ mkDerivation, base, guarded-allocation, storable-complex + , transformers + }: + mkDerivation { + pname = "netlib-ffi"; + version = "0.1.1"; + sha256 = "0irf5gc9kw3pjb339nrzylr1ldz8fhgmpkji26dm3w18vkwic411"; + libraryHaskellDepends = [ + base guarded-allocation storable-complex transformers + ]; + description = "Helper modules for FFI to BLAS and LAPACK"; + license = stdenv.lib.licenses.bsd3; + hydraPlatforms = stdenv.lib.platforms.none; + }) {}; + "netlines" = callPackage ({ mkDerivation, base, bytestring, contstuff, enumerator, HTF , random, text, time @@ -153367,6 +153563,8 @@ self: { pname = "non-empty"; version = "0.3.0.1"; sha256 = "00zbnpcnmchbbdgyw19m1bl3bdhmw89pp9k0mq3z75nz0i40gg9z"; + revision = "1"; + editedCabalFile = "1628z42q77xjvwpyx3rifqf6mh4y6ivdl0lkhngxwz8c21bnf7d3"; libraryHaskellDepends = [ base containers deepseq QuickCheck utility-ht ]; @@ -158218,8 +158416,8 @@ self: { pname = "pandoc"; version = "2.5"; sha256 = "0bi26r2qljdfxq26gaxj1xnhrawrfndfavs3f3g098x0g3dwazfm"; - revision = "1"; - editedCabalFile = "15jzrlf1qnn3qkzy1zk5f300y7748qdz8yk0zg0zy7ygi36b403v"; + revision = "2"; + editedCabalFile = "1z44hcwqqmkmhfak7svrrf950amf008gzhnlxkhwdyjpnpqp21sm"; configureFlags = [ "-fhttps" "-f-trypandoc" ]; isLibrary = true; isExecutable = true; @@ -161854,6 +162052,24 @@ self: { license = stdenv.lib.licenses.bsd3; }) {}; + "persist_0_1_1_1" = callPackage + ({ mkDerivation, base, bytestring, containers, QuickCheck + , test-framework, test-framework-quickcheck2, text + }: + mkDerivation { + pname = "persist"; + version = "0.1.1.1"; + sha256 = "1r14xfaa4rncv7sgrm6lznab8yyj6wh65yvzh2j2prwpjqswy5b7"; + libraryHaskellDepends = [ base bytestring containers text ]; + testHaskellDepends = [ + base bytestring QuickCheck test-framework + test-framework-quickcheck2 text + ]; + description = "Minimal serialization library with focus on performance"; + license = stdenv.lib.licenses.bsd3; + hydraPlatforms = stdenv.lib.platforms.none; + }) {}; + "persist2er" = callPackage ({ mkDerivation, base, optparse-applicative, persistent, text }: mkDerivation { @@ -171271,6 +171487,8 @@ self: { pname = "publish"; version = "0.3.2"; sha256 = "1jkmp5wsd8ffrxvj965z9pch5g8vxkfwv70hxa3lipdh46k6ll7l"; + revision = "1"; + editedCabalFile = "136hi1c3ap2dvhn79dqdn29dfq5ncilg6qap41d0wf4jp7p419a8"; isLibrary = false; isExecutable = true; executableHaskellDepends = [ @@ -173389,6 +173607,37 @@ self: { hydraPlatforms = stdenv.lib.platforms.none; }) {}; + "quickcheck-state-machine_0_5_0" = callPackage + ({ mkDerivation, ansi-wl-pprint, base, bytestring, containers + , directory, doctest, exceptions, filelock, filepath, http-client + , matrix, monad-logger, mtl, network, persistent + , persistent-postgresql, persistent-template, pretty-show, process + , QuickCheck, quickcheck-instances, random, resourcet, servant + , servant-client, servant-server, split, strict, string-conversions + , tasty, tasty-hunit, tasty-quickcheck, text, tree-diff, unliftio + , vector, wai, warp + }: + mkDerivation { + pname = "quickcheck-state-machine"; + version = "0.5.0"; + sha256 = "0wds624fhvzwxcbrr05pgfq802c5namrsqpkdr2388j525374lsj"; + libraryHaskellDepends = [ + ansi-wl-pprint base containers exceptions matrix mtl pretty-show + QuickCheck split tree-diff unliftio vector + ]; + testHaskellDepends = [ + base bytestring containers directory doctest filelock filepath + http-client matrix monad-logger mtl network persistent + persistent-postgresql persistent-template process QuickCheck + quickcheck-instances random resourcet servant servant-client + servant-server strict string-conversions tasty tasty-hunit + tasty-quickcheck text tree-diff unliftio vector wai warp + ]; + description = "Test monadic programs using state machine based models"; + license = stdenv.lib.licenses.bsd3; + hydraPlatforms = stdenv.lib.platforms.none; + }) {}; + "quickcheck-state-machine-distributed" = callPackage ({ mkDerivation, base, binary, containers, directory , distributed-process, mtl, network-transport @@ -176418,8 +176667,8 @@ self: { ({ mkDerivation, base, composition-prelude }: mkDerivation { pname = "recursion"; - version = "2.2.0.1"; - sha256 = "0xf8d9gjqmnp9scz5q06kx473y498iy7kql5200zr4mnr62c2pqj"; + version = "2.2.1.0"; + sha256 = "0f16lk8apql211gy30vm5l0gjhjlp243cdbrrz6wq47pdlxns5pa"; libraryHaskellDepends = [ base composition-prelude ]; description = "A recursion schemes library for GHC"; license = stdenv.lib.licenses.bsd3; @@ -186022,6 +186271,28 @@ self: { license = stdenv.lib.licenses.bsd3; }) {}; + "semigroupoids_5_3_2" = callPackage + ({ mkDerivation, base, base-orphans, bifunctors, Cabal + , cabal-doctest, comonad, containers, contravariant, distributive + , doctest, hashable, tagged, template-haskell, transformers + , transformers-compat, unordered-containers + }: + mkDerivation { + pname = "semigroupoids"; + version = "5.3.2"; + sha256 = "01cxdcflfzx674bhdclf6c7lwgjpbj5yqv8w1fi9dvipyhyj3a31"; + setupHaskellDepends = [ base Cabal cabal-doctest ]; + libraryHaskellDepends = [ + base base-orphans bifunctors comonad containers contravariant + distributive hashable tagged template-haskell transformers + transformers-compat unordered-containers + ]; + testHaskellDepends = [ base doctest ]; + description = "Semigroupoids: Category sans id"; + license = stdenv.lib.licenses.bsd3; + hydraPlatforms = stdenv.lib.platforms.none; + }) {}; + "semigroupoids-syntax" = callPackage ({ mkDerivation, base, comonad, containers, contravariant , directory, distributive, doctest, filepath, QuickCheck @@ -201232,12 +201503,13 @@ self: { }) {}; "strict-tuple" = callPackage - ({ mkDerivation, base }: + ({ mkDerivation, base, deepseq, hashable }: mkDerivation { pname = "strict-tuple"; - version = "0.1.1"; - sha256 = "13r72i95d0aal7i6v1mrviin2i5c6j9zs0f3qvc66wyy7mkr1h5n"; - libraryHaskellDepends = [ base ]; + version = "0.1.2"; + sha256 = "1897l4x7aqadwbvq26di2cd7bsj498dvm3lsshbc37p1f3qry3lj"; + libraryHaskellDepends = [ base deepseq hashable ]; + testHaskellDepends = [ base ]; description = "Strict tuples"; license = stdenv.lib.licenses.bsd3; }) {}; @@ -201871,8 +202143,8 @@ self: { }: mkDerivation { pname = "structured-cli"; - version = "2.5.0.1"; - sha256 = "0a28m0i0fygs1i0lxq27vs2l749saqwph1rjdvv10xvxa16kx552"; + version = "2.5.0.2"; + sha256 = "0ds6rwzja9yrxq14ip4gxg6km6bzar4dxl5v9m3f3d64zqgm7yi5"; isLibrary = true; isExecutable = true; libraryHaskellDepends = [ @@ -202129,6 +202401,34 @@ self: { license = "GPL"; }) {}; + "suavemente" = callPackage + ({ mkDerivation, base, blaze-markup, bytestring, diagrams-core + , diagrams-lib, diagrams-svg, interpolatedstring-perl6, lens, mtl + , servant, servant-blaze, servant-server, servant-websockets, stm + , streaming, svg-builder, transformers, warp, websockets + }: + mkDerivation { + pname = "suavemente"; + version = "0.1.0.0"; + sha256 = "1595jc7lqvdk60p0cc3vjag7lgd90ayfwb16n70i1j9sz3b2qvva"; + isLibrary = true; + isExecutable = true; + libraryHaskellDepends = [ + base blaze-markup bytestring diagrams-core diagrams-lib + diagrams-svg interpolatedstring-perl6 lens mtl servant + servant-blaze servant-server servant-websockets stm streaming + svg-builder transformers warp websockets + ]; + executableHaskellDepends = [ + base blaze-markup bytestring diagrams-core diagrams-lib + diagrams-svg interpolatedstring-perl6 lens mtl servant + servant-blaze servant-server servant-websockets stm streaming + svg-builder transformers warp websockets + ]; + description = "An applicative functor that seamlessly talks to HTML inputs"; + license = stdenv.lib.licenses.bsd3; + }) {}; + "sub-state" = callPackage ({ mkDerivation, base, mtl, QuickCheck, quickcheck-instances, sets , tasty, tasty-hunit, tasty-quickcheck @@ -202927,6 +203227,32 @@ self: { license = stdenv.lib.licenses.bsd3; }) {}; + "sv-core_0_3_1" = callPackage + ({ mkDerivation, attoparsec, base, bifunctors, bytestring + , containers, contravariant, deepseq, lens, mtl, parsec + , profunctors, QuickCheck, readable, semigroupoids, semigroups + , tasty, tasty-quickcheck, text, transformers, trifecta + , utf8-string, validation, vector, void + }: + mkDerivation { + pname = "sv-core"; + version = "0.3.1"; + sha256 = "08j8qin7q04jvrb1gd870cylix7p81f4rws1k31b3azby2mdja6h"; + libraryHaskellDepends = [ + attoparsec base bifunctors bytestring containers contravariant + deepseq lens mtl parsec profunctors readable semigroupoids + semigroups text transformers trifecta utf8-string validation vector + void + ]; + testHaskellDepends = [ + base bytestring profunctors QuickCheck semigroupoids semigroups + tasty tasty-quickcheck text validation vector + ]; + description = "Encode and decode separated values (CSV, PSV, ...)"; + license = stdenv.lib.licenses.bsd3; + hydraPlatforms = stdenv.lib.platforms.none; + }) {}; + "sv-svfactor" = callPackage ({ mkDerivation, base, bytestring, lens, profunctors, sv-core , svfactor, validation @@ -207480,19 +207806,18 @@ self: { }) {}; "terminal-progress-bar" = callPackage - ({ mkDerivation, async, base, HUnit, stm, stm-chans, terminal-size - , test-framework, test-framework-hunit + ({ mkDerivation, base, criterion, deepseq, HUnit, terminal-size + , test-framework, test-framework-hunit, text, time }: mkDerivation { pname = "terminal-progress-bar"; - version = "0.2"; - sha256 = "052az3lxmhfssvm1i5md5d9la7vhfy560ls101kvw73vdzxk9cfn"; - isLibrary = true; - isExecutable = true; - libraryHaskellDepends = [ async base stm stm-chans terminal-size ]; + version = "0.4"; + sha256 = "03c2mjygz5sk4as031v5wvg946x27w3khadp709la942b5725nkn"; + libraryHaskellDepends = [ base deepseq terminal-size text time ]; testHaskellDepends = [ - base HUnit test-framework test-framework-hunit + base HUnit test-framework test-framework-hunit text time ]; + benchmarkHaskellDepends = [ base criterion time ]; description = "A simple progress bar in the terminal"; license = stdenv.lib.licenses.bsd3; }) {}; @@ -209294,12 +209619,27 @@ self: { pname = "tfp"; version = "1.0.0.2"; sha256 = "1njccng7gj8za3ywjydphw054nx6grmgnfzwmwj89xwirf8710cs"; + revision = "1"; + editedCabalFile = "062rvn5ba3x5fjhnqs8lid6mra3vqz5ikaixck1mlmafkqmxhvw9"; libraryHaskellDepends = [ base utility-ht ]; testHaskellDepends = [ base QuickCheck ]; description = "Type-level integers, booleans, lists using type families"; license = stdenv.lib.licenses.bsd3; }) {}; + "tfp_1_0_1_1" = callPackage + ({ mkDerivation, base, QuickCheck, utility-ht }: + mkDerivation { + pname = "tfp"; + version = "1.0.1.1"; + sha256 = "1qkcm4l09qpxy9996lnfn79c1wn1ca45s3i2iz2x3kvp0f999d3i"; + libraryHaskellDepends = [ base utility-ht ]; + testHaskellDepends = [ base QuickCheck ]; + description = "Type-level integers, booleans, lists using type families"; + license = stdenv.lib.licenses.bsd3; + hydraPlatforms = stdenv.lib.platforms.none; + }) {}; + "tfp-th" = callPackage ({ mkDerivation, base, template-haskell, tfp }: mkDerivation { @@ -215421,6 +215761,8 @@ self: { pname = "ty"; version = "0.1.7"; sha256 = "0nn9lr9q0vmkkw25j7yfi3js2qmfmsrhrkviipjj8y7hrhmkfimm"; + revision = "1"; + editedCabalFile = "0sxqrkqchr3zcks68wljp722f5sndxz1fw5a2qi599i984v91y0l"; libraryHaskellDepends = [ base ghc-prim ]; description = "Typed type representations and equality proofs"; license = stdenv.lib.licenses.bsd3; @@ -216079,6 +216421,8 @@ self: { pname = "type-unary"; version = "0.3.2"; sha256 = "12h20xjqr1abb5mb4fmij9j0vkfn7rwbidm2dr7ssbkk7cb5fv37"; + revision = "1"; + editedCabalFile = "0pj81qqwd6cvypn923jlqg42v9zb3sv5kjvd93z2cksy3k80mqk6"; enableSeparateDataOutput = true; libraryHaskellDepends = [ applicative-numbers base constraints newtype-generics ty @@ -217049,6 +217393,8 @@ self: { pname = "unamb"; version = "0.2.7"; sha256 = "0v4c4zyr2fw6g86isa4n8mbflh7mwhzl70sp48mmpr1335n403xs"; + revision = "1"; + editedCabalFile = "0d1kjvxadb25mr7vmiilm3p5r7kgbfkkpklxkr6a136abdbv0pff"; isLibrary = true; isExecutable = true; libraryHaskellDepends = [ base ]; @@ -221353,6 +221699,8 @@ self: { pname = "vector-space"; version = "0.15"; sha256 = "03swlbn0x8gfb7bilxmh3zckprjc6v64bildmhwzlimjvd1v8jb8"; + revision = "1"; + editedCabalFile = "19549mrhg3x0d1ancrxyvrskd6p4x11iprnv0b0d84q7sc40fa8w"; libraryHaskellDepends = [ base Boolean MemoTrie NumInstances ]; description = "Vector & affine spaces, linear maps, and derivatives"; license = stdenv.lib.licenses.bsd3; @@ -222399,20 +222747,24 @@ self: { }) {inherit (pkgs) vrpn;}; "vt-utils" = callPackage - ({ mkDerivation, aeson, base, bytestring, directory, HUnit, parsec - , text, time, unordered-containers, vector + ({ mkDerivation, aeson, aeson-pretty, base, bytestring + , case-insensitive, directory, http-client, http-types, HUnit + , parsec, process, text, time, transformers, unordered-containers + , vector, wai, warp }: mkDerivation { pname = "vt-utils"; - version = "1.0.1.0"; - sha256 = "1a33bxnyyhs4ibnrgz5472bqvg4irqh4z5cv0wcwmmpi8s4i629w"; + version = "1.1.0.0"; + sha256 = "1xqcffipp5hwvmiqxg80zj3v4nzqklqcpy3kblfkw4xkvg57gh87"; libraryHaskellDepends = [ - aeson base bytestring directory HUnit parsec text time - unordered-containers vector + aeson aeson-pretty base bytestring case-insensitive directory + http-client http-types HUnit parsec process text time transformers + unordered-containers vector wai ]; testHaskellDepends = [ - aeson base bytestring directory HUnit parsec text time - unordered-containers vector + aeson aeson-pretty base bytestring case-insensitive directory + http-client http-types HUnit parsec process text time transformers + unordered-containers vector wai warp ]; description = "Vector and Text utilities"; license = stdenv.lib.licenses.mit; @@ -230396,35 +230748,31 @@ self: { }) {}; "yam" = callPackage - ({ mkDerivation, aeson, base, bytestring, conduit, data-default - , hspec, monad-logger, mtl, persistent, persistent-sqlite - , QuickCheck, random, reflection, resource-pool, resourcet, salak - , servant-server, servant-swagger, servant-swagger-ui, text, time - , unliftio-core, vault, wai, wai-extra, warp + ({ mkDerivation, aeson, base, bytestring, data-default, fast-logger + , hspec, monad-logger, mtl, QuickCheck, random, reflection, salak + , servant-server, servant-swagger, servant-swagger-ui, text, vault + , wai, warp }: mkDerivation { pname = "yam"; - version = "0.4.0"; - sha256 = "1kapdqz6pn1x95xffm5w0wclj3hdyazmvvgmgir8kjlchfmdanmi"; + version = "0.5.2"; + sha256 = "1cig29wyyq7dg4hz6iz5fm25xf2zvmrahdg06sq1m3cl4gk6fw6s"; isLibrary = true; isExecutable = true; libraryHaskellDepends = [ - aeson base bytestring conduit data-default monad-logger mtl - persistent random reflection resource-pool resourcet salak - servant-server servant-swagger servant-swagger-ui text - unliftio-core vault wai warp + aeson base bytestring data-default fast-logger monad-logger mtl + random reflection salak servant-server servant-swagger + servant-swagger-ui text vault wai warp ]; executableHaskellDepends = [ - aeson base bytestring conduit data-default monad-logger mtl - persistent persistent-sqlite random reflection resource-pool - resourcet salak servant-server servant-swagger servant-swagger-ui - text time unliftio-core vault wai wai-extra warp + aeson base bytestring data-default fast-logger monad-logger mtl + random reflection salak servant-server servant-swagger + servant-swagger-ui text vault wai warp ]; testHaskellDepends = [ - aeson base bytestring conduit data-default hspec monad-logger mtl - persistent QuickCheck random reflection resource-pool resourcet - salak servant-server servant-swagger servant-swagger-ui text - unliftio-core vault wai warp + aeson base bytestring data-default fast-logger hspec monad-logger + mtl QuickCheck random reflection salak servant-server + servant-swagger servant-swagger-ui text vault wai warp ]; description = "Yam Web"; license = stdenv.lib.licenses.bsd3; @@ -230470,6 +230818,21 @@ self: { license = stdenv.lib.licenses.mit; }) {}; + "yam-datasource" = callPackage + ({ mkDerivation, base, conduit, persistent, resource-pool + , resourcet, unliftio-core, yam + }: + mkDerivation { + pname = "yam-datasource"; + version = "0.5.2"; + sha256 = "06cfjcppkwx82cv7gf56rhypwsc2qxnks50vjslgxp7c0k9qaaza"; + libraryHaskellDepends = [ + base conduit persistent resource-pool resourcet unliftio-core yam + ]; + description = "Yam DataSource Middleware"; + license = stdenv.lib.licenses.bsd3; + }) {}; + "yam-job" = callPackage ({ mkDerivation, base, cron, yam-app }: mkDerivation { @@ -231114,6 +231477,55 @@ self: { hydraPlatforms = stdenv.lib.platforms.none; }) {}; + "yaya" = callPackage + ({ mkDerivation, base, bifunctors, comonad, constraints, containers + , deriving-compat, distributive, either, errors, free, hedgehog + , kan-extensions, lens, profunctors, template-haskell, transformers + , yaya-hedgehog + }: + mkDerivation { + pname = "yaya"; + version = "0.1.0.0"; + sha256 = "1ycxm83j85lyxz9fzydccd0r4lv667a4c03bfbz81gk90hzlsvrv"; + libraryHaskellDepends = [ + base bifunctors comonad constraints containers distributive either + errors free kan-extensions lens profunctors template-haskell + transformers + ]; + testHaskellDepends = [ + base deriving-compat hedgehog yaya-hedgehog + ]; + description = "Total recursion schemes"; + license = stdenv.lib.licenses.agpl3; + }) {}; + + "yaya-hedgehog" = callPackage + ({ mkDerivation, base, deriving-compat, hedgehog, yaya }: + mkDerivation { + pname = "yaya-hedgehog"; + version = "0.1.0.0"; + sha256 = "14q16av76mnhrlz93ihwqaknzihf3nlsa572pqqc6hs6g4vxdikj"; + libraryHaskellDepends = [ base deriving-compat hedgehog yaya ]; + description = "Hedgehog testing support for the Yaya recursion scheme library"; + license = stdenv.lib.licenses.agpl3; + }) {}; + + "yaya-unsafe" = callPackage + ({ mkDerivation, base, bifunctors, comonad, either, free, hedgehog + , lens, yaya, yaya-hedgehog + }: + mkDerivation { + pname = "yaya-unsafe"; + version = "0.1.0.0"; + sha256 = "18zsq1pvfglrxfk2afk7aiqlsfi4dpwhlp34cfi3kjqcg00zzv19"; + libraryHaskellDepends = [ + base bifunctors comonad either free lens yaya + ]; + testHaskellDepends = [ base hedgehog yaya yaya-hedgehog ]; + description = "Non-total extensions to the Yaya recursion scheme library"; + license = stdenv.lib.licenses.agpl3; + }) {}; + "ycextra" = callPackage ({ mkDerivation, base, containers, csv, mtl, uniplate, yhccore }: mkDerivation { From 056227a877f7736de5b57bef203cb68b37d982ae Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Sun, 6 Jan 2019 14:30:37 +0100 Subject: [PATCH 123/247] haskell-yaya: break infinite recursion --- pkgs/development/haskell-modules/configuration-nix.nix | 3 +++ 1 file changed, 3 insertions(+) diff --git a/pkgs/development/haskell-modules/configuration-nix.nix b/pkgs/development/haskell-modules/configuration-nix.nix index 62f2782e8f77..d34d9193c23a 100644 --- a/pkgs/development/haskell-modules/configuration-nix.nix +++ b/pkgs/development/haskell-modules/configuration-nix.nix @@ -550,4 +550,7 @@ self: super: builtins.intersectAttrs super { # The test suite has undeclared dependencies on git. githash = dontCheck super.githash; + # Avoid infitite recursion with yaya. + yaya-hedgehog = super.yaya-hedgehog.override { yaya = dontCheck self.yaya; }; + } From 10b9cc5b06c3b509a74f98698e7e469439c9c236 Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Sun, 6 Jan 2019 14:32:25 +0100 Subject: [PATCH 124/247] pandoc: drop obsolete override --- pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix | 3 --- 1 file changed, 3 deletions(-) diff --git a/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix b/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix index 4d258a5490b2..a3124db97d38 100644 --- a/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix +++ b/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix @@ -64,7 +64,4 @@ self: super: { # Break out of "yaml >=0.10.4.0 && <0.11": https://github.com/commercialhaskell/stack/issues/4485 stack = doJailbreak super.stack; - # Break out of "tasty >= 0.11 && < 1.2": https://github.com/jgm/pandoc/issues/5200 - pandoc = doJailbreak super.pandoc; - } From 6c54f9ea5a4370160483820040fec301389c005a Mon Sep 17 00:00:00 2001 From: Peter Simons Date: Sun, 6 Jan 2019 14:38:03 +0100 Subject: [PATCH 125/247] git-annex: patch to fix build with ghc 8.6.x --- .../configuration-ghc-8.6.x.nix | 3 + .../git-annex-fix-ghc-8.6.x-build.patch | 91 +++++++++++++++++++ 2 files changed, 94 insertions(+) create mode 100644 pkgs/development/haskell-modules/patches/git-annex-fix-ghc-8.6.x-build.patch diff --git a/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix b/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix index a3124db97d38..daa12f711b52 100644 --- a/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix +++ b/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix @@ -64,4 +64,7 @@ self: super: { # Break out of "yaml >=0.10.4.0 && <0.11": https://github.com/commercialhaskell/stack/issues/4485 stack = doJailbreak super.stack; + # Fix build with ghc 8.6.x. + git-annex = appendPatch super.git-annex ./patches/git-annex-fix-ghc-8.6.x-build.patch; + } diff --git a/pkgs/development/haskell-modules/patches/git-annex-fix-ghc-8.6.x-build.patch b/pkgs/development/haskell-modules/patches/git-annex-fix-ghc-8.6.x-build.patch new file mode 100644 index 000000000000..46d7afada4ad --- /dev/null +++ b/pkgs/development/haskell-modules/patches/git-annex-fix-ghc-8.6.x-build.patch @@ -0,0 +1,91 @@ +From 2e0e557e7512ddd0376f179e82c811d8b4cce401 Mon Sep 17 00:00:00 2001 +From: Joey Hess +Date: Sat, 5 Jan 2019 11:54:06 -0400 +Subject: [PATCH] Support being built with ghc 8.0.1 (MonadFail) + +Tested on an older ghc by enabling MonadFailDesugaring globally. + +In TransferQueue, the lack of a MonadFail for STM exposed what would +normally be a bug in the pattern matching, although in this case an +earlier check that the queue was not empty avoided a pattern match +failure. +--- + Annex.hs | 2 ++ + Assistant/Monad.hs | 2 ++ + Assistant/TransferQueue.hs | 21 +++++++++++---------- + CHANGELOG | 1 + + 4 files changed, 16 insertions(+), 10 deletions(-) + +diff --git a/Annex.hs b/Annex.hs +index 0a0368d36..af0ede1f4 100644 +--- a/Annex.hs ++++ b/Annex.hs +@@ -74,6 +74,7 @@ import "mtl" Control.Monad.Reader + import Control.Concurrent + import Control.Concurrent.Async + import Control.Concurrent.STM ++import qualified Control.Monad.Fail as Fail + import qualified Control.Concurrent.SSem as SSem + import qualified Data.Map.Strict as M + import qualified Data.Set as S +@@ -93,6 +94,7 @@ newtype Annex a = Annex { runAnnex :: ReaderT (MVar AnnexState) IO a } + MonadCatch, + MonadThrow, + MonadMask, ++ Fail.MonadFail, + Functor, + Applicative + ) +diff --git a/Assistant/Monad.hs b/Assistant/Monad.hs +index 403ee16a8..ef2ee6012 100644 +--- a/Assistant/Monad.hs ++++ b/Assistant/Monad.hs +@@ -27,6 +27,7 @@ module Assistant.Monad ( + + import "mtl" Control.Monad.Reader + import System.Log.Logger ++import qualified Control.Monad.Fail as Fail + + import Annex.Common + import Assistant.Types.ThreadedMonad +@@ -49,6 +50,7 @@ newtype Assistant a = Assistant { mkAssistant :: ReaderT AssistantData IO a } + Monad, + MonadIO, + MonadReader AssistantData, ++ Fail.MonadFail, + Functor, + Applicative + ) +diff --git a/Assistant/TransferQueue.hs b/Assistant/TransferQueue.hs +index 6a4473262..7c0ab80d0 100644 +--- a/Assistant/TransferQueue.hs ++++ b/Assistant/TransferQueue.hs +@@ -191,17 +191,18 @@ getNextTransfer acceptable = do + sz <- readTVar (queuesize q) + if sz < 1 + then retry -- blocks until queuesize changes +- else do +- (r@(t,info):rest) <- readTList (queuelist q) +- void $ modifyTVar' (queuesize q) pred +- setTList (queuelist q) rest +- if acceptable info +- then do +- adjustTransfersSTM dstatus $ +- M.insert t info +- return $ Just r +- else return Nothing ++ else readTList (queuelist q) >>= \case ++ [] -> retry -- blocks until something is queued ++ (r@(t,info):rest) -> do ++ void $ modifyTVar' (queuesize q) pred ++ setTList (queuelist q) rest ++ if acceptable info ++ then do ++ adjustTransfersSTM dstatus $ ++ M.insert t info ++ return $ Just r ++ else return Nothing + + {- Moves transfers matching a condition from the queue, to the + - currentTransfers map. -} + From bb9edd458e041fafdcc8da6f5bf709bc7c755911 Mon Sep 17 00:00:00 2001 From: rnhmjoj Date: Mon, 7 Jan 2019 11:09:56 +0100 Subject: [PATCH 126/247] python.pkgs.plone-testing: fix build --- pkgs/development/python-modules/plone-testing/default.nix | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/plone-testing/default.nix b/pkgs/development/python-modules/plone-testing/default.nix index 81482414d57f..636028c957a9 100644 --- a/pkgs/development/python-modules/plone-testing/default.nix +++ b/pkgs/development/python-modules/plone-testing/default.nix @@ -1,6 +1,7 @@ { lib , buildPythonPackage , fetchPypi +, six , zope_testing , setuptools }: @@ -14,7 +15,7 @@ buildPythonPackage rec { sha256 = "db71bde0d4d3c273dbba8c7a2ab259a42f038eca74184da36c5aab61e90e8dd7"; }; - propagatedBuildInputs = [ setuptools zope_testing ]; + propagatedBuildInputs = [ six setuptools zope_testing ]; # Huge amount of testing dependencies (including Zope2) doCheck = false; @@ -24,4 +25,4 @@ buildPythonPackage rec { homepage = https://github.com/plone/plone.testing; license = lib.licenses.bsd3; }; -} \ No newline at end of file +} From 985bc6ca5a598471c311ec09c2c86e1e99a0c606 Mon Sep 17 00:00:00 2001 From: rnhmjoj Date: Mon, 7 Jan 2019 11:10:38 +0100 Subject: [PATCH 127/247] searx: 0.14.0 -> 0.15.0 --- pkgs/servers/web-apps/searx/default.nix | 22 ++++++++++++++-------- 1 file changed, 14 insertions(+), 8 deletions(-) diff --git a/pkgs/servers/web-apps/searx/default.nix b/pkgs/servers/web-apps/searx/default.nix index cde8f9fecbc8..59d3a387b606 100644 --- a/pkgs/servers/web-apps/searx/default.nix +++ b/pkgs/servers/web-apps/searx/default.nix @@ -4,26 +4,31 @@ with python3Packages; buildPythonApplication rec { pname = "searx"; - version = "0.14.0"; + version = "0.15.0"; # Can not use PyPI because certain test files are missing. src = fetchFromGitHub { owner = "asciimoo"; repo = "searx"; rev = "v${version}"; - sha256 = "046xg6xcs1mxgahz7kwf3fsmwd99q3hhms6pdjlvyczidlfhpmxl"; + sha256 = "05si0fn57z1g80l6003cs0ypag2m6zyi3dgsi06pvjp066xbrjvd"; }; postPatch = '' substituteInPlace requirements.txt \ --replace 'certifi==2017.11.5' 'certifi' \ - --replace 'flask==0.12.2' 'flask==0.12.*' \ + --replace 'flask==1.0.2' 'flask==1.0.*' \ --replace 'flask-babel==0.11.2' 'flask-babel==0.11.*' \ - --replace 'lxml==4.1.1' 'lxml==4.1.*' \ - --replace 'idna==2.5' 'idna' \ + --replace 'lxml==4.2.3' 'lxml==4.2.*' \ + --replace 'idna==2.7' 'idna' \ --replace 'pygments==2.1.3' 'pygments>=2.1,<3.0' \ - --replace 'pyopenssl==17.4.0' 'pyopenssl' \ - --replace 'python-dateutil==2.6.1' 'python-dateutil==2.6.*' + --replace 'pyopenssl==18.0.0' 'pyopenssl' \ + --replace 'python-dateutil==2.7.3' 'python-dateutil==2.7.*' + substituteInPlace requirements-dev.txt \ + --replace 'plone.testing==5.0.0' 'plone.testing' \ + --replace 'pep8==1.7.1' 'pep8==1.7.*' \ + --replace 'splinter==0.7.5' 'splinter' \ + --replace 'selenium==3.5.0' 'selenium' ''; propagatedBuildInputs = [ @@ -33,7 +38,8 @@ buildPythonApplication rec { ]; checkInputs = [ - splinter mock plone-testing robotsuite unittest2 selenium + Babel mock nose2 covCore pep8 plone-testing splinter + unittest2 zope_testrunner selenium ]; preCheck = '' From bb5c86d4040c21d01c2e03a554da87185a34b5ed Mon Sep 17 00:00:00 2001 From: betaboon Date: Sat, 29 Dec 2018 19:25:28 +0100 Subject: [PATCH 128/247] soapysdr: fix modules-directory for extraPackages --- pkgs/applications/misc/soapysdr/default.nix | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/pkgs/applications/misc/soapysdr/default.nix b/pkgs/applications/misc/soapysdr/default.nix index f14b560bf52c..5a79e9d52a0c 100644 --- a/pkgs/applications/misc/soapysdr/default.nix +++ b/pkgs/applications/misc/soapysdr/default.nix @@ -6,7 +6,11 @@ } : let + version = "0.7.0"; + modulesVersion = with lib; versions.major version + "." + versions.minor version; + modulesPath = "lib/SoapySDR/modules" + modulesVersion; + extraPackagesSearchPath = lib.makeSearchPath modulesPath extraPackages; in stdenv.mkDerivation { name = "soapysdr-${version}"; @@ -18,8 +22,8 @@ in stdenv.mkDerivation { sha256 = "14fjwnfj7jz9ixvim2gy4f52y6s7d4xggzxn2ck7g4q35d879x13"; }; - nativeBuildInputs = [ cmake pkgconfig ]; - buildInputs = [ libusb ncurses numpy swig2 python makeWrapper ]; + nativeBuildInputs = [ cmake makeWrapper pkgconfig ]; + buildInputs = [ libusb ncurses numpy python swig2 ]; cmakeFlags = [ "-DCMAKE_BUILD_TYPE=Release" @@ -31,11 +35,9 @@ in stdenv.mkDerivation { for i in ${toString extraPackages}; do ${lndir}/bin/lndir -silent $i $out done - # Needed for at least the remote plugin server for file in $out/bin/*; do - wrapProgram "$file" \ - --prefix SOAPY_SDR_PLUGIN_PATH : ${lib.makeSearchPath "lib/SoapySDR/modules0.6" extraPackages} + wrapProgram "$file" --prefix SOAPY_SDR_PLUGIN_PATH : ${extraPackagesSearchPath} done ''; @@ -47,4 +49,3 @@ in stdenv.mkDerivation { platforms = platforms.linux; }; } - From 289fe57eea6a2b3c9b5fa37b7c1cc6097e9466e0 Mon Sep 17 00:00:00 2001 From: Tim Steinbach Date: Mon, 7 Jan 2019 07:35:20 -0500 Subject: [PATCH 129/247] urxvt: Allow switching out package --- nixos/modules/services/x11/urxvtd.nix | 28 ++++++++++++++++++--------- 1 file changed, 19 insertions(+), 9 deletions(-) diff --git a/nixos/modules/services/x11/urxvtd.nix b/nixos/modules/services/x11/urxvtd.nix index 5531d7f153c2..d916fa5bb393 100644 --- a/nixos/modules/services/x11/urxvtd.nix +++ b/nixos/modules/services/x11/urxvtd.nix @@ -7,14 +7,24 @@ with lib; let cfg = config.services.urxvtd; in { + options.services.urxvtd = { + enable = mkOption { + type = types.bool; + default = false; + description = '' + Enable urxvtd, the urxvt terminal daemon. To use urxvtd, run + "urxvtc". + ''; + }; - options.services.urxvtd.enable = mkOption { - type = types.bool; - default = false; - description = '' - Enable urxvtd, the urxvt terminal daemon. To use urxvtd, run - "urxvtc". - ''; + package = mkOption { + default = pkgs.rxvt_unicode-with-plugins; + defaultText = "pkgs.rxvt_unicode-with-plugins"; + description = '' + Package to install. Usually pkgs.rxvt_unicode-with-plugins or pkgs.rxvt_unicode + ''; + type = types.package; + }; }; config = mkIf cfg.enable { @@ -24,14 +34,14 @@ in { partOf = [ "graphical-session.target" ]; path = [ pkgs.xsel ]; serviceConfig = { - ExecStart = "${pkgs.rxvt_unicode-with-plugins}/bin/urxvtd -o"; + ExecStart = "${cfg.package}/bin/urxvtd -o"; Environment = "RXVT_SOCKET=%t/urxvtd-socket"; Restart = "on-failure"; RestartSec = "5s"; }; }; - environment.systemPackages = [ pkgs.rxvt_unicode-with-plugins ]; + environment.systemPackages = [ cfg.package ]; environment.variables.RXVT_SOCKET = "/run/user/$(id -u)/urxvtd-socket"; }; From 220aa6713b89203d956eef7156f46c0fa0689bc7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vladim=C3=ADr=20=C4=8Cun=C3=A1t?= Date: Mon, 7 Jan 2019 13:45:52 +0100 Subject: [PATCH 130/247] knot-dns: 2.7.4 -> 2.7.5 https://gitlab.labs.nic.cz/knot/knot-dns/tags/v2.7.5 --- pkgs/servers/dns/knot-dns/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/dns/knot-dns/default.nix b/pkgs/servers/dns/knot-dns/default.nix index 2ff80906c01b..c2b63184bec7 100644 --- a/pkgs/servers/dns/knot-dns/default.nix +++ b/pkgs/servers/dns/knot-dns/default.nix @@ -7,11 +7,11 @@ let inherit (stdenv.lib) optional optionals; in # Note: ATM only the libraries have been tested in nixpkgs. stdenv.mkDerivation rec { name = "knot-dns-${version}"; - version = "2.7.4"; + version = "2.7.5"; src = fetchurl { url = "https://secure.nic.cz/files/knot-dns/knot-${version}.tar.xz"; - sha256 = "0x7xx6jh4x8ljnvj30zh3n1zw5jkhla62dv9i75v0rwgrpxy5sxc"; + sha256 = "7d70d6d8f708285517d1d7c4ff2e5ddfd119cd2962c7a8d3f50a4c695209a086"; }; outputs = [ "bin" "out" "dev" ]; From 97aba92bcd689b7f2a2e5ff956e3dc2297bce805 Mon Sep 17 00:00:00 2001 From: Tim Steinbach Date: Mon, 7 Jan 2019 07:57:32 -0500 Subject: [PATCH 131/247] linux: 4.20-rc7 -> 5.0-rc1 --- pkgs/os-specific/linux/kernel/common-config.nix | 10 +++++----- pkgs/os-specific/linux/kernel/linux-testing.nix | 8 ++++---- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/pkgs/os-specific/linux/kernel/common-config.nix b/pkgs/os-specific/linux/kernel/common-config.nix index c098571bb606..ab4b1cc2fc96 100644 --- a/pkgs/os-specific/linux/kernel/common-config.nix +++ b/pkgs/os-specific/linux/kernel/common-config.nix @@ -88,9 +88,9 @@ let # Include the CFQ I/O scheduler in the kernel, rather than as a # module, so that the initrd gets a good I/O scheduler. scheduler = { - IOSCHED_CFQ = yes; + IOSCHED_CFQ = whenOlder "5.0" yes; # Removed in 5.0-RC1 BLK_CGROUP = yes; # required by CFQ" - IOSCHED_DEADLINE = yes; + IOSCHED_DEADLINE = whenOlder "5.0" yes; # Removed in 5.0-RC1 MQ_IOSCHED_DEADLINE = whenAtLeast "4.11" yes; BFQ_GROUP_IOSCHED = whenAtLeast "4.12" yes; MQ_IOSCHED_KYBER = whenAtLeast "4.12" yes; @@ -365,7 +365,7 @@ let # https://lwn.net/Articles/682582/ # https://bugzilla.kernel.org/show_bug.cgi?id=12309#c655 BLK_WBT = yes; - BLK_WBT_SQ = yes; + BLK_WBT_SQ = whenOlder "5.0" yes; # Removed in 5.0-RC1 BLK_WBT_MQ = yes; }; @@ -382,7 +382,7 @@ let DEVPTS_MULTIPLE_INSTANCES = whenOlder "4.7" yes; BLK_DEV_THROTTLING = yes; - CFQ_GROUP_IOSCHED = yes; + CFQ_GROUP_IOSCHED = whenOlder "5.0" yes; # Removed in 5.0-RC1 CGROUP_PIDS = whenAtLeast "4.3" yes; }; @@ -466,7 +466,7 @@ let MEDIA_DIGITAL_TV_SUPPORT = yes; MEDIA_CAMERA_SUPPORT = yes; MEDIA_RC_SUPPORT = whenOlder "4.14" yes; - MEDIA_CONTROLLER = yes; + MEDIA_CONTROLLER = yes; MEDIA_PCI_SUPPORT = yes; MEDIA_USB_SUPPORT = yes; MEDIA_ANALOG_TV_SUPPORT = yes; diff --git a/pkgs/os-specific/linux/kernel/linux-testing.nix b/pkgs/os-specific/linux/kernel/linux-testing.nix index 1e810a129318..6b92d9be1777 100644 --- a/pkgs/os-specific/linux/kernel/linux-testing.nix +++ b/pkgs/os-specific/linux/kernel/linux-testing.nix @@ -1,13 +1,13 @@ { stdenv, buildPackages, fetchurl, perl, buildLinux, libelf, utillinux, ... } @ args: buildLinux (args // rec { - version = "4.20-rc7"; - modDirVersion = "4.20.0-rc7"; - extraMeta.branch = "4.20"; + version = "5.0-rc1"; + modDirVersion = "5.0.0-rc1"; + extraMeta.branch = "5.0"; src = fetchurl { url = "https://git.kernel.org/torvalds/t/linux-${version}.tar.gz"; - sha256 = "0qga2x4rz1vphi7j044f4b4la24qyk5sm7lm8q991imq5wm5s2rl"; + sha256 = "01gva1hp2jyf137iy5ryaq93ksiw9ysnczpp914scx6k005y7yzz"; }; # Should the testing kernels ever be built on Hydra? From bd7eec5d9cc61302c456cc51868fefb931e0793d Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 05:52:18 -0800 Subject: [PATCH 132/247] pynac: 0.7.22 -> 0.7.23 (#53559) Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/pynac/versions --- pkgs/applications/science/math/pynac/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/science/math/pynac/default.nix b/pkgs/applications/science/math/pynac/default.nix index 9bbb695a331b..032b2ef09643 100644 --- a/pkgs/applications/science/math/pynac/default.nix +++ b/pkgs/applications/science/math/pynac/default.nix @@ -9,14 +9,14 @@ }: stdenv.mkDerivation rec { - version = "0.7.22"; + version = "0.7.23"; name = "pynac-${version}"; src = fetchFromGitHub { owner = "pynac"; repo = "pynac"; rev = "pynac-${version}"; - sha256 = "1ribm5vpbgsja4hbca1ckw4ln9kjkv608aaqsvxxvbs4z76ys6yi"; + sha256 = "02yhl8v9l6aj3wl6dk9iacz4hdv08i1d750rxpygjp43nlgvvb2h"; }; buildInputs = [ From e1d98548167f52425c089b81f594dfa9c58a5e02 Mon Sep 17 00:00:00 2001 From: Michael Weiss Date: Sun, 6 Jan 2019 20:29:52 +0100 Subject: [PATCH 133/247] scons: 3.0.1 -> 3.0.2 A few packages broke due to the SCons upgrade (they depended on deprecated options that got removed), I've kept them on version 3.0.1 for now. The rest of the rebuilds seems fine (the failing ones where already in a broken state before this change). --- pkgs/applications/audio/klick/default.nix | 6 +++--- pkgs/applications/audio/nova-filters/default.nix | 6 +++--- pkgs/development/tools/toluapp/default.nix | 4 ++-- pkgs/games/btanks/default.nix | 4 ++-- pkgs/games/globulation/default.nix | 4 ++-- pkgs/tools/graphics/lprof/default.nix | 4 ++-- pkgs/top-level/all-packages.nix | 2 +- 7 files changed, 15 insertions(+), 15 deletions(-) diff --git a/pkgs/applications/audio/klick/default.nix b/pkgs/applications/audio/klick/default.nix index 4d1ae8ebd58e..5e54609f8bf0 100644 --- a/pkgs/applications/audio/klick/default.nix +++ b/pkgs/applications/audio/klick/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, scons, pkgconfig +{ stdenv, fetchurl, sconsPackages, pkgconfig , libsamplerate, libsndfile, liblo, libjack2, boost }: stdenv.mkDerivation rec { @@ -10,8 +10,8 @@ stdenv.mkDerivation rec { sha256 = "1289533c0849b1b66463bf27f7ce5f71736b655cfb7672ef884c7e6eb957ac42"; }; - nativeBuildInputs = [ pkgconfig ]; - buildInputs = [ scons libsamplerate libsndfile liblo libjack2 boost ]; + nativeBuildInputs = [ sconsPackages.scons_3_0_1 pkgconfig ]; + buildInputs = [ libsamplerate libsndfile liblo libjack2 boost ]; prefixKey = "PREFIX="; NIX_CFLAGS_COMPILE = "-fpermissive"; diff --git a/pkgs/applications/audio/nova-filters/default.nix b/pkgs/applications/audio/nova-filters/default.nix index 1e52ff2d9e40..bb186687c66e 100644 --- a/pkgs/applications/audio/nova-filters/default.nix +++ b/pkgs/applications/audio/nova-filters/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, scons, boost, ladspaH, pkgconfig }: +{stdenv, fetchurl, sconsPackages, boost, ladspaH, pkgconfig }: stdenv.mkDerivation rec { version = "0.2-2"; @@ -9,8 +9,8 @@ stdenv.mkDerivation rec { sha256 = "16064vvl2w5lz4xi3lyjk4xx7fphwsxc14ajykvndiz170q32s6i"; }; - nativeBuildInputs = [ pkgconfig ]; - buildInputs = [ scons boost ladspaH ]; + nativeBuildInputs = [ pkgconfig sconsPackages.scons_3_0_1 ]; + buildInputs = [ boost ladspaH ]; patchPhase = '' # remove TERM: diff --git a/pkgs/development/tools/toluapp/default.nix b/pkgs/development/tools/toluapp/default.nix index 1214058698e2..5ad9a7c58efb 100644 --- a/pkgs/development/tools/toluapp/default.nix +++ b/pkgs/development/tools/toluapp/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, scons, lua }: +{ stdenv, fetchFromGitHub, sconsPackages, lua }: stdenv.mkDerivation rec { version = "1.0.93"; @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { sha256 = "0zd55bc8smmgk9j4cf0jpibb03lgsvl0knpwhplxbv93mcdnw7s0"; }; - nativeBuildInputs = [ scons ]; + nativeBuildInputs = [ sconsPackages.scons_3_0_1 ]; buildInputs = [ lua ]; patches = [ ./environ-and-linux-is-kinda-posix.patch ]; diff --git a/pkgs/games/btanks/default.nix b/pkgs/games/btanks/default.nix index b1c20d72520e..9de90069a375 100644 --- a/pkgs/games/btanks/default.nix +++ b/pkgs/games/btanks/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, fetchpatch, scons, pkgconfig, SDL, libGLU_combined, zlib, smpeg +{ stdenv, fetchurl, fetchpatch, sconsPackages, pkgconfig, SDL, libGLU_combined, zlib, smpeg , SDL_image, libvorbis, expat, zip, lua5_1 }: stdenv.mkDerivation rec { @@ -9,7 +9,7 @@ stdenv.mkDerivation rec { sha256 = "0ha35kxc8xlbg74wsrbapfgxvcrwy6psjkqi7c6adxs55dmcxliz"; }; - nativeBuildInputs = [ scons pkgconfig ]; + nativeBuildInputs = [ sconsPackages.scons_3_0_1 pkgconfig ]; buildInputs = [ SDL libGLU_combined zlib smpeg SDL_image libvorbis expat zip lua5_1 ]; NIX_CFLAGS_COMPILE = "-I${SDL_image}/include/SDL"; diff --git a/pkgs/games/globulation/default.nix b/pkgs/games/globulation/default.nix index a539b79339f9..edfb05d237cd 100644 --- a/pkgs/games/globulation/default.nix +++ b/pkgs/games/globulation/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, libGLU_combined, SDL, scons, SDL_ttf, SDL_image, zlib, SDL_net +{ stdenv, fetchurl, libGLU_combined, SDL, sconsPackages, SDL_ttf, SDL_image, zlib, SDL_net , speex, libvorbis, libogg, boost, fribidi, bsdiff , fetchpatch }: @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { sed -i -e "s@env = Environment()@env = Environment( ENV = os.environ )@" SConstruct ''; - nativeBuildInputs = [ scons ]; + nativeBuildInputs = [ sconsPackages.scons_3_0_1 ]; buildInputs = [ libGLU_combined SDL SDL_ttf SDL_image zlib SDL_net speex libvorbis libogg boost fribidi bsdiff ]; postConfigure = '' diff --git a/pkgs/tools/graphics/lprof/default.nix b/pkgs/tools/graphics/lprof/default.nix index a4a2cfc1a7c4..42ccc4d5022e 100644 --- a/pkgs/tools/graphics/lprof/default.nix +++ b/pkgs/tools/graphics/lprof/default.nix @@ -1,11 +1,11 @@ -{ stdenv, fetchurl, scons, qt3, lcms1, libtiff, vigra }: +{ stdenv, fetchurl, sconsPackages, qt3, lcms1, libtiff, vigra }: /* how to calibrate your monitor: Eg see https://wiki.archlinux.org/index.php/ICC_Profiles#Loading_ICC_Profiles */ stdenv.mkDerivation { name = "lprof-1.11.4.1"; - nativeBuildInputs = [ scons ]; + nativeBuildInputs = [ sconsPackages.scons_3_0_1 ]; buildInputs = [ qt3 lcms1 libtiff vigra ]; hardeningDisable = [ "format" ]; diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index adf85fa0a6ec..7559303bcba4 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -9030,7 +9030,7 @@ in selendroid = callPackage ../development/tools/selenium/selendroid { }; sconsPackages = callPackage ../development/tools/build-managers/scons { }; - scons = sconsPackages.scons_3_0_1; + scons = sconsPackages.scons_3_0_2; scons_2_5_1 = sconsPackages.scons_2_5_1; mill = callPackage ../development/tools/build-managers/mill { }; From d89f092087a84ec2339b0458283e2fef76577800 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 07:08:47 -0800 Subject: [PATCH 134/247] pasystray: 0.7.0 -> 0.7.1 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/pasystray/versions --- pkgs/tools/audio/pasystray/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/audio/pasystray/default.nix b/pkgs/tools/audio/pasystray/default.nix index 57896fd7f637..bd6317bcea19 100644 --- a/pkgs/tools/audio/pasystray/default.nix +++ b/pkgs/tools/audio/pasystray/default.nix @@ -5,13 +5,13 @@ stdenv.mkDerivation rec { name = "pasystray-${version}"; - version = "0.7.0"; + version = "0.7.1"; src = fetchFromGitHub { owner = "christophgysin"; repo = "pasystray"; rev = name; - sha256 = "0cc9hjyw4gr4ip4lw74pzb1l9sxs3ffhf0xn0m1fhmyfbjyixwkh"; + sha256 = "0xx1bm9kimgq11a359ikabdndqg5q54pn1d1dyyjnrj0s41168fk"; }; nativeBuildInputs = [ pkgconfig ]; From 651ee38deaecdc16a54a51331e8af0419b30a16e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B8rn=20Forsman?= Date: Fri, 28 Dec 2018 11:47:13 +0100 Subject: [PATCH 135/247] jnetmap: init at 0.5.4 --- .../networking/jnetmap/default.nix | 33 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 35 insertions(+) create mode 100644 pkgs/applications/networking/jnetmap/default.nix diff --git a/pkgs/applications/networking/jnetmap/default.nix b/pkgs/applications/networking/jnetmap/default.nix new file mode 100644 index 000000000000..af94db23c0ac --- /dev/null +++ b/pkgs/applications/networking/jnetmap/default.nix @@ -0,0 +1,33 @@ +{ stdenv, fetchurl, jre, makeWrapper }: + +stdenv.mkDerivation rec { + name = "jnetmap-${version}"; + version = "0.5.4"; + + src = fetchurl { + url = "mirror://sourceforge/project/jnetmap/jNetMap%20${version}/jNetMap-${version}.jar"; + sha256 = "0nxsfa600jhazwbabxmr9j37mhwysp0fyrvczhv3f1smiy8rjanl"; + }; + + buildInputs = [ jre makeWrapper ]; + + unpackPhase = ":"; + + installPhase = '' + mkdir -p "$out/bin" + mkdir -p "$out/lib" + + cp "${src}" "$out/lib/jnetmap.jar" + makeWrapper "${jre}/bin/java" "$out/bin/jnetmap" \ + --add-flags "-jar \"$out/lib/jnetmap.jar\"" + ''; + + meta = with stdenv.lib; { + description = "Graphical network monitoring and documentation tool"; + homepage = "http://www.rakudave.ch/jnetmap/"; + license = licenses.gpl3Plus; + # Upstream supports macOS and Windows too. + platforms = platforms.linux; + maintainers = [ maintainers.bjornfor ]; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 7559303bcba4..7ac0b9ce6e16 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -16086,6 +16086,8 @@ in bitcoin-xt = altcoins.bitcoin-xt; cryptop = altcoins.cryptop; + jnetmap = callPackage ../applications/networking/jnetmap {}; + libbitcoin = callPackage ../tools/misc/libbitcoin/libbitcoin.nix { secp256k1 = secp256k1.override { enableECDH = true; }; }; From d8378602a9902a463b2f4d9740882a63f357f80b Mon Sep 17 00:00:00 2001 From: Kamil Chmielewski Date: Mon, 7 Jan 2019 17:09:21 +0100 Subject: [PATCH 136/247] qtile: 0.12.0 -> 0.13.0 needs Python 3 to use Clock widget: https://github.com/qtile/qtile/issues/1258#issuecomment-451958978 --- .../applications/window-managers/qtile/default.nix | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/pkgs/applications/window-managers/qtile/default.nix b/pkgs/applications/window-managers/qtile/default.nix index be51a5c46bf3..dc78702b03c5 100644 --- a/pkgs/applications/window-managers/qtile/default.nix +++ b/pkgs/applications/window-managers/qtile/default.nix @@ -1,19 +1,19 @@ -{ stdenv, fetchFromGitHub, python27Packages, glib, cairo, pango, pkgconfig, libxcb, xcbutilcursor }: +{ stdenv, fetchFromGitHub, python37Packages, glib, cairo, pango, pkgconfig, libxcb, xcbutilcursor }: -let cairocffi-xcffib = python27Packages.cairocffi.override { +let cairocffi-xcffib = python37Packages.cairocffi.override { withXcffib = true; }; in -python27Packages.buildPythonApplication rec { +python37Packages.buildPythonApplication rec { name = "qtile-${version}"; - version = "0.12.0"; + version = "0.13.0"; src = fetchFromGitHub { owner = "qtile"; repo = "qtile"; rev = "v${version}"; - sha256 = "0ynmmnh12mr3gwgz0j7l2hvm8c0y5gzsw80jszdkp4s5bh1q0nrj"; + sha256 = "1lyclnn8hs6wl4w9v5b4hh2q0pvmsn7cyibpskhbpw0cgv7bvi90"; }; patches = [ @@ -30,9 +30,9 @@ python27Packages.buildPythonApplication rec { ''; nativeBuildInputs = [ pkgconfig ]; - buildInputs = [ glib libxcb cairo pango python27Packages.xcffib ]; + buildInputs = [ glib libxcb cairo pango python37Packages.xcffib ]; - pythonPath = with python27Packages; [ xcffib cairocffi-xcffib trollius ]; + pythonPath = with python37Packages; [ xcffib cairocffi-xcffib ]; postInstall = '' wrapProgram $out/bin/qtile \ From d1fff1e9e819f62a7517511990c50126c59b2d8a Mon Sep 17 00:00:00 2001 From: Piotr Bogdan Date: Sat, 5 Jan 2019 07:47:15 +0000 Subject: [PATCH 137/247] rxvt_unicode: fix build --- pkgs/applications/misc/rxvt_unicode/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/misc/rxvt_unicode/default.nix b/pkgs/applications/misc/rxvt_unicode/default.nix index 57ce1f081801..2ae33a1eaa51 100644 --- a/pkgs/applications/misc/rxvt_unicode/default.nix +++ b/pkgs/applications/misc/rxvt_unicode/default.nix @@ -47,11 +47,11 @@ stdenv.mkDerivation (rec { configureFlags="--with-terminfo=$terminfo/share/terminfo --enable-256-color ${if perlSupport then "--enable-perl" else "--disable-perl"} ${if unicode3Support then "--enable-unicode3" else "--disable-unicode3"}"; export TERMINFO=$terminfo/share/terminfo # without this the terminfo won't be compiled by tic, see man tic NIX_CFLAGS_COMPILE="$NIX_CFLAGS_COMPILE -I${freetype.dev}/include/freetype2" - NIX_LDFLAGS="$NIX_LDFLAGS -lfontconfig -lXrender " + NIX_LDFLAGS="$NIX_LDFLAGS -lfontconfig -lXrender -lpthread " '' # make urxvt find its perl file lib/perl5/site_perl is added to PERL5LIB automatically + stdenv.lib.optionalString perlSupport '' - mkdir -p $(dirname ${perl.libPrefix}) + mkdir -p $out/$(dirname ${perl.libPrefix}) ln -s $out/lib/urxvt $out/${perl.libPrefix} ''; From 75b4b5fc99f0a9cc8274bb449c780a4232538f71 Mon Sep 17 00:00:00 2001 From: WilliButz Date: Mon, 7 Jan 2019 16:59:27 +0100 Subject: [PATCH 138/247] prometheus-dnsmasq-exporter: unstable-2018-05-05 -> 0.1.0 --- .../prometheus/dnsmasq-exporter-deps.nix | 87 ++++++++++++++----- .../prometheus/dnsmasq-exporter.nix | 7 +- 2 files changed, 70 insertions(+), 24 deletions(-) diff --git a/pkgs/servers/monitoring/prometheus/dnsmasq-exporter-deps.nix b/pkgs/servers/monitoring/prometheus/dnsmasq-exporter-deps.nix index 1acf859e81a6..dd3c1b4d4c2d 100644 --- a/pkgs/servers/monitoring/prometheus/dnsmasq-exporter-deps.nix +++ b/pkgs/servers/monitoring/prometheus/dnsmasq-exporter-deps.nix @@ -1,5 +1,23 @@ -# This file was generated by https://github.com/kamilchm/go2nix v1.2.1 +# This file was generated by https://github.com/kamilchm/go2nix v1.3.0 [ + { + goPackagePath = "github.com/alecthomas/template"; + fetch = { + type = "git"; + url = "https://github.com/alecthomas/template"; + rev = "a0175ee3bccc567396460bf5acd36800cb10c49c"; + sha256 = "0qjgvvh26vk1cyfq9fadyhfgdj36f1iapbmr5xp6zqipldz8ffxj"; + }; + } + { + goPackagePath = "github.com/alecthomas/units"; + fetch = { + type = "git"; + url = "https://github.com/alecthomas/units"; + rev = "2efee857e7cfd4f3d0138cc3cbb1b4966962b93a"; + sha256 = "1j65b91qb9sbrml9cpabfrcf07wmgzzghrl7809hjjhrmbzri5bl"; + }; + } { goPackagePath = "github.com/beorn7/perks"; fetch = { @@ -14,8 +32,8 @@ fetch = { type = "git"; url = "https://github.com/golang/protobuf"; - rev = "b4deda0973fb4c70b50d226b1af49f3da59f5265"; - sha256 = "0ya4ha7m20bw048m1159ppqzlvda4x0vdprlbk5sdgmy74h3xcdq"; + rev = "1d3f30b51784bec5aad268e59fd3c2fc1c2fe73f"; + sha256 = "1wx76776z48qd9pjnrydhj1f3k94qlbcj32ak6am7n7w2nda7sjx"; }; } { @@ -23,8 +41,8 @@ fetch = { type = "git"; url = "https://github.com/matttproud/golang_protobuf_extensions"; - rev = "c12348ce28de40eed0136aa2b644d0ee0650e56c"; - sha256 = "1d0c1isd2lk9pnfq2nk0aih356j30k3h1gi2w0ixsivi5csl7jya"; + rev = "c182affec369e30f25d3eb8cd8a478dee585ae7d"; + sha256 = "1xqsf9vpcrd4hp95rl6kgmjvkv1df4aicfw4l5vfcxcwxknfx2xs"; }; } { @@ -32,8 +50,8 @@ fetch = { type = "git"; url = "https://github.com/miekg/dns"; - rev = "9c76f9827e170bfcd354c2cb02a6fd428faf81a6"; - sha256 = "0yym4jr15cqwlppnqfsp92i7p1ir12ys695wffb3in7gnnm0d38n"; + rev = "5beb9624161b94eaf384fed4bd8dc4235e4d80af"; + sha256 = "1p9ypprs467g31v635zjqn1f2rq1y3r6xw47d29ifg9wfmrpmpc7"; }; } { @@ -41,8 +59,8 @@ fetch = { type = "git"; url = "https://github.com/prometheus/client_golang"; - rev = "82f5ff156b29e276022b1a958f7d385870fb9814"; - sha256 = "111j329yrlgvh73dm80gawwxsh9dgjkw74254kyj5c2rfmra7znz"; + rev = "d2ead25884778582e740573999f7b07f47e171b4"; + sha256 = "1zj7x16xw94jw5l3arajwwcr2f06j2a7z87zqbd6a1jjcsbjj3a5"; }; } { @@ -50,8 +68,8 @@ fetch = { type = "git"; url = "https://github.com/prometheus/client_model"; - rev = "99fa1f4be8e564e8a6b613da7fa6f46c9edafc6c"; - sha256 = "19y4ywsivhpxj7ikf2j0gm9k3cmyw37qcbfi78n526jxcc7kw998"; + rev = "5c3871d89910bfb32f5fcab2aa4b9ec68e65a99f"; + sha256 = "04psf81l9fjcwascsys428v03fx4fi894h7fhrj2vvcz723q57k0"; }; } { @@ -59,8 +77,8 @@ fetch = { type = "git"; url = "https://github.com/prometheus/common"; - rev = "d811d2e9bf898806ecfb6ef6296774b13ffc314c"; - sha256 = "0r4067r4ysmljksqw3awcxx5qplqhykahc5igdzgkky7i4bvaik1"; + rev = "2998b132700a7d019ff618c06a234b47c1f3f681"; + sha256 = "131qmx0rs1nz0ci3qzkks4i6fdmr5c69i48h5cngjizlb9xxwir2"; }; } { @@ -68,17 +86,26 @@ fetch = { type = "git"; url = "https://github.com/prometheus/procfs"; - rev = "8b1c2da0d56deffdbb9e48d4414b4e674bd8083e"; - sha256 = "0x128p15h35mgwqxkigfkk1lfrcz9g697ahl8v6xp9kwvcqvjrrf"; + rev = "b1a0a9a36d7453ba0f62578b99712f3a6c5f82d1"; + sha256 = "00jdvxvg9zy6gm5q1zp3j5kdcrrma46kqcm73pz8wpljlhbb9s8g"; }; } { - goPackagePath = "golang.org/x/net"; + goPackagePath = "github.com/sirupsen/logrus"; fetch = { type = "git"; - url = "https://go.googlesource.com/net"; - rev = "640f4622ab692b87c2f3a94265e6f579fe38263d"; - sha256 = "097m4qhcljhp180171j5fjhq4740iirfkkajfd7yrxqhp4s9hljx"; + url = "https://github.com/sirupsen/logrus"; + rev = "eef6b768ab01a0598a0a6db97bad2a37d31df1d1"; + sha256 = "0h3fy7i08s9wm1nrv3164g68dwdy0493px6xhyms6y3vfnbq2n6m"; + }; + } + { + goPackagePath = "golang.org/x/crypto"; + fetch = { + type = "git"; + url = "https://go.googlesource.com/crypto"; + rev = "ff983b9c42bc9fbf91556e191cc8efb585c16908"; + sha256 = "1hpr06kzn8jnn3gvzp0p9zn4fz4l9h69f7x66idx142w4xdlaanz"; }; } { @@ -86,8 +113,26 @@ fetch = { type = "git"; url = "https://go.googlesource.com/sync"; - rev = "1d60e4601c6fd243af51cc01ddf169918a5407ca"; - sha256 = "046jlanz2lkxq1r57x9bl6s4cvfqaic6p2xybsj8mq1120jv4rs6"; + rev = "37e7f081c4d4c64e13b10787722085407fe5d15f"; + sha256 = "1bb0mw6ckb1k7z8v3iil2qlqwfj408fvvp8m1cik2b46p7snyjhm"; + }; + } + { + goPackagePath = "golang.org/x/sys"; + fetch = { + type = "git"; + url = "https://go.googlesource.com/sys"; + rev = "cb59ee3660675d463e86971646692ea3e470021c"; + sha256 = "0xnhdhwg6xca41m1204yg3qc7ki6l5xzx5fkq25gsmf5sz6ylsnl"; + }; + } + { + goPackagePath = "gopkg.in/alecthomas/kingpin.v2"; + fetch = { + type = "git"; + url = "https://gopkg.in/alecthomas/kingpin.v2"; + rev = "947dcec5ba9c011838740e680966fd7087a71d0d"; + sha256 = "0mndnv3hdngr3bxp7yxfd47cas4prv98sqw534mx7vp38gd88n5r"; }; } ] diff --git a/pkgs/servers/monitoring/prometheus/dnsmasq-exporter.nix b/pkgs/servers/monitoring/prometheus/dnsmasq-exporter.nix index bcfc82adf478..e43488bbaaeb 100644 --- a/pkgs/servers/monitoring/prometheus/dnsmasq-exporter.nix +++ b/pkgs/servers/monitoring/prometheus/dnsmasq-exporter.nix @@ -1,15 +1,16 @@ { stdenv, buildGoPackage, fetchFromGitHub }: buildGoPackage rec { - name = "dnsmasq_exporter-unstable-2018-05-05"; + name = "dnsmasq_exporter-${version}"; + version = "0.1.0"; goPackagePath = "github.com/google/dnsmasq_exporter"; src = fetchFromGitHub { owner = "google"; repo = "dnsmasq_exporter"; - sha256 = "1kzq4h7z28xadx425nbgxadk62yiz6279d300fyiyi83hwq0ay8c"; - rev = "e1f281b435bbefbb2d17fc57c051ede0ab973c59"; + sha256 = "0pl4jkp0kssplv32wbg8yk06x9c2hidilpix32hdvk287l3ys201"; + rev = "v${version}"; }; goDeps = ./dnsmasq-exporter-deps.nix; From 6a6cd025fccd1b2280ae571b2ef780619a747fbf Mon Sep 17 00:00:00 2001 From: Katharina Fey Date: Mon, 7 Jan 2019 19:01:23 +0100 Subject: [PATCH 139/247] void: init at 1.1.5 --- pkgs/tools/misc/void/default.nix | 26 ++++++++++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 28 insertions(+) create mode 100644 pkgs/tools/misc/void/default.nix diff --git a/pkgs/tools/misc/void/default.nix b/pkgs/tools/misc/void/default.nix new file mode 100644 index 000000000000..32747ccbf440 --- /dev/null +++ b/pkgs/tools/misc/void/default.nix @@ -0,0 +1,26 @@ +{ stdenv, fetchFromGitHub, rustPlatform }: + +rustPlatform.buildRustPackage rec { + name = "void-${version}"; + version = "1.1.5"; + + src = fetchFromGitHub { + owner = "spacejam"; + repo = "void"; + rev = "${version}"; + sha256 = "08vazw4rszqscjz988k89z28skyj3grm81bm5iwknxxagmrb20fz"; + }; + + # The tests are long-running and not that useful + checkPhase = null; + + cargoSha256 = "1rq947s82icl7gdkjynjwz426bpmd96dip2dv2y7p8rg7yz29x0m"; + + meta = with stdenv.lib; { + description = "Terminal-based personal organizer"; + homepage = https://github.com/spacejam/void; + license = licenses.mit; + maintainers = with maintainers; [ spacekookie ]; + platforms = platforms.all; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 7ac0b9ce6e16..27a3740f95ed 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -6012,6 +6012,8 @@ in vobsub2srt = callPackage ../tools/cd-dvd/vobsub2srt { }; + void = callPackage ../tools/misc/void { }; + volume_key = callPackage ../development/libraries/volume-key { }; vorbisgain = callPackage ../tools/misc/vorbisgain { }; From 2743be6e3f28f9d7aea59a4b0ba6b1b083fa2e56 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 10:35:09 -0800 Subject: [PATCH 140/247] pdf2djvu: 0.9.11 -> 0.9.12 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/pdf2djvu/versions --- pkgs/tools/typesetting/pdf2djvu/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/typesetting/pdf2djvu/default.nix b/pkgs/tools/typesetting/pdf2djvu/default.nix index fa582d4594cb..ce9056af0e42 100644 --- a/pkgs/tools/typesetting/pdf2djvu/default.nix +++ b/pkgs/tools/typesetting/pdf2djvu/default.nix @@ -1,12 +1,12 @@ { stdenv, fetchurl, pkgconfig, djvulibre, poppler, fontconfig, libjpeg }: stdenv.mkDerivation rec { - version = "0.9.11"; + version = "0.9.12"; name = "pdf2djvu-${version}"; src = fetchurl { url = "https://github.com/jwilk/pdf2djvu/releases/download/${version}/${name}.tar.xz"; - sha256 = "1hscpm5lsqmiv1niwnq999wmcvj9wlajw8wd3diaaxcq207kvsvd"; + sha256 = "10wfgnrkhdzscax5j57wdgqhiw7rwmsfsq945rb6n25ql6d9vyh3"; }; nativeBuildInputs = [ pkgconfig ]; From 3a096b46168a389d4a7873b0920b126bb93460e4 Mon Sep 17 00:00:00 2001 From: Nathan van Doorn Date: Mon, 7 Jan 2019 18:38:22 +0000 Subject: [PATCH 141/247] metamath: 0.168 -> 0.171 --- pkgs/development/interpreters/metamath/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/development/interpreters/metamath/default.nix b/pkgs/development/interpreters/metamath/default.nix index 2fb1ccb24bc4..fedb9f59f80f 100644 --- a/pkgs/development/interpreters/metamath/default.nix +++ b/pkgs/development/interpreters/metamath/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { name = "metamath-${version}"; - version = "0.168"; + version = "0.171"; buildInputs = [ autoreconfHook ]; @@ -13,8 +13,8 @@ stdenv.mkDerivation rec { src = fetchFromGitHub { owner = "Taneb"; repo = "metamath"; - rev = "542bfd5e53d8ce026ce5d29da9e7069ec807f5e0"; - sha256 = "07ssgqh9ipiw1bf60snmjaxngln1an1h9q0vgszadc94wzw06zi4"; + rev = "1c622a844fbdee43f13a629c73d8b33ff7fc4e44"; + sha256 = "0bkz75saddlwinyqwmxx89nilaar401j63kgqfqiak8iw2nk3wln"; }; meta = with stdenv.lib; { From a4f51746f826349c631910b1a67d7556a9a0bf30 Mon Sep 17 00:00:00 2001 From: Joachim Fasting Date: Mon, 7 Jan 2019 19:16:54 +0100 Subject: [PATCH 142/247] Revert "openafs: fix build against linux_hardened" This reverts commit 4bb0a719cf8f6b89ec89cd902a511a7e043d9a0d. Can be reveted once randstruct actually works --- pkgs/servers/openafs/1.6/module.nix | 3 --- pkgs/servers/openafs/1.8/module.nix | 3 --- 2 files changed, 6 deletions(-) diff --git a/pkgs/servers/openafs/1.6/module.nix b/pkgs/servers/openafs/1.6/module.nix index 374046cfdb61..c133161cf576 100644 --- a/pkgs/servers/openafs/1.6/module.nix +++ b/pkgs/servers/openafs/1.6/module.nix @@ -15,9 +15,6 @@ in stdenv.mkDerivation rec { hardeningDisable = [ "pic" ]; - # The RANDSTRUCT gcc plugin rewrites structs using designated initializers - NIX_CFLAGS_COMPILE = [ "-Wno-error=designated-init" ]; - configureFlags = [ "--with-linux-kernel-build=${kernelBuildDir}" "--sysconfdir=/etc" diff --git a/pkgs/servers/openafs/1.8/module.nix b/pkgs/servers/openafs/1.8/module.nix index c60b96f1693e..958fcd578c2b 100644 --- a/pkgs/servers/openafs/1.8/module.nix +++ b/pkgs/servers/openafs/1.8/module.nix @@ -18,9 +18,6 @@ in stdenv.mkDerivation rec { hardeningDisable = [ "pic" ]; - # The RANDSTRUCT gcc plugin rewrites structs using designated initializers - NIX_CFLAGS_COMPILE = [ "-Wno-error=designated-init" ]; - configureFlags = [ "--with-linux-kernel-build=${kernelBuildDir}" "--sysconfdir=/etc" From 865f7a14b49786a2ed55c5ecf3e994f6a3099e8c Mon Sep 17 00:00:00 2001 From: Joachim Fasting Date: Mon, 7 Jan 2019 19:18:13 +0100 Subject: [PATCH 143/247] Revert "Revert "linux-hardened: Disable GCC_PLUGIN_RANDSTRUCT"" This reverts commit c68e8b05f005381ac1caf51bb28282b70242b77b. RANDSTRUCT currently fails to work with out-of-tree modules, as evinced by https://github.com/NixOS/nixpkgs/commit/c68e8b05f005381ac1caf51bb28282b70242b77b#commitcomment-31850284 and https://github.com/NixOS/nixpkgs/issues/53522. Specifically, loading out-of-tree modules results in modsym version mismatches, as in spl: version magic '4.20.0 SMP mod_unload modversions RANDSTRUCT_PLUGIN from the issue above. A working hypothesis is that the randstruct seed is not carried over when building out-of-tree modules but more investigation is needed here. Closes https://github.com/NixOS/nixpkgs/issues/53522 --- pkgs/os-specific/linux/kernel/hardened-config.nix | 5 ----- 1 file changed, 5 deletions(-) diff --git a/pkgs/os-specific/linux/kernel/hardened-config.nix b/pkgs/os-specific/linux/kernel/hardened-config.nix index ed540a9e7518..4fadd4476548 100644 --- a/pkgs/os-specific/linux/kernel/hardened-config.nix +++ b/pkgs/os-specific/linux/kernel/hardened-config.nix @@ -125,11 +125,6 @@ ${optionalString (versionAtLeast version "4.20") '' GCC_PLUGIN_STACKLEAK y # A port of the PaX stackleak plugin ''} -${optionalString (versionAtLeast version "4.13") '' - GCC_PLUGIN_RANDSTRUCT y # A port of the PaX randstruct plugin - GCC_PLUGIN_RANDSTRUCT_PERFORMANCE y -''} - # Disable various dangerous settings ACPI_CUSTOM_METHOD n # Allows writing directly to physical memory PROC_KCORE n # Exposes kernel text image layout From 8fac37db006ad1e6c051525e65becd54ad011923 Mon Sep 17 00:00:00 2001 From: Robin Gloster Date: Mon, 7 Jan 2019 20:08:15 +0100 Subject: [PATCH 144/247] gitlab: 11.6.0 -> 11.6.3 --- .../version-management/gitlab/data.json | 20 +++++++++---------- .../gitlab/rubyEnv-ce/Gemfile | 2 +- .../gitlab/rubyEnv-ce/Gemfile.lock | 4 ++-- .../gitlab/rubyEnv-ce/gemset.nix | 6 ++++-- .../gitlab/rubyEnv-ee/Gemfile | 2 +- .../gitlab/rubyEnv-ee/Gemfile.lock | 4 ++-- .../gitlab/rubyEnv-ee/gemset.nix | 6 ++++-- 7 files changed, 24 insertions(+), 20 deletions(-) diff --git a/pkgs/applications/version-management/gitlab/data.json b/pkgs/applications/version-management/gitlab/data.json index 37925b3be10f..7504adcbf4f1 100644 --- a/pkgs/applications/version-management/gitlab/data.json +++ b/pkgs/applications/version-management/gitlab/data.json @@ -1,12 +1,12 @@ { "ce": { - "version": "11.6.0", - "repo_hash": "1b3vn1s07c5j6cl9javdlixv3583vx54ag4rlalrj0z35a0zggkd", - "deb_hash": "00lb3c41agcdqrdad77dw361y65kwzrfmjzcplzmpi3ign8wa2h4", - "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ce/packages/debian/stretch/gitlab-ce_11.6.0-ce.0_amd64.deb/download.deb", + "version": "11.6.3", + "repo_hash": "0bvmccfybgzbd85bdvwikmxh4asj5ly8yhxazhaqkwmnymnxa4k2", + "deb_hash": "11blasjkdi85sivfjb0s6cssh1p13fyxhqimcx1dsvb5q5v0m6as", + "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ce/packages/debian/stretch/gitlab-ce_11.6.3-ce.0_amd64.deb/download.deb", "owner": "gitlab-org", "repo": "gitlab-ce", - "rev": "v11.6.0", + "rev": "v11.6.3", "passthru": { "GITALY_SERVER_VERSION": "1.7.1", "GITLAB_PAGES_VERSION": "1.3.1", @@ -15,13 +15,13 @@ } }, "ee": { - "version": "11.6.0", - "repo_hash": "0zaif61qf7y0r7sh3vdmxacvzw8hcgj8xhj69iy0jcxf508wbysh", - "deb_hash": "1ksdnfzfdb2qcvq60dhhxi5iab8bjvddfnjbs6zaw0m0ymdrnsxb", - "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ee/packages/debian/stretch/gitlab-ee_11.6.0-ee.0_amd64.deb/download.deb", + "version": "11.6.3", + "repo_hash": "0j31h5i74j94f7qlcxk6pvwaxqqcjbm02lnqslnfs3zs8k2bmd35", + "deb_hash": "1ivap84d5xphxfmzff8i663pf6kw5rh2zxv1bcwn62p8dccr7hcc", + "deb_url": "https://packages.gitlab.com/gitlab/gitlab-ee/packages/debian/stretch/gitlab-ee_11.6.3-ee.0_amd64.deb/download.deb", "owner": "gitlab-org", "repo": "gitlab-ee", - "rev": "v11.6.0-ee", + "rev": "v11.6.3-ee", "passthru": { "GITALY_SERVER_VERSION": "1.7.1", "GITLAB_PAGES_VERSION": "1.3.1", diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile b/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile index 3d25195f9650..a7f5deadb866 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile @@ -181,7 +181,7 @@ gem 'acts-as-taggable-on', '~> 5.0' gem 'sidekiq', '~> 5.2.1' gem 'sidekiq-cron', '~> 0.6.0' gem 'redis-namespace', '~> 1.6.0' -gem 'gitlab-sidekiq-fetcher', '~> 0.1.0', require: 'sidekiq-reliable-fetch' +gem 'gitlab-sidekiq-fetcher', '~> 0.4.0', require: 'sidekiq-reliable-fetch' # Cron Parser gem 'rufus-scheduler', '~> 3.4' diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile.lock b/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile.lock index 7bc8fdbcb09b..96bbfa7d4e1d 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile.lock +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ce/Gemfile.lock @@ -280,7 +280,7 @@ GEM gitlab-default_value_for (3.1.1) activerecord (>= 3.2.0, < 6.0) gitlab-markup (1.6.5) - gitlab-sidekiq-fetcher (0.1.0) + gitlab-sidekiq-fetcher (0.4.0) sidekiq (~> 5) gitlab-styles (2.4.1) rubocop (~> 0.54.0) @@ -1011,7 +1011,7 @@ DEPENDENCIES github-markup (~> 1.7.0) gitlab-default_value_for (~> 3.1.1) gitlab-markup (~> 1.6.5) - gitlab-sidekiq-fetcher (~> 0.1.0) + gitlab-sidekiq-fetcher (~> 0.4.0) gitlab-styles (~> 2.4) gitlab_omniauth-ldap (~> 2.0.4) gon (~> 6.2) diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ce/gemset.nix b/pkgs/applications/version-management/gitlab/rubyEnv-ce/gemset.nix index fc40ae8cb27c..abaecb432245 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ce/gemset.nix +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ce/gemset.nix @@ -1117,12 +1117,14 @@ }; gitlab-sidekiq-fetcher = { dependencies = ["sidekiq"]; + groups = ["default"]; + platforms = []; source = { remotes = ["https://rubygems.org"]; - sha256 = "08bwgagrdryva8vlwiiwfa3v60w9k13nknmjjfadrkn68a4ihk2a"; + sha256 = "1xaag97iclmiay8fx7dkiws8dsws2gi6l0axq4yljq5g7xm78qjr"; type = "gem"; }; - version = "0.1.0"; + version = "0.4.0"; }; gitlab-styles = { dependencies = ["rubocop" "rubocop-gitlab-security" "rubocop-rspec"]; diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile b/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile index 3e8c5112a39b..8258596ed6bd 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile @@ -191,7 +191,7 @@ gem 'acts-as-taggable-on', '~> 5.0' gem 'sidekiq', '~> 5.2.1' gem 'sidekiq-cron', '~> 0.6.0' gem 'redis-namespace', '~> 1.6.0' -gem 'gitlab-sidekiq-fetcher', '~> 0.1.0', require: 'sidekiq-reliable-fetch' +gem 'gitlab-sidekiq-fetcher', '~> 0.4.0', require: 'sidekiq-reliable-fetch' # Cron Parser gem 'rufus-scheduler', '~> 3.4' diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile.lock b/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile.lock index f6ced99bece5..d7c27460c604 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile.lock +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ee/Gemfile.lock @@ -305,7 +305,7 @@ GEM activerecord (>= 3.2.0, < 6.0) gitlab-license (1.0.0) gitlab-markup (1.6.5) - gitlab-sidekiq-fetcher (0.1.0) + gitlab-sidekiq-fetcher (0.4.0) sidekiq (~> 5) gitlab-styles (2.4.1) rubocop (~> 0.54.0) @@ -1046,7 +1046,7 @@ DEPENDENCIES gitlab-default_value_for (~> 3.1.1) gitlab-license (~> 1.0) gitlab-markup (~> 1.6.5) - gitlab-sidekiq-fetcher (~> 0.1.0) + gitlab-sidekiq-fetcher (~> 0.4.0) gitlab-styles (~> 2.4) gitlab_omniauth-ldap (~> 2.0.4) gon (~> 6.2) diff --git a/pkgs/applications/version-management/gitlab/rubyEnv-ee/gemset.nix b/pkgs/applications/version-management/gitlab/rubyEnv-ee/gemset.nix index f85528bb52e7..bd6c9d29a0aa 100644 --- a/pkgs/applications/version-management/gitlab/rubyEnv-ee/gemset.nix +++ b/pkgs/applications/version-management/gitlab/rubyEnv-ee/gemset.nix @@ -1213,12 +1213,14 @@ }; gitlab-sidekiq-fetcher = { dependencies = ["sidekiq"]; + groups = ["default"]; + platforms = []; source = { remotes = ["https://rubygems.org"]; - sha256 = "08bwgagrdryva8vlwiiwfa3v60w9k13nknmjjfadrkn68a4ihk2a"; + sha256 = "1xaag97iclmiay8fx7dkiws8dsws2gi6l0axq4yljq5g7xm78qjr"; type = "gem"; }; - version = "0.1.0"; + version = "0.4.0"; }; gitlab-styles = { dependencies = ["rubocop" "rubocop-gitlab-security" "rubocop-rspec"]; From 66fe6f10fc79bd431ec38f64c7fe98af96f16944 Mon Sep 17 00:00:00 2001 From: Katharina Fey Date: Mon, 7 Jan 2019 21:21:22 +0100 Subject: [PATCH 145/247] void: fixing license and changing test setup --- pkgs/tools/misc/void/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/misc/void/default.nix b/pkgs/tools/misc/void/default.nix index 32747ccbf440..cba897431511 100644 --- a/pkgs/tools/misc/void/default.nix +++ b/pkgs/tools/misc/void/default.nix @@ -12,14 +12,14 @@ rustPlatform.buildRustPackage rec { }; # The tests are long-running and not that useful - checkPhase = null; + doCheck = false; cargoSha256 = "1rq947s82icl7gdkjynjwz426bpmd96dip2dv2y7p8rg7yz29x0m"; meta = with stdenv.lib; { description = "Terminal-based personal organizer"; homepage = https://github.com/spacejam/void; - license = licenses.mit; + license = licenses.gpl3; maintainers = with maintainers; [ spacekookie ]; platforms = platforms.all; }; From b60f8fc6e2a0af1f5e1af3c7e0c9aaa9230a858d Mon Sep 17 00:00:00 2001 From: Franz Pletz Date: Thu, 22 Nov 2018 08:50:59 +0100 Subject: [PATCH 146/247] atlassian modules: don't chown home recursively This can take a long time and should not be necassary anyway. --- nixos/modules/services/web-apps/atlassian/confluence.nix | 2 +- nixos/modules/services/web-apps/atlassian/crowd.nix | 2 +- nixos/modules/services/web-apps/atlassian/jira.nix | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nixos/modules/services/web-apps/atlassian/confluence.nix b/nixos/modules/services/web-apps/atlassian/confluence.nix index f896d92fd6fc..b71887fcc6ee 100644 --- a/nixos/modules/services/web-apps/atlassian/confluence.nix +++ b/nixos/modules/services/web-apps/atlassian/confluence.nix @@ -166,7 +166,7 @@ in ln -sf ${cfg.home}/{logs,work,temp,server.xml} /run/confluence ln -sf ${cfg.home} /run/confluence/home - chown -R ${cfg.user} ${cfg.home} + chown ${cfg.user} ${cfg.home} sed -e 's,port="8090",port="${toString cfg.listenPort}" address="${cfg.listenAddress}",' \ '' + (lib.optionalString cfg.proxy.enable '' diff --git a/nixos/modules/services/web-apps/atlassian/crowd.nix b/nixos/modules/services/web-apps/atlassian/crowd.nix index b6cb9f3b7c41..1fb619da93eb 100644 --- a/nixos/modules/services/web-apps/atlassian/crowd.nix +++ b/nixos/modules/services/web-apps/atlassian/crowd.nix @@ -132,7 +132,7 @@ in mkdir -p /run/atlassian-crowd ln -sf ${cfg.home}/{database,work,server.xml} /run/atlassian-crowd - chown -R ${cfg.user}:${cfg.group} ${cfg.home} + chown ${cfg.user}:${cfg.group} ${cfg.home} sed -e 's,port="8095",port="${toString cfg.listenPort}" address="${cfg.listenAddress}",' \ '' + (lib.optionalString cfg.proxy.enable '' diff --git a/nixos/modules/services/web-apps/atlassian/jira.nix b/nixos/modules/services/web-apps/atlassian/jira.nix index f5ec0a5f31b8..dba970c612bc 100644 --- a/nixos/modules/services/web-apps/atlassian/jira.nix +++ b/nixos/modules/services/web-apps/atlassian/jira.nix @@ -171,7 +171,7 @@ in ln -sf ${cfg.home}/{logs,work,temp,server.xml} /run/atlassian-jira ln -sf ${cfg.home} /run/atlassian-jira/home - chown -R ${cfg.user} ${cfg.home} + chown ${cfg.user} ${cfg.home} sed -e 's,port="8080",port="${toString cfg.listenPort}" address="${cfg.listenAddress}",' \ '' + (lib.optionalString cfg.proxy.enable '' From ece39b063807bc3a582bb5234e6cc05b250a0446 Mon Sep 17 00:00:00 2001 From: Franz Pletz Date: Mon, 22 Oct 2018 17:49:58 +0200 Subject: [PATCH 147/247] atlassian-confluence: 6.11.1 -> 6.12.0 --- pkgs/servers/atlassian/confluence.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/atlassian/confluence.nix b/pkgs/servers/atlassian/confluence.nix index 617ae3ee1d10..181a3fd90305 100644 --- a/pkgs/servers/atlassian/confluence.nix +++ b/pkgs/servers/atlassian/confluence.nix @@ -5,11 +5,11 @@ stdenv.mkDerivation rec { name = "atlassian-confluence-${version}"; - version = "6.11.1"; + version = "6.12.0"; src = fetchurl { url = "https://www.atlassian.com/software/confluence/downloads/binary/${name}.tar.gz"; - sha256 = "0sp1ggllvxdz0pf409yyil1x9dah1jyqspknfzgivkmwhcqj7brr"; + sha256 = "0ip3j6id0554ynrs1rcxck4cs8j2hgxkv1rha9xhqikm89bdml7h"; }; phases = [ "unpackPhase" "buildPhase" "installPhase" ]; From 847bd6e2d43a1c8013798f3677888f6642f025b0 Mon Sep 17 00:00:00 2001 From: Franz Pletz Date: Wed, 21 Nov 2018 02:22:30 +0100 Subject: [PATCH 148/247] atlassian-confluence: 6.12.0 -> 6.12.2 --- pkgs/servers/atlassian/confluence.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/atlassian/confluence.nix b/pkgs/servers/atlassian/confluence.nix index 181a3fd90305..bed9319c7c26 100644 --- a/pkgs/servers/atlassian/confluence.nix +++ b/pkgs/servers/atlassian/confluence.nix @@ -5,11 +5,11 @@ stdenv.mkDerivation rec { name = "atlassian-confluence-${version}"; - version = "6.12.0"; + version = "6.12.2"; src = fetchurl { url = "https://www.atlassian.com/software/confluence/downloads/binary/${name}.tar.gz"; - sha256 = "0ip3j6id0554ynrs1rcxck4cs8j2hgxkv1rha9xhqikm89bdml7h"; + sha256 = "043ng5q1rawmajgvdjzgch8baack8rxsi3qyln79gb00cy3sv9y0"; }; phases = [ "unpackPhase" "buildPhase" "installPhase" ]; From 4a38287887e169805ab88233edc559224deffe8b Mon Sep 17 00:00:00 2001 From: Robin Gloster Date: Mon, 7 Jan 2019 19:12:40 +0100 Subject: [PATCH 149/247] atlassian-confluence: 6.12.2 -> 6.13.0 --- pkgs/servers/atlassian/confluence.nix | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/pkgs/servers/atlassian/confluence.nix b/pkgs/servers/atlassian/confluence.nix index bed9319c7c26..db80682d8993 100644 --- a/pkgs/servers/atlassian/confluence.nix +++ b/pkgs/servers/atlassian/confluence.nix @@ -5,15 +5,13 @@ stdenv.mkDerivation rec { name = "atlassian-confluence-${version}"; - version = "6.12.2"; + version = "6.13.0"; src = fetchurl { url = "https://www.atlassian.com/software/confluence/downloads/binary/${name}.tar.gz"; - sha256 = "043ng5q1rawmajgvdjzgch8baack8rxsi3qyln79gb00cy3sv9y0"; + sha256 = "1ckpcb0dq964gwdls5q71260r0i8zxgx8nzv8y4sizr37jvpi8mw"; }; - phases = [ "unpackPhase" "buildPhase" "installPhase" ]; - buildPhase = '' echo "confluence.home=/run/confluence/home" > confluence/WEB-INF/classes/confluence-init.properties mv conf/server.xml conf/server.xml.dist From 89d24aca9358e07d50f2301800b35a2a0818d36c Mon Sep 17 00:00:00 2001 From: Robin Gloster Date: Mon, 7 Jan 2019 19:13:21 +0100 Subject: [PATCH 150/247] atlassian-crowd: 3.2.5 -> 3.3.3 --- nixos/modules/services/web-apps/atlassian/crowd.nix | 3 ++- pkgs/servers/atlassian/crowd.nix | 7 ++++--- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/nixos/modules/services/web-apps/atlassian/crowd.nix b/nixos/modules/services/web-apps/atlassian/crowd.nix index 1fb619da93eb..9f48d1e16a44 100644 --- a/nixos/modules/services/web-apps/atlassian/crowd.nix +++ b/nixos/modules/services/web-apps/atlassian/crowd.nix @@ -130,9 +130,10 @@ in mkdir -p ${cfg.home}/{logs,database,work} mkdir -p /run/atlassian-crowd - ln -sf ${cfg.home}/{database,work,server.xml} /run/atlassian-crowd + ln -sf ${cfg.home}/{database,logs,work,server.xml} /run/atlassian-crowd chown ${cfg.user}:${cfg.group} ${cfg.home} + chown ${cfg.user}:${cfg.group} ${cfg.home}/{logs,database,work} sed -e 's,port="8095",port="${toString cfg.listenPort}" address="${cfg.listenAddress}",' \ '' + (lib.optionalString cfg.proxy.enable '' diff --git a/pkgs/servers/atlassian/crowd.nix b/pkgs/servers/atlassian/crowd.nix index 4ad0388e8db4..6bde7e187d78 100644 --- a/pkgs/servers/atlassian/crowd.nix +++ b/pkgs/servers/atlassian/crowd.nix @@ -3,11 +3,11 @@ stdenv.mkDerivation rec { name = "atlassian-crowd-${version}"; - version = "3.2.5"; + version = "3.3.3"; src = fetchurl { url = "https://www.atlassian.com/software/crowd/downloads/binary/${name}.tar.gz"; - sha256 = "1h8kxh89d2wm0hkgrzx5dnnfy8sbhpgisgdwn3srhb4js8h4qil6"; + sha256 = "1mdjxr4p56rlsgnv78bfnlwmniv8hv3hdxnfvqzsmvv88s3z7c66"; }; phases = [ "unpackPhase" "buildPhase" "installPhase" "fixupPhase" ]; @@ -16,7 +16,8 @@ stdenv.mkDerivation rec { mv apache-tomcat/conf/server.xml apache-tomcat/conf/server.xml.dist ln -s /run/atlassian-crowd/server.xml apache-tomcat/conf/server.xml - rm -rf apache-tomcat/work + rm -rf apache-tomcat/{logs,work} + ln -s /run/atlassian-crowd/logs apache-tomcat/logs ln -s /run/atlassian-crowd/work apache-tomcat/work ln -s /run/atlassian-crowd/database database From 6f02b8672645ec02967799237b37d3a3825bffc6 Mon Sep 17 00:00:00 2001 From: Robin Gloster Date: Mon, 7 Jan 2019 19:13:39 +0100 Subject: [PATCH 151/247] atlassian-jira: 7.12.3 -> 7.13.0 --- pkgs/servers/atlassian/jira.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/atlassian/jira.nix b/pkgs/servers/atlassian/jira.nix index b9c5951b0b29..8e11ef6163cc 100644 --- a/pkgs/servers/atlassian/jira.nix +++ b/pkgs/servers/atlassian/jira.nix @@ -5,11 +5,11 @@ stdenv.mkDerivation rec { name = "atlassian-jira-${version}"; - version = "7.12.3"; + version = "7.13.0"; src = fetchurl { url = "https://downloads.atlassian.com/software/jira/downloads/atlassian-jira-software-${version}.tar.gz"; - sha256 = "0gna0pr8g78pahm4ci14742w40f0nwfn4hpm3iwbsiw2w6vziahv"; + sha256 = "1dra5h8lgqwzhs95br8x34c5pcrkgrkmpyhiq9vbayf1aarjxfnq"; }; phases = [ "unpackPhase" "buildPhase" "installPhase" "fixupPhase" ]; From 1dcc1f250b03e6b961e737c4c97926887acad060 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 13:48:55 -0800 Subject: [PATCH 152/247] nmon: 16g -> 16h Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/nmon/versions --- pkgs/os-specific/linux/nmon/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/os-specific/linux/nmon/default.nix b/pkgs/os-specific/linux/nmon/default.nix index ae6abeb1f56f..21579f47a0a5 100644 --- a/pkgs/os-specific/linux/nmon/default.nix +++ b/pkgs/os-specific/linux/nmon/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "nmon-${version}"; - version = "16g"; + version = "16h"; src = fetchurl { url = "mirror://sourceforge/nmon/lmon${version}.c"; - sha256 = "127n8xvmg7byp42sm924mdr7hd3bsfsxpryzahl0cfsh7dlxv0ns"; + sha256 = "1snfi6wsnpwhpzi33yhqvrrmxmfw6ilcxjkgjx3jkk0453y2sfz2"; }; buildInputs = [ ncurses ]; From 40d29cb4bd49a22a4c77419a721bf29153567015 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 03:18:09 -0800 Subject: [PATCH 153/247] polar-bookshelf: 1.5.1 -> 1.7.0 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/polar-bookshelf/versions --- pkgs/applications/misc/polar-bookshelf/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/misc/polar-bookshelf/default.nix b/pkgs/applications/misc/polar-bookshelf/default.nix index bcff0db65ab1..2088f59adfac 100644 --- a/pkgs/applications/misc/polar-bookshelf/default.nix +++ b/pkgs/applications/misc/polar-bookshelf/default.nix @@ -10,12 +10,12 @@ stdenv.mkDerivation rec { name = "polar-bookshelf-${version}"; - version = "1.5.1"; + version = "1.7.0"; # fetching a .deb because there's no easy way to package this Electron app src = fetchurl { url = "https://github.com/burtonator/polar-bookshelf/releases/download/v${version}/polar-bookshelf-${version}-amd64.deb"; - sha256 = "1nnbybrzk1ms83490gbw5gakfim0j2c8gp83d9iaqwl4590qgwlg"; + sha256 = "14xpjm5bw1jl74shnpn5pm3p1hdpf6c3wl9pkjvz90g7w8wjc942"; }; buildInputs = [ From 59667421a14622e5f0c09ab7c7addb2699926950 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 02:42:13 -0800 Subject: [PATCH 154/247] pgcli: 2.0.1 -> 2.0.2 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/pgcli/versions --- pkgs/development/tools/database/pgcli/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/tools/database/pgcli/default.nix b/pkgs/development/tools/database/pgcli/default.nix index f9e60e3e492c..f2346480776c 100644 --- a/pkgs/development/tools/database/pgcli/default.nix +++ b/pkgs/development/tools/database/pgcli/default.nix @@ -2,7 +2,7 @@ python3Packages.buildPythonApplication rec { pname = "pgcli"; - version = "2.0.1"; + version = "2.0.2"; # Python 2 won't have prompt_toolkit 2.x.x # See: https://github.com/NixOS/nixpkgs/blob/f49e2ad3657dede09dc998a4a98fd5033fb52243/pkgs/top-level/python-packages.nix#L3408 @@ -10,7 +10,7 @@ python3Packages.buildPythonApplication rec { src = python3Packages.fetchPypi { inherit pname version; - sha256 = "149naq3gp1n922vag7vixs0hd114bpbmbmv70k4kzc1q7jz748l2"; + sha256 = "1p4j2dbcfxd3kz86qi519jkqjx1mg5wdgn1gxdjx3lk1vpsd7x04"; }; propagatedBuildInputs = with python3Packages; [ From f05d8f31ec944eb5b07a9dbf80b606372e47cb21 Mon Sep 17 00:00:00 2001 From: Matthew Bauer Date: Thu, 20 Dec 2018 16:17:05 -0600 Subject: [PATCH 155/247] make-disk-image: use filterSource instead of cleanSource cleanSource does not appear to work correctly in this case. The path does not get coerced to a string, resulting in a dangling symlink produced in channel.nix. Not sure why, but this seems to fix it. Fixes #51025. /cc @elvishjericco --- nixos/lib/make-disk-image.nix | 2 +- nixos/modules/installer/cd-dvd/channel.nix | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/nixos/lib/make-disk-image.nix b/nixos/lib/make-disk-image.nix index bf32a36895c5..6fec322f9095 100644 --- a/nixos/lib/make-disk-image.nix +++ b/nixos/lib/make-disk-image.nix @@ -84,7 +84,7 @@ let format' = format; in let # FIXME: merge with channel.nix / make-channel.nix. channelSources = pkgs.runCommand "nixos-${config.system.nixos.version}" {} '' mkdir -p $out - cp -prd ${nixpkgs} $out/nixos + cp -prd ${nixpkgs.outPath} $out/nixos chmod -R u+w $out/nixos if [ ! -e $out/nixos/nixpkgs ]; then ln -s . $out/nixos/nixpkgs diff --git a/nixos/modules/installer/cd-dvd/channel.nix b/nixos/modules/installer/cd-dvd/channel.nix index 01cfe8a02e10..e946c4abc576 100644 --- a/nixos/modules/installer/cd-dvd/channel.nix +++ b/nixos/modules/installer/cd-dvd/channel.nix @@ -16,7 +16,7 @@ let { } '' mkdir -p $out - cp -prd ${nixpkgs} $out/nixos + cp -prd ${nixpkgs.outPath} $out/nixos chmod -R u+w $out/nixos if [ ! -e $out/nixos/nixpkgs ]; then ln -s . $out/nixos/nixpkgs From 0ca68bddcfce1029b6cde12e6237f610829773a4 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Sun, 6 Jan 2019 17:51:04 -0800 Subject: [PATCH 156/247] python37Packages.xdis: 3.8.8 -> 3.8.9 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/python3.7-xdis/versions --- pkgs/development/python-modules/xdis/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/xdis/default.nix b/pkgs/development/python-modules/xdis/default.nix index 39eb962c0405..b9400530b05b 100644 --- a/pkgs/development/python-modules/xdis/default.nix +++ b/pkgs/development/python-modules/xdis/default.nix @@ -8,11 +8,11 @@ buildPythonPackage rec { pname = "xdis"; - version = "3.8.8"; + version = "3.8.9"; src = fetchPypi { inherit pname version; - sha256 = "4d212df8a85ab55a35f6ad71b2c29818d903c3e6a95e31eb26d5f3fc66a4e015"; + sha256 = "1q2dg3hnsmmpjcc7lzjf5nd041mpbwa2bq3dgr4p6wv65vncny9v"; }; checkInputs = [ pytest ]; From f0fbc76d3ee02c0e5241b3b189d69d2d87e3e017 Mon Sep 17 00:00:00 2001 From: worldofpeace Date: Sun, 6 Jan 2019 21:01:51 -0500 Subject: [PATCH 157/247] pythonPackages.xdis: enable tests --- pkgs/development/python-modules/xdis/default.nix | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/xdis/default.nix b/pkgs/development/python-modules/xdis/default.nix index b9400530b05b..df0ad509e291 100644 --- a/pkgs/development/python-modules/xdis/default.nix +++ b/pkgs/development/python-modules/xdis/default.nix @@ -18,8 +18,9 @@ buildPythonPackage rec { checkInputs = [ pytest ]; propagatedBuildInputs = [ six click ]; - # newest release moves to pytest (tests not packaged with release) - doCheck = false; + checkPhase = '' + make check + ''; meta = with stdenv.lib; { description = "Python cross-version byte-code disassembler and marshal routines"; From 75e12828b657605144955856809e178755015631 Mon Sep 17 00:00:00 2001 From: Vladyslav Mykhailichenko Date: Tue, 8 Jan 2019 01:13:27 +0200 Subject: [PATCH 158/247] alacritty: 0.2.4 -> 0.2.5 --- pkgs/applications/misc/alacritty/default.nix | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/pkgs/applications/misc/alacritty/default.nix b/pkgs/applications/misc/alacritty/default.nix index 5d1e43769b7e..fd4180a8dcbf 100644 --- a/pkgs/applications/misc/alacritty/default.nix +++ b/pkgs/applications/misc/alacritty/default.nix @@ -43,16 +43,16 @@ let ]; in buildRustPackage rec { name = "alacritty-${version}"; - version = "0.2.4"; + version = "0.2.5"; src = fetchFromGitHub { owner = "jwilm"; repo = "alacritty"; rev = "v${version}"; - sha256 = "1mf0x8dc196qf08lqpm0n4a5954cx9qfb09dq8ab7mp3xnyrnqzx"; + sha256 = "17802fgfkp80872wr6qkjhs3gdjjw2cibigcifqnzcfzwabp07iv"; }; - cargoSha256 = "0p3bygvmpmy09h7972nhmma51lxp8q91cdlaw3s6p35i79hq3bmp"; + cargoSha256 = "0adw5zwxy1x9laa1fx11j2bhhs2w7c9n0xnjwxw8vchqi4xwqvy5"; nativeBuildInputs = [ cmake @@ -71,9 +71,6 @@ in buildRustPackage rec { outputs = [ "out" "terminfo" ]; - # https://github.com/NixOS/nixpkgs/issues/49693 - doCheck = !stdenv.isDarwin; - postPatch = '' substituteInPlace copypasta/src/x11.rs \ --replace Command::new\(\"xclip\"\) Command::new\(\"${xclip}/bin/xclip\"\) From 381e1ff25248e411affcf2af5fb9878e6fcad016 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 12:27:06 -0800 Subject: [PATCH 159/247] moe: 1.9 -> 1.10 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/moe/versions --- pkgs/applications/editors/moe/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/editors/moe/default.nix b/pkgs/applications/editors/moe/default.nix index 64843b2f0706..3f7eba73ca49 100644 --- a/pkgs/applications/editors/moe/default.nix +++ b/pkgs/applications/editors/moe/default.nix @@ -6,11 +6,11 @@ with stdenv.lib; stdenv.mkDerivation rec { name = "moe-${version}"; - version = "1.9"; + version = "1.10"; src = fetchurl { url = "mirror://gnu/moe/${name}.tar.lz"; - sha256 = "1wsfzy0iia0c89wnx1ilzw54wqcmlp2nz8mkpvc393z0zagrx48q"; + sha256 = "0fymywdiy9xqppcmvgs7mf7d3gfrky3jp5jkxs2l3v93asml9zcc"; }; prePatch = '' From bb874163fdf8873a03623afc2eb1031b21f44087 Mon Sep 17 00:00:00 2001 From: Matthew Bauer Date: Mon, 7 Jan 2019 19:37:55 -0600 Subject: [PATCH 160/247] cups: use v2.2.6 on darwin This is the last version known to build. Fixes #53609. --- pkgs/misc/cups/default.nix | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/pkgs/misc/cups/default.nix b/pkgs/misc/cups/default.nix index e3649bb821b3..f691444c1afb 100644 --- a/pkgs/misc/cups/default.nix +++ b/pkgs/misc/cups/default.nix @@ -10,13 +10,17 @@ with stdenv.lib; stdenv.mkDerivation rec { name = "cups-${version}"; - version = "2.2.10"; + + # After 2.2.6, CUPS requires headers only available in macOS 10.12+ + version = if stdenv.isDarwin then "2.2.6" else "2.2.10"; passthru = { inherit version; }; src = fetchurl { url = "https://github.com/apple/cups/releases/download/v${version}/cups-${version}-source.tar.gz"; - sha256 = "1fq52aw1mini3ld2czv5gg37wbbvh4n7yc7wzzxvbs3zpfrv5j3p"; + sha256 = if version == "2.2.6" + then "16qn41b84xz6khrr2pa2wdwlqxr29rrrkjfi618gbgdkq9w5ff20" + else "1fq52aw1mini3ld2czv5gg37wbbvh4n7yc7wzzxvbs3zpfrv5j3p"; }; outputs = [ "out" "lib" "dev" "man" ]; From 6b8c09bffca82c1373c38586cac2032088f0e5bf Mon Sep 17 00:00:00 2001 From: Jim Fowler Date: Mon, 7 Jan 2019 21:06:09 -0500 Subject: [PATCH 161/247] more idiomatic nix --- pkgs/tools/security/hashcash/default.nix | 26 ++++++++++++++---------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/pkgs/tools/security/hashcash/default.nix b/pkgs/tools/security/hashcash/default.nix index 337837f3116d..a28822ecd951 100644 --- a/pkgs/tools/security/hashcash/default.nix +++ b/pkgs/tools/security/hashcash/default.nix @@ -1,23 +1,27 @@ { stdenv, fetchurl, openssl }: stdenv.mkDerivation rec { - name = "hashcash-${version}"; + pname = "hashcash"; version = "1.22"; - + buildInputs = [ openssl ]; src = fetchurl { - url = "http://www.hashcash.org/source/hashcash-1.22.tgz"; - sha256 = "15kqaimwb2y8wvzpn73021bvay9mz1gqqfc40gk4hj6f84nz34h1"; + url = "http://www.hashcash.org/source/hashcash-${version}.tgz"; + sha256 = "15kqaimwb2y8wvzpn73021bvay9mz1gqqfc40gk4hj6f84nz34h1"; }; + + makeFlags = [ + "generic-openssl" + "LIBCRYPTO=-lcrypto" + ]; - makeFlags = "generic-openssl LIBCRYPTO=-lcrypto"; - - installPhase = '' - install -D -m 0755 --target $out/bin hashcash sha1 - install -D -m 0444 hashcash.1 $out/share/man/man1/hashcash.1 - ''; - + installFlags = [ + "INSTALL_PATH=${placeholder "out"}/bin" + "MAN_INSTALL_PATH=${placeholder "out"}/share/man/man1" + "DOC_INSTALL_PATH=${placeholder "out"}/share/doc/hashcash-$(version)" + ]; + meta = with stdenv.lib; { description = "Proof-of-work algorithm used as spam and denial-of-service counter measure"; homepage = http://hashcash.org; From 76d8df7b325ab52aecfe68ce839667252e233c3a Mon Sep 17 00:00:00 2001 From: Jan Tojnar Date: Tue, 8 Jan 2019 03:51:22 +0100 Subject: [PATCH 162/247] hashcat: clean up with placeholder --- pkgs/tools/security/hashcat/default.nix | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/pkgs/tools/security/hashcat/default.nix b/pkgs/tools/security/hashcat/default.nix index 68866a8cad4f..8316adb5a1e2 100644 --- a/pkgs/tools/security/hashcat/default.nix +++ b/pkgs/tools/security/hashcat/default.nix @@ -14,18 +14,12 @@ stdenv.mkDerivation rec { buildInputs = [ opencl-headers xxHash ]; makeFlags = [ + "PREFIX=${placeholder "out"}" "OPENCL_HEADERS_KHRONOS=${opencl-headers}/include" "COMPTIME=1337" "VERSION_TAG=${version}" ]; - # $out is not known until the build has started. - configurePhase = '' - runHook preConfigure - makeFlags="$makeFlags PREFIX=$out" - runHook postConfigure - ''; - postFixup = '' wrapProgram $out/bin/hashcat --prefix LD_LIBRARY_PATH : ${ocl-icd}/lib ''; From 04beae0979007f5a5b99e64fc945211824a91572 Mon Sep 17 00:00:00 2001 From: Dylan Simon Date: Mon, 7 Jan 2019 21:39:15 -0500 Subject: [PATCH 163/247] stdenv: allow custom stdenv to take crossOverlays --- pkgs/stdenv/custom/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/stdenv/custom/default.nix b/pkgs/stdenv/custom/default.nix index e86face95195..4c7380118f7d 100644 --- a/pkgs/stdenv/custom/default.nix +++ b/pkgs/stdenv/custom/default.nix @@ -1,5 +1,5 @@ { lib -, localSystem, crossSystem, config, overlays +, localSystem, crossSystem, config, overlays, crossOverlays ? [] }: assert crossSystem == localSystem; From e39ff06b16324025ecfe50e70b890e2286ff4338 Mon Sep 17 00:00:00 2001 From: Kevin Rauscher Date: Mon, 7 Jan 2019 11:21:30 +0100 Subject: [PATCH 164/247] mopidy-iris: 3.31.7 -> 3.31.8 --- pkgs/applications/audio/mopidy/iris.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/audio/mopidy/iris.nix b/pkgs/applications/audio/mopidy/iris.nix index 211e5db43c73..dc129f945fdd 100644 --- a/pkgs/applications/audio/mopidy/iris.nix +++ b/pkgs/applications/audio/mopidy/iris.nix @@ -2,11 +2,11 @@ pythonPackages.buildPythonApplication rec { pname = "Mopidy-Iris"; - version = "3.31.7"; + version = "3.31.8"; src = pythonPackages.fetchPypi { inherit pname version; - sha256 = "0z3lqjncczlddfwdsfqninh2i8dz0kis8lhqfpdzdxhhmxlgmi20"; + sha256 = "16rrvby6rdiz53minfqsbgmymnc4agi2iwp0pf5ahsaxp1xq0cqy"; }; propagatedBuildInputs = [ From f312f66b4d57941a3d090bbca0ba26fe1035ceec Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 19:12:54 -0800 Subject: [PATCH 165/247] kwalletcli: 3.01 -> 3.02 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/kwalletcli/versions --- pkgs/tools/security/kwalletcli/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/security/kwalletcli/default.nix b/pkgs/tools/security/kwalletcli/default.nix index 2831ffd31414..52e8ab8cf570 100644 --- a/pkgs/tools/security/kwalletcli/default.nix +++ b/pkgs/tools/security/kwalletcli/default.nix @@ -7,14 +7,14 @@ let pname = "kwalletcli"; - version = "3.01"; + version = "3.02"; in mkDerivation rec { name = "${pname}-${version}"; src = fetchurl { url = "https://www.mirbsd.org/MirOS/dist/hosted/kwalletcli/${name}.tar.gz"; - sha256 = "03jd7m868dc5dkmm7wbr6dj1h1kp4cb2x8ay8jwvlcbnf7srjzcs"; + sha256 = "05njayi07996ljfl8a6frlk2s60grk5w27f0f445nmvd5n0bzgpn"; }; postPatch = '' From b10f43c1f12ade8ef92c808e596fb7b6ef7dcb2e Mon Sep 17 00:00:00 2001 From: Jack Kelly Date: Tue, 8 Jan 2019 16:30:17 +1100 Subject: [PATCH 166/247] hpc-coveralls: jailbreak for GHC 8.6 --- pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix | 1 + 1 file changed, 1 insertion(+) diff --git a/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix b/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix index daa12f711b52..6190dd9ab931 100644 --- a/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix +++ b/pkgs/development/haskell-modules/configuration-ghc-8.6.x.nix @@ -48,6 +48,7 @@ self: super: { cereal = dontCheck super.cereal; data-clist = doJailbreak super.data-clist; # won't cope with QuickCheck 2.12.x Diff = dontCheck super.Diff; + hpc-coveralls = doJailbreak super.hpc-coveralls; # https://github.com/guillaume-nargeot/hpc-coveralls/issues/82 http-api-data = doJailbreak super.http-api-data; persistent-sqlite = dontCheck super.persistent-sqlite; psqueues = dontCheck super.psqueues; # won't cope with QuickCheck 2.12.x From 4bfdc717c70cb9c05c8647025a6f12f5a88654d0 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Sun, 6 Jan 2019 18:12:45 -0800 Subject: [PATCH 167/247] python37Packages.xarray: 0.11.0 -> 0.11.2 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/python3.7-xarray/versions --- pkgs/development/python-modules/xarray/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/xarray/default.nix b/pkgs/development/python-modules/xarray/default.nix index 094c71bea4b1..c055618b2e60 100644 --- a/pkgs/development/python-modules/xarray/default.nix +++ b/pkgs/development/python-modules/xarray/default.nix @@ -9,11 +9,11 @@ buildPythonPackage rec { pname = "xarray"; - version = "0.11.0"; + version = "0.11.2"; src = fetchPypi { inherit pname version; - sha256 = "06580fg3kgnwci070ivgqzfilmldjk5lxb10jbbfb87wrjx68sb3"; + sha256 = "1cnghx1xcgdq675abmrys311vspmzgjgiji4wh8iyw194qalfwdg"; }; checkInputs = [ pytest ]; From 51230853c80a9097e141a7a53aa1cd60d6b5e358 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 23:02:32 -0800 Subject: [PATCH 168/247] cutelyst: 2.5.1 -> 2.6.0 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/cutelyst/versions --- pkgs/development/libraries/cutelyst/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/cutelyst/default.nix b/pkgs/development/libraries/cutelyst/default.nix index f4a10452eef8..4bc5d7227e17 100644 --- a/pkgs/development/libraries/cutelyst/default.nix +++ b/pkgs/development/libraries/cutelyst/default.nix @@ -4,13 +4,13 @@ stdenv.mkDerivation rec { name = "cutelyst-${version}"; - version = "2.5.1"; + version = "2.6.0"; src = fetchFromGitHub { owner = "cutelyst"; repo = "cutelyst"; rev = "v${version}"; - sha256 = "0iamavr5gj213c8knrh2mynhn8wcrv83x6s46jq93x93kc5127ks"; + sha256 = "092qzam3inmj3kvn1s0ygwf3jcikifzkk5hv02b5ym18nqz1025d"; }; nativeBuildInputs = [ cmake pkgconfig makeWrapper ]; From 8b12798dbdaf6676f02ac408904cded8fa5312ab Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 22:32:31 -0800 Subject: [PATCH 169/247] elementary-icon-theme: 5.0.1 -> 5.0.2 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/elementary-icon-theme/versions --- pkgs/data/icons/elementary-icon-theme/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/data/icons/elementary-icon-theme/default.nix b/pkgs/data/icons/elementary-icon-theme/default.nix index 4c3beaaef2b0..68ece44116e1 100644 --- a/pkgs/data/icons/elementary-icon-theme/default.nix +++ b/pkgs/data/icons/elementary-icon-theme/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "elementary-icon-theme-${version}"; - version = "5.0.1"; + version = "5.0.2"; src = fetchFromGitHub { owner = "elementary"; repo = "icons"; rev = version; - sha256 = "1rw924b3ixfdff368dpv4vgsykwncmrvj9a6yfss0cf236xnvr9b"; + sha256 = "12j582f0kggv2lp935r75xg7q26zpl0f05s11xcs4qxazhj1ly2r"; }; nativeBuildInputs = [ meson ninja python3 gtk3 ]; From 07a7a358780ffa7ebe02554d763e833944521dc5 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 17:01:04 -0800 Subject: [PATCH 170/247] zafiro-icons: 0.8 -> 0.8.1 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/zafiro-icons/versions --- pkgs/data/icons/zafiro-icons/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/data/icons/zafiro-icons/default.nix b/pkgs/data/icons/zafiro-icons/default.nix index c75f1c5ea0fe..76c829c90c6a 100644 --- a/pkgs/data/icons/zafiro-icons/default.nix +++ b/pkgs/data/icons/zafiro-icons/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "zafiro-icons"; - version = "0.8"; + version = "0.8.1"; src = fetchFromGitHub { owner = "zayronxio"; repo = pname; rev = "v${version}"; - sha256 = "05g94ln3xfp8adw09fckjaml1dpl1simphyhd407lx2mmwkgw6rh"; + sha256 = "121fpg74vra8kfvgxi3i7p09qxhck45kv270x6cv5dq1fp2hdm8k"; }; nativeBuildInputs = [ gtk3 ]; From 47a8b13efa502f883034b2e23579d010e840d911 Mon Sep 17 00:00:00 2001 From: Izorkin Date: Mon, 24 Dec 2018 14:16:22 +0300 Subject: [PATCH 171/247] datadog-agent: 6.4.2 -> 6.8.3 --- nixos/modules/services/monitoring/datadog-agent.nix | 2 +- pkgs/tools/networking/dd-agent/6.nix | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/nixos/modules/services/monitoring/datadog-agent.nix b/nixos/modules/services/monitoring/datadog-agent.nix index 5434fe99347d..a4d29d45bacf 100644 --- a/nixos/modules/services/monitoring/datadog-agent.nix +++ b/nixos/modules/services/monitoring/datadog-agent.nix @@ -186,7 +186,7 @@ in { type = types.attrs; default = { init_config = {}; - instances = [ { use-mount = "no"; } ]; + instances = [ { use_mount = "false"; } ]; }; }; diff --git a/pkgs/tools/networking/dd-agent/6.nix b/pkgs/tools/networking/dd-agent/6.nix index b26e915e6909..a4a3cc86f97b 100644 --- a/pkgs/tools/networking/dd-agent/6.nix +++ b/pkgs/tools/networking/dd-agent/6.nix @@ -6,14 +6,14 @@ let in buildGoPackage rec { name = "datadog-agent-${version}"; - version = "6.4.2"; + version = "6.8.3"; owner = "DataDog"; repo = "datadog-agent"; src = fetchFromGitHub { inherit owner repo; - rev = "155fddb3547919bd54530dfdb250e0cb2defae7d"; - sha256 = "0l7ic0p2h27x386k1gzzm20af2s06cpalmqz0h0c5zq4wszmw5zy"; + rev = "${version}"; + sha256 = "18kk3f10pbcxplshxzbblga6bqlkk5mgy536yy27j463l4xps92q"; }; subPackages = [ @@ -57,7 +57,7 @@ in buildGoPackage rec { # into standard paths. postInstall = '' mkdir -p $bin/${python.sitePackages} $bin/share/datadog-agent - cp -R $src/cmd/agent/dist/{conf.d,trace-agent.conf} $bin/share/datadog-agent + cp -R $src/cmd/agent/dist/conf.d $bin/share/datadog-agent cp -R $src/cmd/agent/dist/{checks,utils,config.py} $bin/${python.sitePackages} cp -R $src/pkg/status/dist/templates $bin/share/datadog-agent From 48541ab6b933aefaea80144bea9d7d1260f16dc1 Mon Sep 17 00:00:00 2001 From: Alex Branham Date: Fri, 4 Jan 2019 13:13:01 -0600 Subject: [PATCH 172/247] R: update CRAN and BIOC package sets Closes https://github.com/NixOS/nixpkgs/pull/53414. --- pkgs/development/r-modules/bioc-packages.nix | 3274 +++++++++--------- pkgs/development/r-modules/cran-packages.nix | 746 ++-- 2 files changed, 2064 insertions(+), 1956 deletions(-) diff --git a/pkgs/development/r-modules/bioc-packages.nix b/pkgs/development/r-modules/bioc-packages.nix index 05715a99922b..360a0fc89d50 100644 --- a/pkgs/development/r-modules/bioc-packages.nix +++ b/pkgs/development/r-modules/bioc-packages.nix @@ -6,1642 +6,1642 @@ { self, derive }: let derive2 = derive { biocVersion = "3.8"; }; in with self; { - ABAEnrichment = derive2 { name="ABAEnrichment"; version="1.11.7"; sha256="0gzv8nphchispdrlmbx28ps6k7g8ylqldf7p25pimjba700ydjdd"; depends=[ABAData data_table GOfuncR gplots gtools Rcpp]; }; - ABSSeq = derive2 { name="ABSSeq"; version="1.35.2"; sha256="0x86y1j8h9ad4vyzadb4xngzfihz73jcy2qrn5d2bpigv3m3rar5"; depends=[limma locfit]; }; - ABarray = derive2 { name="ABarray"; version="1.49.0"; sha256="1rnsk81lhybj612rb2b886al567m58ax77kng4ip43ivzd3yssil"; depends=[Biobase multtest]; }; - ACE = derive2 { name="ACE"; version="0.99.10"; sha256="1a2mkw04fdvdfdva0gwsh0d7xkg49gi7dhsxz8ban9g1kn1g5w6z"; depends=[Biobase ggplot2 QDNAseq]; }; - ACME = derive2 { name="ACME"; version="2.37.0"; sha256="1ihpzaxhpdg8lvd30g9xhjhsil34s7w8w06cy04dp7zv117yda55"; depends=[Biobase BiocGenerics]; }; - ADaCGH2 = derive2 { name="ADaCGH2"; version="2.21.1"; sha256="0ph0glq1ngmhgh8vv1zdm0m6flfkp576fk7qdyb3prc5rc730yxr"; depends=[aCGH bit cluster DNAcopy ff ffbase GLAD snapCGH tilingArray waveslim]; }; - AGDEX = derive2 { name="AGDEX"; version="1.29.0"; sha256="0bidzm02g5f4ivnrymg9m7kpmjlg93zv1alpcsjx6ssbaix42r33"; depends=[Biobase GSEABase]; }; - AIMS = derive2 { name="AIMS"; version="1.13.0"; sha256="15ch50fw03q66d7x0asri8ff5xr82r8rxd46i80zij1fg27avkxa"; depends=[Biobase e1071]; }; - ALDEx2 = derive2 { name="ALDEx2"; version="1.13.0"; sha256="01c4bjbybivjqq1hl9dpmndn3mfk595yyjjkljcxbza6wax99rd0"; depends=[BiocParallel GenomicRanges IRanges multtest S4Vectors SummarizedExperiment]; }; - AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.7.0"; sha256="12al115s0h3pylk8dv2d9kn241vqhdqww6y44md0ywwcpfrbkdvi"; depends=[]; }; - ANF = derive2 { name="ANF"; version="1.3.0"; sha256="0386q8bx4r00i12l79k0yi17f9kj1iw5fg3gg760pjspp67v810s"; depends=[Biobase igraph MASS RColorBrewer survival]; }; - ARRmNormalization = derive2 { name="ARRmNormalization"; version="1.21.0"; sha256="1ipryh3wagasfz1kzhdja7mp6sfpl8xf01pi0nh2mwyah7k76h5n"; depends=[ARRmData]; }; - ASAFE = derive2 { name="ASAFE"; version="1.7.0"; sha256="0p6q9zpfqf7cz1lb0cm75ddhhcrdf90dpblrxhn8hkh5wgn3yp0m"; depends=[]; }; - ASEB = derive2 { name="ASEB"; version="1.25.0"; sha256="00wwdg07zgqbaparqail1pnffx5r63007rq65shlxda483f3ywr1"; depends=[]; }; - ASGSCA = derive2 { name="ASGSCA"; version="1.15.0"; sha256="0f9mih8bhv4ibwqni7z94n4v3kz5cm2paqdp5c0y7hvg9i836gyl"; depends=[MASS Matrix]; }; - ASICS = derive2 { name="ASICS"; version="1.1.1"; sha256="18arka0aj4y82ngdx458ilnvxrv45bfjj6dz1wz28frsz7bzhry2"; depends=[BiocParallel ggplot2 gridExtra plyr quadprog ropls speaq SummarizedExperiment zoo]; }; - ASSET = derive2 { name="ASSET"; version="1.99.0"; sha256="1c43xdlgqpmq192cxfbpsq6f767zlcmpm7am539673yr6fc8ql7i"; depends=[MASS msm rmeta]; }; - ASSIGN = derive2 { name="ASSIGN"; version="1.17.4"; sha256="01ly4vislijmaa6vfs4nsawhf3jv7xb5jaa7iaizl7gpm7jnv7bp"; depends=[ggplot2 gplots msm Rlab sva yaml]; }; - ASpli = derive2 { name="ASpli"; version="1.7.2"; sha256="1x30c1srl6sgjpl2milsc06ix5b8ds3kgz2h5wzg9wl4jsfswml3"; depends=[AnnotationDbi BiocGenerics BiocStyle edgeR GenomicAlignments GenomicFeatures GenomicRanges Gviz IRanges Rsamtools S4Vectors]; }; - ATACseqQC = derive2 { name="ATACseqQC"; version="1.5.7"; sha256="06aq30lj97xpxxm5f46qlnl2pik44hh4jr7wcbsvjyf3xx99k3za"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges KernSmooth limma motifStack preseqR randomForest Rsamtools rtracklayer S4Vectors]; }; - AUCell = derive2 { name="AUCell"; version="1.3.6"; sha256="1i88w2jkydspgiw6vdpi1bspajr1y8jwmlxakydm7ww8azib4cwl"; depends=[data_table GSEABase mixtools R_utils shiny SummarizedExperiment]; }; - AffiXcan = derive2 { name="AffiXcan"; version="0.99.15"; sha256="0d5y1s2d30rkwmnr206xjf9rdzn099kirh9pxn0qddjhxl6n6d6c"; depends=[BiocParallel MultiAssayExperiment SummarizedExperiment]; }; - AffyCompatible = derive2 { name="AffyCompatible"; version="1.41.0"; sha256="1gxk7kggb29hhfqz2a1g6yqy8mbg0x7gvajnnqgamdggylg7zz32"; depends=[Biostrings RCurl XML]; }; - AffyExpress = derive2 { name="AffyExpress"; version="1.47.0"; sha256="1ph5vgm6hxifdyg8v3vgcqwm7k1fh4d3jnf10i4p7x4gi00xycan"; depends=[affy limma]; }; - AffyRNADegradation = derive2 { name="AffyRNADegradation"; version="1.27.0"; sha256="17m0sn1rb6485lvrpn677z3y540pc93ykbyjg1plrl3qby6nxc5q"; depends=[affy]; }; - AgiMicroRna = derive2 { name="AgiMicroRna"; version="2.31.0"; sha256="1hxvi9hdx8shikljwbh60k4ylir2hdibkccqd5wr4hb08spnam4j"; depends=[affy affycoretools Biobase limma preprocessCore]; }; - AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.19.1"; sha256="14wh237bkzkczvbsqfv4fsgd1plc7nn2p77a6gcb7pgwz1lbq9is"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; }; - AnalysisPageServer = derive2 { name="AnalysisPageServer"; version="1.15.3"; sha256="1xq8cp8yhjnvrr7wp16zi24qjrwchx3l95w4302qh5hfngr3c8xn"; depends=[Biobase graph log4r rjson]; }; - Anaquin = derive2 { name="Anaquin"; version="2.5.0"; sha256="1cqrm7pmirdd23dw8lvrdjfkjp6rgx15s8h88jbilcv7qajg32jc"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; }; - AneuFinder = derive2 { name="AneuFinder"; version="1.9.1"; sha256="0grk4npv8lkf71s9nacmz29g87f7avrfsyb7lpljpg8ndq9cddx3"; depends=[AneuFinderData bamsignals Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust ReorderCluster reshape2 Rsamtools S4Vectors]; }; - AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.43.1"; sha256="150mxlr5fcid4vnv8gh0imr9y9lzgyxrmvzmah4l8kg7r5rllm6k"; depends=[Biobase BiocGenerics DBI IRanges RSQLite S4Vectors]; }; - AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.5.2"; sha256="12lkv4dg25r5p77s84xzyh3aw8pybcdrkvqf21n8xv41gxpycdkq"; depends=[GenomicRanges lazyeval]; }; - AnnotationForge = derive2 { name="AnnotationForge"; version="1.23.4"; sha256="1q0j4nn6hb9h22cnqdgqb89710j86kiayyaf98n47pcdyb96024d"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; }; - AnnotationFuncs = derive2 { name="AnnotationFuncs"; version="1.31.0"; sha256="1sf2afh9s94k1j9xx7csv7k1cah52s8ks7bhjr13m5c2dad3df1f"; depends=[AnnotationDbi DBI]; }; - AnnotationHub = derive2 { name="AnnotationHub"; version="2.13.10"; sha256="087nk0wmkl3k7i00v9lbxq44gzj7dnyjahbhrq3zjx6qmg4l8dia"; depends=[AnnotationDbi BiocGenerics BiocManager curl httr interactiveDisplayBase RSQLite S4Vectors yaml]; }; - AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.11.14"; sha256="0056p06iyw81pzyy52ydgzibqin84xrmsn5jyaa9a6qs3agm62h6"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite OrganismDbi rBiopaxParser RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; }; - ArrayExpress = derive2 { name="ArrayExpress"; version="1.41.1"; sha256="0x5fvbp959x0pczb8qmy70npdx6p8km5aq6jbfmna5d5l8azd11q"; depends=[Biobase limma oligo XML]; }; - ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.31.0"; sha256="16j2a1qyhykzyqggfwaxvp4ay6l9ckimd4djh1qdp3ayqaign04r"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops DESeq edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; }; - ArrayTV = derive2 { name="ArrayTV"; version="1.19.0"; sha256="1swim5w679hskgwfdm9fbfdwhlra7wp4fgsl38vmainayna90xw9"; depends=[DNAcopy foreach IRanges oligoClasses S4Vectors]; }; - ArrayTools = derive2 { name="ArrayTools"; version="1.41.0"; sha256="1pkv72pkiqxjb0f642p7gdc0gfr7xg9vc96awi149a5z71bbykli"; depends=[affy Biobase limma xtable]; }; - AssessORF = derive2 { name="AssessORF"; version="0.99.21"; sha256="1k2b3psllayv8rwgc7jhhyr73apd51wbwgfhn1lawfvpn2k07gqr"; depends=[Biostrings DECIPHER GenomicRanges IRanges]; }; - BAC = derive2 { name="BAC"; version="1.41.0"; sha256="0jk4drgs8w1fvarkhm4sbkm9ls6vh67vja9f2f29p4n0ykgf06y2"; depends=[]; }; - BADER = derive2 { name="BADER"; version="1.19.0"; sha256="1y2lw5f6l32q3p3bral7bz2h57fvd7mpj00q4ds6l3y8j8grp3vf"; depends=[]; }; - BAGS = derive2 { name="BAGS"; version="2.21.2"; sha256="14h103ycmxwpa02binhla0ys5fls2whdgjqj4g40pv96nj5kpwav"; depends=[Biobase breastCancerVDX]; }; - BASiCS = derive2 { name="BASiCS"; version="1.3.24"; sha256="0rxvwpnfvw3nbr8rbrm64hzxx1vzq7rq9jaq20x1nrkkx46gj5s7"; depends=[BiocGenerics coda data_table ggplot2 KernSmooth MASS matrixStats Rcpp RcppArmadillo S4Vectors scran SingleCellExperiment SummarizedExperiment testthat]; }; - BBCAnalyzer = derive2 { name="BBCAnalyzer"; version="1.11.1"; sha256="1gzivdxz02d27pkad6h6k0n1damph0vncslx70s3h6ypcb3g731j"; depends=[Biostrings GenomicRanges IRanges Rsamtools SummarizedExperiment VariantAnnotation]; }; - BCRANK = derive2 { name="BCRANK"; version="1.43.0"; sha256="06082ki14mb4xrbx32lpi7q06bsnmjsc08ggx0si0fxdbf0584r5"; depends=[Biostrings]; }; - BEARscc = derive2 { name="BEARscc"; version="1.1.1"; sha256="180r40a5f7fmck4jly7d4qrjpyb1xqgp8w6aasvx7qfd9vwqbfbx"; depends=[data_table ggplot2 SingleCellExperiment]; }; - BEAT = derive2 { name="BEAT"; version="1.19.0"; sha256="1c3csghkdbqmaj36bg75fnx626rp2myykwc4hpxlij1sy8a9pjra"; depends=[Biostrings BSgenome GenomicRanges ShortRead]; }; - BEclear = derive2 { name="BEclear"; version="1.13.11"; sha256="1c7bgnpj9wx839dhal4rlfamaxngqxdq2pm3paykqf2cjg278d37"; depends=[BiocParallel data_table futile_logger Matrix Rdpack]; }; - BGmix = derive2 { name="BGmix"; version="1.41.0"; sha256="1v6rpn322g4qp3q3hisvi419nnslzpfqdp37bdc1spmsh88inb1j"; depends=[KernSmooth]; }; - BHC = derive2 { name="BHC"; version="1.33.0"; sha256="18jpic1xk5gnxfw7r4hw0591lmrcncv412qd1q08l2nqw0a24895"; depends=[]; }; - BLMA = derive2 { name="BLMA"; version="1.5.0"; sha256="1cpy2dx1da1bn0wc43fwva2akq473ww4nz241dq5xfrk2hwwkz91"; depends=[Biobase graph GSA limma PADOG ROntoTools]; }; - BPRMeth = derive2 { name="BPRMeth"; version="1.7.14"; sha256="0gbklnxs0g236f839yq9p3x8yacgv4248yyp1fgazr6q9gcgqqdf"; depends=[assertthat BiocStyle cowplot data_table doParallel e1071 earth foreach GenomicRanges ggplot2 IRanges kernlab magrittr MASS matrixcalc mvtnorm randomForest Rcpp RcppArmadillo S4Vectors truncnorm]; }; - BRAIN = derive2 { name="BRAIN"; version="1.27.1"; sha256="04an1yqsfwkpwr31l4l21p09yr3jbdm4v7m89vg4q0rvlmha31ss"; depends=[Biostrings lattice PolynomF]; }; - BSgenome = derive2 { name="BSgenome"; version="1.49.5"; sha256="18z80kskhgmhar2njmpxba5fg4d6fz651n3bc4lvfxpvn3j2nh9f"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools rtracklayer S4Vectors XVector]; }; - BUMHMM = derive2 { name="BUMHMM"; version="1.5.0"; sha256="0qs117jr903zyr55xql7793nr8scyqhfn9acnw4d29im2jwfhclq"; depends=[Biostrings devtools gtools IRanges stringi SummarizedExperiment]; }; - BUS = derive2 { name="BUS"; version="1.37.0"; sha256="0rd0d1wm65q1x821l74y96w48dbqdlbd8gzz04fwz2lbpp4x6645"; depends=[infotheo minet]; }; - BUScorrect = derive2 { name="BUScorrect"; version="0.99.13"; sha256="1cbmr2xq1246cypjkf0l05h077bbrhigdhxx6fqkvzrgixw742r3"; depends=[gplots SummarizedExperiment]; }; - BaalChIP = derive2 { name="BaalChIP"; version="1.7.0"; sha256="18jvr700mqfqalby53jhjskz2wrfbyl3x6bgx28yxzzg0hk7d897"; depends=[coda doBy doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges reshape2 Rsamtools scales]; }; - BadRegionFinder = derive2 { name="BadRegionFinder"; version="1.9.1"; sha256="07m2lj91nk88rjjlqgrqvfwdmvvhsk406bq7wbd3a18hawljrcr6"; depends=[biomaRt GenomicRanges Rsamtools S4Vectors VariantAnnotation]; }; - BaseSpaceR = derive2 { name="BaseSpaceR"; version="1.25.1"; sha256="0636123345m2hgip2l7wpbppkav6nryskq3r8sdby09yw3xf8yny"; depends=[RCurl RJSONIO]; }; - Basic4Cseq = derive2 { name="Basic4Cseq"; version="1.17.0"; sha256="0ynfj4x0hkjxxza8v85kda2a5rrmwzjh1am3ffnv1mvpi3dnb95l"; depends=[Biostrings BSgenome_Ecoli_NCBI_20080805 caTools GenomicAlignments GenomicRanges RCircos]; }; - BasicSTARRseq = derive2 { name="BasicSTARRseq"; version="1.9.0"; sha256="074zndzd7dbz31khkn73a3jqfyacl56dd8b82zq5lykirw647zp4"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges S4Vectors]; }; - BatchQC = derive2 { name="BatchQC"; version="1.9.2"; sha256="0cg9ymwq08a3jxzpzwqgazz98868swp4ijiaz0h1msp8v30bqydd"; depends=[corpcor d3heatmap ggvis gplots knitr limma Matrix matrixStats MCMCpack moments pander reshape2 rmarkdown shiny sva]; }; - BayesKnockdown = derive2 { name="BayesKnockdown"; version="1.7.0"; sha256="0ikq8bk4viw9kj55cci37cdicbmyq9p5fa0vxw0bsa9ichj47cl5"; depends=[Biobase]; }; - BayesPeak = derive2 { name="BayesPeak"; version="1.33.0"; sha256="0grhyp7i834sj1j2kavpk2ydy0970gjcvllxy05l9vs9cilhczgp"; depends=[IRanges]; }; - BeadDataPackR = derive2 { name="BeadDataPackR"; version="1.33.0"; sha256="0asbgmcidblxj82w5bv0g0c5l9w2nzyr7qparbxg2inxcqimsa37"; depends=[]; }; - BgeeDB = derive2 { name="BgeeDB"; version="2.7.2"; sha256="0rk6kfy78xxsd8zbvs2gdklncz5dzr6wayndf3bh7nm575d8jnrd"; depends=[Biobase data_table digest dplyr graph RCurl tidyr topGO]; }; - BiFET = derive2 { name="BiFET"; version="1.1.8"; sha256="0h7lrhfjgxfchk4i1i6y65znr2dxh9zkiy9n6clvrby6aqrswgr3"; depends=[GenomicRanges poibin]; }; - BiGGR = derive2 { name="BiGGR"; version="1.17.1"; sha256="18d57ia7vzgrwc8nzqjp368s7a6hqckcskp807xmk239ggrk9iii"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; }; - BiRewire = derive2 { name="BiRewire"; version="3.13.3"; sha256="09i4mvpbfvnljvg87zgwawv5ahj7kaiqvwx7mlsqkrdzijclfqq3"; depends=[igraph Matrix slam tsne]; }; - BiSeq = derive2 { name="BiSeq"; version="1.21.0"; sha256="12wnihb693dk6ri3hqcm7cjyy0r3dffvjcfybypl75zsj42k7zb7"; depends=[betareg Biobase BiocGenerics Formula GenomeInfoDb GenomicRanges globaltest IRanges lokern rtracklayer S4Vectors SummarizedExperiment]; }; - BicARE = derive2 { name="BicARE"; version="1.39.0"; sha256="1gdglclrkrsxw7lks9rczhjy3ldsrl18qbk6h4f10d3rf6b147b1"; depends=[Biobase GSEABase multtest]; }; - BioCor = derive2 { name="BioCor"; version="1.5.6"; sha256="1zy4yxwgx70f6sz09kva97p2gby4yjyrqn4zshrdr89npnk5h5rz"; depends=[BiocParallel GSEABase Matrix]; }; - BioMVCClass = derive2 { name="BioMVCClass"; version="1.49.0"; sha256="01v6bzq8jsqd3p2cpg0hlfccqzkr9fk9zkby2dg1npwrf27x6j4g"; depends=[Biobase graph MVCClass Rgraphviz]; }; - BioNet = derive2 { name="BioNet"; version="1.41.0"; sha256="039mzwvfamlxkqn9ipn7vab7qnnn0153sg7dcp4g5glfxgmqnngh"; depends=[AnnotationDbi Biobase graph igraph RBGL]; }; - BioNetStat = derive2 { name="BioNetStat"; version="1.1.2"; sha256="17iyf5k9mm3mqvw7vskk7vcmadrs4qxq69sx024j63ihiq6divkb"; depends=[BiocParallel ggplot2 Hmisc igraph knitr pathview pheatmap plyr psych RColorBrewer RJSONIO shiny shinyBS whisker yaml]; }; - BioQC = derive2 { name="BioQC"; version="1.9.0"; sha256="0v9czgv6n57nczg2ijz78dfknvmlbxbdrsi8c90wiyxr888gkb3m"; depends=[Biobase Rcpp]; }; - BioSeqClass = derive2 { name="BioSeqClass"; version="1.39.2"; sha256="1j9mbp6xdnm24a1vzwq3327dhm9nglydib73nrwcw1jn0am78yqv"; depends=[Biobase Biostrings class e1071 foreign ipred klaR nnet party randomForest rpart scatterplot3d tree]; }; - Biobase = derive2 { name="Biobase"; version="2.41.2"; sha256="11wda45crjk2v7zscrhrh0w30qdqvkxf6zcqyg7jqk833327ci0r"; depends=[BiocGenerics]; }; - BiocCaseStudies = derive2 { name="BiocCaseStudies"; version="1.43.0"; sha256="0xdn0zrd034mxzc6khqfnsp0rynfpd7zbxhmcmj5j0h83m9kyfnw"; depends=[Biobase]; }; - BiocCheck = derive2 { name="BiocCheck"; version="1.17.25"; sha256="1h1lwjpzmwiygfrh4gjh3mw7fjk0ync3xbvw5bl39ykgq9b1dw7h"; depends=[BiocManager biocViews codetools graph httr knitr optparse stringdist]; }; - BiocFileCache = derive2 { name="BiocFileCache"; version="1.5.9"; sha256="1prwqr9xrl47knyx1jddw5in1casj7xyz787qqqlf7xfp8z5kqyf"; depends=[curl DBI dbplyr dplyr httr rappdirs RSQLite]; }; - BiocGenerics = derive2 { name="BiocGenerics"; version="0.27.1"; sha256="1v2vqhixnn4caanpnmd0pw7jnczfkc79wlb9c7v0kwpz9h79h023"; depends=[]; }; - BiocInstaller = derive2 { name="BiocInstaller"; version="1.31.3"; sha256="10b20kbp8gqfq7fsdcgfpkghndn5aw8c1cj1l67a8a5qibbfq89x"; depends=[]; }; - BiocNeighbors = derive2 { name="BiocNeighbors"; version="0.99.22"; sha256="006map9pk5q4qk2zardgxgirlil4hhvw7vjs4js426qrxqqmhlxn"; depends=[BiocParallel Rcpp RcppAnnoy S4Vectors]; }; - BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.1.22"; sha256="10dnfzxhhvnmkcpdrzwv8810ss3yljfbq0lswa1149ndqyanhdvj"; depends=[bigrquery ComplexHeatmap DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 httr IRanges magrittr rjson S4Vectors shiny SummarizedExperiment]; }; - BiocParallel = derive2 { name="BiocParallel"; version="1.15.15"; sha256="0iqgcmgq1jzayalkym2s1zvblfrwvgp2rc7v09a6mm0hzgbxvh9y"; depends=[BH futile_logger snow]; }; - BiocPkgTools = derive2 { name="BiocPkgTools"; version="0.99.16"; sha256="1lw8llvhfp8vpy72y3dc8dy6xiq3yl71zfry4h1ag3kxh9c4snvh"; depends=[BiocManager dplyr DT htmltools htmlwidgets httr igraph jsonlite readr rex rvest stringr tibble tidyr xml2]; }; - BiocSklearn = derive2 { name="BiocSklearn"; version="1.3.2"; sha256="0zdakw0yrjkxvspc2sb0z70ipx7jrqcnf0br80nrkvg5sxkm5nd0"; depends=[BBmisc knitr reticulate SummarizedExperiment]; }; - BiocStyle = derive2 { name="BiocStyle"; version="2.9.6"; sha256="1b123p3id4ljqcg3xj9lr5x05k1wa67gcl5v2bfi7nv8i6221bn3"; depends=[BiocManager bookdown knitr rmarkdown yaml]; }; + ABAEnrichment = derive2 { name="ABAEnrichment"; version="1.12.0"; sha256="0bvanqmg1smyckh16m2qn7d68zq4j7n74sgsnbgms5jngbp9158v"; depends=[ABAData data_table GOfuncR gplots gtools Rcpp]; }; + ABSSeq = derive2 { name="ABSSeq"; version="1.36.0"; sha256="0nfz9l6zfnxm7lgq39nyzlhgh55kdnq8rgvjx33rn1ybcn63frsw"; depends=[limma locfit]; }; + ABarray = derive2 { name="ABarray"; version="1.50.0"; sha256="06gy96ppfrix6w9vjfljsj1j0hs7k67j0awzx8hkw301z281akxs"; depends=[Biobase multtest]; }; + ACE = derive2 { name="ACE"; version="1.0.0"; sha256="0ry6yfpzi6g0qnimnpzf3iibhm2bsblhi3604hiy76hl6mz20qg8"; depends=[Biobase ggplot2 QDNAseq]; }; + ACME = derive2 { name="ACME"; version="2.38.0"; sha256="17vr6ifjnmpcclifnzpbz538bmvs4xfym6rq9ndkh9xbjfacfcdm"; depends=[Biobase BiocGenerics]; }; + ADaCGH2 = derive2 { name="ADaCGH2"; version="2.22.0"; sha256="121vjv6xbinkkl6zq7gg3pgqwk1068rh2fpd16w5c7pcslkr7n1q"; depends=[aCGH bit cluster DNAcopy ff ffbase GLAD snapCGH tilingArray waveslim]; }; + AGDEX = derive2 { name="AGDEX"; version="1.30.0"; sha256="0l16sfmm3j9lhyjbl0bcghhkmr77a2rrscfd3ry93z7q0gki0fw8"; depends=[Biobase GSEABase]; }; + AIMS = derive2 { name="AIMS"; version="1.14.0"; sha256="0kvfdr9fk3lvbj2b46ydnhj64j4gqg8ihc1vrdzydxwc8nzmp60h"; depends=[Biobase e1071]; }; + ALDEx2 = derive2 { name="ALDEx2"; version="1.14.0"; sha256="0zgmybmmj7an8cv8396n6q6jc27p4nrac95d61kfqgxm5xqyfd10"; depends=[BiocParallel GenomicRanges IRanges multtest S4Vectors SummarizedExperiment]; }; + AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.8.0"; sha256="0w8h7a8skvwd8ass98y8sx733hz23kczpxsbwi7cdmpx8b0wxqaq"; depends=[]; }; + ANF = derive2 { name="ANF"; version="1.4.0"; sha256="08kd394kz7x0hjb8js9xpz8f1b7rg4yzghgys0il0w1z335ivb8c"; depends=[Biobase igraph MASS RColorBrewer survival]; }; + ARRmNormalization = derive2 { name="ARRmNormalization"; version="1.22.0"; sha256="09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd"; depends=[ARRmData]; }; + ASAFE = derive2 { name="ASAFE"; version="1.8.0"; sha256="0fjiz98cr83cjfakqq7q3prqha5gzr2k6741327jgjibmhbzpyz3"; depends=[]; }; + ASEB = derive2 { name="ASEB"; version="1.26.0"; sha256="0hyi0yncxwqydwcdmw265k6zip5ahry5yx4na3fiz1n6ivi7dxq2"; depends=[]; }; + ASGSCA = derive2 { name="ASGSCA"; version="1.16.0"; sha256="0sbyvwmjsfsrlc4gymzjb3aqs1k600w2zwnz7ih1gspgj4h6yi6l"; depends=[MASS Matrix]; }; + ASICS = derive2 { name="ASICS"; version="1.2.0"; sha256="12dq0ydn35zyjfspaxpn6k8wk8443a666v5ql4d4x5nf5vy39sk7"; depends=[BiocParallel ggplot2 gridExtra plyr quadprog ropls speaq SummarizedExperiment zoo]; }; + ASSET = derive2 { name="ASSET"; version="2.0.0"; sha256="05d788w7l6sd63xzay8yv0zxjbibm6dfm9rm8shihzn74c9wk7i9"; depends=[MASS msm rmeta]; }; + ASSIGN = derive2 { name="ASSIGN"; version="1.18.0"; sha256="1mcjz9nksk0a5jgd4wyjpf7af6c883idllkx4z14w651840sd6lr"; depends=[ggplot2 gplots msm Rlab sva yaml]; }; + ASpli = derive2 { name="ASpli"; version="1.8.0"; sha256="0x51ksxm54bfd4kyrws58wi1r5r4ak16fsx9dazx1a04ibz2sjfc"; depends=[AnnotationDbi BiocGenerics BiocStyle edgeR GenomicAlignments GenomicFeatures GenomicRanges Gviz IRanges Rsamtools S4Vectors]; }; + ATACseqQC = derive2 { name="ATACseqQC"; version="1.6.4"; sha256="1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn"; depends=[BiocGenerics Biostrings BSgenome ChIPpeakAnno GenomeInfoDb GenomicAlignments GenomicRanges GenomicScores IRanges KernSmooth limma motifStack preseqR randomForest Rsamtools rtracklayer S4Vectors]; }; + AUCell = derive2 { name="AUCell"; version="1.4.0"; sha256="0c784r5bm3pi0s5cismsj9p3c27zj8171bgcl2pg9gcllzm15mp7"; depends=[data_table GSEABase mixtools R_utils shiny SummarizedExperiment]; }; + AffiXcan = derive2 { name="AffiXcan"; version="1.0.0"; sha256="1y07gf8f94s2i080a3bh0gam2fx2n4hmbznddkcxv7rkqgcq0adx"; depends=[BiocParallel MultiAssayExperiment SummarizedExperiment]; }; + AffyCompatible = derive2 { name="AffyCompatible"; version="1.42.0"; sha256="1vkjlpxpckmpgpf2svz866sa2pjpkhp4nc06vzpjfa8sqj5dl6n4"; depends=[Biostrings RCurl XML]; }; + AffyExpress = derive2 { name="AffyExpress"; version="1.48.0"; sha256="0zkk74dnbihc3xna4hlypyyqg3arhdsjqbc7q3dji8j9kz76kmcw"; depends=[affy limma]; }; + AffyRNADegradation = derive2 { name="AffyRNADegradation"; version="1.28.0"; sha256="04lvkd8m1arzilgs0i9f8f52f3yc7himhv4igbxhvhqmz4fln3xi"; depends=[affy]; }; + AgiMicroRna = derive2 { name="AgiMicroRna"; version="2.32.0"; sha256="0iqns14hihxr2rf4g3x47k9sniy6qsfmqq1r4jd8alcis22pl4gx"; depends=[affy affycoretools Biobase limma preprocessCore]; }; + AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.20.0"; sha256="03524lj6aw9cskbpxzjmi9g708x6p94mf26yz4j941g1d0mc3z91"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; }; + AnalysisPageServer = derive2 { name="AnalysisPageServer"; version="1.16.0"; sha256="088f4h87bvlckf4s4q8iy9n9d9hw9njj6y4wwr3f62xax264glj0"; depends=[Biobase graph log4r rjson]; }; + Anaquin = derive2 { name="Anaquin"; version="2.6.0"; sha256="0d3jnxc5dxj0dk5h9m9b5fyi2jd00i7jvdgsn5q1zhrqnddiwhym"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; }; + AneuFinder = derive2 { name="AneuFinder"; version="1.10.1"; sha256="1409vacjj27gm7ck5b888rys2gjnqb46z96ibgam6z2gglhf38mk"; depends=[AneuFinderData bamsignals Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust ReorderCluster reshape2 Rsamtools S4Vectors]; }; + AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.44.0"; sha256="1954vimkx5yb9irppq8vssq0f3yjkg36w38b9r0rqmijx1ps7x5d"; depends=[Biobase BiocGenerics DBI IRanges RSQLite S4Vectors]; }; + AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.6.0"; sha256="0wrr10cxjzmxx46vjzq2nsf6xlqz1sqwx4xm0sk3d77ff8wmph4x"; depends=[GenomicRanges lazyeval]; }; + AnnotationForge = derive2 { name="AnnotationForge"; version="1.24.0"; sha256="13yvhf3yskmvhs8szs6rkw93h81h5xqa3h19h91pp6nprhc8s3ll"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; }; + AnnotationFuncs = derive2 { name="AnnotationFuncs"; version="1.32.0"; sha256="1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss"; depends=[AnnotationDbi DBI]; }; + AnnotationHub = derive2 { name="AnnotationHub"; version="2.14.2"; sha256="17fgrvcnbii9siv5rq5j09bxhqffx47f6jf10418qvr7hh61ic1g"; depends=[AnnotationDbi BiocGenerics BiocManager curl httr interactiveDisplayBase RSQLite S4Vectors yaml]; }; + AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.12.0"; sha256="1xim76sxldx70h13fpkhz7fxr5rcq0gp7558w4v1iqjjzd4gp3mh"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite OrganismDbi rBiopaxParser RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; }; + ArrayExpress = derive2 { name="ArrayExpress"; version="1.42.0"; sha256="1a61miwsyqghmqnfnfpd7b0p712mz9cpcrq00p9b7jr8j4jd5vla"; depends=[Biobase limma oligo XML]; }; + ArrayExpressHTS = derive2 { name="ArrayExpressHTS"; version="1.32.0"; sha256="1k8qq2l1jvnm0kqmixk4pjw8k2cz9viyh14pkbn93sv8j0bvqn0n"; depends=[Biobase BiocGenerics biomaRt Biostrings bitops DESeq edgeR GenomicRanges Hmisc IRanges R2HTML RColorBrewer rJava Rsamtools sampling sendmailR ShortRead snow svMisc XML]; }; + ArrayTV = derive2 { name="ArrayTV"; version="1.20.0"; sha256="00azibnfaa7w9gzlx8l21l9xlkzagwb0zbd70f95wvbr5qiq9w93"; depends=[DNAcopy foreach IRanges oligoClasses S4Vectors]; }; + ArrayTools = derive2 { name="ArrayTools"; version="1.42.0"; sha256="08wklnb3wi0yzxis5nic5g7w8shn9n3j6h7vbvxjv8n92bqmc0y1"; depends=[affy Biobase limma xtable]; }; + AssessORF = derive2 { name="AssessORF"; version="1.0.2"; sha256="1kkdds8mmrnh72j267xhyfn40i5czdfwhy8zlxxlm376mxipxwgj"; depends=[Biostrings DECIPHER GenomicRanges IRanges]; }; + BAC = derive2 { name="BAC"; version="1.42.0"; sha256="02r74rwsn59b1f9l3n51xh6jj5bwjcg9qp63i1jczfnglwga01av"; depends=[]; }; + BADER = derive2 { name="BADER"; version="1.20.0"; sha256="1aizqvi86wkn7d98sh55c24zx9zh55n4w5xfya50h9yg70rl4wgg"; depends=[]; }; + BAGS = derive2 { name="BAGS"; version="2.22.0"; sha256="13zlmffg8y1vrkpj62wawfzx9h68q1p42bizrwzq0cdh6jyafp3z"; depends=[Biobase breastCancerVDX]; }; + BASiCS = derive2 { name="BASiCS"; version="1.4.0"; sha256="0b8qjd9pyva8hjc5083dwrfij9j3khin01n1wyc2qs0df0785xjf"; depends=[BiocGenerics coda data_table ggplot2 KernSmooth MASS matrixStats Rcpp RcppArmadillo S4Vectors scran SingleCellExperiment SummarizedExperiment testthat]; }; + BBCAnalyzer = derive2 { name="BBCAnalyzer"; version="1.12.0"; sha256="0k49ad1k3szjawsn7s97k7y2j7c03cqjcg8kmx8wmypjivjv1nv0"; depends=[Biostrings GenomicRanges IRanges Rsamtools SummarizedExperiment VariantAnnotation]; }; + BCRANK = derive2 { name="BCRANK"; version="1.44.0"; sha256="0zrmrc4dsz9jl0n7a0fsnmfws54hpda21sxpdqdq86qhj4ljz2nd"; depends=[Biostrings]; }; + BDMMAcorrect = derive2 { name="BDMMAcorrect"; version="1.0.0"; sha256="0l6p0nbzik4vcdw1wkvp2xnvz7y66mim3p4mkyf5s1pwblfzg456"; depends=[ape ellipse ggplot2 Rcpp RcppArmadillo RcppEigen SummarizedExperiment vegan]; }; + BEARscc = derive2 { name="BEARscc"; version="1.2.0"; sha256="0i8qvj3j3cj6pvmckwqfc97gfyrmv40a2fscc71ihnp0xjbagm5m"; depends=[data_table ggplot2 SingleCellExperiment]; }; + BEAT = derive2 { name="BEAT"; version="1.20.0"; sha256="1m9mi0wgzz8v1f85j168d1hs3ksvz3qgj21hkq95swi45x3bmqs2"; depends=[Biostrings BSgenome GenomicRanges ShortRead]; }; + BEclear = derive2 { name="BEclear"; version="1.14.0"; sha256="0xwmq59hbkxki573brhp2rvmn06dyysk64n4fs0vna0h729d8lhj"; depends=[BiocParallel data_table futile_logger Matrix Rdpack]; }; + BGmix = derive2 { name="BGmix"; version="1.42.0"; sha256="19n8cqdfrp8br20g7gw787w2sa3sgs41vfnic6l9gdbqphb702d1"; depends=[KernSmooth]; }; + BHC = derive2 { name="BHC"; version="1.34.0"; sha256="0wsz5ak60fd69mds7f3siv4g3hygbzwdapm6jkldnph2x3sv0f2w"; depends=[]; }; + BLMA = derive2 { name="BLMA"; version="1.6.0"; sha256="12fxafyyffgmbnqqpq15wfawa5s1lmygkjxbh08sl34a9d5g2apf"; depends=[Biobase graph GSA limma PADOG ROntoTools]; }; + BPRMeth = derive2 { name="BPRMeth"; version="1.8.0"; sha256="1pnmpwmd30c0c2pm59wkqr95p4a8fm93fdkrk6r239z7z810svyh"; depends=[assertthat BiocStyle cowplot data_table doParallel e1071 earth foreach GenomicRanges ggplot2 IRanges kernlab magrittr MASS matrixcalc mvtnorm randomForest Rcpp RcppArmadillo S4Vectors truncnorm]; }; + BRAIN = derive2 { name="BRAIN"; version="1.28.0"; sha256="13sqj6mxx1wyv0ii2lag4qcd95ly9c2r4bh0ds8f40gfz2dx1z62"; depends=[Biostrings lattice PolynomF]; }; + BSgenome = derive2 { name="BSgenome"; version="1.50.0"; sha256="07z4zxx0khrc86qqvc7vxww8df9fh6pyks9ajxkc9gdqr5nn79j7"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools rtracklayer S4Vectors XVector]; }; + BUMHMM = derive2 { name="BUMHMM"; version="1.6.0"; sha256="1bbqx3ywh7yr49az3xyhgpyjbiqmkpv2p63s3mnywwxbccn0fxh3"; depends=[Biostrings devtools gtools IRanges stringi SummarizedExperiment]; }; + BUS = derive2 { name="BUS"; version="1.38.0"; sha256="04lk2rq8cv6hw64ssl1v64gqg7fz2jm7hd4hwkf6q6nhivr7skpi"; depends=[infotheo minet]; }; + BUScorrect = derive2 { name="BUScorrect"; version="1.0.0"; sha256="1z841bjyyqah232dhdpm7j77irjim09h3lpy2659n5llgzr7cdi2"; depends=[gplots SummarizedExperiment]; }; + BaalChIP = derive2 { name="BaalChIP"; version="1.8.0"; sha256="0xscwx5afwcyrg8pcq3fd80m9h8mqiswyvnk3x13r020r1jgxr9l"; depends=[coda doBy doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges reshape2 Rsamtools scales]; }; + BadRegionFinder = derive2 { name="BadRegionFinder"; version="1.10.0"; sha256="1d29hnaxyvlpdbzadnjp3x1jba1d4vis797iak81b217wrq34g1z"; depends=[biomaRt GenomicRanges Rsamtools S4Vectors VariantAnnotation]; }; + BaseSpaceR = derive2 { name="BaseSpaceR"; version="1.26.0"; sha256="1w7iz4nhgpx25004s9bd6mw9pm1z8dr8p7nxr6ck8wbdv19j1srp"; depends=[RCurl RJSONIO]; }; + Basic4Cseq = derive2 { name="Basic4Cseq"; version="1.18.0"; sha256="0g0nzmh073f8pvrmf9cb4sjv61cn227s84ysb4arb852xap4369l"; depends=[Biostrings BSgenome_Ecoli_NCBI_20080805 caTools GenomicAlignments GenomicRanges RCircos]; }; + BasicSTARRseq = derive2 { name="BasicSTARRseq"; version="1.10.0"; sha256="03micn3sy861i7218vcx7fpzflvlh5rsgx0gnc4irzvi1xh478j9"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges S4Vectors]; }; + BatchQC = derive2 { name="BatchQC"; version="1.10.1"; sha256="1clsabpfnaiy0dlb0m88z72kmwslny9rinrgzcb9ljjma3yarx8q"; depends=[corpcor d3heatmap ggvis gplots knitr limma Matrix matrixStats MCMCpack moments pander reshape2 rmarkdown shiny sva]; }; + BayesKnockdown = derive2 { name="BayesKnockdown"; version="1.8.0"; sha256="0ziaciznv926xq6xjj22afcwpvz6ha0g93fgyw0y6cr4kx8mlphd"; depends=[Biobase]; }; + BayesPeak = derive2 { name="BayesPeak"; version="1.34.0"; sha256="0zj06b8r0hqjczhlryfy8z7jf799gglisv4cxszlzw4wj7byyi9x"; depends=[IRanges]; }; + BeadDataPackR = derive2 { name="BeadDataPackR"; version="1.34.0"; sha256="0scdvj7d6gh78h6l1iv6nrd100i0n51a5dki9nvb7sk76sw06zzk"; depends=[]; }; + BgeeDB = derive2 { name="BgeeDB"; version="2.8.0"; sha256="1bhin7h1bd3wc74af1fms0ha3fy9drij26d1np27knpjs95wygiq"; depends=[Biobase data_table digest dplyr graph RCurl tidyr topGO]; }; + BiFET = derive2 { name="BiFET"; version="1.2.0"; sha256="0s4wrl9c5p7vn52y1kn4vxmpy2d2bppz8qqa00782fmy59b73mrf"; depends=[GenomicRanges poibin]; }; + BiGGR = derive2 { name="BiGGR"; version="1.18.0"; sha256="0p42i0j2sqz9kc79nh0wi7hb7r8y01cs5gczanza59q3amhjidqq"; depends=[hyperdraw hypergraph LIM limSolve rsbml stringr]; }; + BiRewire = derive2 { name="BiRewire"; version="3.14.0"; sha256="0zawg7gjywf8bsxmr33dj4x0xxy06rxcmimdmwx6flx0igf8xrx0"; depends=[igraph Matrix slam tsne]; }; + BiSeq = derive2 { name="BiSeq"; version="1.22.0"; sha256="0bvq2qn4pn632x8ppqx99ar44xh1nazn34f2jqzhg3m8mc7q5h7c"; depends=[betareg Biobase BiocGenerics Formula GenomeInfoDb GenomicRanges globaltest IRanges lokern rtracklayer S4Vectors SummarizedExperiment]; }; + BicARE = derive2 { name="BicARE"; version="1.40.0"; sha256="1dl1jv927l1ywsccmf662j3dl7m4pnkw8v1lpv47nq49pns0qqsw"; depends=[Biobase GSEABase multtest]; }; + BioCor = derive2 { name="BioCor"; version="1.6.0"; sha256="07xldgqdddx1ax1djp5hgp9xp0qmi4zxz938mkm8y1v6iqwjdcc6"; depends=[BiocParallel GSEABase Matrix]; }; + BioMVCClass = derive2 { name="BioMVCClass"; version="1.50.0"; sha256="0kkjj1c0s443agk7kaa1dxda4d1bsmlkxmivz2gvf5bhnbaxjn13"; depends=[Biobase graph MVCClass Rgraphviz]; }; + BioNet = derive2 { name="BioNet"; version="1.42.0"; sha256="1hxlwh3jwgnhs8ma0ky6nk9hm2yphd0g7a7ic32vibmw1xcs8znd"; depends=[AnnotationDbi Biobase graph igraph RBGL]; }; + BioNetStat = derive2 { name="BioNetStat"; version="1.2.2"; sha256="0d2kh6bbvbxwd48c9wa6nbaj12mmgikknrsdm13r4va7218d24f5"; depends=[BiocParallel ggplot2 Hmisc igraph knitr pathview pheatmap plyr psych RColorBrewer RJSONIO shiny shinyBS whisker yaml]; }; + BioQC = derive2 { name="BioQC"; version="1.10.0"; sha256="0ip0vvq6ln8ci14g2ynxi2ipz60df6bll3ynk5dchz2zybj9l2c2"; depends=[Biobase Rcpp]; }; + BioSeqClass = derive2 { name="BioSeqClass"; version="1.40.0"; sha256="1wx8pc9xv23w1lh1lz5qgv911yh38dz9h1wa3lp1jwb5hsk1lkzv"; depends=[Biobase Biostrings class e1071 foreign ipred klaR nnet party randomForest rpart scatterplot3d tree]; }; + Biobase = derive2 { name="Biobase"; version="2.42.0"; sha256="10nr6nrkj5vlq8hsgbhbhv669z0dbpz4m3vz9k32rx1czbrrqwin"; depends=[BiocGenerics]; }; + BiocCaseStudies = derive2 { name="BiocCaseStudies"; version="1.44.0"; sha256="0sidi2rynhbxmjwd90nccgximv4c60qdw4lc6yrgfi00928xms8d"; depends=[Biobase]; }; + BiocCheck = derive2 { name="BiocCheck"; version="1.18.0"; sha256="0zamvs5jar38293ff27imvwy0ra25y64ls9z8w3q1y4jcp8p8pg7"; depends=[BiocManager biocViews codetools graph httr knitr optparse stringdist]; }; + BiocFileCache = derive2 { name="BiocFileCache"; version="1.6.0"; sha256="0ykcr9saxs0sd03ng6g6r6dzqx28rc6590vfa2jq5sq84w95lxr0"; depends=[curl DBI dbplyr dplyr httr rappdirs RSQLite]; }; + BiocGenerics = derive2 { name="BiocGenerics"; version="0.28.0"; sha256="0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"; depends=[]; }; + BiocInstaller = derive2 { name="BiocInstaller"; version="1.32.1"; sha256="1s1f9qhyf3mc73ir25x2zlgi9hf45a37lg4z8fbva4i21hqisgsl"; depends=[]; }; + BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.0.0"; sha256="1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"; depends=[BiocParallel Rcpp RcppAnnoy S4Vectors]; }; + BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.2.0"; sha256="0bipd4s5qpa4nkvl362dvv966zyib5r77jpwj5821dajghxhwz6p"; depends=[bigrquery ComplexHeatmap DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 httr IRanges magrittr rjson S4Vectors shiny SummarizedExperiment]; }; + BiocParallel = derive2 { name="BiocParallel"; version="1.16.4"; sha256="0wlj7pc53yv6287a294zvkrsq4n0066r6bj4q1vbcsmbkgp6s9yg"; depends=[BH futile_logger snow]; }; + BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.0.2"; sha256="0ypiagphwlj5jmxxwbdfrwnmm593rsizkchfdb0kkascdbqzqs55"; depends=[BiocManager dplyr DT htmltools htmlwidgets httr igraph jsonlite readr rex rvest stringr tibble tidyr xml2]; }; + BiocSklearn = derive2 { name="BiocSklearn"; version="1.4.0"; sha256="08a1jaxhqaxqrhbgkm11isi3d83sbpfjh02nki7rbwffcjim3fy0"; depends=[BBmisc knitr reticulate SummarizedExperiment]; }; + BiocStyle = derive2 { name="BiocStyle"; version="2.10.0"; sha256="01lm8xljilj666fcl3wnw82dxkcxnlr294lddr553rm8xr5nwg31"; depends=[BiocManager bookdown knitr rmarkdown yaml]; }; BiocVersion = derive2 { name="BiocVersion"; version="3.8.0"; sha256="1kyqzca8n7wggz6lfx7xj0i1h1s3rma15v11iycgkdka58443qqr"; depends=[]; }; - BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.7.5"; sha256="1k39zcfdwzddrfaakh3nchwc3xlq63x2dzybj7xj0xhjj14klyr1"; depends=[BiocStyle bookdown devtools git2r httr knitr rmarkdown rstudioapi stringr]; }; - Biostrings = derive2 { name="Biostrings"; version="2.49.2"; sha256="0fm0vfi5s7d0xzwanq5rrdh0fp394qnd7jcmlsib6naqjch0zqaf"; depends=[BiocGenerics IRanges S4Vectors XVector]; }; - BitSeq = derive2 { name="BitSeq"; version="1.25.2"; sha256="05vkx8wr53qfsyjcmfp31768qycmrcbanqfwh1x0l7456v0hmbcv"; depends=[IRanges Rsamtools S4Vectors zlibbioc]; }; - BrainStars = derive2 { name="BrainStars"; version="1.25.0"; sha256="0svlrnd131m2lrpafxcpzbjqj3pvzcsi6azk1f4l2f21yimmx2iq"; depends=[Biobase RCurl RJSONIO]; }; - BridgeDbR = derive2 { name="BridgeDbR"; version="1.15.2"; sha256="1rmdyh16qkhqad0xdhqi2vxzi1ga3gmxfl81nqnb5pm1vp0rr4ns"; depends=[RCurl rJava]; }; - BrowserViz = derive2 { name="BrowserViz"; version="2.3.0"; sha256="0f4hayj2iinfqiwpl53nmnw0cfv9p6sz25ggwpz1pyib24n2n9b6"; depends=[BiocGenerics httpuv jsonlite]; }; - BubbleTree = derive2 { name="BubbleTree"; version="2.11.0"; sha256="0a69azv8v67jfdyg9mfaf58g1v3b09brhr2fvgl2lq7d48gi0cbh"; depends=[Biobase BiocGenerics BiocStyle biovizBase dplyr e1071 GenomicRanges ggplot2 gridExtra gtable gtools IRanges limma magrittr plyr RColorBrewer WriteXLS]; }; - BufferedMatrix = derive2 { name="BufferedMatrix"; version="1.45.0"; sha256="0qr9dsdh04msxva28n37shjk4j6a4m0i5v4plkk7qpvb6ccbvrf8"; depends=[]; }; - BufferedMatrixMethods = derive2 { name="BufferedMatrixMethods"; version="1.45.0"; sha256="1v2yh5pvjc3x25nq6cdqazm1x80ir2qz4jlmssgd31n1bz8r4x48"; depends=[BufferedMatrix]; }; - CAFE = derive2 { name="CAFE"; version="1.17.1"; sha256="057pw96g13h5sak0scqyn2qsfm3dqz7qmqrasjf4vnp2zz059blp"; depends=[affy annotate Biobase biovizBase GenomicRanges ggbio ggplot2 gridExtra IRanges]; }; - CAGEfightR = derive2 { name="CAGEfightR"; version="1.1.5"; sha256="0604b35q82x6brwmg31ks3k77r9f287fr4azgl0bcphj71g9ijc3"; depends=[assertthat BiocGenerics BiocParallel GenomeInfoDb GenomicFeatures GenomicFiles GenomicInteractions GenomicRanges grr Gviz InteractionSet IRanges Matrix Matrix_utils pryr rtracklayer S4Vectors SummarizedExperiment]; }; - CAGEr = derive2 { name="CAGEr"; version="1.23.5"; sha256="181vj5kmny36vdvyzvjpxvj7n0q35cq1nv28ph5v6i5xf6ymyj47"; depends=[beanplot BiocGenerics BiocParallel BSgenome data_table DelayedArray formula_tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise MultiAssayExperiment plyr reshape Rsamtools rtracklayer S4Vectors som stringdist stringi SummarizedExperiment vegan VGAM]; }; - CALIB = derive2 { name="CALIB"; version="1.47.0"; sha256="1j486knj1l7chda7gdlkkzrrs7vwi39brzkshj1zcsn87r9j1j09"; depends=[limma]; }; - CAMERA = derive2 { name="CAMERA"; version="1.37.0"; sha256="0n0xvhcy3y84cq6q45ms56z4nrs6q762iqgxp266kpl93z16rw4v"; depends=[Biobase graph Hmisc igraph RBGL xcms]; }; - CAMTHC = derive2 { name="CAMTHC"; version="0.99.7"; sha256="1m2qpf3ssn7h7qj96021kbg3h8sfkbggq4dfxd4xz3px8vra5q82"; depends=[apcluster Biobase BiocParallel corpcor DMwR geometry NMF pcaPP rJava SummarizedExperiment]; }; - CATALYST = derive2 { name="CATALYST"; version="1.5.9"; sha256="1xxa2sv7a75wr2py7ah8lwqhgrbbic25cq9lf3gb73iaid994fy9"; depends=[Biobase circlize ComplexHeatmap ConsensusClusterPlus dplyr drc DT flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra htmltools limma magrittr Matrix matrixStats nnls plotly RColorBrewer reshape2 Rtsne S4Vectors scales shiny shinyBS shinydashboard shinyjs SummarizedExperiment tidyr]; }; - CAnD = derive2 { name="CAnD"; version="1.13.0"; sha256="07ypm7zz4hf64q478b7s2q46m3imcs0kjc77gkwxky3ymsvid07y"; depends=[ggplot2 reshape]; }; - CCPROMISE = derive2 { name="CCPROMISE"; version="1.7.0"; sha256="1yb8idgdka7psnwa7w94lsld8ghphhdz8kcyvp1na6l88lyc2iyi"; depends=[Biobase CCP GSEABase PROMISE]; }; - CEMiTool = derive2 { name="CEMiTool"; version="1.5.1"; sha256="1jvnpinmyjcpss3wm7kchdksjc5a5a64vdymj9ada38q3j9ni3fd"; depends=[clusterProfiler data_table DT fgsea ggdendro ggplot2 ggpmisc ggrepel ggthemes gRbase gridExtra gtable htmltools igraph intergraph knitr matrixStats network pracma rmarkdown scales sna stringr WGCNA]; }; - CFAssay = derive2 { name="CFAssay"; version="1.15.0"; sha256="06xq5rwbbgxknymn061ck1vyqlb8l715cpf7k40w3l4v95h02jiz"; depends=[]; }; - CGEN = derive2 { name="CGEN"; version="3.17.0"; sha256="1i31ckwfw6nx0fpfg2g8zq83r6zykvkxfrqkib9kj4wvxx24kvcx"; depends=[mvtnorm survival]; }; - CGHbase = derive2 { name="CGHbase"; version="1.41.2"; sha256="1ncy4lxvzpbs3nrwdyk56scmirgi2a3byi6dcja35syqpw2hdqip"; depends=[Biobase marray]; }; - CGHcall = derive2 { name="CGHcall"; version="2.43.0"; sha256="1r8df0xvnhzwhbg1l1wp474f85j6l1g2ivvzmqxcqr5va1clz6g9"; depends=[Biobase CGHbase DNAcopy impute snowfall]; }; - CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.35.0"; sha256="0bas6wmdw9h8ablm85ggbb776nfxrf4lpfvv5rkahd10b35y3x4b"; depends=[Biobase CGHbase CGHcall]; }; - CGHregions = derive2 { name="CGHregions"; version="1.39.0"; sha256="0r3gvrinr7f5qn89v6rs5bxx4sjalsjl0f2cf6vzbzgnmdysarns"; depends=[Biobase CGHbase]; }; - CHARGE = derive2 { name="CHARGE"; version="1.1.0"; sha256="05zqkiqnc82bmb580f16v6d02kfq55sdrm0nxk86h5kp1cs8fryk"; depends=[cluster diptest factoextra FactoMineR GenomicRanges IRanges matrixStats modes plyr SummarizedExperiment]; }; - CHRONOS = derive2 { name="CHRONOS"; version="1.9.2"; sha256="01r3zd0vq4qp40sxvcp7h23713addck5d463b3vyimz7y1x07cqv"; depends=[biomaRt circlize doParallel foreach graph openxlsx RBGL RCurl XML]; }; - CINdex = derive2 { name="CINdex"; version="1.9.1"; sha256="1g24rbbhpq90c6cqjx96pxz4vlj3kyxvc9ad3hibbkljr705rs77"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; }; - CMA = derive2 { name="CMA"; version="1.39.0"; sha256="05yx2rwnrzdsgbyv86iyy17qiz6sy91bl6y3qf29aid3yndawc1s"; depends=[Biobase]; }; - CNAnorm = derive2 { name="CNAnorm"; version="1.27.0"; sha256="152cwha5mg66vc1ax6k2mwnahwj0cgcs3khii747y3xxn4p8m0z5"; depends=[DNAcopy]; }; - CNEr = derive2 { name="CNEr"; version="1.17.4"; sha256="1pyv4j04ls6l5b1y80rrwjygyp2bii8psxvswyb70flpi18gs0jp"; depends=[annotate BiocGenerics Biostrings DBI GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 GO_db IRanges KEGGREST poweRlaw R_utils readr reshape2 RSQLite rtracklayer S4Vectors XVector]; }; - CNORdt = derive2 { name="CNORdt"; version="1.23.1"; sha256="044sgjrziy70b4xdlyl56y90p5cddcp5iwfbfcwbzfpz9hbqas4l"; depends=[abind CellNOptR]; }; - CNORfeeder = derive2 { name="CNORfeeder"; version="1.21.1"; sha256="1dvwj9q37hx6jrvzvlnkzqs3gl7abhm5b9v4xghp8ak00cwx19n6"; depends=[CellNOptR graph]; }; - CNORfuzzy = derive2 { name="CNORfuzzy"; version="1.23.1"; sha256="13dn4lnm5z0j817hxp513yas96918nvk363bwqy4gd6aps5nhi6k"; depends=[CellNOptR nloptr]; }; - CNORode = derive2 { name="CNORode"; version="1.23.1"; sha256="0f5lfyfvch8bp0prl5q3i8zmj0dbw50v6i48padgq3ajyszp86dx"; depends=[CellNOptR genalg]; }; - CNPBayes = derive2 { name="CNPBayes"; version="1.11.8"; sha256="007r98f177iw6qbsrz33pa6jsr236j45pdm6h4alg7c813blhiq3"; depends=[BiocGenerics coda combinat dplyr GenomeInfoDb GenomicRanges ggplot2 gtools IRanges magrittr matrixStats mclust purrr RColorBrewer Rcpp reshape2 S4Vectors scales SummarizedExperiment tibble tidyr]; }; - CNTools = derive2 { name="CNTools"; version="1.37.0"; sha256="1hzdyjkbwv5iwapkf7a04r55gi1m0bg2ckjkmj4v94kfc5031nwc"; depends=[genefilter]; }; - CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.13.2"; sha256="0mzssf1w9yal8z9lg6b6wjhr3wgs7r03k2rsdi9baiwaiwvqjca5"; depends=[exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; }; - CNVrd2 = derive2 { name="CNVrd2"; version="1.19.0"; sha256="0xdkckwys2963ylj2mid10k9dwwwmsks29pdp5z4266z0z3r9x9b"; depends=[DNAcopy ggplot2 gridExtra IRanges rjags Rsamtools VariantAnnotation]; }; - CNVtools = derive2 { name="CNVtools"; version="1.75.0"; sha256="1x70y389szy3b6vimlpzjsqdg4kykmx01wfw8aks5hxq9z23vaik"; depends=[survival]; }; - COCOA = derive2 { name="COCOA"; version="0.99.8"; sha256="07r7lv3kaf4lq4mgbgp5yym373mm949qs6wiwc5zvkkaka3rm6zx"; depends=[Biobase BiocGenerics ComplexHeatmap data_table GenomicRanges ggplot2 IRanges MIRA S4Vectors tidyr]; }; - CODEX = derive2 { name="CODEX"; version="1.13.1"; sha256="0mrr40660358n2f31phzmagwfg7fxdmmyhmcaqf17cdcyp9cnslb"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb IRanges Rsamtools S4Vectors]; }; - COHCAP = derive2 { name="COHCAP"; version="1.27.5"; sha256="13b7ms1j1p6qfyvipzipm2qnr50rhzf0hm9h6h8g6rwvkxxqbvci"; depends=[BH COHCAPanno gplots RColorBrewer Rcpp RcppArmadillo WriteXLS]; }; - COMPASS = derive2 { name="COMPASS"; version="1.19.4"; sha256="061jy33qvsvadi3a8ccwqh02nmnhhs8khy7vixf9akndl2jqbzqz"; depends=[abind BiocStyle clue data_table dplyr knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang rmarkdown scales tidyr]; }; - CONFESS = derive2 { name="CONFESS"; version="1.9.1"; sha256="0v334w2252mvc4qmpz5wnwz7xk99nj2izj61qhaafiaqq9wk3f5i"; depends=[changepoint cluster contrast data_table EBImage ecp flexmix flowClust flowCore flowMeans flowMerge flowPeaks foreach ggplot2 limma MASS moments outliers plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo]; }; - CORREP = derive2 { name="CORREP"; version="1.47.0"; sha256="061hyv2jxhjpwycv9c0s0881nsq1z3pm0jcn9simdha55hzb20hs"; depends=[e1071]; }; - COSNet = derive2 { name="COSNet"; version="1.15.0"; sha256="0irkzh1rm430y5a67rx0rzc4bgb9zg9jyh768bgl1mcf3hjdqsgl"; depends=[]; }; - CRISPRseek = derive2 { name="CRISPRseek"; version="1.21.4"; sha256="1ck8pqwm2g4fwibd5lbj9r04ryqhw93r7rn1djp7mfxp829asfl7"; depends=[BiocGenerics BiocParallel Biostrings BSgenome data_table hash IRanges S4Vectors seqinr]; }; - CRImage = derive2 { name="CRImage"; version="1.29.0"; sha256="1b5giadnwi8h4x8bmkw5064grhaijmnkidbbd8fi2pc1pz406fli"; depends=[aCGH DNAcopy e1071 EBImage foreach MASS sgeostat]; }; - CSAR = derive2 { name="CSAR"; version="1.33.0"; sha256="1i2amxpka75l91bhvfdwzs85hcl9c11rz82l2xsjybj0ff3v0m91"; depends=[GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; - CSSP = derive2 { name="CSSP"; version="1.19.0"; sha256="1ic79b6cg68ylwj9r7ak21m1fbwrys3kwcllmhpdf8v0fldk6qld"; depends=[]; }; - CTDquerier = derive2 { name="CTDquerier"; version="1.1.2"; sha256="1sy46i32ylyny88992x6l9csn9aji7vjki6i47wdp6a0zi2s9q23"; depends=[BiocFileCache ggplot2 gridExtra igraph rappdirs RCurl S4Vectors stringdist stringr]; }; - CVE = derive2 { name="CVE"; version="1.7.13"; sha256="1sw0kiivd411hbr3jhvdpgl8b56f7w8vlxykyjgr47dbyn6nwbcd"; depends=[ape ConsensusClusterPlus ggplot2 gplots jsonlite plyr RColorBrewer shiny tidyverse WGCNA]; }; - CancerInSilico = derive2 { name="CancerInSilico"; version="2.1.0"; sha256="1rpphiy5bda3gpfscgyzci5dynyqdia5nb720pdjzxbz9xkr87f5"; depends=[BH Rcpp]; }; - CancerMutationAnalysis = derive2 { name="CancerMutationAnalysis"; version="1.23.0"; sha256="1dxw34fbr25q20k7z9isl4r0w5gz8jj1a0hd9kb4nqhm1yzilpai"; depends=[AnnotationDbi limma qvalue]; }; - CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.7.0"; sha256="09c7k5789i4afsgk1vxbz036s5gyxlnwmmwwpcgq0v4y920s37w3"; depends=[cluster ConsensusClusterPlus iCluster impute limma NMF sigclust SNFtool survival]; }; - Cardinal = derive2 { name="Cardinal"; version="1.99.1"; sha256="0pd5b3bvgcpylml6fkw5zr6kalzjqzkdyygrj2jcqyr73ln2hvxg"; depends=[Biobase BiocGenerics BiocParallel dplyr EBImage irlba lattice magrittr matter ProtGenerics S4Vectors signal sp]; }; - Category = derive2 { name="Category"; version="2.47.1"; sha256="1lg7adkrj3gsvbzkwdvrrpqv911p7ysqwimgj8silrk1vb21pghv"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; }; - CausalR = derive2 { name="CausalR"; version="1.13.0"; sha256="0npjg5zg4ckqhgjayb0rxvaaggbd52n61bs7mba6f20dnq1x0q5j"; depends=[igraph]; }; - CellMapper = derive2 { name="CellMapper"; version="1.7.1"; sha256="18w6mxmx58rh93alrxfvqnkg3m28wrycvm5pcm5zr7kvckgd9zlr"; depends=[S4Vectors]; }; - CellNOptR = derive2 { name="CellNOptR"; version="1.27.1"; sha256="1rbn2dbch4mf7ckgbh16zv85imz3wrv97gc618m3q0swp03589ay"; depends=[ggplot2 graph hash RBGL RCurl Rgraphviz XML]; }; - CellScore = derive2 { name="CellScore"; version="1.1.1"; sha256="1fwnzggm0kldackdcr8ssb0g9448gkddv632aipp6ksqw609qn52"; depends=[Biobase gplots lsa RColorBrewer squash]; }; - CellTrails = derive2 { name="CellTrails"; version="0.99.15"; sha256="0pg0wqcfwwq7y8xqm0dcpkmn7j1vd3c0ivcyij11li2znmhamsm9"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; }; - CexoR = derive2 { name="CexoR"; version="1.19.3"; sha256="1cia3bhplk559pz1znmqnfxy3zpzbg55489gadankpz3kz7n73xd"; depends=[genomation GenomeInfoDb GenomicRanges idr IRanges RColorBrewer Rsamtools rtracklayer S4Vectors]; }; - ChAMP = derive2 { name="ChAMP"; version="2.11.5"; sha256="1m6br9h75j9c659a4zhadghwf7aisc3sm2mz9s67fy3hlncmlska"; depends=[bumphunter ChAMPdata combinat dendextend DMRcate DNAcopy doParallel FEM GenomicRanges globaltest goseq Hmisc Illumina450ProbeVariants_db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest illuminaio impute isva limma marray matrixStats minfi missMethyl plotly plyr preprocessCore prettydoc quadprog qvalue RColorBrewer rmarkdown RPMM shiny shinythemes sva wateRmelon]; }; - ChIC = derive2 { name="ChIC"; version="1.1.09"; sha256="1730yssk9ig84mbzbvs0rhszscp00sbqqhhvl559gfacajs5gv85"; depends=[BiocGenerics caret caTools ChIC_data GenomicRanges IRanges progress S4Vectors spp]; }; - ChIPComp = derive2 { name="ChIPComp"; version="1.11.0"; sha256="0lia22xjj1w8m7hwpfcyaf6cldk05f78v93x3p947xdrkymx6lgc"; depends=[BiocGenerics BSgenome_Hsapiens_UCSC_hg19 BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicRanges IRanges limma Rsamtools rtracklayer S4Vectors]; }; - ChIPQC = derive2 { name="ChIPQC"; version="1.17.1"; sha256="0cpii7sxp1vab5wnnm00kifqnmxxr8hc4rnb8l4wmk5ib4ijqpra"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; }; - ChIPSeqSpike = derive2 { name="ChIPSeqSpike"; version="1.1.0"; sha256="15w26zchxjggz8236afgykdncdzim9n3lyr4bm5p7qxzqs8aigbv"; depends=[BiocGenerics corrplot GenomicRanges ggplot2 IRanges LSD Rsamtools rtracklayer S4Vectors seqplots stringr]; }; - ChIPXpress = derive2 { name="ChIPXpress"; version="1.25.0"; sha256="0px8vpyiay60fb2qvjax7mkijkmix41vaa34g9s6ahzp7mxxhwyz"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; }; - ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.3.7"; sha256="0lrpymicyi3fphw7vj1bcrgl00fpld7436kfffdwrmjla7m6539w"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; }; - ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.5.1"; sha256="1691808rn2jw08aivd2vsys279kbzs9ndf7brlgyaxaii3lxm2hc"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; }; - ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.15.2"; sha256="1b5kg8vh37pslj5ckavz401pxpy1xgak9jsanfjb76wjbpyadzm0"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager biomaRt Biostrings BSgenome DBI DelayedArray ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GO_db graph idr IRanges limma matrixStats multtest RBGL regioneR Rsamtools S4Vectors seqinr SummarizedExperiment VennDiagram]; }; - ChIPseeker = derive2 { name="ChIPseeker"; version="1.17.2"; sha256="0gnb451jh6fscpgywbclk0plfmha4zxpzpf3lq6y9kyvxk9v2cqp"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gridBase gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene UpSetR]; }; - ChIPseqR = derive2 { name="ChIPseqR"; version="1.35.2"; sha256="11pw2265qni3j20jn7kmxmw5gjf01x34vzsfnv6j4cn8k4hpl6l7"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; }; - ChIPsim = derive2 { name="ChIPsim"; version="1.35.2"; sha256="0nrwi9xy224g9r923gwkmmcq7ld4vnfwsgafiw7i1n20vsj85gyj"; depends=[Biostrings IRanges ShortRead XVector]; }; - ChemmineOB = derive2 { name="ChemmineOB"; version="1.19.3"; sha256="0c2xlkf1y15lqp7yibzp1wlknyf4l5wm8zwqf0s2grp3snc3zcv0"; depends=[BH BiocGenerics Rcpp zlibbioc]; }; - ChemmineR = derive2 { name="ChemmineR"; version="3.33.5"; sha256="0ydl1hz4hjiln4kpym7kdswbn7rddafpvsanblqbivy58p8vxkhk"; depends=[base64enc BH BiocGenerics DBI digest DT ggplot2 gridExtra png Rcpp RCurl rjson rsvg]; }; - Chicago = derive2 { name="Chicago"; version="1.9.0"; sha256="0b3j250w0piasfs3jbyycy9w4snvrn7vbaq31hhj150gjvphsgzk"; depends=[data_table Delaporte Hmisc MASS matrixStats]; }; - ChromHeatMap = derive2 { name="ChromHeatMap"; version="1.35.0"; sha256="18xgngy77rj8q91bj9v8kpzqijz15ax5w9db0xiyrspvi39z4fx4"; depends=[annotate AnnotationDbi Biobase BiocGenerics GenomicRanges IRanges rtracklayer]; }; - ClassifyR = derive2 { name="ClassifyR"; version="2.1.32"; sha256="1v82c9s3g7j6da528571nsw1d4yjl502zw5q7zfjdd23nz6kppzz"; depends=[BiocParallel locfit MultiAssayExperiment plyr S4Vectors]; }; - Clomial = derive2 { name="Clomial"; version="1.17.4"; sha256="0w0qnl7ihmkgl568wimx13cc4lhpxb1ll68iwkibnihz604rcnq6"; depends=[matrixStats permute]; }; - Clonality = derive2 { name="Clonality"; version="1.29.0"; sha256="0hlrj9rl7d0wzyk6a95p68gx76m34bfgxvpz68r3qhdzi0z0lxbn"; depends=[DNAcopy]; }; - ClusterJudge = derive2 { name="ClusterJudge"; version="1.3.0"; sha256="1zc019s15skjnzjm0vb5y3z4rd5cnk1awnvwxwj062y3pzr5kp62"; depends=[httr infotheo jsonlite lattice latticeExtra]; }; - ClusterSignificance = derive2 { name="ClusterSignificance"; version="1.9.2"; sha256="13mgd8sxj65f7lv4jlbslq27zj3hsqd57fg34xkrvgvir2a7jcmp"; depends=[pracma princurve RColorBrewer scatterplot3d]; }; - CoCiteStats = derive2 { name="CoCiteStats"; version="1.53.0"; sha256="0xy1zy4951r9xpjmhia8krrc429azbfg22nqzd9p0jcqflfj2sq7"; depends=[AnnotationDbi org_Hs_eg_db]; }; - CoGAPS = derive2 { name="CoGAPS"; version="3.1.6"; sha256="15x5pp83i1wzzs5h9gdllzb4qffi6ciw1kf63h1x6b42sk37kzia"; depends=[BH cluster doParallel foreach ggplot2 gplots RColorBrewer Rcpp reshape2 shiny]; }; - CoRegNet = derive2 { name="CoRegNet"; version="1.19.1"; sha256="0ywa8d80vgk222161ks0mgxi0ahswm3mil0lxgxanny8ad1vxvx2"; depends=[arules igraph shiny]; }; - CompGO = derive2 { name="CompGO"; version="1.17.0"; sha256="04f22n17b4cyv1mapimkmc913d22cpvifdznfgqgbmrkjsyygg2k"; depends=[GenomicFeatures ggplot2 pathview pcaMethods RDAVIDWebService reshape2 Rgraphviz rtracklayer TxDb_Mmusculus_UCSC_mm9_knownGene]; }; - ComplexHeatmap = derive2 { name="ComplexHeatmap"; version="1.19.3"; sha256="1pczcx26i30izg7iwi7ljnwqzf2k8mfw09dhmgbrcvy5siv7vn03"; depends=[circlize colorspace GetoptLong GlobalOptions RColorBrewer]; }; - ConsensusClusterPlus = derive2 { name="ConsensusClusterPlus"; version="1.45.0"; sha256="1ypfclg252j9d7v78r81n14f0gsaxgzk6n1509rdv010h0xbaw2q"; depends=[ALL Biobase cluster]; }; - CopywriteR = derive2 { name="CopywriteR"; version="2.13.1"; sha256="1w3raf6756lnf1fmarcwsr10808ggih71v0gzky4xcbhgy5d9dkh"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; }; - CorMut = derive2 { name="CorMut"; version="1.23.0"; sha256="0y0sbnz3rlv98b87i7qcqv7zy1js180hmpy45fw55kmzjvd4j6vq"; depends=[igraph seqinr]; }; - Cormotif = derive2 { name="Cormotif"; version="1.27.0"; sha256="0spl1qg0p8za8w6ikiwsf4d1spx55g1b73vcbpxbipmjymwc408i"; depends=[affy limma]; }; - CountClust = derive2 { name="CountClust"; version="1.9.1"; sha256="06vqcmb53h7h329kvq51gka8gzbz811wnrbi92wr9p0vy2pwm3hy"; depends=[cowplot flexmix ggplot2 gtools limma maptpx picante plyr reshape2 slam SQUAREM]; }; - CoverageView = derive2 { name="CoverageView"; version="1.19.0"; sha256="0alj0908pfih5z5zyi5szkimcm73sfsbqwpg6w594iglgyvbfbck"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; }; - CrispRVariants = derive2 { name="CrispRVariants"; version="1.9.2"; sha256="09ilj21fr59kw51msyazl3lcypla5dd0sc3z60jrr4ygs3fyw91q"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; }; - CytoDx = derive2 { name="CytoDx"; version="1.1.2"; sha256="1d2kdsiarfz9hpr87qq94ybiyg8cg40j6p2pryw6qnkkj43qdmgj"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; }; - CytoML = derive2 { name="CytoML"; version="1.7.14"; sha256="0xflcjjzigq08xpjjsyz67v80x0qmxnrkjq9h4241f7s0vxx7pl2"; depends=[base64enc Biobase data_table flowCore flowUtils flowWorkspace ggcyto graph jsonlite ncdfFlow openCyto plyr RBGL Rgraphviz XML]; }; - DAPAR = derive2 { name="DAPAR"; version="1.13.15"; sha256="1yxkipp01zdx5xlj479a6f2hzrhs72fh8qyk5b5nbqvbrb2jipfh"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter imp4p impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot vsn]; }; - DART = derive2 { name="DART"; version="1.29.0"; sha256="1akgln0w3xbvis0pcgjdm07jbbfsg0yn732gkvh1hzkpg26iwgfr"; depends=[igraph]; }; - DBChIP = derive2 { name="DBChIP"; version="1.25.0"; sha256="1c3s5ffbdbhsr35q5mxs1vhl3glrjfwnpng11xlrcsj9h3jpxhva"; depends=[DESeq edgeR]; }; - DChIPRep = derive2 { name="DChIPRep"; version="1.11.1"; sha256="1kp0lsqlrnr815rp0g7jcppbrp1h62pa60j1jgav78bwh51l4dpq"; depends=[assertthat ChIPpeakAnno DESeq2 fdrtool GenomicRanges ggplot2 plyr purrr reshape2 S4Vectors smoothmest soGGi SummarizedExperiment tidyr]; }; - DECIPHER = derive2 { name="DECIPHER"; version="2.9.2"; sha256="0lvg0kcv6rryb39aini5s9b4aacbld67z7427w9gvpsj7zcapgvz"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; }; - DEComplexDisease = derive2 { name="DEComplexDisease"; version="1.1.1"; sha256="007wgj3kpdk7nvx8qribm6vqfca4vp7n1ih8y866xlqgdcr5ad61"; depends=[BiocParallel ComplexHeatmap DESeq2 edgeR Rcpp SummarizedExperiment]; }; - DEDS = derive2 { name="DEDS"; version="1.55.0"; sha256="0823ycm0j30dh1pbpxbcfwqglpff72675cr4h18rk0fx0v742vhy"; depends=[]; }; - DEFormats = derive2 { name="DEFormats"; version="1.9.1"; sha256="1hcxamc82wyp8xgrx4mxhw3q15g32y8z66qgv1gbm7h17wykssih"; depends=[checkmate data_table DESeq2 edgeR GenomicRanges S4Vectors SummarizedExperiment]; }; - DEGraph = derive2 { name="DEGraph"; version="1.33.1"; sha256="19fcsjz6bgc1bvnympvq0ms5d7mvj2681jbnq5inrr4pxq2qz0p0"; depends=[graph KEGGgraph lattice mvtnorm NCIgraph R_methodsS3 R_utils RBGL Rgraphviz rrcov]; }; - DEGreport = derive2 { name="DEGreport"; version="1.17.8"; sha256="02z93g0fy594dhj7dk16fglw4jakyb44zcn22k1c64d8wvhq8rfa"; depends=[Biobase BiocGenerics broom circlize cluster ComplexHeatmap ConsensusClusterPlus cowplot DESeq2 dplyr edgeR ggdendro ggplot2 ggrepel knitr lasso2 logging magrittr Nozzle_R1 psych RColorBrewer reshape rlang S4Vectors scales stringr SummarizedExperiment tibble tidyr]; }; - DEGseq = derive2 { name="DEGseq"; version="1.35.1"; sha256="1mb9chwazmsj9j4dz92kw2mhc3b5lx5v2y3xgdcc9s4bjmb21xrz"; depends=[qvalue]; }; - DEP = derive2 { name="DEP"; version="1.3.3"; sha256="0wmzinv369svfwfmgv2gsz471bnh5vz77p5w1q4ycgd6lj5l2ckn"; depends=[assertthat circlize cluster ComplexHeatmap dplyr DT fdrtool ggplot2 ggrepel gridExtra imputeLCMD limma MSnbase purrr RColorBrewer readr rmarkdown shiny shinydashboard SummarizedExperiment tibble tidyr vsn]; }; - DEScan2 = derive2 { name="DEScan2"; version="1.1.2"; sha256="04xla8cr3f3r1dwvahs55l93bzlnds04c42kx93lgyn5r2ksqr8n"; depends=[BiocGenerics BiocParallel ChIPpeakAnno data_table DelayedArray GenomeInfoDb GenomicAlignments GenomicRanges glue IRanges plyr Rcpp RcppArmadillo rtracklayer S4Vectors SummarizedExperiment]; }; - DESeq = derive2 { name="DESeq"; version="1.33.0"; sha256="1h56v3d1kj8inh3xy08k6kfc31czyq9a2zwy1v2kibcaa79z4zrn"; depends=[Biobase BiocGenerics genefilter geneplotter lattice locfit MASS RColorBrewer]; }; - DESeq2 = derive2 { name="DESeq2"; version="1.21.25"; sha256="1ll8fdpqyml171vsxsnggsx09963jz15rivvn32xihwas9dxwksv"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; }; - DEXSeq = derive2 { name="DEXSeq"; version="1.27.1"; sha256="0jppj3yl1jibxj2ci07sf4lbbx9rbjlx172ynp2vg3ic7j7y6z61"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; }; - DEqMS = derive2 { name="DEqMS"; version="0.99.44"; sha256="01754m7rwrc1in1ls8vd0c94p2p4jyspb0nwx42scb8kjpnmcbdq"; depends=[ggplot2 limma]; }; - DEsingle = derive2 { name="DEsingle"; version="1.1.5"; sha256="0biail9qfp0sp7f2sp4mx55ajba2waqsfllx2sndjls0673pv215"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; }; - DEsubs = derive2 { name="DEsubs"; version="1.7.4"; sha256="0v4yd63zzd0k7y19pcx5mb7iq17dijjldf64c6nwlf69d8gv5lp9"; depends=[circlize DESeq DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; }; - DFP = derive2 { name="DFP"; version="1.39.0"; sha256="10yamzm28gnayrjc58jvj6mjg2j6gr266f65i9rrz5shnz9244wl"; depends=[Biobase]; }; - DMCHMM = derive2 { name="DMCHMM"; version="1.3.1"; sha256="01r9kzyjsk43ncw7xbr95r4apxchpkfjl4qilxvgsq8icg0mhqx4"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; }; - DMRScan = derive2 { name="DMRScan"; version="1.7.5"; sha256="1x6nv3688p4lh8bsv3brg35xpn4pk6i1fks2zfdfspvagbq4bqvp"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; }; - DMRcaller = derive2 { name="DMRcaller"; version="1.13.8"; sha256="0lp27mbx6sqh4b7fwsbm0gxk5ng9qabdimxhw4f8dqhsza6mp73p"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; }; - DMRcate = derive2 { name="DMRcate"; version="1.17.6"; sha256="0ynh5q7shl6as7vafg0z7z4ld2ikk785vhw656viipix4q71k1iv"; depends=[DMRcatedata DSS GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors]; }; - DMRforPairs = derive2 { name="DMRforPairs"; version="1.17.0"; sha256="0094pw863dnc57kfif490fabcsggplfdr5xh41asldydp2x1pwcy"; depends=[GenomicRanges Gviz R2HTML]; }; - DNABarcodes = derive2 { name="DNABarcodes"; version="1.11.0"; sha256="1hpsdybpj3dszjxvlh7x2j5xdrgyhx03sv15hlg2bn4jj6am4iiy"; depends=[BH Matrix Rcpp]; }; - DNAcopy = derive2 { name="DNAcopy"; version="1.55.0"; sha256="1bmd22nmfbrcwvz9qk6rh4f81faxh7f71fk2pgvgdcz97kzl4g8w"; depends=[]; }; - DNAshapeR = derive2 { name="DNAshapeR"; version="1.9.6"; sha256="1v29k18l3wqrnhfzgj3lff5pzzgwn5n9956xlx94nbblh01x96lc"; depends=[Biostrings fields GenomicRanges Rcpp]; }; - DOQTL = derive2 { name="DOQTL"; version="1.17.5"; sha256="1z1qbzg0fw6ygskk1p339dlkmbm6nj8wmwng9izhmipfn6jpfzfv"; depends=[annotate annotationTools Biobase BiocGenerics biomaRt BSgenome_Mmusculus_UCSC_mm10 corpcor doParallel foreach fpc GenomicRanges hwriter IRanges iterators mclust QTLRel regress rhdf5 Rsamtools RUnit VariantAnnotation XML]; }; - DOSE = derive2 { name="DOSE"; version="3.7.1"; sha256="0dldsqs807hgnfx59vl1q90hh1lv9x2dbxndbfi97yvzlkhnar55"; depends=[AnnotationDbi BiocParallel DO_db fgsea ggplot2 GOSemSim qvalue reshape2 S4Vectors]; }; - DRIMSeq = derive2 { name="DRIMSeq"; version="1.9.2"; sha256="0kpfvphzighq7iryxbn7s6v7k3mi09cv49r2c9gsyklqypv5cvsq"; depends=[BiocGenerics BiocParallel edgeR GenomicRanges ggplot2 IRanges limma MASS reshape2 S4Vectors]; }; - DSS = derive2 { name="DSS"; version="2.29.0"; sha256="1jwjyfx1356j0jxryf8f3mnl764fd5bz5p395z6ax8xsafzkabq1"; depends=[Biobase bsseq DelayedArray]; }; - DTA = derive2 { name="DTA"; version="2.27.0"; sha256="129hvbvdgq7whh1f63gdh28w0g5avl3xqwvjm61makyyqyx47ipf"; depends=[LSD scatterplot3d]; }; - DaMiRseq = derive2 { name="DaMiRseq"; version="1.5.3"; sha256="0zxw6ls834cizk6nw8kpbi7p9c2xr2s0892qmizzqbgag8d0mjif"; depends=[arm caret corrplot DESeq2 e1071 EDASeq edgeR FactoMineR FSelector ggplot2 Hmisc ineq kknn limma lubridate MASS pheatmap pls plsVarSel randomForest RColorBrewer reshape2 RSNNS SummarizedExperiment sva]; }; - DeMAND = derive2 { name="DeMAND"; version="1.11.1"; sha256="00rbd5mwrh9g2ppx0z0kaf1245l7r5rgiyzhrhkrkp6vvbjrhd4i"; depends=[KernSmooth]; }; - DeconRNASeq = derive2 { name="DeconRNASeq"; version="1.23.0"; sha256="0hnnw6k246a0dsj0ppfrj40ddrl3czpdq28gvkahyig64ljwfrbm"; depends=[ggplot2 limSolve pcaMethods]; }; - DeepBlueR = derive2 { name="DeepBlueR"; version="1.7.0"; sha256="198apfr10nfnk82zhmsnk9vpq2ykfi6yh79gwdnnkls8h2r5nqz9"; depends=[data_table diffr dplyr filehash foreach GenomeInfoDb GenomicRanges R_utils RCurl rjson rtracklayer settings stringr withr XML]; }; - DelayedArray = derive2 { name="DelayedArray"; version="0.7.49"; sha256="0nkpnxa91prhfnd0dwfmfr0g3r8i93gy6xcw403s81zw74imn1jk"; depends=[BiocGenerics BiocParallel IRanges matrixStats S4Vectors]; }; - DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.3.11"; sha256="0m3dx01ibmxqn4syv5cw88m7b30qlby6fiwjhd3927zmfi3jwl2s"; depends=[BiocParallel DelayedArray HDF5Array IRanges Matrix matrixStats S4Vectors]; }; - DiffBind = derive2 { name="DiffBind"; version="2.9.0"; sha256="0ka72zizphm2sphr8gm53602wgm7rkfc6hx0fql3cb34yjg11wi1"; depends=[amap BiocParallel DESeq2 dplyr edgeR GenomicAlignments GenomicRanges ggplot2 ggrepel gplots IRanges lattice limma locfit RColorBrewer Rcpp Rsamtools S4Vectors SummarizedExperiment systemPipeR zlibbioc]; }; - DiffLogo = derive2 { name="DiffLogo"; version="2.5.0"; sha256="00vk5qj0byh8ggg5nmaa94ddbi42rl59y049bxx37qr98qyw79yj"; depends=[cba]; }; - Director = derive2 { name="Director"; version="1.7.3"; sha256="1yin749xl3v3h01gccvlgkb91l2dn1rkm7asb3q9bxnr389sm4yr"; depends=[htmltools]; }; - DirichletMultinomial = derive2 { name="DirichletMultinomial"; version="1.23.0"; sha256="1wxb094p90628bbkm4vzjrpxcagcpm17iqa0f1hjfy7b8a1my9wh"; depends=[BiocGenerics IRanges S4Vectors]; }; - DominoEffect = derive2 { name="DominoEffect"; version="1.1.2"; sha256="1ri0224my8imjjd95ccdg3gmpq4npji67f01skvycn7j2z5illq8"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; }; - Doscheda = derive2 { name="Doscheda"; version="1.3.0"; sha256="1yfywqzxjj88wwnwmrm3yd9z1al74w2xzijzk1zqdjy5lg8vc1qn"; depends=[affy calibrate corrgram d3heatmap drc DT ggplot2 gridExtra httr jsonlite limma matrixStats prodlim readxl reshape2 shiny shinydashboard stringr vsn]; }; - DriverNet = derive2 { name="DriverNet"; version="1.21.0"; sha256="0ja7jpnh2rh4gkcv0h99mma19rk07y1vmh4hpkyxg1m1mb1q4vyv"; depends=[]; }; - DropletUtils = derive2 { name="DropletUtils"; version="1.1.13"; sha256="1qpds9drjvxwjdlv844lsv081iyp4syzvhpkm90skd5wpsfiriy7"; depends=[beachmat BiocParallel edgeR HDF5Array Matrix Rcpp rhdf5 Rhdf5lib S4Vectors SingleCellExperiment]; }; - DrugVsDisease = derive2 { name="DrugVsDisease"; version="2.23.0"; sha256="01hrd65q8h9r09y91vnl7x8gczgi3q8vlxihyingxjdc09qn86xd"; depends=[affy annotate ArrayExpress BiocGenerics biomaRt cMap2data DrugVsDiseasedata GEOquery hgu133a_db hgu133a2_db hgu133plus2_db limma qvalue RUnit xtable]; }; - DupChecker = derive2 { name="DupChecker"; version="1.19.1"; sha256="0a8vaamkpqwir3w3clfihpwcbjfmaaccwb86b6i6lydglkbdhnpq"; depends=[R_utils RCurl]; }; - DynDoc = derive2 { name="DynDoc"; version="1.59.0"; sha256="1cdyv6ylgdz7fyj8dnndy5y0khg0na8r7sss5p1pja73idxdqpvf"; depends=[]; }; - EBImage = derive2 { name="EBImage"; version="4.23.2"; sha256="0q91m78i1s5ds5971rbdgrlv6d4mj30ljssbg75gw1gxzhlhaczg"; depends=[abind BiocGenerics fftwtools htmltools htmlwidgets jpeg locfit png RCurl tiff]; }; - EBSEA = derive2 { name="EBSEA"; version="1.9.0"; sha256="14bgrkfx93gcr0j9fj48krnfvhnbjxnqanvnx85n5x48bk40s2jr"; depends=[edgeR limma plyr]; }; - EBSeq = derive2 { name="EBSeq"; version="1.21.0"; sha256="0nbw3mkqgify3yijwizdznafvfyd4qizfqaj5f3w04nx0h8m8b2h"; depends=[blockmodeling gplots testthat]; }; - EBSeqHMM = derive2 { name="EBSeqHMM"; version="1.15.0"; sha256="067fi2vy35y3n6a5264a7af3j03jg46fp7vzl80ca7x8vqji4xvy"; depends=[EBSeq]; }; - EBarrays = derive2 { name="EBarrays"; version="2.45.0"; sha256="1wvim2qldy74qccgqkj6hwqxjhwm3sgj2gsr88qqh16gvfqy1w9z"; depends=[Biobase cluster lattice]; }; - EBcoexpress = derive2 { name="EBcoexpress"; version="1.25.0"; sha256="1xpihh3pxm492kqrf7pnz6sarz98hqhrgw3ybicja3cvn5ihlk1j"; depends=[EBarrays mclust minqa]; }; - EDASeq = derive2 { name="EDASeq"; version="2.15.4"; sha256="0lsp0cgix7qkqry6hk2a6wqp8cfqcr3apdsi31jgjnxqz7fn7jlj"; depends=[AnnotationDbi aroma_light Biobase BiocGenerics biomaRt Biostrings DESeq GenomicFeatures GenomicRanges IRanges Rsamtools ShortRead]; }; - EDDA = derive2 { name="EDDA"; version="1.19.1"; sha256="0cs962g60shzywbp4q33hxv03qwrkr6cn12c63i8wfp49kz1g7h1"; depends=[baySeq DESeq edgeR Rcpp ROCR snow]; }; - EGAD = derive2 { name="EGAD"; version="1.9.2"; sha256="0xb1lcrzivadfnwl2v0x0aldsqzilcg7ygy6mizbijpfr79g8y42"; depends=[affy arrayQualityMetrics Biobase GEOquery gplots igraph impute limma MASS Matrix plyr RColorBrewer RCurl zoo]; }; - EGSEA = derive2 { name="EGSEA"; version="1.9.2"; sha256="1mphjnwvwnphq2iby76w49rlwflxvhm72488gv0ls5pyvvj68r32"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 Glimma globaltest gplots GSVA HTMLUtils htmlwidgets hwriter limma metap org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db PADOG pathview plotly RColorBrewer safe stringi topGO]; }; - ELBOW = derive2 { name="ELBOW"; version="1.17.1"; sha256="1wz4msw03g9c6732zciqpcabq8q3arxng5cbzpfgym22n0gsri82"; depends=[]; }; - ELMER = derive2 { name="ELMER"; version="2.5.7"; sha256="0a987d542rgydny6fwpvgrhjr0729b8mpr2nyv3j7ic65c1hzibf"; depends=[biomaRt circlize ComplexHeatmap doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr readr reshape rmarkdown rvest S4Vectors stringr SummarizedExperiment TCGAbiolinks xml2]; }; - EMDomics = derive2 { name="EMDomics"; version="2.11.0"; sha256="0snk2fcikj34s2hhfg9i5di92nd8lbg26ypvc1b1zcf7rj5yy07p"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; }; - ENCODExplorer = derive2 { name="ENCODExplorer"; version="2.7.0"; sha256="01sjpf4s0gdsiv6pqjmh0jq582wax9za47qf619igyzhwy2crvp1"; depends=[data_table dplyr DT jsonlite RCurl shiny shinythemes stringi stringr tidyr]; }; - ENVISIONQuery = derive2 { name="ENVISIONQuery"; version="1.29.0"; sha256="1pj6r1sb3izyr2ilv95j3nl92297zxiypjipl1x3nrqpnjn7k032"; depends=[rJava XML]; }; - ENmix = derive2 { name="ENmix"; version="1.17.0"; sha256="0hk2qj8y976ybz2pxj5ldnr13z3l64s8z7na18ry85yvbv90xzs3"; depends=[doParallel foreach geneplotter impute MASS minfi preprocessCore SummarizedExperiment sva wateRmelon]; }; - ERSSA = derive2 { name="ERSSA"; version="0.99.8"; sha256="0l56mvag5y1svm18l093037ilarna51zz56bxnbidzgvqgw1cdfc"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; }; - EasyqpcR = derive2 { name="EasyqpcR"; version="1.23.2"; sha256="1fdfhclpyv6ls6misnwa4kvm9qlgnv65pqg58q2rqd2w012kic02"; depends=[gWidgetsRGtk2 matrixStats plotrix plyr]; }; - EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.9.0"; sha256="131xg14zp0kqxwk1y2yfxb0sysf4ad97klrgsrnqkdbvjfz8wfa0"; depends=[]; }; - EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="0.99.16"; sha256="0r5v611wckw7i6qyd5zhdi7m98hqvypn3zxqy4gbis2khmblnhq0"; depends=[ggplot2 ggrepel]; }; - EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.11.3"; sha256="1y0w504rvh9zrr8dr57zdrlm8pjv34jcvlvd8d20f11yxc9c82yx"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; }; - EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.11.19"; sha256="15jcfandrlihhiw12w4akdhavr8z1pkg9cd6jb5n88dhm4hb7f72"; depends=[AnnotationDbi BiocFileCache biocGraph BiocManager ComplexHeatmap DESeq2 EDASeq edgeR geneplotter GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma MASS pathview rappdirs ReportingTools Rgraphviz S4Vectors safe SPIA SummarizedExperiment topGO]; }; - EpiDISH = derive2 { name="EpiDISH"; version="1.3.0"; sha256="07ln6hyq2lfil1xwackvhb2biay3ig6bvsyf2ll5n3glk938x02d"; depends=[e1071 MASS quadprog]; }; - EventPointer = derive2 { name="EventPointer"; version="1.99.3"; sha256="01fbip59zzhy5fg5vr1yw36dbfzcmfr23rfxz7f0r6ymihz892m3"; depends=[affxparser cobs doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges graph igraph IRanges limma MASS Matrix matrixStats nnls prodlim qvalue RBGL rhdf5 S4Vectors SGSeq stringr SummarizedExperiment]; }; - ExCluster = derive2 { name="ExCluster"; version="0.99.13"; sha256="1f9qw645bir2sxb3h3pzswhjm6p1fd2dlj6bmlsqlb9awxsj8r47"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; }; - ExiMiR = derive2 { name="ExiMiR"; version="2.23.0"; sha256="01syzl0q719fif0pdhn31hrwpbq14idwpyppcwl0b0156aid7lwv"; depends=[affy affyio Biobase limma preprocessCore]; }; - ExperimentHub = derive2 { name="ExperimentHub"; version="1.7.7"; sha256="002wzd5nll3vxncqqq95slsadj40gdj6bd59qhdhz4v6gz005h60"; depends=[AnnotationHub BiocGenerics BiocManager curl S4Vectors]; }; - ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.7.5"; sha256="1q6pc9hl5q7r8vmpk1ixb95xjh6lbikab76yhjp89xzapiprd1sl"; depends=[AnnotationHubData BiocCheck BiocGenerics BiocManager biocViews curl DBI ExperimentHub graph httr S4Vectors]; }; - ExpressionAtlas = derive2 { name="ExpressionAtlas"; version="1.9.1"; sha256="0pg30fbiz2q45b06p5jmav4gncbl01003m9m8lk2ifi0sxvx4jn6"; depends=[Biobase httr limma S4Vectors SummarizedExperiment XML xml2]; }; - ExpressionView = derive2 { name="ExpressionView"; version="1.33.0"; sha256="14h6jgdaikyjpf5bqban0ixscw3k28pczh0bsvnkhyb5916qfxch"; depends=[AnnotationDbi bitops caTools eisa GO_db isa2 KEGG_db]; }; - FCBF = derive2 { name="FCBF"; version="0.99.3"; sha256="0drpbnx5sampabr17rwjj7biw5bpngdmrrma2p3h5yq5llb409jr"; depends=[ggplot2 gridExtra SummarizedExperiment]; }; - FELLA = derive2 { name="FELLA"; version="1.1.6"; sha256="1d284qaz74d7lgxl3gn0c9i6a33x6j0xf9sbjbpm8bpl0kbhr0ln"; depends=[igraph KEGGREST Matrix plyr]; }; - FEM = derive2 { name="FEM"; version="3.9.2"; sha256="0nbg1rbx7gszbqf0xjibsgwapjrv8lniiv7kw0j50ppab69qxiqq"; depends=[AnnotationDbi BiocGenerics corrplot graph igraph impute limma marray Matrix org_Hs_eg_db]; }; - FGNet = derive2 { name="FGNet"; version="3.15.4"; sha256="1pnadm9c3ckdd5k9jgq3jmfny8mfc3w7j5w08vn0khnqlq9cp3x8"; depends=[hwriter igraph plotrix png R_utils RColorBrewer reshape2 XML]; }; - FISHalyseR = derive2 { name="FISHalyseR"; version="1.15.0"; sha256="0izn77dhzhsg69i893r9sy6qalw4qr120m6k5x5k6z9w01dgq47x"; depends=[abind EBImage]; }; - FRGEpistasis = derive2 { name="FRGEpistasis"; version="1.17.1"; sha256="17qmq5mgqhfzw3v4gl9waa1ni6h8llz2hz63p3mwrx1yixinsn20"; depends=[fda MASS]; }; - FamAgg = derive2 { name="FamAgg"; version="1.9.0"; sha256="1vqkaa1cpzd2cdyql66skz3jkrnp5ibdbhwipkj82dgww9zwwkbx"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; }; - FastqCleaner = derive2 { name="FastqCleaner"; version="0.99.40"; sha256="1hfrlr3lwcqvb1c5w6n5ffml5znjil4dchhcz4jwm2qnf6zcha0n"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; }; - FindMyFriends = derive2 { name="FindMyFriends"; version="1.11.2"; sha256="0mxpv5c2fyvcxwzaiig9qy8lg78fd8ms35nchd86nj1n4265kkx2"; depends=[Biobase BiocGenerics BiocParallel Biostrings digest dplyr filehash ggdendro ggplot2 gtable igraph IRanges kebabs Matrix Rcpp reshape2 S4Vectors]; }; - FitHiC = derive2 { name="FitHiC"; version="1.7.1"; sha256="07d3lywhc665qm3kp6f89dnvjvkgsdsvqk0ms6b3w402j12jvxsb"; depends=[data_table fdrtool Rcpp]; }; - FlowRepositoryR = derive2 { name="FlowRepositoryR"; version="1.13.1"; sha256="1vbc2bl5afa2zvqj8xp4ajdij44732689n1c28i1s32y92wzgjng"; depends=[jsonlite RCurl XML]; }; - FlowSOM = derive2 { name="FlowSOM"; version="1.13.0"; sha256="0vw98kxlcyd9rwa2r9rgjwfp5f5pmb122w2xk1gfhsf9kqh7db7g"; depends=[BiocGenerics ConsensusClusterPlus flowCore flowUtils igraph tsne XML]; }; - FoldGO = derive2 { name="FoldGO"; version="0.99.10"; sha256="0df75rvpc0031rjrx5pwfwprm1nrli2l2yafa8jbqnycz02z0dz4"; depends=[ggplot2 tidyr topGO]; }; - FourCSeq = derive2 { name="FourCSeq"; version="1.15.0"; sha256="0d8qnalv97a37l0xqxi4qi7s03zxs81122h4rw6rpi03pn5h7i10"; depends=[Biobase Biostrings DESeq2 fda GenomicAlignments GenomicRanges ggbio ggplot2 gtools LSD Matrix reshape2 Rsamtools rtracklayer SummarizedExperiment]; }; - FunChIP = derive2 { name="FunChIP"; version="1.7.0"; sha256="15pfl68yynvidx9r69xxf3zavn79savabam5yjjwqq7g9yvhzjw5"; depends=[doParallel fda foreach GenomeInfoDb GenomicAlignments GenomicRanges RColorBrewer Rcpp Rsamtools shiny]; }; - FunciSNP = derive2 { name="FunciSNP"; version="1.25.3"; sha256="0w9wqlkj52dwzrhxwq193435camj12kjv1a70rdnzdlvi3y849hm"; depends=[Biobase BiocGenerics ChIPpeakAnno FunciSNP_data GenomicRanges ggplot2 IRanges plyr reshape Rsamtools rtracklayer S4Vectors scales snpStats TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; - GA4GHclient = derive2 { name="GA4GHclient"; version="1.5.0"; sha256="1bcskcxcmv47rdgrw0i8rm4cn27jqy86rx8z83qnanbzqp4g7kgg"; depends=[BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges httr IRanges jsonlite S4Vectors VariantAnnotation]; }; - GA4GHshiny = derive2 { name="GA4GHshiny"; version="1.3.0"; sha256="031p9qa6cp4gxlgp8whswl7b11d24d4zl3m9fkqg3i461kjyswxj"; depends=[AnnotationDbi BiocGenerics dplyr DT GA4GHclient GenomeInfoDb GenomicFeatures openxlsx purrr S4Vectors shiny shinyjs shinythemes tidyr]; }; - GARS = derive2 { name="GARS"; version="1.1.1"; sha256="004i5nkmdi61fkkxps1frlhs4gd8ix6s3yypzrl6s4afvm05hw4p"; depends=[cluster DaMiRseq ggplot2 MLSeq SummarizedExperiment]; }; - GAprediction = derive2 { name="GAprediction"; version="1.7.0"; sha256="04bxpyc13mq7klkpkyw574cbk6xsjn9n91za7hvmzg5xfzgdr2rg"; depends=[glmnet Matrix]; }; - GDCRNATools = derive2 { name="GDCRNATools"; version="1.1.9"; sha256="134f9264b1br2s2d99dlad1r8nwzkv78qkr7iqym8s1anl7xsh9j"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; }; - GDSArray = derive2 { name="GDSArray"; version="1.1.1"; sha256="0cgs1fhzqax8nbihifhmgd6clk4wf3586x85cmg06ydxdh9yyzlv"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; }; - GEM = derive2 { name="GEM"; version="1.7.1"; sha256="0sxlqkd2rhi511jmi2c82ib0krx9pynssvw0gcr2mrrxj5gy2vcz"; depends=[ggplot2]; }; - GENESIS = derive2 { name="GENESIS"; version="2.11.17"; sha256="1czvvmqnmpx9wpq6hw4xfwhj1vjrwdrwbj8b4zcs1x7dv8qkvyb5"; depends=[Biobase BiocGenerics data_table dplyr foreach gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; }; - GENIE3 = derive2 { name="GENIE3"; version="1.3.1"; sha256="0zp1g97xmigjarpbmfnay1gac5fjhcslrdp656gzafdah32k2nzl"; depends=[reshape2]; }; - GEOmetadb = derive2 { name="GEOmetadb"; version="1.43.0"; sha256="05ad0h84vqkcp9b9966dsmgwl4r2xsg9wjjgwcfx00yc9jgg94lj"; depends=[GEOquery RSQLite]; }; - GEOquery = derive2 { name="GEOquery"; version="2.49.1"; sha256="1vxhz9drmj90j67ga7jflzb602bs1b9qdamz7vgazlpl0xj7ls5s"; depends=[Biobase dplyr httr limma magrittr readr tidyr xml2]; }; - GEOsubmission = derive2 { name="GEOsubmission"; version="1.33.0"; sha256="17qck1a7szkgaixkjzq2c4vw7kb7cy8sv609z3i8h0pljrprvx07"; depends=[affy Biobase]; }; - GEWIST = derive2 { name="GEWIST"; version="1.25.0"; sha256="0dr7vz9v8cfjg8vxxqs0c7i4vzvfdnp741b82radwb0ya4crfml0"; depends=[car]; }; - GGBase = derive2 { name="GGBase"; version="3.43.2"; sha256="1kwh6di0kgw821mh0gmgrm8b0mlbcyji5yc0pn4v836w0wc0amqb"; depends=[AnnotationDbi Biobase BiocGenerics digest genefilter GenomicRanges IRanges limma Matrix S4Vectors snpStats SummarizedExperiment]; }; - GGtools = derive2 { name="GGtools"; version="5.17.1"; sha256="1p7wczch0nnb5ax5g1889iz3qr5ffwyhgvlrln19ypb20c454cnk"; depends=[AnnotationDbi biglm Biobase BiocGenerics Biostrings bit data_table ff GenomeInfoDb GenomicRanges GGBase ggplot2 Gviz hexbin Homo_sapiens IRanges iterators reshape2 ROCR Rsamtools rtracklayer S4Vectors snpStats VariantAnnotation]; }; - GIGSEA = derive2 { name="GIGSEA"; version="0.99.25"; sha256="0k6njipzq9r6g9gkn9g2blkmhq752yv4n2127wxvxfi4kkwf8nfc"; depends=[locfdr MASS Matrix]; }; - GISPA = derive2 { name="GISPA"; version="1.5.0"; sha256="1030cwbkccj2scjmszlzbxd28qgwga26hf86jly8xmw9qvpa77y1"; depends=[Biobase changepoint data_table genefilter GSEABase HH lattice latticeExtra plyr scatterplot3d]; }; - GLAD = derive2 { name="GLAD"; version="2.45.1"; sha256="1cpjai8dxqb35xf2933rf4z08zmli760scz6s1zdzbgpc92dl2zl"; depends=[aws]; }; - GMRP = derive2 { name="GMRP"; version="1.9.0"; sha256="06q87139z5dgl0c4i8jhry15q9ah9k19kgjmadkb55lfsb3akazn"; depends=[diagram GenomicRanges plotrix]; }; - GOFunction = derive2 { name="GOFunction"; version="1.29.1"; sha256="05yz8kl6m3ypdvi5mb813nvc8s75ybbc16ppdza6pkrf5cdawy55"; depends=[AnnotationDbi Biobase DBI GO_db graph Rgraphviz SparseM]; }; - GOSemSim = derive2 { name="GOSemSim"; version="2.7.1"; sha256="1q1h4ak6ki9hn9psrx17psf7kmcn2c7jy5q428qvwk4raq5fhdh0"; depends=[AnnotationDbi GO_db Rcpp]; }; - GOSim = derive2 { name="GOSim"; version="1.19.0"; sha256="0irpycjkzzdymg50zf2szgf7v4s2s0skfpjf5ckdrzskkjr2jzc1"; depends=[annotate AnnotationDbi cluster corpcor flexmix GO_db graph Matrix org_Hs_eg_db RBGL Rcpp topGO]; }; - GOTHiC = derive2 { name="GOTHiC"; version="1.17.1"; sha256="00na8sn5fszb9z0z58xwlrxzwvxsahhisn2sc8g6xqcfld231pfr"; depends=[BiocGenerics Biostrings BSgenome data_table GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors ShortRead]; }; - GOexpress = derive2 { name="GOexpress"; version="1.15.0"; sha256="0k1hiinzn4553gh6app0kvd84md0g3jydv1y2rlzrcasamba7xvv"; depends=[Biobase biomaRt ggplot2 gplots randomForest RColorBrewer RCurl stringr]; }; - GOfuncR = derive2 { name="GOfuncR"; version="1.1.6"; sha256="10bvn7hq8igd1wj4izg6nb06v4dn88gc65r7pq02z29dz1n5rbnv"; depends=[AnnotationDbi GenomicRanges gtools IRanges mapplots Rcpp vioplot]; }; - GOpro = derive2 { name="GOpro"; version="1.7.1"; sha256="0np0df5nfgcr435ngs8bbfiklp8b3v01842jkfdf2wwasx7c4mlw"; depends=[AnnotationDbi BH dendextend doParallel foreach GO_db IRanges MultiAssayExperiment org_Hs_eg_db Rcpp S4Vectors]; }; - GOstats = derive2 { name="GOstats"; version="2.47.0"; sha256="1dxzr3xnn60iy2xv8k0j1r9bz1lq1g1n792gzl308dsy35p25cim"; depends=[annotate AnnotationDbi AnnotationForge Biobase Category GO_db graph RBGL Rgraphviz]; }; - GOsummaries = derive2 { name="GOsummaries"; version="2.17.2"; sha256="1ndpqr43rs3wrsrm5i0bn4xhcjylpddf95vnmyzq3rn3vc0y89sd"; depends=[ggplot2 gProfileR gtable limma plyr Rcpp reshape2]; }; - GRENITS = derive2 { name="GRENITS"; version="1.33.0"; sha256="1jgsk0wcrkcvf6cgypmdyj6zjfxwxan5xm88l1ycdrilfrx1g582"; depends=[ggplot2 Rcpp RcppArmadillo reshape2]; }; - GRmetrics = derive2 { name="GRmetrics"; version="1.7.3"; sha256="1xnbfqqw63inh1fyfclb369b6j3ihn6jnvglkmrvp609x104sakb"; depends=[drc ggplot2 plotly S4Vectors SummarizedExperiment]; }; - GRridge = derive2 { name="GRridge"; version="1.5.3"; sha256="1bdv13j5vk38mrj06dms6xgyl21xqf5rzp8f5y8p7a0q36npflcr"; depends=[glmnet graph Iso mvtnorm penalized survival]; }; - GSALightning = derive2 { name="GSALightning"; version="1.9.0"; sha256="1qwq8yawf0llik4880y9j3qzbl9py404wrp6p2738qjb1mxyx9nr"; depends=[data_table Matrix]; }; - GSAR = derive2 { name="GSAR"; version="1.15.1"; sha256="185ywirc49x7dy3vzy346avzsc16xjzsdr4njfr7f5bc421xkyxz"; depends=[igraph]; }; - GSCA = derive2 { name="GSCA"; version="2.11.1"; sha256="1ahkd5ivr38c4igmwdr5fk5kaysw3128a4y15ydz2ab2488vgsd4"; depends=[ggplot2 gplots RColorBrewer reshape2 rhdf5 shiny sp]; }; - GSEABase = derive2 { name="GSEABase"; version="1.43.2"; sha256="1zhzvcjv9m9d0qmhf5csafq5inb1czkmwxm1ivyh2zrn2a66f8kl"; depends=[annotate AnnotationDbi Biobase BiocGenerics graph XML]; }; - GSEABenchmarkeR = derive2 { name="GSEABenchmarkeR"; version="1.1.1"; sha256="102hvayxljl0nk4593aw0hdpdr929v5yhknyppnxyqrnmply8vqp"; depends=[AnnotationDbi AnnotationHub Biobase BiocFileCache BiocParallel edgeR EnrichmentBrowser ExperimentHub GEOquery KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO rappdirs S4Vectors SummarizedExperiment]; }; - GSEAlm = derive2 { name="GSEAlm"; version="1.41.0"; sha256="1di0d7zpsigi6k4bxfnq0yniyssxrmzdih3xayg6facpwgyhkp6n"; depends=[Biobase]; }; - GSRI = derive2 { name="GSRI"; version="2.29.0"; sha256="0g3nncckasyx3n6nq5aihahzk73h6xb1m8xmq3m046vz245ny76x"; depends=[Biobase fdrtool genefilter GSEABase les]; }; - GSReg = derive2 { name="GSReg"; version="1.15.0"; sha256="1qazhsx6gfnywwkhxip962v4jr5njbf97k36nbnq20q0yavwgzhz"; depends=[AnnotationDbi GenomicFeatures Homo_sapiens org_Hs_eg_db]; }; - GSVA = derive2 { name="GSVA"; version="1.29.3"; sha256="12x52iq2c9y7y3hfza849754xf8z8ysh41dk0id7dy9mbjawvz7d"; depends=[Biobase BiocGenerics geneplotter GSEABase shiny shinythemes]; }; - GUIDEseq = derive2 { name="GUIDEseq"; version="1.11.0"; sha256="1qxb0mrrldyac16zfzkqcy11750hakr4hgqm8ai1cabr6xd5yna1"; depends=[BiocGenerics BiocParallel Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table GenomeInfoDb GenomicAlignments GenomicRanges hash IRanges limma matrixStats Rsamtools S4Vectors]; }; - GWASTools = derive2 { name="GWASTools"; version="1.27.3"; sha256="0snjz7vqfq5izfk68z3r7d0356almksxbsc79m2ryk7mkfjfw5bx"; depends=[Biobase DBI DNAcopy gdsfmt GWASExactHW lmtest logistf quantsmooth RSQLite sandwich survival]; }; - GateFinder = derive2 { name="GateFinder"; version="1.1.0"; sha256="1blj8407nl6nsn8dyg31xj4ii8rr2rfkg35g1hf97j60dk53bmwf"; depends=[diptest flowCore flowFP mvoutlier splancs]; }; - GenRank = derive2 { name="GenRank"; version="1.9.0"; sha256="05g9mram44zs76m48rvplwdhdlhkygfxrzgdsd43was2xvyj6nvb"; depends=[matrixStats reshape2 survcomp]; }; - GenVisR = derive2 { name="GenVisR"; version="1.13.2"; sha256="1ca47n9ddnm20vjj7070wfmmd9ff8w58d5rd79sq23hszmzwyzlf"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome data_table DBI FField GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales VariantAnnotation viridis]; }; - GeneAccord = derive2 { name="GeneAccord"; version="0.99.13"; sha256="1rw3wrgvqxznia7p0vm55dkq5rfks1gq5nixcf4ljzd9kcwc4ggs"; depends=[biomaRt caTools dplyr ggplot2 ggpubr gtools magrittr maxLik RColorBrewer reshape2 tibble]; }; - GeneAnswers = derive2 { name="GeneAnswers"; version="2.23.1"; sha256="0nxilnnhb48jwbplwhndwd8y5rlmhyjfjywc1whcij3hz9f6yzp9"; depends=[annotate Biobase downloader Heatplus igraph MASS RBGL RColorBrewer RCurl RSQLite XML]; }; - GeneBreak = derive2 { name="GeneBreak"; version="1.11.1"; sha256="0pyvj6grznl5qjki857zfhqcn05xwhicm6l1jxa1jc0aav91y764"; depends=[CGHbase CGHcall GenomicRanges QDNAseq]; }; - GeneExpressionSignature = derive2 { name="GeneExpressionSignature"; version="1.27.0"; sha256="0bmhxzrg5d7v4lv4k2igl7ah8fncrggyziwqyhawavig17i1iqzc"; depends=[Biobase PGSEA]; }; - GeneGA = derive2 { name="GeneGA"; version="1.31.0"; sha256="0fdfb6x7rjg4ak5xbikwj6fmmrnr3hnsi97amn69w81087228b5g"; depends=[hash seqinr]; }; - GeneGeneInteR = derive2 { name="GeneGeneInteR"; version="1.7.0"; sha256="03kkfv7vj717brzdw346yapxfg414v84wncqqrv3si03q4w450mz"; depends=[data_table FactoMineR GenomicRanges GGtools igraph IRanges kernlab mvtnorm plspm rioja Rsamtools snpStats]; }; - GeneMeta = derive2 { name="GeneMeta"; version="1.53.0"; sha256="18f1nca21drjpv55b4d92zkgqr3zqhzp98slq6xfqvsj3rip6y5v"; depends=[Biobase genefilter]; }; - GeneNetworkBuilder = derive2 { name="GeneNetworkBuilder"; version="1.23.2"; sha256="1nikjknsfy99i3b3r384gjlw8rzk4wv1wqflwpnrnffvzxh3sr5d"; depends=[graph htmlwidgets plyr Rcpp Rgraphviz rjson XML]; }; - GeneOverlap = derive2 { name="GeneOverlap"; version="1.17.0"; sha256="0dqsq1sd1ly6gvnpq3xcv9idr30kazx97jha9icv1g64d337l289"; depends=[gplots RColorBrewer]; }; - GeneRegionScan = derive2 { name="GeneRegionScan"; version="1.37.0"; sha256="1672nriz5r0gpgb6c9bsa864ap3ap68n1igvpf9q8mf3sw659m3b"; depends=[affxparser Biobase Biostrings RColorBrewer S4Vectors]; }; - GeneSelectMMD = derive2 { name="GeneSelectMMD"; version="2.25.0"; sha256="1lwszjpxp9bj0hd5z1kasq2qv49swji3ib1ljlph22wh0j9jimid"; depends=[Biobase limma MASS survival]; }; - GeneSelector = derive2 { name="GeneSelector"; version="2.31.2"; sha256="1z346x227rs0nlyzf1idmcb2s05fhp68i3cjiib2d2328fs0yzyw"; depends=[Biobase limma multtest samr siggenes]; }; - GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.1.0"; sha256="0w8ydly5qi8cvdhhda2q3k8fj9k9v1sg3c45h4ki02vx19j2kap0"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; }; - GeneticsDesign = derive2 { name="GeneticsDesign"; version="1.49.0"; sha256="1n9d1i45dcmp2irnsc5ak9pk33r68nzd84iixylwaj302l7yphjs"; depends=[gmodels gtools mvtnorm]; }; - GeneticsPed = derive2 { name="GeneticsPed"; version="1.43.1"; sha256="0agd99r4jhp4y2ix5qrbwrycy3r8pc1cwa09ib3mhg5jdszm6jr8"; depends=[gdata genetics MASS]; }; - GenoGAM = derive2 { name="GenoGAM"; version="1.99.0"; sha256="18s3hh2gis61sakld098ffpihy2fd11sia94cxxq9cy0wl49bzci"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; }; - GenomeGraphs = derive2 { name="GenomeGraphs"; version="1.41.0"; sha256="07vwj2pbrxgj3k673m8xrf3cpqc1g753fvj950qwmy4jmz6s8w04"; depends=[biomaRt]; }; - GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.17.4"; sha256="1kma1ywai2l8lknng1hpp5nxgv45rwiih0ac9nxmg5ydb910m2z0"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; }; - GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.17.3"; sha256="17kdllb2griy85qdk8nkx1qislc424kpibsrfb2pirf6xjm82rxn"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; }; - GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.5.8"; sha256="0gp8izsk2kb2adv8ykmsjzba39lbkw02061f5j82ysvgzmb2gh16"; depends=[dplyr GenomicRanges httr IRanges jsonlite lazyeval magrittr rappdirs readr S4Vectors SummarizedExperiment xml2]; }; - GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.33.6"; sha256="0qq5yh524qxd3qa9i10niqk3aw4ff7b6xfr10041gk1r94l7apyv"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; - GenomicFiles = derive2 { name="GenomicFiles"; version="1.17.4"; sha256="160mnxz41wzlqigc9r40pkn5jc0raa84y1yjiyhj1406fv2aaj6n"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; - GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.15.1"; sha256="0jga57bna3fbfrzp9525mzp9c6amy8i6i1j65vf3l7hw75d8q20z"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; }; - GenomicRanges = derive2 { name="GenomicRanges"; version="1.33.14"; sha256="1vmvmrd65dxhm06r879kqmncs9f4sg5z70fi0409b2078ia4qiyp"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; }; - GenomicScores = derive2 { name="GenomicScores"; version="1.5.6"; sha256="1fyich4fdz3pfxi95mdz6mmnva9kb7ak5wslzlh6sar62cfk17mx"; depends=[AnnotationHub Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors XML]; }; - GenomicTuples = derive2 { name="GenomicTuples"; version="1.15.2"; sha256="0hgnz5f5d3wh54icj36v6j06q87w19acnyd696aw78fk590mkvs5"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; - Genominator = derive2 { name="Genominator"; version="1.35.0"; sha256="0qvzw9r8hn19gzkj6r94v4787h9lbw8y2s9k7zasn2cdyx55074i"; depends=[BiocGenerics DBI GenomeGraphs IRanges RSQLite]; }; - Glimma = derive2 { name="Glimma"; version="1.9.2"; sha256="1njcjla1az23lrg5j93s1hxjrrjsf808plmvdhiai14fdlgzfb8w"; depends=[edgeR jsonlite S4Vectors]; }; - GlobalAncova = derive2 { name="GlobalAncova"; version="3.99.3"; sha256="1d38kp53qw25g2pdsiz4g38nm5hjr537i6ly7lvabvh5zim7h0bn"; depends=[annotate AnnotationDbi Biobase corpcor dendextend globaltest GSEABase VGAM]; }; - GoogleGenomics = derive2 { name="GoogleGenomics"; version="2.3.2"; sha256="00qf7zadaryylkkizfdaapdppzxkfwdzwkv4qxkvwz1pkvr1yc5r"; depends=[Biobase Biostrings GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges rjson Rsamtools S4Vectors VariantAnnotation]; }; - GraphAT = derive2 { name="GraphAT"; version="1.53.0"; sha256="0wsn0nfj4qds2kxm3gxfx8wwyf00l0ifvk660czm7zc6ppfj1sb8"; depends=[graph MCMCpack]; }; - GraphAlignment = derive2 { name="GraphAlignment"; version="1.45.0"; sha256="0mdy8g3i4b7wy9zqfbb1zia1h84kv2av4yl6japzz5ymiipjaimy"; depends=[]; }; - GraphPAC = derive2 { name="GraphPAC"; version="1.23.1"; sha256="1xr4ys2ckzyc8w5c3pmywp341viac9xv9hz691lgm61krafyh370"; depends=[igraph iPAC RMallow TSP]; }; - GreyListChIP = derive2 { name="GreyListChIP"; version="1.13.0"; sha256="0m9qvb3rw1hr119vq2k5fdbywq8vfgfhxwm6r9nfmxdhdir6178j"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; }; - Guitar = derive2 { name="Guitar"; version="1.19.0"; sha256="0khy7vhr8r56r14kiqz83py227jaji46aqlqs8yhj7kh6cgh59c5"; depends=[GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rsamtools rtracklayer]; }; - Gviz = derive2 { name="Gviz"; version="1.25.0"; sha256="0c64bn8dqvcwi3jdfx0yg2jc7x1v41h4py7ily9z82ms8lfv7jh8"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; }; - HDF5Array = derive2 { name="HDF5Array"; version="1.9.19"; sha256="01421q7hz1kmj4s4iwzb01ibq3ssz3sh67smg0ap52d1ykqqx8mx"; depends=[BiocGenerics DelayedArray IRanges rhdf5 S4Vectors]; }; - HDTD = derive2 { name="HDTD"; version="1.15.1"; sha256="08h1wnsacr74ynjwn4aw98lwf9pjf081g1yi4557xb7cfzf4l6pn"; depends=[Rcpp RcppArmadillo]; }; - HELP = derive2 { name="HELP"; version="1.39.0"; sha256="1sb43vndrk5qbazxwx3n0lmkb43525vmarj3hbkqplid5bppcddp"; depends=[Biobase]; }; - HEM = derive2 { name="HEM"; version="1.53.0"; sha256="090k94d4bfmf1fqbxhlp2vb70x7934xwq8fjmgc2wlrq5d1iqjff"; depends=[Biobase]; }; - HIBAG = derive2 { name="HIBAG"; version="1.17.2"; sha256="08fdgnrzx113cqk7v6wv7kfj13lhg2j4f86ap4ily1wirbb0q8y2"; depends=[]; }; - HIREewas = derive2 { name="HIREewas"; version="0.99.8"; sha256="1df575f0fld051il5cpz27syvfmm70idvhr2af82r2lqbzz4ik8v"; depends=[gplots quadprog]; }; - HMMcopy = derive2 { name="HMMcopy"; version="1.23.0"; sha256="1ciawdh971fwfa60lb1469pqgmw9giyqksqk5zkfbal967pia1ck"; depends=[geneplotter IRanges]; }; - HPAanalyze = derive2 { name="HPAanalyze"; version="0.99.19"; sha256="1s5inkcpsga791ranlf7c3bbdq42s05h4q7ba465lym685gpz18l"; depends=[cowplot dplyr ggplot2 hpar magrittr readr reshape2 tibble tidyr XLConnect xml2]; }; - HTSFilter = derive2 { name="HTSFilter"; version="1.21.0"; sha256="1c85v66fax6h00dkny5308mv1vsdinj590x6w4aghd6b4nb16qgr"; depends=[Biobase BiocParallel DESeq DESeq2 edgeR]; }; - HTSanalyzeR = derive2 { name="HTSanalyzeR"; version="2.33.0"; sha256="10agvn6dcmzczj5xdpviisnamfs6642xskh7zgh14c0p13gv76xs"; depends=[AnnotationDbi biomaRt BioNet cellHTS2 graph GSEABase igraph RankProd]; }; - HTSeqGenie = derive2 { name="HTSeqGenie"; version="4.11.0"; sha256="0k6ql5pkn2yjvmf13g4lzrqb0jcnp0rqsvakkqmirpj2b40wynj1"; depends=[BiocGenerics BiocParallel Biostrings Cairo chipseq GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR hwriter IRanges Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment VariantAnnotation VariantTools]; }; - HTqPCR = derive2 { name="HTqPCR"; version="1.35.0"; sha256="09wc412znd92fi3lm909mrz3xd9cjiwiw6b0ncki1yc186faizr4"; depends=[affy Biobase gplots limma RColorBrewer]; }; - Harman = derive2 { name="Harman"; version="1.9.1"; sha256="1nk5szn0zgw1301m6jn9kr6qp3z1766a2nzp8sp9x6fnigc7zmsi"; depends=[Rcpp]; }; - Harshlight = derive2 { name="Harshlight"; version="1.53.0"; sha256="0nlghc13lmhvsy06spvzhc7cihpzayli1iyid7h7ifa8zik6dz72"; depends=[affy altcdfenvs Biobase]; }; - Heatplus = derive2 { name="Heatplus"; version="2.27.0"; sha256="1fyz7272w2ixisvg0gsv30svppd6xd47r79xg1r1y2qy62q04bca"; depends=[RColorBrewer]; }; - HelloRanges = derive2 { name="HelloRanges"; version="1.7.0"; sha256="1h88zrvx3h4s7jsadyf3f3x6p0hbkn2f6smnkdmm7fva4lhlg7hl"; depends=[BiocGenerics Biostrings BSgenome docopt GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; - HiCBricks = derive2 { name="HiCBricks"; version="0.99.16"; sha256="11rafxnh91mgl73xvqw83q9fhvm1gy6ma3c6r1xrwbjkwib5iam5"; depends=[BiocFileCache curl data_table digest GenomeInfoDb GenomicRanges ggplot2 IRanges R6 rappdirs RColorBrewer reshape2 rhdf5 S4Vectors scales stringr viridis]; }; - HiCcompare = derive2 { name="HiCcompare"; version="1.3.2"; sha256="0mqslkc98yz8hhil6fapxwzs4qy5v784knnakkm01rz0sjpb8jbp"; depends=[BiocParallel data_table dplyr GenomicRanges ggplot2 gridExtra gtools InteractionSet IRanges KernSmooth mgcv pheatmap QDNAseq S4Vectors]; }; - HiTC = derive2 { name="HiTC"; version="1.25.0"; sha256="1mryn42bsvswb0gf027aw4qbrk57w8859zyvicymdi3d78pw8rmv"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; }; - HilbertCurve = derive2 { name="HilbertCurve"; version="1.11.2"; sha256="0kxl5ihmgvsafiwi576kgyz1g60a25w6r8m4g9w6pzdwcxzp871d"; depends=[circlize GenomicRanges HilbertVis IRanges png]; }; - HilbertVis = derive2 { name="HilbertVis"; version="1.39.2"; sha256="1qmnv0m4ywcjwqljvs9kbif63cyr842lzsj2flh5f3bf7pha1s7f"; depends=[lattice]; }; - HilbertVisGUI = derive2 { name="HilbertVisGUI"; version="1.39.0"; sha256="1jq70si8q74jg22zg4gx4c6nbi8zszgiqrbc6cavn4v578fam3z1"; depends=[HilbertVis]; }; - HybridMTest = derive2 { name="HybridMTest"; version="1.25.0"; sha256="0g667li0fhf085ha9210xwj3r0sy7ks9lj5v8lpiyz48yi8w2nfn"; depends=[Biobase fdrtool MASS survival]; }; - IHW = derive2 { name="IHW"; version="1.9.2"; sha256="10lwbvr33xsxxs0sy8skyym81gw4328xxwdkhhmz0cyqgy23k3jr"; depends=[BiocGenerics fdrtool lpsymphony slam]; }; - IMAS = derive2 { name="IMAS"; version="1.5.1"; sha256="0p5rhnvkzms8bvwc5lhkgi8hyqsm82mdwmsk245xxrrjdn6ir6ff"; depends=[AnnotationDbi BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfortify ggplot2 gridExtra IRanges IVAS lattice lme4 Matrix Rsamtools S4Vectors survival]; }; - IMMAN = derive2 { name="IMMAN"; version="1.1.0"; sha256="0sgyiq7wif4imq81qqgwhbrx54dr26gb22j79mzzjyprv8yxgdkj"; depends=[BiocFileCache Biostrings igraph seqinr STRINGdb]; }; - IMPCdata = derive2 { name="IMPCdata"; version="1.17.0"; sha256="0r5j70i1mdrpxjznmb6i561076n1vk1h371kvlxkb8y343ajz7sq"; depends=[rjson]; }; - INDEED = derive2 { name="INDEED"; version="0.99.17"; sha256="0v9vx1zb3r6861h7zb2bg15a541q04v8k2pf3j0i8vd5az32knlv"; depends=[devtools glasso]; }; - INPower = derive2 { name="INPower"; version="1.17.0"; sha256="1ilqffcbaxwk54m297f4znhbphjjipjfd82554z4mwdrkf0cz2lw"; depends=[mvtnorm]; }; - INSPEcT = derive2 { name="INSPEcT"; version="1.11.0"; sha256="1na92547w6qn6dkhy3zp3gj1g3vr2y3kx6j78hnq0ch9l8k9s2c7"; depends=[Biobase BiocGenerics BiocParallel deSolve GenomicAlignments GenomicFeatures GenomicRanges IRanges preprocessCore pROC rootSolve Rsamtools S4Vectors]; }; - IONiseR = derive2 { name="IONiseR"; version="2.5.0"; sha256="0gn75w73ahyk3vm70vq003rlg1wsazfy7qygdp4dnq0g9qpz8dyy"; depends=[BiocGenerics BiocParallel Biostrings bit64 dplyr ggplot2 magrittr rhdf5 ShortRead stringr tibble tidyr XVector]; }; - IPO = derive2 { name="IPO"; version="1.7.1"; sha256="0hgflvvy840y822bk3bm2sj8yqc8q3nipxxqa5j6if17w10icvvn"; depends=[BiocParallel CAMERA rsm xcms]; }; - IPPD = derive2 { name="IPPD"; version="1.29.0"; sha256="1gwsq17ipba4q7jby4hj7bwrpbfzach5spsvnb4571x7nr6yx7qg"; depends=[bitops digest MASS Matrix XML]; }; - IRanges = derive2 { name="IRanges"; version="2.15.19"; sha256="096d7hil68zhy2l2vhd0q5prkrzybbwl28fa00k7rbail5vh8r8v"; depends=[BiocGenerics S4Vectors]; }; - ISoLDE = derive2 { name="ISoLDE"; version="1.9.0"; sha256="111p1wxyn3kqx6gdnrl55jwnlnqfa98wljkiw4wqqf2cdrykb7pr"; depends=[]; }; - ITALICS = derive2 { name="ITALICS"; version="2.41.0"; sha256="1lj5n1xgq49xn8yv8q6lfg01hw8l4yc5ffc98falzhlcvqxhkvzc"; depends=[affxparser DBI GLAD ITALICSData oligo oligoClasses pd_mapping50k_xba240]; }; - IVAS = derive2 { name="IVAS"; version="2.1.0"; sha256="0ipw8834ag1j2qg3i5nnfcncrjpzhd2m5hzhn1bjpvhd357r1gn1"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges ggfortify ggplot2 IRanges lme4 Matrix S4Vectors]; }; - IWTomics = derive2 { name="IWTomics"; version="1.5.2"; sha256="1rmlr66mgg5nfm2b50g0a83ahs0xkkji1is930vjprrfcn6clmn2"; depends=[fda GenomicRanges gtable IRanges KernSmooth S4Vectors]; }; - Icens = derive2 { name="Icens"; version="1.53.0"; sha256="16cxm1i6ir74l2x80wsp544ykffy91m4fv8v283nki0hx434pkn7"; depends=[survival]; }; - IdMappingAnalysis = derive2 { name="IdMappingAnalysis"; version="1.25.0"; sha256="025zqjc36whlraq3hjz0p5dzj5m19y50clrlgrimrz4ag5bfmf2q"; depends=[Biobase boot mclust R_oo rChoiceDialogs RColorBrewer]; }; - IdMappingRetrieval = derive2 { name="IdMappingRetrieval"; version="1.29.0"; sha256="0fn8xp7ybpg0z3bnk9sab53y7kflzys0r1cvikyp5n8pfkrr95g2"; depends=[AffyCompatible biomaRt ENVISIONQuery R_methodsS3 R_oo rChoiceDialogs RCurl XML]; }; - IdeoViz = derive2 { name="IdeoViz"; version="1.17.0"; sha256="0yr7yisb9hr2jsdlv7m59p9kiaxssv6rj8x4rqzraaipd7cn0gcy"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges RColorBrewer rtracklayer]; }; - Imetagene = derive2 { name="Imetagene"; version="1.11.0"; sha256="1zswp6h2c9nn4p73knp4wsnbqv77gp86njzpxjvgqjmvfj57y8nc"; depends=[d3heatmap ggplot2 metagene shiny shinyBS shinyFiles shinythemes]; }; - ImmuneSpaceR = derive2 { name="ImmuneSpaceR"; version="1.9.3"; sha256="1dlb8dklkizcbmy7kc8mgr8d60k59j1zwgdfs9lf2zlxmzqz44zv"; depends=[Biobase curl data_table ggplot2 gplots gtools heatmaply httr pheatmap plotly preprocessCore R6 reshape2 rjson Rlabkey rmarkdown scales]; }; - ImpulseDE = derive2 { name="ImpulseDE"; version="1.7.0"; sha256="0g34jfff5lsvzak21fdi2fdx9a2v0n1f2cmjsk62jkjzr9jpyp2f"; depends=[amap boot]; }; - ImpulseDE2 = derive2 { name="ImpulseDE2"; version="1.5.0"; sha256="1f9nymih6fwq6p53x9f7zjblkdrrj0f89w1lv9f8bdz1y4icn1y4"; depends=[Biobase BiocParallel circlize ComplexHeatmap cowplot DESeq2 ggplot2 knitr Matrix S4Vectors SummarizedExperiment]; }; - InPAS = derive2 { name="InPAS"; version="1.13.1"; sha256="0wj459bay4ywq9aymdp2snw6fzhbrdfg80ya96z8kgprxvp2r21z"; depends=[AnnotationDbi Biobase BiocParallel BSgenome cleanUpdTSeq depmixS4 GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges limma preprocessCore S4Vectors seqinr]; }; - InTAD = derive2 { name="InTAD"; version="1.1.0"; sha256="0pm720gl7apzbcqxd53gj4ynkglv4bb0xrzibcwbpwgsmi75g55c"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggpubr IRanges mclust MultiAssayExperiment qvalue rtracklayer S4Vectors SummarizedExperiment]; }; - IntEREst = derive2 { name="IntEREst"; version="1.5.2"; sha256="0vm9bp8cp8igmxcsd8n8s9y5nmcm98fsj1albcn8p87iq2jgkvix"; depends=[BiocGenerics BiocParallel Biostrings DBI DESeq2 DEXSeq edgeR GenomicAlignments GenomicFeatures GenomicRanges IRanges RMySQL Rsamtools S4Vectors seqinr seqLogo SummarizedExperiment]; }; - InterMineR = derive2 { name="InterMineR"; version="1.3.3"; sha256="0x8nlvffa4i4rnk7ib11a29f5cr4vmvc4hspm0gir186zqcg7dw8"; depends=[Biostrings GenomicRanges httr igraph IRanges RCurl RJSONIO S4Vectors sqldf SummarizedExperiment XML xml2]; }; - InteractionSet = derive2 { name="InteractionSet"; version="1.9.5"; sha256="1dmk08y0416ffljinh16qvvnm7hifdbbfzpg59r9l0lqwgpkligk"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix Rcpp S4Vectors SummarizedExperiment]; }; - IntramiRExploreR = derive2 { name="IntramiRExploreR"; version="1.3.0"; sha256="015mjy0fcch4z3nsy5jvyl6jcc6zigvfh4s35nm3yjw2plg06jm4"; depends=[FGNet igraph knitr]; }; - IsoCorrectoR = derive2 { name="IsoCorrectoR"; version="0.99.3"; sha256="11py0fpn0lz62my2zfs1p5aahjjda259gnfwsa47jid6dx9lghw4"; depends=[dplyr magrittr pracma quadprog readr readxl stringr tibble WriteXLS]; }; - IsoGeneGUI = derive2 { name="IsoGeneGUI"; version="2.17.0"; sha256="0fx9zkvg8471kcyda3hvp7zjv6d1z1pr2sq5882xn1amhcjpwws1"; depends=[Biobase ff geneplotter goric Iso IsoGene jpeg multtest ORCME ORIClust orQA RColorBrewer Rcpp relimp tkrplot xlsx]; }; - IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.3.10"; sha256="1r1y2fzhiv1r86jrd1miij164lq5pa6425shcd8jfza9igpnlmz6"; depends=[Biostrings BSgenome DBI DEXSeq dplyr DRIMSeq edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr plyr RColorBrewer readr reshape2 rtracklayer stringr tximport VennDiagram]; }; - JunctionSeq = derive2 { name="JunctionSeq"; version="1.11.2"; sha256="1hhfam0yfrwyjvkzsn5pnx2564zggzw2y9163g4sxjxr5a0y5ggb"; depends=[Biobase BiocGenerics BiocParallel DESeq2 genefilter geneplotter GenomicRanges Hmisc IRanges locfit plotrix Rcpp RcppArmadillo S4Vectors statmod stringr SummarizedExperiment]; }; - KCsmart = derive2 { name="KCsmart"; version="2.39.0"; sha256="1y5lrcl4inkdmbr9bma02j7g4r0my49jvc434mzgvjmv6zfilm4k"; depends=[BiocGenerics KernSmooth multtest siggenes]; }; - KEGGREST = derive2 { name="KEGGREST"; version="1.21.2"; sha256="1xbs8c2p4y0igwazh0iy7g0bsjqvrp76gdn3bfgvyig75x7fkiv0"; depends=[Biostrings httr png]; }; - KEGGgraph = derive2 { name="KEGGgraph"; version="1.41.0"; sha256="0sd2m80q2igal5qh03qcdjpcyi6rxk8w3mxgd9rjars6ykcj0g84"; depends=[graph XML]; }; - KEGGlincs = derive2 { name="KEGGlincs"; version="1.7.3"; sha256="0mrzrcg0327hgp11i704qiyc53pplzmjdwbjxx12pqwaxrrkfijf"; depends=[AnnotationDbi gtools hgu133a_db httr igraph KEGGgraph KEGGREST KOdata org_Hs_eg_db plyr RJSONIO XML]; }; - KEGGprofile = derive2 { name="KEGGprofile"; version="1.23.2"; sha256="02yqlbav775sx6cipc93rnz2qrhay93k4vrgs9h4gcz949rchhwh"; depends=[AnnotationDbi biomaRt KEGG_db KEGGREST png RCurl TeachingDemos XML]; }; - KinSwingR = derive2 { name="KinSwingR"; version="0.99.10"; sha256="1mj7bdqlg7rsxpha7x1wcjkkavcmnb9bdz92xigksip5qsdcs2r1"; depends=[BiocParallel data_table sqldf]; }; - LBE = derive2 { name="LBE"; version="1.49.0"; sha256="07r55w9f7a5fdp183rjx5f15jzkw73q6r7ra7drk887xylzmxvd0"; depends=[]; }; - LEA = derive2 { name="LEA"; version="2.3.0"; sha256="1k7zxl6aa09kr2gmh6lhg1hdb332fqggdi8hk4gbjcgsa533sqcc"; depends=[]; }; - LINC = derive2 { name="LINC"; version="1.9.0"; sha256="1295829apimwfiyhxzyl61wlabd7j18zdycrrai2f3d42005pfjw"; depends=[ape Biobase clusterProfiler DOSE ggplot2 ggtree gridExtra org_Hs_eg_db png Rcpp ReactomePA reshape2 sva]; }; - LMGene = derive2 { name="LMGene"; version="2.37.0"; sha256="1pkgkn12bgmamfcbdi5c352v92q31rzwcq69kh00z7wb07flcmf2"; depends=[affy Biobase multtest survival]; }; - LOBSTAHS = derive2 { name="LOBSTAHS"; version="1.7.2"; sha256="1j14x79xmzxc64jr3k4mxhfsv20pwvzr253jnchywfagky8ad3a5"; depends=[CAMERA xcms]; }; - LOLA = derive2 { name="LOLA"; version="1.11.1"; sha256="1dk4b0cc1kgqd0b171pigvk445hl82bsx8izxwlg86zgrgmsb0sx"; depends=[BiocGenerics data_table GenomicRanges IRanges reshape2 S4Vectors]; }; - LPE = derive2 { name="LPE"; version="1.55.0"; sha256="08pghdnq4l4zj21q3jz77x2hryjps1jk0rpdlv9kr207f535ww9l"; depends=[]; }; - LPEadj = derive2 { name="LPEadj"; version="1.41.0"; sha256="0sjhx44m1rfkhpq87996wc7n8axz2k8c4ni818rx78cqpha5ybjl"; depends=[LPE]; }; - LRBaseDbi = derive2 { name="LRBaseDbi"; version="0.99.22"; sha256="0yvsj66hdxmw9nqysb0a7jih5fi8jp1fdaccrkjs7mkp3zz6hzpp"; depends=[AnnotationDbi Biobase DBI RSQLite]; }; - LVSmiRNA = derive2 { name="LVSmiRNA"; version="1.31.0"; sha256="0wgjvy0r0p254kr686nnvjdwbqhbq06q1izy2idh9aaa043swaqn"; depends=[affy Biobase BiocGenerics limma MASS quantreg SparseM vsn zlibbioc]; }; - LedPred = derive2 { name="LedPred"; version="1.15.1"; sha256="0h2rw9mx67ilcm61z1m2ddwpvq53rzvn1kbsgzqdszx0r63gfkxm"; depends=[akima e1071 ggplot2 irr jsonlite plot3D plyr RCurl ROCR testthat]; }; - LineagePulse = derive2 { name="LineagePulse"; version="1.1.0"; sha256="00y0xcw89c1kdmcdj4pw620szrhxy2sykb7iblfbxz04cbj7vygs"; depends=[BiocParallel circlize ComplexHeatmap ggplot2 gplots knitr Matrix RColorBrewer SingleCellExperiment SummarizedExperiment]; }; - Linnorm = derive2 { name="Linnorm"; version="2.5.0"; sha256="013i53zmjgrkb4icgzp9mdmn7wqfm8r24izm6vifigczqphm0g0i"; depends=[amap apcluster ellipse fastcluster fpc ggdendro ggplot2 gmodels igraph limma MASS mclust Rcpp RcppArmadillo Rtsne statmod vegan zoo]; }; - LiquidAssociation = derive2 { name="LiquidAssociation"; version="1.35.0"; sha256="0ggrhgdlw44k0q5nddn60m91225xx4c58ydjgd98b4rz4a0l9qjy"; depends=[Biobase geepack org_Sc_sgd_db yeastCC]; }; - Logolas = derive2 { name="Logolas"; version="1.5.1"; sha256="14db1h5caklijdn0g4hk89n6h82fd932j9sxfzw2smhkg3k71xhw"; depends=[Biostrings ggplot2 gridBase LaplacesDemon SQUAREM]; }; - LowMACA = derive2 { name="LowMACA"; version="1.11.2"; sha256="1ir6vfjiwjhi6hj6pzksh2wfrcsmhkd80zwc135md0gmxr5bhhw8"; depends=[BiocParallel Biostrings cgdsr data_table httr LowMACAAnnotation motifStack RColorBrewer reshape2 stringr]; }; - LymphoSeq = derive2 { name="LymphoSeq"; version="1.9.2"; sha256="1q0xs2d7lgg0vz2ca84kv1igaf48y42g94xxdxmi1nmpz901pr8a"; depends=[Biostrings circlize data_table dplyr ggplot2 ggtree ineq LymphoSeqDB msa phangorn plyr RColorBrewer reshape stringdist UpSetR VennDiagram]; }; - M3C = derive2 { name="M3C"; version="1.3.991"; sha256="0wzg8rsfc1xgfdyl3l1y87cqvicpmj30ng45wfwp0d4vkd1llvqp"; depends=[cluster dendextend doParallel doSNOW foreach ggplot2 Matrix matrixcalc NMF RColorBrewer Rtsne sigclust survival]; }; - M3D = derive2 { name="M3D"; version="1.15.0"; sha256="1fdfahbdfx3csn27q61djp27a2w6jr9yl9hw6rakjnj7mk5s1xrj"; depends=[BiocGenerics BiSeq GenomicRanges IRanges Rcpp S4Vectors SummarizedExperiment]; }; - M3Drop = derive2 { name="M3Drop"; version="1.7.1"; sha256="1gscdkrnyk2qghkpidwj6abbxc53ivyxyc43297yja6hj73nz8mw"; depends=[bbmle gplots numDeriv RColorBrewer statmod]; }; - MACPET = derive2 { name="MACPET"; version="1.1.4"; sha256="0g9adhig02s6r45ax7335i2zsq8r2319111c0ijp6c6y5z52rcrp"; depends=[BH bigmemory BiocParallel Biostrings futile_logger GenomeInfoDb GenomicAlignments GenomicRanges GEOquery gtools InteractionSet intervals IRanges knitr plyr rbamtools Rbowtie Rcpp Rsamtools rtracklayer S4Vectors ShortRead]; }; - MADSEQ = derive2 { name="MADSEQ"; version="1.7.1"; sha256="1x8cfif8var04bdfgdws8zql33a67lf7r0kkalansy5w64wkjm8n"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 coda GenomeInfoDb GenomicAlignments GenomicRanges IRanges preprocessCore rjags Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation vcfR VGAM zlibbioc]; }; - MAGeCKFlute = derive2 { name="MAGeCKFlute"; version="1.1.9"; sha256="1bx9nawmjf2bsnk8iilplph90hdipyqf8mw24cbaaivajnsk6cz0"; depends=[biomaRt clusterProfiler data_table DOSE ggExtra ggplot2 ggrepel ggsci gridExtra pathview pheatmap png RColorBrewer sva]; }; - MAIT = derive2 { name="MAIT"; version="1.15.0"; sha256="0z1wl9hxqcfy7nlwqccz244kljdjra58drlhjfvc38kiy4q7nsyg"; depends=[agricolae CAMERA caret class e1071 gplots MASS pls plsgenomics Rcpp xcms]; }; - MANOR = derive2 { name="MANOR"; version="1.53.2"; sha256="1ss77yxivvgv2nswdp5qbbjc21ghrnwvj3w33xj4zv79bdb92qga"; depends=[GLAD]; }; - MAST = derive2 { name="MAST"; version="1.7.2"; sha256="07v6gjlh645w60c5fq206lmm2qpld1qqirdszrnrz00zrxzrnpz0"; depends=[abind Biobase BiocGenerics data_table ggplot2 plyr reshape2 S4Vectors SingleCellExperiment stringr SummarizedExperiment]; }; - MBASED = derive2 { name="MBASED"; version="1.15.0"; sha256="19zn2xmarpiszs3jfmmlgc5nflc2gafbby3x68l38sich2jn1kix"; depends=[BiocGenerics BiocParallel GenomicRanges RUnit SummarizedExperiment]; }; - MBAmethyl = derive2 { name="MBAmethyl"; version="1.15.0"; sha256="19lgv7lcy5qc6xbsngqvfxbaqcyk3rz907983ngqa9magr7xy2r1"; depends=[]; }; - MBCB = derive2 { name="MBCB"; version="1.35.0"; sha256="0cmmyj0c13b47apdk04qqqfg35rywh5fa0d2inhi31lfvbfd8bcx"; depends=[preprocessCore tcltk2]; }; - MBttest = derive2 { name="MBttest"; version="1.9.3"; sha256="1g443ynnk46blficdzygnksirfnwwgggl6d2j0jw0qfvkdsks2bz"; depends=[gplots gtools]; }; - MCRestimate = derive2 { name="MCRestimate"; version="2.37.0"; sha256="1b1cp4aan1wnzspihjm2snp16qjd3flr3ixx19mvsqzy5p38pf69"; depends=[Biobase e1071 golubEsets pamr randomForest RColorBrewer]; }; - MCbiclust = derive2 { name="MCbiclust"; version="1.5.0"; sha256="1zkxh6gax7rnp6n5dd6kwcljwds33fv5ps4crn41hzndllpbbc93"; depends=[AnnotationDbi BiocParallel cluster GGally ggplot2 GO_db org_Hs_eg_db scales WGCNA]; }; - MDTS = derive2 { name="MDTS"; version="1.1.2"; sha256="0q3v06za1wdkrzp711gs7awpk4dvrxj0xy6m5lzjyjz5qdd2nym5"; depends=[Biostrings DNAcopy GenomicAlignments GenomicRanges IRanges Rsamtools stringr]; }; - MEAL = derive2 { name="MEAL"; version="1.11.7"; sha256="11l3rbfwnh8yrbi33ii0mcmi63wgmhdwyffx8790gm3dj99l1626"; depends=[Biobase BiocGenerics DMRcate GenomicRanges ggplot2 Gviz IRanges isva limma matrixStats minfi missMethyl MultiDataSet permute S4Vectors SmartSVA SummarizedExperiment vegan]; }; - MEDIPS = derive2 { name="MEDIPS"; version="1.33.3"; sha256="0a2jypw2k9kpdh86gvgchvqlww72gb55aw9vhz67dkd7mfwnsqyc"; depends=[biomaRt Biostrings BSgenome DNAcopy edgeR GenomicRanges gtools IRanges preprocessCore Rsamtools rtracklayer]; }; - MEDME = derive2 { name="MEDME"; version="1.41.0"; sha256="1l0i3vz1zp9lmvvfn5h6baf9kzvdyb9m1qffwlg3dvzdzdqadx0l"; depends=[Biostrings drc MASS]; }; - MEIGOR = derive2 { name="MEIGOR"; version="1.15.1"; sha256="1vfklcm9yppy3rr2l5ddnp20r368hsr08vy26agr5jqharw7qik9"; depends=[CNORode deSolve Rsolnp snowfall]; }; - MGFM = derive2 { name="MGFM"; version="1.15.1"; sha256="1pd7c9d66c4b1bz6l24mhrwxwdivl47kc57c7mp79z1h9hf66ipf"; depends=[annotate AnnotationDbi]; }; - MGFR = derive2 { name="MGFR"; version="1.7.0"; sha256="11vw9yyv6j2pjj4cmlw0f3blxz4iwx3p9r0xpzis5zs12x7pn17f"; depends=[annotate biomaRt]; }; - MIGSA = derive2 { name="MIGSA"; version="1.5.2"; sha256="02yqj1srxh41wmda686y0nh88rnvmffr5f6p46h7vmz8kb1pi9cf"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel data_table edgeR futile_logger ggdendro ggplot2 GO_db GOstats graph GSEABase ismev limma matrixStats org_Hs_eg_db RBGL reshape2 Rgraphviz RJSONIO vegan]; }; - MIMOSA = derive2 { name="MIMOSA"; version="1.19.0"; sha256="1z3hj0ivv4zw4sprzr5bhxp5fpzkg37m1sk1y90cfm42p4vyqagg"; depends=[Biobase coda data_table Formula ggplot2 MASS MCMCpack modeest plyr pracma Rcpp RcppArmadillo reshape scales testthat]; }; - MIRA = derive2 { name="MIRA"; version="1.3.1"; sha256="139wlx2c0bpgljjxrzrcn7s8kvqrs53lrw6nsdnb3v4y7wx2fc8y"; depends=[Biobase BiocGenerics bsseq data_table GenomicRanges ggplot2 IRanges S4Vectors]; }; - MLInterfaces = derive2 { name="MLInterfaces"; version="1.61.1"; sha256="1nmcxaa3r34xhzcs063pwggck2yhwvc1ckzyhqabbb41jflnnw3g"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rda rpart sfsmisc shiny threejs]; }; - MLP = derive2 { name="MLP"; version="1.29.0"; sha256="0fqrpnqb9031f3y1qgmvxr0ynygp1rzjg2dsy4g2z98jzwbncznk"; depends=[affy AnnotationDbi gdata gmodels gplots gtools plotrix]; }; - MLSeq = derive2 { name="MLSeq"; version="1.99.9"; sha256="0bjgj44j6xxipp6wskd1cq3kj2j9g3jl8365r9rv5m8vp58nvkl2"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma plyr sSeq SummarizedExperiment xtable]; }; - MMDiff2 = derive2 { name="MMDiff2"; version="1.9.0"; sha256="1l3frx6myj4jglypv5il3pgjpm3szq5xfp5p8k8xilahmg98ykh1"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; }; - MODA = derive2 { name="MODA"; version="1.7.0"; sha256="0wm5sc2fh5j191128xlxdqmfsh8ix8k33gkcz6yn8rfpj3rdfhzg"; depends=[AMOUNTAIN cluster dynamicTreeCut igraph RColorBrewer WGCNA]; }; - MPFE = derive2 { name="MPFE"; version="1.17.0"; sha256="1jalc9ny5lv3h7awrkg5mmagjh15js5rmpqfl7pn15499186fajp"; depends=[]; }; - MPRAnalyze = derive2 { name="MPRAnalyze"; version="0.99.11"; sha256="0vqy590j0jfx00lifmavdvl6bd93k85kpm67575z3hd7lffrmawm"; depends=[BiocParallel progress SummarizedExperiment]; }; - MSGFgui = derive2 { name="MSGFgui"; version="1.15.1"; sha256="01mdpd0ph49zjvhynb4cq8m60k1bd4xw72bay2ly19akp72lwcpz"; depends=[MSGFplus mzID mzR shiny shinyFiles xlsx]; }; - MSGFplus = derive2 { name="MSGFplus"; version="1.15.1"; sha256="15ljj766719690mb37alih2001vcm8az92j0qgyfdb80c9gm8my6"; depends=[mzID ProtGenerics]; }; - MSnID = derive2 { name="MSnID"; version="1.15.1"; sha256="08z17czddqlfj6hppqg43s45ldh3ck6qay14iyrpsa809xqda1yw"; depends=[Biobase data_table doParallel dplyr foreach iterators MSnbase mzID mzR ProtGenerics R_cache Rcpp reshape2]; }; - MSnbase = derive2 { name="MSnbase"; version="2.7.12"; sha256="15vs3dca3ml859005wpwk84c0d1si0h65g9hnkvd0nw05wsp7g81"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS mzID mzR pcaMethods plyr preprocessCore ProtGenerics Rcpp S4Vectors scales vsn XML]; }; - MSstats = derive2 { name="MSstats"; version="3.13.5"; sha256="06rhwn9fk5dr52p73mxi04x86s1c8ixvw3kw01qxygd6x0acshy4"; depends=[data_table doSNOW dplyr foreach ggplot2 ggrepel gplots limma lme4 marray MASS minpack_lm preprocessCore randomForest reshape2 snow stringr survival tidyr]; }; - MSstatsQC = derive2 { name="MSstatsQC"; version="1.99.3"; sha256="1rbkn12pgy8g6s15lizaymkbc5k5cb07gndzy65w0zsbm2w5vaz4"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics RecordLinkage]; }; - MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.1.1"; sha256="0s3invrc3601y8hai3pxbd1k0v6vvr7n95zpbxj5cjqdv3yn52ir"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly RecordLinkage shiny]; }; - MSstatsTMT = derive2 { name="MSstatsTMT"; version="0.99.9"; sha256="08plgvwwhrjyby45gq5s4b3nxb53az6dayhgsk96fhxa3q7dbmds"; depends=[data_table dplyr ggplot2 limma lme4 matrixStats MSstats nlme reshape2 tidyr]; }; - MVCClass = derive2 { name="MVCClass"; version="1.55.0"; sha256="0xkwwvq66cnmac52ik95siq78ny9nfbgp4xncdamq7gmn7wasacr"; depends=[]; }; - MWASTools = derive2 { name="MWASTools"; version="1.5.6"; sha256="1axhfzvinhg8lfgn703rl76bxj0b1dz0rmiapssqvzzm6bg8lgmf"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; }; - MantelCorr = derive2 { name="MantelCorr"; version="1.51.0"; sha256="03sqqfi06hcprya25aj3p9sa35x9n2m9ffnplnh6gqmcv22fj75k"; depends=[]; }; - MassArray = derive2 { name="MassArray"; version="1.33.0"; sha256="1ni7dw8lk73n3b19m0rnd8cszb4p6la6msld0z63lgvih4m3z805"; depends=[]; }; - MassSpecWavelet = derive2 { name="MassSpecWavelet"; version="1.47.0"; sha256="0mq6xfdj11m49xi6x14lp6kh9idfbrmy9kx7jpjm90hwdjnl48ym"; depends=[waveslim]; }; - MatrixRider = derive2 { name="MatrixRider"; version="1.13.0"; sha256="0plcabv6wc7s4q7ippi7i9ckc3lg4pwxdm32gpsmmssff37jx41c"; depends=[Biostrings IRanges S4Vectors TFBSTools XVector]; }; - MaxContrastProjection = derive2 { name="MaxContrastProjection"; version="1.5.1"; sha256="1ybz5ij152pdbnn47p5sprlm8lzdgzazv0h890dbh9z3k9b7vbli"; depends=[EBImage]; }; - MeSHDbi = derive2 { name="MeSHDbi"; version="1.17.1"; sha256="1qxbpvl97j187bl9nqib6z580f692apdrsdw8qlpk1lw197sv7np"; depends=[AnnotationDbi Biobase BiocGenerics RSQLite]; }; - MeasurementError_cor = derive2 { name="MeasurementError.cor"; version="1.53.0"; sha256="0j6v368naid00b1igibjp94yxyz0sqhsr8lxgxv0xwy85ivsqlbi"; depends=[]; }; - MergeMaid = derive2 { name="MergeMaid"; version="2.53.0"; sha256="1dn5shrkyhph13x5qyygvp10jd8acs6rka9vr3g9dh0rq4mx4114"; depends=[Biobase MASS survival]; }; - Mergeomics = derive2 { name="Mergeomics"; version="1.9.1"; sha256="0gz7vx1gvng7dlkwfz45i1cpsdhazv9w5idbxjsh3rxwpll4yvd5"; depends=[]; }; - MetCirc = derive2 { name="MetCirc"; version="1.11.3"; sha256="12f9cj5wzavd51kbyiz380fhb2zrlybakm4z7rnpvcx0g8q7l3y3"; depends=[amap circlize scales shiny]; }; - MetID = derive2 { name="MetID"; version="0.99.8"; sha256="196ha93x99p7dhhwnr4b4xddkjjw2m1q30bn238msndz4l5chmri"; depends=[ChemmineR devtools igraph Matrix stringr]; }; - MetNet = derive2 { name="MetNet"; version="0.99.24"; sha256="15gqzi23r7g43awk67qnqxlpgyq0zb9z06gq60kd0j05pwhfpgqz"; depends=[BiocParallel bnlearn mpmi parmigene ppcor rfPermute sna stabs WGCNA]; }; - MetaCyto = derive2 { name="MetaCyto"; version="1.3.4"; sha256="0j97f77ailb5ih6ky3svcf7lmr6qk352p59mbx7rcxgg7fdajc0l"; depends=[cluster fastcluster flowCore FlowSOM ggplot2 metafor tidyr]; }; - MetaNeighbor = derive2 { name="MetaNeighbor"; version="1.1.0"; sha256="1jj4jh27ysl3ilhw20pf1srw0n47c0dbc3s760blwbf5qnrlhivv"; depends=[beanplot gplots RColorBrewer SummarizedExperiment]; }; - Metab = derive2 { name="Metab"; version="1.15.0"; sha256="12l43jyrsq1dcbbrkr6k66hrcwkx8ynyniz3cfs17im09nrj20jz"; depends=[pander svDialogs xcms]; }; - MetaboSignal = derive2 { name="MetaboSignal"; version="1.11.0"; sha256="0cpmbq55d7bf9mky0m0ydg1qs60sxq8wl2apkhvnyfhifv3f316q"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; }; - MethPed = derive2 { name="MethPed"; version="1.9.1"; sha256="0x83lz61vn74z9nps99a0f8jh34impkm1523wzp0gr24gcmikb8y"; depends=[Biobase randomForest]; }; - MethTargetedNGS = derive2 { name="MethTargetedNGS"; version="1.13.0"; sha256="02kc184ql68rqll95sza94qnzjgh8wvg76h3z5r3lqmxdd7bblz9"; depends=[Biostrings gplots seqinr stringr]; }; - MethylAid = derive2 { name="MethylAid"; version="1.15.0"; sha256="15xkcbjj7mcmbm5di1bxslfiipnbdarsfsg16kmd530v9lmll331"; depends=[Biobase BiocGenerics BiocParallel ggplot2 gridBase hexbin matrixStats minfi RColorBrewer shiny SummarizedExperiment]; }; - MethylMix = derive2 { name="MethylMix"; version="2.11.2"; sha256="02wsil0s5jp6lh4jlh9sppz9ir8lk849jlxagj48s9napxbw65fc"; depends=[data_table digest foreach ggplot2 impute limma R_matlab RColorBrewer RCurl RPMM]; }; - MethylSeekR = derive2 { name="MethylSeekR"; version="1.21.1"; sha256="18hcd43z15949vsd7s02zg85dpyf9gkc7dky70xz8jv8gbmizl56"; depends=[BSgenome geneplotter GenomicRanges IRanges mhsmm rtracklayer]; }; - Mfuzz = derive2 { name="Mfuzz"; version="2.41.0"; sha256="0hdjkg90kk7igjx26hfm9wfh7lymm0cgxsn263a7sy1cb6ld7nx8"; depends=[Biobase e1071 tkWidgets]; }; - MiChip = derive2 { name="MiChip"; version="1.35.0"; sha256="19w0kzyg6s950g0p4a4gdkkblsz30zv57rs3dqzqh1rgcrcb4gpf"; depends=[Biobase]; }; - MiPP = derive2 { name="MiPP"; version="1.53.0"; sha256="0ii5vlx5gwkz01ivg0qjml8q5zqdvz21rrxgqhx2zdqwi6cbfww0"; depends=[Biobase e1071 MASS]; }; - MiRaGE = derive2 { name="MiRaGE"; version="1.23.3"; sha256="02nrjckzywcfm0b34f076qkpsaa9n6p57pjd9chhcnns0i7kl2ji"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; }; - MineICA = derive2 { name="MineICA"; version="1.21.0"; sha256="1n711vz5g1rrz6hnm88w3ycm0yczq4a0h2rg635g7x33sszjr3dk"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; }; - MinimumDistance = derive2 { name="MinimumDistance"; version="1.25.2"; sha256="1pv6h2p0y6r32dz99b61bdgyd86nnmzs7dph9xk7a5rrgzaj1bb8"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; }; - Mirsynergy = derive2 { name="Mirsynergy"; version="1.17.0"; sha256="0n8vspalfwisnfk486i90pxi2hd2xi32b36pfl3ifrpqyr2rylix"; depends=[ggplot2 gridExtra igraph Matrix RColorBrewer reshape scales]; }; - MmPalateMiRNA = derive2 { name="MmPalateMiRNA"; version="1.31.0"; sha256="10cdaprs899j3fswds8vx4gm2xp5kcx11l53ymxlyjr5592887fm"; depends=[Biobase lattice limma statmod vsn xtable]; }; - MoPS = derive2 { name="MoPS"; version="1.15.1"; sha256="0nmk4iapypdak2z4zmlwv2crvgzh10l8vvajkiszwakdpsc734fd"; depends=[Biobase]; }; - MoonlightR = derive2 { name="MoonlightR"; version="1.7.2"; sha256="1j2k09hcg5z65yxaml6yhxffsz3dmh56j64w625rqxmfk0b1zyii"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; - MotIV = derive2 { name="MotIV"; version="1.37.0"; sha256="0wzf7dzw063i613gx8pa3sf1hvqc52yhb8dqpy87g3smalfj3qr3"; depends=[BiocGenerics Biostrings IRanges lattice rGADEM S4Vectors]; }; - MotifDb = derive2 { name="MotifDb"; version="1.23.14"; sha256="0v7n0682w9gsnp7vknhwfc6baimsjcqb5gm3bglnsp6kr4khjhkx"; depends=[BiocGenerics Biostrings IRanges rtracklayer S4Vectors splitstackshape]; }; - Mulcom = derive2 { name="Mulcom"; version="1.31.0"; sha256="0l8wn2ma3s55w86wv3779y39vsp45rfa5nkjj1cjn26qc2ay0r0f"; depends=[Biobase fields]; }; - MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.7.22"; sha256="1pw80vr48jii32mxd8rwshi3q6ccr4c3x3fr0bxdkbf9ypa2l57j"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; }; - MultiDataSet = derive2 { name="MultiDataSet"; version="1.9.1"; sha256="19j4jd5gh363l6p3jmjfcp14y1vmixg20lcpqjs78zxk1saalhz3"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; }; - MultiMed = derive2 { name="MultiMed"; version="2.3.0"; sha256="085vmkq1hd9x1za5c21gvndyl46ymd7w5hwixvhnsclzb4r7gav7"; depends=[]; }; - MutationalPatterns = derive2 { name="MutationalPatterns"; version="1.7.3"; sha256="1krq37chmnqzl9dlk6dwjy6kasa511s2qc8hndg5l0am12lmn5bg"; depends=[BiocGenerics Biostrings cowplot GenomeInfoDb GenomicRanges ggdendro ggplot2 IRanges NMF plyr pracma reshape2 S4Vectors SummarizedExperiment VariantAnnotation]; }; - NADfinder = derive2 { name="NADfinder"; version="1.5.4"; sha256="0qgnpq9ci3344kjba8jfs6lbnrdhsyjvb5vxrd0p4v08j3fg4q55"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap rbamtools Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; }; - NBSplice = derive2 { name="NBSplice"; version="0.99.9"; sha256="181msya2wpcqsn3xyiqzghl58r394ilw5khmzihyq5b1bq3x7rmr"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; }; - NCIgraph = derive2 { name="NCIgraph"; version="1.29.0"; sha256="06jmifga56d9cnqp4wb9hm6g32fhsk6n0g70qqw1k4l5k7m2v5wv"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; }; - NGScopy = derive2 { name="NGScopy"; version="1.15.1"; sha256="0azw7zq7bz7haifmng9y59jbhh7nfhz6k886gffdvlnbrn3k4kbr"; depends=[changepoint rbamtools Xmisc]; }; - NOISeq = derive2 { name="NOISeq"; version="2.25.1"; sha256="094jrp87nhjyi31qbg719ny0dqki5blf6k86d4sbh3vqngakcjg3"; depends=[Biobase Matrix]; }; - NTW = derive2 { name="NTW"; version="1.31.0"; sha256="183y8sqf3h4ik1cm6zhvzmijc8kanmv3lvqh4v4cb7qhvgrgb3ln"; depends=[mvtnorm]; }; - NanoStringDiff = derive2 { name="NanoStringDiff"; version="1.11.0"; sha256="0sl0chkrx8s4625ch43x9r8n5k7cd0y18cinafrligqfrwnc5yx0"; depends=[Biobase matrixStats Rcpp]; }; - NanoStringQCPro = derive2 { name="NanoStringQCPro"; version="1.13.0"; sha256="1km8i428rn4q5b89d56bcnwkrpvhf67bzmxwzxfdwm1qr956vab2"; depends=[AnnotationDbi Biobase knitr NMF org_Hs_eg_db png RColorBrewer]; }; - NarrowPeaks = derive2 { name="NarrowPeaks"; version="1.25.1"; sha256="1lqs0rcx52c3hnx89wngmyyhn02a7nf007x95z85rqzrclgy27ki"; depends=[BiocGenerics CSAR fda GenomeInfoDb GenomicRanges ICSNP IRanges S4Vectors]; }; - NeighborNet = derive2 { name="NeighborNet"; version="0.99.5"; sha256="1xwpzkfmhgiswwyls5q9cm8qnz7xvp3axhm95cvwfqxwbp8j81mc"; depends=[graph]; }; - NetPathMiner = derive2 { name="NetPathMiner"; version="1.17.1"; sha256="0hfdi6359vl27m5fa8fr9pr4xw8pqdx3qjbw6laigylapn8vwy6n"; depends=[igraph]; }; - NetSAM = derive2 { name="NetSAM"; version="1.21.1"; sha256="0h1wld8p7pvyf7jfgcdgykg34dccf7ykrfc7jqv0i5aip4zjxpd0"; depends=[graph igraph seriation]; }; - NormalyzerDE = derive2 { name="NormalyzerDE"; version="0.99.25"; sha256="00x86np9265klpvzv72xcdnnqfkaa1ygja4hrlpx3iaz9r2x3k4z"; depends=[ape Biobase car ggplot2 limma MASS matrixStats preprocessCore raster RcmdrMisc SummarizedExperiment vsn]; }; - NormqPCR = derive2 { name="NormqPCR"; version="1.27.2"; sha256="18bsw0hp7m48vh85ajyxhp447agrzhs5x0jy4684p77xrlhqfmqz"; depends=[Biobase qpcR RColorBrewer ReadqPCR]; }; - NuPoP = derive2 { name="NuPoP"; version="1.31.0"; sha256="1sfv98q0z3x5lzmvhbjh1k65flxhsjfx5nqhlhhihcs5rjx8pa3h"; depends=[]; }; - OCplus = derive2 { name="OCplus"; version="1.55.0"; sha256="0nn2adv9v0j0dhz93kd2d3bh1fx31vg3qk9sygrf1xbwqppmcyp9"; depends=[akima multtest]; }; - OGSA = derive2 { name="OGSA"; version="1.11.0"; sha256="063y4bzxiwjb0nvh3lkkgd39p59sy9drzcckpkxm5yxm3scrdy2f"; depends=[Biobase gplots limma]; }; - OLIN = derive2 { name="OLIN"; version="1.59.0"; sha256="0q0cr7yfprvzl01dgb4mwpbwnj1yfpn4myf8jksckiy0s2cwinra"; depends=[limma locfit marray]; }; - OLINgui = derive2 { name="OLINgui"; version="1.55.0"; sha256="1wjsb9h443d82x6vq70plhv7cgc3n7imvjlian1a0hd9dbcx9ss3"; depends=[marray OLIN tkWidgets widgetTools]; }; - OMICsPCA = derive2 { name="OMICsPCA"; version="0.99.17"; sha256="1na9swmy7z5xnbvp7h2x6s1jgdhifwdh36ad7g7jlhfc7v8a3kqh"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; }; - OPWeight = derive2 { name="OPWeight"; version="1.3.1"; sha256="17xrv1ad4wv20q4lwgxpr58sn73klx165h2pvjwly8v68hx1713s"; depends=[MASS qvalue tibble]; }; - ORFik = derive2 { name="ORFik"; version="1.1.14"; sha256="1cq43ha9brllyn1p72978xcvb45iapkz2hsfh6anbh4xdhv9pbxg"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp Rsamtools rtracklayer S4Vectors]; }; - OSAT = derive2 { name="OSAT"; version="1.29.0"; sha256="174jna1bl6vkbr3zypyfnhakfm7bm6llfcgghr4m9bvc8a6hxq6b"; depends=[]; }; - OTUbase = derive2 { name="OTUbase"; version="1.31.0"; sha256="0p86dn54pipqy3v74iwgvs2xqxypq6iq58y9m0pqbncryrszcs0p"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; }; - OUTRIDER = derive2 { name="OUTRIDER"; version="0.99.31"; sha256="1wihfldpj8hq86z9ln5c06rr5kv8cjx5bmcqz5cx58vxg3sr86h4"; depends=[BBmisc Biobase BiocGenerics BiocParallel data_table DESeq2 GenomicFeatures GenomicRanges ggplot2 ggpubr gplots IRanges matrixStats pcaMethods plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reticulate S4Vectors scales SummarizedExperiment]; }; - OmaDB = derive2 { name="OmaDB"; version="1.1.4"; sha256="192wpb9f7vwkrlq2y2r7kicppqc5c9hb7nk00im06588mdldbp4p"; depends=[ape Biostrings GenomicRanges httr IRanges jsonlite plyr topGO]; }; - OmicCircos = derive2 { name="OmicCircos"; version="1.19.0"; sha256="03laa1vjjxgrpcz2sxdq9dq0fa2s04jvf56q03h5gx8hkfn4rv7v"; depends=[GenomicRanges]; }; - OmicsMarkeR = derive2 { name="OmicsMarkeR"; version="1.13.1"; sha256="0fx2jjyn196344indfpdiaf63abvxm1rw7ris378rzpl282kch2m"; depends=[assertive assertive_base caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; }; - Onassis = derive2 { name="Onassis"; version="1.3.7"; sha256="11ifi7bsdy6yrgs54pglaqhgw86zndn98qhygzkw7sxgb8b7ly18"; depends=[AnnotationDbi data_table DT GEOmetadb knitr OnassisJavaLibs RCurl rJava RSQLite]; }; - OncoScore = derive2 { name="OncoScore"; version="1.9.3"; sha256="07pvd6alsbvm4wjlz3m3dnl0hyzv33fvznzxhcsgh1sz2kv92aya"; depends=[biomaRt]; }; - OncoSimulR = derive2 { name="OncoSimulR"; version="2.11.1"; sha256="1nkwfc2gcmfn8pnz6zk7bywr1n75jrrfyhmbj0mzzhp4cjxsrj8d"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph nem RColorBrewer Rcpp Rgraphviz smatr]; }; - OrderedList = derive2 { name="OrderedList"; version="1.53.0"; sha256="1pdv3pih594x3bkrzmm7ab418mxjsa17qbv0dpmw4w1yyvrlyz5m"; depends=[Biobase twilight]; }; - Organism_dplyr = derive2 { name="Organism.dplyr"; version="1.9.2"; sha256="1n87ajas2wrrpkpmy0n9zim6f1by9vvqk9wh25kk4rxp3500d8gh"; depends=[AnnotationDbi AnnotationFilter BiocFileCache DBI dbplyr dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges RSQLite S4Vectors]; }; - OrganismDbi = derive2 { name="OrganismDbi"; version="1.23.2"; sha256="18l7ki8vaavzy0380gw1bhpjf5xs3naaq44xfam307pl5h7xr8c0"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager DBI GenomicFeatures GenomicRanges graph IRanges RBGL S4Vectors]; }; - Oscope = derive2 { name="Oscope"; version="1.11.0"; sha256="1x8z5i3v42787iv9hddp65cggnlvr7xa9kippi0sn0wr7gd79zcw"; depends=[BiocParallel cluster EBSeq testthat]; }; - OutlierD = derive2 { name="OutlierD"; version="1.45.0"; sha256="085nk41icxzx8halczi4kjd262y8dfxq6lrhwiy8qjb216hbrln6"; depends=[Biobase quantreg]; }; - PAA = derive2 { name="PAA"; version="1.15.2"; sha256="16w6xc05gs9ynj01xkrk7gf0qvqknfpicayik5qlm7gmm1k43hm8"; depends=[e1071 gplots gtools limma MASS mRMRe randomForest Rcpp ROCR sva]; }; - PADOG = derive2 { name="PADOG"; version="1.23.0"; sha256="10libml1j14yy70s22yf8i4mh8awmnx5a94b3krmh6py2xlw41nj"; depends=[AnnotationDbi Biobase doRNG foreach GSA hgu133a_db hgu133plus2_db KEGG_db KEGGdzPathwaysGEO limma nlme]; }; - PANR = derive2 { name="PANR"; version="1.27.0"; sha256="0zr55whhmqyic41chlzxhrn081ray8gl90llb6rwigvmzhfjabyr"; depends=[igraph MASS pvclust RedeR]; }; - PAPi = derive2 { name="PAPi"; version="1.21.0"; sha256="1qnbqa72w1734j6rbdbays1f4ysl2b1r65p2hi580zwwi6isaa3i"; depends=[KEGGREST svDialogs]; }; - PCAN = derive2 { name="PCAN"; version="1.9.0"; sha256="14ph4mk4svinwpy0rw2b3n96dswahw6273lggw2blp9s24a56a1h"; depends=[BiocParallel]; }; - PCpheno = derive2 { name="PCpheno"; version="1.43.0"; sha256="004qx7rclh2q9bbrqf4d54jlzpha8vg0lbaf67gf42ivav0fl908"; depends=[annotate AnnotationDbi Biobase Category GO_db graph GSEABase KEGG_db ppiData ppiStats ScISI SLGI]; }; - PECA = derive2 { name="PECA"; version="1.17.0"; sha256="0p4vg0kcrypxm4g8al50rcvrk10lqs23mc00hrd1s8ydycvgd26a"; depends=[affy aroma_affymetrix aroma_core genefilter limma preprocessCore ROTS]; }; - PGA = derive2 { name="PGA"; version="1.11.4"; sha256="1dcig05dglia3ixymm1s7hzxf5fa7p6bgcwlf66qdx72iagr9ivp"; depends=[AnnotationDbi biomaRt Biostrings customProDB data_table GenomicFeatures GenomicRanges ggplot2 IRanges Nozzle_R1 pheatmap RCurl Rsamtools RSQLite rTANDEM rtracklayer S4Vectors stringr VariantAnnotation]; }; - PGSEA = derive2 { name="PGSEA"; version="1.55.0"; sha256="07ynkcxppvm8s525y10ly6jcc0ga93a8sqihdxhs1yg092pcbx64"; depends=[annaffy AnnotationDbi Biobase GO_db KEGG_db]; }; - PICS = derive2 { name="PICS"; version="2.25.0"; sha256="1qfv4ddkym5s7171i0c4s5v3x8liaxngpv40y362cr895wa63mwm"; depends=[BiocGenerics GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; }; - PING = derive2 { name="PING"; version="2.25.0"; sha256="1lgvn09a1frb6cqrnrvmyzlwm7rgis61wd1gqv5y6pf0w6m6ya9k"; depends=[BiocGenerics BSgenome chipseq fda GenomicRanges Gviz IRanges PICS S4Vectors]; }; - PLPE = derive2 { name="PLPE"; version="1.41.0"; sha256="11a1wsgzssn5nqbmxxrfqk7js6h3y0zcxgfyqr5hvfz6licl2q3v"; depends=[Biobase LPE MASS]; }; - POST = derive2 { name="POST"; version="1.5.0"; sha256="099q5w5sgpamgncga096szl40i3lzjnphki2kfby0svkkvjiyrhl"; depends=[Biobase CompQuadForm GSEABase Matrix survival]; }; - PPInfer = derive2 { name="PPInfer"; version="1.7.0"; sha256="0pvhfc3qyxx6vxww6fx7jx8hb72sl4jna1c3bnyw6z7lvp7a8cxw"; depends=[biomaRt fgsea ggplot2 igraph kernlab STRINGdb yeastExpData]; }; - PREDA = derive2 { name="PREDA"; version="1.27.1"; sha256="00wwfvcahrhyxylcg5wjsbv3aqsvw230lcggkk3jrwdyb5x902p2"; depends=[annotate Biobase lokern multtest]; }; - PROMISE = derive2 { name="PROMISE"; version="1.33.0"; sha256="1gkbpj9cd5fbrrp2zmffnckynbn81kqyg5wvy2g88spa1zxsx6vp"; depends=[Biobase GSEABase]; }; - PROPER = derive2 { name="PROPER"; version="1.13.0"; sha256="1w77rishajj0azrcf0cfsg9is98w1f1w3hfh72rgi7kc93d0k4v0"; depends=[edgeR]; }; - PROPS = derive2 { name="PROPS"; version="1.3.0"; sha256="15md6zvsa9ismdwbhlzwxkyj38n4bqv4kpbvxbzg7kb50hc109w6"; depends=[Biobase bnlearn reshape2 sva]; }; - PROcess = derive2 { name="PROcess"; version="1.57.0"; sha256="1sb25yfpvq4z6famifk951gwx75dd51srf1khm96psz9k0klxbqg"; depends=[Icens]; }; - PSEA = derive2 { name="PSEA"; version="1.15.0"; sha256="1rcz03n4asjajlncppvfhmlnar6f9qzb6m9bg99nmp0gdkjcwa2j"; depends=[Biobase MASS]; }; - PSICQUIC = derive2 { name="PSICQUIC"; version="1.19.1"; sha256="0554irz5sxq3vglxq1jlr0fip3hfd41zw5wfd05gn5k0h8s3ff7j"; depends=[BiocGenerics biomaRt httr IRanges plyr RCurl]; }; - PWMEnrich = derive2 { name="PWMEnrich"; version="4.17.0"; sha256="1mknim17d0wl7vhn6cffjasisd9nmgs4b3fjz42yjj9y5xqjxwv9"; depends=[BiocGenerics Biostrings evd gdata seqLogo]; }; - PanVizGenerator = derive2 { name="PanVizGenerator"; version="1.9.0"; sha256="0x1rzblyy45xdr3hnjbacip7v1pbr54wfc2abldgij9mgc0hmhl9"; depends=[FindMyFriends igraph jsonlite pcaMethods shiny]; }; - Path2PPI = derive2 { name="Path2PPI"; version="1.11.0"; sha256="1f6qc6cvsrnhh26lkprjan9fxc1kw4hbb1wbr83rswg0lj8nyg6r"; depends=[igraph]; }; - PathNet = derive2 { name="PathNet"; version="1.21.2"; sha256="1ihd81wwx0w1alzylc2wydg9kx9x3m2hw3zyp8qjhxxjf9pps507"; depends=[]; }; - PathoStat = derive2 { name="PathoStat"; version="1.7.8"; sha256="1lnv8x2im6nw4kckv62cmxi06hjxw3ivj9jyzxi9wc0yylyrbp6j"; depends=[ape BiocStyle ComplexHeatmap corpcor DESeq2 devtools dplyr DT edgeR ggplot2 glmnet gmodels knitr limma matrixStats phyloseq plotly plyr RColorBrewer rentrez reshape2 ROCR scales shiny shinyjs tidyr vegan webshot XML]; }; - PathwaySplice = derive2 { name="PathwaySplice"; version="1.5.2"; sha256="1dj56ssc31yxn3g29485phmjjd9a4nndx455yvvig8p74630149w"; depends=[annotate AnnotationDbi AnnotationHub BiasedUrn Biobase BiocGenerics DOSE dplyr EnrichmentBrowser ensembldb gdata geneLenDataBase GO_db goseq gplots gridExtra htmlwidgets igraph JunctionSeq KEGGREST mgcv org_Hs_eg_db org_Mm_eg_db plotly RColorBrewer reshape2 S4Vectors tibble VennDiagram webshot]; }; - Pbase = derive2 { name="Pbase"; version="0.21.3"; sha256="0945vdb18879j269fd16rac4pmlnqbddp6nn1vkfyprfqv3aqdq8"; depends=[AnnotationFilter Biobase BiocGenerics BiocParallel biomaRt Biostrings cleaver ensembldb GenomicRanges Gviz IRanges MSnbase mzID mzR Pviz Rcpp rtracklayer S4Vectors]; }; - PharmacoGx = derive2 { name="PharmacoGx"; version="1.11.3"; sha256="14dib394xhrdapli5lwrzvf4fmbbgpcrgnbrv80749y9ivmg2jb1"; depends=[Biobase caTools downloader lsa magicaxis piano RColorBrewer reshape2]; }; - PhenStat = derive2 { name="PhenStat"; version="2.17.0"; sha256="1fvkaqg1ignyknjgrnj359a5276rrscrkdk9029851rjpyzwypd5"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; }; - Pi = derive2 { name="Pi"; version="1.9.3"; sha256="0h3a40bhj2410w8ibfbfp2nl76c5anh62pva8phf6y2g4bxvhi9p"; depends=[caret dnet GenomeInfoDb GenomicRanges ggbio ggplot2 ggrepel glmnet Gviz igraph lattice MASS Matrix plot3D randomForest ROCR scales supraHex XGR]; }; - Pigengene = derive2 { name="Pigengene"; version="1.7.8"; sha256="0spdvc7wl8y7nsvyfrzni666wpbi8021ff2nlc4f6chhx6zqvg2i"; depends=[bnlearn C50 GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; }; - Polyfit = derive2 { name="Polyfit"; version="1.15.0"; sha256="0k3apzd7szmglba2s51grmp4lbvv2wmv6kvv43mvbvrvc59cyxq5"; depends=[DESeq]; }; - PowerExplorer = derive2 { name="PowerExplorer"; version="1.1.1"; sha256="06igcls1khn3dvajp7289v4ax6yr5cgg0da0d81dkr38cb6lwnpx"; depends=[Biobase BiocParallel data_table DESeq2 ggplot2 gridExtra MASS ROTS S4Vectors SummarizedExperiment vsn]; }; - Prize = derive2 { name="Prize"; version="1.11.0"; sha256="0fk26mk97l3jdj9n20ha7m8gcfxc20w4c9c5xshnphfij56brrr5"; depends=[diagram ggplot2 gplots matrixcalc reshape2 stringr]; }; - ProCoNA = derive2 { name="ProCoNA"; version="1.19.0"; sha256="1648ly7mpqfhj1phnvwrkzsj31wdk5ddg7cc073kbwwgmz859r0d"; depends=[BiocGenerics flashClust GOstats MSnbase WGCNA]; }; - Prostar = derive2 { name="Prostar"; version="1.13.16"; sha256="0kfqzibwkwbggjs5isgf9s1nk3zssahcicf9vpr3s2rkkmn18y8j"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets webshot XML]; }; - ProtGenerics = derive2 { name="ProtGenerics"; version="1.13.0"; sha256="0mcdiy93c01ki2zfv90a5q00hss8i4mds4gw6n6gp32f40ap7h2j"; depends=[]; }; - ProteoMM = derive2 { name="ProteoMM"; version="0.99.8"; sha256="0j9sjj7r6jbgwv2vfsgd61xk5sd6rlw6ns5j0qvpcry6a5a26z3s"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; }; - ProteomicsAnnotationHubData = derive2 { name="ProteomicsAnnotationHubData"; version="1.11.1"; sha256="1zlwsfk1f0pc6diqmd5r6cfxz48zz1m1hxagly7rw3v52qmjqynh"; depends=[AnnotationHub AnnotationHubData Biobase BiocManager Biostrings GenomeInfoDb MSnbase mzR RCurl]; }; - PureCN = derive2 { name="PureCN"; version="1.11.20"; sha256="0nznlpqpj1lrxn0lymq5xksn8zs6hda4jmq57mks9nj8ilq1sw0r"; depends=[BiocGenerics Biostrings data_table DNAcopy futile_logger GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra IRanges Matrix RColorBrewer rhdf5 Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VGAM]; }; - Pviz = derive2 { name="Pviz"; version="1.15.0"; sha256="08kkrhxmy60lkvmjwpkv3nv7w8mybv5465923a9hghzs291qjvn4"; depends=[Biostrings biovizBase data_table GenomicRanges Gviz IRanges]; }; - QDNAseq = derive2 { name="QDNAseq"; version="1.17.0"; sha256="113s3ir4dxhxxpfy700hp2lgvx6qgzy1nbqin0g3fz7z0y50m2ns"; depends=[Biobase BiocParallel CGHbase CGHcall DNAcopy GenomicRanges IRanges matrixStats R_utils Rsamtools]; }; - QSutils = derive2 { name="QSutils"; version="0.99.8"; sha256="03840r3xw83gd1k56p66qang26g26gilrddfdnjjilpkcshmbksd"; depends=[ape BiocGenerics Biostrings psych]; }; - QUALIFIER = derive2 { name="QUALIFIER"; version="1.25.1"; sha256="1acaga0zc3vnjmr15xmyd05xp2cdwh96armg47qbpb4kygfh433g"; depends=[Biobase data_table flowCore flowViz flowWorkspace hwriter lattice latticeExtra MASS ncdfFlow reshape XML]; }; - QUBIC = derive2 { name="QUBIC"; version="1.9.1"; sha256="0akvph9v1rqiq5a4ygi3wcpi82n4py59fdwvzbphnkd1wpva61wn"; depends=[biclust Matrix Rcpp RcppArmadillo]; }; - QuartPAC = derive2 { name="QuartPAC"; version="1.13.1"; sha256="105jl05hai0jiy240618zbb861d7ya0x51hds6h9af189jgc98jz"; depends=[data_table GraphPAC iPAC SpacePAC]; }; - QuasR = derive2 { name="QuasR"; version="1.21.2"; sha256="1wz8mq86ffws24akwf0idvq3s2ys8dgwcm47ajv59589x75a9qwv"; depends=[Biobase BiocGenerics BiocManager BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges IRanges Rbowtie Rsamtools rtracklayer S4Vectors ShortRead zlibbioc]; }; - QuaternaryProd = derive2 { name="QuaternaryProd"; version="1.15.3"; sha256="0k3a64j3zkvqqg04hlx94iiw5g2hndnl99m2bbn6asjx3vyjj237"; depends=[dplyr Rcpp yaml]; }; - R3CPET = derive2 { name="R3CPET"; version="1.13.1"; sha256="182h5zgq496lg284ncjk5qrqfnzab2cs8lkjrrxf4yzvf8h38bgl"; depends=[BiocGenerics clues clValid data_table GenomeInfoDb GenomicRanges ggbio ggplot2 Hmisc igraph IRanges pheatmap Rcpp RCurl reshape2 S4Vectors]; }; - R453Plus1Toolbox = derive2 { name="R453Plus1Toolbox"; version="1.31.0"; sha256="16cri94hg585804xaq5gfbs9nn62nhmcayapvwpb2y7vs855g4qx"; depends=[Biobase BiocGenerics biomaRt Biostrings BSgenome GenomicRanges IRanges R2HTML Rsamtools S4Vectors ShortRead SummarizedExperiment TeachingDemos VariantAnnotation xtable XVector]; }; - R4RNA = derive2 { name="R4RNA"; version="1.9.0"; sha256="08jrmdcdwk9dzk38sjc6rxn4nf3s5lg6x9w540drhiynd3jw9nxw"; depends=[Biostrings]; }; - RBGL = derive2 { name="RBGL"; version="1.57.0"; sha256="0bm2wfsi3himissj2x1v16rgrz3j2wz9s1kisaxxpgv27a4bvp0i"; depends=[graph]; }; - RBM = derive2 { name="RBM"; version="1.13.1"; sha256="1yc0cqw84b5bzwnp85x50q3ibq7zr3awnc0ndrf05q38jbqrgskc"; depends=[limma marray]; }; - RBioinf = derive2 { name="RBioinf"; version="1.41.0"; sha256="1bi7dx51nhq7y2s0395hncbfbwfhdixwwn5n238f6fq6sxg95v1h"; depends=[graph]; }; - RCAS = derive2 { name="RCAS"; version="1.7.3"; sha256="1k8frzidrg88j0mzbhn4njm2jfgxi5lv91yszarl43fhl19zrdl2"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; }; - RCASPAR = derive2 { name="RCASPAR"; version="1.27.0"; sha256="00r0p6hzzjsgpwc0ja6ws2sn7fp5qzlcajvwq3l5zd99zcn3lds8"; depends=[]; }; - RCy3 = derive2 { name="RCy3"; version="2.1.26"; sha256="0j8ynimcgr0jbnlfib17vr4zjf3k5j5159aq1v8y3dxcx21hqh0d"; depends=[BiocGenerics graph httr igraph RJSONIO XML]; }; - RCyjs = derive2 { name="RCyjs"; version="2.3.11"; sha256="1q74r04h169mix224jcahh8mir17dc1ifasfcgjir9szw3gh97lv"; depends=[base64enc BiocGenerics BrowserViz graph httpuv]; }; - RDAVIDWebService = derive2 { name="RDAVIDWebService"; version="1.19.0"; sha256="0in7bnx1v9z9z55b88hmix8fgrjysbzjxp0c53psq3k7fm46yxg7"; depends=[Category ggplot2 GO_db GOstats graph RBGL rJava]; }; - RDRToolbox = derive2 { name="RDRToolbox"; version="1.31.0"; sha256="0zm1319g4b0jfqi7ix7insqadilccmlcc1bnwf4hwgw1d2bsby1p"; depends=[MASS rgl]; }; - REBET = derive2 { name="REBET"; version="0.99.6"; sha256="1q8ksqv13rnk2rv0xs1cfkskp8j701pi231b5m14s41gxq85f689"; depends=[ASSET]; }; - REDseq = derive2 { name="REDseq"; version="1.27.0"; sha256="0s1v5qlbzz54pck44vy0bzhkm0ga7wa01nrr4x1fbswxbkz80djy"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome BSgenome_Celegans_UCSC_ce2 ChIPpeakAnno IRanges multtest]; }; - REMP = derive2 { name="REMP"; version="1.5.2"; sha256="04jg8c2x1k3wbf1gr8ncdgy4z09r2zk1fhbxpgz8cv2hngdpwhfi"; depends=[AnnotationHub BiocGenerics BiocParallel Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 caret doParallel foreach GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 impute IRanges iterators kernlab minfi org_Hs_eg_db ranger S4Vectors settings SummarizedExperiment]; }; - RGMQL = derive2 { name="RGMQL"; version="1.1.0"; sha256="1z7dj3lmw40b08x33bl9fb4asr22syn0cinl12ya60nawh5rlxsi"; depends=[BiocGenerics data_table dplyr GenomicRanges glue httr plyr RGMQLlib rJava rtracklayer S4Vectors xml2]; }; - RGSEA = derive2 { name="RGSEA"; version="1.15.0"; sha256="1c0i33lz0cl983dk520g2caf0844jknd39h71fy6kynknqxmnqqs"; depends=[BiocGenerics]; }; - RGalaxy = derive2 { name="RGalaxy"; version="1.25.0"; sha256="04xs1w3yndlrdbac2ybzhdk8fdbg95a3qmjjqyykhfl5mck97d97"; depends=[Biobase BiocGenerics optparse roxygen2 XML]; }; - RGraph2js = derive2 { name="RGraph2js"; version="1.9.0"; sha256="0y7fnysz9rljyrk4gs1r29zgxzzcpwk3jayv6km20l6abxzbfccr"; depends=[digest graph rjson whisker]; }; - RIPSeeker = derive2 { name="RIPSeeker"; version="1.21.1"; sha256="0vxllhd0pyq1a3z0gqpiv5llyb18qi8ph6h8jmqbjsknba243j30"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; - RITAN = derive2 { name="RITAN"; version="1.5.5"; sha256="0p2dpn6zas3wndzr9dbs1l97s5w7qzj0y7db7796jysd3mlzlvz1"; depends=[BgeeDB dynamicTreeCut ggplot2 gplots gridExtra gsubfn hash igraph knitr linkcomm MCL plotrix png RColorBrewer reshape2 RITANdata sqldf STRINGdb]; }; - RIVER = derive2 { name="RIVER"; version="1.5.1"; sha256="1c7li0kihq3rxqv7ykz12accyqpiwwvjdlma137mfh5dhpjlx5cr"; depends=[Biobase ggplot2 glmnet pROC]; }; - RImmPort = derive2 { name="RImmPort"; version="1.9.0"; sha256="0amhihh6g8j817xr05bqcp9sx564gp0jlg34iinmjqzizksflv1g"; depends=[data_table DBI dplyr plyr reshape2 RSQLite sqldf]; }; - RJMCMCNucleosomes = derive2 { name="RJMCMCNucleosomes"; version="1.5.0"; sha256="008nmql2f1qw246bj50w38kabcfw2bvgqb086ch9h9cv4b976dwi"; depends=[BiocGenerics BiocParallel consensusSeekeR GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; - RLMM = derive2 { name="RLMM"; version="1.43.0"; sha256="1hfr0w56jai1v3x0b6w4z5y00yf8j2aa2yhcd994lj48klwgjacp"; depends=[MASS]; }; - RMassBank = derive2 { name="RMassBank"; version="2.9.2"; sha256="0yvbd1425ygp3xmn1danhbx5865cyl2h340yscs4r6g9whciw1vn"; depends=[Biobase digest httr MSnbase mzR rcdk Rcpp RCurl rjson S4Vectors XML yaml]; }; - RNASeqPower = derive2 { name="RNASeqPower"; version="1.21.0"; sha256="0gd3mbish7k4zwfv4kadcnifwm485p7zizvdj8pk1ns1fl5cwpbz"; depends=[]; }; - RNASeqR = derive2 { name="RNASeqR"; version="0.99.25"; sha256="03mka6s8s064agyrvl3xzdds1dr03jimgcqgnisr61ypdy9lyih0"; depends=[ballgown Biostrings clusterProfiler corrplot DESeq2 DOSE edgeR factoextra FactoMineR ggplot2 gridExtra org_Hs_eg_db org_Sc_sgd_db pathview PerformanceAnalytics pheatmap rafalib reshape2 reticulate Rsamtools stringr systemPipeR systemPipeRdata]; }; - RNAdecay = derive2 { name="RNAdecay"; version="1.1.2"; sha256="09z07f5x0h19dbk47lwmp9h9ijvmdznr8hxxyihazqvr66qb5ghn"; depends=[ggplot2 gplots nloptr TMB]; }; - RNAinteract = derive2 { name="RNAinteract"; version="1.29.1"; sha256="1wq1b3z8yqslw4l4103x28lv063m5f1wi1dr43q9h345gcb4kyvs"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; }; - RNAither = derive2 { name="RNAither"; version="2.29.0"; sha256="0w90awkmdi2h6q2hpvl6i5qbkdggbpvac1cbxx2995hmx8lc6pwa"; depends=[biomaRt car geneplotter limma prada RankProd splots topGO]; }; - RNAprobR = derive2 { name="RNAprobR"; version="1.13.0"; sha256="0hjhk0ap6n17ccjkjfxq8c8cfg166gcwbapmwixac4dqwqg5k997"; depends=[BiocGenerics Biostrings GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr Rsamtools rtracklayer S4Vectors]; }; - ROC = derive2 { name="ROC"; version="1.57.0"; sha256="1glip25d37gz13b2c4zpk1vm34kvfxvgbsz302ww0g8wqq3cc0i5"; depends=[]; }; - ROTS = derive2 { name="ROTS"; version="1.9.1"; sha256="061z3cnwaz5fgbpikg6vqazp1bqsxp7ln8krn3i1fz20k4ny800z"; depends=[Biobase Rcpp]; }; - ROntoTools = derive2 { name="ROntoTools"; version="2.9.0"; sha256="1ivsr52qf9sz08zpp1vbvwyqpsfd55m4jj8g62mb5khkmrf8mnwl"; depends=[boot graph KEGGgraph KEGGREST Rgraphviz]; }; - RPA = derive2 { name="RPA"; version="1.37.2"; sha256="16yr6qp6wcdrb4zpyrs30zv0q4zb74s04fzpddk6c7v1phmakk0a"; depends=[affy BiocGenerics phyloseq]; }; - RProtoBufLib = derive2 { name="RProtoBufLib"; version="1.3.7"; sha256="0f68ziylg1pp3wakxr08i6hlhf3grnvfmsr7fc1v1phsz8amg676"; depends=[]; }; - RRHO = derive2 { name="RRHO"; version="1.21.0"; sha256="00wy53vmfdzfv56ib277cl7rnv2l6klyixyjq93whmzr39d8mbwi"; depends=[VennDiagram]; }; - RSVSim = derive2 { name="RSVSim"; version="1.21.0"; sha256="0l7wq0cvws0n78xp14rwagrjhm3pxzf2jg3k1w5pv6w778mhm9dw"; depends=[Biostrings GenomicRanges IRanges ShortRead]; }; - RSeqAn = derive2 { name="RSeqAn"; version="1.1.0"; sha256="186qcffr5f1g5x5didd8gkhfdl9wxdivqjwxbcn001i3k71h11mm"; depends=[]; }; - RTCA = derive2 { name="RTCA"; version="1.33.0"; sha256="0wyvn004xjxgr80ar5a0bcc6jpz9ksi03is8yc8ijsdlssk9cs71"; depends=[Biobase gtools RColorBrewer]; }; - RTCGA = derive2 { name="RTCGA"; version="1.11.3"; sha256="1r0c2lj73brq174lfnxlwvjz34wckf2kd5hkzmymwv6vgy83j98q"; depends=[assertthat data_table dplyr ggplot2 ggthemes knitr purrr rvest scales stringi survival survminer viridis XML xml2]; }; - RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.11.8"; sha256="0sb5n88vbx24dfn66i4xd71c8kswsgwd14zky172lrjhplb1lkwm"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges IRanges limma RaggedExperiment RCircos RCurl RJSONIO S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; }; - RTN = derive2 { name="RTN"; version="2.5.6"; sha256="01r5hv1xc3znllqknc06x8zs9nxs2d9y2fxi8mv8ggxplaw05mwz"; depends=[data_table igraph IRanges limma minet mixtools RedeR S4Vectors snow viper]; }; - RTNduals = derive2 { name="RTNduals"; version="1.5.4"; sha256="1kjx590l4q2g9khph4xfkj2nqnq9aycyy16havv2ll4i48k4j4i7"; depends=[RTN]; }; - RTNsurvival = derive2 { name="RTNsurvival"; version="1.5.4"; sha256="0gn6s0lpxag113v1smh20k1w0yyhpr2wp4i0hvihxlqascmrp73j"; depends=[RColorBrewer RTN RTNduals scales survival viper]; }; - RTopper = derive2 { name="RTopper"; version="1.27.0"; sha256="1d2bnvjlwgrahxjd1x6gzdhz70wyd990iq9204kc072qyi40l2yz"; depends=[Biobase limma multtest]; }; - RUVSeq = derive2 { name="RUVSeq"; version="1.15.1"; sha256="0j60afjrnbi8x00nw5y0l8m2j7i4n1aq31k8swxinsniawhidbvn"; depends=[Biobase EDASeq edgeR MASS]; }; - RUVcorr = derive2 { name="RUVcorr"; version="1.13.0"; sha256="0cfq69vvajn2s8gyrr4g9vzf8l8wp7p6hg6jlfffv2kfn3yhd05g"; depends=[BiocParallel bladderbatch corrplot gridExtra lattice MASS psych reshape2 snowfall]; }; - RUVnormalize = derive2 { name="RUVnormalize"; version="1.15.0"; sha256="02v5kj8hbzgcckqq671zypfkf460j3rxiqxh4w5izp9bxqdv9g3g"; depends=[Biobase RUVnormalizeData]; }; - RVS = derive2 { name="RVS"; version="1.3.1"; sha256="02y68m30aqmcyf1bv0aicrijdx87gzaa9a5f2dlfjfd6jgk2ijn9"; depends=[gRain kinship2 snpStats]; }; - RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.5.7"; sha256="1wvczzqhsgdj0f6a2v7ls4c51vm9wik10wnlkxsw06h3xz6c3xmf"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; - RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.1.1"; sha256="0p9qvbsmxvca615h6pk51n8dm21265bmciix3ddnhljq1c6lgc7x"; depends=[dnet igraph Matrix]; }; - RankProd = derive2 { name="RankProd"; version="3.7.0"; sha256="1zqawks6i567dk4ylnyh0jddnp62nqygshv4ihy39xhjab4j04wx"; depends=[gmp Rmpfr]; }; - RareVariantVis = derive2 { name="RareVariantVis"; version="2.9.0"; sha256="1466zh50n0f1apkbd38lp84r8byras0pna5bm49bc7i7s9agkp14"; depends=[BiocGenerics BSgenome BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores googleVis gtools IRanges phastCons100way_UCSC_hg19 S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; - Rariant = derive2 { name="Rariant"; version="1.17.0"; sha256="0nm0k2d1bhqsk9gir38gd0py6xn5wk0b985kpix8ghi64mypmqmr"; depends=[BiocGenerics dplyr exomeCopy GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges reshape2 Rsamtools S4Vectors shiny SomaticSignatures VariantAnnotation VGAM]; }; - RbcBook1 = derive2 { name="RbcBook1"; version="1.49.0"; sha256="1ar8jl97fillw0g7kf09mxkr9215dw3jmw2b6qaq9pch7qg8qnr7"; depends=[Biobase graph rpart]; }; - Rbowtie = derive2 { name="Rbowtie"; version="1.21.2"; sha256="1l5mllfa4kfdrf65xmssd3wpfvqnl9p0lajg2fz1hl98xwm7yl31"; depends=[]; }; - Rbowtie2 = derive2 { name="Rbowtie2"; version="1.3.1"; sha256="1ss2i77lq3fazv6ipv543cfizchp9gh566d7xbjkggh1a0vcm1db"; depends=[]; }; - Rcade = derive2 { name="Rcade"; version="1.23.0"; sha256="0d6cyn6b06g0qkps2d7b65p7pa7bz6iv71lv4hbzmdc581azg4fq"; depends=[baySeq GenomeInfoDb GenomicAlignments GenomicRanges IRanges plotrix rgl Rsamtools S4Vectors]; }; - Rchemcpp = derive2 { name="Rchemcpp"; version="2.19.0"; sha256="17kz0ld7hnrvdv69hz3kj3mhv2f4qms9i65lrwam63g0aydfzyrx"; depends=[ChemmineR Rcpp]; }; - RchyOptimyx = derive2 { name="RchyOptimyx"; version="2.21.0"; sha256="0fzmw1kxnaqmk5h61r2dkwq0xp8ir7gg7kq2wkhyvpd68hr3ir3d"; depends=[flowType graph Rgraphviz sfsmisc]; }; - RcisTarget = derive2 { name="RcisTarget"; version="1.1.3"; sha256="09zkvl5hwcds9w5n5h51zgpilmygljmar3fqd5wihr8dd6bj1qnk"; depends=[AUCell BiocGenerics data_table feather GSEABase R_utils SummarizedExperiment]; }; - Rcpi = derive2 { name="Rcpi"; version="1.17.2"; sha256="1d77jnlw2jsg8f2ij7ax8ngwb99bngiq0vvdpx2q5nmhkzn9w5vq"; depends=[Biostrings ChemmineR doParallel fmcsR foreach GOSemSim rcdk RCurl rjson]; }; - Rdisop = derive2 { name="Rdisop"; version="1.41.0"; sha256="038bgrf5bcdwy8bji5wprq55ypajwp68lqv1i24bk6hikfm2g7p9"; depends=[Rcpp RcppClassic]; }; - ReQON = derive2 { name="ReQON"; version="1.27.0"; sha256="1dvsnbsl5ljwfirn61rbcxvrdy74qv96xbs4d8x1wmkfs2bsm2gy"; depends=[rJava Rsamtools seqbias]; }; - ReactomePA = derive2 { name="ReactomePA"; version="1.25.1"; sha256="1kqhm5n1g8r1rci0n1135pcka2x0p8h565m609bfljiqnmgaza9v"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite igraph reactome_db]; }; - ReadqPCR = derive2 { name="ReadqPCR"; version="1.27.2"; sha256="1mbaqp0xj0ncdja7rgb84j54bv1vricsabnfj6d8v55yrp1jp7p6"; depends=[Biobase]; }; - RedeR = derive2 { name="RedeR"; version="1.29.0"; sha256="00j3yr07qg363ghbgv76ydyar0jp48zdfw5pdpxnv13mzm48wa4r"; depends=[igraph]; }; - RefNet = derive2 { name="RefNet"; version="1.17.0"; sha256="0lcbg131gxkvsvmbwj4gpqdpfqjik91jmyd2g745yb7rayly252g"; depends=[AnnotationHub BiocGenerics IRanges PSICQUIC RCurl shiny]; }; - RefPlus = derive2 { name="RefPlus"; version="1.51.0"; sha256="0wq0l2883ns2sl8ia5qdx6wn9227lxaz7m0g3lqmr36xkflc1ka1"; depends=[affy affyPLM Biobase preprocessCore]; }; - Repitools = derive2 { name="Repitools"; version="1.27.0"; sha256="1anh3fn4wyn69838y7jr5h6bhi8m7d7r1n68rbqvsvbr4bik54vr"; depends=[aroma_affymetrix BiocGenerics Biostrings BSgenome cluster DNAcopy edgeR GenomeInfoDb GenomicAlignments GenomicRanges gplots gsmoothr IRanges MASS Ringo Rsamtools Rsolnp rtracklayer S4Vectors]; }; - ReportingTools = derive2 { name="ReportingTools"; version="2.21.1"; sha256="0rdndxizkbx8bdjcx82x59y326ypsxrlmzyrgkgkmm3hgq041n97"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category DESeq2 edgeR ggbio ggplot2 GOstats GSEABase hwriter IRanges knitr lattice limma PFAM_db R_utils XML]; }; - Rgin = derive2 { name="Rgin"; version="1.1.0"; sha256="1yqif2dpw0c3p4kg8pni80ggh3f6430nd7k3k0fxirz74ljv642h"; depends=[RcppEigen]; }; - Rgraphviz = derive2 { name="Rgraphviz"; version="2.25.1"; sha256="1l98pa3zp18xp64phrp5k7sn9an3a8mqp124ik8a2gk8hs021glx"; depends=[graph]; }; - Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.3.3"; sha256="19r2afmvik4as8cwgk0adh3rm94bjp9vll3c63845swrsk13smzz"; depends=[]; }; - Rhtslib = derive2 { name="Rhtslib"; version="1.13.4"; sha256="0g60pz7ssy872ppws7qvsv7miph3yhx48p6sqmxi3qbz0qs6dq15"; depends=[zlibbioc]; }; - RiboProfiling = derive2 { name="RiboProfiling"; version="1.11.0"; sha256="0l76dfz2r2grx31v8ic80k3mry78m20znssrh5i7v6xfh33ghg6c"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr reshape2 Rsamtools rtracklayer S4Vectors sqldf]; }; - Ringo = derive2 { name="Ringo"; version="1.45.0"; sha256="0pwyfjv8f91g7i1h9qpzwgbkgyh04dyvmrm9v4rdabmfbhr38c6g"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; }; - Risa = derive2 { name="Risa"; version="1.23.2"; sha256="0ng31ms4ndfgwna99qqf73ad9klgi7d477x3my4wkd6896hk7xg3"; depends=[affy Biobase biocViews Rcpp xcms]; }; - Rmagpie = derive2 { name="Rmagpie"; version="1.37.0"; sha256="1qzxifxdkc86p4q8l7qz8bmxlh5an7zkmgbzb72chwm6bby774m8"; depends=[Biobase e1071 kernlab pamr]; }; - RmiR = derive2 { name="RmiR"; version="1.37.0"; sha256="0zz0jgqfqph0rhkbx0bgm8kcwm81hsk1cml8a917gfymfpzj93s8"; depends=[DBI RmiR_Hs_miRNA RSVGTipsDevice]; }; - Rmmquant = derive2 { name="Rmmquant"; version="0.99.11"; sha256="0lj7dnjf5msrn7fbr68krv2rgav8qrpahgj37qa64k5cn0xyiblw"; depends=[BiocStyle DESeq2 devtools GenomicRanges org_Mm_eg_db Rcpp S4Vectors SummarizedExperiment TBX20BamSubset TxDb_Mmusculus_UCSC_mm9_knownGene]; }; - RnBeads = derive2 { name="RnBeads"; version="1.99.0"; sha256="1gmhq1rp5jlkm0dmbzzxzpylyxzpbf2529j3v7a37fq4pia0nylk"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; }; - RnaSeqSampleSize = derive2 { name="RnaSeqSampleSize"; version="1.13.0"; sha256="0d27jiw016fkmzpd4lsjnrkd122amqi37cr5rpnwviyw47rw5dxj"; depends=[biomaRt edgeR heatmap3 KEGGREST matlab Rcpp RnaSeqSampleSizeData]; }; - Rnits = derive2 { name="Rnits"; version="1.15.0"; sha256="0vg3rx87fw9y792b9icf1qliwsbi7h74csk7n9ya8jwjsyb0fcv2"; depends=[affy Biobase boot ggplot2 impute limma qvalue reshape2]; }; - Roleswitch = derive2 { name="Roleswitch"; version="1.19.0"; sha256="12pqrclq4vfsv0y9ykisri5l2zy3pz3sz22xqlqfkmlldqvngy4v"; depends=[Biobase biomaRt Biostrings DBI microRNA plotrix pracma reshape]; }; - RpsiXML = derive2 { name="RpsiXML"; version="2.23.0"; sha256="061r9c1lb3qrm4lwpk87ynsi6nqjwqv2cxk9z6l01b14cb2mn6r3"; depends=[annotate AnnotationDbi Biobase graph hypergraph RBGL XML]; }; - Rqc = derive2 { name="Rqc"; version="1.15.1"; sha256="0hb3115hrq4vgl32w01fagkbyisxxkbhs96fbxrz3rlkw982b636"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings biovizBase digest GenomicAlignments GenomicFiles ggplot2 IRanges knitr markdown plyr Rcpp reshape2 Rsamtools S4Vectors shiny ShortRead]; }; - Rsamtools = derive2 { name="Rsamtools"; version="1.33.7"; sha256="1jlhfjdby0cgsjfjcbf6kgcc8g1c6nfwlyp67yrn6x577cf9vl40"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges S4Vectors XVector zlibbioc]; }; - Rsubread = derive2 { name="Rsubread"; version="1.31.23"; sha256="1n59sxlfmwvk9yfp88lcffbqpbxdg5b1hgawkz0d3sy9f4wv6vg1"; depends=[]; }; - Rtreemix = derive2 { name="Rtreemix"; version="1.43.0"; sha256="0wkszdsbpkai8snqvgr46mc0kqlgha76hclr4kbgddlbg9cmbymh"; depends=[Biobase graph Hmisc]; }; - S4Vectors = derive2 { name="S4Vectors"; version="0.19.24"; sha256="0r8plfk310jkymlpkxvkqh9b5y9xd00iy2jn28w5ajf7zxrdbxl2"; depends=[BiocGenerics]; }; - SAGx = derive2 { name="SAGx"; version="1.55.0"; sha256="1xriaf6qhmisx7415jgrpk6p0jhhv0mn3ab1zj4g6dvm495s0579"; depends=[Biobase multtest]; }; - SANTA = derive2 { name="SANTA"; version="2.19.0"; sha256="0qfzmsqssb62bab9csak82s0dhrrpz93q0825sdjk7sy2qnp3c6l"; depends=[igraph Matrix snow]; }; - SBMLR = derive2 { name="SBMLR"; version="1.77.0"; sha256="0xhs5adrirlplm8m3ldsw0m085wqi7mgjn3c7ldkhmlr9w9vc7wg"; depends=[deSolve XML]; }; - SC3 = derive2 { name="SC3"; version="1.9.1"; sha256="1nj5sjxgv0ic0s74w9vy3dwnrwywwj2kaydnn5s1p1hnrc6xsm11"; depends=[BiocGenerics cluster doParallel doRNG e1071 foreach ggplot2 pheatmap Rcpp RcppArmadillo robustbase ROCR rrcov S4Vectors shiny SingleCellExperiment SummarizedExperiment WriteXLS]; }; - SCAN_UPC = derive2 { name="SCAN.UPC"; version="2.23.0"; sha256="1l7h4r4msq8gdiklmnb8cnh29babknzsbncxg3qkrf28q6gihz29"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; }; - SCBN = derive2 { name="SCBN"; version="0.99.2"; sha256="10rcvn19k2034dgcc5lyv24ir5ql9qsikr5fplsp4qc4v9z8v658"; depends=[]; }; - SCnorm = derive2 { name="SCnorm"; version="1.3.3"; sha256="0vbyvvx3pf5k9j9fy0jkfawic3l54kj5sjmsgb1bb6b5x1njdz0h"; depends=[BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SingleCellExperiment SummarizedExperiment]; }; - SDAMS = derive2 { name="SDAMS"; version="1.1.2"; sha256="0zd1y03g9dxflvj3adg2jqlzcipbaz87vm927l1cd3pdzgzvx294"; depends=[qvalue SummarizedExperiment trust]; }; - SELEX = derive2 { name="SELEX"; version="1.13.0"; sha256="0n2xpdyr6sy8mnbq9vqccaphfa5pjbldcnmpm4zb9w2zdg27g24k"; depends=[Biostrings rJava]; }; - SEPA = derive2 { name="SEPA"; version="1.11.0"; sha256="19904q9pxbxwaj8vfqk1nvwb5sn69g15zfk9xyb7wwnwxrrkph0r"; depends=[ggplot2 org_Hs_eg_db org_Mm_eg_db reshape2 segmented shiny topGO]; }; - SEPIRA = derive2 { name="SEPIRA"; version="1.1.2"; sha256="1v6xqrvvnkf5r5cl6k4akq9450qhii0hwbysc76ndnwyc7lgmjws"; depends=[corpcor limma]; }; - SGSeq = derive2 { name="SGSeq"; version="1.15.0"; sha256="09ksqyszgh84lwv0vzy8kp4vdhczdqpk1mr7h18ja5rpilnk60r0"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges igraph IRanges Rsamtools rtracklayer RUnit S4Vectors SummarizedExperiment]; }; - SIAMCAT = derive2 { name="SIAMCAT"; version="1.1.0"; sha256="0aaw372yl2b74ni3hr788bqglma679vqfzhfad2903ln0lx54rl3"; depends=[beanplot glmnet gridBase gridExtra LiblineaR matrixStats mlr ParamHelpers phyloseq pROC PRROC RColorBrewer]; }; - SICtools = derive2 { name="SICtools"; version="1.11.0"; sha256="1jgq6acqqfx6fcwkyqn49p94m399dblc86s3hf7xgdml61jjxa81"; depends=[Biostrings doParallel GenomicRanges IRanges matrixStats plyr Rsamtools stringr]; }; - SIM = derive2 { name="SIM"; version="1.51.0"; sha256="0z23b4pgiyah5qcixhww7csmkq01gw0bd9hmzrwrn046yy3mmnql"; depends=[globaltest quantreg quantsmooth]; }; - SIMAT = derive2 { name="SIMAT"; version="1.13.4"; sha256="142lafcpbmfnx1ywwas9dba4gz2vxnds4pia4dcxya6r254pbw9b"; depends=[ggplot2 mzR Rcpp reshape2]; }; - SIMD = derive2 { name="SIMD"; version="0.99.10"; sha256="17m05cvc1yzdjlyx7j971cais8lyacil2vjfl09vvj93ygfks1sy"; depends=[edgeR methylMnM statmod]; }; - SIMLR = derive2 { name="SIMLR"; version="1.7.4"; sha256="0pgz774i1ffix5s37qxxm78wa283zaghshwrj1chqzsk2hw1vy21"; depends=[Matrix pracma Rcpp RcppAnnoy RSpectra]; }; - SISPA = derive2 { name="SISPA"; version="1.11.0"; sha256="1cw4xzcqjp8pdaglar9dfgr25zqyb6h31k3hn66hyxg9cyagj4k4"; depends=[changepoint data_table genefilter ggplot2 GSVA plyr]; }; - SLGI = derive2 { name="SLGI"; version="1.41.0"; sha256="0ihb43dmab2188641l5zpn98djj68mm5xq2v79wqrh136n9cam9j"; depends=[AnnotationDbi Biobase BiocGenerics GO_db lattice ScISI]; }; - SLqPCR = derive2 { name="SLqPCR"; version="1.47.0"; sha256="0m2qhkc6l158phg5hwfcs5wlq2n2nrhsjprrmzjv3q9rsdhwid8c"; depends=[]; }; - SMAP = derive2 { name="SMAP"; version="1.45.0"; sha256="1i94sywcxp3pg30b93v5p9n70va1mixk67jxxfyhc6dlbfpx7d3y"; depends=[]; }; - SMITE = derive2 { name="SMITE"; version="1.9.0"; sha256="1hvmbsz7p4ibjfh2a45aqpvv1kridkfg3zk3kzgbmws5l1vf154z"; depends=[AnnotationDbi Biobase BioNet geneLenDataBase GenomicRanges ggplot2 goseq Hmisc igraph IRanges KEGG_db org_Hs_eg_db plyr reactome_db S4Vectors scales]; }; - SNAGEE = derive2 { name="SNAGEE"; version="1.21.0"; sha256="0lsb2rqb1a3dgfgv5bijgb87y3zdl3mp1p38nzzi05n180yrgpzr"; depends=[SNAGEEdata]; }; - SNPRelate = derive2 { name="SNPRelate"; version="1.15.5"; sha256="19lzy5jcp64kvg569x0688v03jalpbigmxpbaqsyc61j9h3gqkh7"; depends=[gdsfmt]; }; - SNPchip = derive2 { name="SNPchip"; version="2.27.0"; sha256="15cf2nrwixiqiyav5634qlv7md5dmv17h3z97j5771dv75fkl2gr"; depends=[Biobase foreach GenomeInfoDb GenomicRanges IRanges lattice oligoClasses S4Vectors SummarizedExperiment]; }; - SNPediaR = derive2 { name="SNPediaR"; version="1.7.1"; sha256="1lly6gajffcia6kjb3bshy401w2ydrwj674kas3dipamchp7k7p9"; depends=[jsonlite RCurl]; }; - SNPhood = derive2 { name="SNPhood"; version="1.11.0"; sha256="03dami2l6y21fh7sazh3bzjhj1n9vqc0fva4ig1kkdansd1bvp0f"; depends=[BiocGenerics BiocParallel Biostrings checkmate cluster data_table DESeq2 GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges lattice RColorBrewer reshape2 Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; - SPEM = derive2 { name="SPEM"; version="1.21.0"; sha256="19l21yaqcazymnapqalrkb6az10jkmzy8zvp5wh28rb8bl2p88f3"; depends=[Biobase Rsolnp]; }; - SPIA = derive2 { name="SPIA"; version="2.33.0"; sha256="06si8xr8hc4sr87gafaphv9rfiq9w82gwd4xzwn0js00fgalffvd"; depends=[KEGGgraph]; }; - SPLINTER = derive2 { name="SPLINTER"; version="1.7.4"; sha256="007h0y808cylwkr9bjgsdvf4d4bfvz0xpalh06drq666cr9cxdzr"; depends=[biomaRt Biostrings BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 googleVis Gviz IRanges plyr S4Vectors seqLogo stringr]; }; - SPONGE = derive2 { name="SPONGE"; version="1.3.0"; sha256="0xnrzzlm12rrr54ymfa10pcmzgq7njqhgynv9ki9msxrvn1rhcd4"; depends=[Biobase data_table doRNG expm foreach glmnet gRbase igraph iterators logging MASS ppcor]; }; - SQUADD = derive2 { name="SQUADD"; version="1.31.0"; sha256="0dh04i31lzdpkmqhawm1krn132hqj6qz5i6cj2sxxvk4chqq1xmf"; depends=[RColorBrewer]; }; - SRAdb = derive2 { name="SRAdb"; version="1.43.2"; sha256="01nr09lkm4lwc6p0mfl1nn8g4fkzsw8c157snkcclqzn829121bp"; depends=[GEOquery graph RCurl RSQLite]; }; - SRGnet = derive2 { name="SRGnet"; version="1.7.0"; sha256="1b6y5wq18vb41wvjdgbwr5mhwbyi0brzj941950w9if4hm1xrxs6"; depends=[DMwR EBcoexpress gbm Hmisc igraph limma MASS matrixStats pvclust]; }; - SSPA = derive2 { name="SSPA"; version="2.21.0"; sha256="1bsn84xsapnfdfrv6nbp4a7604y2jfkf7zj1xzhv582klawwxzyg"; depends=[lattice limma qvalue]; }; - STAN = derive2 { name="STAN"; version="2.9.0"; sha256="0i8y0a2i60irdg3061l4fmwdmnfrf0fc5byhx1bwbr8w5g4ahpnh"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; }; - STATegRa = derive2 { name="STATegRa"; version="1.17.1"; sha256="1k55kb5x108iq3f2hbbair96x9kn8cci0753jkmd485j3mizfqq4"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; }; - STRINGdb = derive2 { name="STRINGdb"; version="1.21.0"; sha256="079y5h2jfx40vr5yvvpafzzld1z7jc9z98gm31qy7gvm2lyzvgl5"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; }; - STROMA4 = derive2 { name="STROMA4"; version="1.5.2"; sha256="1c7cjzrvbb62j8lyq8fn6xl375yhzghw1a4zy6pp0s8sd1r6vpmn"; depends=[Biobase BiocParallel cluster matrixStats]; }; - SVAPLSseq = derive2 { name="SVAPLSseq"; version="1.7.0"; sha256="0g27ik0m7z6wya7z2xgaip0c8dingv1c2jq9qbwpwipvk2yl8f50"; depends=[edgeR ggplot2 limma lmtest pls SummarizedExperiment]; }; - SVM2CRM = derive2 { name="SVM2CRM"; version="1.13.0"; sha256="0bnd0bpxwd2c33xdp9bfn8lsvf9dm8an4n43py6akshf6q2l9x3y"; depends=[AnnotationDbi GenomicRanges IRanges LiblineaR mclust pls ROCR rtracklayer squash SVM2CRMdata verification zoo]; }; - SWATH2stats = derive2 { name="SWATH2stats"; version="1.11.7"; sha256="1j8c18kiijzz1sc28n4asspljdgxmd000ms6qq5pzac36gkjwn98"; depends=[biomaRt data_table ggplot2 reshape2]; }; - SamSPECTRAL = derive2 { name="SamSPECTRAL"; version="1.35.2"; sha256="0dzapl17bgykgsd9qapc1v0ihzn229n25zvagjp1kdx3r4jqmkbb"; depends=[]; }; - ScISI = derive2 { name="ScISI"; version="1.53.0"; sha256="02m4ma2izak4vg4240hnny0b84x440myayjwqcysg8r5gr6pzd83"; depends=[annotate AnnotationDbi apComplex GO_db org_Sc_sgd_db RpsiXML]; }; - Scale4C = derive2 { name="Scale4C"; version="1.3.0"; sha256="1a97dchcinhp24k0r5f7agca33zk3qyh1scz8250aiilhfa4w37y"; depends=[GenomicRanges IRanges smoothie SummarizedExperiment]; }; - Sconify = derive2 { name="Sconify"; version="1.1.3"; sha256="1v5g6w51xfh8gs026k68lhrkzp4fkd5bwkjr7vxlbxggwp523sia"; depends=[dplyr flowCore FNN ggplot2 magrittr readr Rtsne tibble]; }; - SemDist = derive2 { name="SemDist"; version="1.15.2"; sha256="1mqv1xj3wwadrvf7qv2fpqhjgmvlipsy8afljl67i2y5ik025svi"; depends=[annotate AnnotationDbi GO_db]; }; - SeqArray = derive2 { name="SeqArray"; version="1.21.8"; sha256="03mv656dyvpxpqpxayr0d5zd47zjk0rn20jj58ma0cyln2a1rly8"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; - SeqGSEA = derive2 { name="SeqGSEA"; version="1.21.0"; sha256="10900fdl0g6izlpxwc3x2yix3cxpqfx6xxvbdq66mx2zqaksrq88"; depends=[Biobase biomaRt DESeq doParallel]; }; - SeqSQC = derive2 { name="SeqSQC"; version="1.3.1"; sha256="0avzc9h0xabr2j54gbfpbj5dvf0yr690ckzj9phqz1g4xj16sa25"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; }; - SeqVarTools = derive2 { name="SeqVarTools"; version="1.19.4"; sha256="0cqf6lmqa0r9rzslcgrvfislkmf0cx5ylp6mqqxfzi09q7f74s6q"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf Matrix S4Vectors SeqArray tidyr]; }; - ShortRead = derive2 { name="ShortRead"; version="1.39.0"; sha256="1cwpd5xf40gwpcnwmvxysxsl21cgfx3rdgigrawlzlzfd7j9kdig"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rsamtools S4Vectors XVector zlibbioc]; }; - SigCheck = derive2 { name="SigCheck"; version="2.13.0"; sha256="1cbdry06knmycqyc7p0z598rxlyyrw6yc8an8qm74b9p8vbnwp1a"; depends=[Biobase BiocParallel e1071 MLInterfaces survival]; }; - SigFuge = derive2 { name="SigFuge"; version="1.19.0"; sha256="07j9nzw5c4g99yf458n8jwkndr79mam2n4a6kcz9fpcsyjq4plp4"; depends=[GenomicRanges ggplot2 matlab reshape sigclust]; }; - SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.19.0"; sha256="0916ml80crldixb8jn5sbzp156ba0r9lc7wc2ri8wmrslv3w97lv"; depends=[Biobase limma mclust Ringo]; }; - SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.3.12"; sha256="1f4c1ma86rzxxqfmyr6w29fmclm6yrmlinkvsdfs8g5ynvlr272m"; depends=[BiocGenerics S4Vectors SummarizedExperiment]; }; - SomaticSignatures = derive2 { name="SomaticSignatures"; version="2.17.0"; sha256="1xq3m2i0b9rklg741796i8n1x0d07mn3xbdmvlc3islh368661jw"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; }; - SpacePAC = derive2 { name="SpacePAC"; version="1.19.3"; sha256="0i74bxw99bbs83zvs625pxqbjgkcp0jw076g3j6k5mqlhq98bj7i"; depends=[iPAC]; }; - SparseSignatures = derive2 { name="SparseSignatures"; version="1.1.5"; sha256="148x34p90x90lkl1ijj0s9gab3k295dbw2hyyy2hmx6hsmvp6hbl"; depends=[Biostrings BSgenome BSgenome_Hsapiens_1000genomes_hs37d5 data_table GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges NMF nnlasso nnls]; }; - SpeCond = derive2 { name="SpeCond"; version="1.35.0"; sha256="0sqb84sa7yf34lwwkchh5wb3dp6n4wk8kzqmsydx5lsaz6fxg32r"; depends=[Biobase fields hwriter mclust RColorBrewer]; }; - SpidermiR = derive2 { name="SpidermiR"; version="1.11.1"; sha256="0mxl07rzcs9agly7hx8f1xyjwfv8bi7yq93y2jzw0bfmxnn7b0rr"; depends=[AnnotationDbi gdata ggplot2 gplots gridExtra httr igraph lattice latticeExtra miRNAtap miRNAtap_db networkD3 org_Hs_eg_db TCGAbiolinks visNetwork]; }; - SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.21.0"; sha256="08n37qnhfk6j6gf0scm5m6i7q8ags821v4lp8aw670kij8xm4j5w"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; }; - StarBioTrek = derive2 { name="StarBioTrek"; version="1.7.1"; sha256="14a7rj8386iaqi3l47ahkpijh7bwwr8sir9ncmzj55fvk3m7c05g"; depends=[AnnotationDbi e1071 igraph KEGGREST org_Hs_eg_db ROCR SpidermiR]; }; - Starr = derive2 { name="Starr"; version="1.37.0"; sha256="0is2fy9zf2cgl3ywkn89v7n134sh812gibr3mpb8iccplvis7dks"; depends=[affxparser affy MASS pspline Ringo zlibbioc]; }; - Streamer = derive2 { name="Streamer"; version="1.27.0"; sha256="14wdvp51cgmzahqqr9dv5whgrl85yjj72sj1v3kqislqvfkn7lww"; depends=[BiocGenerics graph RBGL]; }; - SummarizedBenchmark = derive2 { name="SummarizedBenchmark"; version="1.99.3"; sha256="00a6wnysxmxlanjh8zy3bycl9grvzlpsfc7p8qnslyz446dnqdp8"; depends=[BiocGenerics BiocParallel crayon digest dplyr ggplot2 mclust rlang S4Vectors sessioninfo stringr SummarizedExperiment tibble tidyr UpSetR]; }; - SummarizedExperiment = derive2 { name="SummarizedExperiment"; version="1.11.6"; sha256="1wzp1yvn5vrfrr54v208i63rvb9awv7aplppv3lvwgk0j09hl4hh"; depends=[Biobase BiocGenerics DelayedArray GenomeInfoDb GenomicRanges IRanges Matrix S4Vectors]; }; - Sushi = derive2 { name="Sushi"; version="1.19.2"; sha256="12dz0l0lkvayqcvr21i2jdlpbfpvvd3rnzchar2yq7k7cwwa3v9s"; depends=[biomaRt zoo]; }; - SwathXtend = derive2 { name="SwathXtend"; version="2.3.1"; sha256="185rdcmdrahcmga3rkqniszg2i6scynspf7hh77q1ld7hi62ikcq"; depends=[e1071 lattice openxlsx VennDiagram]; }; - SwimR = derive2 { name="SwimR"; version="1.19.1"; sha256="1nbcan63p8jplrc1w7ljkmfisczgi9jg5rasdfm2iws5azpa36w9"; depends=[gplots heatmap_plus R2HTML signal]; }; - TCC = derive2 { name="TCC"; version="1.21.5"; sha256="140fhqn6yk8yayqhq47zpb6g3a1pwqhxdi6np5szz1h45scxzw01"; depends=[baySeq DESeq DESeq2 edgeR ROC]; }; - TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.9.5"; sha256="1lw67yvmhh24yh6rhanvpxp1ma9qwy8klia4py29jskw86vva3ca"; depends=[biomaRt circlize ComplexHeatmap ConsensusClusterPlus data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma matlab plyr R_utils RColorBrewer readr rvest S4Vectors scales selectr stringr SummarizedExperiment survival survminer sva tibble XML xml2]; }; - TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.7.3"; sha256="0h4cax1nl2f1ly5q7019jsadfmpva5ykg3qhz9zak8vph8jbwxyv"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel IlluminaHumanMethylation27kanno_ilmn12_hg19 IlluminaHumanMethylation27kmanifest IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest maftools minfi pathview plotly readr shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; }; - TCGAutils = derive2 { name="TCGAutils"; version="1.1.24"; sha256="1564ssv2f3xkc0lg4k8a4jlccbad9y8zbqx2iyy9ib31rjcysswj"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; }; - TCseq = derive2 { name="TCseq"; version="1.5.0"; sha256="1xir0481s72jwp0jnrb9134pv9vwy3g8mhk0rpzwr4qvxxxy7zxn"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; }; - TDARACNE = derive2 { name="TDARACNE"; version="1.31.0"; sha256="19qk0kc7yi4z8kqg7a9msxdiazad3y7xvshmf6pk0999ypacqws4"; depends=[Biobase GenKern Rgraphviz]; }; - TEQC = derive2 { name="TEQC"; version="4.3.0"; sha256="1ldjq8ap4si95zqywhp27rzd8kgij2p9hvcb0w8qvzw2ndk950z4"; depends=[Biobase BiocGenerics hwriter IRanges Rsamtools]; }; - TFARM = derive2 { name="TFARM"; version="1.3.0"; sha256="1c4gks6kvp8x68vnq7npxbq0q94gavbxvx3155prvx5qhsxw4jb8"; depends=[arules fields GenomicRanges stringr]; }; - TFBSTools = derive2 { name="TFBSTools"; version="1.19.3"; sha256="1zv3wid1jbjd8gn789an6khhsjw6kj10xzs1l2k3vji2ma4by4xd"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome caTools CNEr DBI DirichletMultinomial GenomeInfoDb GenomicRanges gtools IRanges RSQLite rtracklayer S4Vectors seqLogo TFMPvalue XML XVector]; }; - TFEA_ChIP = derive2 { name="TFEA.ChIP"; version="1.1.1"; sha256="0n71va6mqdcgqagjr2ga5g7zrbp1a3xnl4hh3yjzsaa1g5fyx1yz"; depends=[biomaRt dplyr GenomicFeatures GenomicRanges IRanges org_Hs_eg_db R_utils TxDb_Hsapiens_UCSC_hg19_knownGene]; }; - TFHAZ = derive2 { name="TFHAZ"; version="1.3.0"; sha256="1j03dp2n459b373ig3yds88f1x5yawr9jqr91w2s8smx5vqqicm8"; depends=[GenomicRanges IRanges S4Vectors]; }; - TFutils = derive2 { name="TFutils"; version="1.1.9"; sha256="097fn90mzyafhw27hc3m0dwyls7fc5d5c4rsrp0ris90c5m9lwbb"; depends=[dplyr magrittr miniUI shiny]; }; - TIN = derive2 { name="TIN"; version="1.13.0"; sha256="0iphf37gff3m1hyvijbbpp46bmjvwdppqrrwgf1yj660r01cyvyl"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; }; - TMixClust = derive2 { name="TMixClust"; version="1.3.0"; sha256="1ga7mxlaxv4hglixlqa3kjrvqikzc46mrs1435aihhf649h8zz6j"; depends=[Biobase BiocParallel cluster flexclust gss mvtnorm SPEM zoo]; }; - TPP = derive2 { name="TPP"; version="3.9.6"; sha256="152hnfxadkcr0dirwxjx428r94pxsmb2j8fpw89mnblr0l28y36g"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown sme stringr tidyr VennDiagram VGAM]; }; - TRONCO = derive2 { name="TRONCO"; version="2.13.3"; sha256="0s57yxz8kdjg2rs3njlay7fan4v241nq6aqv9g08wkhnd60220av"; depends=[bnlearn cgdsr circlize doParallel foreach gridExtra gtable gtools igraph iterators R_matlab RColorBrewer Rgraphviz scales xtable]; }; - TSCAN = derive2 { name="TSCAN"; version="1.19.0"; sha256="05zkydpl57j6b02bq0v3896612lbq33jbm896kimygbk4k2wa3g5"; depends=[combinat fastICA ggplot2 gplots igraph mclust mgcv plyr shiny]; }; - TSRchitect = derive2 { name="TSRchitect"; version="1.7.2"; sha256="0fprnylwnwrbya0zpya578ljxwj2xbrnbwwc9qb31nanhwr7p68a"; depends=[AnnotationHub BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; - TSSi = derive2 { name="TSSi"; version="1.27.0"; sha256="1a4xvqmbx2wlhad1pb6013sas5gqm27kc7jhyqp49ccbwm7ayz4r"; depends=[Biobase BiocGenerics Hmisc IRanges minqa plyr S4Vectors]; }; - TTMap = derive2 { name="TTMap"; version="1.3.0"; sha256="0fg0d930icbm62rvfv0d177ld126f1shm5knird50da4vx3qr1a9"; depends=[Biobase colorRamps rgl SummarizedExperiment]; }; - TVTB = derive2 { name="TVTB"; version="1.7.0"; sha256="1514rfqdrp3s1z4zf53zprslqdbsdl1w3crfbqgsv6hisqrrwlm2"; depends=[AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz IRanges limma reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation]; }; - TarSeqQC = derive2 { name="TarSeqQC"; version="1.11.2"; sha256="0h8vpdy4ja0i8jpdk87qk2dkfrz4izg2m7lgqx18fl490plii1bk"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; }; - TargetScore = derive2 { name="TargetScore"; version="1.19.0"; sha256="1phdg2ncvsjgjsfggxv37n74fwj8asw73vccb8iaqj8x7vlkci85"; depends=[Matrix pracma]; }; - TargetSearch = derive2 { name="TargetSearch"; version="1.37.8"; sha256="1cgk9sg5d0m0njs75lj5c9kz5agyy89xn4vfznh2j06w6l60dvil"; depends=[ncdf4]; }; - TissueEnrich = derive2 { name="TissueEnrich"; version="1.1.9"; sha256="11254f58mqhwa54kz83iac5sblcbpz6myw8gkwg06gx393yald22"; depends=[dplyr ensurer ggplot2 GSEABase SummarizedExperiment tidyr]; }; - TitanCNA = derive2 { name="TitanCNA"; version="1.19.1"; sha256="0j84k2bysiizbzr5mfsnv7xmcmi74m7x8a14i375mahp6x9krp4v"; depends=[data_table dplyr foreach GenomeInfoDb GenomicRanges IRanges Rsamtools VariantAnnotation]; }; - TnT = derive2 { name="TnT"; version="1.3.6"; sha256="0j64j32v1d83qqil3bfb6zxlp4k92qr6khzak5lkk7vdkhpbpckk"; depends=[Biobase data_table GenomeInfoDb GenomicRanges htmlwidgets IRanges jsonlite knitr S4Vectors]; }; - ToPASeq = derive2 { name="ToPASeq"; version="1.15.1"; sha256="13wzyspyipi122g976hp2haqyjhhgnwpaj844w2by8x65nh1hicl"; depends=[graph graphite Rcpp]; }; - TransView = derive2 { name="TransView"; version="1.25.2"; sha256="0b1bx8smkfp5a282rrmlmqgfgfkiqsvzn6jnkvgn4v3pq7w3752c"; depends=[BiocGenerics GenomicRanges gplots IRanges Rsamtools S4Vectors zlibbioc]; }; - Trendy = derive2 { name="Trendy"; version="1.3.11"; sha256="01k4ryaymr3c6m3gfdqv1wq8g47x5sr4vcnp6x92gcnncmm8m1qh"; depends=[BiocParallel DT gplots magrittr S4Vectors segmented shiny shinyFiles SummarizedExperiment]; }; - TurboNorm = derive2 { name="TurboNorm"; version="1.29.0"; sha256="15k6cxxwjkb56r9b1r17va2ssq4da7z72dvvgj91bd3x6vqph13q"; depends=[affy convert lattice limma marray]; }; - TxRegInfra = derive2 { name="TxRegInfra"; version="1.1.4"; sha256="1fv107daivcila7j3wkgc413138jza7s8x5g9ksgyr8kxjfs9w7b"; depends=[BiocParallel GenomeInfoDb GenomicRanges IRanges mongolite RaggedExperiment rjson S4Vectors SummarizedExperiment]; }; - TypeInfo = derive2 { name="TypeInfo"; version="1.47.0"; sha256="1nh15bs814s09cck4829r48n18g0w4haglbn826razjrcj5k46y0"; depends=[]; }; - UNDO = derive2 { name="UNDO"; version="1.23.0"; sha256="0csl0kh2ksswmv53cmy10b35ns5l9yg917m99f9pjrnql1n3ciq6"; depends=[Biobase BiocGenerics boot MASS nnls]; }; - Ularcirc = derive2 { name="Ularcirc"; version="0.99.24"; sha256="0dq4lwx2q6lga1cd9smqrmngvsd26xj83amfhg8192jg6jys9i70"; depends=[AnnotationHub Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicFeatures gsubfn httpuv mirbase_db moments shiny shinyFiles Sushi yaml]; }; - UniProt_ws = derive2 { name="UniProt.ws"; version="2.21.4"; sha256="1dsz47zs47mqrijiybs4p1syrf975ff2g1waxpcixbi3jr20gq80"; depends=[AnnotationDbi BiocFileCache BiocGenerics rappdirs RCurl RSQLite]; }; - Uniquorn = derive2 { name="Uniquorn"; version="2.1.4"; sha256="13xgw133kbrmm1idb21hdgm2mn619gvwq1k5bk6nw9m3qcwnp69l"; depends=[data_table doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; }; - VanillaICE = derive2 { name="VanillaICE"; version="1.43.4"; sha256="0wdmcmynsrk6ir4sxmgdpvsfdqnb1cgjc3n7vvsa8rsa6b22a15d"; depends=[Biobase BiocGenerics BSgenome_Hsapiens_UCSC_hg18 crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment]; }; - VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.27.9"; sha256="0vh50jil9ksjs6d9d9f457v31s8l4rn8cdm0wamj71gcdmp9x2f7"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; }; - VariantFiltering = derive2 { name="VariantFiltering"; version="1.17.3"; sha256="16jgpja0mxlb2sny6ccnc4aqvgxkl1kna3j8dnn5gyxbd11vzxri"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores graph Gviz IRanges RBGL Rsamtools S4Vectors shiny shinyjs shinythemes shinyTree SummarizedExperiment VariantAnnotation XVector]; }; - VariantTools = derive2 { name="VariantTools"; version="1.23.0"; sha256="1kr4w5c1rwsamb168ahj74f379rk87qldm2mivhn73zq75qrawaf"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; - Vega = derive2 { name="Vega"; version="1.29.1"; sha256="04yvxrv7m78dxg2k7pjcz6hz4clywb2lrldqs6pixyli2ifal8fq"; depends=[]; }; - VegaMC = derive2 { name="VegaMC"; version="3.19.1"; sha256="1dah8j41qd9ym00nlv8k0kpz3vsl7y3f6h4nyzv8bwa3nf9ip9qy"; depends=[Biobase biomaRt genoset]; }; - Wrench = derive2 { name="Wrench"; version="0.99.10"; sha256="1wm4zrh8wiyvjw246a4xwc3y278qyyvgx02n7kgnwznzg6wvh05s"; depends=[limma locfit matrixStats]; }; - XBSeq = derive2 { name="XBSeq"; version="1.13.1"; sha256="1dkwk181glpqq3g6ks5mpx39p106a8vkhky40hh7zny1pdycbzzh"; depends=[Biobase DESeq2 dplyr ggplot2 locfit magrittr matrixStats pracma roar]; }; - XDE = derive2 { name="XDE"; version="2.27.1"; sha256="1kj5wdn3w49zzi43hp8qs17v173nlgf215hm5pjy6l6pgvjjffjm"; depends=[Biobase BiocGenerics genefilter GeneMeta gtools MergeMaid mvtnorm RColorBrewer siggenes]; }; - XINA = derive2 { name="XINA"; version="0.99.13"; sha256="1vyawdy8z1lisnpfdy6rxmkbjxzs9dzb5f8i6wqiyx726z68fcpc"; depends=[alluvial Biobase ggplot2 gridExtra igraph mclust plyr STRINGdb]; }; - XVector = derive2 { name="XVector"; version="0.21.4"; sha256="1zb01pi6dm424ky95sli7h0a2qy2px6as0bz9ic48b3nwd7az2mn"; depends=[BiocGenerics IRanges S4Vectors zlibbioc]; }; - YAPSA = derive2 { name="YAPSA"; version="1.7.0"; sha256="1ny51v4papa067aylq7njyi2f17yp44y955szpark0lj0p759vjb"; depends=[circlize ComplexHeatmap corrplot dendextend GenomeInfoDb GenomicRanges GetoptLong ggplot2 gridExtra gtrellis KEGGREST lsei PMCMR reshape2 SomaticSignatures VariantAnnotation]; }; - a4 = derive2 { name="a4"; version="1.29.0"; sha256="0anj0gkbiccvb93xqzi7k1xxw2kqlwcf82pf4pqadc2fvmb1yfd7"; depends=[a4Base a4Classif a4Core a4Preproc a4Reporting]; }; - a4Base = derive2 { name="a4Base"; version="1.29.0"; sha256="03lnbfg94xwrib8g40y4bazp122zy9nnpv4v1m18wjc10hi7z7qp"; depends=[a4Core a4Preproc annaffy AnnotationDbi Biobase genefilter glmnet gplots limma mpm multtest]; }; - a4Classif = derive2 { name="a4Classif"; version="1.29.0"; sha256="1q5axh2494x2w40rqcj6kvrc3nbdyz117mxn39p1340ga7y2wxb7"; depends=[a4Core a4Preproc glmnet MLInterfaces pamr ROCR varSelRF]; }; - a4Core = derive2 { name="a4Core"; version="1.29.0"; sha256="1vv7x9iijn88vkj4yp66swkipsdm347m2hs59g76bdypsd926slv"; depends=[Biobase glmnet]; }; - a4Preproc = derive2 { name="a4Preproc"; version="1.29.0"; sha256="1yhdsx23rd1mihj18jwvb7rl6kgyvbh4a75lsv0faqvsh9bk2k77"; depends=[AnnotationDbi]; }; - a4Reporting = derive2 { name="a4Reporting"; version="1.29.0"; sha256="1m79clrlf0f5f108vyamy2ia8sbxi3mm2kf8ckhbbsr6qgmnqcsb"; depends=[annaffy xtable]; }; - aCGH = derive2 { name="aCGH"; version="1.59.0"; sha256="17nqy2sgkvjzhm3l8ypg93i7yzsniy536b2wz7rd6km52spldp7r"; depends=[Biobase cluster multtest survival]; }; - abseqR = derive2 { name="abseqR"; version="0.99.11"; sha256="1fzcchzxzpmiv2az8cg7nyx4pxkabfviyzm2nyx36kbyl4mfhwbb"; depends=[BiocParallel BiocStyle circlize flexdashboard ggcorrplot ggdendro ggplot2 gridExtra knitr plotly plyr png RColorBrewer reshape2 rmarkdown stringr vegan VennDiagram]; }; - acde = derive2 { name="acde"; version="1.11.0"; sha256="18551wkanalxk32g37j2yg766qgddsxid0lzv2rb61gqjb7qrmpa"; depends=[boot]; }; - adSplit = derive2 { name="adSplit"; version="1.51.0"; sha256="1azczbx6w17a1awwpfc1bbgx14562mr41mgii7skm9r8jb9pxn4n"; depends=[AnnotationDbi Biobase cluster GO_db KEGG_db multtest]; }; - adaptest = derive2 { name="adaptest"; version="1.1.1"; sha256="02dlhbnfl11x8hpampzz2d76i958k6lm4d3yc4kicpdsl5vmv6mk"; depends=[calibrate origami SummarizedExperiment tmle]; }; - affxparser = derive2 { name="affxparser"; version="1.53.2"; sha256="15i7rnwhc602y2c2i0h07z7fw29ynjq0jw1hqsjinw5df4afnxj7"; depends=[]; }; - affy = derive2 { name="affy"; version="1.59.1"; sha256="08fppshnnj1rxjd0kkmlrsz9nhqllzbzha5r1jbcly1f3dgy0799"; depends=[affyio Biobase BiocGenerics BiocManager preprocessCore zlibbioc]; }; - affyContam = derive2 { name="affyContam"; version="1.39.0"; sha256="1mh1yqrdh47ggqibgghnlmjfq46n0w4q1hdji7cv1js6kry7wqcf"; depends=[affy affydata Biobase]; }; - affyILM = derive2 { name="affyILM"; version="1.33.0"; sha256="0q41aznln8kngmv0q6036zvzbbk5sw46lhmss3npk7r6q0ryyvwr"; depends=[affxparser affy Biobase gcrma]; }; - affyPLM = derive2 { name="affyPLM"; version="1.57.0"; sha256="17vy0knf0vb3l824q2ib4hp0izw4s8phbjalsrzbwvmm7gg25xv7"; depends=[affy Biobase BiocGenerics gcrma preprocessCore zlibbioc]; }; - affyPara = derive2 { name="affyPara"; version="1.41.0"; sha256="1j81wl9ivx24jag4jnnv6viblpqba72c72nmcxs60cdqq44vs87h"; depends=[affy affyio aplpack snow vsn]; }; - affyQCReport = derive2 { name="affyQCReport"; version="1.59.0"; sha256="16sz9rii38vph2qiplab0f7fakd2vl77df543mfiykk3w5f0why2"; depends=[affy affyPLM Biobase genefilter lattice RColorBrewer simpleaffy xtable]; }; - affycomp = derive2 { name="affycomp"; version="1.57.0"; sha256="167bgzq82zsl2mdgzai95msh188j10hwrmp4bqab5qh9h2s8phvb"; depends=[Biobase]; }; - affycoretools = derive2 { name="affycoretools"; version="1.53.4"; sha256="13vacl5a4rnizn6pgchyd8xxpf3sd4cdwxfyvmslwaci4dh0mlk5"; depends=[affy AnnotationDbi Biobase BiocGenerics DBI edgeR gcrma ggplot2 GOstats gplots hwriter lattice limma oligoClasses ReportingTools RSQLite S4Vectors xtable]; }; - affyio = derive2 { name="affyio"; version="1.51.0"; sha256="1p10bycid4dlhxhllalffywrc06xj1qjzs9f9fvj1y1yzj3xgmqz"; depends=[zlibbioc]; }; - affylmGUI = derive2 { name="affylmGUI"; version="1.55.3"; sha256="0x6f92w8gqk2vs2p3walg2f0z0vx0gkiyz1jpnq01lz9zklwvhq9"; depends=[affy affyio affyPLM BiocGenerics BiocManager gcrma limma R2HTML tkrplot xtable]; }; - affypdnn = derive2 { name="affypdnn"; version="1.55.0"; sha256="11gwlr0ghw5c0977sgyhvghb953cgppp3vz3g1gfd3mdgkckvpqw"; depends=[affy]; }; - agilp = derive2 { name="agilp"; version="3.13.0"; sha256="1z7bxkdmqpz4kn1m2z91knnp36mp7z5awzj6qqwj7xwydc85m8np"; depends=[]; }; - alpine = derive2 { name="alpine"; version="1.7.0"; sha256="0d5r1izkx7lvl9f7sy0sy97mpvxaj05010vxmgw0c5yfpzzi3hz1"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors speedglm stringr SummarizedExperiment]; }; - alsace = derive2 { name="alsace"; version="1.17.0"; sha256="0p17f29n1z3n4x2rpv4hja10aq5349653ra4hwl5fbli3fa0ww43"; depends=[ALS ptw]; }; - altcdfenvs = derive2 { name="altcdfenvs"; version="2.43.0"; sha256="1md8rb732bpsxs1r1mgvd9f98ixg596rn28pw6pq8bl8hj5jh3l9"; depends=[affy Biobase BiocGenerics Biostrings hypergraph makecdfenv S4Vectors]; }; - ampliQueso = derive2 { name="ampliQueso"; version="1.19.4"; sha256="0nznv4cdjxr1lcr4cf2jpipcqn9s90kd97rqnv5kild2yv8srbhq"; depends=[DESeq doParallel edgeR foreach genefilter ggplot2 gplots knitr rgl rnaSeqMap samr statmod VariantAnnotation xtable]; }; - amplican = derive2 { name="amplican"; version="1.3.5"; sha256="0yf9wjgg22ry89cs9in66gwfana8c9cqaq7anfkpa3ng27llakd7"; depends=[BiocGenerics BiocParallel Biostrings clusterCrit data_table dplyr GenomeInfoDb GenomicRanges ggforce ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats rmarkdown S4Vectors ShortRead stringr waffle]; }; - anamiR = derive2 { name="anamiR"; version="1.9.2"; sha256="0l0lgan8zs04dyk972prvdng4xb8rig5g9rv55z1pplxvla4grqk"; depends=[agricolae DBI DESeq2 gage gplots limma lumi RMySQL S4Vectors SummarizedExperiment]; }; - annaffy = derive2 { name="annaffy"; version="1.53.0"; sha256="0z97liznk6by9a7klw0wirpchd9n57ycsf80xsprnlgy60slypvc"; depends=[AnnotationDbi Biobase DBI GO_db KEGG_db]; }; - annmap = derive2 { name="annmap"; version="1.23.0"; sha256="0m74p8zrqhyfgpbqf4s98174y7gz9p1nh9q272xbsqn8ckdk8c0a"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; }; - annotate = derive2 { name="annotate"; version="1.59.1"; sha256="016sgwqd0s3jhpqw4056y0xa7p1jc99i8b7biq754vzzbapjvyb0"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl XML xtable]; }; - annotationTools = derive2 { name="annotationTools"; version="1.55.0"; sha256="18rxyi7sx93l52agbxnla1b7gn2bk3fpby0qj224nqinydjxkmjj"; depends=[Biobase]; }; - annotatr = derive2 { name="annotatr"; version="1.7.2"; sha256="0q18fmb7wbbhqm3rwgf3d3cm9rpryrybv35jglsjsa3ca7y0550d"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges readr regioneR reshape2 rtracklayer S4Vectors]; }; - anota = derive2 { name="anota"; version="1.29.0"; sha256="1najgyj4qn9954jxbq0c4psarsq8mrg6fz0w3p9vmcm68l8lz3ig"; depends=[multtest qvalue]; }; - anota2seq = derive2 { name="anota2seq"; version="1.3.1"; sha256="1gp5f852kiz1ck19iasvkm1idgdcv636jdkmfp4j76r7k3vjzk36"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; }; - antiProfiles = derive2 { name="antiProfiles"; version="1.21.0"; sha256="166mx0y4b3j1vd3daxr9wd48d007qh1sj1vjssjfails6j4sy9lh"; depends=[locfit matrixStats]; }; - apComplex = derive2 { name="apComplex"; version="2.47.0"; sha256="0pqgrzfvljvinsalki5sc31c38k959g5gzag7sn33iilqw7s8grx"; depends=[graph org_Sc_sgd_db RBGL Rgraphviz]; }; - apeglm = derive2 { name="apeglm"; version="1.3.2"; sha256="1w7g7vfzqs109b2bihw7vgsyxrc65j31zlxf4v9bn5y144hzrn2j"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; }; - appreci8R = derive2 { name="appreci8R"; version="0.99.5"; sha256="0jr8qfrxdigddw1nwlzgqs7whzvs5h1c8xzmlzrbwrzn3ymgka54"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 COSMIC_67 DT GenomicFeatures GenomicRanges GenomicScores Homo_sapiens IRanges MafDb_1Kgenomes_phase3_hs37d5 MafDb_ESP6500SI_V2_SSA137_hs37d5 MafDb_ExAC_r1_0_hs37d5 MafDb_gnomADex_r2_0_1_hs37d5 openxlsx PolyPhen_Hsapiens_dbSNP131 rentrez Rsamtools rsnps S4Vectors seqinr shiny shinyjs SIFT_Hsapiens_dbSNP137 SNPlocs_Hsapiens_dbSNP144_GRCh37 stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation XtraSNPlocs_Hsapiens_dbSNP144_GRCh37]; }; - aroma_light = derive2 { name="aroma.light"; version="3.11.2"; sha256="0m03zkil79axvrmvaaimlv5pas6h19ylc4l5pm7f2xnc5150n8vp"; depends=[matrixStats R_methodsS3 R_oo R_utils]; }; - arrayMvout = derive2 { name="arrayMvout"; version="1.39.0"; sha256="1yrqx8vkbhwsdh0x3ig5wmy3ynx56154wgc69hzssvw38jdlp9vy"; depends=[affy affyContam Biobase lumi mdqc parody simpleaffy]; }; - arrayQuality = derive2 { name="arrayQuality"; version="1.59.0"; sha256="1nhavhn4vnxvmj2hw8qlrnbyp3nsv3m90qcj20ijiv85jkr10mpa"; depends=[gridBase hexbin limma marray RColorBrewer]; }; - arrayQualityMetrics = derive2 { name="arrayQualityMetrics"; version="3.37.1"; sha256="1pn3q37dmx2drqiq9k1y0s9n9hmh5njp70ljgkf4z83a3wwgz6fk"; depends=[affy affyPLM beadarray Biobase Cairo genefilter gridSVG Hmisc hwriter lattice latticeExtra limma RColorBrewer setRNG vsn XML]; }; - artMS = derive2 { name="artMS"; version="0.99.101"; sha256="0id199zy5cmbjap8zwp2if5hnr20cbsk9fsvfvkvg29pa01bi3x0"; depends=[AnnotationDbi biomaRt bit64 circlize cluster ComplexHeatmap corrplot data_table dplyr factoextra FactoMineR getopt ggdendro ggplot2 ggrepel gplots gProfileR limma MSstats openxlsx org_Hs_eg_db org_Mm_eg_db PerformanceAnalytics pheatmap plotly plyr RColorBrewer reshape2 seqinr stringr tidyr UpSetR VennDiagram yaml]; }; - attract = derive2 { name="attract"; version="1.33.2"; sha256="15mrqxcqflm3f77s336dyh8q57ipr27ca81aap6pwfxgpqykay49"; depends=[AnnotationDbi Biobase cluster GOstats KEGGREST limma org_Hs_eg_db reactome_db]; }; - bacon = derive2 { name="bacon"; version="1.9.0"; sha256="018082c3g5cdi3i1z1q26cq4v1f529d1c2q92p6qyzblcs8m2j2m"; depends=[BiocParallel ellipse ggplot2]; }; - ballgown = derive2 { name="ballgown"; version="2.13.1"; sha256="16464any97gpy6jmg61w58cryfd4z0c7qrq29vb28pbfxiwv4mmz"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; }; - bamsignals = derive2 { name="bamsignals"; version="1.13.2"; sha256="1w8jqk8iz63cfhnbnf2r4k15052kp2cyq6da9zl4my9kc237nr14"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; }; - banocc = derive2 { name="banocc"; version="1.5.2"; sha256="1sdj9gd43a7pz8sbzm0l9d7ifsmdpgksq6f52zs06blsy31aca99"; depends=[coda mvtnorm rstan stringr]; }; - basecallQC = derive2 { name="basecallQC"; version="1.5.0"; sha256="1g6hisqbg41kwz16iw7ai2rbw6hvndv560m7jxa85cm3kl9s5dxh"; depends=[data_table dplyr DT ggplot2 knitr lazyeval magrittr prettydoc raster rmarkdown ShortRead stringr tidyr XML yaml]; }; - bayNorm = derive2 { name="bayNorm"; version="0.99.19"; sha256="1vk4rlc9vchlvidhykqb75ljxhy0v9pbm2jdd5md4dswwq74psad"; depends=[BB BiocParallel doSNOW fitdistrplus foreach iterators locfit MASS Rcpp RcppArmadillo RcppProgress SingleCellExperiment SummarizedExperiment]; }; - baySeq = derive2 { name="baySeq"; version="2.15.2"; sha256="01iv53gsrqm0ia44dzirdfpfqdrav46xxwml7xmb6cfgafx118qd"; depends=[abind edgeR GenomicRanges]; }; - bcSeq = derive2 { name="bcSeq"; version="1.3.3"; sha256="14lmv9zlrh1xqdm0d0xyfi2rbjk8h3hkiaq74mbrygcgy8i9n77b"; depends=[Biostrings Matrix Rcpp]; }; - beachmat = derive2 { name="beachmat"; version="1.3.11"; sha256="06nb379rwpfb216qizxmmviljnm92vw52q9qlba8hsgrn189fbzl"; depends=[BiocGenerics DelayedArray HDF5Array Rcpp rhdf5 Rhdf5lib]; }; - beadarray = derive2 { name="beadarray"; version="2.31.1"; sha256="1vnhdw4gcv35xbj6s2rhwf4w90ghpmyjqcp5r4hnh3f829921xvf"; depends=[AnnotationDbi BeadDataPackR Biobase BiocGenerics GenomicRanges ggplot2 illuminaio IRanges limma reshape2]; }; - beadarraySNP = derive2 { name="beadarraySNP"; version="1.47.0"; sha256="1x4byqw6d2xy4db6pgbadsdwakw39lvw58dckijk2fwgrimzipn0"; depends=[Biobase quantsmooth]; }; - bgafun = derive2 { name="bgafun"; version="1.43.0"; sha256="02pv0b72m7xy2hqjdhz881qkp83api8lwbjngq7v29xhp7mpmgq3"; depends=[ade4 made4 seqinr]; }; - bgx = derive2 { name="bgx"; version="1.47.0"; sha256="1vh2hhjsfyx8laq1xym7zaxsakgwcp0ybha6xxdc18mwlwr3q412"; depends=[affy Biobase gcrma]; }; - bigmelon = derive2 { name="bigmelon"; version="1.7.4"; sha256="10sypnsvj561v9fdii047xvy2hamljss3rdw89b5l478flh5h3bx"; depends=[Biobase BiocGenerics gdsfmt GEOquery methylumi minfi wateRmelon]; }; - bigmemoryExtras = derive2 { name="bigmemoryExtras"; version="1.29.0"; sha256="0cxbd4zdvrpqycnvgw7svvngknscc4s9ycqp3csa8v1gpc9bj9cd"; depends=[bigmemory]; }; - bioCancer = derive2 { name="bioCancer"; version="1.9.8"; sha256="0dzsa1v2w8x73vz41h1h7gfv6yk1csffmn453cpzvvy2sy6v7pls"; depends=[AlgDesign AnnotationFuncs Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier htmlwidgets org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; }; - bioDist = derive2 { name="bioDist"; version="1.53.0"; sha256="04pazvkmw36ghicyzbqvb7rq3kvpw7qrj01k7gddrg4c1dc2rdd2"; depends=[Biobase KernSmooth]; }; - bioassayR = derive2 { name="bioassayR"; version="1.19.3"; sha256="1p7akwrsa22qrngsyksin8xxldfmlfp63yypgsqackj1qni1p4gs"; depends=[BiocGenerics ChemmineR DBI Matrix rjson RSQLite XML]; }; - biobroom = derive2 { name="biobroom"; version="1.13.2"; sha256="02mgb1rqdn616xgs1gjfmn84z6565v41m9zg16m6waba8p348chn"; depends=[Biobase broom dplyr tidyr]; }; - biocGraph = derive2 { name="biocGraph"; version="1.43.0"; sha256="1ps4r6rkffmqisfz5wip981r3dbx57n3r1j6whw9l6dbs043fjql"; depends=[BiocGenerics geneplotter graph Rgraphviz]; }; - biocViews = derive2 { name="biocViews"; version="1.49.10"; sha256="1dzd4ag0m2cprih66787aqgmm6fn68w6r7l5x6palsgix382m4m2"; depends=[Biobase graph RBGL RCurl RUnit XML]; }; - biomaRt = derive2 { name="biomaRt"; version="2.37.9"; sha256="196glcsp4cp0wfw2hrlvpxrx9r7ncfd775gfpmy298xldsxqf319"; depends=[AnnotationDbi httr progress RCurl stringr XML]; }; - biomformat = derive2 { name="biomformat"; version="1.9.1"; sha256="1kjk6agznq63a48jhj2yxkxr1nmwjlhb4zwmh1i1aawhzk1d04z1"; depends=[jsonlite Matrix plyr rhdf5]; }; - biomvRCNS = derive2 { name="biomvRCNS"; version="1.21.0"; sha256="193cfwknlm28pm5n7ydmrnaczw7xisiz07l29jyk0h05jrmrvna0"; depends=[GenomicRanges Gviz IRanges mvtnorm]; }; - biosigner = derive2 { name="biosigner"; version="1.9.0"; sha256="0v33vksq23byv5ybkb0mmvcb5fag3ghy9gcvb9aj16i7r0bs61ql"; depends=[Biobase e1071 randomForest ropls]; }; - biosvd = derive2 { name="biosvd"; version="2.17.0"; sha256="19l7mc1pbsbbzsb635iiqb778xq1lrlnmsnyd324471c3rnb1yn7"; depends=[Biobase BiocGenerics NMF]; }; - biotmle = derive2 { name="biotmle"; version="1.5.1"; sha256="0ihc1g60j1lkz3na23vvpd9c8xcz0p8wm5ksa6169zxjgqb90mmv"; depends=[BiocGenerics BiocParallel doFuture dplyr future ggplot2 ggsci limma S4Vectors SummarizedExperiment superheat tmle]; }; - biovizBase = derive2 { name="biovizBase"; version="1.29.2"; sha256="0xhwnjjwv41wsn3knl3pyswdwnrmsj49nwrxpmdlmivgqz6f0kz7"; depends=[AnnotationDbi AnnotationFilter BiocGenerics Biostrings dichromat ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Hmisc IRanges RColorBrewer rlang Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; - birta = derive2 { name="birta"; version="1.25.0"; sha256="0c8rvf63cq6rzax2vhgk4y2xjgylnygihgv8yw7iznhpvqxxqm5g"; depends=[Biobase limma MASS]; }; - birte = derive2 { name="birte"; version="1.17.0"; sha256="14xgvv12457yai92vvbpnc2fn4bnc129nrpwxl4kck09mh7kzfii"; depends=[Biobase glmnet limma MASS nem Rcpp RcppArmadillo]; }; - blima = derive2 { name="blima"; version="1.15.1"; sha256="06j3ibg62kxv0qvn1rmals6y6g1h8a3y1icvypjanl2r96l3h8hv"; depends=[beadarray Biobase BiocGenerics Rcpp]; }; - bnbc = derive2 { name="bnbc"; version="1.3.0"; sha256="07jzc55x31zn5ak5rlpc0xpqgnkl03vhpdrd8ay12n450zggd77q"; depends=[BiocGenerics EBImage GenomeInfoDb GenomicRanges IRanges matrixStats preprocessCore Rcpp S4Vectors SummarizedExperiment sva]; }; - brainImageR = derive2 { name="brainImageR"; version="0.99.13"; sha256="0yfp5z27iawr9m1avmlk6fwyxfzh030j6a6amz50zssmxx3girld"; depends=[BiocGenerics ExperimentHub ggplot2 gridExtra randomForest RColorBrewer testthat]; }; - branchpointer = derive2 { name="branchpointer"; version="1.7.0"; sha256="0ii7y3as43g7yp2qbzxv0bz66ayng8pxgk95303fp2l2akjb7gnx"; depends=[biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg38 caret cowplot data_table gbm GenomeInfoDb GenomicRanges ggplot2 IRanges kernlab plyr rtracklayer S4Vectors stringr]; }; - breakpointR = derive2 { name="breakpointR"; version="0.99.11"; sha256="1d6s3zvr0sjif63czd8z0d67ysdvjyfcqfcvcjzwcv158h59h7vj"; depends=[BiocGenerics breakpointRdata cowplot doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges Rsamtools S4Vectors]; }; - bridge = derive2 { name="bridge"; version="1.45.0"; sha256="11rqvigax6j1bqj1nyf4x6ssmqi0892m1rhak1wz3xcj4adb8vwz"; depends=[rama]; }; - bsseq = derive2 { name="bsseq"; version="1.17.7"; sha256="1ch766hhahn70nsi2a0r6438q5b3b3z1a7l65ldbhr8c3w4x1wp3"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp Rhdf5lib S4Vectors scales SummarizedExperiment]; }; - bumphunter = derive2 { name="bumphunter"; version="1.23.0"; sha256="1dn6z7q8k54vd59dqirvdy6048ywa3c4njc2vrja8f5i2lsvfwc8"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; }; - cTRAP = derive2 { name="cTRAP"; version="0.99.12"; sha256="0wg8phma29ijgfwp992l3dcqb64q7fzvamsiphrr3swn5dzs8kbv"; depends=[biomaRt cowplot data_table fgsea ggplot2 httr limma pbapply piano plyr R_utils readr rhdf5]; }; - caOmicsV = derive2 { name="caOmicsV"; version="1.11.0"; sha256="0lxlk5wlfna009k2jk8kgj61ks3hfcx1lvpymidb2yjx0kk2n7sg"; depends=[bc3net igraph]; }; - canceR = derive2 { name="canceR"; version="1.15.3"; sha256="03ib2ydmb26zc91hwy5w2sysvqay1087yjs03ki83spr4hh4hqmx"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; }; - cancerclass = derive2 { name="cancerclass"; version="1.25.0"; sha256="059nw8y6319m8k3i4l4crbydia2xz8v3dzc1dgj0hz6v3gfkxh8v"; depends=[binom Biobase]; }; - casper = derive2 { name="casper"; version="2.15.0"; sha256="129grx8bb2scjsvcqgyxigsw1n36miqbpf8val5yzm0lv9zwv24s"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; }; - categoryCompare = derive2 { name="categoryCompare"; version="1.25.1"; sha256="1qxfkqzyq6q4imhi517bbxn785i0qzwcy4ac68k1iw0c8frcn1hg"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; }; - cbaf = derive2 { name="cbaf"; version="1.3.5"; sha256="08gr3axl77gyall3hd97gf5npqz588p24aafqf4p31djqxmv64wn"; depends=[BiocFileCache cgdsr genefilter gplots RColorBrewer xlsx]; }; - ccfindR = derive2 { name="ccfindR"; version="1.1.23"; sha256="14gl5jmjp23q0kh9wrv5ds5l0qly9x07h4ny1ivm3sqqlbs8ya9h"; depends=[ape gtools irlba Matrix RColorBrewer Rcpp RcppEigen Rmpi Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; }; - ccmap = derive2 { name="ccmap"; version="1.7.2"; sha256="1f0b24c0is8nxkfxxjnbdbmqv4p9ifcsdw49skkwnsc5n9k6w54c"; depends=[AnnotationDbi BiocManager ccdata data_table doParallel foreach lsa xgboost]; }; - ccrepe = derive2 { name="ccrepe"; version="1.17.0"; sha256="1k464wrgigq0yyr2w7pw8qwkql49jnl58ayr26785ajdn79lfcq4"; depends=[infotheo]; }; - celaref = derive2 { name="celaref"; version="0.99.3"; sha256="1nmdqadrj5hgqijjywk8754ajj4i59bmrpah9xdginpiakdbskra"; depends=[BiocGenerics dplyr ggplot2 magrittr MAST Matrix readr rlang S4Vectors SummarizedExperiment tibble]; }; - cellGrowth = derive2 { name="cellGrowth"; version="1.25.0"; sha256="12flwz3pzjhwqxsljy5g2ylgxiygln24z5zydc62xrkjcg3wqgn0"; depends=[lattice locfit]; }; - cellHTS2 = derive2 { name="cellHTS2"; version="2.45.1"; sha256="0ccl152v44380666xhqj5s1vwd9xqih3a7ysdjb5n8mwpq1kq0av"; depends=[Biobase BiocGenerics Category genefilter GSEABase hwriter locfit prada RColorBrewer splots vsn]; }; - cellTree = derive2 { name="cellTree"; version="1.11.1"; sha256="026f59jj07j5jbv0j3048c44sz2zr50lzwy07m0i6yvl0w1pc57h"; depends=[gplots igraph maptpx slam topGO topicmodels xtable]; }; - cellbaseR = derive2 { name="cellbaseR"; version="1.5.0"; sha256="0067s59gq395ha4kjmdvqx3bdjgkgczwvchwjswr23hm6ffbgss3"; depends=[BiocParallel data_table doParallel foreach httr jsonlite pbapply R_utils Rsamtools tidyr]; }; - cellity = derive2 { name="cellity"; version="1.9.2"; sha256="0hc8whsqq066drwbk3aiz8pdy7zd3qx7fmsa5knw0xk1dpbpglcg"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; }; - cellscape = derive2 { name="cellscape"; version="1.5.1"; sha256="1fi9qxnhrh9n9br1gjpss8acpfd2fm22nd9ih2flng0hgy4aymyc"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; }; - cghMCR = derive2 { name="cghMCR"; version="1.39.0"; sha256="119nk170b8a8lr1hi2nmj2bgaydkxf11732bqxhpm13hn9cyvnpr"; depends=[BiocGenerics CNTools DNAcopy limma]; }; - charm = derive2 { name="charm"; version="2.27.0"; sha256="0cgrh027qjy34nb0xd0fl7fxifpgb1i9qcy3g7w7vv0sgj5g2gxc"; depends=[Biobase Biostrings BSgenome ff fields genefilter gtools IRanges limma nor1mix oligo oligoClasses preprocessCore RColorBrewer siggenes SQN sva]; }; - chimera = derive2 { name="chimera"; version="1.23.0"; sha256="16l1y016wdmdqm4psnl3rxs4gw1d8b0hvfr29x9sv7153fpvqxhf"; depends=[AnnotationDbi Biobase BSgenome_Hsapiens_UCSC_hg19 GenomicAlignments GenomicRanges Homo_sapiens Rsamtools TxDb_Hsapiens_UCSC_hg19_knownGene]; }; - chimeraviz = derive2 { name="chimeraviz"; version="1.7.5"; sha256="0k0yn24v3lgkzwbx1597n5k81igjmvmz232mwfsazd3znwdbwm7b"; depends=[AnnotationDbi AnnotationFilter ArgumentCheck BiocStyle Biostrings data_table dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph Gviz IRanges org_Hs_eg_db org_Mm_eg_db plyr RCircos RColorBrewer Rgraphviz rmarkdown Rsamtools S4Vectors]; }; - chipenrich = derive2 { name="chipenrich"; version="2.5.0"; sha256="1ssvmnnlf6s37hbj0cdpcjyfz3qj7mv1nfxbdsb3cbq541lxidlv"; depends=[AnnotationDbi BiocGenerics chipenrich_data GenomeInfoDb GenomicRanges IRanges lattice latticeExtra mgcv org_Dm_eg_db org_Dr_eg_db org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db plyr rms rtracklayer S4Vectors stringr]; }; - chipseq = derive2 { name="chipseq"; version="1.31.0"; sha256="0pfi2jyi3cb73c6k0300k1yvk2nvzh6lc19qmgs9qxqm0zjh5vly"; depends=[BiocGenerics GenomicRanges IRanges lattice S4Vectors ShortRead]; }; - chopsticks = derive2 { name="chopsticks"; version="1.47.0"; sha256="0lvd5fpvlkwzplm6wpxrmi6gl35vg9li8zs8kiyf65yggp8azkd7"; depends=[survival]; }; - chroGPS = derive2 { name="chroGPS"; version="1.99.4"; sha256="10grx4zwj2w2wcf4bf09m97fi4nn31q99jrlnmpm5zfwfyh9y1nk"; depends=[Biobase changepoint cluster DPpackage ellipse GenomicRanges ICSNP IRanges MASS vegan]; }; - chromDraw = derive2 { name="chromDraw"; version="2.11.0"; sha256="17lb88jp4997nmdb7g3rmi509vn552rda603diq5qxjd8hxszhj7"; depends=[GenomicRanges Rcpp]; }; - chromPlot = derive2 { name="chromPlot"; version="1.9.0"; sha256="0g7vnv12m9db563p99kcdv9mjb5h2saxmvq810ckw3vd9hxla4sm"; depends=[biomaRt GenomicRanges]; }; - chromVAR = derive2 { name="chromVAR"; version="1.3.2"; sha256="0wg1ajyff9ly82q0468cy33iysj59dfidp2qqgkp85vik0aci1sx"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicRanges ggplot2 IRanges Matrix miniUI nabor plotly RColorBrewer Rcpp RcppArmadillo Rsamtools Rtsne S4Vectors shiny SummarizedExperiment TFBSTools]; }; - chromstaR = derive2 { name="chromstaR"; version="1.7.3"; sha256="0nbfzh7ks9816yllyd125nd4qm7fk5i4x36jd7wd81hp0cpb7ia5"; depends=[bamsignals chromstaRData doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges mvtnorm reshape2 Rsamtools S4Vectors]; }; - chromswitch = derive2 { name="chromswitch"; version="1.3.2"; sha256="1ls6007vz2b0ij543vgdpxv5dqbjaklv9ps81c3z6n91qf9ld2an"; depends=[Biobase BiocParallel cluster dplyr GenomicRanges gplots IRanges lazyeval magrittr matrixStats NMF rtracklayer S4Vectors tidyr]; }; - cicero = derive2 { name="cicero"; version="0.99.57"; sha256="1gj0ckn4b3ifkvvb8lbwl83fdnmcayk3wmd83piq95j8nkaba0c8"; depends=[assertthat Biobase BiocGenerics data_table dplyr FNN GenomicRanges ggplot2 glasso Gviz igraph IRanges Matrix monocle plyr reshape2 S4Vectors stringr tibble VGAM]; }; - cisPath = derive2 { name="cisPath"; version="1.21.1"; sha256="06s9ch9av414vqi8l6rsz8y49bklygv9m7wrvv8nmx14h6fvpbmq"; depends=[]; }; - cleanUpdTSeq = derive2 { name="cleanUpdTSeq"; version="1.19.1"; sha256="12izlkfqx1cshb48qzn987hhanqxjfhaiiwl6lrn0xpqbw384k3y"; depends=[BiocGenerics BSgenome BSgenome_Drerio_UCSC_danRer7 e1071 GenomicRanges seqinr]; }; - cleaver = derive2 { name="cleaver"; version="1.19.0"; sha256="19jrmz8bjj9yg52j002zyf6v1as2k7m0g0msvmgvlsf0nvgk5h72"; depends=[Biostrings IRanges S4Vectors]; }; - clippda = derive2 { name="clippda"; version="1.31.0"; sha256="18jsfx4y09mzsah8w2pqwarl7h1kn76cm6sjh6r3dqikbzq24rak"; depends=[Biobase lattice limma rgl scatterplot3d statmod]; }; - clipper = derive2 { name="clipper"; version="1.21.1"; sha256="19gkqz94sxamw8gx1rib17j7sxivzflrhypkp4bsyqshkydyzgcq"; depends=[Biobase corpcor graph gRbase igraph KEGGgraph Matrix qpgraph RBGL Rcpp]; }; - clonotypeR = derive2 { name="clonotypeR"; version="1.19.0"; sha256="03hyifp94i9fj391gz0p73g2jkgfc4cjscsgiszmm99j4mjp6641"; depends=[]; }; - clst = derive2 { name="clst"; version="1.29.0"; sha256="0bz0hd7zjr9a225hg1jl0r86zvdz4i9i63grg0nm0dvs32pbaf2g"; depends=[lattice ROC]; }; - clstutils = derive2 { name="clstutils"; version="1.29.0"; sha256="0fsqlx06qd7bqdnk746pcn1w29xbpcpjazsnvk1dibxyxqkbqvjh"; depends=[ape clst lattice rjson RSQLite]; }; - clustComp = derive2 { name="clustComp"; version="1.9.0"; sha256="1lmg17d3n97kp5z21wl2kyx140kmqlfwsm4q6qcq7j9zyfq2jrdc"; depends=[sm]; }; - clusterExperiment = derive2 { name="clusterExperiment"; version="2.1.6"; sha256="0wgi8qil7vyqlqsbqm0fbk9337wvcz53xid8qy4qc5l9pipf7s4r"; depends=[ape BiocGenerics cluster DelayedArray dendextend edgeR HDF5Array howmany kernlab limma locfdr matrixStats NMF phylobase RColorBrewer Rcpp RSpectra S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; }; - clusterProfiler = derive2 { name="clusterProfiler"; version="3.9.2"; sha256="1y9kss22c64yk3abbcz12ph2q38xp6x38cvffnr3wcm71pa26aj2"; depends=[AnnotationDbi DOSE enrichplot ggplot2 GO_db GOSemSim magrittr plyr qvalue rvcheck tidyr]; }; - clusterSeq = derive2 { name="clusterSeq"; version="1.5.1"; sha256="0y8a5ik310pvhbrpaf77dpdlhgsggv8b4ziw9270lw552wq6m2s2"; depends=[baySeq BiocGenerics BiocParallel]; }; - clusterStab = derive2 { name="clusterStab"; version="1.53.0"; sha256="1fz5l64c7sfzxvqrfxbwvla6k72dq32r9v9nsc4cycpmyyfvgqfg"; depends=[Biobase]; }; - cn_farms = derive2 { name="cn.farms"; version="1.29.1"; sha256="0dysp6kvdgxbzjhm9sd0h9l2ckl7kvlg910bxzz192p9nlwpgc25"; depends=[affxparser Biobase DBI DNAcopy ff lattice oligo oligoClasses preprocessCore snow]; }; - cn_mops = derive2 { name="cn.mops"; version="1.27.0"; sha256="1fzsp4amldbfg2msll3synvwlwdsda1fajwsl5qxg83pcy0v8rm2"; depends=[Biobase BiocGenerics exomeCopy GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; - cnvGSA = derive2 { name="cnvGSA"; version="1.25.0"; sha256="0ha9nh485r7x67q25cj6r7m8lckw9bm1kvd1rvkrwn6nnlld8bn1"; depends=[brglm doParallel foreach GenomicRanges splitstackshape]; }; - coGPS = derive2 { name="coGPS"; version="1.25.0"; sha256="081ljzlc0vq19h7w31ccqxbdhi2rivi8qrrvnxw6imj0pfckn1hn"; depends=[]; }; - coMET = derive2 { name="coMET"; version="1.13.4"; sha256="0fzgwy11jcscp207giwdwpkq5zad72sdhcd4d5qrprda8565kx33"; depends=[biomaRt colortools corrplot GenomicRanges gridExtra Gviz hash IRanges psych rtracklayer S4Vectors]; }; - coRdon = derive2 { name="coRdon"; version="0.99.11"; sha256="1fa2zzqrnj5ggk3czvdqkn1ixha1a991xjv27plw9hvy8snvyjzc"; depends=[Biobase Biostrings data_table dplyr ggplot2 purrr]; }; - cobindR = derive2 { name="cobindR"; version="1.19.1"; sha256="1n4yr8izd1fhn6qzcifamhvd1shah0hv06v1a097xjnghnr46r8q"; depends=[BiocGenerics biomaRt Biostrings BSgenome gmp gplots IRanges mclust rtfbs seqinr yaml]; }; - codelink = derive2 { name="codelink"; version="1.49.0"; sha256="0fqxdmzwx6vhclsamc4i0kshdnqpjpqgzrmjm2lwvjai2bnbiaz4"; depends=[annotate Biobase BiocGenerics limma]; }; - coexnet = derive2 { name="coexnet"; version="1.3.0"; sha256="0kqzvi5zs1nvcnbvgrq06fzzcfdsga5fz0r70drcsx449nkqrj5c"; depends=[acde affy Biobase GEOquery igraph limma minet rmarkdown siggenes STRINGdb SummarizedExperiment vsn]; }; - cogena = derive2 { name="cogena"; version="1.15.1"; sha256="0ch85p3abar0cahb3f8hrd28ylwbd1m7z7s28gh4wrrxx9cfqjmx"; depends=[amap apcluster Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots kohonen mclust reshape2]; }; - compEpiTools = derive2 { name="compEpiTools"; version="1.15.3"; sha256="06m6kd2c6cadnsl8lq3dna1kxyc7sgr14g9qbjr3qf40kc2njmka"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges GO_db gplots IRanges methylPipe Rsamtools S4Vectors topGO XVector]; }; - compcodeR = derive2 { name="compcodeR"; version="1.17.2"; sha256="0p8mv2pw8hrv23yswqavagii5ascppmgm89zq7589xnc20bl70yh"; depends=[caTools edgeR gdata ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS modeest ROCR sm stringr vioplot]; }; - condcomp = derive2 { name="condcomp"; version="0.99.2"; sha256="1wckrk43h6ab30caqvffrxlssib2iigagqlpbifwf6l2856c642i"; depends=[cluster ggplot2 ggrepel outliers]; }; - consensus = derive2 { name="consensus"; version="0.99.17"; sha256="0ipdx2qazvh2aliz1k48cq6k21vn40wql1h67qgcnb5s8s10k24a"; depends=[gplots matrixStats RColorBrewer]; }; - consensusDE = derive2 { name="consensusDE"; version="0.99.10"; sha256="1zx233m9d65xvsjwgm1m54sqqvp3fjjcxi0yj1j7by3a96yhy7my"; depends=[airway AnnotationDbi Biobase BiocParallel Biostrings dendextend DESeq2 EDASeq edgeR GenomicAlignments GenomicFeatures limma pcaMethods RColorBrewer Rsamtools RUVSeq S4Vectors SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm3_ensGene]; }; - consensusOV = derive2 { name="consensusOV"; version="1.3.0"; sha256="0jk776svh4krp1cj77sy9lrp3rx6ka8vbc4xz1armf9vd9sn0ln8"; depends=[Biobase gdata genefu GSVA limma matrixStats randomForest]; }; - consensusSeekeR = derive2 { name="consensusSeekeR"; version="1.9.0"; sha256="0hdfnvvd06s2pbrsbrcp6nky7clvj2xqdf3d6x728mxfv17yflrl"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges IRanges rtracklayer S4Vectors stringr]; }; - contiBAIT = derive2 { name="contiBAIT"; version="1.9.1"; sha256="0nli8r7wn20f92wax39gk8nawbiy8xjdxfv7r8267n9cmfdywxhm"; depends=[BH BiocParallel clue cluster colorspace data_table diagram DNAcopy exomeCopy GenomicAlignments GenomicFiles GenomicRanges ggplot2 gplots gtools IRanges Rcpp reshape2 Rsamtools rtracklayer S4Vectors TSP]; }; - conumee = derive2 { name="conumee"; version="1.15.0"; sha256="1xpq77j6zwqj3s8qxjvnzvrwk27g6cipqp8k8g1x61ayalw5mwn9"; depends=[DNAcopy GenomeInfoDb GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest IRanges minfi rtracklayer]; }; - convert = derive2 { name="convert"; version="1.57.0"; sha256="1bfwmxcvg3dxygzbl290l645ri610fxymvba349hj785w9v09hgi"; depends=[Biobase limma marray]; }; - copa = derive2 { name="copa"; version="1.49.0"; sha256="08myzip07f28iyyf1v28y60pwmyabv7yhbd1y9avmmfa8swh4zav"; depends=[Biobase]; }; - copynumber = derive2 { name="copynumber"; version="1.21.0"; sha256="1qcrq5ls1rj5had0v2abcya5bbm1mpni97lxvlm75yxpalkrbmg1"; depends=[BiocGenerics GenomicRanges IRanges S4Vectors]; }; - coseq = derive2 { name="coseq"; version="1.5.2"; sha256="1hx8brqi422k5q9isbdfrp1799c161yjkfad2hq9zw3rkjj3hbyf"; depends=[BiocParallel capushe compositions corrplot DESeq2 e1071 edgeR ggplot2 HTSCluster HTSFilter mvtnorm Rmixmod S4Vectors scales SummarizedExperiment]; }; - cosmiq = derive2 { name="cosmiq"; version="1.15.2"; sha256="1n91gp3v27924pavlm4kkidihzhdgj5p679x5krxkqf430f3kbk4"; depends=[faahKO MassSpecWavelet pracma Rcpp xcms]; }; - countsimQC = derive2 { name="countsimQC"; version="0.99.4"; sha256="0fnjl8pan117fcaxvpbcplrlqcd3sx2pq7ddcwy4qvhphbksk148"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; }; - covEB = derive2 { name="covEB"; version="1.7.0"; sha256="01qy9713bixj1nbdhafyappbm0m6q6k769akzysvcb4cs74isq3x"; depends=[Biobase gsl igraph LaplacesDemon Matrix mvtnorm]; }; - covRNA = derive2 { name="covRNA"; version="1.7.1"; sha256="09915p41xmb4gxl9nhpy8qrlpf4z1dlc9g3yi1j73a49kvgamlaa"; depends=[ade4 Biobase genefilter]; }; - cpvSNP = derive2 { name="cpvSNP"; version="1.13.0"; sha256="0wv304nisngcbc8as6anlb7i090wl078rs0pclix975akj9s4zpw"; depends=[BiocParallel corpcor GenomicFeatures ggplot2 GSEABase plyr]; }; - cqn = derive2 { name="cqn"; version="1.27.0"; sha256="1680ww5rr4y1jqhb267hbgk77ha87awbjrl3id5cz7d7ps75a7fb"; depends=[mclust nor1mix preprocessCore quantreg]; }; - crisprseekplus = derive2 { name="crisprseekplus"; version="1.7.3"; sha256="07fcgm24mfxxa7nv68kdd5pawkq46n2p9i3k2pmpfa07irywizf6"; depends=[AnnotationDbi BiocManager BSgenome CRISPRseek DT GenomicFeatures GenomicRanges GUIDEseq hash shiny shinyjs]; }; - crlmm = derive2 { name="crlmm"; version="1.39.1"; sha256="1mb7zpqb9qfpjg8samrdd5pxgj64ganm7mkh2y7aa3vlhj450rmx"; depends=[affyio beanplot Biobase BiocGenerics ellipse ff foreach illuminaio lattice limma matrixStats mvtnorm oligoClasses preprocessCore RcppEigen SNPchip VGAM]; }; - crossmeta = derive2 { name="crossmeta"; version="1.7.1"; sha256="0n5g234ghcan9jx1cavpzngypjjcrg7lz621czfg8d0rfj8wavs9"; depends=[affxparser affy AnnotationDbi Biobase BiocGenerics BiocManager ccmap data_table doParallel doRNG DT fdrtool foreach GEOquery ggplot2 limma matrixStats metaMA metap miniUI oligo pander plotly RColorBrewer rdrop2 reshape shiny stringr sva]; }; - csaw = derive2 { name="csaw"; version="1.15.9"; sha256="0p5clsxqfy8ihsh8lxvhl8ally5gi1k6v7cclvp8kvvwj5mvcg6p"; depends=[AnnotationDbi BiocGenerics BiocParallel edgeR GenomeInfoDb GenomicFeatures GenomicRanges IRanges limma Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment zlibbioc]; }; - ctc = derive2 { name="ctc"; version="1.55.0"; sha256="0zkzdv3yrrr671bvr0j7xi1c358r7k09f96x5sciljg95gwpq6fm"; depends=[amap]; }; - ctsGE = derive2 { name="ctsGE"; version="1.7.2"; sha256="1qykz2w7c0v7zs9ga0crvdydi57sqbfkg0i14rfr9mrh2cn874la"; depends=[ccaPP ggplot2 limma reshape2 shiny stringr]; }; - cummeRbund = derive2 { name="cummeRbund"; version="2.23.0"; sha256="12npw9nr02fs1lyj1fism4zbw1vbd47rxyyc21z8kx9ra5c76df9"; depends=[Biobase BiocGenerics fastcluster ggplot2 Gviz plyr reshape2 RSQLite rtracklayer S4Vectors]; }; - customProDB = derive2 { name="customProDB"; version="1.21.5"; sha256="01fkp1bhk21flb3ik38i533zxdzv2g1qfp9bp0b91r29z5rp8nz9"; depends=[AhoCorasickTrie AnnotationDbi biomaRt Biostrings DBI GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr RCurl Rsamtools RSQLite rtracklayer S4Vectors stringr VariantAnnotation]; }; - cycle = derive2 { name="cycle"; version="1.35.0"; sha256="0wij6y9alg55kric7bs8syrw8ypd5w0iayh057qcl9qqr5lp1vq7"; depends=[Biobase Mfuzz]; }; - cydar = derive2 { name="cydar"; version="1.5.9"; sha256="0c7k6c02yqs5nr8pirvcgdmjgqhg7ynml1sf4fsjj6m0jbqrp29p"; depends=[Biobase BiocGenerics BiocNeighbors BiocParallel flowCore Rcpp S4Vectors shiny SingleCellExperiment SummarizedExperiment viridis]; }; - cytofkit = derive2 { name="cytofkit"; version="1.13.0"; sha256="0dl0y609w2y3wpncw4mxhflrnq1ymdmzp8qwnrlc13ykkrcwh40w"; depends=[Biobase colourpicker destiny doParallel e1071 flowCore FlowSOM ggplot2 ggrepel gplots igraph pdist plyr RANN Rcpp reshape2 Rtsne shiny shinyFiles vegan VGAM]; }; - cytolib = derive2 { name="cytolib"; version="1.3.2"; sha256="10c9f7fqa5qbcxbs985ad3lljbmgfnwgcgfkp95yhahr97jb7w3s"; depends=[BH RProtoBufLib]; }; - dSimer = derive2 { name="dSimer"; version="1.7.0"; sha256="0ra9y6df21s97pa8810dzbcwjhbh9br86mlqkgvvrq5rxwj97a35"; depends=[AnnotationDbi ggplot2 GO_db igraph org_Hs_eg_db Rcpp reshape2]; }; - daMA = derive2 { name="daMA"; version="1.53.0"; sha256="1ahmx5c58az3s3jybz3gx7g853n0qy7b84rm7gq157yi4iil01wf"; depends=[MASS]; }; - dada2 = derive2 { name="dada2"; version="1.9.3"; sha256="1qqw51pvgvwznx3v81xbn9qakxd6s9yl8f2pxbzr0ampgm22s9yn"; depends=[BiocGenerics Biostrings data_table ggplot2 IRanges Rcpp RcppParallel reshape2 ShortRead XVector]; }; - dagLogo = derive2 { name="dagLogo"; version="1.19.1"; sha256="1y966jzzy7357gr2vdq0qgkwvbdq8pls51vfmmwka9c2zqnsdxdm"; depends=[biomaRt Biostrings grImport motifStack pheatmap]; }; - dcGSA = derive2 { name="dcGSA"; version="1.9.0"; sha256="0d85qpq1v9sky5x8nv5w0hfry9w833kkljq5laa2x3n10czp1hb3"; depends=[BiocParallel Matrix]; }; - ddCt = derive2 { name="ddCt"; version="1.37.1"; sha256="1bysg67mqyrx6fqxsfbxbn4fw3brpyw0nyrvxkgbh6kwwwaccwaw"; depends=[Biobase BiocGenerics lattice RColorBrewer xtable]; }; - ddPCRclust = derive2 { name="ddPCRclust"; version="1.1.2"; sha256="0d09vdwrv9kifgld4g3342xrcfi85y46nnl1pq4yv1n8dx14k3ms"; depends=[clue flowCore flowDensity flowPeaks ggplot2 openxlsx plotrix R_utils SamSPECTRAL]; }; - debrowser = derive2 { name="debrowser"; version="1.9.21"; sha256="0a4nzgw4066a9ryanvdjrbscbns6a74js3c0gadw7q19b824gv6i"; depends=[annotate AnnotationDbi baySeq clusterProfiler colourpicker d3heatmap DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 googleAuthR gplots Harman heatmaply igraph IRanges jsonlite limma org_Hs_eg_db org_Mm_eg_db pathview plotly RColorBrewer RCurl reshape2 S4Vectors shiny shinyBS shinydashboard shinyjs stringi SummarizedExperiment sva V8]; }; - decontam = derive2 { name="decontam"; version="1.1.2"; sha256="0p3kdcwl0gph9mdffd7jmycpcj1kbk8rgcwhp0idkm2xbfnra4n2"; depends=[ggplot2 reshape2]; }; - deepSNV = derive2 { name="deepSNV"; version="1.27.3"; sha256="02wn7y8dbikllpmgbq5fksxvbw6dnz3hkl1lvjd9ff6avsrpyzjs"; depends=[Biostrings GenomicRanges IRanges Rhtslib SummarizedExperiment VariantAnnotation VGAM]; }; - deltaGseg = derive2 { name="deltaGseg"; version="1.21.1"; sha256="1mrm1j816j8b9myzy8az16sg8v1g5ynxv1j2dpwbqg003pm9b2zn"; depends=[changepoint fBasics ggplot2 pvclust reshape scales tseries wavethresh]; }; - derfinder = derive2 { name="derfinder"; version="1.15.4"; sha256="1qyblw4iy33r37k9zfsbf6rbgx8fnz89wv99dy3xibiw07hahgf1"; depends=[AnnotationDbi BiocGenerics BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; }; - derfinderHelper = derive2 { name="derfinderHelper"; version="1.15.2"; sha256="1xgzx1q2fzglnrn3xyqmhbzf9rl56wbfdc4n0fy0lfrg13rb5kq1"; depends=[IRanges Matrix S4Vectors]; }; - derfinderPlot = derive2 { name="derfinderPlot"; version="1.15.2"; sha256="0vp6x6dd8ykvgaic82crykhddykiz9y3ji7nmg2j66cklsvp018s"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer RefManageR reshape2 S4Vectors scales]; }; - destiny = derive2 { name="destiny"; version="2.11.3"; sha256="0z9z0frhif84rshnpffizjjv2ckr1mp7vqlk9r3fyyxzz1pkrl29"; depends=[Biobase BiocGenerics ggplot2 ggthemes igraph Matrix proxy Rcpp RcppEigen scales scatterplot3d smoother SummarizedExperiment VIM]; }; - dexus = derive2 { name="dexus"; version="1.21.1"; sha256="00yld22dj4i9ci2jniqycxcli0xg0k06n02cg3i0lj03g4ml202h"; depends=[BiocGenerics]; }; - diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.63.0"; sha256="19g9azy3s359k84rg677l0yndq13h48fs0rmddrs4z8z8w4k2n9h"; depends=[minpack_lm]; }; - diffHic = derive2 { name="diffHic"; version="1.13.7"; sha256="07w2djzjsla6z7dy2g2dr0zfc7p1r88i6vgs4fmp0jr0ifsc3dal"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment zlibbioc]; }; - diffcoexp = derive2 { name="diffcoexp"; version="1.1.2"; sha256="1nrhdhzz5768ah9p3z5xszn48q6swawz3k9d72lxywm1yx0yqy5c"; depends=[BiocGenerics DiffCorr igraph psych SummarizedExperiment WGCNA]; }; - diffcyt = derive2 { name="diffcyt"; version="1.1.11"; sha256="1chm02ixzh7627xmdpb91zhymamxnc2j3n7di97yc1fgv83bm0bx"; depends=[circlize ComplexHeatmap dplyr edgeR flowCore FlowSOM limma lme4 magrittr multcomp reshape2 S4Vectors SummarizedExperiment tidyr]; }; - diffloop = derive2 { name="diffloop"; version="1.9.0"; sha256="0wfnh79xkfkkzm3rkx90i0ij81l33ssm03b91mfq02yzijqv5dzv"; depends=[Biobase biomaRt data_table dplyr edgeR foreach GenomeInfoDb GenomicRanges ggplot2 IRanges limma locfit matrixStats pbapply plyr readr reshape2 rtracklayer S4Vectors statmod Sushi]; }; - diffuStats = derive2 { name="diffuStats"; version="1.1.0"; sha256="02269q356hvddnsi87p141cdyl1bmprarm9hqvpyjj244a8nirrv"; depends=[expm igraph MASS Matrix plyr precrec Rcpp RcppArmadillo RcppParallel]; }; - diggit = derive2 { name="diggit"; version="1.13.1"; sha256="1sryn5n6vrc9cf7gsz9xgg6hp9gn18m7h9zz286l1p5cvmk4y1i9"; depends=[Biobase ks viper]; }; - discordant = derive2 { name="discordant"; version="1.5.2"; sha256="011vh7xzxldfmid6w4g29b7s4w81lqifwxfj6r0d6725pa3bcxb4"; depends=[Biobase biwt gtools MASS]; }; - dks = derive2 { name="dks"; version="1.27.0"; sha256="04da9f6ckqzw8dppxrrcc7aqgkb980jq1g15dkmzx9ys54bnhh78"; depends=[cubature]; }; - dmrseq = derive2 { name="dmrseq"; version="1.1.21"; sha256="15jvpy5n27vdb387qmcv63c2fs5pnx5zdsg1h2b99cil650b1c0s"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; }; - doppelgangR = derive2 { name="doppelgangR"; version="1.9.6"; sha256="07y79wbb82j4iqh04rcjg66qkngply7s4b2hcmc5i6g5ycar5cmv"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; }; - drawProteins = derive2 { name="drawProteins"; version="1.1.1"; sha256="12n5pi0yj692k9wridiwnjazcajknlpvjbl7wav6408lg4ph5z6p"; depends=[dplyr ggplot2 httr readr stringr]; }; - dualKS = derive2 { name="dualKS"; version="1.41.0"; sha256="125gpaykiy2cplkvixghj2c1xh08zga7jvi2xmsh0j1illdssab5"; depends=[affy Biobase]; }; - dupRadar = derive2 { name="dupRadar"; version="1.11.1"; sha256="0myl9j77gpjgkqz24vxnf8x889qa06xr54bgmr32jhb0n6i9km90"; depends=[Rsubread]; }; - dyebias = derive2 { name="dyebias"; version="1.41.2"; sha256="0mjin0pvpi9z9vq8pj5smbz4968za5n31aclgwaiydy5lfmqd6zz"; depends=[Biobase marray]; }; - easyRNASeq = derive2 { name="easyRNASeq"; version="2.17.0"; sha256="0siki1k4qvkgkyhldrz7i05vhria9nd9yvf848a4gkx4l68v2189"; depends=[Biobase BiocGenerics BiocParallel biomaRt Biostrings DESeq edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD Rsamtools S4Vectors ShortRead SummarizedExperiment]; }; - ecolitk = derive2 { name="ecolitk"; version="1.53.0"; sha256="14df276m23zlmz6q2lhbv2j91wj2jaxhs6wnl5x5gnjj1p8jv6wj"; depends=[Biobase]; }; - edge = derive2 { name="edge"; version="2.13.2"; sha256="1qjsxydfdzr2zrz5ns69w743rsfhxcmp7i13ax7pz5kry2sf0hl1"; depends=[Biobase jackstraw MASS qvalue snm sva]; }; - edgeR = derive2 { name="edgeR"; version="3.23.7"; sha256="0mwx3qqf2c8g9p03qxy2qixri8jm2wxd642zskl2173r05iba2sm"; depends=[limma locfit Rcpp]; }; - eegc = derive2 { name="eegc"; version="1.7.5"; sha256="1dhfzsi0avamj3bnp0p99ba3lc5dw83b0pl7idfhnh5yp4imv6nf"; depends=[AnnotationDbi clusterProfiler DESeq2 DOSE edgeR ggplot2 gplots igraph limma org_Hs_eg_db org_Mm_eg_db pheatmap R_utils S4Vectors sna wordcloud]; }; - eiR = derive2 { name="eiR"; version="1.21.1"; sha256="0zk1jf0n2kpajqpnlwwi2814vrbmy8gixnnkapflcbdl0z25m25z"; depends=[BiocGenerics ChemmineR DBI digest gespeR RcppAnnoy RCurl RUnit snow snowfall]; }; - eisa = derive2 { name="eisa"; version="1.33.0"; sha256="18jk4iwav2r95wfjynl9dwnhsm5n97kq0i7xv5dhgw2gqh5yfv64"; depends=[AnnotationDbi Biobase BiocGenerics Category DBI genefilter isa2]; }; - enrichplot = derive2 { name="enrichplot"; version="1.1.7"; sha256="14i800cnlgc8bm8g5rlgl4rd9ajbpgljg3bhqh89zfgvvj6xy3v1"; depends=[AnnotationDbi cowplot DOSE europepmc ggplot2 ggplotify ggraph ggridges GOSemSim gridExtra igraph purrr RColorBrewer reshape2 UpSetR]; }; - ensemblVEP = derive2 { name="ensemblVEP"; version="1.23.1"; sha256="0sh1c2pmyp3lxabm2if4266mczb1as562hbyzxd3dq79n7s0wijj"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; }; - ensembldb = derive2 { name="ensembldb"; version="2.5.9"; sha256="0sbrcfg4d8yqpls11ba05qgddg1y8s23fpq68560wrzippz4j2p7"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; }; - epiNEM = derive2 { name="epiNEM"; version="1.5.2"; sha256="1wqn5mqjxw6i21byig7b0cypiws6kjq6vjwcafg6dxry2fx675iw"; depends=[BoolNet e1071 graph gtools igraph lattice latticeExtra minet nem pcalg RColorBrewer]; }; - epigenomix = derive2 { name="epigenomix"; version="1.21.0"; sha256="11vcdklmg7ghwr3da1n5bnm272m0wgqinhc1gj3i6wpgcvijnwr3"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; }; - epivizr = derive2 { name="epivizr"; version="2.11.1"; sha256="08x7zbqpi3mrgkilibm0nrkqv7v4zr4l6a0xzgln3y4ns226lvy1"; depends=[epivizrData epivizrServer GenomicRanges IRanges S4Vectors]; }; - epivizrChart = derive2 { name="epivizrChart"; version="1.3.4"; sha256="18j25cyimifrblfipfjlazhpp10h606shgw9rq7b351gnr6a92ac"; depends=[BiocGenerics epivizrData epivizrServer htmltools rjson]; }; - epivizrData = derive2 { name="epivizrData"; version="1.9.4"; sha256="0fscvaq46rvnvpcbzli8mrk4ig7ik6q7yprgf1dmj40a7pcx48j3"; depends=[Biobase ensembldb epivizrServer GenomeInfoDb GenomicFeatures GenomicRanges IRanges OrganismDbi S4Vectors SummarizedExperiment]; }; - epivizrServer = derive2 { name="epivizrServer"; version="1.9.4"; sha256="0pxpmqbkwsh4g72zdr7c0dsxwxm538cs1fv6y1ns1mpiv9k4wmcl"; depends=[httpuv mime R6 rjson]; }; - epivizrStandalone = derive2 { name="epivizrStandalone"; version="1.9.1"; sha256="0snqd11np3zksrxmya5pb6fbwx5k3iipqika1ig3wmvry1czrsr9"; depends=[BiocGenerics epivizr epivizrServer GenomeInfoDb GenomicFeatures git2r S4Vectors]; }; - erccdashboard = derive2 { name="erccdashboard"; version="1.15.0"; sha256="0g8b2ngfc5a6cagpiqh1q2k66s3d275r03z1yb2lvaqv1bprx0s7"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr]; }; - erma = derive2 { name="erma"; version="0.13.1"; sha256="01s2rpcbhd9hi2md5nzccral4ffp3xjl3qkkhm42q114dfbk5ccp"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel GenomeInfoDb GenomicFiles GenomicRanges ggplot2 Homo_sapiens IRanges rtracklayer S4Vectors shiny SummarizedExperiment]; }; - esATAC = derive2 { name="esATAC"; version="1.3.6"; sha256="1qwq2vchc1jyqy6h141ygkibz1i5nxfvciv7mqkz7sp6a3i2a149"; depends=[AnnotationDbi BiocGenerics BiocManager Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr motifmatchr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; }; - esetVis = derive2 { name="esetVis"; version="1.7.3"; sha256="0yr2rbpj2rddr50v4ws21jl16ylnjan5ag7m629lcrp34lxn7b73"; depends=[Biobase hexbin MASS MLP mpm Rtsne]; }; - eudysbiome = derive2 { name="eudysbiome"; version="1.11.0"; sha256="0372hl9jsk225zjm3ca63q95x4rcnj4i13r7192gfxzisy7y9i36"; depends=[Biostrings plyr R_utils Rsamtools]; }; - exomeCopy = derive2 { name="exomeCopy"; version="1.27.0"; sha256="003r5750vnadkvc19aaw8rf4qlfs1015nmndmsaazbg70dwkkdyl"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; }; - exomePeak = derive2 { name="exomePeak"; version="2.15.0"; sha256="1xyx8c1sflf98fp2588cvwmpz7f4bji6mwaw0297cj7h4893nb2a"; depends=[GenomicAlignments GenomicFeatures Rsamtools rtracklayer]; }; - explorase = derive2 { name="explorase"; version="1.45.0"; sha256="18cch1m5k8sr9fjgfqv6ya2miwin89viq7sigpdv15r0xiz1js77"; depends=[limma rggobi RGtk2]; }; - fCCAC = derive2 { name="fCCAC"; version="1.7.2"; sha256="18hbjv0c53mr9751h27b1spn1kc47wvbkh0p35y68akjk815gfrw"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; }; - fCI = derive2 { name="fCI"; version="1.11.1"; sha256="0b9n1vigqd7hvyqpgdaqdpz1iqmng2xl3zkgbasqyq71crcfchwv"; depends=[FNN gtools psych rgl VennDiagram zoo]; }; - fabia = derive2 { name="fabia"; version="2.27.0"; sha256="0lp2h8px9f4czvld93v1cpra31375qwvyfaq336jc7ib2myvdclz"; depends=[Biobase]; }; - factDesign = derive2 { name="factDesign"; version="1.57.0"; sha256="1kf98xygnq5pwjl7ak5jasrkgnrqhzpb81gljgsc0xp3a1mj37gn"; depends=[Biobase]; }; - farms = derive2 { name="farms"; version="1.33.0"; sha256="1xbndc128m1f5jv8firhgsbgyqvwrxma22182p5axxjf5qwymnl9"; depends=[affy Biobase MASS]; }; - fastLiquidAssociation = derive2 { name="fastLiquidAssociation"; version="1.17.0"; sha256="1j3zhxcn21d81dh0afb5h84xh6lrfj0z7ldfdsqlr5f7l9niljfc"; depends=[doParallel Hmisc impute LiquidAssociation preprocessCore WGCNA]; }; - fastseg = derive2 { name="fastseg"; version="1.27.0"; sha256="079yskkxy0fvjckgc8n5nd3rs96q44v6078k3p95kgyr57sxa56s"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors]; }; - fdrame = derive2 { name="fdrame"; version="1.53.0"; sha256="1vxh7hjpqkl6wp1ycm11rfjn3xw56n4jj61j7gmzcb8x5f6nchr8"; depends=[]; }; - ffpe = derive2 { name="ffpe"; version="1.25.0"; sha256="0pkzf7rh51bb4ha8aimb7l49qd7zfm7hb6fambwwdf91l842d5i7"; depends=[affy Biobase BiocGenerics lumi methylumi sfsmisc TTR]; }; - fgsea = derive2 { name="fgsea"; version="1.7.1"; sha256="1aiiqc3jbanlxa6q3inqzj1h81dpar2i05bmaja38k7inciaysa0"; depends=[BiocParallel data_table fastmatch ggplot2 gridExtra Matrix Rcpp]; }; - flagme = derive2 { name="flagme"; version="1.37.0"; sha256="0pjyi90l7k2i7bm93p9yyvrx18jmwcg0gaj2wixa0inyx9w5bymc"; depends=[CAMERA gcspikelite gplots MASS SparseM xcms]; }; - flipflop = derive2 { name="flipflop"; version="1.19.0"; sha256="0283bks3jbscnvyj51jm3z47rvdpfmaj40bc2h1ck8md82jrhiqj"; depends=[GenomicRanges IRanges Matrix]; }; - flowAI = derive2 { name="flowAI"; version="1.11.3"; sha256="1ha80s8w2mcy72r2h6kj5sq0qrwkan4vzxpy2lf9frbpxrdkw696"; depends=[changepoint flowCore ggplot2 knitr plyr RColorBrewer reshape2 rmarkdown scales]; }; - flowBeads = derive2 { name="flowBeads"; version="1.19.0"; sha256="16h0jd88nada5lsaxl7q1m3nqf7gzqc1hw9cv5q96qa8n13a50la"; depends=[Biobase flowCore knitr rrcov xtable]; }; - flowBin = derive2 { name="flowBin"; version="1.17.0"; sha256="0axib7fny5n1h0fcisy2ll67m1illv41swwi1xdc37d2v605c6jk"; depends=[BiocGenerics class flowCore flowFP limma snow]; }; - flowCHIC = derive2 { name="flowCHIC"; version="1.15.0"; sha256="1qsa6lkdang9x44wva0dwkgvv4kxqadk3jvjkg0q59bdf137irrs"; depends=[EBImage flowCore ggplot2 hexbin vegan]; }; - flowCL = derive2 { name="flowCL"; version="1.19.3"; sha256="0rp3lrxk3sdwjv939kjkc246pwifidn6bvm6lk115yqa03ymii3w"; depends=[graph Rgraphviz SPARQL]; }; - flowClean = derive2 { name="flowClean"; version="1.19.0"; sha256="091d79vx5w76xhhjm1zvjfyfv9pn4ni91a85yq2ca4laplsd0nqn"; depends=[bit changepoint flowCore sfsmisc]; }; - flowClust = derive2 { name="flowClust"; version="3.19.1"; sha256="0sdssv5bingj6zs0jp0ddfckkmbx3kljhh7snv74b0k0f3lndg4h"; depends=[Biobase BiocGenerics clue corpcor ellipse flowCore flowViz graph mnormt]; }; - flowCore = derive2 { name="flowCore"; version="1.47.9"; sha256="03wzl92yv5zg4rgbffd07lzb69xk3flf1fg640b8kw6527wbgfkz"; depends=[BH Biobase BiocGenerics corpcor graph MASS matrixStats Rcpp rrcov]; }; - flowCyBar = derive2 { name="flowCyBar"; version="1.17.0"; sha256="1c3a12slk8z8y1vr8j09p2k5h2pw697ysk0a74p6n20sfl1zd3h9"; depends=[gplots vegan]; }; - flowDensity = derive2 { name="flowDensity"; version="1.15.2"; sha256="1qadx0lxvk74rapgmibp9fix19zdyg3illgl7qfnzkkadbjc1bbw"; depends=[car flowCore flowWorkspace gplots RFOC rgeos sp]; }; - flowFP = derive2 { name="flowFP"; version="1.39.0"; sha256="02n85dv2qvxzwdi44mc7awvxc26nbwpbzawb0ikjv8gwf4www9ch"; depends=[Biobase BiocGenerics flowCore flowViz]; }; - flowFit = derive2 { name="flowFit"; version="1.19.1"; sha256="0v7qdrskm47d2j16gag2lv63051hz182l7j5j2m36jh1fbddwhz6"; depends=[flowCore flowViz gplots kza minpack_lm]; }; - flowMap = derive2 { name="flowMap"; version="1.19.1"; sha256="1q3gvb4q2d3lh8828hlnxdrqzlsfm4chl5rvf99nbmapazz37r7g"; depends=[abind ade4 doParallel Matrix reshape2 scales]; }; - flowMatch = derive2 { name="flowMatch"; version="1.17.1"; sha256="0ymvn6nyxp95yb23y6lr0ks297m1djqaisz34wssxqk524zjrgbr"; depends=[Biobase flowCore Rcpp]; }; - flowMeans = derive2 { name="flowMeans"; version="1.41.0"; sha256="1ixzwry1435w20w40z87yhscbgskbldqmrz0x7nqvlqp5yn1ax71"; depends=[Biobase feature flowCore rrcov]; }; - flowMerge = derive2 { name="flowMerge"; version="2.29.0"; sha256="0imabypbjyn83jyb3isichi7fy4p4nkmsphcqbkimpjrfgc391kw"; depends=[feature flowClust flowCore foreach graph Rgraphviz rrcov snow]; }; - flowPeaks = derive2 { name="flowPeaks"; version="1.27.1"; sha256="07r0l4iyc9jrraswmd0j2lzrjw2ch7wkfniisr148k3a6gvhl0wq"; depends=[]; }; - flowPloidy = derive2 { name="flowPloidy"; version="1.7.3"; sha256="1m7vr6z9ca04xk876s9mc36hjr1wd9bb3kgx1hi7zd1aazzis1rb"; depends=[car caTools flowCore knitr minpack_lm rmarkdown shiny]; }; - flowPlots = derive2 { name="flowPlots"; version="1.29.0"; sha256="0ylxkvhzghzybsi20lpprz430sl2d6mnrkbwp8bbsysr2ymsjml6"; depends=[]; }; - flowQ = derive2 { name="flowQ"; version="1.41.1"; sha256="15n2w9958hp3w0rigx80p2gj5l4bg8zycv8h2l31ysdg34lij5r7"; depends=[BiocGenerics bioDist flowCore flowViz geneplotter IRanges lattice latticeExtra mvoutlier outliers parody RColorBrewer]; }; - flowQB = derive2 { name="flowQB"; version="2.9.0"; sha256="0d4n8qxja851z4d7ran9wr4rhfa64mnkhz7rqwa0vggrq1y0ksja"; depends=[extremevalues flowCore]; }; - flowStats = derive2 { name="flowStats"; version="3.39.4"; sha256="1cj7dwvqa9x3lxblfvxmsl88zc91fbjhh1viy3s2m88kxl6517vr"; depends=[Biobase BiocGenerics cluster fda flowCore flowViz flowWorkspace KernSmooth ks lattice MASS ncdfFlow RColorBrewer]; }; - flowTime = derive2 { name="flowTime"; version="1.5.0"; sha256="0qh2p696xh8xsi0j7d6s75kbf8ajm4virfs8c6c1rn48n4grhlpy"; depends=[flowCore plyr]; }; - flowTrans = derive2 { name="flowTrans"; version="1.33.0"; sha256="1fqw49s9dgz4khq3m73bf8f7vy9xzhdl91n0rkmcnwq7kd6wm5n9"; depends=[flowClust flowCore flowViz]; }; - flowType = derive2 { name="flowType"; version="2.19.0"; sha256="1313ak0n79pvhzpckrapbkzrzxhd8qnxawpvagm92lsdg5p79mfc"; depends=[BH Biobase flowClust flowCore flowMeans flowMerge Rcpp rrcov sfsmisc]; }; - flowUtils = derive2 { name="flowUtils"; version="1.45.2"; sha256="1x6ng8wvwqhq76r3wm62xyi29dq0086yvklv2ddv2gfc7ifzk8nl"; depends=[Biobase corpcor flowCore graph RUnit XML]; }; - flowVS = derive2 { name="flowVS"; version="1.13.0"; sha256="16r8ig33ym1d8hp2hvxnlszifc0qpmd4vnqzg1nn31a4j3xf575r"; depends=[flowCore flowStats flowViz]; }; - flowViz = derive2 { name="flowViz"; version="1.45.0"; sha256="076hjz0mvc7pygmlrapsgg6scsxkzd714yg4wq8r8fbbpblqhkxf"; depends=[Biobase flowCore hexbin IDPmisc KernSmooth lattice latticeExtra MASS RColorBrewer]; }; - flowWorkspace = derive2 { name="flowWorkspace"; version="3.29.10"; sha256="0qch9hbpxqwma1kg9jrmnyf7d9zc714pjybpzphkgx9c9cdbaqzy"; depends=[BH Biobase BiocGenerics cytolib data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra matrixStats ncdfFlow RBGL RColorBrewer Rcpp Rgraphviz RProtoBufLib scales stringr XML]; }; - flowcatchR = derive2 { name="flowcatchR"; version="1.15.3"; sha256="04njcbq0bi53pwkfrf489l3fws63w9l981cf4iadkadbk5dl2hav"; depends=[abind BiocParallel colorRamps EBImage plotly shiny]; }; - fmcsR = derive2 { name="fmcsR"; version="1.23.3"; sha256="1f2la9cx08yd3y96n2hkc6dzqvj5kya58rghr711axjmjfcigw2y"; depends=[BiocGenerics ChemmineR RUnit]; }; - focalCall = derive2 { name="focalCall"; version="1.15.0"; sha256="1vnihlpxaplnjp7h9n3k3py0103qz98dnkm1p7hns93pf185ih05"; depends=[CGHcall]; }; - frma = derive2 { name="frma"; version="1.33.0"; sha256="02n251fwg34f0mkvingrsv1n0v77cvmpmd44rs1a4qyl5nj3x9v6"; depends=[affy Biobase BiocGenerics DBI MASS oligo oligoClasses preprocessCore]; }; - frmaTools = derive2 { name="frmaTools"; version="1.33.0"; sha256="1w62s3i6q92ka44dy8sqid21fgpjjghmnyavj3swx5czpn476vny"; depends=[affy Biobase DBI preprocessCore]; }; - funtooNorm = derive2 { name="funtooNorm"; version="1.5.1"; sha256="0pqh1hiblr6989wvdx7fmxkkj451xijjj6z9jgqz2c08qpk2d4h8"; depends=[GenomeInfoDb IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest matrixStats minfi pls]; }; - gCMAP = derive2 { name="gCMAP"; version="1.25.0"; sha256="0mp0cg33slfpnqzk2fsggpb3dfgq95isj42lia0i3hkwkdfcisly"; depends=[annotate AnnotationDbi bigmemory bigmemoryExtras Biobase Category DESeq genefilter GSEABase GSEAlm limma Matrix]; }; - gCMAPWeb = derive2 { name="gCMAPWeb"; version="1.21.0"; sha256="15fmiii9kkiy1p9d2h7hg9fi3kacifz6113hpkzkk0lic4phncg5"; depends=[annotate AnnotationDbi Biobase BiocGenerics brew gCMAP GSEABase hwriter Rook yaml]; }; - gCrisprTools = derive2 { name="gCrisprTools"; version="1.9.3"; sha256="1msp2xfd3h1bj04abad714r9rmgbr9w6g26lj7s8j451jjlw57na"; depends=[Biobase ggplot2 limma PANTHER_db rmarkdown RobustRankAggreg]; }; - gQTLBase = derive2 { name="gQTLBase"; version="1.13.0"; sha256="0rszhclakgc0xyg8jdb9mxgwaqcb28rcs9pyrg31d0wxi44c90w2"; depends=[BatchJobs BBmisc BiocGenerics bit doParallel ff ffbase foreach GenomicFiles GenomicRanges rtracklayer S4Vectors SummarizedExperiment]; }; - gQTLstats = derive2 { name="gQTLstats"; version="1.13.1"; sha256="0apicd22s2yx57ypqvnmxkh3ca06r5cq3mj7x3hz57z9sv99bq1w"; depends=[AnnotationDbi BatchJobs BBmisc beeswarm Biobase BiocGenerics doParallel dplyr erma ffbase foreach GenomeInfoDb GenomicFeatures GenomicFiles GenomicRanges ggbeeswarm ggplot2 gQTLBase HardyWeinberg Homo_sapiens IRanges limma mgcv plotly reshape2 S4Vectors shiny snpStats SummarizedExperiment VariantAnnotation]; }; - gaga = derive2 { name="gaga"; version="2.27.0"; sha256="09q5xfki8nnp5z4ia0l07pnvsmiwag7ahr1bxbic9aajql873ipk"; depends=[Biobase coda EBarrays mgcv]; }; - gage = derive2 { name="gage"; version="2.31.2"; sha256="0m4mp78g3sxa19rkw9p4d6sxw1ic9km6z5hir8d1lqg0hmv9y2ki"; depends=[AnnotationDbi graph KEGGREST]; }; - gaggle = derive2 { name="gaggle"; version="1.49.0"; sha256="0bi19b9ndccrky2i89scjzgna5b2gj0p74licynn8pm1jfwla584"; depends=[graph rJava RUnit]; }; - gaia = derive2 { name="gaia"; version="2.25.3"; sha256="10qcjcfqiwa2xcgh2jpiq5hp8i8ihbl4nz503ndcz3j54rw3pjfn"; depends=[]; }; - garfield = derive2 { name="garfield"; version="1.9.1"; sha256="1fj196imnr9vb8pg6rxf46n5yw7v3g1w0q8h49psrvw7zrmzknsg"; depends=[]; }; - gcapc = derive2 { name="gcapc"; version="1.5.1"; sha256="1fk3vqxl6xpf4xhmacsn3ywwixs1brm24pfyshlbwp27rwj3jpzw"; depends=[BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS matrixStats Rsamtools S4Vectors]; }; - gcatest = derive2 { name="gcatest"; version="1.11.0"; sha256="0x0k557fydigj81610a39b8hg973wbjsfj0ailpjfa1grp77csa1"; depends=[lfa]; }; - gcrma = derive2 { name="gcrma"; version="2.53.1"; sha256="0qlvr4lgkddyrdvf81z60zzlbq0x7abdlgsgw1xr1xabmp7wbkrs"; depends=[affy affyio Biobase BiocManager Biostrings XVector]; }; - gdsfmt = derive2 { name="gdsfmt"; version="1.17.6"; sha256="0x44n0qrcq82kxd8w1zlbfsgmf2yxxnf1i5h9z7ajlcz46cwgaxn"; depends=[]; }; - geNetClassifier = derive2 { name="geNetClassifier"; version="1.21.1"; sha256="0fjkm6bg4g2qr5xyjjyhrpm9iijhmgy6rwd38iwimlq3qqgnm819"; depends=[Biobase e1071 EBarrays minet]; }; - geecc = derive2 { name="geecc"; version="1.15.0"; sha256="0wfa0a4hlwvjsjvxk7m6lgjxjvph3392a4kskg2y1vphh916qnxr"; depends=[gplots hypergea MASS Rcpp]; }; - genArise = derive2 { name="genArise"; version="1.57.0"; sha256="08hrc2y06prmacdzrd3qnlbyzrr9127jgglq7babrnhw0dffjl96"; depends=[locfit tkrplot xtable]; }; - genbankr = derive2 { name="genbankr"; version="1.9.2"; sha256="1ba891irw0carh6pg2r6v50g5g7am1k09zyw450rz878sfka50cj"; depends=[Biobase BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors VariantAnnotation]; }; - geneAttribution = derive2 { name="geneAttribution"; version="1.7.0"; sha256="1snpd1xy66kaj2mb8xjasgm3bipydxbrbcpvp5bny9shvk6di0cf"; depends=[BiocGenerics GenomeInfoDb GenomicFeatures GenomicRanges IRanges org_Hs_eg_db rtracklayer]; }; - geneClassifiers = derive2 { name="geneClassifiers"; version="1.5.0"; sha256="0qwqb1sq6bw688br5c5lxvc7dxwg1qwwb30dn9pklgfgpnjwp86n"; depends=[Biobase BiocGenerics]; }; - geneRecommender = derive2 { name="geneRecommender"; version="1.53.0"; sha256="1qrlk46y1hkgva2yrf8x2smy82p4kmzjpr7kyk9381rfl64nn18q"; depends=[Biobase]; }; - geneRxCluster = derive2 { name="geneRxCluster"; version="1.17.0"; sha256="0vlhskyymdnbigdq1qj9gimklcmzvybh74zn7f65if5ssqdgmj10"; depends=[GenomicRanges IRanges]; }; - geneXtendeR = derive2 { name="geneXtendeR"; version="1.7.11"; sha256="1kws224q6rhzmdrgfv2695l5aah3hz6r5vacwl5akg2bja2v42yv"; depends=[AnnotationDbi BiocStyle data_table dplyr GO_db networkD3 org_Rn_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; }; - genefilter = derive2 { name="genefilter"; version="1.63.2"; sha256="0kx0fv9gjknffhvgz65y36hxcfi25rii6m35caxdrkcfm3cnrc6l"; depends=[annotate AnnotationDbi Biobase S4Vectors survival]; }; - genefu = derive2 { name="genefu"; version="2.13.1"; sha256="0b1xrxfp1swfsvvrr1nkkkmjjb6bxbjhvvm2fl2463mmgy3qdsn6"; depends=[AIMS amap biomaRt iC10 limma mclust survcomp]; }; - geneplast = derive2 { name="geneplast"; version="1.7.2"; sha256="18g39wzkcnkpp4v2fwbh3ff84b8fcwfn723hpfyla7857qjm6krp"; depends=[ape igraph snow]; }; - geneplotter = derive2 { name="geneplotter"; version="1.59.0"; sha256="1yqxqxchjn31sqw3csk5y3jmshb3v5580q245skam5r5v2nw5lhb"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; }; - genoCN = derive2 { name="genoCN"; version="1.33.0"; sha256="1rcly2dfm93lbsc1inm3z669l19k213zyq31kb4kkg1cnam2cflv"; depends=[]; }; - genomation = derive2 { name="genomation"; version="1.13.1"; sha256="038fnkv0m2r47mm2cg2fmrzq776j0jfskppi7p0872rx59r0vl6y"; depends=[Biostrings BSgenome data_table GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridBase impute IRanges matrixStats plotrix plyr Rcpp readr reshape2 Rsamtools rtracklayer RUnit S4Vectors seqPattern]; }; - genomeIntervals = derive2 { name="genomeIntervals"; version="1.37.0"; sha256="1xinqj7zzwjxx6qxi6mxrws2ajjm8cy7g9v1773x7mh47w9rz7mw"; depends=[BiocGenerics GenomeInfoDb GenomicRanges intervals IRanges S4Vectors]; }; - genomes = derive2 { name="genomes"; version="3.11.0"; sha256="0vvc43ih4idj6jakm4jvwynvi4v90nndvbz18kb7nxb7fh1bl9m3"; depends=[curl readr]; }; - genoset = derive2 { name="genoset"; version="1.37.0"; sha256="0awbbvhz1qzra92ghal5wrqrkya4v0wd15q75dmqxb5xx36s8if6"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; - genotypeeval = derive2 { name="genotypeeval"; version="1.13.2"; sha256="10zz9jd1xsk09gh3mkm23jmqi4j5kv7d5fbjwlr2bxq4z2yjl8h4"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer VariantAnnotation]; }; - genphen = derive2 { name="genphen"; version="1.9.49"; sha256="0mdr79x7a036rrjdh1aqxnxskgsvvjbzyvlgcrf9jxh2yf45ciq1"; depends=[Biostrings doParallel e1071 foreach ranger rstan]; }; - gep2pep = derive2 { name="gep2pep"; version="1.1.1"; sha256="0h6qf7fl2hmg5chv6g9qfj5ih4mfc6xmihqny9pzg277i5gwmdsj"; depends=[Biobase digest foreach GSEABase iterators repo rhdf5 XML]; }; - gespeR = derive2 { name="gespeR"; version="1.13.0"; sha256="1qc9d8vp5s5rzw7bqbfm2n5l23yfk9d3kpmhyd4hnr9jb2h4jypp"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; }; - ggbio = derive2 { name="ggbio"; version="1.29.5"; sha256="1aqj3m7jkjdzwvnk8il74v05gybd3n6b056mlwq8slmmpyngjnc6"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 rlang Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; }; - ggcyto = derive2 { name="ggcyto"; version="1.9.13"; sha256="0dhwv19dny4490jg2p7bbmzqnpyf04zms33vwssaf7xwy7i8h0q9"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra ncdfFlow plyr RColorBrewer rlang scales]; }; - ggtree = derive2 { name="ggtree"; version="1.13.6"; sha256="0hbw03ixzvmiqgacvi41mb8kjnh7s78z39900b532qd1ghmg8xrq"; depends=[ape dplyr ggplot2 magrittr purrr rlang rvcheck scales tibble tidyr tidytree treeio]; }; - girafe = derive2 { name="girafe"; version="1.33.2"; sha256="1b7sqnbj3a6p8zdaf8w7s19fijiw5ciqchxsi8i7ali46fqvqhbs"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; }; - glmSparseNet = derive2 { name="glmSparseNet"; version="0.99.36"; sha256="1qhjrpd70qfizkk64kl4spwwq8gjk7zg6ypj5gyk6pn98myvk2bm"; depends=[biomaRt dplyr forcats futile_logger ggplot2 glmnet loose_rock Matrix MultiAssayExperiment readr reshape2 rlang sparsebn sparsebnUtils STRINGdb stringr SummarizedExperiment survminer]; }; - globalSeq = derive2 { name="globalSeq"; version="1.9.4"; sha256="146zfaz0w3gdic5q50vqzynr6gzv6b0c417yi1x350ir3qn2vczk"; depends=[]; }; - globaltest = derive2 { name="globaltest"; version="5.35.1"; sha256="0q72cvh11qffkr6c17pz7a5d2wi2csk37pq9fjda11mmx1g01paq"; depends=[annotate AnnotationDbi Biobase survival]; }; - gmapR = derive2 { name="gmapR"; version="1.23.1"; sha256="0qyn39vcp7a84xjn7n4cyhk47yw9yxn9mwq81kz3fjljafy2pv9z"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; - goProfiles = derive2 { name="goProfiles"; version="1.43.0"; sha256="19r3h8rnfs826aldlgkjgsllk4wj95rq7lq37qd927bjgvi4kbnj"; depends=[AnnotationDbi Biobase CompQuadForm GO_db stringr]; }; - goSTAG = derive2 { name="goSTAG"; version="1.5.1"; sha256="1nazixjbh90460iqc7hgsgsilzaknjym639c5mmxcxdas96vmry1"; depends=[AnnotationDbi biomaRt GO_db memoise]; }; - goTools = derive2 { name="goTools"; version="1.55.0"; sha256="1lzgsdqvwrxckg5pdbmnxldifrsm7zyvl72pl3sz8x2997b4lc97"; depends=[AnnotationDbi GO_db]; }; - goseq = derive2 { name="goseq"; version="1.33.0"; sha256="102w1cxz2ab0gyzamy9rcdbf73bgkvqrm0lxasz6m2h79j9gfmc9"; depends=[AnnotationDbi BiasedUrn BiocGenerics geneLenDataBase GO_db mgcv]; }; - gpart = derive2 { name="gpart"; version="0.99.19"; sha256="05nzlyn7n1a73qdrg8wrwjwcix4i7y43g6bycbfw07zxps8a3472"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; }; - gpls = derive2 { name="gpls"; version="1.53.0"; sha256="02yca8lllmq7lmbg55kn3yhsb0s9d2b828aj08lsp5hxmyill36k"; depends=[]; }; - gprege = derive2 { name="gprege"; version="1.25.2"; sha256="0qlbvss2hk3f3bfi4k4jcpyqwishkxsqq9cv846cbnkryn1xnrih"; depends=[gptk]; }; - graph = derive2 { name="graph"; version="1.59.2"; sha256="1vncpr60yl63kwlxdp1b15r81ymf28whzkkd9mz5r8f6jz184h0g"; depends=[BiocGenerics]; }; - graphite = derive2 { name="graphite"; version="1.27.6"; sha256="009gjkmnjr8y6j8dz9h19bn16qkzhvknqazrdm4pf86pn8w2gy2w"; depends=[AnnotationDbi checkmate graph httr rappdirs]; }; - groHMM = derive2 { name="groHMM"; version="1.15.1"; sha256="1a6c40bfsskh0adaqjvimn6bysfgz24lga9byznp2cf2757i9bps"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; }; - gsean = derive2 { name="gsean"; version="1.1.0"; sha256="0aar598qdhppzkzrrmhzd1nkn7i3xci401yz3w5dsgz27fy12c18"; depends=[fgsea PPInfer]; }; - gtrellis = derive2 { name="gtrellis"; version="1.13.3"; sha256="0pg30gnbmsn498isqw3g26a5pzxbq1k0hbz4sd986ak1whgac1q3"; depends=[circlize GenomicRanges GetoptLong IRanges]; }; - gwascat = derive2 { name="gwascat"; version="2.13.5"; sha256="0p4l8skyyjblqzlcb13sj29sy6x62fakb5i56d757z6ic8pi84kx"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 gQTLstats graph Gviz Homo_sapiens IRanges Rsamtools rtracklayer S4Vectors snpStats SummarizedExperiment VariantAnnotation]; }; - gwasurvivr = derive2 { name="gwasurvivr"; version="0.99.46"; sha256="137a4vclz7h462xf2aia47kaigz2gchlhxl6v7ycv4rq48i6qjrq"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; }; - h5vc = derive2 { name="h5vc"; version="2.15.1"; sha256="1gfch3p8ylws4g22kd6xs79wsm6x65yfdaqxjhqp0cgsjlyrr29h"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra h5vcData IRanges reshape rhdf5 Rsamtools S4Vectors]; }; - hapFabia = derive2 { name="hapFabia"; version="1.23.0"; sha256="0dhq26aqqmnzmx3cnwmmrqa8zx5gxq48is1wmljvfn86qixr70xr"; depends=[Biobase fabia]; }; - heatmaps = derive2 { name="heatmaps"; version="1.5.0"; sha256="0lz2cxw3fxyvnmnzk95k791x8x3vjn5cif2bqp3zv2rlkwgdjd7m"; depends=[BiocGenerics Biostrings EBImage GenomeInfoDb GenomicRanges IRanges KernSmooth Matrix plotrix RColorBrewer]; }; - hiAnnotator = derive2 { name="hiAnnotator"; version="1.15.0"; sha256="12q17c31j1q1jbh1z1ddlcml1wxin5s32yz9xk7dd7bxa81frpmg"; depends=[BSgenome dplyr foreach GenomicRanges ggplot2 iterators rtracklayer scales]; }; - hiReadsProcessor = derive2 { name="hiReadsProcessor"; version="1.17.0"; sha256="1qad1winpzjwjn9wnr7xvmspza2j0islsdqh7aig767svipw8870"; depends=[BiocGenerics BiocParallel Biostrings dplyr GenomicAlignments GenomicRanges hiAnnotator readxl rSFFreader sonicLength]; }; - hicrep = derive2 { name="hicrep"; version="1.5.1"; sha256="0vjif93dnjjqrd15gxflwlhncrr3sdrp3hw9944p4pmd1xq38i3i"; depends=[]; }; - hierGWAS = derive2 { name="hierGWAS"; version="1.11.0"; sha256="0wfv8pxnm8v1lwj1cbk4d7v0cyjzra8nm8gaawwr0aqcsg7ksp2f"; depends=[fastcluster fmsb glmnet]; }; - hierinf = derive2 { name="hierinf"; version="0.99.3"; sha256="0rwwdwgx1p96vgfszp01i85wa56d9djkrjnzphgcv5962smd0wka"; depends=[fmsb glmnet]; }; - hipathia = derive2 { name="hipathia"; version="1.1.3"; sha256="08yx1jpfz08zsldxvjsz9957rp1wk2744kb8248k5rwf4fmcdp4w"; depends=[AnnotationHub coin DelayedArray igraph limma matrixStats MultiAssayExperiment preprocessCore S4Vectors servr SummarizedExperiment]; }; - hmdbQuery = derive2 { name="hmdbQuery"; version="1.1.3"; sha256="0gvbfiibnb3w588ri385wwyg1x3my7a3ay6sacbjhh0j6amx9g7p"; depends=[S4Vectors XML]; }; - hopach = derive2 { name="hopach"; version="2.41.0"; sha256="1i329clrw9bjxkchinadprix36xjak5x6i1zqpdj27kyr8w26gn2"; depends=[Biobase BiocGenerics cluster]; }; - hpar = derive2 { name="hpar"; version="1.23.4"; sha256="0nf8w8qn63zrq2y5i5imrwv242cc884lzi92jldd24ainybp362h"; depends=[]; }; - htSeqTools = derive2 { name="htSeqTools"; version="1.29.5"; sha256="0rigcwd8mc3kjsj0kxzxnspzqz0d1i58vav71p7a4cx76yrzi5z1"; depends=[Biobase BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges MASS S4Vectors]; }; - hyperdraw = derive2 { name="hyperdraw"; version="1.33.0"; sha256="0qcp9p3n7gxskvw8afz7yr2msm0gikl7v3dvzvrhfypad9czplx0"; depends=[graph hypergraph Rgraphviz]; }; - hypergraph = derive2 { name="hypergraph"; version="1.53.0"; sha256="1mj14bgkbs3p0smf6phfig2rcf7kd88d85djr6rq1c3vpiyhpyx3"; depends=[graph]; }; - iASeq = derive2 { name="iASeq"; version="1.25.0"; sha256="0p4m13k5n974469xh8vhz8xd5b37ill3i9jmglq0fa47n7rbdjz1"; depends=[]; }; - iBBiG = derive2 { name="iBBiG"; version="1.25.0"; sha256="1dbcazr88ac38g58jgr9byqaql36jvfn5bmr8gibn3hr187c5ypf"; depends=[ade4 biclust xtable]; }; - iBMQ = derive2 { name="iBMQ"; version="1.21.1"; sha256="11bkzp25bv5j4x2xanj5cq173pwhl1av5l7kb94vhw80yhbk9l4r"; depends=[Biobase ggplot2]; }; - iCARE = derive2 { name="iCARE"; version="1.9.7"; sha256="0bbzn5yx2i7ijfvsglzsi3f7rv6c0043qvv46n859bpq83pgng5p"; depends=[gtools Hmisc plotrix]; }; - iCNV = derive2 { name="iCNV"; version="1.1.1"; sha256="0rwr2di8215fxjv0wz75ipwdipyxr043yv72m0c03iwq5rccglxd"; depends=[CODEX data_table dplyr fields ggplot2 rlang tidyr truncnorm]; }; - iCOBRA = derive2 { name="iCOBRA"; version="1.9.1"; sha256="08nzcsph0w5zp6l2lwrg2624gsgs939rkv1662ic72jf8759i4s1"; depends=[dplyr DT ggplot2 limma reshape2 ROCR scales shiny shinyBS shinydashboard UpSetR]; }; - iCheck = derive2 { name="iCheck"; version="1.11.0"; sha256="0bs9zzcc1pbdvvzq912yqr2waic72jj4pv6ksqjg6s9wz390a4gc"; depends=[affy Biobase GeneSelectMMD gplots limma lmtest lumi MASS preprocessCore randomForest rgl scatterplot3d]; }; - iChip = derive2 { name="iChip"; version="1.35.1"; sha256="0yaf4q92fjdw80v3ln596f7088wlp7nmwhdxgnbkj0x4kwa9mr2b"; depends=[limma]; }; - iClusterPlus = derive2 { name="iClusterPlus"; version="1.17.2"; sha256="1da6hn0hysmbsd3mma9aq3qh2bj15hdc83p3lj0725c52xi6f2kx"; depends=[]; }; - iGC = derive2 { name="iGC"; version="1.11.1"; sha256="02j3bfv5r8cjjp2k7d3w9y80gvygslcgawmhvzp70chjr12a5nds"; depends=[data_table plyr]; }; - iPAC = derive2 { name="iPAC"; version="1.25.2"; sha256="15jvpz8qmmlcvarnxidmw2x3hn98ngwf2pxa6a8a0rl8qhgis3wb"; depends=[Biostrings gdata multtest scatterplot3d]; }; - iSEE = derive2 { name="iSEE"; version="1.1.14"; sha256="057shg5ayy1c2xss12jknnfj9riavnd50nv6l39bfbxymmn5gwp1"; depends=[AnnotationDbi BiocGenerics colourpicker cowplot dplyr DT ggplot2 igraph mgcv rentrez reshape2 rintrojs S4Vectors scales shiny shinyAce shinydashboard shinyjs SingleCellExperiment SummarizedExperiment vipor viridisLite]; }; - iSeq = derive2 { name="iSeq"; version="1.33.1"; sha256="1cw7fmzd0v6rdrqqkaxx0g5fz763sfwf4kyafmvw00chs4rzi21n"; depends=[]; }; - iasva = derive2 { name="iasva"; version="0.99.3"; sha256="1ax0594b3d2glam0lb4dzqzx8bbfdln0wglr96szjdxa6qi31ghk"; depends=[BiocParallel cluster irlba SummarizedExperiment]; }; - ibh = derive2 { name="ibh"; version="1.29.0"; sha256="07954bdkijs41r0h39fhlzpd8d75vhlk8gl4zlbaky93prsmi1hf"; depends=[simpIntLists]; }; - icetea = derive2 { name="icetea"; version="0.99.10"; sha256="14yzjsydnv2k8x183l7a94jmxsd27p2ndwzdvkd93d5nkh5iq36l"; depends=[BiocGenerics BiocParallel Biostrings csaw edgeR GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges limma Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm6_ensGene VariantAnnotation]; }; - ideal = derive2 { name="ideal"; version="1.5.6"; sha256="1k2h2nn0s6pmy5m2l3c6nri11am49c4s2js1q6iywbhmlcxk5dh5"; depends=[AnnotationDbi BiocParallel d3heatmap DESeq2 dplyr DT GenomicRanges ggplot2 GO_db goseq GOstats gplots IHW IRanges knitr limma pcaExplorer pheatmap rentrez rintrojs rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; }; - idiogram = derive2 { name="idiogram"; version="1.57.0"; sha256="0nsldgh780amhdafafrkp1lzriwskm3l89fkn2licxvpw63rlajn"; depends=[annotate Biobase plotrix]; }; - igvR = derive2 { name="igvR"; version="1.1.17"; sha256="1hqd65n1qkdf54jqghj9jxcbi6sl918ymarwbrgrfrm6dk1mxzsn"; depends=[BiocGenerics BrowserViz GenomicRanges httpuv rtracklayer VariantAnnotation]; }; - illuminaio = derive2 { name="illuminaio"; version="0.23.2"; sha256="05m18f0ipc89lak30rdlg1b1aafsgjsjzbr6scn18168m12qkd5i"; depends=[base64]; }; - imageHTS = derive2 { name="imageHTS"; version="1.31.0"; sha256="0d7l8w5i0nlfks1iak0qdkxrarfx280wyqbpig38bhbmzkv31xrg"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; }; - immunoClust = derive2 { name="immunoClust"; version="1.13.4"; sha256="04wjiyqp4fcbgyllpqrandvl20cjayymyi35gs3cdg9g2dwci3aq"; depends=[flowCore lattice]; }; - impute = derive2 { name="impute"; version="1.55.0"; sha256="1nb2zpnx9ia2br0044jky4kcqj2vw1vw35s34869i35n90n3vqqc"; depends=[]; }; - intansv = derive2 { name="intansv"; version="1.21.3"; sha256="0aqq5mc63s5gyz82wp37m0y3b7rkv2rxxkfld0jw6dn3fp6dapqp"; depends=[BiocGenerics GenomicRanges ggbio IRanges plyr]; }; - interactiveDisplay = derive2 { name="interactiveDisplay"; version="1.19.3"; sha256="1lmc0x0gfi8jhzl3z8pmkbqmx56xn6fim0ydsrqcaygz25gif6fp"; depends=[AnnotationDbi BiocGenerics Category ggplot2 gridSVG interactiveDisplayBase plyr RColorBrewer reshape2 shiny XML]; }; - interactiveDisplayBase = derive2 { name="interactiveDisplayBase"; version="1.19.2"; sha256="02b3sps2irfb83zii5c0zxzjp2138xfr2jfdhwvh4h6wzqn2a21q"; depends=[BiocGenerics shiny]; }; - inveRsion = derive2 { name="inveRsion"; version="1.29.1"; sha256="0bwr76l30sxzdfjjsf7py4i78diwazfjkf237yx8n4kzb0jlkilp"; depends=[haplo_stats]; }; - ipdDb = derive2 { name="ipdDb"; version="0.99.10"; sha256="1k1giv6jvgy54pa5yqcy0yrmn53x1ggbryg9c7mmpb4dljw7vnrj"; depends=[AnnotationDbi AnnotationHub assertthat Biostrings DBI GenomicRanges IRanges RSQLite]; }; - isobar = derive2 { name="isobar"; version="1.27.1"; sha256="0kznz8h6b8wq1z8xqkhn0k6gmc7wbxdfv3vy19s93njdk7w3gn5d"; depends=[Biobase biomaRt distr ggplot2 plyr]; }; - isomiRs = derive2 { name="isomiRs"; version="1.9.5"; sha256="08xvxpl1x46rs4zh34irypq0bsici3xhh52dzirhr0671p9ihqa6"; depends=[AnnotationDbi assertive_sets Biobase BiocGenerics cluster cowplot DEGreport DESeq2 DiscriMiner dplyr GenomicRanges GGally ggplot2 gplots gridExtra gtools IRanges limma RColorBrewer readr reshape rlang S4Vectors SummarizedExperiment tibble tidyr]; }; - iterClust = derive2 { name="iterClust"; version="1.3.2"; sha256="1gkqnpyhispjbzc30dfs1hdv1vq6r33sqkmjnzcil4mbr529gvc3"; depends=[Biobase cluster]; }; - iterativeBMA = derive2 { name="iterativeBMA"; version="1.39.0"; sha256="07xy5vjmgzglab6hp82xkd6gc67lb58n8g26zvssldpzm1kir70j"; depends=[Biobase BMA leaps]; }; - iterativeBMAsurv = derive2 { name="iterativeBMAsurv"; version="1.39.0"; sha256="1cj63g97xm05clix5cv3dmjdwb806rb5va262hfhvmd2aa6bgq2k"; depends=[BMA leaps survival]; }; - iteremoval = derive2 { name="iteremoval"; version="1.1.1"; sha256="09qdb60ndjljn4wgpgnxcy2yvivlpvzgr6vs04ssjwq9dk8vwc9l"; depends=[GenomicRanges ggplot2 magrittr SummarizedExperiment]; }; - ivygapSE = derive2 { name="ivygapSE"; version="1.3.0"; sha256="1730rd55ws484q4iwgd06cps8jfg7f1wzryjr0gzaykxq7n2yi94"; depends=[ggplot2 hwriter plotly S4Vectors shiny SummarizedExperiment survival survminer UpSetR]; }; - joda = derive2 { name="joda"; version="1.29.0"; sha256="0n76l7mrkqrsvjq67hp9am3b6ixi2v9vz7hppj36y37r02myhdlb"; depends=[bgmm RBGL]; }; - karyoploteR = derive2 { name="karyoploteR"; version="1.7.17"; sha256="1ks87kkw12gr4598rpq262axaszk4kppm5dhs4hjhy0gkwlm4lhh"; depends=[bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors]; }; - kebabs = derive2 { name="kebabs"; version="1.15.2"; sha256="1d08ad2cbrd77qlgmf3y6frya8g5kn8x9k7paabch1fxpzx4sj2g"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; }; - keggorthology = derive2 { name="keggorthology"; version="2.33.0"; sha256="11a1d08pycj99xzhwblgrjwl6idm6l90i0ya1c0q0bwmaiyqqbwp"; depends=[AnnotationDbi DBI graph hgu95av2_db]; }; - kimod = derive2 { name="kimod"; version="1.9.0"; sha256="1q2ndbpw13c9a6g5vs29w5zzrw3ac5y5rjnndw660xljfphid6x4"; depends=[Biobase cluster]; }; - kissDE = derive2 { name="kissDE"; version="1.1.3"; sha256="0gm63ixcr3gfg64bg253n9vp1gasmdg3xpb4i27gq7njsx7hs6bw"; depends=[aod Biobase DESeq2 doParallel DSS foreach ggplot2 gplots matrixStats]; }; - kmknn = derive2 { name="kmknn"; version="0.99.16"; sha256="14gvgdz4gvpv5bvr3l7rbn356cqvg3nqq7vcavgyd7bqsvk6mmg3"; depends=[BiocParallel DelayedArray Rcpp]; }; - lapmix = derive2 { name="lapmix"; version="1.47.0"; sha256="08qj6i6y42ax82j29maf89zs0k03iv6p30v1zlvgixfh1p86ffk4"; depends=[Biobase]; }; - ldblock = derive2 { name="ldblock"; version="1.11.1"; sha256="0z53xkh2khlfsnvr0nqsw8k6s375ba2y5a3njbr9qnif3r0846km"; depends=[BiocGenerics erma GenomeInfoDb GenomicFiles GO_db Homo_sapiens Matrix Rsamtools snpStats VariantAnnotation]; }; - les = derive2 { name="les"; version="1.31.0"; sha256="11ad0v5j31s8kcg4572ga4znnpx9ry83m994bqbk3h51cb48pzm8"; depends=[boot fdrtool gplots RColorBrewer]; }; - levi = derive2 { name="levi"; version="0.99.13"; sha256="0n1sl3l7xdp346jz5s6xgfmdy0i71k05khkjygkp0yqnlnapd48z"; depends=[colorspace dplyr DT ggplot2 httr igraph knitr RColorBrewer Rcpp reshape2 shiny shinydashboard shinyjs testthat xml2]; }; - lfa = derive2 { name="lfa"; version="1.11.0"; sha256="1vww3lfzb3kx2hp1cm48vg1rmnazgklz1qz1y36yydg53lbl8igi"; depends=[corpcor]; }; - limma = derive2 { name="limma"; version="3.37.10"; sha256="16jdx417iahrvai0p32qaf6cgknb2pc7bjas5ba4brd2p255sn8i"; depends=[]; }; - limmaGUI = derive2 { name="limmaGUI"; version="1.57.1"; sha256="09dykl3gd231j0xi45j23mv0p9vk0xdhyjls1z5026vclnv6037s"; depends=[limma R2HTML tkrplot xtable]; }; - lmdme = derive2 { name="lmdme"; version="1.23.0"; sha256="0192ffh3qmqx31d67zxr8sg7qvwd4wmcgzxq44w9sflb947sn8ds"; depends=[limma pls stemHypoxia]; }; - loci2path = derive2 { name="loci2path"; version="1.1.1"; sha256="1mgnx1dji2dc3jd9biv4bs5f8sgpkxzk6mwsfivfbjll9m7hprb7"; depends=[BiocParallel data_table GenomicRanges pheatmap RColorBrewer S4Vectors wordcloud]; }; - logicFS = derive2 { name="logicFS"; version="2.1.18"; sha256="14jdnjlgsgbciahljmp8wb5zn3dbqy2r3pywbn2iqqx628hl0li6"; depends=[LogicReg mcbiopi survival]; }; - logitT = derive2 { name="logitT"; version="1.39.0"; sha256="0ynd7h26ask2i15cxikx9igcm9cdmmihg561l1dv3m9zw84s6mvb"; depends=[affy]; }; - lol = derive2 { name="lol"; version="1.29.0"; sha256="050i433xkj365q7k5i7gw07z8li29myd3zgavjg14p9lkdcwia0w"; depends=[Matrix penalized]; }; - lpNet = derive2 { name="lpNet"; version="2.13.0"; sha256="1k94rsji8p9ri8mvs6xc23dm4fq4pxcd9323c6jllq9bdljxffkp"; depends=[lpSolve nem]; }; - lpsymphony = derive2 { name="lpsymphony"; version="1.9.0"; sha256="1lsxg37yc6ddnw13dfg79yy7gz0ppv5mp92cvxc8pyh7x4m4mbaq"; depends=[]; }; - lumi = derive2 { name="lumi"; version="2.33.0"; sha256="1i192shbsczsnc7j6z1hqks6bsxq4rbkfkxbb99y77m7xzzw642i"; depends=[affy annotate AnnotationDbi Biobase DBI GenomicFeatures GenomicRanges KernSmooth lattice MASS methylumi mgcv nleqslv preprocessCore RSQLite]; }; - mAPKL = derive2 { name="mAPKL"; version="1.11.0"; sha256="093kg8mildsmq7w6xa0ml86m8lyn00rafz3q3p9adw6i2x3lpm1b"; depends=[AnnotationDbi apcluster Biobase clusterSim e1071 igraph limma multtest parmigene reactome_db]; }; - mBPCR = derive2 { name="mBPCR"; version="1.35.0"; sha256="1nyzymd036biskr5b5gpz8z14mqjsxrbj2mn0sv9vp22lkcj0ls3"; depends=[Biobase oligoClasses SNPchip]; }; - mCSEA = derive2 { name="mCSEA"; version="1.1.1"; sha256="1fj53j42p62rr1chyb22wvqd25iqd1cwgw1bdgdzpx8n0d9lh64d"; depends=[fgsea GenomicFeatures GenomicRanges ggplot2 Gviz Homo_sapiens IRanges limma mCSEAdata S4Vectors SummarizedExperiment]; }; - mQTL_NMR = derive2 { name="mQTL.NMR"; version="1.15.0"; sha256="1xmhzllrj06g33pa1yq4mkg9sg8dhi1fz4239763pnid8l2jz40y"; depends=[MASS outliers qtl]; }; - maCorrPlot = derive2 { name="maCorrPlot"; version="1.51.0"; sha256="0hj93i05fqjx03c7lbdk81985v1qyy89yjwqjd75pqiy4jx2yy8f"; depends=[lattice]; }; - maPredictDSC = derive2 { name="maPredictDSC"; version="1.19.0"; sha256="1hn35cgd9571b5vz3wv76lhg2hr77kl1s6r6nmpnjph4asqhj7yg"; depends=[affy AnnotationDbi caret class e1071 gcrma hgu133plus2_db limma LungCancerACvsSCCGEO MASS ROC ROCR]; }; - maSigPro = derive2 { name="maSigPro"; version="1.53.0"; sha256="0gf80ff0jhag6mj6r888ivla5fccrdg63d7wh1g322ygp5b27h4s"; depends=[Biobase MASS mclust venn]; }; - maanova = derive2 { name="maanova"; version="1.51.0"; sha256="0az1jxfmjjpz3aqb5hvxpw912rh188b6gf02jj3q4v294131rqw4"; depends=[Biobase]; }; - macat = derive2 { name="macat"; version="1.55.3"; sha256="0ywngyddagavml8fyr3m2g9aic1bvy49r3mw8kbx1gy4mcqp0q9a"; depends=[annotate Biobase]; }; - made4 = derive2 { name="made4"; version="1.55.2"; sha256="16r6dsg0ayj26xmblzlwmp93jhw8j1b7cv2z372id2cy1girfdxs"; depends=[ade4 gplots RColorBrewer scatterplot3d]; }; - maftools = derive2 { name="maftools"; version="1.7.51"; sha256="1gvnbcyipjl13yj6yix693d6wibkamwqnmh2zds31hlbj0m2f09a"; depends=[Biostrings BSgenome cometExactTest ComplexHeatmap cowplot data_table ggplot2 ggrepel gridExtra mclust NMF RColorBrewer rjson survival wordcloud]; }; - maigesPack = derive2 { name="maigesPack"; version="1.45.0"; sha256="04ihpaqpkimf5k2j8hf2zwjqm6s75nkr1bn8gsvg21m88gajsh3x"; depends=[convert graph limma marray]; }; - makecdfenv = derive2 { name="makecdfenv"; version="1.57.0"; sha256="1v9a3r9gxijglxyhjb52jqm6p9vqkn549cim9zbw6mhngn2cqnzs"; depends=[affy affyio Biobase zlibbioc]; }; - manta = derive2 { name="manta"; version="1.27.2"; sha256="15hqw96xpprmq38f0gq50ik6ynqk6k51fp3gxcsy1qbpk9kp89jx"; depends=[caroline edgeR Hmisc]; }; - mapscape = derive2 { name="mapscape"; version="1.5.1"; sha256="1aqxpwz9a87y5kfxnz98axzc7q7d59qkw61jnj5sq9qv2s565q5v"; depends=[base64enc htmlwidgets jsonlite stringr]; }; - marray = derive2 { name="marray"; version="1.59.0"; sha256="01kgc79bhg5yg1zkglkpm85zrhm3dl5j63hvxbll3xsrrmy4bhs9"; depends=[limma]; }; - martini = derive2 { name="martini"; version="1.1.0"; sha256="1aj39flz18cnl9042hqlnqzyq6ff9j4dl5b2fm29y150s0j2wz5p"; depends=[igraph Matrix Rcpp RcppEigen Rgin S4Vectors snpStats]; }; - maser = derive2 { name="maser"; version="0.99.16"; sha256="12dchpcxjj3bc4qz0viqxg20c1yv42830l8jc38k3nx90iafs93g"; depends=[BiocGenerics data_table dplyr DT GenomeInfoDb GenomicRanges ggplot2 Gviz IRanges reshape2 rtracklayer]; }; - maskBAD = derive2 { name="maskBAD"; version="1.25.0"; sha256="09g28yd1jwxrvqh59lbcnni8ba1kk0gkgcxb2x7s9m35nx8sdr04"; depends=[affy gcrma]; }; - massiR = derive2 { name="massiR"; version="1.17.0"; sha256="0gf0j965ssrawvyx4i3mq5xrwbjy73vplig3d5518425l38g3ajp"; depends=[Biobase cluster diptest gplots]; }; - matchBox = derive2 { name="matchBox"; version="1.23.1"; sha256="134bv5pplxb2vg75wwb6x7b0mi5qscidrz9xpnf3wfk446mvpzyd"; depends=[]; }; - matter = derive2 { name="matter"; version="1.7.6"; sha256="029qb75k8ps0d979wrvv99666dn6513mhk26x7s0ahj5b75iyymk"; depends=[biglm BiocGenerics digest irlba]; }; - mcaGUI = derive2 { name="mcaGUI"; version="1.29.1"; sha256="0klxp5g2s7c6k93imdkc9dxvzzvb89d5jf7x7p7v0mmsm6rbhg95"; depends=[bpca foreign gWidgets gWidgetsRGtk2 lattice MASS OTUbase proto vegan]; }; - mdgsa = derive2 { name="mdgsa"; version="1.13.1"; sha256="06p6dfffc7h80wzsypq1xk80q1ilzqpjxrwmvi70sdqv9fc9ac17"; depends=[AnnotationDbi cluster DBI GO_db KEGG_db Matrix]; }; - mdp = derive2 { name="mdp"; version="1.1.0"; sha256="0a5r860nywkd35h16vsgqqj0iin0ldbra0b8cs1ql2bwmdjccl7i"; depends=[ggplot2]; }; - mdqc = derive2 { name="mdqc"; version="1.43.0"; sha256="1h0pk6amx5vj9zxxwa3aydhnph0cn2qcibz7xk5whpr3fqrzk1b4"; depends=[cluster MASS]; }; - meshes = derive2 { name="meshes"; version="1.7.2"; sha256="03zhlaz7z6z6z9k4c0apqa871g1z5597szk7zq9vsdp210bbws7y"; depends=[AnnotationDbi DOSE enrichplot GOSemSim MeSH_db rvcheck]; }; - meshr = derive2 { name="meshr"; version="1.17.2"; sha256="07y38icgvdncfqw4n4dmigwgl4dwwxmxypwi2rzd586m1wb3diy6"; depends=[BiocGenerics Category cummeRbund fdrtool MeSH_Aca_eg_db MeSH_AOR_db MeSH_Bsu_168_eg_db MeSH_db MeSH_Hsa_eg_db MeSH_PCR_db MeSH_Syn_eg_db MeSHDbi org_Hs_eg_db RSQLite S4Vectors]; }; - messina = derive2 { name="messina"; version="1.17.0"; sha256="0zllyp3azgv0yyx0hdcad1bv41shqvkyw143nb7nc79x34zgm11m"; depends=[foreach ggplot2 plyr Rcpp survival]; }; - metaArray = derive2 { name="metaArray"; version="1.59.0"; sha256="0xp7qnvgj9qa83lwv6dcbs3fw41jyp1lsw17n87jr9x2gnz9v2ly"; depends=[Biobase MergeMaid]; }; - metaCCA = derive2 { name="metaCCA"; version="1.9.0"; sha256="1i8qgq7qxngkrgibwqh8c6yigpi5w7bf1jivpmkk1swzlsa620y8"; depends=[]; }; - metaMS = derive2 { name="metaMS"; version="1.17.0"; sha256="194pw7fbf9nr0wxq7fbg4j45lh36va6ypr62aj8zc6l2hh42d2b5"; depends=[BiocGenerics CAMERA Matrix robustbase xcms]; }; - metaSeq = derive2 { name="metaSeq"; version="1.21.0"; sha256="0fcwfk0vz0pa5pykxlf4g8zg5iyd40qncq40kh8zydymkkz7njqg"; depends=[NOISeq Rcpp snow]; }; - metabomxtr = derive2 { name="metabomxtr"; version="1.15.0"; sha256="09mx5a26maf4zm670r17xs9bfyn7xz6hhyjh9bbbkm4lf0fyph22"; depends=[Biobase BiocParallel Formula ggplot2 multtest optimx plyr]; }; - metagene = derive2 { name="metagene"; version="2.13.3"; sha256="19g9nh13b8wr4kbpr57vhnm2237zzx2iv4pvsvabsswr9ls09pfl"; depends=[BiocParallel data_table DBChIP EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats muStat purrr R6 Rsamtools rtracklayer stringr]; }; - metagenomeFeatures = derive2 { name="metagenomeFeatures"; version="2.1.0"; sha256="1dbw7cvyrh4w8cjqdvslph3lbrxxyxnpc71l69myasf4w1hwwsjb"; depends=[ape Biobase Biostrings dbplyr DECIPHER dplyr lattice lazyeval magrittr purrr RSQLite S4Vectors stringr]; }; - metagenomeSeq = derive2 { name="metagenomeSeq"; version="1.23.1"; sha256="141hm3dbbcpjy743gwcn0ajvkb6af4g4cxqq7lads1zxhfpl6fq4"; depends=[Biobase foreach glmnet gplots limma Matrix matrixStats RColorBrewer]; }; - metahdep = derive2 { name="metahdep"; version="1.39.0"; sha256="1zm6j0i9myn4q4lwc2almy6d6khg1kqb8ij11cr5dhxmwx444ma8"; depends=[]; }; - metaseqR = derive2 { name="metaseqR"; version="1.21.2"; sha256="1vyjn9v0z3wx69ncqp2gzswwz6b47aarqf3dk1hpzwhrr30sqli8"; depends=[baySeq biomaRt brew corrplot DESeq EDASeq edgeR gplots limma log4r NBPSeq NOISeq qvalue rjson vsn]; }; - metavizr = derive2 { name="metavizr"; version="1.5.1"; sha256="1wvdzqvjlr2ygxkq2pvkfw5xdr09yafmalf4k5ya7mc70cg6w7nb"; depends=[Biobase data_table digest epivizr epivizrData epivizrServer epivizrStandalone GenomeInfoDb httr metagenomeSeq phyloseq vegan]; }; - methInheritSim = derive2 { name="methInheritSim"; version="1.3.1"; sha256="0grqjwv75yd0v3ji99cwnbbgp6s488kyh5d3kan1x88wqy6p00cw"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges methylKit msm S4Vectors]; }; - methVisual = derive2 { name="methVisual"; version="1.33.0"; sha256="0pyj09zkan51w6w0wnkg3ww49hlwqarl5sfw7wrbarfdvxvlyqpa"; depends=[Biostrings ca gridBase gsubfn IRanges plotrix sqldf]; }; - methimpute = derive2 { name="methimpute"; version="1.3.2"; sha256="1nd5ay6ymf0hchv1q62qpj3by4h7c83x59b8d72w1hrv5xcgqhi6"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges ggplot2 IRanges minpack_lm Rcpp reshape2]; }; - methyAnalysis = derive2 { name="methyAnalysis"; version="1.23.0"; sha256="1fhhk2yqcq2rh30369izn32w7jzcyzhlwaa5wcds4mb2caiyr4kj"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges genoset Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; }; - methylGSA = derive2 { name="methylGSA"; version="0.99.16"; sha256="1jxwys6dlhqs8fq9f8vw63d5llzcbvyyczw2qgi94qwispb5s5bi"; depends=[AnnotationDbi clusterProfiler ggplot2 GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 missMethyl org_Hs_eg_db reactome_db RobustRankAggreg stringr]; }; - methylInheritance = derive2 { name="methylInheritance"; version="1.5.2"; sha256="0vvwzxabm5xz94zfvi1yjw43d8asmv7wmcngjx571qphcl1hlyab"; depends=[BiocParallel GenomicRanges ggplot2 gridExtra IRanges methylKit rebus S4Vectors]; }; - methylKit = derive2 { name="methylKit"; version="1.7.10"; sha256="1m8cb5w8rhcnsdh01ahcr16hnjpvzb77albxlbqcprhndvd7cxgh"; depends=[data_table emdbook fastseg GenomeInfoDb GenomicRanges gtools IRanges KernSmooth limma mclust qvalue R_utils Rcpp Rhtslib Rsamtools rtracklayer S4Vectors zlibbioc]; }; - methylMnM = derive2 { name="methylMnM"; version="1.19.1"; sha256="1h0ydwljbrdyb5vn688303zp61np5a0zaah974g6v8mgs4izdqvk"; depends=[edgeR statmod]; }; - methylPipe = derive2 { name="methylPipe"; version="1.15.0"; sha256="0v00cc5jiw0n6nxq5nvbmaknbanp0gbzk8d3p5igfj3pva6zvpjy"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; }; - methylumi = derive2 { name="methylumi"; version="2.27.0"; sha256="1carjnp9fbldzyms0cnc5lv92y4cxgzri9wxd5m4svrdfagnj75z"; depends=[annotate AnnotationDbi Biobase BiocGenerics FDb_InfiniumMethylation_hg19 genefilter GenomeInfoDb GenomicRanges ggplot2 illuminaio IRanges lattice matrixStats minfi reshape2 S4Vectors scales SummarizedExperiment]; }; - methyvim = derive2 { name="methyvim"; version="1.3.1"; sha256="1jycwzqf7147pcdfais5n876x9w61xsr41jq2kgqhnmxz05rhwkb"; depends=[BiocGenerics BiocParallel bumphunter cluster doFuture dplyr future GenomeInfoDb ggplot2 ggsci gridExtra gtools IRanges limma minfi S4Vectors SummarizedExperiment superheat tmle]; }; - mfa = derive2 { name="mfa"; version="1.3.1"; sha256="1nn35lxbq6dqsgc21pkbl7x803v385n360wnjv1qxjs9b8w8xqjk"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; }; - mgsa = derive2 { name="mgsa"; version="1.29.0"; sha256="1vhp23qx5vzaqmn06vngfd9c3y5ygizc6hhx1ccv7m5x4lz2a4jg"; depends=[gplots]; }; - miRBaseConverter = derive2 { name="miRBaseConverter"; version="1.5.6"; sha256="0r6cgvslm1lsg1mhrxzdghglk55zh7f3n1lhk136hk5nqh58nhk9"; depends=[]; }; - miRLAB = derive2 { name="miRLAB"; version="1.11.1"; sha256="18bqx7gxx3hs9mfvgidnngf57grlxnapq8axp2cyhvbvspwaabb6"; depends=[Category ctc dplyr energy entropy glmnet GOstats gplots heatmap_plus Hmisc httr impute InvariantCausalPrediction limma org_Hs_eg_db pcalg RCurl Roleswitch stringr SummarizedExperiment TCGAbiolinks]; }; - miRNAmeConverter = derive2 { name="miRNAmeConverter"; version="1.9.0"; sha256="116zkdwspzb0rp6yhz9bjfarbi2mvvlngsb53zs1js59kzsrw06a"; depends=[AnnotationDbi DBI miRBaseVersions_db reshape2]; }; - miRNApath = derive2 { name="miRNApath"; version="1.41.0"; sha256="1hndq9aq3r3mci5j9ysfkb8kdw2zp7bbi3j7qfcdchm9q3g78rya"; depends=[]; }; - miRNAtap = derive2 { name="miRNAtap"; version="1.15.1"; sha256="030kl4i7m1apxb4r3r3p2fbq2429zcm2aja96vdr6x2vmrna3nr5"; depends=[AnnotationDbi DBI plyr RSQLite sqldf stringr]; }; - miRSM = derive2 { name="miRSM"; version="0.99.28"; sha256="04liw858ihv2ljg4w14gj0mrkfrsycnfg0k0pp041pz158d4wn78"; depends=[BiBitR BicARE biclust Biobase dynamicTreeCut fabia flashClust GFA GSEABase iBBiG igraph isa2 linkcomm MCL miRsponge NMF PMA Rcpp rqubic runibic s4vd SummarizedExperiment WGCNA]; }; - miRcomp = derive2 { name="miRcomp"; version="1.11.1"; sha256="1am0pxrdp297z12wbg1nlf7lbc37d9v01nb6hp4zw5gdkf3rfagd"; depends=[Biobase KernSmooth miRcompData]; }; - miRmine = derive2 { name="miRmine"; version="1.3.0"; sha256="10j2f6ldxxf78aps1ygvdzpvga5smb4xv9m4mhgbhl9qfbkqvkd1"; depends=[SummarizedExperiment]; }; - miRsponge = derive2 { name="miRsponge"; version="1.7.6"; sha256="1isl9mi8bqwxxsm1miv7bh0xahsg3lb22q0lyj35ij0bhkdr1sw7"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL Rcpp ReactomePA survival varhandle]; }; - microRNA = derive2 { name="microRNA"; version="1.39.0"; sha256="0c1dvhp81kxv1kxr77rl7wgq5wr92gj37m8qsgn0b40zs5b1b49i"; depends=[Biostrings]; }; - microbiome = derive2 { name="microbiome"; version="1.3.3"; sha256="17gnyy8qwxjg86i8nx4mpyhrsy8mkmzyhgmxfngkvlyb3cqqvbdl"; depends=[dplyr ggplot2 phyloseq reshape2 tidyr vegan]; }; - mimager = derive2 { name="mimager"; version="1.5.3"; sha256="1zpp71qjws6qm1cdl7s057mgijbsqhahklaq0flc4izvjn7awkrs"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; }; - minet = derive2 { name="minet"; version="3.39.0"; sha256="0lbga3id91swx8vnfcw4vgwq5bypr3a110il3a84kwr9naq9vnvi"; depends=[infotheo]; }; - minfi = derive2 { name="minfi"; version="1.27.8"; sha256="0vizm0alsczrjqryzhl7za6n3gc6dmr3z6h2dihn31fc74z0lqyn"; depends=[beanplot Biobase BiocGenerics BiocParallel Biostrings bumphunter data_table DelayedArray DelayedMatrixStats genefilter GenomeInfoDb GenomicRanges GEOquery HDF5Array illuminaio IRanges lattice limma MASS mclust nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; }; - mirIntegrator = derive2 { name="mirIntegrator"; version="1.11.0"; sha256="1f6xi68rgc5xgmcpv25lfz9khdwh94k59a2r2lj81y7h1fg3asck"; depends=[AnnotationDbi ggplot2 graph org_Hs_eg_db Rgraphviz ROntoTools]; }; - missMethyl = derive2 { name="missMethyl"; version="1.15.5"; sha256="0p2mgq5njh830vhi2najh3slzhqz56fzi947xvrbyz5crqn8aq02"; depends=[AnnotationDbi BiasedUrn GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest limma methylumi minfi org_Hs_eg_db ruv statmod stringr]; }; - missRows = derive2 { name="missRows"; version="1.1.1"; sha256="09s34cd47hylqwi4qmcnba4qmwiz0n1n3z0m7pabqmw7ysn20mi8"; depends=[ggplot2 gtools MultiAssayExperiment plyr S4Vectors]; }; - mitoODE = derive2 { name="mitoODE"; version="1.19.0"; sha256="1qkhf4y5cnwxv39lacdph3r030d9d4jc76lzgg9gl7gyk9801rhh"; depends=[KernSmooth MASS minpack_lm mitoODEdata]; }; - mixOmics = derive2 { name="mixOmics"; version="6.4.6"; sha256="1id5zcqqdzh72k41sc267fi7cbqyzlfwb8758xnxibgp9a3mjqci"; depends=[corpcor dplyr ellipse ggplot2 gridExtra igraph lattice MASS matrixStats rARPACK RColorBrewer reshape2 tidyr]; }; - mlm4omics = derive2 { name="mlm4omics"; version="0.99.22"; sha256="0yrz6cg6w8nsv5lkpzs43jla0wgmvb4bv66q5wb5f3p38fvym4c1"; depends=[BH ggplot2 MASS Matrix Rcpp RcppEigen rstan rstantools StanHeaders]; }; - mogsa = derive2 { name="mogsa"; version="1.15.0"; sha256="02a9p3awa8lix75ghw8x0nm9dzccg57ydyg1hr5kxx3bq51lvj3v"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; }; - monocle = derive2 { name="monocle"; version="2.9.0"; sha256="15m4221g6m5r8w3af9qk8jxqnqjjj31xvfcxi2n7dhfvqw4f35a1"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; }; - mosaics = derive2 { name="mosaics"; version="2.19.0"; sha256="1d5b7rhxzzzlyapfq4fmml8k41fpha2bw398jzq6xsk52wfjjbiv"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; }; - motifRG = derive2 { name="motifRG"; version="1.25.0"; sha256="0ramq5yk9ri04waj16vgcvr8jgd93afn2q8yr4avzaq9a1klsh7a"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 IRanges seqLogo XVector]; }; - motifStack = derive2 { name="motifStack"; version="1.25.3"; sha256="1qvillm4aflyws82gi6sk6wd8f0zpnm0srgv420l0plmiv9v8gaj"; depends=[ade4 Biostrings grImport htmlwidgets MotIV scales XML]; }; - motifbreakR = derive2 { name="motifbreakR"; version="1.11.1"; sha256="1mpwxh7yigxplm3pczmqczqbs9nbfz1f5jpl4j5wkgcxh634s42l"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges grImport Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr TFMPvalue VariantAnnotation]; }; - motifcounter = derive2 { name="motifcounter"; version="1.5.5"; sha256="1zf3sgl3d8wazbd673bmns3fx5r3ppbzlgrms3z2svzh9997z4gc"; depends=[Biostrings]; }; - motifmatchr = derive2 { name="motifmatchr"; version="1.3.0"; sha256="0p1v2nbxw889ck8jsvw0qkxqxnpzqvha2k64r9f8xg2d06pfr7ya"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment TFBSTools]; }; - mpra = derive2 { name="mpra"; version="1.3.0"; sha256="1bh73npgphq2xanx9sc9yz0dpcilcvwnwz030fpy2mvaipnrqpjc"; depends=[BiocGenerics limma S4Vectors scales statmod SummarizedExperiment]; }; - msPurity = derive2 { name="msPurity"; version="1.7.2"; sha256="018gawlqn1syhhqmg9dbdzxg2knrp4vwqpbbazdayxk8adsr4ak2"; depends=[DBI doSNOW fastcluster foreach ggplot2 mzR plyr Rcpp reshape2 RSQLite stringr]; }; - msa = derive2 { name="msa"; version="1.13.1"; sha256="0fcs489fmx6vhdmqmksqwlakg1a9cn44s9mbdcjqkx15lhcqaa9r"; depends=[BiocGenerics Biostrings IRanges Rcpp S4Vectors]; }; - msgbsR = derive2 { name="msgbsR"; version="1.5.0"; sha256="1hlpg3zd4w514f1p0c36jsgg0dlirmnw1fq5l734yabgbf6zkv3l"; depends=[BSgenome easyRNASeq edgeR GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr R_utils Rsamtools S4Vectors SummarizedExperiment]; }; - msmsEDA = derive2 { name="msmsEDA"; version="1.19.0"; sha256="0xni6k9ij49zzxlhnbhn6v0nij49m26cxyv6xdlwfp0jh37390gk"; depends=[gplots MASS MSnbase RColorBrewer]; }; - msmsTests = derive2 { name="msmsTests"; version="1.19.0"; sha256="1kz9s9dc4rxz77k743ql6j84h2hv8fkbwl7707gqfs5789gj7w41"; depends=[edgeR msmsEDA MSnbase qvalue]; }; - multiClust = derive2 { name="multiClust"; version="1.11.6"; sha256="1g5zxy0x3fipmdiw3dkwzjnrni9r7rcqc71jilq0jfr8z52h5kik"; depends=[amap cluster ctc dendextend mclust survival]; }; - multiHiCcompare = derive2 { name="multiHiCcompare"; version="0.99.46"; sha256="0f2h2xdprarri4x19jvac9irm7gba2x1dhaab1r6pl6hkkmasi01"; depends=[BiocParallel BLMA data_table dplyr edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges HiCcompare metap pbapply pheatmap qqman]; }; - multiMiR = derive2 { name="multiMiR"; version="1.3.2"; sha256="19my81w8q1zva7p1k7wbjr69x3bmqwwkz2phmfmb6gaa2361gn6l"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; }; - multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.5.1"; sha256="0zjp90z00dmd6k96ffmb1iljzf22asij7m90lj764z2xskii9nz0"; depends=[doParallel foreach SummarizedExperiment]; }; - multiscan = derive2 { name="multiscan"; version="1.41.0"; sha256="08s4rpikrjzhip9zpb5dc0fi98hj304qlcvxm1agi881awlvpkig"; depends=[Biobase]; }; - multtest = derive2 { name="multtest"; version="2.37.0"; sha256="1xlizjdzvxn0i9gs1jpkb07fkkx1prrr1v5n6kfvff9izh40cx6j"; depends=[Biobase BiocGenerics MASS survival]; }; - muscle = derive2 { name="muscle"; version="3.23.0"; sha256="110wvrf2isiw2by15vkxsds5sxy68l1vav8fq55f5f8lx77450yp"; depends=[Biostrings]; }; - mygene = derive2 { name="mygene"; version="1.17.2"; sha256="1fi43b84q73kfyq6dincnkx7glhzxw8c42vy63k2j19dqygzc0k7"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; }; - myvariant = derive2 { name="myvariant"; version="1.11.1"; sha256="0p4wan3cwmag2nnxza6zqc3rvidgcg6xdk3aqp1d40v1vyxd4j8c"; depends=[GenomeInfoDb Hmisc httr jsonlite magrittr plyr S4Vectors VariantAnnotation]; }; - mzID = derive2 { name="mzID"; version="1.19.0"; sha256="0czwvilzp756qfyjzf6x4wskg7w35zwl3df3md4p03v95c1ynbdk"; depends=[doParallel foreach iterators plyr ProtGenerics XML]; }; - mzR = derive2 { name="mzR"; version="2.15.5"; sha256="1kbnxini43zw1mvmbv15ms1na4d2piirzqq79w3d45a4dsdyjkkq"; depends=[Biobase BiocGenerics ncdf4 ProtGenerics Rcpp Rhdf5lib zlibbioc]; }; - ncdfFlow = derive2 { name="ncdfFlow"; version="2.27.0"; sha256="0m29ncb8i4xndialy9x8iagyvamiacq6jvdbl8v9m0f18ygv9y81"; depends=[BH Biobase BiocGenerics flowCore flowViz Rcpp RcppArmadillo Rhdf5lib zlibbioc]; }; - ndexr = derive2 { name="ndexr"; version="1.3.1"; sha256="1nann1ndc6zy04inb4ag7axi5hl407xr7v283lad1gvqmhrjnzii"; depends=[httr igraph jsonlite plyr tidyr]; }; - nem = derive2 { name="nem"; version="2.55.0"; sha256="0y0yp1bq3ixkxdqjx4lbx5h1yfx2vsia2zpqnjjvp9hzqjddvvbl"; depends=[boot e1071 graph limma plotrix RBGL RColorBrewer Rgraphviz statmod]; }; - netReg = derive2 { name="netReg"; version="1.5.1"; sha256="0zw8q4dy893jdsjmb3zhy66g8y0w6m9iqvf360bhrnr5kzdfi8ac"; depends=[Rcpp RcppArmadillo]; }; - netSmooth = derive2 { name="netSmooth"; version="1.1.1"; sha256="0pfqn3wmkmh4wvyy72pvy4f0z3h9vnpnnqp9l1cwgkpwwzlqsk9z"; depends=[cluster clusterExperiment data_table entropy Matrix scater SingleCellExperiment SummarizedExperiment]; }; - netbenchmark = derive2 { name="netbenchmark"; version="1.13.0"; sha256="0ssagk6gwdbrqwc037y05xjbnaiv7k5mq8rmwmx6y3d74jwwpb3d"; depends=[c3net corpcor fdrtool GeneNet GENIE3 grndata Matrix minet PCIT pracma Rcpp]; }; - netbiov = derive2 { name="netbiov"; version="1.15.0"; sha256="1njiy14g8pf4yps4npwsm4x883qgixwvv0f3p2pb69p9r4kg0phy"; depends=[igraph]; }; - nethet = derive2 { name="nethet"; version="1.13.1"; sha256="1rsgm1war7y5hjxcihjjfnha52jphlh3sayh1wmxwxn56cqfnsdr"; depends=[CompQuadForm GeneNet ggm ggplot2 glasso glmnet GSA huge ICSNP limma mclust multtest mvtnorm network parcor]; }; - netprioR = derive2 { name="netprioR"; version="1.7.0"; sha256="076b72g6b9k2zz277i6whjw49jcl6b3bmr9n652nc11d1ydwq3ic"; depends=[doParallel dplyr foreach ggplot2 gridExtra Matrix pROC sparseMVN]; }; - netresponse = derive2 { name="netresponse"; version="1.41.0"; sha256="1spzd74z279rvpw0vpw3bw19gimhcdrcxk6hgxv1w7b0nllih606"; depends=[dmt ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape2 Rgraphviz]; }; - networkBMA = derive2 { name="networkBMA"; version="2.21.0"; sha256="1gax5312r6cz4s1qxxlg8k63dlk4ja8b57c2br1q0kpcdgbwhrqr"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; }; - nnNorm = derive2 { name="nnNorm"; version="2.45.0"; sha256="0m8zcv7kyv7ll6bw599nlihmssfizivkrfm1sqr1ndjwmc8b6blp"; depends=[marray nnet]; }; - nondetects = derive2 { name="nondetects"; version="2.11.0"; sha256="0iiwvad8cb3g2a7701vci7g2qkvhc43arw4cw7zpmg46qk6yhvv0"; depends=[arm Biobase HTqPCR limma mvtnorm]; }; - normalize450K = derive2 { name="normalize450K"; version="1.9.0"; sha256="01j9gp2d7b8n30ckf61ywncw0il81lf6d0sfczr39bqdq2x2xyj3"; depends=[Biobase illuminaio quadprog]; }; - normr = derive2 { name="normr"; version="1.7.2"; sha256="16f73sigq43f5fy74zhcz9pzcvd9hra5yzq4fp5sdkhnsnjd0b02"; depends=[bamsignals GenomeInfoDb GenomicRanges IRanges qvalue Rcpp rtracklayer]; }; - npGSEA = derive2 { name="npGSEA"; version="1.17.0"; sha256="0fw33zgrp9wkchddagsd93ijkspi20d8p7yvsqspqrjy3yv6yq3i"; depends=[Biobase BiocGenerics GSEABase]; }; - nuCpos = derive2 { name="nuCpos"; version="0.99.1"; sha256="0p1nijap5a66q9ldh3mqdjg7b29wz1pfixy3zrwhmr05gar5c78y"; depends=[]; }; - nucleR = derive2 { name="nucleR"; version="2.13.1"; sha256="19y523lg3a2jb9ajqyz0qky292makxmirj9f9244n9xmcm84sm2w"; depends=[Biobase BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr Rsamtools S4Vectors ShortRead]; }; - nucleoSim = derive2 { name="nucleoSim"; version="1.9.0"; sha256="0bn8gihg4b70gmdyvn91i5adzfbkfaqcb59kv3y56dss04ss736j"; depends=[IRanges S4Vectors]; }; - occugene = derive2 { name="occugene"; version="1.41.0"; sha256="13dqbp1kaan56xqlgfdqrld0l3qwky6487mf9j0g7788yxwl1fnm"; depends=[]; }; - odseq = derive2 { name="odseq"; version="1.9.0"; sha256="0yyg4y77ch7x0f6xa10wnz8kydc2pjrrpbvdc448388acmmbpdbl"; depends=[kebabs mclust msa]; }; - oligo = derive2 { name="oligo"; version="1.45.2"; sha256="01z9jhnnnnaprpp7zcl4727wkwrhn25djb94fiw7ycb830nqnkxv"; depends=[affxparser affyio Biobase BiocGenerics Biostrings DBI ff oligoClasses preprocessCore RSQLite zlibbioc]; }; - oligoClasses = derive2 { name="oligoClasses"; version="1.43.3"; sha256="13c7hkbifylm315h4qgqbn9fv5i0742k4rmcjf72ll9wj1yqjzf9"; depends=[affyio Biobase BiocGenerics BiocManager Biostrings DBI ff foreach GenomicRanges IRanges RSQLite S4Vectors SummarizedExperiment]; }; - omicRexposome = derive2 { name="omicRexposome"; version="1.3.1"; sha256="14dqybpgj57avgsmjhf63lcy5n8r4g77idlpnblkqj0c232mpq6v"; depends=[Biobase ggplot2 ggrepel gridExtra isva limma MultiDataSet omicade4 PMA rexposome SmartSVA stringr SummarizedExperiment sva]; }; - omicade4 = derive2 { name="omicade4"; version="1.21.0"; sha256="055jnv8m9fhj2hixbc997mqv56p07azg40k8qb91mdc8fidypka6"; depends=[ade4 made4]; }; - omicplotR = derive2 { name="omicplotR"; version="1.1.4"; sha256="0d2jhnjhxl2kl8s33fl45v2yyb85gjx9api8qwhpiny4bh12rq3q"; depends=[ALDEx2 compositions knitr matrixStats rmarkdown shiny vegan zCompositions]; }; - omicsPrint = derive2 { name="omicsPrint"; version="1.1.0"; sha256="0zsx8zabz07jyfl1xj28ak6k69jfrrig38psl7qny82ydz8bnbas"; depends=[MASS matrixStats MultiAssayExperiment RaggedExperiment SummarizedExperiment]; }; - oncomix = derive2 { name="oncomix"; version="1.3.0"; sha256="0rpwkksxakhwhqvir646gj0x8b1nqsnc2cvjzvh0mlxvv4zmmc0n"; depends=[ggplot2 ggrepel mclust RColorBrewer SummarizedExperiment]; }; - oneSENSE = derive2 { name="oneSENSE"; version="1.3.1"; sha256="15790wlbw8ff752lqipmib5mq1chq1wvrrq6yj5zargdv4lffrik"; depends=[flowCore gplots plotly Rtsne scatterplot3d shiny shinyFiles webshot]; }; - onlineFDR = derive2 { name="onlineFDR"; version="0.99.7"; sha256="18naq5jfds1njalqqsi6b1hs2sld55flnv63s8yk2cnhpjcfyq47"; depends=[]; }; - ontoProc = derive2 { name="ontoProc"; version="1.3.5"; sha256="0xv0hin8khcpyj6dxnadncy62isdixjgaq8m1n8i49b0f368bgji"; depends=[AnnotationDbi Biobase ontologyIndex S4Vectors shiny]; }; - openCyto = derive2 { name="openCyto"; version="1.19.2"; sha256="0m2lalpd9hn1vn62n6lfz4kflfdq188m5vcxdjmlj7wzkxijdcmw"; depends=[Biobase BiocGenerics clue data_table flowClust flowCore flowStats flowViz flowWorkspace graph gtools ks lattice MASS ncdfFlow plyr R_utils RBGL RColorBrewer Rcpp rrcov]; }; - openPrimeR = derive2 { name="openPrimeR"; version="1.3.2"; sha256="0fc12pzp2b7ns1k039v43ns1d10k9lmww6pjrgvyxhrwdd16b9vn"; depends=[ape BiocGenerics Biostrings DECIPHER digest distr distrEx dplyr fitdistrplus foreach GenomicRanges ggplot2 Hmisc IRanges lpSolveAPI magrittr openxlsx plyr RColorBrewer reshape2 S4Vectors scales seqinr stringdist stringr tinytex uniqtag XML]; }; - openPrimeRui = derive2 { name="openPrimeRui"; version="1.3.1"; sha256="10hky16l94bx0n3r12kq8951wjcm30kgp8qciqgji563kjq9lbww"; depends=[DT openPrimeR rmarkdown shiny shinyBS shinyjs]; }; - oposSOM = derive2 { name="oposSOM"; version="1.99.0"; sha256="1k85a2ixnxzclfaw5is9myppmb3slpyd6n1jyg67y0ii6zac2aig"; depends=[ape Biobase biomaRt fastICA fdrtool igraph pixmap Rcpp RcppParallel scatterplot3d tsne]; }; - oppar = derive2 { name="oppar"; version="1.9.1"; sha256="0irzz17xd1vf5syqzr8sp2rv7076xi64mr2anwp63xfx2xh02wrp"; depends=[Biobase GSEABase GSVA]; }; - pRoloc = derive2 { name="pRoloc"; version="1.21.9"; sha256="11l2jssdrg3lz0svnjskk280xlkyzfymfhkq13517zv6jshn23gl"; depends=[Biobase BiocGenerics BiocParallel biomaRt caret class coda dendextend e1071 FNN ggplot2 gtools hexbin kernlab knitr LaplacesDemon lattice MASS mclust mixtools MLInterfaces MSnbase mvtnorm nnet plyr proxy randomForest RColorBrewer Rcpp RcppArmadillo sampling scales]; }; - pRolocGUI = derive2 { name="pRolocGUI"; version="1.15.2"; sha256="0yljbianwqb214g47s9s5s80sfiay6vxrgkzciibyr0bmn7bmrmb"; depends=[Biobase dplyr DT ggplot2 MSnbase pRoloc scales shiny]; }; - paircompviz = derive2 { name="paircompviz"; version="1.19.0"; sha256="1glli54k00gpm04p177hwgsdq352ypc7r8swbksk18j8xghk8cq4"; depends=[Rgraphviz]; }; - pandaR = derive2 { name="pandaR"; version="1.13.0"; sha256="13mv40jsclngfzcapscw0wxv67dd2ym4kkpcvy2v03z37ak3n1fk"; depends=[Biobase BiocGenerics ggplot2 hexbin igraph matrixStats plyr reshape RUnit]; }; - panelcn_mops = derive2 { name="panelcn.mops"; version="1.3.1"; sha256="13p3rrmkjv58f3hac26bxgwrknx6bhdhxkg2c4z1yxh9jny96h9a"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; - panp = derive2 { name="panp"; version="1.51.0"; sha256="1yrxsjc0r9z0nfgbc9n9p5mhqhyx7x76v7vcjah6hdv4svi78csc"; depends=[affy Biobase]; }; - parglms = derive2 { name="parglms"; version="1.13.3"; sha256="0x8j7ffz8h7303n90v27wcb71x75m7j1rq4yz59iv9fpis16yj27"; depends=[BatchJobs BiocGenerics doParallel foreach]; }; - parody = derive2 { name="parody"; version="1.39.1"; sha256="0213vnj1mbnc9zhrxidqjz5ls8nrgz7ljmz0f9hrbixn2k369ccl"; depends=[]; }; - pathRender = derive2 { name="pathRender"; version="1.49.0"; sha256="1ln36h3jy35398r92i5hm4qvcjfsmc0frpy4dpgi75ab1wgjzb1s"; depends=[AnnotationDbi cMAP graph RColorBrewer Rgraphviz]; }; - pathVar = derive2 { name="pathVar"; version="1.11.2"; sha256="1v0pia06qx995b9y4vllp844f5846877zyl587xz5026mnbr5p5l"; depends=[data_table EMT ggplot2 gridExtra Matching mclust]; }; - pathifier = derive2 { name="pathifier"; version="1.19.0"; sha256="0sazl4wi6pivvr2r098parc8j68hq8apfjb0nk6vicfisx0dqk1h"; depends=[princurve R_oo]; }; - pathprint = derive2 { name="pathprint"; version="1.11.3"; sha256="14x9i2gkra49aqnpi0xd94430nl05sw3yr85ramaxrzavm7lxvsf"; depends=[]; }; - pathview = derive2 { name="pathview"; version="1.21.2"; sha256="14021aqb36s56w9j439ydgbv2b4yk7sbsndrmyzbdxrisi6q3xyw"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; }; - paxtoolsr = derive2 { name="paxtoolsr"; version="1.15.1"; sha256="13rc66d9fyd85haylmc55irvshrfrxgny3l539ga1zq4h6bhlxz6"; depends=[httr igraph jsonlite plyr R_utils readr rJava rjson XML]; }; - pbcmc = derive2 { name="pbcmc"; version="1.9.0"; sha256="1hxhpxixl5jfpiqpwqvkfcnp2k7sw43asc5ikj6qpl4p5xrrfn0d"; depends=[Biobase BiocGenerics BiocParallel cowplot genefu ggplot2 gridExtra limma reshape2]; }; - pcaExplorer = derive2 { name="pcaExplorer"; version="2.7.6"; sha256="0dwhd5ybli05wlv8j0l639phbksm0h9g418bdq2x9f7h1vskr3z5"; depends=[AnnotationDbi biomaRt d3heatmap DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats IRanges knitr limma NMF pheatmap plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; }; - pcaGoPromoter = derive2 { name="pcaGoPromoter"; version="1.25.1"; sha256="1dfvd3bb7v5dz58icb7j802fj358waa6xs8sasz0kvlvapma9kx1"; depends=[AnnotationDbi Biostrings ellipse]; }; - pcaMethods = derive2 { name="pcaMethods"; version="1.73.1"; sha256="0vslvglp2j6zkkbjcwj66bbv683qzjnqlpa8adb8wmgc2l4a1rkv"; depends=[Biobase BiocGenerics MASS Rcpp]; }; - pcot2 = derive2 { name="pcot2"; version="1.49.0"; sha256="0ffg35602h7k904dq47sgnfyky041alnypaf3gvx7m6f8yszq46c"; depends=[amap Biobase]; }; - pcxn = derive2 { name="pcxn"; version="2.3.1"; sha256="0yp9hfbval7ind2nqa2n4nfafgbrfr4gq7hm7dkrfampp7if66j3"; depends=[pcxnData pheatmap]; }; - pdInfoBuilder = derive2 { name="pdInfoBuilder"; version="1.45.0"; sha256="15whr6rjdf75z6wg9k8zsyvfn08vidimzx2rw6ki1zmbh0fz8in6"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; }; - pepStat = derive2 { name="pepStat"; version="1.15.0"; sha256="08dpwiphw9s8dafy4m946jxi1jfyc3lzzdg4h0ax7d6knzq0za73"; depends=[Biobase data_table fields GenomicRanges ggplot2 IRanges limma plyr]; }; - pepXMLTab = derive2 { name="pepXMLTab"; version="1.15.0"; sha256="1bwp82zvg65yrhlx1xk2jci9fqsgc83h1x7124ci2afzlvx56ms5"; depends=[XML]; }; - perturbatr = derive2 { name="perturbatr"; version="1.1.0"; sha256="0cwk2f0bm9vlgdngb9blcpcwg2gl8ik0rdx0a6i36qzdd256qk91"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; }; - pgca = derive2 { name="pgca"; version="1.5.1"; sha256="11la42gqiqxwlms84lc1dsvpys3bmrzwz5d8vcx4xwnl9pc3lqhh"; depends=[]; }; - phantasus = derive2 { name="phantasus"; version="1.1.5"; sha256="148mxhmc0qymjdkx64ji4karaazx89vmwmyrrk8d1g7m3lj1qpvl"; depends=[assertthat Biobase ccaPP fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix Matrix_utils opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; }; - phenoTest = derive2 { name="phenoTest"; version="1.29.0"; sha256="10mw83ivb99ipndjjc5r69wpsanfvzx01bfpzhq5pygjzhl6m8jb"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach HTSanalyzeR limma mgcv SNPchip survival xtable]; }; - phenopath = derive2 { name="phenopath"; version="1.5.0"; sha256="05a1d7apyhg4d4nahl97i0794fji6dnnd454wfww89adjx68nfnc"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; }; - philr = derive2 { name="philr"; version="1.7.3"; sha256="1nzn6xv5kkm1babdimhvcjd5ql58hhj772asjd1i6r4qbidzyjfd"; depends=[ape ggplot2 ggtree phangorn tidyr]; }; - phosphonormalizer = derive2 { name="phosphonormalizer"; version="1.5.1"; sha256="1bvbjm42nr1mjxixbcd39g4qz4171qrb7x7ssz5jkrf8y3j26yxa"; depends=[matrixStats plyr]; }; - phyloseq = derive2 { name="phyloseq"; version="1.25.3"; sha256="081f1fwkda6am9i64y2zq8z6xiz9z7hfz3agrlxkfrrfc455ch65"; depends=[ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data_table foreach ggplot2 igraph multtest plyr reshape2 scales vegan]; }; - piano = derive2 { name="piano"; version="1.21.1"; sha256="1adwsk3vkdg3695yjfw6sip1ww8zfd90dmmbzsf1kryidlkl60nz"; depends=[Biobase BiocGenerics fgsea gplots igraph marray relations]; }; - pickgene = derive2 { name="pickgene"; version="1.53.0"; sha256="1nklcgm3wryljq22hc3fcja6x2kwa9bilp76gzhy8zpj8swwjszl"; depends=[MASS]; }; - pint = derive2 { name="pint"; version="1.31.0"; sha256="10kwlp947h03w8xqcs9qcyp21wvx60sl47k2cnbrdhva3wf35vp3"; depends=[dmt Matrix mvtnorm]; }; - pkgDepTools = derive2 { name="pkgDepTools"; version="1.47.2"; sha256="12bc56a5l3p9mdi15ryinicvyyzv58qwprksixjwm54mx42r5kw2"; depends=[graph RBGL]; }; - plateCore = derive2 { name="plateCore"; version="1.39.0"; sha256="0vf42ms3vky8n2n7x16kc284252zifjmch32lsww0lmsxv0h857n"; depends=[Biobase flowCore flowStats flowViz lattice latticeExtra MASS robustbase]; }; - plethy = derive2 { name="plethy"; version="1.19.1"; sha256="0pmrryxkxpgrb8c4pr25ajfn3v6m53810xz9da1j3hnyk9l42ha7"; depends=[Biobase BiocGenerics DBI ggplot2 IRanges plyr RColorBrewer reshape2 RSQLite S4Vectors Streamer]; }; - plgem = derive2 { name="plgem"; version="1.53.0"; sha256="04hwkr3v126mildi76jfr5b8s8lly9z60iydh5i3dc5zsyd6h84f"; depends=[Biobase MASS]; }; - plier = derive2 { name="plier"; version="1.51.0"; sha256="1m7bwaypnaw7kk756k0wl6xi3s0j9awi986lpa8ncjv587q0442h"; depends=[affy Biobase]; }; - plotGrouper = derive2 { name="plotGrouper"; version="0.99.43"; sha256="1b36ay09h0fx3kcyiw1pd48750b6slqzidw8g2bvjpgw2i03f4ww"; depends=[colourpicker dplyr egg ggplot2 ggpubr gridExtra gtable Hmisc magrittr readr readxl rlang scales shiny shinythemes stringr tibble tidyr]; }; - plrs = derive2 { name="plrs"; version="1.21.0"; sha256="18k3xad3gmkw74klyvqzbvnlr1pq93is6dqxm2bxb4cmzar12f6k"; depends=[Biobase BiocGenerics CGHbase ic_infer marray quadprog Rcsdp]; }; - plw = derive2 { name="plw"; version="1.41.0"; sha256="0q9dwj7rznhdj1h34ygnw0snfswnr8ycx0927jzsiiycz31n8z0f"; depends=[affy MASS]; }; - plyranges = derive2 { name="plyranges"; version="1.1.10"; sha256="0q9dsgnflr9gly3x4kbvr8ambfz5k5mvgn6hj9qyyb2vy6viqvni"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyr tidyselect]; }; - pmm = derive2 { name="pmm"; version="1.13.0"; sha256="0p0xnkz6hgnpvai7947861kw5hmjwwf3zj2y423whdr7x2lpdayw"; depends=[lme4]; }; - podkat = derive2 { name="podkat"; version="1.13.1"; sha256="0brp4d5y0708yv1b2jylywp4j7fknxy5vayss5jr9xp82sbahagz"; depends=[Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp Rsamtools]; }; - pogos = derive2 { name="pogos"; version="1.1.0"; sha256="1135bxxhamcxs5hn6hq43hc7s7cr9v0jy2884dz7f9qvgnrqhymi"; depends=[ggplot2 httr ontoProc rjson S4Vectors shiny]; }; - polyester = derive2 { name="polyester"; version="1.17.2"; sha256="1f2vd15qfkbka9pi88n61mrsmxx7pnl88aiarm5ahy4nmdv3fyrq"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; }; - powerTCR = derive2 { name="powerTCR"; version="1.1.4"; sha256="0zf2ip194y5ad7xzzkplv1lbilpns2l78flf8snrvi14n8588gjj"; depends=[cubature doParallel evmix foreach magrittr purrr tcR truncdist vegan VGAM]; }; - ppiStats = derive2 { name="ppiStats"; version="1.47.0"; sha256="0prrs1g99g55i993689c6s497crijnl96z2qzgga1y9w4zbf6g88"; depends=[Biobase Category graph lattice ppiData RColorBrewer ScISI]; }; - pqsfinder = derive2 { name="pqsfinder"; version="1.9.2"; sha256="1hj0mx9ii7rxjcwn8mg2ywhlzpf4ckwxf8w9ms7fkj7kk37r9wy1"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; }; - prada = derive2 { name="prada"; version="1.57.0"; sha256="0isj6w4lzfsqwwzs3njddabn2xznjqhp0bbihwfvc31kiya9k8di"; depends=[Biobase BiocGenerics MASS RColorBrewer rrcov]; }; - prebs = derive2 { name="prebs"; version="1.21.3"; sha256="0gqgl5sqsn92b5rck85nn4ri5b6mzvgyk13n9dp5qa0hxvdifhx4"; depends=[affy Biobase GenomeInfoDb GenomicAlignments GenomicRanges IRanges RPA S4Vectors]; }; - predictionet = derive2 { name="predictionet"; version="1.27.0"; sha256="0ls88pw7k1vy3qjzl91dj6kfbkgvz67448zhj1b3g308b33qasqk"; depends=[catnet igraph MASS penalized RBGL]; }; - preprocessCore = derive2 { name="preprocessCore"; version="1.43.0"; sha256="13859ip42jk6j6ngs8bwkzfarrqzd0jzhq9kdgsnicl9kf9k9vj6"; depends=[]; }; - primirTSS = derive2 { name="primirTSS"; version="0.99.29"; sha256="17d2x3y5iiz0r840d8adkb7lypdyhp76izxbkj42b89rqsfm5v2j"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg38 dplyr GenomicRanges GenomicScores Gviz IRanges JASPAR2018 phastCons100way_UCSC_hg38 purrr R_utils rtracklayer S4Vectors shiny stringr TFBSTools tibble tidyr]; }; - proBAMr = derive2 { name="proBAMr"; version="1.15.0"; sha256="1cl1ns7m1d1n3ayhga7f45xrjx9cy2a8l9xs2z7x3074kx8h8xxg"; depends=[AnnotationDbi Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer]; }; - proFIA = derive2 { name="proFIA"; version="1.7.0"; sha256="1qx79xamr77rjdfr50ms0dzrmwqwc2fzd24k2njbknxvz8kay5is"; depends=[Biobase BiocParallel minpack_lm missForest pracma ropls xcms]; }; - procoil = derive2 { name="procoil"; version="2.9.1"; sha256="1dhb7aphl93rxqk2k3fx8nrwgbd07wckrfx44c72fq0biam5qi5j"; depends=[Biostrings kebabs S4Vectors]; }; - profileScoreDist = derive2 { name="profileScoreDist"; version="1.9.0"; sha256="1jv9szg451ljggx458sgcgiaf1p6i7sin62lhbh6b8jn1s4h7qrw"; depends=[BiocGenerics Rcpp]; }; - progeny = derive2 { name="progeny"; version="1.3.0"; sha256="0rini10n59yzyq7bzckbyxvvl2lgj35k4dzm72lx47cws8nlqyl0"; depends=[Biobase]; }; - prot2D = derive2 { name="prot2D"; version="1.19.1"; sha256="141f38lcvrm0nirghx31gr3qzfq3q5zmqvvzcf5071s60hhm3syb"; depends=[Biobase fdrtool impute limma MASS Mulcom qvalue samr st]; }; - proteinProfiles = derive2 { name="proteinProfiles"; version="1.21.1"; sha256="1s35xglin78hv8f83jzi1racvklmnpf3gyjqxl60fj2i8b2r27dz"; depends=[]; }; - proteoQC = derive2 { name="proteoQC"; version="1.17.0"; sha256="17a6wmkxr8jfb7nbwykfc562fgj4p8addq5idajag2ijaiycvzz5"; depends=[dplyr ggplot2 MSnbase Nozzle_R1 plotly plyr reshape2 rmarkdown rpx rTANDEM seqinr tidyr VennDiagram XML]; }; - psichomics = derive2 { name="psichomics"; version="1.7.0"; sha256="0vj20pw305p4i08s7kxj0np1xxi8mhdlasagypc76ysnlhq0w6bn"; depends=[AnnotationHub cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma miscTools pairsD3 plyr R_utils Rcpp shiny shinyBS shinyjs stringr survival XML xtable]; }; - psygenet2r = derive2 { name="psygenet2r"; version="1.13.3"; sha256="0ldyrzhxw7m146yfm5fjr917g089f0mnhddinsqmd7h5pykhidb2"; depends=[BgeeDB Biobase BiocManager biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; }; - puma = derive2 { name="puma"; version="3.23.3"; sha256="0jk8696hna14c261ni1xpi5klfpgzjci9yd62nkqfvf3pynl12a9"; depends=[affy affyio Biobase mclust oligo oligoClasses]; }; - pvac = derive2 { name="pvac"; version="1.29.2"; sha256="087bmn6snyvw7z3j3xzga31rq4w81fxx46c54drapz6pfjmc0gzy"; depends=[affy Biobase]; }; - pvca = derive2 { name="pvca"; version="1.21.1"; sha256="0j2hqix5ih462rr5mpxav8whvkvng3v497qiznb7nlv20p6swgbi"; depends=[Biobase lme4 Matrix vsn]; }; - pwOmics = derive2 { name="pwOmics"; version="1.13.0"; sha256="0y4jsybxd6bcv9hqa25zij5lsbh55790njdy0p383pywbsn2dwvs"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics biomaRt data_table GenomicRanges gplots graph igraph rBiopaxParser STRINGdb]; }; - qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="0.99.12"; sha256="11q97nx0yss8w69jvq58mw34lma700rzkkkxs0qlga4hijjkm3v7"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr GenomicRanges ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer statmod stringr tibble tidyr]; }; - qcmetrics = derive2 { name="qcmetrics"; version="1.19.2"; sha256="043ybq0ykry2r5xh2gv76lbg16723zsflic930q12hc1pxncxa8m"; depends=[Biobase knitr Nozzle_R1 pander S4Vectors xtable]; }; - qpcrNorm = derive2 { name="qpcrNorm"; version="1.39.0"; sha256="18h58d58c0hs804n0xzsn0ydp4xw5cvab447zxq50g4adajjf7r8"; depends=[affy Biobase limma]; }; - qpgraph = derive2 { name="qpgraph"; version="2.15.2"; sha256="0lw5wfcw9br8k4wr70vp9xqgfjhbnzhjxfw4hzyp9z9h54vb9fay"; depends=[annotate AnnotationDbi Biobase BiocParallel GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges Matrix mvtnorm qtl Rgraphviz S4Vectors]; }; - qrqc = derive2 { name="qrqc"; version="1.35.0"; sha256="1mcb7gpncr91lq95vmbf6skjm5hxqlzx25inac3zwj3j4q07ipnk"; depends=[Biostrings biovizBase brew ggplot2 plyr reshape Rsamtools testthat xtable]; }; - qsea = derive2 { name="qsea"; version="1.7.4"; sha256="1rnm4f9skig9p8i0qz9nrfm6vxnjgi67s8r2665c3c87j52r4gga"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges gtools HMMcopy IRanges limma Rsamtools rtracklayer zoo]; }; - quantro = derive2 { name="quantro"; version="1.15.2"; sha256="0lf3d17b9d5gszpjknzhc5s2k8m31f8qf4k8y2lsrs7kaqr0skq0"; depends=[Biobase doParallel foreach ggplot2 iterators minfi RColorBrewer]; }; - quantsmooth = derive2 { name="quantsmooth"; version="1.47.0"; sha256="1w2gwaxy90s6laghgdhxqb0c0s93ci8g61zbrn7xjpd6af1vz1md"; depends=[quantreg]; }; - qusage = derive2 { name="qusage"; version="2.15.1"; sha256="03fxcg63mlxkc3m3pj5y828spk42h3f5h8l9zcfjmf93qacal6s7"; depends=[Biobase limma lsmeans nlme]; }; - qvalue = derive2 { name="qvalue"; version="2.13.0"; sha256="1g6lfgn73z68imy6qmh9s1zyniaq1wyx8jyllrk4lxpgk17i5dgh"; depends=[ggplot2 reshape2]; }; - r3Cseq = derive2 { name="r3Cseq"; version="1.27.0"; sha256="13cswnxp8ikv95xb3szn7br7xm5ml3mpj365vxhaky2s1x9kxr9p"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges IRanges qvalue RColorBrewer Rsamtools rtracklayer sqldf VGAM]; }; - rBiopaxParser = derive2 { name="rBiopaxParser"; version="2.21.1"; sha256="15lzqw4frw59scwarzcncp1a75xaf274bfy17ypwq0y7fnvqvlh5"; depends=[data_table XML]; }; - rCGH = derive2 { name="rCGH"; version="1.11.2"; sha256="10284xrdqh0pbn8a3ibwr2znf3lajnimli93lrhs4d60cna8wp9n"; depends=[aCGH affy AnnotationDbi DNAcopy GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges lattice limma mclust org_Hs_eg_db plyr shiny TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; }; - rDGIdb = derive2 { name="rDGIdb"; version="1.7.1"; sha256="195z5zifd48sq96rx9ayijfpqbrs5rygjsgjm42h4zylm2niasxi"; depends=[httr jsonlite]; }; - rGADEM = derive2 { name="rGADEM"; version="2.29.0"; sha256="1bqzmawhz1m00zcbnvznxzvak5f1b65xalr7sgas2sbrd77lvrhr"; depends=[Biostrings BSgenome IRanges seqLogo]; }; - rGREAT = derive2 { name="rGREAT"; version="1.13.3"; sha256="0fkcv2nz674i66yd3x34ba3897sdq96c1cns2kj7hjnv92l88qv3"; depends=[GenomicRanges GetoptLong IRanges RCurl rjson]; }; - rHVDM = derive2 { name="rHVDM"; version="1.47.0"; sha256="1y8dkws06j7jh6rnlq3y91bn5wy8fn2ha224mmvx4qchp6y9xcxd"; depends=[affy Biobase minpack_lm R2HTML]; }; - rMAT = derive2 { name="rMAT"; version="3.31.0"; sha256="0d2hn2jjs6c5xjwf6w0m9v53bb9mfpqvmms5vnzhwh6z3jankavm"; depends=[affxparser Biobase BiocGenerics IRanges]; }; - rRDP = derive2 { name="rRDP"; version="1.15.1"; sha256="0m00070c87za48a4in8bqzb3l77177jqys2ya6wv6xylmfig899j"; depends=[Biostrings]; }; - rSFFreader = derive2 { name="rSFFreader"; version="0.29.0"; sha256="1302ln1sshljannk1wkig4hf4cr5zk98z091jvbgs8icfg7k12by"; depends=[Biostrings IRanges S4Vectors ShortRead XVector]; }; - rTANDEM = derive2 { name="rTANDEM"; version="1.21.0"; sha256="1n7yaycgh5822j119si8i66yn0asg1mz9a9g7idiyvj8gpq54fv5"; depends=[data_table Rcpp XML]; }; - rTRM = derive2 { name="rTRM"; version="1.19.0"; sha256="1x8gbrn4b80v52isxg8a5rhkwijnlx649xyipnj206ky6ihzd3hc"; depends=[AnnotationDbi DBI igraph RSQLite]; }; - rTRMui = derive2 { name="rTRMui"; version="1.19.0"; sha256="0gw5yx609nzk8r8qc7q9zgkfs32s79d8v1zpw2njcb5d6figs7b1"; depends=[MotifDb org_Hs_eg_db org_Mm_eg_db rTRM shiny]; }; - rWikiPathways = derive2 { name="rWikiPathways"; version="1.1.7"; sha256="180pfczj66sm1a7g7r4ykl0qv8bncq7gqp0vf6hr39jmi985shin"; depends=[caTools httr RJSONIO]; }; - rain = derive2 { name="rain"; version="1.15.0"; sha256="0zrxh7bmc9x9rh6zbb0zmv3nvz6l7hqq21h4gh3rzzyjy79vw3aj"; depends=[gmp multtest]; }; - rama = derive2 { name="rama"; version="1.55.0"; sha256="0kmp25yw86vqxf43br2j75svvaprz97s5nvnxxjxbjwiigbjla7h"; depends=[]; }; - ramwas = derive2 { name="ramwas"; version="1.5.1"; sha256="1ixis62wpg0mzrzirgyfmp3k4kglsnw0vhgd1n4mvwa3v49vlbgi"; depends=[BiocGenerics biomaRt Biostrings digest filematrix GenomicAlignments glmnet KernSmooth Rsamtools]; }; - randPack = derive2 { name="randPack"; version="1.27.0"; sha256="0s7460iz01vmkf4a8g3vn6hrfx94bp5mihfyjkcv46nd9p3k6af5"; depends=[Biobase]; }; - rbsurv = derive2 { name="rbsurv"; version="2.39.0"; sha256="08lh9hn97sc0rx9vmkd977kpijs6gqa6r89my7afsvmkm8v7n7ls"; depends=[Biobase survival]; }; - rcellminer = derive2 { name="rcellminer"; version="2.3.2"; sha256="0fmg98pcv20gx5c4cbcdcs2cd1a84sg29xld5c7sa76i60ajy6ij"; depends=[Biobase fingerprint ggplot2 gplots rcdk rcellminerData shiny stringr]; }; - readat = derive2 { name="readat"; version="1.7.2"; sha256="0wskar887f6hyrp7p69z50kilwz0kb2d1f6rllbkgrchlh3zn53g"; depends=[assertive_base assertive_files assertive_numbers assertive_properties assertive_sets assertive_types Biobase data_table dplyr magrittr openxlsx pathological reshape2 stringi SummarizedExperiment testthat tidyr]; }; - reb = derive2 { name="reb"; version="1.59.0"; sha256="0sdlhx64sh55waxj47hz9kfb6bvxrw4ycyzj5cycr1w3sk2idszc"; depends=[Biobase idiogram]; }; - recount = derive2 { name="recount"; version="1.7.6"; sha256="03gk0h8aqzky7q1jgmn4f27cm18602m5nqbql9nyfxpbdpy9gdwb"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; }; - recoup = derive2 { name="recoup"; version="1.9.2"; sha256="0c6zd42xr7068yfnsag8xfjix83m3wa3s8fsc2dv5fz2gnmhbfm2"; depends=[BiocGenerics biomaRt circlize ComplexHeatmap GenomicAlignments GenomicRanges ggplot2 plyr rtracklayer]; }; - regionReport = derive2 { name="regionReport"; version="1.15.5"; sha256="02fhvjx5pj5hb3bdmm417rdjd8bzx81icdd8yqc4q7layhjrqb5q"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitcitations knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; }; - regioneR = derive2 { name="regioneR"; version="1.13.3"; sha256="1rmh4xq596yb8kd411j5h02b6g2rflkwy9a1g38djj7lhzihy2im"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; }; - regsplice = derive2 { name="regsplice"; version="1.7.1"; sha256="07g7jhwsb6yqhjvapr7kyqd8cwvn5jq9nrrf1ywifbf54x0kgzm1"; depends=[edgeR glmnet limma pbapply S4Vectors SummarizedExperiment]; }; - restfulSE = derive2 { name="restfulSE"; version="1.3.23"; sha256="1cpxkqnffmhj6js1a4y3k85jmrcciw1sih35akj8v6rpv4fsy7xa"; depends=[AnnotationDbi AnnotationHub bigrquery Biobase DBI DelayedArray dplyr ExperimentHub GO_db magrittr reshape2 rhdf5client rlang S4Vectors SummarizedExperiment]; }; - rexposome = derive2 { name="rexposome"; version="1.3.4"; sha256="0w5w4agdphrv935y3415hcrbgsxw27yk7h1xrjl5vk1ymkrj767z"; depends=[Biobase circlize corrplot FactoMineR ggplot2 ggrepel glmnet gplots gridExtra gtools Hmisc imputeLCMD lme4 lsr mice pryr reshape2 S4Vectors scales scatterplot3d stringr]; }; - rfPred = derive2 { name="rfPred"; version="1.19.0"; sha256="0xnb68s8iw01cnxma5iqyfki4f30i4if7kxc9p0i8w1nv3jf28xj"; depends=[data_table GenomicRanges IRanges Rsamtools]; }; - rgsepd = derive2 { name="rgsepd"; version="1.13.0"; sha256="128dqx7qzs9pf7ffxn94g8krkyryhcvj4wq9m1mdfj024yl4s04i"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots hash org_Hs_eg_db SummarizedExperiment]; }; - rhdf5 = derive2 { name="rhdf5"; version="2.25.11"; sha256="02xa4pc743k7q523p8x9njzqk8j0zv5kmprx5srnmrr1r1m4am8g"; depends=[Rhdf5lib]; }; - rhdf5client = derive2 { name="rhdf5client"; version="1.3.13"; sha256="0pcppacx3n1pr67amd5y7r25sm2w9k8vhxn8k8v66ndp08i0pd9b"; depends=[DelayedArray httr R6 rjson S4Vectors]; }; - riboSeqR = derive2 { name="riboSeqR"; version="1.15.0"; sha256="0cwf51cish38slfv3cqfn4rqjs8k9wwwph0n4w7wd4dh7c9p2rmn"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools seqLogo]; }; - rnaSeqMap = derive2 { name="rnaSeqMap"; version="2.39.0"; sha256="07q9dblld6ns943ppjdl1xlbzhg3yvxci8v1x2kbifqwlvv2lzs6"; depends=[Biobase DBI DESeq edgeR GenomicAlignments GenomicRanges IRanges Rsamtools]; }; - rnaseqcomp = derive2 { name="rnaseqcomp"; version="1.11.0"; sha256="0r1n74x5xbp264ap9xsndiich89cv2140whi6ax179dpjs57ikaa"; depends=[RColorBrewer]; }; - roar = derive2 { name="roar"; version="1.17.0"; sha256="09wmsfn4lqzj8ffqlf5z9npx4v0y3bpvxrm6b5rggc3prlq9m4qb"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicRanges IRanges rtracklayer S4Vectors SummarizedExperiment]; }; - rols = derive2 { name="rols"; version="2.9.4"; sha256="15qvqv3gi33ihdh0nlqqrv7raqs8g5hskaz2gk4pw0v24bzh1579"; depends=[Biobase BiocGenerics httr jsonlite progress]; }; - ropls = derive2 { name="ropls"; version="1.13.8"; sha256="1ryxjnpd7q0pwi8sd2ha3jlfwkk6v4cqz2751bv952k8c9mldna7"; depends=[Biobase]; }; - rpx = derive2 { name="rpx"; version="1.17.2"; sha256="0h0y31bi5f9z64ilcsgx1bj52qwfh1rv9ar00v3xkgx0zax5aw2m"; depends=[RCurl xml2]; }; - rqt = derive2 { name="rqt"; version="1.7.2"; sha256="1nnacv0vgf9y3abrph04hmibjm08bmhi32ik7vrbr5pv5bbmdhrn"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; }; - rqubic = derive2 { name="rqubic"; version="1.27.0"; sha256="06pp8ha9va9hkr5s7dmw6xsxs55sv0cn9vwysja0n4hdbbh5fx9v"; depends=[biclust Biobase BiocGenerics]; }; - rsbml = derive2 { name="rsbml"; version="2.39.0"; sha256="0ch87r9v7yxxqab81n99silsi6am7vwf1fzg43jg8x5726yz4pip"; depends=[BiocGenerics graph]; }; - rtracklayer = derive2 { name="rtracklayer"; version="1.41.8"; sha256="029qzy68il0mn7bkjhqdainl93a6v6k044ihgg5mndyhhhadjv03"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl Rsamtools S4Vectors XML XVector zlibbioc]; }; - runibic = derive2 { name="runibic"; version="1.3.3"; sha256="038afzgh06f908m1rlr0v58vfgm97q3shd174772k9rllzqr0q0j"; depends=[biclust Rcpp SummarizedExperiment testthat]; }; - sRAP = derive2 { name="sRAP"; version="1.21.0"; sha256="1mfailybmpa5ikc372qcfp57rnsksv6kn4x48bf6c0g5vln2kpjh"; depends=[gplots pls qvalue ROCR WriteXLS]; }; - sSeq = derive2 { name="sSeq"; version="1.19.0"; sha256="19d7xj3bqvvlxl23i08ab8ja53342nzi658a1f7xzf7khgp58fg9"; depends=[caTools RColorBrewer]; }; - safe = derive2 { name="safe"; version="3.21.0"; sha256="12h9d3dradnnkmhxz94d1b191q6xvx74nvp9y9y46yla7rxqpzma"; depends=[AnnotationDbi Biobase SparseM]; }; - sagenhaft = derive2 { name="sagenhaft"; version="1.51.0"; sha256="0mvj275rrqvz53fsv48c5gd3lzxmwh036353bmw7jswb1mrrv5qz"; depends=[SparseM]; }; - samExploreR = derive2 { name="samExploreR"; version="1.5.1"; sha256="1qzi9vn2hj9ph23mf8v0m6m587qisqvp0fmvkavxm8v3y07mcnpk"; depends=[edgeR ggplot2 RNAseqData_HNRNPC_bam_chr14 Rsubread]; }; - sampleClassifier = derive2 { name="sampleClassifier"; version="1.5.1"; sha256="1a4y3nnibjkv51i0m1qpj8mb675r9gz9zdpyra18c19ga245bwih"; depends=[annotate e1071 ggplot2 MGFM MGFR]; }; - sangerseqR = derive2 { name="sangerseqR"; version="1.17.0"; sha256="02v0khp8dksvj8h0p3py5cdxwgbla9hv60mrj6ay2d6yyv2w0vz6"; depends=[Biostrings shiny]; }; - sapFinder = derive2 { name="sapFinder"; version="1.19.0"; sha256="0f0k3afijnj0h6bh46cnkm3gajdsvngamcw2q5xbdrafidrk6npm"; depends=[pheatmap Rcpp rTANDEM]; }; - savR = derive2 { name="savR"; version="1.19.0"; sha256="1lzlrpv244pnwmf3347r7l5vwz0cd4hlm9nvlpdlvv8glvf7v4ay"; depends=[ggplot2 gridExtra reshape2 scales XML]; }; - scDD = derive2 { name="scDD"; version="1.5.0"; sha256="1s2a4nz3ys4vllk9dphwskqrw2bb9shkqx4bismprn0b7qcmnv9j"; depends=[arm BiocParallel EBSeq fields ggplot2 mclust outliers S4Vectors scran SingleCellExperiment SummarizedExperiment]; }; - scFeatureFilter = derive2 { name="scFeatureFilter"; version="1.1.1"; sha256="0xsbyqlflmphrdc0rqbgjyc93fmm2b747wn2lswq24r6g87084cs"; depends=[dplyr ggplot2 magrittr rlang tibble]; }; - scPipe = derive2 { name="scPipe"; version="1.3.8"; sha256="0c250q77rwcmns0m5px7485axbrflb7xmkrw58fxyzn58i13y3bc"; depends=[AnnotationDbi BiocGenerics biomaRt GGally ggplot2 MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib robustbase S4Vectors scales SingleCellExperiment SummarizedExperiment testthat zlibbioc]; }; - scater = derive2 { name="scater"; version="1.9.24"; sha256="062afh547brk3jxjxkyapz66agkdyvsn62ppx1n2qcpbhxlpppnd"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dplyr ggbeeswarm ggplot2 Matrix plyr Rcpp reshape2 Rhdf5lib S4Vectors SingleCellExperiment SummarizedExperiment viridis]; }; - scde = derive2 { name="scde"; version="2.9.0"; sha256="1zmhbjdy9v2v11q261l7gwjm77qpiyqdskgbkcaxf7a65wbzs90r"; depends=[BiocParallel Cairo edgeR extRemes flexmix MASS mgcv nnet pcaMethods quantreg RColorBrewer Rcpp RcppArmadillo rjson RMTstat Rook]; }; - scfind = derive2 { name="scfind"; version="1.3.0"; sha256="08xkvmjd6p6vsnfk7a5y4586b9r3ap7l9ig0g6cd6cj8pjhvf51b"; depends=[bit dplyr hash Rcpp reshape2 SingleCellExperiment SummarizedExperiment]; }; - scmap = derive2 { name="scmap"; version="1.3.0"; sha256="0pnflc49ysq7sxcg0ddcapi65vfjq3zl9pnz119hjr6avp8sjmhy"; depends=[Biobase BiocGenerics dplyr e1071 ggplot2 googleVis matrixStats proxy randomForest Rcpp RcppArmadillo reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; }; - scmeth = derive2 { name="scmeth"; version="1.1.8"; sha256="1fkf2pxbnhl992cql5nd73qq0kqzhvhl8g7rjfyx2zlfnb0a2m22"; depends=[AnnotationHub annotatr Biostrings BSgenome bsseq DelayedArray DT GenomeInfoDb GenomicRanges HDF5Array knitr reshape2 rmarkdown SummarizedExperiment]; }; - scone = derive2 { name="scone"; version="1.5.1"; sha256="0sqnwq34ixlpaq8zrpqjwvpfx985yzyc7wdymfkwfy2ysclrcbn6"; depends=[aroma_light BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SummarizedExperiment]; }; - scoreInvHap = derive2 { name="scoreInvHap"; version="1.3.1"; sha256="1nysi4blc9rxfsq4kwyyq9nbzdww7xfwgrcw8czvnfca59dbfgdq"; depends=[BiocParallel Biostrings GenomicRanges snpStats SummarizedExperiment VariantAnnotation]; }; - scran = derive2 { name="scran"; version="1.9.39"; sha256="174s3jymh8w1gbaq60m4lwhk038bfzrwva2a8xry3ampns818a6b"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel DelayedArray DelayedMatrixStats dynamicTreeCut edgeR igraph limma Matrix Rcpp Rhdf5lib S4Vectors scater SingleCellExperiment statmod SummarizedExperiment]; }; - scruff = derive2 { name="scruff"; version="0.99.39"; sha256="1za3d79p6cm19m3xqwbfgvrnfhjrr3j54s5vqhaaxxxvj9xbpv06"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr refGenome Rsamtools S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; }; - scsR = derive2 { name="scsR"; version="1.17.0"; sha256="1ppw53nl05rfs7jkgr464pa24yrczlvh7yfgmn5apd3yxbmf9i9w"; depends=[BiocGenerics Biostrings ggplot2 hash IRanges plyr RColorBrewer sqldf STRINGdb]; }; - segmentSeq = derive2 { name="segmentSeq"; version="2.15.1"; sha256="10qjyzzi4vr43p66rgpxkm5hlgfpg6s76g19vdyzs8lh0mn4shfw"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; }; - semisup = derive2 { name="semisup"; version="1.5.3"; sha256="13xmxl1915hk000l2kg120h4cqyw1372j2b92vfz5mn45ngmg99k"; depends=[SummarizedExperiment VGAM]; }; - seq2pathway = derive2 { name="seq2pathway"; version="1.13.2"; sha256="15fvc4dqn7adl3jsphin60krbm29mbm3w8000plcmk8n5bxdxqvj"; depends=[biomaRt GenomicRanges GSA nnet seq2pathway_data WGCNA]; }; - seqCAT = derive2 { name="seqCAT"; version="1.3.7"; sha256="10c5y3d63zk6zsyjx38srw73xj03nk7apa2p81z91jwwmva2ab2m"; depends=[dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges lazyeval S4Vectors scales SummarizedExperiment tidyr VariantAnnotation]; }; - seqCNA = derive2 { name="seqCNA"; version="1.27.0"; sha256="03zxkdcvxgjjhciv1w9l9gdj21ljqrw3c9cgkf2pqp3jk0swpaa7"; depends=[adehabitatLT doSNOW GLAD seqCNA_annot]; }; - seqLogo = derive2 { name="seqLogo"; version="1.47.0"; sha256="1hqfgxd7yvh7lm5q3qfhlkiy0pq5ffxls317miivsgid28shwmwk"; depends=[]; }; - seqPattern = derive2 { name="seqPattern"; version="1.13.0"; sha256="1xm7f3z29ahyiiy8586yfy5m4cqalws8hsyp8yc9xybw0mwdpyhg"; depends=[Biostrings GenomicRanges IRanges KernSmooth plotrix]; }; - seqTools = derive2 { name="seqTools"; version="1.15.0"; sha256="0qnj79xhgflhjcrd2n61fmx099q83iil8hy6pq7jzhnzhg4572pj"; depends=[zlibbioc]; }; - seqbias = derive2 { name="seqbias"; version="1.29.0"; sha256="1lv6wcqzlr40jmwac9s07ixx9vyikkc5a8f5wjmip9gglyy7m5f4"; depends=[Biostrings GenomicRanges Rsamtools zlibbioc]; }; - seqcombo = derive2 { name="seqcombo"; version="1.3.0"; sha256="1l4n2472kr4kimf4aq8v5whqwjpzwbkisfrf74wjljdj43903dr2"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr rvcheck]; }; - seqplots = derive2 { name="seqplots"; version="1.19.3"; sha256="0drjn6l80xqy3lij4qzg48chrwi0sjhv0xnqgg9m6qyq9xb7hy5l"; depends=[BiocManager Biostrings BSgenome class DBI digest DT fields GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges jsonlite kohonen plotrix RColorBrewer reshape2 Rsamtools RSQLite rtracklayer S4Vectors shiny]; }; - seqsetvis = derive2 { name="seqsetvis"; version="1.1.7"; sha256="01yd5lbkad79s274yc0byfvi4pp51b8ikrdnrza9r6jffaalzi60"; depends=[data_table eulerr GenomicRanges ggplot2 IRanges limma png RColorBrewer Rsamtools rtracklayer S4Vectors]; }; - sesame = derive2 { name="sesame"; version="0.99.7"; sha256="19l3cl5202aysf8bahhb4sm53q3x2jlz424ykw9zdf0ab9m3zbnc"; depends=[DNAcopy GenomicRanges ggplot2 illuminaio IRanges MASS preprocessCore R6 randomForest S4Vectors sesameData wheatmap]; }; - sevenC = derive2 { name="sevenC"; version="1.1.4"; sha256="16x95kb8264r5z55r635lyy13i37jsnyghmn27mw4wj8acdgv6gb"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; }; - sevenbridges = derive2 { name="sevenbridges"; version="1.11.5"; sha256="07pndfkcx4ixh5sk2hq64r5xzz2b6h26km50dk4pizj03lpcgalr"; depends=[curl docopt dplyr httr jsonlite miniUI objectProperties rstudioapi S4Vectors shiny stringr uuid yaml]; }; - shinyMethyl = derive2 { name="shinyMethyl"; version="1.17.1"; sha256="18s9m1yxqvpzqaq87c09k5wvjxpxijz6b9gi7nr1b4jxfglkxrdl"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; }; - shinyTANDEM = derive2 { name="shinyTANDEM"; version="1.19.0"; sha256="0yvf4rxpki7xb7f7yckxrm7ycsx2clqn13smc2m7ihdyvg5kw941"; depends=[mixtools rTANDEM shiny xtable]; }; - sigFeature = derive2 { name="sigFeature"; version="0.99.5"; sha256="08fs7pa4r4gbsg8j1f630lz9b0p4z4cq9r54akv0ix5q1mi71n2p"; depends=[BiocParallel biocViews e1071 Matrix nlme openxlsx pheatmap RColorBrewer SparseM SummarizedExperiment]; }; - sigPathway = derive2 { name="sigPathway"; version="1.49.0"; sha256="0fzqf17xqb0f2af9lz392l656naddann4wsxn233d28dajdvw5rx"; depends=[]; }; - sigaR = derive2 { name="sigaR"; version="1.29.0"; sha256="0lmv6m0rb7pnrqp6gd8klni3vd0rb98xscfx7qb5xpkihqcnya9s"; depends=[Biobase CGHbase corpcor igraph limma marray MASS mvtnorm penalized quadprog snowfall]; }; - siggenes = derive2 { name="siggenes"; version="1.55.0"; sha256="1lfw6ny0s76jcypqin49raz1zrbl1rwds3646c8h52rd37c4hdx0"; depends=[Biobase multtest]; }; - sights = derive2 { name="sights"; version="1.7.1"; sha256="05zny8xlsxzyp9bbv4jlgrpkmy0ppzqf97809ic6myfch547x7gp"; depends=[ggplot2 lattice MASS qvalue reshape2]; }; - signeR = derive2 { name="signeR"; version="1.7.2"; sha256="1ranfb4kik0k6cpi8zhsnqhvccrlizrkrijcp1yzhhaq5w33xj5b"; depends=[BiocGenerics Biostrings class GenomicRanges nloptr NMF PMCMR Rcpp RcppArmadillo VariantAnnotation]; }; - signet = derive2 { name="signet"; version="1.1.1"; sha256="0fcrwsimxx9j7m5x7civv9qrlcgnn6dyb7kcblsfxw6lidqhv59n"; depends=[graph igraph RBGL]; }; - sigsquared = derive2 { name="sigsquared"; version="1.13.0"; sha256="11bjd0bq2kf4inkybx7hkf970ma8rhwvagrlwxnxafh8nzw5amn8"; depends=[Biobase survival]; }; - similaRpeak = derive2 { name="similaRpeak"; version="1.13.0"; sha256="1lgs161banaxsi22ydgmw1jpf04h7js92sqzir5v7ms0h12nym15"; depends=[R6]; }; - simpleaffy = derive2 { name="simpleaffy"; version="2.57.0"; sha256="0yc44svjmh2vr1z3a77nvmas7kfcl0p6rjygq6ax477rvzldw7rq"; depends=[affy Biobase BiocGenerics gcrma genefilter]; }; - simulatorZ = derive2 { name="simulatorZ"; version="1.15.1"; sha256="16vzgni41r2jj8g8lbf3hh7r7202j0zq77shdaivrfzas19gaxwc"; depends=[Biobase BiocGenerics CoxBoost gbm GenomicRanges Hmisc SummarizedExperiment survival]; }; - sincell = derive2 { name="sincell"; version="1.13.2"; sha256="1h43wmx7l2sl9ka9lklqxfd35zkjbxvwsza979vxp6c8j8plp03g"; depends=[cluster entropy fastICA fields ggplot2 igraph MASS proxy Rcpp reshape2 Rtsne scatterplot3d statmod TSP]; }; - singleCellTK = derive2 { name="singleCellTK"; version="1.1.26"; sha256="1caw8cyw9f0ky3mj1fsk5lfgb4v0g3ghqb0l32j70q1r1yipdl87"; depends=[AnnotationDbi ape Biobase circlize cluster colourpicker ComplexHeatmap data_table DelayedArray DESeq2 DT enrichR ggplot2 ggtree gridExtra GSVA GSVAdata limma MAST matrixStats multtest plotly RColorBrewer reshape2 Rtsne S4Vectors shiny shinyalert shinycssloaders shinyjs SingleCellExperiment SummarizedExperiment sva]; }; - singscore = derive2 { name="singscore"; version="1.1.1"; sha256="12qqx0xnjza2rlyy1isq8mp28baphmb5yld3av5wvackyn0mwmf7"; depends=[Biobase BiocParallel edgeR ggplot2 ggrepel ggsci GSEABase magrittr matrixStats plotly plyr RColorBrewer reshape SummarizedExperiment tidyr]; }; - sizepower = derive2 { name="sizepower"; version="1.51.0"; sha256="0g0f5z0ccypk7m81b2nhrrj86fv1fin96qm8wba2j6ib2wf0p4np"; depends=[]; }; - skewr = derive2 { name="skewr"; version="1.13.2"; sha256="01ks1ir4sclf2gpwjn0mahxg9iz9iz66axxni190x7gnn076byc4"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; }; - slalom = derive2 { name="slalom"; version="1.3.1"; sha256="0qjw9zqyxnm6s6glw5j9iaqalnb5rbnrzkmwha2gswq9g6jd803n"; depends=[BH ggplot2 GSEABase Rcpp RcppArmadillo rsvd SingleCellExperiment SummarizedExperiment]; }; - slingshot = derive2 { name="slingshot"; version="0.99.13"; sha256="0w7ii3npq0qgjlszmsmn82sks9rdavhzqvxnn3d7p6c5y5bhz51j"; depends=[ape clusterExperiment igraph matrixStats princurve rgl SingleCellExperiment SummarizedExperiment]; }; - slinky = derive2 { name="slinky"; version="0.99.20"; sha256="1k41hw11wv9lnwkfbfbwdcajfac0sm0c7cspk8iwnkpzkj2qns8c"; depends=[curl dplyr foreach httr jsonlite readr rhdf5 SummarizedExperiment tidyr]; }; - snapCGH = derive2 { name="snapCGH"; version="1.51.0"; sha256="0qfkc3sa8inlnviw5wx36nyy71b59xas9rqsmfb4j32nxdhqj64p"; depends=[aCGH cluster DNAcopy GLAD limma tilingArray]; }; - snm = derive2 { name="snm"; version="1.29.0"; sha256="052mayih2hdgsgklqhvzmvnvx82ch8q4jvpx8ch5rp4k4g0qlqyj"; depends=[corpcor lme4]; }; - snpStats = derive2 { name="snpStats"; version="1.31.0"; sha256="1pxdf5qnibp6szwsllcayqxm9164yl30awfizlv6jmphfkah2i35"; depends=[BiocGenerics Matrix survival zlibbioc]; }; - soGGi = derive2 { name="soGGi"; version="1.13.0"; sha256="1xg6yaprmafl861g66j5pymlg1hpjanyibyi3zkrd15avvxw23g9"; depends=[BiocGenerics BiocParallel Biostrings chipseq GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges preprocessCore reshape2 Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; - sparseDOSSA = derive2 { name="sparseDOSSA"; version="1.5.0"; sha256="15vpj6v1x84zfy7vblhkm1vsv8hp5qa0fhfgfxbnzc5v28g1g41h"; depends=[MASS MCMCpack optparse tmvtnorm]; }; - sparsenetgls = derive2 { name="sparsenetgls"; version="0.99.7"; sha256="05n4c3gic10hy68kkc8mvh7d51sfbzvr8wr04y160pmlgrjslps4"; depends=[glmnet huge MASS Matrix parcor]; }; - specL = derive2 { name="specL"; version="1.15.0"; sha256="1xdfsvq7i9g2pbr0fh0awdwvl3j5ggk1r0n5bxhq7s2p4kjppxc6"; depends=[DBI protViz RSQLite seqinr]; }; - spikeLI = derive2 { name="spikeLI"; version="2.41.0"; sha256="1wx57idxn0wbg9mcfxdydcs5fbxmarsvv4hjcp62r5dpp4ymhcsb"; depends=[]; }; - spkTools = derive2 { name="spkTools"; version="1.37.0"; sha256="12nwaifk726dr0lh6yf8xaxdmhlybiy88fwc1qypm3kvw6jff6ma"; depends=[Biobase gtools RColorBrewer]; }; - splatter = derive2 { name="splatter"; version="1.5.8"; sha256="1bcjrywp49inr59xc01c7iz925wm2jpghx0anj97w08w0z5pn59s"; depends=[akima BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats scales scater SingleCellExperiment SummarizedExperiment]; }; - spliceSites = derive2 { name="spliceSites"; version="1.29.0"; sha256="1ivw3zsy5jggacvcby2nx9g9h0r1vvj331qpxxnvzajp9j0187yq"; depends=[Biobase BiocGenerics Biostrings doBy IRanges rbamtools refGenome seqLogo]; }; - splicegear = derive2 { name="splicegear"; version="1.53.0"; sha256="15bc3wmz3rz2jipgfj51bj2shr5cy941vnzxnk277yzh5wvz9hvc"; depends=[annotate Biobase XML]; }; - splineTimeR = derive2 { name="splineTimeR"; version="1.9.0"; sha256="114c641vyi585yl11czkq5n8gl01q6h8q34g427sj7aspqpf8lkc"; depends=[Biobase FIs GeneNet GSEABase gtools igraph limma longitudinal]; }; - splots = derive2 { name="splots"; version="1.47.0"; sha256="18yb8ifayd8cjs7najls4bzw0z3s9pyyid54vhcg1ll6860crymw"; depends=[RColorBrewer]; }; - spotSegmentation = derive2 { name="spotSegmentation"; version="1.55.0"; sha256="16zbzf05pg39vs6k1yvdsi880vfa3im4bq7rvyg8fvffb07pxr5l"; depends=[mclust]; }; - srnadiff = derive2 { name="srnadiff"; version="1.1.0"; sha256="1zn43lad3q5cvajr5zw07rcd1q95528xr3kcvr0b0j2c2wqd9q5v"; depends=[BiocParallel BiocStyle DESeq2 devtools GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; - sscore = derive2 { name="sscore"; version="1.53.0"; sha256="0p6klmcl2zd4i8qmmqj043p310grjmi6b2d610wanas03f0jdv71"; depends=[affy affyio]; }; - sscu = derive2 { name="sscu"; version="2.11.0"; sha256="0hnzxyyp82psjddh97kw3g533aiczkji858jl1xqi1kbr02avwc0"; depends=[BiocGenerics Biostrings seqinr]; }; - ssize = derive2 { name="ssize"; version="1.55.0"; sha256="061gpsj4dlzxii5ar3rdbc0kpvwby9639l3pk8vfslvcbl290w9f"; depends=[gdata xtable]; }; - ssviz = derive2 { name="ssviz"; version="1.15.1"; sha256="0q7xzn5xy8xx660711klssbi996218yvi9map04qinb9n60h0bbw"; depends=[Biostrings ggplot2 RColorBrewer reshape Rsamtools]; }; - staRank = derive2 { name="staRank"; version="1.23.0"; sha256="1gqvfbs15hdg7fkz6yxjxwn227am7lj372yhiiadgm629bwgcyxi"; depends=[cellHTS2]; }; - stageR = derive2 { name="stageR"; version="1.3.28"; sha256="1k7by1vds39xyxn3yas181si96v8q8rqxwv34b12ihsb4z7nsxpi"; depends=[SummarizedExperiment]; }; - statTarget = derive2 { name="statTarget"; version="1.11.7"; sha256="06vvha2dp1wf3lbpxxf2p4w1jvicd7fcicc525km7qkw9wp7bl5j"; depends=[impute pdist pls plyr randomForest ROC rrcov]; }; - stepNorm = derive2 { name="stepNorm"; version="1.53.0"; sha256="1iq4kv3dj8nr9nqd4nnrndss4ypc87a9pl389ha9q671ifqahaii"; depends=[marray MASS]; }; - strandCheckR = derive2 { name="strandCheckR"; version="0.99.15"; sha256="02g18vb3adnk5vd5khpi61whall2vrpj9ghwf7dh43d37q7x3kz9"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges magrittr reshape2 Rsamtools S4Vectors stringr TxDb_Hsapiens_UCSC_hg38_knownGene]; }; - subSeq = derive2 { name="subSeq"; version="1.11.1"; sha256="1xhfxccbdgzy8k3y41vjr7pi42z7lyffvyrfa6w24dvyqxbg5cb0"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; }; - supraHex = derive2 { name="supraHex"; version="1.19.1"; sha256="0gkp192jg1xnpy8g320hr89qd1w55dlbc3lir3mmx1yyfcdmiclv"; depends=[ape hexbin MASS]; }; - survcomp = derive2 { name="survcomp"; version="1.31.2"; sha256="029fzp9gpmcrswyd9347kghg1swqkwvi886q4hqffrddwm7dx4a6"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; }; - sva = derive2 { name="sva"; version="3.29.1"; sha256="0864qxajs9r26x7051hfnf9ns813j8v1l7wgkwjndk8i4h0bbchg"; depends=[BiocParallel genefilter limma matrixStats mgcv]; }; - swfdr = derive2 { name="swfdr"; version="1.7.0"; sha256="1bnqmz6vcj79j6cp15gla9lmsa3d96m790f5yl9vffbcj48n0rlc"; depends=[dplyr ggplot2 reshape2]; }; - switchBox = derive2 { name="switchBox"; version="1.17.1"; sha256="06k771nrdzmr8w5k9d5a7b83bwvnahwahdmx5q4cg7n6la1yll91"; depends=[gplots pROC]; }; - switchde = derive2 { name="switchde"; version="1.7.1"; sha256="14n3h4afr3sfv08vxip3i8hnn77npcwvhrfg759da8qaqmyb9dky"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; }; - synapter = derive2 { name="synapter"; version="2.5.2"; sha256="04gxig9cya85xha19zrgqh8hkl43nhpdgvhxh7kl2pnfgx0q82nf"; depends=[Biobase Biostrings cleaver knitr lattice MSnbase multtest qvalue RColorBrewer readr rmarkdown]; }; - synergyfinder = derive2 { name="synergyfinder"; version="1.7.0"; sha256="0v76jdh7dh9hhjgxfbls529lrv1wkjvaym39s7ahm3p1njycx05d"; depends=[drc ggplot2 gplots gridBase lattice nleqslv reshape2 SpatialExtremes]; }; - synlet = derive2 { name="synlet"; version="1.11.0"; sha256="0ijhssagav4hw7nm8x5157crdv4i8yhikrk6qf9w134lkkl0mviq"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; }; - systemPipeR = derive2 { name="systemPipeR"; version="1.15.4"; sha256="174nh3p7rhfdhpl0rpyg14z3nr9gkv5j57csazdsqn6qd6fgblxy"; depends=[annotate BatchJobs BiocGenerics Biostrings DESeq2 edgeR GenomicFeatures GenomicRanges ggplot2 GO_db GOstats limma pheatmap rjson Rsamtools ShortRead SummarizedExperiment VariantAnnotation]; }; - tRNA = derive2 { name="tRNA"; version="0.99.11"; sha256="1ahqh4jrlgjdb25v47ilwx84dibgg0birqxz4jxmbkya0sah36i9"; depends=[assertive BiocGenerics Biostrings GenomicRanges ggplot2 IRanges S4Vectors scales stringr XVector]; }; - tRNAdbImport = derive2 { name="tRNAdbImport"; version="0.99.7"; sha256="0rys26q9vrblpkjq1hhsv924k9k3vf40dnqsbmwc7xbwxi3cb434"; depends=[assertive Biostrings GenomicRanges httr IRanges S4Vectors stringr tRNA xml2]; }; - tRNAscanImport = derive2 { name="tRNAscanImport"; version="1.1.9"; sha256="0r971lja5fb352yzvhnvbynci78rpni3rli4kx5pyshh7bymiml2"; depends=[assertive BiocGenerics Biostrings GenomeInfoDb GenomicRanges rtracklayer S4Vectors stringr tRNA]; }; - tRanslatome = derive2 { name="tRanslatome"; version="1.19.5"; sha256="1li5qwwmsq5pgawkb2ffd6yqh8qr88dan624fm938rj0iqdwaxz8"; depends=[anota Biobase DESeq edgeR GOSemSim gplots Heatplus limma org_Hs_eg_db plotrix RankProd sigPathway topGO]; }; - tenXplore = derive2 { name="tenXplore"; version="1.3.1"; sha256="1jam1x14hr8rcgxq21yrpvfxcap3rcpcyz4pxh0d5z9n8ry7m2mr"; depends=[AnnotationDbi matrixStats ontoProc org_Mm_eg_db restfulSE shiny SummarizedExperiment]; }; - ternarynet = derive2 { name="ternarynet"; version="1.25.1"; sha256="01yzfiyrbkdgzzkdnn2ifa879j8pal38k8zm83d4ad9y06v8ndbm"; depends=[igraph]; }; - tigre = derive2 { name="tigre"; version="1.35.3"; sha256="0ya16fnif6ww3xviadhrnkh7hdgpi7bb2rbj27lxahd7kpigja2v"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; }; - tilingArray = derive2 { name="tilingArray"; version="1.59.0"; sha256="1kbw2hj4x3wizqia245kfb1x7rkd6prij7ywif8w3wcv9c8p919m"; depends=[affy Biobase genefilter pixmap RColorBrewer strucchange vsn]; }; - timecourse = derive2 { name="timecourse"; version="1.53.0"; sha256="1424s2ai9mkmxxswy6i928gzkk6kk5yz59nxkz91icg39xlf0rl5"; depends=[Biobase limma marray MASS]; }; - timescape = derive2 { name="timescape"; version="1.5.1"; sha256="0525j832iffyjcb1ii82jy0ix8mdfyf7w9frmc5zrwkflq0x2ds2"; depends=[dplyr gtools htmlwidgets jsonlite stringr]; }; - tkWidgets = derive2 { name="tkWidgets"; version="1.59.0"; sha256="0nxvgfl8kmasb1i6s3sq46qz0f7sjbqlwm5hpww1856bqd8dyyld"; depends=[DynDoc widgetTools]; }; - tofsims = derive2 { name="tofsims"; version="1.9.1"; sha256="12agad74lcnmg6v5g0rjzvk0qa7abav5giaz45rha61f7lz2lv12"; depends=[ALS ChemometricsWithR KernSmooth ProtGenerics Rcpp RcppArmadillo signal]; }; - topGO = derive2 { name="topGO"; version="2.33.1"; sha256="0g6kpxn0x4v55x2p28ikc556hcy3xy1d4wgag01k19ch9bmfaqhs"; depends=[AnnotationDbi Biobase BiocGenerics DBI GO_db graph lattice matrixStats SparseM]; }; - topdownr = derive2 { name="topdownr"; version="1.3.6"; sha256="0wsicb1m9r3a2gzx0masrfbmdd2ind415rp9iba22blj5ykqx4x0"; depends=[Biobase BiocGenerics Biostrings ggplot2 Matrix MSnbase mzR ProtGenerics S4Vectors]; }; - trackViewer = derive2 { name="trackViewer"; version="1.17.8"; sha256="196c6inqnvxb0hdlnmi8dyp9sx9jyx6f3ks4gvlv3687yfb0b3fv"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph grImport Gviz htmlwidgets InteractionSet IRanges plotrix Rgraphviz Rsamtools rtracklayer S4Vectors scales]; }; - tracktables = derive2 { name="tracktables"; version="1.15.0"; sha256="05glrr3f9clix43nvbsknicm9lyckswc5vj654444zhx08dmgnj5"; depends=[GenomicRanges IRanges RColorBrewer Rsamtools stringr tractor_base XML XVector]; }; - transcriptR = derive2 { name="transcriptR"; version="1.9.1"; sha256="09ikxr69d54kskrpx18z8gsmbv3fa120x9qncmkmxczddkmswh6j"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; }; - transcriptogramer = derive2 { name="transcriptogramer"; version="1.3.6"; sha256="0yzb4yzd5qbcq8gnmni0bprjz2bni2ak08v75ln51k4hcnjdqsxa"; depends=[biomaRt data_table doSNOW foreach ggplot2 igraph limma progress RedeR snow tidyr topGO]; }; - transite = derive2 { name="transite"; version="0.99.4"; sha256="0iikbbpa9ih6jwz3dmcyqr7698axsr4zim9zfmvw5s516q939h2w"; depends=[BiocGenerics Biostrings dplyr GenomicRanges ggplot2 ggseqlogo gridExtra Rcpp scales TFMPvalue]; }; - traseR = derive2 { name="traseR"; version="1.11.0"; sha256="18s4sy6v9wzcyd0i33zh1kf4nbxmsmzpvqsz6nz7d26xprmir450"; depends=[BSgenome_Hsapiens_UCSC_hg19 GenomicRanges IRanges]; }; - treeio = derive2 { name="treeio"; version="1.5.5"; sha256="1nvk2hr75zram3kiw5j65hlzf4gng2j0kbpscn3iwnhv8ja1a08h"; depends=[ape dplyr jsonlite magrittr rlang rvcheck tibble tidytree]; }; - trena = derive2 { name="trena"; version="1.3.1"; sha256="0yzspka8j9iyr4lb8vqsyzap3ps74bjnan3crq2b8qjfpmr0qrcy"; depends=[AnnotationDbi BiocParallel biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI flare GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 vbsr]; }; - triform = derive2 { name="triform"; version="1.23.0"; sha256="0rmxaa6hfslpqg5zngcy8s659v9n5mry6kjm1svniz347z7smdrj"; depends=[BiocGenerics IRanges yaml]; }; - trigger = derive2 { name="trigger"; version="1.27.0"; sha256="0yi3r23yw1vsz5y5wxzql0gmvwks0i6kn7f4r53swzmb12fkgs7h"; depends=[corpcor qtl qvalue sva]; }; - trio = derive2 { name="trio"; version="3.19.0"; sha256="1zix49bxx0qiz535cl8pmzjdbh4n4g5qa6bzd87p6ylrzzyxcq0j"; depends=[]; }; - triplex = derive2 { name="triplex"; version="1.21.0"; sha256="0y7r8b1a21cmys6l0li20bnlhi644i3085k8mkh80rzqin30aqgf"; depends=[Biostrings GenomicRanges IRanges S4Vectors XVector]; }; - tspair = derive2 { name="tspair"; version="1.39.0"; sha256="0anbb202pazdryadm7ww68nlrmyzand8kiwjfxnf59n6ansls8nd"; depends=[Biobase]; }; - tweeDEseq = derive2 { name="tweeDEseq"; version="1.27.0"; sha256="0aycx0ixg6bj05wz9am84jxbwa9qbbh3hmjp0w4pppzbmv6xrydw"; depends=[cqn edgeR limma MASS]; }; - twilight = derive2 { name="twilight"; version="1.57.0"; sha256="0mhx126yqlq76smabagwjxdff6n3vn9vzsr38nn0v8cs4vzq7v20"; depends=[Biobase]; }; - twoddpcr = derive2 { name="twoddpcr"; version="1.5.2"; sha256="0vs1hhlpsn08g5vf5yza0lb055x3lj0xwhgnd4lnq1qc8d1ksz1r"; depends=[class ggplot2 hexbin RColorBrewer S4Vectors scales shiny]; }; - tximeta = derive2 { name="tximeta"; version="0.99.18"; sha256="1x5vv6w34w3fqrp04i3zbq11zb8mblkvdqgmd790ll0f5y1qhq58"; depends=[AnnotationDbi BiocFileCache ensembldb GenomeInfoDb GenomicFeatures jsonlite rappdirs S4Vectors SummarizedExperiment tibble tximport]; }; - tximport = derive2 { name="tximport"; version="1.9.12"; sha256="1s5h5kxzb8nq9qc68rq5ik894yx7jl0315cn1b4k97i12rpajyjf"; depends=[]; }; - uSORT = derive2 { name="uSORT"; version="1.7.0"; sha256="1f5dabc7ksz6fhx7x87dm8whlxrhzh5zzfysgs18fv6yn815x747"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; }; - unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.17.0"; sha256="0rf9hrilb6d9jr2lbw20d3almds9lmhbdkmm130kx26kybp6vi1i"; depends=[BiocGenerics HTqPCR]; }; - variancePartition = derive2 { name="variancePartition"; version="1.11.14"; sha256="091j76x1jcc6g8vnzsjfnpf8q6d35rmvmv7sxcjx1jdyshl7gfjd"; depends=[Biobase colorRamps doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS pbkrtest reshape2 scales]; }; - vbmp = derive2 { name="vbmp"; version="1.49.0"; sha256="0h2lwkqx765s6iyyr3mivj83zdg761bci0jz1g8q9wl8xk72ajif"; depends=[]; }; - vidger = derive2 { name="vidger"; version="1.1.4"; sha256="1a48x1jjyccxbz792j7g538w82ascmm4aja10q0r60994h6hx6f2"; depends=[Biobase DESeq2 edgeR GGally ggplot2 ggrepel knitr RColorBrewer rmarkdown scales SummarizedExperiment tidyr]; }; - viper = derive2 { name="viper"; version="1.15.1"; sha256="1mi1qcznr8xcz5n5wr8mcbq5wxvb00rz4zahyv90aa5py62sxagw"; depends=[Biobase e1071 KernSmooth mixtools]; }; - vsn = derive2 { name="vsn"; version="3.49.1"; sha256="1lklwnxvwv1x68nyywxkdgla5pz8d94a86whf5x9vcbvcmk92x2i"; depends=[affy Biobase ggplot2 lattice limma]; }; - vtpnet = derive2 { name="vtpnet"; version="0.21.0"; sha256="0f89b3s1412sxwp64dlnc8rlawy2w86d1y5g1c7n2hd290m51dvp"; depends=[doParallel foreach GenomicRanges graph gwascat]; }; - vulcan = derive2 { name="vulcan"; version="1.3.1"; sha256="0lviq4mgnpfqb0rrh64r73xlqb50q2k4qagbn8gn9ifj35wvv2lr"; depends=[Biobase caTools ChIPpeakAnno csaw DESeq DiffBind GenomicRanges gplots locfit S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene viper wordcloud zoo]; }; - wateRmelon = derive2 { name="wateRmelon"; version="1.25.2"; sha256="0cqy6kp2d4bms235sdzr9vy8j0956wyqr80q2kk4jqywxcb6l1yn"; depends=[Biobase IlluminaHumanMethylation450kanno_ilmn12_hg19 illuminaio limma lumi matrixStats methylumi ROC]; }; - wavClusteR = derive2 { name="wavClusteR"; version="2.15.0"; sha256="0pngqm1b5z8zm5sdnqprq5mibrfm5rwzi0sa0mgwg9gsrn8wcg09"; depends=[BiocGenerics Biostrings foreach GenomicFeatures GenomicRanges ggplot2 Hmisc IRanges mclust Rsamtools rtracklayer S4Vectors seqinr stringr wmtsa]; }; - waveTiling = derive2 { name="waveTiling"; version="1.23.0"; sha256="018vhrv092qfyd5vmdbq216h3rsr6xk9nnknb4x0vnk1l7yckrk8"; depends=[affy Biobase Biostrings GenomeGraphs GenomicRanges IRanges oligo oligoClasses preprocessCore waveslim]; }; - weaver = derive2 { name="weaver"; version="1.47.0"; sha256="096sgg9xrnlf819bh6gz6a9phbhn7a54phd4nl8gz7xfjxscfrhi"; depends=[codetools digest]; }; - webbioc = derive2 { name="webbioc"; version="1.53.1"; sha256="0wjkfa6s1a0vhbfpplsvy0qzkrs94x2zd3s1kpcg5p6j4v9x9ph4"; depends=[affy annaffy Biobase BiocManager gcrma multtest qvalue vsn]; }; - widgetTools = derive2 { name="widgetTools"; version="1.59.0"; sha256="1ypz4rpi6yw6dg1w1dgnjx389xldmjzh484bs9dqzz27ly8b860v"; depends=[]; }; - wiggleplotr = derive2 { name="wiggleplotr"; version="1.5.1"; sha256="01d237s89qkj5i2d377g20h2ibqz1f4m087xchq1lnfmkb3mq0fm"; depends=[assertthat cowplot dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges purrr rtracklayer S4Vectors]; }; - xcms = derive2 { name="xcms"; version="3.3.6"; sha256="17mj4jlw0r48l311nhh44qpmgjcw4bq535xj7ljvg5mkxx74zlxj"; depends=[Biobase BiocGenerics BiocParallel lattice MassSpecWavelet MSnbase multtest mzR plyr ProtGenerics RANN RColorBrewer robustbase S4Vectors]; }; - xmapbridge = derive2 { name="xmapbridge"; version="1.39.0"; sha256="075yj9vqy4gf5ijirpfnm08rxqzg3bflirlr5j6qmr146jsj5cky"; depends=[]; }; - xps = derive2 { name="xps"; version="1.41.2"; sha256="01da8wc01fry7z8ma880h5g6vvqi3rdwqg5wmx9x56yfg0c293im"; depends=[]; }; - yamss = derive2 { name="yamss"; version="1.7.0"; sha256="1h8wz9cm042n9scgpm0m3c7v3wik8nr7lrm4nb47bikzcij7ymd3"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; }; - yaqcaffy = derive2 { name="yaqcaffy"; version="1.41.0"; sha256="044gyqh9pk2ml6f99mfjfw7zp2ygnis74jh4x8z7i99q6jip8pbn"; depends=[simpleaffy]; }; - yarn = derive2 { name="yarn"; version="1.7.1"; sha256="02km8cd5l2l7whzb585c741qkzv6zlmxrl0fjfp13nsww69vg914"; depends=[Biobase biomaRt downloader edgeR gplots limma matrixStats preprocessCore quantro RColorBrewer readr]; }; - zFPKM = derive2 { name="zFPKM"; version="1.3.0"; sha256="12yj97g1y37aq4qfyqchgvp93kkb0bzxmk196s1vygh4dk0b36lp"; depends=[checkmate dplyr ggplot2 SummarizedExperiment tidyr]; }; - zinbwave = derive2 { name="zinbwave"; version="1.3.4"; sha256="0px2v20plqnshb41wy7fk9vh00l45m8mm7paqd4m197wjpxbyf3s"; depends=[BiocParallel copula edgeR genefilter glmnet Matrix SingleCellExperiment softImpute SummarizedExperiment]; }; - zlibbioc = derive2 { name="zlibbioc"; version="1.27.0"; sha256="17jr4jgl30qlnmjfzzc1qd1rah5c9bwbp08dsnkhy7fxpwimqm2i"; depends=[]; }; + BiocWorkflowTools = derive2 { name="BiocWorkflowTools"; version="1.8.0"; sha256="1wpihkd5j3v2qls2n67dwydvxk2mjb6cx27if5vxh7v99x3vph04"; depends=[BiocStyle bookdown devtools git2r httr knitr rmarkdown rstudioapi stringr]; }; + Biostrings = derive2 { name="Biostrings"; version="2.50.1"; sha256="1qyv1ps7vy6gy78pm2rcikg0bgf1mv7falahjp3pkwqq1272hrl8"; depends=[BiocGenerics IRanges S4Vectors XVector]; }; + BitSeq = derive2 { name="BitSeq"; version="1.26.0"; sha256="0z78cwsqx7r8rdy5laaamdbd6jl0w8i4rkpbv8z9z21j3namr9fn"; depends=[IRanges Rsamtools S4Vectors zlibbioc]; }; + BrainStars = derive2 { name="BrainStars"; version="1.26.0"; sha256="0ki6jm4ycm3dzdv5fhv7nflpy4zifx364mlq02fq701hjgm36fwf"; depends=[Biobase RCurl RJSONIO]; }; + BridgeDbR = derive2 { name="BridgeDbR"; version="1.16.1"; sha256="09xfcbf9ix25zm7djp306iz6vyx73giamslsndzzpsgcbmg0wadb"; depends=[RCurl rJava]; }; + BrowserViz = derive2 { name="BrowserViz"; version="2.4.0"; sha256="09rdysgw9dxk5qpg7sxw0w3rpcrqjdibvwj3chcpgk6kv5ysfwgj"; depends=[BiocGenerics httpuv jsonlite]; }; + BubbleTree = derive2 { name="BubbleTree"; version="2.12.0"; sha256="0g40mh7b6awdvhqy70mamb33p2qn93z64p770phr8ccyi91dd93j"; depends=[Biobase BiocGenerics BiocStyle biovizBase dplyr e1071 GenomicRanges ggplot2 gridExtra gtable gtools IRanges limma magrittr plyr RColorBrewer WriteXLS]; }; + BufferedMatrix = derive2 { name="BufferedMatrix"; version="1.46.0"; sha256="0llfqpjbb4q8m6gjx0jq6nxpylqi7r715srkk41rx1bjs0ykbksg"; depends=[]; }; + BufferedMatrixMethods = derive2 { name="BufferedMatrixMethods"; version="1.46.0"; sha256="089wh0rvcvagfx1v3y3r2k8ncm14j9cls2yaywlza8damlz4fbb5"; depends=[BufferedMatrix]; }; + CAFE = derive2 { name="CAFE"; version="1.18.0"; sha256="0x3hn8c7p3p5m215kjbcgxak4c7807ikxs7k4b1immqzz8m5rfqd"; depends=[affy annotate Biobase biovizBase GenomicRanges ggbio ggplot2 gridExtra IRanges]; }; + CAGEfightR = derive2 { name="CAGEfightR"; version="1.2.0"; sha256="1xnsbwjnirhh4dsfpxc8f16wxnvabr07yzbbizxqyna0h3hr61s0"; depends=[assertthat BiocGenerics BiocParallel GenomeInfoDb GenomicFeatures GenomicFiles GenomicInteractions GenomicRanges grr Gviz InteractionSet IRanges Matrix Matrix_utils pryr rtracklayer S4Vectors SummarizedExperiment]; }; + CAGEr = derive2 { name="CAGEr"; version="1.24.0"; sha256="1vin6inq3rlj365bhxpx28rp28isi7967r1plpdyi2lwx2f2d4im"; depends=[beanplot BiocGenerics BiocParallel BSgenome data_table DelayedArray formula_tools GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges KernSmooth memoise MultiAssayExperiment plyr reshape Rsamtools rtracklayer S4Vectors som stringdist stringi SummarizedExperiment vegan VGAM]; }; + CALIB = derive2 { name="CALIB"; version="1.48.0"; sha256="118sy35hi5p1nkm7ygh4pn7m3855vhywsj66j0v74iis00blpv1z"; depends=[limma]; }; + CAMERA = derive2 { name="CAMERA"; version="1.38.0"; sha256="0685lpqigi26w90j61xspdhwqjny2qkni8rvxsira51r705k9bwj"; depends=[Biobase graph Hmisc igraph RBGL xcms]; }; + CAMTHC = derive2 { name="CAMTHC"; version="1.0.0"; sha256="1n2hn4snmlfrwr5c9di214sqvgmmihyxnbzbf0n2hx99rrjlzvpg"; depends=[apcluster Biobase BiocParallel corpcor DMwR geometry NMF pcaPP rJava SummarizedExperiment]; }; + CATALYST = derive2 { name="CATALYST"; version="1.6.0"; sha256="0h4r6fl6p52j5d6l9hh48ws27y8j41ccw7yj4ws16gsnm0hc2s4z"; depends=[Biobase circlize ComplexHeatmap ConsensusClusterPlus dplyr drc DT flowCore FlowSOM ggplot2 ggrepel ggridges gridExtra htmltools limma magrittr Matrix matrixStats nnls plotly RColorBrewer reshape2 Rtsne S4Vectors scales shiny shinyBS shinydashboard shinyjs SummarizedExperiment tidyr]; }; + CAnD = derive2 { name="CAnD"; version="1.14.0"; sha256="0h1ry4z9g4daga7jqnm2wh631d4yzp738yf1vpxvf2d3f2qci8dv"; depends=[ggplot2 reshape]; }; + CCPROMISE = derive2 { name="CCPROMISE"; version="1.8.0"; sha256="1kpz5cwx0bk55w8paldvmvmgprxsrgyqf8r3vxns136ksv1a1zhx"; depends=[Biobase CCP GSEABase PROMISE]; }; + CEMiTool = derive2 { name="CEMiTool"; version="1.6.10"; sha256="0db77vjkpv4a62hl9ralrdimrb02aqjp4iq102z9yhnjh0abn3ld"; depends=[clusterProfiler data_table dplyr DT ff ffbase fgsea GeneOverlap ggdendro ggplot2 ggpmisc ggrepel ggthemes gRbase gridExtra gtable htmltools igraph intergraph knitr limma matrixStats network plyr pracma RColorBrewer rmarkdown scales sna stringr tidyr WGCNA]; }; + CFAssay = derive2 { name="CFAssay"; version="1.16.0"; sha256="140nalnr7r9v3a91slviqmin6h4ag0w1x2cysqin85zabv4xj1ya"; depends=[]; }; + CGEN = derive2 { name="CGEN"; version="3.18.0"; sha256="0p0c05axpj94v3gksy065244vlxh9q4g6ifv07jxrvl23ji4bnyi"; depends=[mvtnorm survival]; }; + CGHbase = derive2 { name="CGHbase"; version="1.42.0"; sha256="0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"; depends=[Biobase marray]; }; + CGHcall = derive2 { name="CGHcall"; version="2.44.0"; sha256="1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"; depends=[Biobase CGHbase DNAcopy impute snowfall]; }; + CGHnormaliter = derive2 { name="CGHnormaliter"; version="1.36.0"; sha256="1j92x5dyxp6hjj87g1hgw5q8fd4k2q5rb97ir47xkalkcskg0ddh"; depends=[Biobase CGHbase CGHcall]; }; + CGHregions = derive2 { name="CGHregions"; version="1.40.0"; sha256="04j87bd2ygda6np72vs1bx857y5mbaga19ky6pgyxv9lahi62xyw"; depends=[Biobase CGHbase]; }; + CHARGE = derive2 { name="CHARGE"; version="1.2.0"; sha256="0230pvgsf775lq4n9cpxb95bqq438f4z0wx9mmbj4yir8bljy0mk"; depends=[cluster diptest factoextra FactoMineR GenomicRanges IRanges matrixStats modes plyr SummarizedExperiment]; }; + CHRONOS = derive2 { name="CHRONOS"; version="1.10.0"; sha256="1r0gm20a5ivg1c0h338rzxby69ww4vlw32gmis06k3pmsqq49g13"; depends=[biomaRt circlize doParallel foreach graph openxlsx RBGL RCurl XML]; }; + CINdex = derive2 { name="CINdex"; version="1.10.0"; sha256="0c4p3v9a0njf28gdhvdbnydlhjgpnwzakhnvkvngs3mhbwpy9ih5"; depends=[bitops dplyr GenomeInfoDb GenomicRanges gplots gridExtra IRanges png S4Vectors som stringr]; }; + CMA = derive2 { name="CMA"; version="1.40.0"; sha256="1v77yiqmvd90pxbs64xfpglwy006w88b4zrb5rk90r0vasnvdl5n"; depends=[Biobase]; }; + CNAnorm = derive2 { name="CNAnorm"; version="1.28.0"; sha256="050yhjqqqm5kqjpw2ar8gf0yjqzmr0xzwa0c10dfry6hml63d6m3"; depends=[DNAcopy]; }; + CNEr = derive2 { name="CNEr"; version="1.18.1"; sha256="1h8p7fibhyn7117qwjrl9f7y5cczv50qihzfd83pj76z5k5ylzry"; depends=[annotate BiocGenerics Biostrings DBI GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 GO_db IRanges KEGGREST poweRlaw R_utils readr reshape2 RSQLite rtracklayer S4Vectors XVector]; }; + CNORdt = derive2 { name="CNORdt"; version="1.24.0"; sha256="1bik2sqmjfmij20l9jxphg9l85xl61x5cpb5017p5vyhgyrm0mrc"; depends=[abind CellNOptR]; }; + CNORfeeder = derive2 { name="CNORfeeder"; version="1.22.0"; sha256="1kvr3jbxm95qg6pa3wfki2d8rg7cqwdd5bgjlb5yhapwll5xcz2s"; depends=[CellNOptR graph]; }; + CNORfuzzy = derive2 { name="CNORfuzzy"; version="1.24.0"; sha256="140a42s9h7li597y45z3dmb8y1nf53xxl7vnipi8k0rgcix465dl"; depends=[CellNOptR nloptr]; }; + CNORode = derive2 { name="CNORode"; version="1.24.0"; sha256="0chx9fgrlqwvlzjnkh45lr4qjfd1q3830kr3yjjniqrhr85x76zg"; depends=[CellNOptR genalg]; }; + CNPBayes = derive2 { name="CNPBayes"; version="1.12.0"; sha256="1vlbnlr63vv2s5nyndiqcb3kh737apswqqygwqn5pz6973nvlcl3"; depends=[BiocGenerics coda combinat dplyr GenomeInfoDb GenomicRanges ggplot2 gtools IRanges magrittr matrixStats mclust purrr RColorBrewer Rcpp reshape2 S4Vectors scales SummarizedExperiment tibble tidyr]; }; + CNTools = derive2 { name="CNTools"; version="1.38.0"; sha256="038nbqgjahc9b646s9avxgccxz1qsly8vqj84dzqwgpyvx7hxqpi"; depends=[genefilter]; }; + CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.14.0"; sha256="0fh94iv66li3zsnadxyxwzhs1jcz63vpmc6khp0srac2kzvc1kcs"; depends=[exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; }; + CNVrd2 = derive2 { name="CNVrd2"; version="1.20.0"; sha256="10141xwwkzrkgkad8x5y1ha779b47vp7b2qk32hgw19ys4lraj79"; depends=[DNAcopy ggplot2 gridExtra IRanges rjags Rsamtools VariantAnnotation]; }; + CNVtools = derive2 { name="CNVtools"; version="1.76.0"; sha256="0xmqqq3j3xxm1pnldw6l3vnww9lfjlghvkrfzfbwxmq8gkxmyzji"; depends=[survival]; }; + COCOA = derive2 { name="COCOA"; version="1.0.1"; sha256="1j53vvkh5y8icmzx7p6i33jw227wxdgsddqlb7wzjpdhv7x55c1j"; depends=[Biobase BiocGenerics ComplexHeatmap data_table GenomicRanges ggplot2 IRanges MIRA S4Vectors tidyr]; }; + CODEX = derive2 { name="CODEX"; version="1.14.0"; sha256="0g76myd81kbmda6j3bi9gzlj74bwg1z6lzwlsas644m2gi7xvy0s"; depends=[Biostrings BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb IRanges Rsamtools S4Vectors]; }; + COHCAP = derive2 { name="COHCAP"; version="1.28.1"; sha256="1zn0skpi7h2nws877bj1van3358cmh88prvj9691kwcwj47h1zny"; depends=[BH COHCAPanno gplots RColorBrewer Rcpp RcppArmadillo WriteXLS]; }; + COMPASS = derive2 { name="COMPASS"; version="1.20.0"; sha256="1ghm2l3m7csg3jwwckbqa0js4hv7ksj67qdggr6w78pwypi8qwp8"; depends=[abind BiocStyle clue data_table dplyr knitr magrittr pdist plyr RColorBrewer Rcpp reshape2 rlang rmarkdown scales tidyr]; }; + CONFESS = derive2 { name="CONFESS"; version="1.10.0"; sha256="1gzxd2vbg68s53yv8g8nq63am6f7vzgbb21zpxvv61sagypycix0"; depends=[changepoint cluster contrast data_table EBImage ecp flexmix flowClust flowCore flowMeans flowMerge flowPeaks foreach ggplot2 limma MASS moments outliers plotrix raster readbitmap reshape2 SamSPECTRAL waveslim wavethresh zoo]; }; + CORREP = derive2 { name="CORREP"; version="1.48.0"; sha256="1jg2j61f3cz7c7xf9wm96gvl5ykc8vbb14vhrbcmibjzxf7zfd1r"; depends=[e1071]; }; + COSNet = derive2 { name="COSNet"; version="1.16.0"; sha256="1bw979xx2g17p3pisvbvskv8xq26pqrn9lcq8jh6av8m592b90gp"; depends=[]; }; + CRISPRseek = derive2 { name="CRISPRseek"; version="1.22.0"; sha256="0v8mz0bxrw6v43hsmiqq9xx1crfyy522m99fisf53j2dfy7m4456"; depends=[BiocGenerics BiocParallel Biostrings BSgenome data_table hash IRanges S4Vectors seqinr]; }; + CRImage = derive2 { name="CRImage"; version="1.30.0"; sha256="11pzsg1bjsg12ad4vrp8slzr53nynb93i6j9zqgcvzh0dl004ss9"; depends=[aCGH DNAcopy e1071 EBImage foreach MASS sgeostat]; }; + CSAR = derive2 { name="CSAR"; version="1.34.0"; sha256="0r8rqgz95bk7piwhgh4ljr8zvnvgxz7w7h7cjwqywsg259sf54sj"; depends=[GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; + CSSP = derive2 { name="CSSP"; version="1.20.0"; sha256="06yzh3kgxwg512ycncxj0ann0m918wyij6xwyz0kskln2vsq84jm"; depends=[]; }; + CTDquerier = derive2 { name="CTDquerier"; version="1.2.0"; sha256="0lpf49gdp5bj83sqv3hnaa4l3lib112m0h4k8zbjvjgkw6inn9wb"; depends=[BiocFileCache ggplot2 gridExtra igraph rappdirs RCurl S4Vectors stringdist stringr]; }; + CVE = derive2 { name="CVE"; version="1.8.0"; sha256="0fjisya8iipc4ghslaw3di62mmi93v34w1c39a57mqk5gng2pzr7"; depends=[ape ConsensusClusterPlus ggplot2 gplots jsonlite plyr RColorBrewer shiny tidyverse WGCNA]; }; + CancerInSilico = derive2 { name="CancerInSilico"; version="2.2.0"; sha256="01042wxyi9kr4x9ga0vx957xqa2xns291w7h47f2v8d76yfk469j"; depends=[BH Rcpp]; }; + CancerMutationAnalysis = derive2 { name="CancerMutationAnalysis"; version="1.24.0"; sha256="10768i5ijrwr7hcshk60r5w6ckqacqk3f9jhs3qkm2ic0g47vgwb"; depends=[AnnotationDbi limma qvalue]; }; + CancerSubtypes = derive2 { name="CancerSubtypes"; version="1.8.0"; sha256="1cg1im5p53n5afz0pzfg7l7wp6lm8cl0dr5x8di62va71n9qdk77"; depends=[cluster ConsensusClusterPlus iCluster impute limma NMF sigclust SNFtool survival]; }; + Cardinal = derive2 { name="Cardinal"; version="2.0.2"; sha256="0xq765ajy884q8ldjd8cvyyy5k9ykhy1zhxwzhpmigvp72yzmg0j"; depends=[Biobase BiocGenerics BiocParallel dplyr EBImage irlba lattice magrittr matter ProtGenerics S4Vectors signal sp]; }; + Category = derive2 { name="Category"; version="2.48.0"; sha256="1jdm83bwdfhpfm1y6hwgvxzj6l83h1bdkqv23799kzywnwm016kv"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI genefilter graph GSEABase Matrix RBGL]; }; + CausalR = derive2 { name="CausalR"; version="1.14.0"; sha256="0dm34x84zwyn0l508rbh1x9xqq5135q6i75z9m952g0fa8s1v152"; depends=[igraph]; }; + CellMapper = derive2 { name="CellMapper"; version="1.8.0"; sha256="0qaw5pf3lgdkfcki0z2hp9g0b07j2khinwh9r0ajvji4j7hiwrw5"; depends=[S4Vectors]; }; + CellNOptR = derive2 { name="CellNOptR"; version="1.28.0"; sha256="0ihi72c7dshmv536lyn7ym4pr3cygzl6bwwd31q17qis3bhsihxg"; depends=[ggplot2 graph hash RBGL RCurl Rgraphviz XML]; }; + CellScore = derive2 { name="CellScore"; version="1.2.0"; sha256="0rc77c7z9nsid22yrdny6kd4yg6031njznsdvk6n82mv2sadk51b"; depends=[Biobase gplots lsa RColorBrewer squash]; }; + CellTrails = derive2 { name="CellTrails"; version="1.0.0"; sha256="14iw57n4pac43iad7gd47jbvwcxh3k0fdamsxkbbrk36r1mcrbsx"; depends=[Biobase BiocGenerics cba dendextend dtw EnvStats ggplot2 ggrepel igraph maptree mgcv reshape2 Rtsne SingleCellExperiment SummarizedExperiment]; }; + CexoR = derive2 { name="CexoR"; version="1.20.0"; sha256="1pwjq3r7l9hinab38g2v5sjrnbhxva1jfjvh20wh75l2hzfjs62j"; depends=[genomation GenomeInfoDb GenomicRanges idr IRanges RColorBrewer Rsamtools rtracklayer S4Vectors]; }; + ChAMP = derive2 { name="ChAMP"; version="2.12.2"; sha256="0j3qw7kflj9q4v90w4f8h1a4g5d49932lswf7i1497z36yvs1m0w"; depends=[bumphunter ChAMPdata combinat dendextend DMRcate DNAcopy doParallel FEM GenomicRanges globaltest goseq Hmisc Illumina450ProbeVariants_db IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest illuminaio impute isva kpmt limma marray matrixStats minfi missMethyl plotly plyr preprocessCore prettydoc quadprog qvalue RColorBrewer rmarkdown RPMM shiny shinythemes sva wateRmelon]; }; + ChIC = derive2 { name="ChIC"; version="1.2.0"; sha256="190jc1k318bk1xh93h726bxl0711qzn672lri3lwsrbjm76w8m1g"; depends=[BiocGenerics caret caTools ChIC_data GenomicRanges IRanges progress S4Vectors spp]; }; + ChIPComp = derive2 { name="ChIPComp"; version="1.12.0"; sha256="1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"; depends=[BiocGenerics BSgenome_Hsapiens_UCSC_hg19 BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicRanges IRanges limma Rsamtools rtracklayer S4Vectors]; }; + ChIPQC = derive2 { name="ChIPQC"; version="1.18.0"; sha256="1pc7j9nfsjryjgxs6vi6hw2918h29rchbagxa2xdra0bj34i0605"; depends=[Biobase BiocGenerics BiocParallel chipseq DiffBind GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gtools IRanges Nozzle_R1 reshape2 Rsamtools S4Vectors TxDb_Celegans_UCSC_ce6_ensGene TxDb_Dmelanogaster_UCSC_dm3_ensGene TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Mmusculus_UCSC_mm10_knownGene TxDb_Mmusculus_UCSC_mm9_knownGene TxDb_Rnorvegicus_UCSC_rn4_ensGene]; }; + ChIPSeqSpike = derive2 { name="ChIPSeqSpike"; version="1.2.0"; sha256="10hdk94b2j2aam7mjbdjygn86sz0az1hxvd7dkwh65lcvl6hvphl"; depends=[BiocGenerics corrplot GenomicRanges ggplot2 IRanges LSD Rsamtools rtracklayer S4Vectors seqplots stringr]; }; + ChIPXpress = derive2 { name="ChIPXpress"; version="1.26.0"; sha256="1b5ss7s8chjm8zgpxkwmghgf2dh1xn225y1qfad838gs0d2rmd5h"; depends=[affy biganalytics bigmemory Biobase ChIPXpressData frma GEOquery]; }; + ChIPanalyser = derive2 { name="ChIPanalyser"; version="1.4.0"; sha256="115ycr6s5lb9888sz9xxdsip22vnbj1gfavrm61ks12rqf0ch2b6"; depends=[BiocManager Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges RcppRoll ROCR rtracklayer S4Vectors]; }; + ChIPexoQual = derive2 { name="ChIPexoQual"; version="1.6.0"; sha256="1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"; depends=[BiocParallel biovizBase broom data_table dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 hexbin IRanges RColorBrewer rmarkdown Rsamtools S4Vectors scales viridis]; }; + ChIPpeakAnno = derive2 { name="ChIPpeakAnno"; version="3.16.0"; sha256="09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager biomaRt Biostrings BSgenome DBI DelayedArray ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GO_db graph idr IRanges limma matrixStats multtest RBGL regioneR Rsamtools S4Vectors seqinr SummarizedExperiment VennDiagram]; }; + ChIPseeker = derive2 { name="ChIPseeker"; version="1.18.0"; sha256="08d8m4svnyki4pg0mwy17p7wi7anw9ba347ck36x8lzbjb8xcmwg"; depends=[AnnotationDbi BiocGenerics boot dplyr enrichplot GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gplots gridBase gtools IRanges magrittr plotrix RColorBrewer rtracklayer S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene UpSetR]; }; + ChIPseqR = derive2 { name="ChIPseqR"; version="1.36.0"; sha256="0m9xrb1aksmrh0zm6sa0nklwbn0mydz70dydhycfknv96l0rrxqn"; depends=[BiocGenerics Biostrings fBasics GenomicRanges HilbertVis IRanges S4Vectors ShortRead timsac]; }; + ChIPsim = derive2 { name="ChIPsim"; version="1.36.0"; sha256="096dlqis3mcbhz837ys0n9yimgrh5fw5cpx16kjg9hfs48253nxs"; depends=[Biostrings IRanges ShortRead XVector]; }; + ChemmineOB = derive2 { name="ChemmineOB"; version="1.20.0"; sha256="037j2hwmrbk0k2abygkrkmdshsh1c434dj0iqdmqsnbyyvv34q2m"; depends=[BH BiocGenerics Rcpp zlibbioc]; }; + ChemmineR = derive2 { name="ChemmineR"; version="3.34.1"; sha256="0pzvwaycvz61156ypqf24a42nhhmlhx2hccyra3g0jm97adm69iw"; depends=[base64enc BH BiocGenerics DBI digest DT ggplot2 gridExtra png Rcpp RCurl rjson rsvg]; }; + Chicago = derive2 { name="Chicago"; version="1.10.0"; sha256="01w2z7jc2aizf6v149h5akvzm24bz9i476pfvhl17yhywkmnwsrm"; depends=[data_table Delaporte Hmisc MASS matrixStats]; }; + ChromHeatMap = derive2 { name="ChromHeatMap"; version="1.36.0"; sha256="0ah133mzrwxdhfazpw41h2h0bz555al9yjlyhahm249d4wbdzr8d"; depends=[annotate AnnotationDbi Biobase BiocGenerics GenomicRanges IRanges rtracklayer]; }; + ClassifyR = derive2 { name="ClassifyR"; version="2.2.4"; sha256="1sjkrxak6sh2iq9wj5a9cjaq6vdvpfvlyp7g3qflfm31s5n4ajh0"; depends=[BiocParallel locfit MultiAssayExperiment plyr S4Vectors]; }; + Clomial = derive2 { name="Clomial"; version="1.18.0"; sha256="17yplh5d2a96m17karvhr0n5jd0mck66whf8m3v4xsys75pspf83"; depends=[matrixStats permute]; }; + Clonality = derive2 { name="Clonality"; version="1.30.0"; sha256="0nhlrzy6z8kcfghw3ciy4ymbnmwb7y68bb1ikz7fxi4d5pywzm03"; depends=[DNAcopy]; }; + ClusterJudge = derive2 { name="ClusterJudge"; version="1.4.0"; sha256="1yi3hcbk8ka9krrc2q8jv0sq5szpwp3iw3wnn8x9ibn1qyimzwc5"; depends=[httr infotheo jsonlite lattice latticeExtra]; }; + ClusterSignificance = derive2 { name="ClusterSignificance"; version="1.10.0"; sha256="1jwl2v9qja11rrdllqkc2hlqiirzcav7s6343d66qaajq02iagzj"; depends=[pracma princurve RColorBrewer scatterplot3d]; }; + CoCiteStats = derive2 { name="CoCiteStats"; version="1.54.0"; sha256="0ar66vhlw6zhrrf6bpd82hqwxh4g6apic56mx9xir40302ikc1h4"; depends=[AnnotationDbi org_Hs_eg_db]; }; + CoGAPS = derive2 { name="CoGAPS"; version="3.2.1"; sha256="1f51jf63h9axpxgyvgzlxq63hs88v4qh58g74s88cbjnl7rrjbbf"; depends=[BH BiocParallel cluster data_table gplots RColorBrewer Rcpp S4Vectors SingleCellExperiment SummarizedExperiment]; }; + CoRegNet = derive2 { name="CoRegNet"; version="1.20.0"; sha256="1z8ihzn4i9zzn7cw2376j92cx1b0w543vr9f47xkhnsj871f2v6c"; depends=[arules igraph shiny]; }; + CompGO = derive2 { name="CompGO"; version="1.18.0"; sha256="1hzps1isfpdmcxdlpfqhanl0qafydgsgjc5xqxgd8zvib4zb28za"; depends=[GenomicFeatures ggplot2 pathview pcaMethods RDAVIDWebService reshape2 Rgraphviz rtracklayer TxDb_Mmusculus_UCSC_mm9_knownGene]; }; + ComplexHeatmap = derive2 { name="ComplexHeatmap"; version="1.20.0"; sha256="0s01dzcfj1lmpqfpsbqw7r4858krfzy499lz4cwx4fq3mbyvy2aj"; depends=[circlize colorspace GetoptLong GlobalOptions RColorBrewer]; }; + ConsensusClusterPlus = derive2 { name="ConsensusClusterPlus"; version="1.46.0"; sha256="00q1xbi7znfvvcqb1szqlw7zh4vvpf1si80k5zylys512ixg9sns"; depends=[ALL Biobase cluster]; }; + CopywriteR = derive2 { name="CopywriteR"; version="2.14.0"; sha256="0aamxafdk98n7s92jyqs65d6ljpnc2463vanvsw80p44qn6l6awn"; depends=[BiocParallel chipseq CopyhelpeR data_table DNAcopy futile_logger GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges matrixStats Rsamtools S4Vectors]; }; + CorMut = derive2 { name="CorMut"; version="1.24.0"; sha256="1p4xj8f5hf1z31943s51inc0mc28bphzy5qs4ay2nccwshbypq0l"; depends=[igraph seqinr]; }; + Cormotif = derive2 { name="Cormotif"; version="1.28.0"; sha256="0lb691mvr9zim7z5yplncmlzyr799jym1wvrgfm1diqjz2daixai"; depends=[affy limma]; }; + CountClust = derive2 { name="CountClust"; version="1.10.0"; sha256="0v10145s9qplg8qd4vd7p6kq1x7dndbiw5i06mjnan1qgwc994n0"; depends=[cowplot flexmix ggplot2 gtools limma maptpx picante plyr reshape2 slam SQUAREM]; }; + CoverageView = derive2 { name="CoverageView"; version="1.20.0"; sha256="14zkmpc2zmashx987qa61y9db0wgfywgg6cinwjk50jsica6l40y"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors]; }; + CrispRVariants = derive2 { name="CrispRVariants"; version="1.10.0"; sha256="02fyl6gap84pppfqp3wjhx86i7h54qyfrjdx9gs0wbypp0ia47j5"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; }; + CytoDx = derive2 { name="CytoDx"; version="1.2.0"; sha256="1h037kwxdldcg8g9diaj414sz1mrr15zq8wkxzhjj74qzazm83nl"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; }; + CytoML = derive2 { name="CytoML"; version="1.8.0"; sha256="0iljvwys5cx4rvmphf3nwha1q32qrxd8kwhrgkddqbig9s0iiq0h"; depends=[base64enc Biobase data_table flowCore flowUtils flowWorkspace ggcyto graph jsonlite ncdfFlow openCyto plyr RBGL Rgraphviz XML]; }; + DAPAR = derive2 { name="DAPAR"; version="1.14.3"; sha256="1j9zcifwmaw3zq8cn8114r2z902s3d2b8811dng5039w3d8cd2s2"; depends=[AnnotationDbi Cairo clusterProfiler cp4p DAPARdata doParallel dplyr factoextra FactoMineR foreach ggplot2 gplots graph highcharter imp4p impute knitr lattice limma lme4 Matrix MSnbase norm openxlsx pcaMethods png preprocessCore RColorBrewer readxl reshape2 scales siggenes stringr tidyr tidyverse tmvtnorm vioplot vsn]; }; + DART = derive2 { name="DART"; version="1.30.0"; sha256="0dxwy95p43c0shx30y95sj1pl64kqkh2bsnj680q196zgyg937s6"; depends=[igraph]; }; + DBChIP = derive2 { name="DBChIP"; version="1.26.0"; sha256="1wk8nvfcfhsymhbi6id0kd1jzcykh6hhikl2040g0v6gi252gv2v"; depends=[DESeq edgeR]; }; + DChIPRep = derive2 { name="DChIPRep"; version="1.12.0"; sha256="1avcjr7r54grh3yn5pjbzji3syc8vvah9as7asv3cwmyqzaya4r0"; depends=[assertthat ChIPpeakAnno DESeq2 fdrtool GenomicRanges ggplot2 plyr purrr reshape2 S4Vectors smoothmest soGGi SummarizedExperiment tidyr]; }; + DECIPHER = derive2 { name="DECIPHER"; version="2.10.0"; sha256="0qqk5wjv42sjs986dkzdkcqj1jy662p7mkvbi951kjs8sf1rk75r"; depends=[Biostrings DBI IRanges RSQLite S4Vectors XVector]; }; + DEComplexDisease = derive2 { name="DEComplexDisease"; version="1.2.0"; sha256="1a4m4xs8dd0459vh5bhi96w6vchmqgap3snrj8x6jjlpvkkhwl8l"; depends=[BiocParallel ComplexHeatmap DESeq2 edgeR Rcpp SummarizedExperiment]; }; + DEDS = derive2 { name="DEDS"; version="1.56.0"; sha256="1zfgaar3bpss49zhs81mwlfzkx5lv92j8a64xd12ig88is24cw2c"; depends=[]; }; + DEFormats = derive2 { name="DEFormats"; version="1.10.0"; sha256="0m1z6w5w98lhcc6w8z9a5qzjp24bv4ygkjnx2mr734s65swlbkh8"; depends=[checkmate data_table DESeq2 edgeR GenomicRanges S4Vectors SummarizedExperiment]; }; + DEGraph = derive2 { name="DEGraph"; version="1.34.0"; sha256="1vrv3lkda2dhcb9ig38xv0bvnk68z9bpsxr4846fq31dvxp6b5al"; depends=[graph KEGGgraph lattice mvtnorm NCIgraph R_methodsS3 R_utils RBGL Rgraphviz rrcov]; }; + DEGreport = derive2 { name="DEGreport"; version="1.18.0"; sha256="1yvm1ci8kv5yqw5lzlz0q2zzi1x4yhz96y1a9ifiam21msg5mxa4"; depends=[Biobase BiocGenerics broom circlize cluster ComplexHeatmap ConsensusClusterPlus cowplot DESeq2 dplyr edgeR ggdendro ggplot2 ggrepel knitr lasso2 logging magrittr Nozzle_R1 psych RColorBrewer reshape rlang S4Vectors scales stringr SummarizedExperiment tibble tidyr]; }; + DEGseq = derive2 { name="DEGseq"; version="1.36.1"; sha256="1p4ldk2wagsnjbxrq3s6fa3l6phqp77hjwv43gbdsh7ph8rzd33g"; depends=[qvalue]; }; + DEP = derive2 { name="DEP"; version="1.4.0"; sha256="171571da6vqid9lp9djbncyr4pwmg04vvrrd8f1kgd09994whz20"; depends=[assertthat circlize cluster ComplexHeatmap dplyr DT fdrtool ggplot2 ggrepel gridExtra imputeLCMD limma MSnbase purrr RColorBrewer readr rmarkdown shiny shinydashboard SummarizedExperiment tibble tidyr vsn]; }; + DEScan2 = derive2 { name="DEScan2"; version="1.2.0"; sha256="02j2jp1q2sjnlagr7z6nz24imalrl0hcmaffbyzakls3ha4d9c11"; depends=[BiocGenerics BiocParallel ChIPpeakAnno data_table DelayedArray GenomeInfoDb GenomicAlignments GenomicRanges glue IRanges plyr Rcpp RcppArmadillo rtracklayer S4Vectors SummarizedExperiment]; }; + DESeq = derive2 { name="DESeq"; version="1.34.0"; sha256="1klv1xrh3173srywr6dnq6i7m9djn4gc9aflr1p3a6yjlqcq6fya"; depends=[Biobase BiocGenerics genefilter geneplotter lattice locfit MASS RColorBrewer]; }; + DESeq2 = derive2 { name="DESeq2"; version="1.22.1"; sha256="1b2bmvcsfzvks47d7w46zplcwz0kgcdhx5xmx3x9lp2gvx2p84r5"; depends=[Biobase BiocGenerics BiocParallel genefilter geneplotter GenomicRanges ggplot2 Hmisc IRanges locfit Rcpp RcppArmadillo S4Vectors SummarizedExperiment]; }; + DEXSeq = derive2 { name="DEXSeq"; version="1.28.0"; sha256="0jh1640cnzpk8x3155cqc8dvrs1rciw3d6nv2k70baw96bhrynp8"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel biomaRt DESeq2 genefilter geneplotter GenomicRanges hwriter IRanges RColorBrewer Rsamtools S4Vectors statmod stringr SummarizedExperiment]; }; + DEqMS = derive2 { name="DEqMS"; version="1.0.0"; sha256="1x17m172k4s92mbsb8pn4x3yskmqv3km2gs7alykr0dh2zfgwnzh"; depends=[ggplot2 limma]; }; + DEsingle = derive2 { name="DEsingle"; version="1.2.1"; sha256="0w3b7pz04l60hrbw4k7rkp4xmf8hzxca7pgrjyalf946z6yvky0s"; depends=[bbmle BiocParallel gamlss MASS Matrix maxLik pscl VGAM]; }; + DEsubs = derive2 { name="DEsubs"; version="1.8.1"; sha256="0whs5q02lgis04zyf6abd9b5phv3bw508k4ngp197ka02pbpvxxz"; depends=[circlize DESeq DESeq2 EBSeq edgeR ggplot2 graph igraph jsonlite limma locfit Matrix NBPSeq pheatmap RBGL]; }; + DFP = derive2 { name="DFP"; version="1.40.0"; sha256="12kb7cjsfdscdwanjbzvwgp1ra0kmijrp1qyx87sxsk4hxk236ml"; depends=[Biobase]; }; + DMCHMM = derive2 { name="DMCHMM"; version="1.4.0"; sha256="12jn77dxbcbzbfdsy4l1vycf68bnw2wdhrwnnjc3829arcz2mkph"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; }; + DMRScan = derive2 { name="DMRScan"; version="1.8.0"; sha256="0vwmkw3abs0v8z49qdkrqxia0kn5i3pl7yqzv42l5xz7d2498s7q"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; }; + DMRcaller = derive2 { name="DMRcaller"; version="1.14.0"; sha256="1ds6paic8g9gynqqy4mciycr6apyxjagwiasnjcpw0j3j1l8rki6"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; }; + DMRcate = derive2 { name="DMRcate"; version="1.18.0"; sha256="0930rrz2aps91mcqihap9830km9x7if6vgpvjplmacvs1x2k3wyh"; depends=[DMRcatedata DSS GenomicRanges Gviz IRanges limma minfi missMethyl plyr S4Vectors]; }; + DMRforPairs = derive2 { name="DMRforPairs"; version="1.18.0"; sha256="11gbnxlkgkx9ynmslxvinfnq39rpg392zbff6g36fd5nsr3dppxd"; depends=[GenomicRanges Gviz R2HTML]; }; + DNABarcodes = derive2 { name="DNABarcodes"; version="1.12.0"; sha256="0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"; depends=[BH Matrix Rcpp]; }; + DNAcopy = derive2 { name="DNAcopy"; version="1.56.0"; sha256="04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"; depends=[]; }; + DNAshapeR = derive2 { name="DNAshapeR"; version="1.10.0"; sha256="1rplgi36jn33npihhmk0vdsiali814y5v1wz5fdna3k9b47id6b6"; depends=[Biostrings fields GenomicRanges Rcpp]; }; + DOQTL = derive2 { name="DOQTL"; version="1.18.0"; sha256="0ligqm4l2x5dz794djapri770j27rhibhdzc48y980768gjpkm8k"; depends=[annotate annotationTools Biobase BiocGenerics biomaRt BSgenome_Mmusculus_UCSC_mm10 corpcor doParallel foreach fpc GenomicRanges hwriter IRanges iterators mclust QTLRel regress rhdf5 Rsamtools RUnit VariantAnnotation XML]; }; + DOSE = derive2 { name="DOSE"; version="3.8.0"; sha256="1ipdyzwk8znqmm1gby7ib8g5zsgzdjpv420ld6jmp7kz9x9pk1yf"; depends=[AnnotationDbi BiocParallel DO_db fgsea ggplot2 GOSemSim qvalue reshape2 S4Vectors]; }; + DRIMSeq = derive2 { name="DRIMSeq"; version="1.10.0"; sha256="0yjhp1rfczs1f8931n0y9f136hyqacdak2z5f9n60n8zbfkca170"; depends=[BiocGenerics BiocParallel edgeR GenomicRanges ggplot2 IRanges limma MASS reshape2 S4Vectors]; }; + DSS = derive2 { name="DSS"; version="2.30.0"; sha256="02q74s98k52bvql5bpk5yri137jc4j8lr3a1bjdbna9r5cl1v0dq"; depends=[Biobase bsseq DelayedArray]; }; + DTA = derive2 { name="DTA"; version="2.28.0"; sha256="1gsc6sbi1awi92w1wnqddybz2n2n8f8pvsg95sp90xp11sjrnvvx"; depends=[LSD scatterplot3d]; }; + DaMiRseq = derive2 { name="DaMiRseq"; version="1.6.1"; sha256="08pibsbipbqpn77q3j3ky45l5fycydba9ll8wfllmxjqj2salcfh"; depends=[arm caret corrplot DESeq2 e1071 EDASeq edgeR FactoMineR FSelector ggplot2 Hmisc ineq kknn limma lubridate MASS pheatmap pls plsVarSel randomForest RColorBrewer reshape2 RSNNS SummarizedExperiment sva]; }; + DeMAND = derive2 { name="DeMAND"; version="1.12.0"; sha256="06hip99jzi5z89v1mprmqxrziv1zf6lysmg6ixsxaq8f0l9x2m38"; depends=[KernSmooth]; }; + DeconRNASeq = derive2 { name="DeconRNASeq"; version="1.24.0"; sha256="1j5mlnx0n3xn2agnp2wwdbyyf36lh277giapz0sknlnpfdhzc4jn"; depends=[ggplot2 limSolve pcaMethods]; }; + DeepBlueR = derive2 { name="DeepBlueR"; version="1.8.0"; sha256="0gc1g4w1finbv8ash79x6nsmvjvx8vz44dr0dpx1vmdfb54qlz3c"; depends=[data_table diffr dplyr filehash foreach GenomeInfoDb GenomicRanges R_utils RCurl rjson rtracklayer settings stringr withr XML]; }; + DelayedArray = derive2 { name="DelayedArray"; version="0.8.0"; sha256="0cl5anqkjwvqx19snjhz0zj8cp8ibckiifl28h821h50g62nvb2f"; depends=[BiocGenerics BiocParallel IRanges matrixStats S4Vectors]; }; + DelayedMatrixStats = derive2 { name="DelayedMatrixStats"; version="1.4.0"; sha256="03fk2avl1vyjv2wslczkc82qr0zmp1ra8iimd47pbmnnm839ly4w"; depends=[BiocParallel DelayedArray HDF5Array IRanges Matrix matrixStats S4Vectors]; }; + DiffBind = derive2 { name="DiffBind"; version="2.10.0"; sha256="0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"; depends=[amap BiocParallel DESeq2 dplyr edgeR GenomicAlignments GenomicRanges ggplot2 ggrepel gplots IRanges lattice limma locfit RColorBrewer Rcpp Rsamtools S4Vectors SummarizedExperiment systemPipeR zlibbioc]; }; + DiffLogo = derive2 { name="DiffLogo"; version="2.6.0"; sha256="1an8c2h0vsy8x3q90bgy7gfigz11k460gpi4wlyj6gq8h6bd1fmy"; depends=[cba]; }; + Director = derive2 { name="Director"; version="1.8.0"; sha256="0xzds7gi9bp6hp8dpw9c4ls6b1rcfk4w4my1wacf0z9hnwpd60r3"; depends=[htmltools]; }; + DirichletMultinomial = derive2 { name="DirichletMultinomial"; version="1.24.0"; sha256="19bzn0a5jal1xv0ad6wikxc7wrk582hczqamlln0vb2ffwkj1z3f"; depends=[BiocGenerics IRanges S4Vectors]; }; + DominoEffect = derive2 { name="DominoEffect"; version="1.2.0"; sha256="08wrblpsliyshdv8kldr8mwp3zkkr1255120vy780x6b2n6jczsz"; depends=[AnnotationDbi biomaRt Biostrings data_table GenomeInfoDb GenomicRanges IRanges SummarizedExperiment VariantAnnotation]; }; + Doscheda = derive2 { name="Doscheda"; version="1.4.0"; sha256="0m9x9cyz6lqrfy1gzv6psl0758ybjyr0bry20d4ily6wcmr8xgwd"; depends=[affy calibrate corrgram d3heatmap drc DT ggplot2 gridExtra httr jsonlite limma matrixStats prodlim readxl reshape2 shiny shinydashboard stringr vsn]; }; + DriverNet = derive2 { name="DriverNet"; version="1.22.0"; sha256="13yd9inyqkaw363m6apiyclkjpb3f5khbi0vwc90whi8q9wvsl8f"; depends=[]; }; + DropletUtils = derive2 { name="DropletUtils"; version="1.2.1"; sha256="17dcc4w6dm90cmgz08izhjxggasbj400mhww5c1m18nhq7840w07"; depends=[beachmat BiocParallel edgeR HDF5Array Matrix Rcpp rhdf5 Rhdf5lib S4Vectors SingleCellExperiment]; }; + DrugVsDisease = derive2 { name="DrugVsDisease"; version="2.24.2"; sha256="17x0smsb1kdj87ndw0dakqjb4c2dq2kkv5z8cs3i4x87hz56yrbd"; depends=[affy annotate ArrayExpress BiocGenerics biomaRt cMap2data DrugVsDiseasedata GEOquery hgu133a_db hgu133a2_db hgu133plus2_db limma qvalue RUnit xtable]; }; + DupChecker = derive2 { name="DupChecker"; version="1.20.0"; sha256="114g9qx4v2lz521pndha3gk0cl2pq1jxqw1z9pzijgdj9lyj0jzv"; depends=[R_utils RCurl]; }; + DynDoc = derive2 { name="DynDoc"; version="1.60.0"; sha256="0k18f07mg7hg085l0pi5j6l8c04m5zd6jx3ha6cpjv6nd0m2lljw"; depends=[]; }; + EBImage = derive2 { name="EBImage"; version="4.24.0"; sha256="18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx"; depends=[abind BiocGenerics fftwtools htmltools htmlwidgets jpeg locfit png RCurl tiff]; }; + EBSEA = derive2 { name="EBSEA"; version="1.10.0"; sha256="1cbc21a6habvlslavdpn5v1nxkdhcpqp27fwg5y7hy9c8fqixqq0"; depends=[edgeR limma plyr]; }; + EBSeq = derive2 { name="EBSeq"; version="1.22.0"; sha256="1z8armk0b30dipx232m51r36vk750zyk3z79f57yq0a1azwpp3vn"; depends=[blockmodeling gplots testthat]; }; + EBSeqHMM = derive2 { name="EBSeqHMM"; version="1.16.0"; sha256="0b5cd5i09d48fyncfcjc6wnpjnrxr4jccmx2k94jfhcnmmbyjjf9"; depends=[EBSeq]; }; + EBarrays = derive2 { name="EBarrays"; version="2.46.0"; sha256="1qz1z9v3dc0rdwm33v47avvgvqfxhbzw34idcxa1ap7ynx9c2sqs"; depends=[Biobase cluster lattice]; }; + EBcoexpress = derive2 { name="EBcoexpress"; version="1.26.0"; sha256="12hh2qvv0jfpsd8jz41jvzs605mccj35c5rz54697lgi7pdhwm4l"; depends=[EBarrays mclust minqa]; }; + EDASeq = derive2 { name="EDASeq"; version="2.16.0"; sha256="1gjqzn1kg9qwyz2gwjyy9xzzr1lnc7xd5zwdyvzkadz97gckzxwf"; depends=[AnnotationDbi aroma_light Biobase BiocGenerics biomaRt Biostrings DESeq GenomicFeatures GenomicRanges IRanges Rsamtools ShortRead]; }; + EDDA = derive2 { name="EDDA"; version="1.20.0"; sha256="0yjnwbikclc912wh75gs8h633vc16ldjpf7p4gi76b70qzlf8gzv"; depends=[baySeq DESeq edgeR Rcpp ROCR snow]; }; + EGAD = derive2 { name="EGAD"; version="1.10.0"; sha256="1krwqspyw63zddgksvjvcidfzcxv9165p5dl3cgh1qsb3s427gla"; depends=[affy arrayQualityMetrics Biobase GEOquery gplots igraph impute limma MASS Matrix plyr RColorBrewer RCurl zoo]; }; + EGSEA = derive2 { name="EGSEA"; version="1.10.0"; sha256="1jcbskcadfjyh1iq1appbywfqdvd66q13gg5bhhcpfiam4may1cn"; depends=[AnnotationDbi Biobase DT edgeR EGSEAdata gage ggplot2 Glimma globaltest gplots GSVA HTMLUtils htmlwidgets hwriter limma metap org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db PADOG pathview plotly RColorBrewer safe stringi topGO]; }; + ELBOW = derive2 { name="ELBOW"; version="1.18.0"; sha256="04i3nw6vrmjld0nypp6xxbq8wxdbpjryc6rsvb13j5jaxak7yjcw"; depends=[]; }; + ELMER = derive2 { name="ELMER"; version="2.6.1"; sha256="1675yr1f54cqyzir8rswndgcxb0pjb3c4bka9kdgfnjynk8w7ssv"; depends=[biomaRt circlize ComplexHeatmap doParallel downloader dplyr ELMER_data GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra Gviz IRanges lattice magrittr Matrix MultiAssayExperiment plotly plyr readr reshape rmarkdown rvest S4Vectors stringr SummarizedExperiment TCGAbiolinks tibble tidyr xml2]; }; + EMDomics = derive2 { name="EMDomics"; version="2.12.0"; sha256="1savm8vh1cl8s9rw5jy341a6azx1d8pm0935jvl10ai0cs6q1f22"; depends=[BiocParallel CDFt emdist ggplot2 matrixStats preprocessCore]; }; + ENCODExplorer = derive2 { name="ENCODExplorer"; version="2.8.0"; sha256="1836v5yj5rr3mvmsakbz5ccqc0h3dngipigszbrzcb2qb9m55gqf"; depends=[data_table dplyr DT jsonlite RCurl shiny shinythemes stringi stringr tidyr]; }; + ENVISIONQuery = derive2 { name="ENVISIONQuery"; version="1.30.0"; sha256="0ciilgg8mw4lzclfqqgfrc6crig15m418qfpcfk9s4ykcnjzzial"; depends=[rJava XML]; }; + ENmix = derive2 { name="ENmix"; version="1.18.0"; sha256="0hl5k7ng0mrs7bqjpi693mdfa31l6lvflflz7cs80l7cr82h4raj"; depends=[doParallel foreach geneplotter impute MASS minfi preprocessCore SummarizedExperiment sva wateRmelon]; }; + ERSSA = derive2 { name="ERSSA"; version="1.0.0"; sha256="1dlz57mmh166di7rp0ps322qdy0f4r5xdkn6br2594g7s2a3f5qc"; depends=[BiocParallel DESeq2 edgeR ggplot2 plyr RColorBrewer]; }; + EasyqpcR = derive2 { name="EasyqpcR"; version="1.24.0"; sha256="1znawlhb44j21jhspn703d62pi1zknv1khklmsdlspn5db67wpin"; depends=[gWidgetsRGtk2 matrixStats plotrix plyr]; }; + EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.10.0"; sha256="05n0984x77kvxjj80vx4sh7sz2v90wzf4vqsgbkn7wm45ly6x3h0"; depends=[]; }; + EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="1.0.0"; sha256="0n87yacfrydxrr7rb5f5bkwdfxl7ga2xcj3rn012zy0kknzpcj3z"; depends=[ggplot2 ggrepel]; }; + EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.12.0"; sha256="1bg3nrlsbfqvkrmwnwyilaniqzkaf2mirdjq58bwvz2022lwyzyg"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; }; + EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.12.0"; sha256="0v1c8w28z77z4h944gzdg4p938pd31j0r44mf4x485ps9ah2qhai"; depends=[AnnotationDbi BiocFileCache biocGraph BiocManager ComplexHeatmap DESeq2 EDASeq edgeR geneplotter GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma MASS pathview rappdirs ReportingTools Rgraphviz S4Vectors safe SPIA SummarizedExperiment topGO]; }; + EpiDISH = derive2 { name="EpiDISH"; version="1.4.1"; sha256="1qd4sglib4852igc1hxrrxsr108mil4mj4xxmf61fz45cxq0v262"; depends=[e1071 MASS quadprog]; }; + EventPointer = derive2 { name="EventPointer"; version="2.0.1"; sha256="0rx31xj13m340m1jfms4bzb5c6shmnh4rrzlv3qcjf6zfgh3n118"; depends=[affxparser cobs doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges graph igraph IRanges limma MASS Matrix matrixStats nnls prodlim qvalue RBGL rhdf5 S4Vectors SGSeq stringr SummarizedExperiment]; }; + ExCluster = derive2 { name="ExCluster"; version="1.0.0"; sha256="1vw99avx3d5zwpjzbv28qj4yrzj6bbz82w1qr9pagjam1d5mxhlf"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; }; + ExiMiR = derive2 { name="ExiMiR"; version="2.24.0"; sha256="1nyyvznjvp9rrgzdp63klq3gah8w1qvgi4hkjf9icwc5liszr48j"; depends=[affy affyio Biobase limma preprocessCore]; }; + ExperimentHub = derive2 { name="ExperimentHub"; version="1.8.0"; sha256="1cxdkzkb4rkzsxcva9ich7p9ysdhijqrmacq1hvciyjrj0ql69w4"; depends=[AnnotationHub BiocGenerics BiocManager curl S4Vectors]; }; + ExperimentHubData = derive2 { name="ExperimentHubData"; version="1.8.0"; sha256="09b64x0rh6j83cwvv0hbwydlcxyp032c8m3h20k8kylkpiyx3csq"; depends=[AnnotationHubData BiocCheck BiocGenerics BiocManager biocViews curl DBI ExperimentHub graph httr S4Vectors]; }; + ExpressionAtlas = derive2 { name="ExpressionAtlas"; version="1.10.0"; sha256="0ll7nhzqn25jwfkxg7cq156hhaiwdcm3fbbwy4891fb8pl4fj81a"; depends=[Biobase httr limma S4Vectors SummarizedExperiment XML xml2]; }; + ExpressionView = derive2 { name="ExpressionView"; version="1.34.0"; sha256="0rar2h2qfhqbxs4haxfm6gfvhdmlr1wdp8ashkxkpx97svd4pa3x"; depends=[AnnotationDbi bitops caTools eisa GO_db isa2 KEGG_db]; }; + FCBF = derive2 { name="FCBF"; version="1.0.0"; sha256="0790n8daxwkyas9rjxqwm0pjp7h6584k4sbj54c6146virjcqbk2"; depends=[ggplot2 gridExtra SummarizedExperiment]; }; + FELLA = derive2 { name="FELLA"; version="1.2.0"; sha256="09ljq7wfmm30h93k3ig4iqa7hq13lv961s446wiq0b5yi9s0y72g"; depends=[igraph KEGGREST Matrix plyr]; }; + FEM = derive2 { name="FEM"; version="3.10.0"; sha256="1cqba4j2ajyrjyqwp3q2f89afx74603m5pbsjgflc8zfpf498rgl"; depends=[AnnotationDbi BiocGenerics corrplot graph igraph impute limma marray Matrix org_Hs_eg_db]; }; + FGNet = derive2 { name="FGNet"; version="3.16.0"; sha256="12wv1r60nga4llvrx6blv9s6vlpcy22rz72qbf0ixpf16g16yc1x"; depends=[hwriter igraph plotrix png R_utils RColorBrewer reshape2 XML]; }; + FISHalyseR = derive2 { name="FISHalyseR"; version="1.16.0"; sha256="0gkghipxbdpb3x55j9n583mi1z9cai8g8xcmyj5337dccx91lfag"; depends=[abind EBImage]; }; + FRGEpistasis = derive2 { name="FRGEpistasis"; version="1.18.0"; sha256="0pw7r0w4ppv7jkjrx88a3bj85d96si1f0hqh7a5gpfb2593fd14k"; depends=[fda MASS]; }; + FamAgg = derive2 { name="FamAgg"; version="1.10.0"; sha256="1ry4p8yjq0zhgvv9wx9b085hq5k1q7q60hc5w5pmk94cswvv82vd"; depends=[BiocGenerics gap igraph kinship2 Matrix survey]; }; + FastqCleaner = derive2 { name="FastqCleaner"; version="1.0.0"; sha256="0v18zhzh8xd5b7828nnvlxc8gzwjgc9hnhznjd3w62js2yg9xv4l"; depends=[Biostrings DT htmltools IRanges Rcpp S4Vectors shiny shinyBS ShortRead]; }; + FindMyFriends = derive2 { name="FindMyFriends"; version="1.12.0"; sha256="1yyzqw9hzyxh2sjw8wj3xi5cvkcr9ssnahhwaqrln5zsiq72kn70"; depends=[Biobase BiocGenerics BiocParallel Biostrings digest dplyr filehash ggdendro ggplot2 gtable igraph IRanges kebabs Matrix Rcpp reshape2 S4Vectors]; }; + FitHiC = derive2 { name="FitHiC"; version="1.8.0"; sha256="15xd8mz7660q4zr9p74mq1pqps4iz7pxp8f9ifn21gwg94aq1avn"; depends=[data_table fdrtool Rcpp]; }; + FlowRepositoryR = derive2 { name="FlowRepositoryR"; version="1.14.0"; sha256="1dz0r4f21xhfi6jkxq33y85ayg5jbmic8zyxx5ry7fs6rjx4n75d"; depends=[jsonlite RCurl XML]; }; + FlowSOM = derive2 { name="FlowSOM"; version="1.14.0"; sha256="1inbc49acj02v6rxbk8kzlvi09a61cgkn5rs18zzx7wls9mpqwkv"; depends=[BiocGenerics ConsensusClusterPlus flowCore flowUtils igraph tsne XML]; }; + FoldGO = derive2 { name="FoldGO"; version="1.0.1"; sha256="193bxmsv37k9cj1f8f6qmy1yq74qap18fk46id229ydfp5sd57wg"; depends=[ggplot2 tidyr topGO]; }; + FourCSeq = derive2 { name="FourCSeq"; version="1.16.0"; sha256="1mknsjif4rv1wg5whv8dvkam2fblm2mnvj4qzv12ypnay0hdj8jq"; depends=[Biobase Biostrings DESeq2 fda GenomicAlignments GenomicRanges ggbio ggplot2 gtools LSD Matrix reshape2 Rsamtools rtracklayer SummarizedExperiment]; }; + FunChIP = derive2 { name="FunChIP"; version="1.8.0"; sha256="1b8a2hd5i4zwq28i7zwz8g3b9w2wgrhdrghr70z5n62cxdrbdwd9"; depends=[doParallel fda foreach GenomeInfoDb GenomicAlignments GenomicRanges RColorBrewer Rcpp Rsamtools shiny]; }; + FunciSNP = derive2 { name="FunciSNP"; version="1.26.0"; sha256="1l3p3s9l56ivgwzkixxr51n86s2p91rqayhz605iqpfpxyywyxzg"; depends=[Biobase BiocGenerics ChIPpeakAnno FunciSNP_data GenomicRanges ggplot2 IRanges plyr reshape Rsamtools rtracklayer S4Vectors scales snpStats TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; + GA4GHclient = derive2 { name="GA4GHclient"; version="1.6.0"; sha256="03jk92nrd8n34z0kb88qsv7pxwwrwy7vjhczxz4a9mqwsb2gv891"; depends=[BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges httr IRanges jsonlite S4Vectors VariantAnnotation]; }; + GA4GHshiny = derive2 { name="GA4GHshiny"; version="1.4.0"; sha256="18g9bhn9wkmfw4f55lly97hf00f6ngh560b87nxyx0c9ls0a6wyg"; depends=[AnnotationDbi BiocGenerics dplyr DT GA4GHclient GenomeInfoDb GenomicFeatures openxlsx purrr S4Vectors shiny shinyjs shinythemes tidyr]; }; + GARS = derive2 { name="GARS"; version="1.2.0"; sha256="1i9dfh9g4sx40r8jdwiv81609jgpaby38hvrvgcf6bw06hip6da4"; depends=[cluster DaMiRseq ggplot2 MLSeq SummarizedExperiment]; }; + GAprediction = derive2 { name="GAprediction"; version="1.8.0"; sha256="0a56jgw36h1fcpsclb36hwg612qv0qpxqs6smz4pq8s4apcdvzn0"; depends=[glmnet Matrix]; }; + GDCRNATools = derive2 { name="GDCRNATools"; version="1.2.0"; sha256="0d33sbyc3zn09ak6wzi6qdpna2c65lmdn1qdqhnb94saiaw4x1zk"; depends=[BiocParallel biomaRt clusterProfiler DESeq2 DOSE DT edgeR GenomicDataCommons ggplot2 gplots jsonlite limma org_Hs_eg_db pathview rjson shiny survival survminer XML]; }; + GDSArray = derive2 { name="GDSArray"; version="1.2.0"; sha256="1yjrdnkbgxdfs5i2s10idy3szc9p6fcq6mv246hbsibl6zxxlqlh"; depends=[BiocGenerics DelayedArray gdsfmt S4Vectors SeqArray SNPRelate]; }; + GEM = derive2 { name="GEM"; version="1.8.0"; sha256="008y135dahsrbk2ik5b7hrsjkhg23cxmsfnbyggm000dap6j4a3w"; depends=[ggplot2]; }; + GENESIS = derive2 { name="GENESIS"; version="2.12.1"; sha256="0w3wvi3h86xg14lbhzwcxi41yqba58qfsgaix5vdx6r3jnp073j0"; depends=[Biobase BiocGenerics data_table dplyr foreach gdsfmt GenomicRanges GWASTools igraph IRanges Matrix reshape2 S4Vectors SeqArray SeqVarTools SNPRelate]; }; + GENIE3 = derive2 { name="GENIE3"; version="1.4.0"; sha256="0aks72imjyqxilfj1h9p8hqvkq9hipk2kb503xmclrhgma07195p"; depends=[reshape2]; }; + GEOmetadb = derive2 { name="GEOmetadb"; version="1.44.0"; sha256="05iwq2qglkc3xdkvc1049m1mzyiw91dmfb41vkqbqkyw7jc4561h"; depends=[GEOquery RSQLite]; }; + GEOquery = derive2 { name="GEOquery"; version="2.50.5"; sha256="074dl00c8yi1ihpjkw7vl9vy2hggvipib0jn0hli0wrw7x1h9hg6"; depends=[Biobase dplyr httr limma magrittr readr tidyr xml2]; }; + GEOsubmission = derive2 { name="GEOsubmission"; version="1.34.0"; sha256="1wiaik74yr84jppvq3hqijha2z4m3jr77q2k9zsr6kw0d82ianvw"; depends=[affy Biobase]; }; + GEWIST = derive2 { name="GEWIST"; version="1.26.0"; sha256="0gdq54rjfwlriv61sn0d9v08cfiz1p80p4asb13r05paa25w7vkm"; depends=[car]; }; + GGBase = derive2 { name="GGBase"; version="3.44.0"; sha256="023yzz4sin86fmkl2d0855mkn7iffhvinnz1hchx88f17rn8ysgz"; depends=[AnnotationDbi Biobase BiocGenerics digest genefilter GenomicRanges IRanges limma Matrix S4Vectors snpStats SummarizedExperiment]; }; + GGtools = derive2 { name="GGtools"; version="5.18.0"; sha256="1iqzqmcz8v4gmbcmxmla60848pmwlsbhrj9g8skxfclg7w21qx1m"; depends=[AnnotationDbi biglm Biobase BiocGenerics Biostrings bit data_table ff GenomeInfoDb GenomicRanges GGBase ggplot2 Gviz hexbin Homo_sapiens IRanges iterators reshape2 ROCR Rsamtools rtracklayer S4Vectors snpStats VariantAnnotation]; }; + GIGSEA = derive2 { name="GIGSEA"; version="1.0.0"; sha256="08q4askg07y6pz4j04rd4l1rralx22z4nfw6r2y8b79lcm6svawl"; depends=[locfdr MASS Matrix]; }; + GISPA = derive2 { name="GISPA"; version="1.6.0"; sha256="0xdqfv6ihn4qm1mv1xixyav921scvi406jz00n92jb7lwqm4aadw"; depends=[Biobase changepoint data_table genefilter GSEABase HH lattice latticeExtra plyr scatterplot3d]; }; + GLAD = derive2 { name="GLAD"; version="2.46.0"; sha256="0mj250k9q78z9s5xy2jra3lazv8nva6ngln8pqxdxhlcnrsrw0nk"; depends=[aws]; }; + GMRP = derive2 { name="GMRP"; version="1.10.1"; sha256="187h6fqy5rcrfb5wnvyg078bzxlb5fhbb4xs34r27pyj8xzbza9r"; depends=[diagram GenomicRanges plotrix]; }; + GOFunction = derive2 { name="GOFunction"; version="1.30.0"; sha256="1rsx1nkxyxd4dv4bn4mm1wyq6l0qn7a1gm60j03y9h4idp3hrgr8"; depends=[AnnotationDbi Biobase DBI GO_db graph Rgraphviz SparseM]; }; + GOSemSim = derive2 { name="GOSemSim"; version="2.8.0"; sha256="0ckihpy8jmgn2np1avprz76v9z7i5hqm2gj514c6dmmq3csbc7ib"; depends=[AnnotationDbi GO_db Rcpp]; }; + GOSim = derive2 { name="GOSim"; version="1.20.0"; sha256="00pl7xhs7mskkkmv45fcr448gbvr92v7xc43y0wyj3zrjh1fdm11"; depends=[annotate AnnotationDbi cluster corpcor flexmix GO_db graph Matrix org_Hs_eg_db RBGL Rcpp topGO]; }; + GOTHiC = derive2 { name="GOTHiC"; version="1.18.0"; sha256="0r699dy31kvq6rw734v30jsvna18fnk1by2qmj2gjqyjmkfj1hp3"; depends=[BiocGenerics Biostrings BSgenome data_table GenomicRanges ggplot2 IRanges Rsamtools rtracklayer S4Vectors ShortRead]; }; + GOexpress = derive2 { name="GOexpress"; version="1.16.0"; sha256="0b6fvbm7bj08m4in892qdpm564iki0d56a9jyhg8d8pdmrp960rb"; depends=[Biobase biomaRt ggplot2 gplots randomForest RColorBrewer RCurl stringr]; }; + GOfuncR = derive2 { name="GOfuncR"; version="1.2.0"; sha256="021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk"; depends=[AnnotationDbi GenomicRanges gtools IRanges mapplots Rcpp vioplot]; }; + GOpro = derive2 { name="GOpro"; version="1.8.0"; sha256="1z2lyhnzqvrqfjzavwriaxxzbvbjhjaciyr9azkq296mj3cdih3v"; depends=[AnnotationDbi BH dendextend doParallel foreach GO_db IRanges MultiAssayExperiment org_Hs_eg_db Rcpp S4Vectors]; }; + GOstats = derive2 { name="GOstats"; version="2.48.0"; sha256="0wlqqgfynwqnqhckhsfjwg9zkj6hkmzwd5y76dhqz720vy21rcln"; depends=[annotate AnnotationDbi AnnotationForge Biobase Category GO_db graph RBGL Rgraphviz]; }; + GOsummaries = derive2 { name="GOsummaries"; version="2.18.0"; sha256="0cmb08w5xjqpdjqjkrwqdfiyf1sfj1xqqlyjq9hv0ynjab6skhvm"; depends=[ggplot2 gProfileR gtable limma plyr Rcpp reshape2]; }; + GRENITS = derive2 { name="GRENITS"; version="1.34.0"; sha256="0a2wdsaga0k5x37qad53fdvpp4smmpkfp9f7vy8r9mvr69j3ji9n"; depends=[ggplot2 Rcpp RcppArmadillo reshape2]; }; + GRmetrics = derive2 { name="GRmetrics"; version="1.8.0"; sha256="1ziarcrdhcy5n145m0hjmzwz14k79pdysn0n5qda4nlvd5dpl0hr"; depends=[drc ggplot2 plotly S4Vectors SummarizedExperiment]; }; + GRridge = derive2 { name="GRridge"; version="1.6.0"; sha256="0l6r36kzdmgcamjzzrjchz0q4k9dsxvmdvrrnq1br1xlhgscqc85"; depends=[glmnet graph Iso mvtnorm penalized survival]; }; + GSALightning = derive2 { name="GSALightning"; version="1.10.0"; sha256="0d1zfxzhcgb6h6p8pcfra9ck031n4yb309m17zbql1ld911nv297"; depends=[data_table Matrix]; }; + GSAR = derive2 { name="GSAR"; version="1.16.0"; sha256="1jdjr432i0njpfmymzbv4irf786hrp1wk4vy4sk2x0hcbjigds5z"; depends=[igraph]; }; + GSCA = derive2 { name="GSCA"; version="2.12.0"; sha256="08j8n9hjaf872c1n7ilzhm96d0hb4qa6l30qq516jpynxf326g2w"; depends=[ggplot2 gplots RColorBrewer reshape2 rhdf5 shiny sp]; }; + GSEABase = derive2 { name="GSEABase"; version="1.44.0"; sha256="110al7x0ig8plzrprvhwc7xshi1jzpj2n8llhhg2fh6v6k0k6awr"; depends=[annotate AnnotationDbi Biobase BiocGenerics graph XML]; }; + GSEABenchmarkeR = derive2 { name="GSEABenchmarkeR"; version="1.2.0"; sha256="1b55w2lc5qfzja07i3ddgnll3dm5f4df8x5nkfy034kdmpmvzkma"; depends=[AnnotationDbi AnnotationHub Biobase BiocFileCache BiocParallel edgeR EnrichmentBrowser ExperimentHub GEOquery KEGGandMetacoreDzPathwaysGEO KEGGdzPathwaysGEO rappdirs S4Vectors SummarizedExperiment]; }; + GSEAlm = derive2 { name="GSEAlm"; version="1.42.0"; sha256="16xflz0ad07qy3cl9r4qvi98hlxs2j9wm7dsbw518qkacynpc29g"; depends=[Biobase]; }; + GSRI = derive2 { name="GSRI"; version="2.30.0"; sha256="16zxia3ksgx14rafkjbxbic2rnskh7hql7ifi45n8gg0mkhw535c"; depends=[Biobase fdrtool genefilter GSEABase les]; }; + GSReg = derive2 { name="GSReg"; version="1.16.0"; sha256="08fasaa8inivgs3li8z0yhs2qaa878lrjymk67f8622wlskvmqcd"; depends=[AnnotationDbi GenomicFeatures Homo_sapiens org_Hs_eg_db]; }; + GSVA = derive2 { name="GSVA"; version="1.30.0"; sha256="0q8jwmxv2w5m7z4i7ggdzm2z627484vn5rm0qfxkkqna3hpjnl4i"; depends=[Biobase BiocGenerics geneplotter GSEABase shiny shinythemes]; }; + GUIDEseq = derive2 { name="GUIDEseq"; version="1.12.0"; sha256="0lv59ppr2g5n96mjhllkg6maq9xrm3yd9a98pdrg1w7c40251bxk"; depends=[BiocGenerics BiocParallel Biostrings BSgenome ChIPpeakAnno CRISPRseek data_table GenomeInfoDb GenomicAlignments GenomicRanges hash IRanges limma matrixStats Rsamtools S4Vectors]; }; + GWASTools = derive2 { name="GWASTools"; version="1.28.0"; sha256="1g039bg6pcbxnz9zyzknrl9qx6wzncqjw4lpiy1lq4pc91lqzjln"; depends=[Biobase DBI DNAcopy gdsfmt GWASExactHW lmtest logistf quantsmooth RSQLite sandwich survival]; }; + GateFinder = derive2 { name="GateFinder"; version="1.2.0"; sha256="16whipxykribkcyjar4xxg5736zkb256vy538a4q1hz52dz44s59"; depends=[diptest flowCore flowFP mvoutlier splancs]; }; + GenRank = derive2 { name="GenRank"; version="1.10.0"; sha256="1fs9kfpm1xcdkyfc52hyysxwdb86aghcgig0jam3cvvfgnpm4xk9"; depends=[matrixStats reshape2 survcomp]; }; + GenVisR = derive2 { name="GenVisR"; version="1.14.1"; sha256="1c49fgh4k5018xg0cxy2vx2lz4d9s8xm1kv2b2834cjviianzvhz"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome data_table DBI FField GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra gtable gtools IRanges plyr reshape2 Rsamtools scales VariantAnnotation viridis]; }; + GeneAccord = derive2 { name="GeneAccord"; version="1.0.0"; sha256="1g1rjgvqnf3bqa4phj0q4gzrm3y6ijbxzyjz83ilwdmwxd4vs5rw"; depends=[biomaRt caTools dplyr ggplot2 ggpubr gtools magrittr maxLik RColorBrewer reshape2 tibble]; }; + GeneAnswers = derive2 { name="GeneAnswers"; version="2.24.0"; sha256="0cx6k2m3cllj0hvfmznkydwnw96q5a6k4781jiix7n9j97ys1rf5"; depends=[annotate Biobase downloader Heatplus igraph MASS RBGL RColorBrewer RCurl RSQLite XML]; }; + GeneBreak = derive2 { name="GeneBreak"; version="1.12.0"; sha256="049876x0665zv2apxf48hc5yqi7nbh89sqxlgyfqc2vk4knjgkbj"; depends=[CGHbase CGHcall GenomicRanges QDNAseq]; }; + GeneExpressionSignature = derive2 { name="GeneExpressionSignature"; version="1.28.0"; sha256="12ww6hlgpxchlvrcc0va4x0ayb3119kakmm4yfscbp2xiy1dlinj"; depends=[Biobase PGSEA]; }; + GeneGA = derive2 { name="GeneGA"; version="1.32.0"; sha256="1z83rrlp82q56wp3ywbacrh8ws5rhqn572p94hqj895jb3b2w3km"; depends=[hash seqinr]; }; + GeneGeneInteR = derive2 { name="GeneGeneInteR"; version="1.8.0"; sha256="12bx94xw3pmsnwqb4ksgz9ydn8581x2pdvbdba8p7cwcwbkp2lfk"; depends=[data_table FactoMineR GenomicRanges GGtools igraph IRanges kernlab mvtnorm plspm rioja Rsamtools snpStats]; }; + GeneMeta = derive2 { name="GeneMeta"; version="1.54.0"; sha256="0cwnhr98sc2xb9y7k4c502r1s1pwlwimpajfp7q34qs3w10sj8my"; depends=[Biobase genefilter]; }; + GeneNetworkBuilder = derive2 { name="GeneNetworkBuilder"; version="1.24.0"; sha256="1vrp2ns29fna1wkzzpfwp30ax9y6fr37w9a89lf2391hdpr3hls4"; depends=[graph htmlwidgets plyr Rcpp Rgraphviz rjson XML]; }; + GeneOverlap = derive2 { name="GeneOverlap"; version="1.18.0"; sha256="1p87ngk0lfbb86hwx63x4xjnw77xslh5a7136l1dwia24r9dccls"; depends=[gplots RColorBrewer]; }; + GeneRegionScan = derive2 { name="GeneRegionScan"; version="1.38.0"; sha256="1f266nq1179gyxqwn0pbbwia04hsshs4653flgm2730cyczq58ki"; depends=[affxparser Biobase Biostrings RColorBrewer S4Vectors]; }; + GeneSelectMMD = derive2 { name="GeneSelectMMD"; version="2.26.0"; sha256="1kv81bn9kr3lf41zhixr56ipsxf2ig1zny742494r3j8d4wi947p"; depends=[Biobase limma MASS survival]; }; + GeneSelector = derive2 { name="GeneSelector"; version="2.32.0"; sha256="0hjrwj7z67j6rmfvcd44j4284v3dq7qjcm24arnfskja5zk8zb6j"; depends=[Biobase limma multtest samr siggenes]; }; + GeneStructureTools = derive2 { name="GeneStructureTools"; version="1.2.0"; sha256="1nww8hvbw9s7j1isjkprm3rqxwi8hkhjvsjhjw25yapl72nhk398"; depends=[Biostrings BSgenome_Mmusculus_UCSC_mm10 data_table GenomicRanges Gviz IRanges plyr rtracklayer S4Vectors stringdist stringr]; }; + GeneticsDesign = derive2 { name="GeneticsDesign"; version="1.50.0"; sha256="1pzqdrny4hx6sxnc9glhb5plgrahfdckmcr7symykcc8d896payl"; depends=[gmodels gtools mvtnorm]; }; + GeneticsPed = derive2 { name="GeneticsPed"; version="1.44.0"; sha256="00v32167gl0kkglrzl3xm5bw7p8mfc933k074mf9lpbbf9s1liy7"; depends=[gdata genetics MASS]; }; + GenoGAM = derive2 { name="GenoGAM"; version="2.0.2"; sha256="1vnvsw3jsp9psdd3vlzxvxhsny15j15b3fhyb07fsr26hgd0k5jh"; depends=[BiocParallel Biostrings data_table DelayedArray DESeq2 futile_logger GenomeInfoDb GenomicAlignments GenomicRanges HDF5Array IRanges Matrix Rcpp RcppArmadillo rhdf5 Rsamtools S4Vectors sparseinv SummarizedExperiment]; }; + GenomeGraphs = derive2 { name="GenomeGraphs"; version="1.42.0"; sha256="0n3nbhgwnd09fnn7pyaa8n46hhjrz1gkvzbjjf7p9clv6p937y18"; depends=[biomaRt]; }; + GenomeInfoDb = derive2 { name="GenomeInfoDb"; version="1.18.1"; sha256="049pyzr8iszv3g7wdqf3pz7vg7bzd450c20ln6fgw4g5xnkkr10s"; depends=[BiocGenerics GenomeInfoDbData IRanges RCurl S4Vectors]; }; + GenomicAlignments = derive2 { name="GenomicAlignments"; version="1.18.0"; sha256="0a3zhwripfw2508fvgx3wzqa8nq8vnslg97a911znpwvxh53jl24"; depends=[BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors SummarizedExperiment]; }; + GenomicDataCommons = derive2 { name="GenomicDataCommons"; version="1.6.0"; sha256="00xlskvrcjmj28mqkdi2d4ksqsb603g6wckqvzqyjr417xyyanrl"; depends=[dplyr GenomicRanges httr IRanges jsonlite lazyeval magrittr rappdirs readr S4Vectors SummarizedExperiment xml2]; }; + GenomicFeatures = derive2 { name="GenomicFeatures"; version="1.34.1"; sha256="0slq6hv5bmc3bgrl824jzmr6db3fvaj6b7ihwmdn76pgqqbq2fq6"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings DBI GenomeInfoDb GenomicRanges IRanges RCurl RSQLite rtracklayer S4Vectors XVector]; }; + GenomicFiles = derive2 { name="GenomicFiles"; version="1.18.0"; sha256="0qf2yj4lfnnk64fk125n8sqms01shfqiik04nasx2z3k129ykpxp"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; + GenomicInteractions = derive2 { name="GenomicInteractions"; version="1.16.0"; sha256="0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"; depends=[Biobase BiocGenerics data_table dplyr GenomeInfoDb GenomicRanges ggplot2 gridExtra Gviz igraph InteractionSet IRanges Rsamtools rtracklayer S4Vectors stringr]; }; + GenomicRanges = derive2 { name="GenomicRanges"; version="1.34.0"; sha256="0bgh14d15dpf2iy36qinw45r6n45rqkf0ghazrdl3jfva6vbrb29"; depends=[BiocGenerics GenomeInfoDb IRanges S4Vectors XVector]; }; + GenomicScores = derive2 { name="GenomicScores"; version="1.6.0"; sha256="0lrhkcblvnki6kncwpavs01gbcz22yza6ma8zvfmbrrkfaxqzh8n"; depends=[AnnotationHub Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges S4Vectors XML]; }; + GenomicTuples = derive2 { name="GenomicTuples"; version="1.16.0"; sha256="1d5bdsrs521rxnwiy2xg09d95p45n68dsqq17m4xw3xnfyfzpn3s"; depends=[BiocGenerics data_table GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; + Genominator = derive2 { name="Genominator"; version="1.36.0"; sha256="0lv8ar4z086k8hfjl187klv4yqsb2dawp0xvly6bz6pj3prrih50"; depends=[BiocGenerics DBI GenomeGraphs IRanges RSQLite]; }; + Glimma = derive2 { name="Glimma"; version="1.10.0"; sha256="0cbsi6g8k1whkh21jxfn22sj7wry2g3rshiracf5nyvrl2fnl947"; depends=[edgeR jsonlite S4Vectors]; }; + GlobalAncova = derive2 { name="GlobalAncova"; version="4.0.0"; sha256="1fzd5122z8d68f4brsp2cv8bqcz9yjh5p41pgn6phqkkzjwj9ivg"; depends=[annotate AnnotationDbi Biobase corpcor dendextend globaltest GSEABase VGAM]; }; + GoogleGenomics = derive2 { name="GoogleGenomics"; version="2.4.0"; sha256="0xcj10r85hxh5qy43cjb6ypd849b5wphhhv528simxq4glhgrhxp"; depends=[Biobase Biostrings GenomeInfoDb GenomicAlignments GenomicRanges httr IRanges rjson Rsamtools S4Vectors VariantAnnotation]; }; + GraphAT = derive2 { name="GraphAT"; version="1.54.0"; sha256="1xfd0i0j1fai58c15mc3lrg2jc4iwswyfpyg0ff5hnyhmgr3wnsa"; depends=[graph MCMCpack]; }; + GraphAlignment = derive2 { name="GraphAlignment"; version="1.46.0"; sha256="1qql33ikps9x0dkvc31sxvyf8w119ax7519v5bv35s3i5yxh16i6"; depends=[]; }; + GraphPAC = derive2 { name="GraphPAC"; version="1.24.0"; sha256="0dwh3xshp74isq3rljlivks04mw4r0vgzg74qwyc2ar5b2j96bbg"; depends=[igraph iPAC RMallow TSP]; }; + GreyListChIP = derive2 { name="GreyListChIP"; version="1.14.0"; sha256="1hsjv4r88ldb7pgl5a3im8vdhmbiaj0rrn0clij7jfh5p5r81r1r"; depends=[BSgenome GenomeInfoDb GenomicAlignments GenomicRanges MASS Rsamtools rtracklayer SummarizedExperiment]; }; + Guitar = derive2 { name="Guitar"; version="1.20.0"; sha256="1yxjgm2znqzaxjn3apk4m0nzwzjc7xhv98pxma8sissmcsy63id1"; depends=[GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rsamtools rtracklayer]; }; + Gviz = derive2 { name="Gviz"; version="1.26.4"; sha256="0jvcivgw0ahv2rjadxmrww76xambhf7silczmh38nn4yn4qw6w9y"; depends=[AnnotationDbi Biobase BiocGenerics biomaRt Biostrings biovizBase BSgenome digest GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges lattice latticeExtra matrixStats RColorBrewer Rsamtools rtracklayer S4Vectors XVector]; }; + HDF5Array = derive2 { name="HDF5Array"; version="1.10.1"; sha256="1qwdsygcadl58qj598hfyvs8hp0hqcl9ghnhknahrlhmb7k2bd2d"; depends=[BiocGenerics DelayedArray IRanges rhdf5 S4Vectors]; }; + HDTD = derive2 { name="HDTD"; version="1.16.0"; sha256="1girysaq3w4vfmrdb4vx2g0z9f4nb7ly44b72yhvw9fxsdjzbsc5"; depends=[Rcpp RcppArmadillo]; }; + HELP = derive2 { name="HELP"; version="1.40.0"; sha256="0l6ysv1wdivimvn895alshz6v6avvp7y2gmdphg4iqrmvmjzsd36"; depends=[Biobase]; }; + HEM = derive2 { name="HEM"; version="1.54.0"; sha256="0nkxr9kihihmvap24ir3mgzyq5zq2ng484z9byq5yrbm69wrk887"; depends=[Biobase]; }; + HIBAG = derive2 { name="HIBAG"; version="1.18.1"; sha256="0wgkvqkyv526hdq5n3z27qfk1axbpj5ab6rdlrvjf4fw1v54whmv"; depends=[]; }; + HIREewas = derive2 { name="HIREewas"; version="1.0.2"; sha256="1l0q9x8c4fapa3qkcb3ny3bfvlwwmyl1mvv1hmxqw514ch5ylaiy"; depends=[gplots quadprog]; }; + HMMcopy = derive2 { name="HMMcopy"; version="1.24.0"; sha256="0kn9cqslx6hf70r2gr8x7dwcmvgnf9c3hxrwmvr4vbkl4d3xg8ic"; depends=[geneplotter IRanges]; }; + HPAanalyze = derive2 { name="HPAanalyze"; version="1.0.0"; sha256="1z17384m893wyf7a9v31ghcmsfvly8llbzh98kjz91a6mlqj2aqf"; depends=[cowplot dplyr ggplot2 hpar magrittr readr reshape2 tibble tidyr XLConnect xml2]; }; + HTSFilter = derive2 { name="HTSFilter"; version="1.22.0"; sha256="1j36cdpmagk65wx2rzr6m2gih3j6y12w34qsz870iv42lv3l62ld"; depends=[Biobase BiocParallel DESeq DESeq2 edgeR]; }; + HTSanalyzeR = derive2 { name="HTSanalyzeR"; version="2.34.0"; sha256="1aiv4692avzgl8431bq547jaxxd3klzrfmi0fg8nwj0x1k5syxh8"; depends=[AnnotationDbi biomaRt BioNet cellHTS2 graph GSEABase igraph RankProd]; }; + HTSeqGenie = derive2 { name="HTSeqGenie"; version="4.12.0"; sha256="1rj81n21y6n4zlh0ck2i5zxani6hryb7xzf8azl03qk6q9yy09c5"; depends=[BiocGenerics BiocParallel Biostrings Cairo chipseq GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR hwriter IRanges Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment VariantAnnotation VariantTools]; }; + HTqPCR = derive2 { name="HTqPCR"; version="1.36.0"; sha256="15raybys2fks10a5w1084yy5sx7r4n61rran7xk7yp0cifg9k8ji"; depends=[affy Biobase gplots limma RColorBrewer]; }; + Harman = derive2 { name="Harman"; version="1.10.0"; sha256="0j116k1gkxxbg210y4knc0wdbqjmb2ql72pzsh9r07zcaw2y8fzj"; depends=[Rcpp]; }; + Harshlight = derive2 { name="Harshlight"; version="1.54.0"; sha256="133b98p7b9shxz4nf6qg9qs5bb8yqxdw83cljjblxh5nngpm0s5b"; depends=[affy altcdfenvs Biobase]; }; + Heatplus = derive2 { name="Heatplus"; version="2.28.0"; sha256="0drspjzgb23ra2kdvpxhsd8mdifsf97fcf668llyz2hr0r39fc48"; depends=[RColorBrewer]; }; + HelloRanges = derive2 { name="HelloRanges"; version="1.8.0"; sha256="1brx8bj4xxn63iwfv7ys1fzw7aa1ir8k6jhdq26rzpk973nl6cyy"; depends=[BiocGenerics Biostrings BSgenome docopt GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation]; }; + HiCBricks = derive2 { name="HiCBricks"; version="1.0.0"; sha256="0w3qw22jln44qxx635miaa807q08w010gad7bnqwr0z0zpwrw769"; depends=[BiocFileCache curl data_table digest GenomeInfoDb GenomicRanges ggplot2 IRanges R6 rappdirs RColorBrewer reshape2 rhdf5 S4Vectors scales stringr viridis]; }; + HiCcompare = derive2 { name="HiCcompare"; version="1.4.0"; sha256="08sk4sgjnjchyl1p3dbgr0yjbxl5qg35k4l5gzs08xa9pypw9jjq"; depends=[BiocParallel data_table dplyr GenomicRanges ggplot2 gridExtra gtools InteractionSet IRanges KernSmooth mgcv pheatmap QDNAseq S4Vectors]; }; + HiTC = derive2 { name="HiTC"; version="1.26.0"; sha256="11f96k1707g6milpjgnrjf3b5r42hsrxhb5d8znkcr3y3mrskdbj"; depends=[Biostrings GenomeInfoDb GenomicRanges IRanges Matrix RColorBrewer rtracklayer]; }; + HilbertCurve = derive2 { name="HilbertCurve"; version="1.12.0"; sha256="1yagxajf5paj45a35d1l9aqb5mxwrh06b5jcrw2gldgndmxss9a8"; depends=[circlize GenomicRanges HilbertVis IRanges png]; }; + HilbertVis = derive2 { name="HilbertVis"; version="1.40.0"; sha256="1b6cfzycskklhxp4fw8hyxgnxdrzx047n2igrqdhbh8pv59cdsfa"; depends=[lattice]; }; + HilbertVisGUI = derive2 { name="HilbertVisGUI"; version="1.40.0"; sha256="1qjfbgzzhj54fvgbvzlk37n1p32bc2vbf2yqkbn5y5ml6hsnmccw"; depends=[HilbertVis]; }; + HybridMTest = derive2 { name="HybridMTest"; version="1.26.0"; sha256="1xjykw1j81bai77nhxhxyib5z118isfr755q700934zh8zmsra61"; depends=[Biobase fdrtool MASS survival]; }; + IHW = derive2 { name="IHW"; version="1.10.0"; sha256="0d88l7yr8gvpjflwvyyl4k87g0cd1ylm5knw3aazfb5pkfh7j0rx"; depends=[BiocGenerics fdrtool lpsymphony slam]; }; + IMAS = derive2 { name="IMAS"; version="1.6.0"; sha256="1q90x47w3516qkdr3kkfij1gcf8bmnai3xjj90az6xl9m80d5yvx"; depends=[AnnotationDbi BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfortify ggplot2 gridExtra IRanges IVAS lattice lme4 Matrix Rsamtools S4Vectors survival]; }; + IMMAN = derive2 { name="IMMAN"; version="1.2.0"; sha256="1z8bxi7szjqzp630yg1hh1jkswy4iqnly325f11bhkaj8d04df21"; depends=[BiocFileCache Biostrings igraph seqinr STRINGdb]; }; + IMPCdata = derive2 { name="IMPCdata"; version="1.18.0"; sha256="0qqdpi4g29kf3y2cj7y3db40myacl368alc72lrv1qbw3qncjyjd"; depends=[rjson]; }; + INDEED = derive2 { name="INDEED"; version="1.0.0"; sha256="16yg0abp58kzip3j1vpx6rylsp14q9ypp03axyk3b9nbrl96ra3j"; depends=[devtools glasso]; }; + INPower = derive2 { name="INPower"; version="1.18.0"; sha256="074fylal7rn880vidi10d78s4zcxakq8f4gcxlgpq2hg0ivhd8rk"; depends=[mvtnorm]; }; + INSPEcT = derive2 { name="INSPEcT"; version="1.12.1"; sha256="07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"; depends=[Biobase BiocGenerics BiocParallel DESeq2 deSolve GenomicAlignments GenomicFeatures GenomicRanges IRanges plgem preprocessCore pROC rootSolve Rsamtools S4Vectors shiny SummarizedExperiment TxDb_Mmusculus_UCSC_mm9_knownGene]; }; + IONiseR = derive2 { name="IONiseR"; version="2.6.0"; sha256="01lqisdlsvym8nhgpzn7lpcddk9lv9253dy9v65r2dicb5xqhj00"; depends=[BiocGenerics BiocParallel Biostrings bit64 dplyr ggplot2 magrittr rhdf5 ShortRead stringr tibble tidyr XVector]; }; + IPO = derive2 { name="IPO"; version="1.8.0"; sha256="0r8ybi8jd0bz4a94knf94sa4ncbqbhsbwmg5shj19kn42xmjba9d"; depends=[BiocParallel CAMERA rsm xcms]; }; + IPPD = derive2 { name="IPPD"; version="1.30.0"; sha256="19g39k2cxfrbfh8hzmwk6hh67mp3na8447kd7jrdshd6zd2raaas"; depends=[bitops digest MASS Matrix XML]; }; + IRanges = derive2 { name="IRanges"; version="2.16.0"; sha256="0ljppsk611xi72gc8mbdx1311b63b1ijd401jz5xmxk5frla1nc1"; depends=[BiocGenerics S4Vectors]; }; + ISoLDE = derive2 { name="ISoLDE"; version="1.10.0"; sha256="05c3dsvargd3qk51zmbflvc2qrh07raxdbyzph1nwj21vpc8a1qs"; depends=[]; }; + ITALICS = derive2 { name="ITALICS"; version="2.42.0"; sha256="1k55pd3zz9zzwc04m1cjlv1ib3w78n8qzxdhzhpw0pwaw6bzfpmr"; depends=[affxparser DBI GLAD ITALICSData oligo oligoClasses pd_mapping50k_xba240]; }; + IVAS = derive2 { name="IVAS"; version="2.2.0"; sha256="1x77qs6v7n8jn8i10vjpn9fd72v082xs9bsb6mnxxb8173r1kkjk"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel doParallel foreach GenomeInfoDb GenomicFeatures GenomicRanges ggfortify ggplot2 IRanges lme4 Matrix S4Vectors]; }; + IWTomics = derive2 { name="IWTomics"; version="1.6.0"; sha256="0xn12qjac2kxpyvpm8ly58q41cqz0v3q6pl6cn7hb0lvxcplp86s"; depends=[fda GenomicRanges gtable IRanges KernSmooth S4Vectors]; }; + Icens = derive2 { name="Icens"; version="1.54.0"; sha256="0l70vj53cnvgp5ls205ign47zhl12xbaxl5hdkjs73gbdvx2aagk"; depends=[survival]; }; + IdMappingAnalysis = derive2 { name="IdMappingAnalysis"; version="1.26.0"; sha256="0s6s02awa5i86rcp12ijaqb8cga00kpwiap2nj6s2jdg3kh1ady6"; depends=[Biobase boot mclust R_oo rChoiceDialogs RColorBrewer]; }; + IdMappingRetrieval = derive2 { name="IdMappingRetrieval"; version="1.30.0"; sha256="1knaavzdvm1iz6crhqhxsxhvlrpa9k6n6d82q21w6qag8lkvwc2x"; depends=[AffyCompatible biomaRt ENVISIONQuery R_methodsS3 R_oo rChoiceDialogs RCurl XML]; }; + IdeoViz = derive2 { name="IdeoViz"; version="1.18.0"; sha256="067bd18pb3xyw58xxl0fxa09kcyh4dhdzxbci6i7b82fa17s9hkb"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges RColorBrewer rtracklayer]; }; + Imetagene = derive2 { name="Imetagene"; version="1.12.0"; sha256="0lh15nqjxwgjlhhzrrjj9bpbbkxnq2nlgx3v4fik6q4d5rqx0zbb"; depends=[d3heatmap ggplot2 metagene shiny shinyBS shinyFiles shinythemes]; }; + ImmuneSpaceR = derive2 { name="ImmuneSpaceR"; version="1.10.1"; sha256="16fmlrly3mhcwyhibynqywc8ymk1cjim8inmy37g16acl1rr3l3q"; depends=[Biobase curl data_table ggplot2 gplots gtools heatmaply httr pheatmap plotly preprocessCore R6 reshape2 rjson Rlabkey rmarkdown scales]; }; + ImpulseDE = derive2 { name="ImpulseDE"; version="1.8.0"; sha256="0jiqclcm0w6nh7j3w5wqv0c6lw0pyn4wczld2fmkqyv71mshmakn"; depends=[amap boot]; }; + ImpulseDE2 = derive2 { name="ImpulseDE2"; version="1.6.0"; sha256="0r6sdhg95c99z3dm5vxxjrispnja1lj5a0sif3v4pf7c3wgz3vvr"; depends=[Biobase BiocParallel circlize ComplexHeatmap cowplot DESeq2 ggplot2 knitr Matrix S4Vectors SummarizedExperiment]; }; + InPAS = derive2 { name="InPAS"; version="1.14.1"; sha256="0r1b5f13yq1nqrfk2ry88m5dnz86pjmf9g158c45jzvw0b9czxyd"; depends=[AnnotationDbi Biobase BiocParallel BSgenome cleanUpdTSeq depmixS4 GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges limma preprocessCore S4Vectors seqinr]; }; + InTAD = derive2 { name="InTAD"; version="1.2.1"; sha256="0r4qln2cgqab7rpahm94v4321nn4md5yh0479s0px8zbnrmq3cnn"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggpubr IRanges mclust MultiAssayExperiment qvalue rtracklayer S4Vectors SummarizedExperiment]; }; + IntEREst = derive2 { name="IntEREst"; version="1.6.1"; sha256="0vkrzs96jmkj68pxyi9wm5xxn7p5l8zh86j68pw1857dj0sy8wkr"; depends=[BiocGenerics BiocParallel Biostrings DBI DESeq2 DEXSeq edgeR GenomicAlignments GenomicFeatures GenomicRanges IRanges RMySQL Rsamtools S4Vectors seqinr seqLogo SummarizedExperiment]; }; + InterMineR = derive2 { name="InterMineR"; version="1.4.1"; sha256="1v11h22nw3chxkscdmbc9z4186x885lpnh537yyijp9429bab44l"; depends=[Biostrings GenomicRanges httr igraph IRanges RCurl RJSONIO S4Vectors sqldf SummarizedExperiment XML xml2]; }; + InteractionSet = derive2 { name="InteractionSet"; version="1.10.0"; sha256="0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges Matrix Rcpp S4Vectors SummarizedExperiment]; }; + IntramiRExploreR = derive2 { name="IntramiRExploreR"; version="1.4.0"; sha256="0cv7g8cca447gvzy13xpx7h5sxg2w9n3pmj74rfqpbcpd1m9h2p4"; depends=[FGNet igraph knitr]; }; + IsoCorrectoR = derive2 { name="IsoCorrectoR"; version="1.0.5"; sha256="0qvcck4ky4mlib49xfmmkhmv4ndxnbfn8bssim8m5c7xl5zqxj7a"; depends=[dplyr magrittr pracma quadprog readr readxl stringr tibble WriteXLS]; }; + IsoGeneGUI = derive2 { name="IsoGeneGUI"; version="2.18.0"; sha256="0k7l3h56m4l7l9d7c1vg06dg6a986n4v7v0w6yrmpspajkx302ar"; depends=[Biobase ff geneplotter goric Iso IsoGene jpeg multtest ORCME ORIClust orQA RColorBrewer Rcpp relimp tkrplot xlsx]; }; + IsoformSwitchAnalyzeR = derive2 { name="IsoformSwitchAnalyzeR"; version="1.4.0"; sha256="1fbrbshan00r8qidz1yran84hj4higf1g4iw1qx58h13laqs1yi0"; depends=[Biostrings BSgenome DBI DEXSeq dplyr DRIMSeq edgeR futile_logger GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges limma magrittr plyr RColorBrewer readr reshape2 rtracklayer stringr tximport VennDiagram]; }; + JunctionSeq = derive2 { name="JunctionSeq"; version="1.12.0"; sha256="167m4qh3hb62y0hslrxlb6lksjb8v1fq2s7118vq9g8whrdc35f5"; depends=[Biobase BiocGenerics BiocParallel DESeq2 genefilter geneplotter GenomicRanges Hmisc IRanges locfit plotrix Rcpp RcppArmadillo S4Vectors statmod stringr SummarizedExperiment]; }; + KCsmart = derive2 { name="KCsmart"; version="2.40.0"; sha256="1jhw1w964hvjxcxxzyx03mm5w98a15x4hak9r1bbhi1q38x0vs6p"; depends=[BiocGenerics KernSmooth multtest siggenes]; }; + KEGGREST = derive2 { name="KEGGREST"; version="1.22.0"; sha256="0blpd5a7whd2sswfhqd17h58hg06ymaf80gapdr9ja43hnnlj309"; depends=[Biostrings httr png]; }; + KEGGgraph = derive2 { name="KEGGgraph"; version="1.42.0"; sha256="0ry0pfqc61r0cz98j6zlyhh4qh6568l0w0j61xmysayyp046mgy3"; depends=[graph XML]; }; + KEGGlincs = derive2 { name="KEGGlincs"; version="1.8.0"; sha256="188c5cq2yrcwd991cicgh9ivh5xingdd6d46hahvwmvz3y9qyi7a"; depends=[AnnotationDbi gtools hgu133a_db httr igraph KEGGgraph KEGGREST KOdata org_Hs_eg_db plyr RJSONIO XML]; }; + KEGGprofile = derive2 { name="KEGGprofile"; version="1.24.0"; sha256="140f834dlwry5h6kl3z2zm8ch31syl72l4jkmri4vwy5cyvin5bg"; depends=[AnnotationDbi biomaRt KEGG_db KEGGREST png RCurl TeachingDemos XML]; }; + KinSwingR = derive2 { name="KinSwingR"; version="1.0.3"; sha256="156ins4fqr4kdc5pnikl71pn2ppqknfxf1dcl3ffk82sby1xclkd"; depends=[BiocParallel data_table sqldf]; }; + LBE = derive2 { name="LBE"; version="1.50.0"; sha256="1padaxr7hdqrbwgkma4r64ndxhig7ygl7dvbixziz4qdl7cwi869"; depends=[]; }; + LEA = derive2 { name="LEA"; version="2.4.0"; sha256="1bbcsk6k2w8bbjksbnvd7zi4m1zldmjj5pwspjcciqssk10abwn9"; depends=[]; }; + LINC = derive2 { name="LINC"; version="1.10.0"; sha256="1lbpqdhiyh52m3jrsqlwshaz0ncflx5gpyp7lknw4z1vgyvi4ad5"; depends=[ape Biobase clusterProfiler DOSE ggplot2 ggtree gridExtra org_Hs_eg_db png Rcpp ReactomePA reshape2 sva]; }; + LMGene = derive2 { name="LMGene"; version="2.38.0"; sha256="0ynyknm86lvcimva5krmy3xwi2ni7js6jrvkkjsy7w3q90cr2q6q"; depends=[affy Biobase multtest survival]; }; + LOBSTAHS = derive2 { name="LOBSTAHS"; version="1.8.0"; sha256="0i23z7jwnykhawf1w50rdjzvfbarh7pc30x4d94si0i4qdn7vvv6"; depends=[CAMERA xcms]; }; + LOLA = derive2 { name="LOLA"; version="1.12.0"; sha256="1ysdxkaarwwzw06c9d5xh617g284wk57wpj9lbkfv8rrxkla33d0"; depends=[BiocGenerics data_table GenomicRanges IRanges reshape2 S4Vectors]; }; + LPE = derive2 { name="LPE"; version="1.56.0"; sha256="0ryvbkjx9x394a9za4wyy6rk9avjpwqsgdz6rywp9rr4di551a4h"; depends=[]; }; + LPEadj = derive2 { name="LPEadj"; version="1.42.0"; sha256="11pvvh42idpi7636wrm52whaavl4wnbwki1p82p196m0rvac1jy5"; depends=[LPE]; }; + LRBaseDbi = derive2 { name="LRBaseDbi"; version="1.0.0"; sha256="0idf0gn593b6k0fnpkaphh59cpr6a8582namxrvik1b6zpi5kfzl"; depends=[AnnotationDbi Biobase DBI RSQLite]; }; + LVSmiRNA = derive2 { name="LVSmiRNA"; version="1.32.0"; sha256="14880gimbgw7lmvdq965nm3jgkss1qfakl8xnf66kx4f8mczrvps"; depends=[affy Biobase BiocGenerics limma MASS quantreg SparseM vsn zlibbioc]; }; + LedPred = derive2 { name="LedPred"; version="1.16.0"; sha256="1nimsxm841fnqn0v0x0laq5dcwrp46k9vxaxwd86ayn9sdlgx6fj"; depends=[akima e1071 ggplot2 irr jsonlite plot3D plyr RCurl ROCR testthat]; }; + LineagePulse = derive2 { name="LineagePulse"; version="1.2.0"; sha256="1j5sxcvapra3ddzsd1mwdd07n03pfpk8qra4y7dxxgzkgx4dh32q"; depends=[BiocParallel circlize ComplexHeatmap ggplot2 gplots knitr Matrix RColorBrewer SingleCellExperiment SummarizedExperiment]; }; + Linnorm = derive2 { name="Linnorm"; version="2.6.0"; sha256="1lksh544ds7hq0q47dqk5m3ym12wpjnyhgslnrwabrb972qz43f7"; depends=[amap apcluster ellipse fastcluster fpc ggdendro ggplot2 gmodels igraph limma MASS mclust Rcpp RcppArmadillo Rtsne statmod vegan zoo]; }; + LiquidAssociation = derive2 { name="LiquidAssociation"; version="1.36.0"; sha256="0hz60m9m0098mqwajw83xkraajlbh4q8617d85mfjcbdgmc483a1"; depends=[Biobase geepack org_Sc_sgd_db yeastCC]; }; + Logolas = derive2 { name="Logolas"; version="1.6.0"; sha256="0asi528yb65vwdkxxlsdv9g06fr2y5mzxa3m1669byjb6fjzzs1y"; depends=[Biostrings ggplot2 gridBase LaplacesDemon SQUAREM]; }; + LoomExperiment = derive2 { name="LoomExperiment"; version="1.0.1"; sha256="15p15x840vgnwldzqrlksvlxsl8r0xdn2jkcl9xykhm3frzp5z6v"; depends=[DelayedArray GenomicRanges HDF5Array rhdf5 rtracklayer S4Vectors SingleCellExperiment SummarizedExperiment]; }; + LowMACA = derive2 { name="LowMACA"; version="1.12.0"; sha256="027nrw2qypw3iqs4dwr6gn6bhbq8kx6ba3fjvk7cd9lp3pqw580s"; depends=[BiocParallel Biostrings cgdsr data_table httr LowMACAAnnotation motifStack RColorBrewer reshape2 stringr]; }; + LymphoSeq = derive2 { name="LymphoSeq"; version="1.10.0"; sha256="024d13hrw0s0zmza9bd8nm9s79imwajqvzxiaxj5348pj2d212hr"; depends=[Biostrings circlize data_table dplyr ggplot2 ggtree ineq LymphoSeqDB msa phangorn plyr RColorBrewer reshape stringdist UpSetR VennDiagram]; }; + M3C = derive2 { name="M3C"; version="1.4.0"; sha256="1cbh9q95zx06inz9y7gc85rscv2wrd5d49mdk5107rnkr4hsidpz"; depends=[cluster dendextend doParallel doSNOW foreach ggplot2 Matrix matrixcalc NMF RColorBrewer Rtsne sigclust survival]; }; + M3D = derive2 { name="M3D"; version="1.16.0"; sha256="0a7xs3kqvyxswsa4zcdakij4rvpv1pr4fmplnvxyskhh2zps7xyl"; depends=[BiocGenerics BiSeq GenomicRanges IRanges Rcpp S4Vectors SummarizedExperiment]; }; + M3Drop = derive2 { name="M3Drop"; version="1.8.0"; sha256="1jblfjk186lxqaczln1b8xj7pbiajwpnklh9czk0fdr4w5x77nqy"; depends=[bbmle gplots numDeriv RColorBrewer statmod]; }; + MACPET = derive2 { name="MACPET"; version="1.2.0"; sha256="0799d3pr5b6g7xbi75pf693768nspdc73qay72naghyql6g91s96"; depends=[BH bigmemory BiocParallel Biostrings futile_logger GenomeInfoDb GenomicAlignments GenomicRanges GEOquery gtools InteractionSet intervals IRanges knitr plyr rbamtools Rbowtie Rcpp Rsamtools rtracklayer S4Vectors ShortRead]; }; + MADSEQ = derive2 { name="MADSEQ"; version="1.8.0"; sha256="1b7d6niz8lhvd17xjl4hy1yyki049cg6wd3g8wp38bm3zs6dzfd1"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 coda GenomeInfoDb GenomicAlignments GenomicRanges IRanges preprocessCore rjags Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation vcfR VGAM zlibbioc]; }; + MAGeCKFlute = derive2 { name="MAGeCKFlute"; version="1.2.2"; sha256="0jl5k0c0146b5mv34wrn0ld9icgdppvhyqnbx0rk18vgyf81bzjn"; depends=[biomaRt bladderbatch clusterProfiler data_table DOSE ggExtra ggplot2 ggrepel ggsci gridExtra pathview pheatmap png sva]; }; + MAIT = derive2 { name="MAIT"; version="1.16.0"; sha256="05m31mhzs0lfw8644gsnby55gyk5ljjkfwnav2mbw76wxsb3sk5g"; depends=[agricolae CAMERA caret class e1071 gplots MASS pls plsgenomics Rcpp xcms]; }; + MANOR = derive2 { name="MANOR"; version="1.54.0"; sha256="102s71adp93n47sz2hcqs5ihykwcvha6sz7v24p409a7rj8ary38"; depends=[GLAD]; }; + MAST = derive2 { name="MAST"; version="1.8.1"; sha256="0vbx4400g1szr3lzbrj540fzcvqkld754j9mbwvdpwyagakjcdvy"; depends=[abind Biobase BiocGenerics data_table ggplot2 plyr progress reshape2 S4Vectors SingleCellExperiment stringr SummarizedExperiment]; }; + MBASED = derive2 { name="MBASED"; version="1.16.0"; sha256="0046yjpjdczxjqkpvsdsj8fnah1kmz4m038k49laqlrricyl6f2f"; depends=[BiocGenerics BiocParallel GenomicRanges RUnit SummarizedExperiment]; }; + MBAmethyl = derive2 { name="MBAmethyl"; version="1.16.0"; sha256="05jwqlvmjhcfqjqxv6m5mmc72q8lfv2qqwm0f8j1dddpvvyh8fzd"; depends=[]; }; + MBCB = derive2 { name="MBCB"; version="1.36.0"; sha256="0yizhggn77arg1pnl3qd25xc5awwv1f1hi3mk6p2c5pdk48mz679"; depends=[preprocessCore tcltk2]; }; + MBttest = derive2 { name="MBttest"; version="1.10.0"; sha256="05cwwqj8qjj66ndy2hdx2jxna07xjqg7qv4z1gar6r91p482zsp0"; depends=[gplots gtools]; }; + MCRestimate = derive2 { name="MCRestimate"; version="2.38.0"; sha256="1hl5bqibajwscir94dla23544sg866hqx1h793fj7m38xcjhxlzn"; depends=[Biobase e1071 golubEsets pamr randomForest RColorBrewer]; }; + MCbiclust = derive2 { name="MCbiclust"; version="1.6.0"; sha256="1rd31c0hxkvhkhyzx0m9scmxhlmibifgymgzhhmlmrg7wj1c11i5"; depends=[AnnotationDbi BiocParallel cluster GGally ggplot2 GO_db org_Hs_eg_db scales WGCNA]; }; + MDTS = derive2 { name="MDTS"; version="1.2.0"; sha256="1h0vpbi62j0g1cdp06xkp0y4aymnqqhp7frhwi6f7hsiviaz2c0p"; depends=[Biostrings DNAcopy GenomicAlignments GenomicRanges IRanges Rsamtools stringr]; }; + MEAL = derive2 { name="MEAL"; version="1.12.0"; sha256="05cfyq3fffxj802cyh3bghfn2gg6z0yhy2spii9n8pxmsfcsr7pn"; depends=[Biobase BiocGenerics DMRcate GenomicRanges ggplot2 Gviz IRanges isva limma matrixStats minfi missMethyl MultiDataSet permute S4Vectors SmartSVA SummarizedExperiment vegan]; }; + MEDIPS = derive2 { name="MEDIPS"; version="1.34.0"; sha256="1bb8k0jzxfji79qxb4v6pdp9jyf6hv83g5mmqj74k3x2cglycwia"; depends=[biomaRt Biostrings BSgenome DNAcopy edgeR GenomicRanges gtools IRanges preprocessCore Rsamtools rtracklayer]; }; + MEDME = derive2 { name="MEDME"; version="1.42.0"; sha256="0yg04lghqc3sfyakf8id3dc5gd0bfhaf9lp903g5jpiai5779byy"; depends=[Biostrings drc MASS]; }; + MEIGOR = derive2 { name="MEIGOR"; version="1.16.0"; sha256="1jxl2bcsbrlab6ss66388l64k5xcjr5g3gpgya2rk4yq237mghl6"; depends=[CNORode deSolve Rsolnp snowfall]; }; + MGFM = derive2 { name="MGFM"; version="1.16.0"; sha256="08ngcr1a979amjdl8x5a7mn1zdvrpa4h35rkhimi9kr0fn68kj34"; depends=[annotate AnnotationDbi]; }; + MGFR = derive2 { name="MGFR"; version="1.8.0"; sha256="0whjr6b2dj6wmagd706q7hxp3nsr3mxsw5p7shv6kdf352pc7xv3"; depends=[annotate biomaRt]; }; + MIGSA = derive2 { name="MIGSA"; version="1.6.0"; sha256="19gfb98qmb8wbi343lw92sf7d29xliyzb3wz095pd2npsjr69qkl"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel data_table edgeR futile_logger ggdendro ggplot2 GO_db GOstats graph GSEABase ismev limma matrixStats org_Hs_eg_db RBGL reshape2 Rgraphviz RJSONIO vegan]; }; + MIMOSA = derive2 { name="MIMOSA"; version="1.20.0"; sha256="0ai8z8m4hvx4widz4kwk2hp4vbwxyw7z4hgz6yy1fzyqa1zh869a"; depends=[Biobase coda data_table Formula ggplot2 MASS MCMCpack modeest plyr pracma Rcpp RcppArmadillo reshape scales testthat]; }; + MIRA = derive2 { name="MIRA"; version="1.4.0"; sha256="1jilw2brpipppl8rwyad5gbmkjj37y8416igpnqnhk2ig5h7h107"; depends=[Biobase BiocGenerics bsseq data_table GenomicRanges ggplot2 IRanges S4Vectors]; }; + MLInterfaces = derive2 { name="MLInterfaces"; version="1.62.0"; sha256="12bgplyzfh0hkwmdp5w4cs5zw3ygdhzmiqzm8vhjyni6m9nrxwy8"; depends=[annotate Biobase BiocGenerics cluster fpc gbm gdata genefilter ggvis hwriter MASS mlbench pls RColorBrewer rda rpart sfsmisc shiny threejs]; }; + MLP = derive2 { name="MLP"; version="1.30.0"; sha256="03h7k5v620x2hw6k3gddaba40fwh6zvpmlnhf6mcml7ldsni95y9"; depends=[affy AnnotationDbi gdata gmodels gplots gtools plotrix]; }; + MLSeq = derive2 { name="MLSeq"; version="2.0.0"; sha256="0v6mv7j46g0ilqxq3bw72zw8mznazqpw3y3bzs2v6577gim7idj1"; depends=[Biobase caret DESeq2 edgeR foreach ggplot2 limma plyr sSeq SummarizedExperiment xtable]; }; + MMDiff2 = derive2 { name="MMDiff2"; version="1.10.0"; sha256="0ljdr6y3plzpf9j70ghw41x3jpb8p52lqb9987gm1mw7lxw9iraf"; depends=[Biobase Biostrings BSgenome GenomicRanges ggplot2 locfit RColorBrewer Rsamtools S4Vectors shiny]; }; + MODA = derive2 { name="MODA"; version="1.8.0"; sha256="0jarqlyfx81pamdl5z1kx96ri6kjq59lv144ifw8ga6kzs5bng58"; depends=[AMOUNTAIN cluster dynamicTreeCut igraph RColorBrewer WGCNA]; }; + MPFE = derive2 { name="MPFE"; version="1.18.0"; sha256="02lnymmsl1k770jh41sak6dxkzsb0c38934aslbd890dibc2c04i"; depends=[]; }; + MPRAnalyze = derive2 { name="MPRAnalyze"; version="1.0.0"; sha256="0irwgb1466gca77s2cfv1m915r0m7li9h0xqc47na5wjnm89xx40"; depends=[BiocParallel progress SummarizedExperiment]; }; + MSGFgui = derive2 { name="MSGFgui"; version="1.16.0"; sha256="1s875q1r5sraxm0lnvcv6vznkna3r0pp0ssnxpw2hwbfdrhs7zp1"; depends=[MSGFplus mzID mzR shiny shinyFiles xlsx]; }; + MSGFplus = derive2 { name="MSGFplus"; version="1.16.0"; sha256="0q1bpb6f73syngq6y1y53vqkpr4ma3nlv5scvl3ps6s70qim7183"; depends=[mzID ProtGenerics]; }; + MSnID = derive2 { name="MSnID"; version="1.16.1"; sha256="077n6ljcnnl7q4w0qj8v46vm4sjk9vzzfqf7wsc6lz0wmyzqdng3"; depends=[Biobase data_table doParallel dplyr foreach iterators MSnbase mzID mzR ProtGenerics R_cache Rcpp reshape2]; }; + MSnbase = derive2 { name="MSnbase"; version="2.8.2"; sha256="1c90xxr743mackcghimnc0912zzy33p13m6azmz6d6daiahqrzkz"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS mzID mzR pcaMethods plyr preprocessCore ProtGenerics Rcpp S4Vectors scales vsn XML]; }; + MSstats = derive2 { name="MSstats"; version="3.14.0"; sha256="0fp5xp9mk8lg8s737fivgbvj51sxzzh1f6rdkcj9hifjc7r18s2y"; depends=[data_table doSNOW dplyr foreach ggplot2 ggrepel gplots limma lme4 marray MASS minpack_lm preprocessCore randomForest reshape2 snow stringr survival tidyr]; }; + MSstatsQC = derive2 { name="MSstatsQC"; version="2.0.0"; sha256="12s1d4dv7dg95fm80mkaa7nd28j7yi9kxngbwbmzfgkrypjii4ap"; depends=[dplyr ggExtra ggplot2 MSnbase plotly qcmetrics RecordLinkage]; }; + MSstatsQCgui = derive2 { name="MSstatsQCgui"; version="1.2.0"; sha256="1dwhr39gpkknk8920zpb2fvjkskkljkj9d4ah0yi7gwl45vv2gll"; depends=[dplyr ggExtra gridExtra MSstatsQC plotly RecordLinkage shiny]; }; + MSstatsTMT = derive2 { name="MSstatsTMT"; version="1.0.0"; sha256="0mpkzj3vzw3hcwf4fm07ywqdchwbmggs4xzrvalgwk5nbmvis9ai"; depends=[data_table dplyr ggplot2 limma lme4 matrixStats MSstats nlme reshape2 tidyr]; }; + MTseeker = derive2 { name="MTseeker"; version="1.0.6"; sha256="0fsb7k6pkl15q8csygpsjrz4jvy20mfd5rfmhl7q7ffj4d7sprxh"; depends=[Biobase BiocGenerics Biostrings circlize GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gmapR Homo_sapiens IRanges jsonlite Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VariantTools viridis xml2]; }; + MVCClass = derive2 { name="MVCClass"; version="1.56.0"; sha256="1hw36gd1z19dir6fl7j3dzqzi5p1668zbwpcz7l21hbyycv27l0j"; depends=[]; }; + MWASTools = derive2 { name="MWASTools"; version="1.6.0"; sha256="0bkl7vgyac6xhjj636vlmynq75zyp6smvjvzg1ymkgg800wylg4c"; depends=[boot car ComplexHeatmap ggplot2 glm2 gridExtra igraph KEGGgraph KEGGREST ppcor qvalue RCurl SummarizedExperiment]; }; + MantelCorr = derive2 { name="MantelCorr"; version="1.52.0"; sha256="1z0f6g5zbxl1sqcl6rdx7y6vh637i6209ya9fsan6wi5r8rcsamn"; depends=[]; }; + MassArray = derive2 { name="MassArray"; version="1.34.0"; sha256="0xi1d4bhn2iy3dignw2ar6c42axrcaab207ww7zbg2yv8ndhzn9m"; depends=[]; }; + MassSpecWavelet = derive2 { name="MassSpecWavelet"; version="1.48.0"; sha256="08l4113qh9rc0zi1b2745dgwbalcg030bx7vx0kqpjmq5lm6vw8c"; depends=[waveslim]; }; + MatrixRider = derive2 { name="MatrixRider"; version="1.14.0"; sha256="17n3s0gdj3jjlf4pangnbdb00ak62j5wvdqd8yhackhs4z9zbchb"; depends=[Biostrings IRanges S4Vectors TFBSTools XVector]; }; + MaxContrastProjection = derive2 { name="MaxContrastProjection"; version="1.6.0"; sha256="0i3kk071m6n3p93kkbnyriigyb3xilw1nm6ascilj746iapqnjpf"; depends=[EBImage]; }; + MeSHDbi = derive2 { name="MeSHDbi"; version="1.18.0"; sha256="1if3jrrxlrsrza7404d7banrdfbz5g1v69wydxglldzfim3g9jw3"; depends=[AnnotationDbi Biobase BiocGenerics RSQLite]; }; + MeasurementError_cor = derive2 { name="MeasurementError.cor"; version="1.54.0"; sha256="0s39wlfcqag15y73dapmnz0zrywsnd9flz1n7yl20r9p8dfmhv12"; depends=[]; }; + MergeMaid = derive2 { name="MergeMaid"; version="2.54.0"; sha256="07cgcfvppdvyrb0hhi24126ysdcal8vjyplqxfkqxxyjpv0p8ap8"; depends=[Biobase MASS survival]; }; + Mergeomics = derive2 { name="Mergeomics"; version="1.10.0"; sha256="16xv75q790r0apdb1yb10j6mcjs67a891av1kjf21xyp5g5bgpja"; depends=[]; }; + MetCirc = derive2 { name="MetCirc"; version="1.12.0"; sha256="0jbxfg57xc1sggglcl5daddc7iy7jn3mjvqyfzbppivkl5mgfqyp"; depends=[amap circlize scales shiny]; }; + MetID = derive2 { name="MetID"; version="1.0.0"; sha256="12nrbdq4xracd6p7xz3l0dvqp4xlj34jr7wj90wmk09i89h7sfjj"; depends=[ChemmineR devtools igraph Matrix stringr]; }; + MetNet = derive2 { name="MetNet"; version="1.0.0"; sha256="0xsifgrxhvxiy04qm2agr3i14zl8r2d3knmjs4b5m2panl6zancj"; depends=[BiocParallel bnlearn mpmi parmigene ppcor rfPermute sna stabs WGCNA]; }; + MetaCyto = derive2 { name="MetaCyto"; version="1.4.0"; sha256="1d6pshk81dg3jjz5hkm3qgzs4jzfag2lrhr65ff7skj38wlslzcz"; depends=[cluster fastcluster flowCore FlowSOM ggplot2 metafor tidyr]; }; + MetaNeighbor = derive2 { name="MetaNeighbor"; version="1.2.0"; sha256="1wa5i8b8pa2hj9sx1cf01vqvc3pklbjkq7h6pr0i2m3czcc72d09"; depends=[beanplot gplots RColorBrewer SummarizedExperiment]; }; + Metab = derive2 { name="Metab"; version="1.16.0"; sha256="0a6sxn4833nm1jrdybcsl50vw9gkmx746x4552i1fd0m7i6srrlm"; depends=[pander svDialogs xcms]; }; + MetaboSignal = derive2 { name="MetaboSignal"; version="1.12.0"; sha256="1wgpcn25cpql6dwgwpxw16w8hizny92xfbgs4rjz4dpssg9n1qq3"; depends=[AnnotationDbi biomaRt EnsDb_Hsapiens_v75 hpar igraph KEGGgraph KEGGREST MWASTools mygene org_Hs_eg_db RCurl]; }; + MethPed = derive2 { name="MethPed"; version="1.10.0"; sha256="17snj89b00pafns713qqp9ljspjciip7zfskl29bzmvi5b2rgch7"; depends=[Biobase randomForest]; }; + MethTargetedNGS = derive2 { name="MethTargetedNGS"; version="1.14.0"; sha256="0by77378lml6ncz53c7xkh29dayach31p3fn0jrf31x947larnzy"; depends=[Biostrings gplots seqinr stringr]; }; + MethylAid = derive2 { name="MethylAid"; version="1.16.0"; sha256="03qf2j12nq6nqfs96lsdk7jny2ak6258j5bq0brp7wmpijlnjrak"; depends=[Biobase BiocGenerics BiocParallel ggplot2 gridBase hexbin matrixStats minfi RColorBrewer shiny SummarizedExperiment]; }; + MethylMix = derive2 { name="MethylMix"; version="2.12.0"; sha256="062jr6qskp3psmpirqn5aiq5mhw3k1ipyb0m16ds2i95n8v3ky5p"; depends=[data_table digest foreach ggplot2 impute limma R_matlab RColorBrewer RCurl RPMM]; }; + MethylSeekR = derive2 { name="MethylSeekR"; version="1.22.0"; sha256="1nqwza5bqkn0k664j1a2p518a3pj27zwlc5pkvjbh09cjvfibyf0"; depends=[BSgenome geneplotter GenomicRanges IRanges mhsmm rtracklayer]; }; + Mfuzz = derive2 { name="Mfuzz"; version="2.42.0"; sha256="105xk52hxc2d5yy0fy4cb0zhrpnansvyb0dzx9jc1dfjvxzq4vjg"; depends=[Biobase e1071 tkWidgets]; }; + MiChip = derive2 { name="MiChip"; version="1.36.0"; sha256="10v9vvyr4bs7l0x6cb6frhni8sa16sdllykjsbnjxd3jynvzrpy9"; depends=[Biobase]; }; + MiPP = derive2 { name="MiPP"; version="1.54.0"; sha256="08g19yw9hbrwsm630rz907dqlfs7qg2xvaby9bx3mjiwlr7d15wx"; depends=[Biobase e1071 MASS]; }; + MiRaGE = derive2 { name="MiRaGE"; version="1.24.0"; sha256="00qhq68nai3kl6ysrq8m8b008b0zmmr9d3sg7j88g55fqx2c810q"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager S4Vectors]; }; + MineICA = derive2 { name="MineICA"; version="1.22.0"; sha256="1n10x9y5x1h06k1kv2jv3ym5n950dhcd20g34rarx0zyihd2ln4j"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt cluster colorspace fastICA foreach fpc ggplot2 GOstats graph gtools Hmisc igraph JADE lumi lumiHumanAll_db marray mclust plyr RColorBrewer Rgraphviz scales xtable]; }; + MinimumDistance = derive2 { name="MinimumDistance"; version="1.26.0"; sha256="0rv7pgzbrscc8raa49x1nbvbp3ivr8kwdr8rf6hvfw8y1xk3rnba"; depends=[Biobase BiocGenerics data_table DNAcopy ff foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment VanillaICE]; }; + Mirsynergy = derive2 { name="Mirsynergy"; version="1.18.0"; sha256="19nw7yapcxvidzzdbhjzplajfmss65drqq5xrsz1ycr87jgh8h5b"; depends=[ggplot2 gridExtra igraph Matrix RColorBrewer reshape scales]; }; + MmPalateMiRNA = derive2 { name="MmPalateMiRNA"; version="1.32.0"; sha256="045089yfj5aakabxhpjld9fa62sfr48xqb88j8m3xm7561ml20ql"; depends=[Biobase lattice limma statmod vsn xtable]; }; + MoPS = derive2 { name="MoPS"; version="1.16.0"; sha256="0wypkl5kdjmwf78pwbgdsin8fxiycfwkf3kwrbqxc7r27lplgwyj"; depends=[Biobase]; }; + MoonlightR = derive2 { name="MoonlightR"; version="1.8.0"; sha256="16jhqygppfy82h3jnldigf1mgirbh6wcrqd61nn335kgj1d016p0"; depends=[Biobase circlize clusterProfiler doParallel DOSE foreach GEOquery gplots HiveR limma parmigene randomForest RColorBrewer RISmed SummarizedExperiment TCGAbiolinks]; }; + MotIV = derive2 { name="MotIV"; version="1.38.0"; sha256="1qrpydwc5bn8f0843qkyhw6920xk8kvq452ird0ij96g6faiv9a8"; depends=[BiocGenerics Biostrings IRanges lattice rGADEM S4Vectors]; }; + MotifDb = derive2 { name="MotifDb"; version="1.24.1"; sha256="1q454k3p4ib2z79rcgwyx9s9s7gg5j0vlhca1b579qzi3692m8xi"; depends=[BiocGenerics Biostrings IRanges rtracklayer S4Vectors splitstackshape]; }; + Mulcom = derive2 { name="Mulcom"; version="1.32.0"; sha256="0k3illh3dchd5nwa4y87v1n0lkil7p5yiqzg9v65nxv35mhkg0vv"; depends=[Biobase fields]; }; + MultiAssayExperiment = derive2 { name="MultiAssayExperiment"; version="1.8.1"; sha256="1lr4mhj15vhhx644i6k91c8cvnam2fam9r7hy480kd0qlc5n54sc"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors SummarizedExperiment tidyr]; }; + MultiDataSet = derive2 { name="MultiDataSet"; version="1.10.0"; sha256="1sr93zdirjqgsffmkv9plaqbg3rfsz8lh96mqv7xrnc3nmhmm65y"; depends=[Biobase BiocGenerics GenomicRanges ggplot2 ggrepel IRanges limma qqman S4Vectors SummarizedExperiment]; }; + MultiMed = derive2 { name="MultiMed"; version="2.4.0"; sha256="1dfcqh7px0zzgrg96r3930jxzcgvc91xlfm4q9fnn3w85nzgdnrb"; depends=[]; }; + MutationalPatterns = derive2 { name="MutationalPatterns"; version="1.8.0"; sha256="0w9lg1zs106h6rqvy8mhikq6q6q9syw6c1prcxr38ssh85rcih12"; depends=[BiocGenerics Biostrings cowplot GenomeInfoDb GenomicRanges ggdendro ggplot2 IRanges NMF plyr pracma reshape2 S4Vectors SummarizedExperiment VariantAnnotation]; }; + NADfinder = derive2 { name="NADfinder"; version="1.6.0"; sha256="01jr6pds2r5h7fmm9z0rajiavx7fh4zxf623s1rdjg9ir6njq5m5"; depends=[ATACseqQC baseline BiocGenerics corrplot csaw EmpiricalBrownsMethod GenomeInfoDb GenomicAlignments GenomicRanges IRanges limma metap rbamtools Rsamtools rtracklayer S4Vectors signal SummarizedExperiment trackViewer]; }; + NBSplice = derive2 { name="NBSplice"; version="1.0.1"; sha256="155cyb7h7sn7q6m63cv33wbackdq7ryvnnidcy86321yrfjyx023"; depends=[BiocParallel car edgeR ggplot2 MASS mppa reshape2]; }; + NCIgraph = derive2 { name="NCIgraph"; version="1.30.0"; sha256="16mxxrq6g4szig29cah2a13qp1ybsh8ci37izlq6gpxn0h00maym"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; }; + NGScopy = derive2 { name="NGScopy"; version="1.16.0"; sha256="1d5r841g5h4siazhkah2xz1all77kgi2q1a0hhhqsnwrnq7f774v"; depends=[changepoint rbamtools Xmisc]; }; + NOISeq = derive2 { name="NOISeq"; version="2.26.0"; sha256="0xf13vxwdlgi6ybg038lq1mw8zypj0aajvc4vn0rc7587m7l1vnd"; depends=[Biobase Matrix]; }; + NTW = derive2 { name="NTW"; version="1.32.0"; sha256="10ndg6mina5wz3w87wpv4mnbxdyj6rhvc9jqf954wmh6gj04vyin"; depends=[mvtnorm]; }; + NanoStringDiff = derive2 { name="NanoStringDiff"; version="1.12.0"; sha256="1927ry931ckjrci6yfk3fh774bizh4yb5f7p7x1ra1yxzfizq7k3"; depends=[Biobase matrixStats Rcpp]; }; + NanoStringQCPro = derive2 { name="NanoStringQCPro"; version="1.14.0"; sha256="1kisr7j27iwyxjxsylnlrqz9ac5kbwr4indg0qkc3ycdlqqxbqvl"; depends=[AnnotationDbi Biobase knitr NMF org_Hs_eg_db png RColorBrewer]; }; + NarrowPeaks = derive2 { name="NarrowPeaks"; version="1.26.0"; sha256="06lppn4pbp0f3yb3lbpqmk7fqw6i754h9c8v1akvhg22wgb8428x"; depends=[BiocGenerics CSAR fda GenomeInfoDb GenomicRanges ICSNP IRanges S4Vectors]; }; + NeighborNet = derive2 { name="NeighborNet"; version="1.0.0"; sha256="16fmsh71sx65g505mwbhkv9sf1y7niy24zpygxv3aqklqqrnk97r"; depends=[graph]; }; + NetPathMiner = derive2 { name="NetPathMiner"; version="1.18.0"; sha256="1pyqplxzmdd3sjwlr3dzhb39gfhkbd5a550inrvxh4gqnw9r2lpl"; depends=[igraph]; }; + NetSAM = derive2 { name="NetSAM"; version="1.22.0"; sha256="10wmq1vgzdsp6iyia7gqh1d685cj1nikgvygpl69hgciabn3kzz5"; depends=[graph igraph seriation]; }; + NormalyzerDE = derive2 { name="NormalyzerDE"; version="1.0.0"; sha256="1ql62i9mgnr3vafz0yfi8zxxlkccjlrjkb4lnrxv0sshhs5kw4di"; depends=[ape Biobase car ggplot2 limma MASS matrixStats preprocessCore raster RcmdrMisc SummarizedExperiment vsn]; }; + NormqPCR = derive2 { name="NormqPCR"; version="1.28.0"; sha256="1b4j0ngqlkpc1fhfnkmk6h917has6ldi1876rsincl28yfvghz25"; depends=[Biobase qpcR RColorBrewer ReadqPCR]; }; + NuPoP = derive2 { name="NuPoP"; version="1.32.0"; sha256="0p1v7v5shvcbiwgi6fy1fkh55ikks6svh17f2h7biw5j29zwg878"; depends=[]; }; + OCplus = derive2 { name="OCplus"; version="1.56.0"; sha256="0brkcx3vapi7gnw8v6023j56pi6mgki26hx71fq4ldwchwrg4pxr"; depends=[akima multtest]; }; + OGSA = derive2 { name="OGSA"; version="1.12.0"; sha256="0qcnc6658ggv4is9a0s9lid41ns9845qbwd5m0l8r9qjzgmix2s7"; depends=[Biobase gplots limma]; }; + OLIN = derive2 { name="OLIN"; version="1.60.0"; sha256="0vmmxx74i3ch00xsaw60b82h7nbh8rgv6xzbzmcnpa79anaamv3l"; depends=[limma locfit marray]; }; + OLINgui = derive2 { name="OLINgui"; version="1.56.0"; sha256="03n5xlh6fhcw7mvsdaihxn0b39zyhf3f2fayql40nkcinfmbmr50"; depends=[marray OLIN tkWidgets widgetTools]; }; + OMICsPCA = derive2 { name="OMICsPCA"; version="1.0.0"; sha256="1n7rl4xnm58dbp34fhhm7ijhzj190j1xghdgjjnc6pgaqnzv9yl4"; depends=[cluster clValid corrplot cowplot data_table factoextra FactoMineR fpc GenomeInfoDb ggplot2 HelloRanges IRanges kableExtra magick MASS MultiAssayExperiment NbClust OMICsPCAdata pdftools PerformanceAnalytics reshape2 rgl rmarkdown rtracklayer tidyr]; }; + OPWeight = derive2 { name="OPWeight"; version="1.4.0"; sha256="1b6p6fxq0m7j85wmrmb2p3af8shh3wbd0m0522dwcw7jn7mj1lai"; depends=[MASS qvalue tibble]; }; + ORFik = derive2 { name="ORFik"; version="1.2.0"; sha256="15kbz7kgklf9ysajlvxxckm2s09h34hvdlms8k94g5a1dmjij1xa"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rcpp Rsamtools rtracklayer S4Vectors]; }; + OSAT = derive2 { name="OSAT"; version="1.30.0"; sha256="12cswkscavbkx8cxj0kzk6gz1h8xwp24mwy53dgyr771sch76k7j"; depends=[]; }; + OTUbase = derive2 { name="OTUbase"; version="1.32.0"; sha256="0xhwa9yd0qd86j03190riff5z64h93pn7q0b6qb2awwf5zrda8fs"; depends=[Biobase Biostrings IRanges S4Vectors ShortRead vegan]; }; + OUTRIDER = derive2 { name="OUTRIDER"; version="1.0.1"; sha256="065j21agl5ckqhr5gmi2ymy7mms15gb4dydcl08nfhy8anj5vxb1"; depends=[BBmisc Biobase BiocGenerics BiocParallel data_table DESeq2 GenomicFeatures GenomicRanges ggplot2 ggpubr gplots IRanges matrixStats pcaMethods plotly plyr PRROC RColorBrewer Rcpp RcppArmadillo reticulate S4Vectors scales SummarizedExperiment]; }; + OmaDB = derive2 { name="OmaDB"; version="1.2.0"; sha256="01ibhq35gd8z2qvmrlfkl82x9gpx7rhm84i5qhm07jh9a637yf1f"; depends=[ape Biostrings GenomicRanges httr IRanges jsonlite plyr topGO]; }; + OmicCircos = derive2 { name="OmicCircos"; version="1.20.0"; sha256="1akb3djkq0waq1f81zi3nnv8svqf2i8w9agaac732vbdr4cf821d"; depends=[GenomicRanges]; }; + OmicsMarkeR = derive2 { name="OmicsMarkeR"; version="1.14.0"; sha256="00a8wwk0z73ipdhjlwkwz4nqpjpyylafds88g8dhz0imk8f24gnj"; depends=[assertive assertive_base caret caTools data_table DiscriMiner e1071 foreach gbm glmnet pamr permute plyr randomForest]; }; + Onassis = derive2 { name="Onassis"; version="1.4.5"; sha256="17s3d2wb6mnckpxaq4ppll6fwc6fag4mg9921bf3islkb7vrbxfz"; depends=[AnnotationDbi data_table DT GEOmetadb knitr OnassisJavaLibs RCurl rJava RSQLite]; }; + OncoScore = derive2 { name="OncoScore"; version="1.10.0"; sha256="1q5xirwr184fn3fbkldp5v4cwmkkpggp2xnnh3s3prl4masdf6pk"; depends=[biomaRt]; }; + OncoSimulR = derive2 { name="OncoSimulR"; version="2.12.0"; sha256="0pbq9qbxx35zzpzsc3b18qhcdwskkg5xk6pf4kgbzisa8jkjyxfd"; depends=[car data_table dplyr ggplot2 ggrepel graph gtools igraph nem RColorBrewer Rcpp Rgraphviz smatr]; }; + OrderedList = derive2 { name="OrderedList"; version="1.54.0"; sha256="1hvw6lc39gq867gvz426qyj79yz85k2shwlw4mnk6xaib652gqwf"; depends=[Biobase twilight]; }; + Organism_dplyr = derive2 { name="Organism.dplyr"; version="1.10.0"; sha256="1s2rqzdmzmbif92466x2mgmbjism68c62590pj8swx853f9x668s"; depends=[AnnotationDbi AnnotationFilter BiocFileCache DBI dbplyr dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges RSQLite S4Vectors]; }; + OrganismDbi = derive2 { name="OrganismDbi"; version="1.24.0"; sha256="11pyv56cy4iy095h40k6k0mpjdlh6gsb4ld3s57nfa9nd4ypx3yi"; depends=[AnnotationDbi Biobase BiocGenerics BiocManager DBI GenomicFeatures GenomicRanges graph IRanges RBGL S4Vectors]; }; + Oscope = derive2 { name="Oscope"; version="1.12.0"; sha256="197l7d2rj1s47blwg96f0xcwyc9rw1zr79j5r5l3iyax9c2gvxsz"; depends=[BiocParallel cluster EBSeq testthat]; }; + OutlierD = derive2 { name="OutlierD"; version="1.46.0"; sha256="1xbkasaf47qmfqqrm1k3mgnjj63rv30094r0f968q7rxfpdmq90f"; depends=[Biobase quantreg]; }; + PAA = derive2 { name="PAA"; version="1.16.0"; sha256="03hd7vvkqfr369wp8r0i9y29li9q91s76wzvbh9scvqd0ngmh9cv"; depends=[e1071 gplots gtools limma MASS mRMRe randomForest Rcpp ROCR sva]; }; + PADOG = derive2 { name="PADOG"; version="1.24.0"; sha256="0xia09m11j70n2gfmka620pk66vjvzr1376y2lb0g18k5n6k2zxv"; depends=[AnnotationDbi Biobase doRNG foreach GSA hgu133a_db hgu133plus2_db KEGG_db KEGGdzPathwaysGEO limma nlme]; }; + PANR = derive2 { name="PANR"; version="1.28.0"; sha256="0xl1raw6ns1zzmljs0gp3rxg6gvq1qz16c38jwq8nbaqgb85c3qr"; depends=[igraph MASS pvclust RedeR]; }; + PAPi = derive2 { name="PAPi"; version="1.22.0"; sha256="0bpidgraqkxh7jb8nx597ml4xcmmv48gx09nmrc80jlbqx0h5wxn"; depends=[KEGGREST svDialogs]; }; + PCAN = derive2 { name="PCAN"; version="1.10.0"; sha256="08im6jwzbnnb4z01ayiv1jk8yqna8ncg6z65bfh0ba4jjvjwywfi"; depends=[BiocParallel]; }; + PCpheno = derive2 { name="PCpheno"; version="1.44.0"; sha256="1svdqnfp7ggi29rm5la35p96vmr7nzcfy5a458f1ra0kd4a6nd5l"; depends=[annotate AnnotationDbi Biobase Category GO_db graph GSEABase KEGG_db ppiData ppiStats ScISI SLGI]; }; + PECA = derive2 { name="PECA"; version="1.18.0"; sha256="10hhwvlr5gzcal0g62zimr79a3v2cpp95cb7nafnlq8v3ndg69hd"; depends=[affy aroma_affymetrix aroma_core genefilter limma preprocessCore ROTS]; }; + PGA = derive2 { name="PGA"; version="1.12.0"; sha256="1mr4v3d12igbrzi0zka7ynjfg9l68pincmlknh7vgv2hjmgl2jy6"; depends=[AnnotationDbi biomaRt Biostrings customProDB data_table GenomicFeatures GenomicRanges ggplot2 IRanges Nozzle_R1 pheatmap RCurl Rsamtools RSQLite rTANDEM rtracklayer S4Vectors stringr VariantAnnotation]; }; + PGSEA = derive2 { name="PGSEA"; version="1.56.0"; sha256="0nmgjfw32flc42qj0vih8r4nsc01qv01cnqrr2nxv30zdwbnfk7w"; depends=[annaffy AnnotationDbi Biobase GO_db KEGG_db]; }; + PICS = derive2 { name="PICS"; version="2.26.0"; sha256="10djnd38jdbyk18yqsypkpxqwnfiy8441zpmx1bhzzn8p5q2jpsv"; depends=[BiocGenerics GenomicAlignments GenomicRanges IRanges Rsamtools S4Vectors]; }; + PING = derive2 { name="PING"; version="2.26.0"; sha256="16iygwjsk8n40jp4giik0d4ypd8i4dmd8xdl7dhh81jmjpmycd92"; depends=[BiocGenerics BSgenome chipseq fda GenomicRanges Gviz IRanges PICS S4Vectors]; }; + PLPE = derive2 { name="PLPE"; version="1.42.0"; sha256="1i5a9nzravs4qzlxz4byvrcg0jnhcfd56ir4bm33056l4ymbia9r"; depends=[Biobase LPE MASS]; }; + POST = derive2 { name="POST"; version="1.6.0"; sha256="1grwyy2lisix5iv7brw85vii04yyhqhfkp8srirb0wh6i4q07wwf"; depends=[Biobase CompQuadForm GSEABase Matrix survival]; }; + PPInfer = derive2 { name="PPInfer"; version="1.8.1"; sha256="1ifp7gxvdlvn7wh6aizjfkaj53bcg4hbq2m54ksk2a7n86fympr5"; depends=[biomaRt fgsea ggplot2 igraph kernlab STRINGdb yeastExpData]; }; + PREDA = derive2 { name="PREDA"; version="1.28.0"; sha256="1bm08y242hikgxh8icld6mvnydq2hg4wh6m3km5j3hw3hzv5qmv5"; depends=[annotate Biobase lokern multtest]; }; + PROMISE = derive2 { name="PROMISE"; version="1.34.0"; sha256="0g4qkk7yc7b4idhy78xnwplfwg5ng7y9qwhap90hhw7nnxdvvb3i"; depends=[Biobase GSEABase]; }; + PROPER = derive2 { name="PROPER"; version="1.14.0"; sha256="05b7k8471gqi5kh9hhpnqzvnrn65a0x90ajyp5bslzviy84akh5b"; depends=[edgeR]; }; + PROPS = derive2 { name="PROPS"; version="1.4.0"; sha256="150apwa4c80741kavf2ilz62575pbmjqkwnbgb095ddfqb2wp4ly"; depends=[Biobase bnlearn reshape2 sva]; }; + PROcess = derive2 { name="PROcess"; version="1.58.0"; sha256="0c3zahyj47s5rj3jplmzp6kjnij1kd7prly0m479l1ias0za7pnm"; depends=[Icens]; }; + PSEA = derive2 { name="PSEA"; version="1.16.0"; sha256="0zw1jrrdl17fmdn3z18rdr86lb9lmpqrsdf9ilm172cxhjbq7iba"; depends=[Biobase MASS]; }; + PSICQUIC = derive2 { name="PSICQUIC"; version="1.20.0"; sha256="0h42hsvh2n0hib9gw4fqpri9lqdnaz6ivzcf406x54zdsgwalyzd"; depends=[BiocGenerics biomaRt httr IRanges plyr RCurl]; }; + PWMEnrich = derive2 { name="PWMEnrich"; version="4.18.0"; sha256="1v8yqczf5784w7a9d21jp3p2dcirrkg6ydccd8k8i0355x8yxxc9"; depends=[BiocGenerics Biostrings evd gdata seqLogo]; }; + PanVizGenerator = derive2 { name="PanVizGenerator"; version="1.10.0"; sha256="0rkkrriik0l010vzn46zm2zm87k38aihz6l5llp1wawwkyac8cla"; depends=[FindMyFriends igraph jsonlite pcaMethods shiny]; }; + Path2PPI = derive2 { name="Path2PPI"; version="1.12.0"; sha256="1yc4hqycjd2zc87wiq9rrswb5f0x33vsd6d23gckn1sqvam2clqj"; depends=[igraph]; }; + PathNet = derive2 { name="PathNet"; version="1.22.0"; sha256="1n4g960m0j38snignsahaq7nr6bahln0cbqhgx530vwzsdv2xzx3"; depends=[]; }; + PathoStat = derive2 { name="PathoStat"; version="1.8.4"; sha256="15n8lmv9vgwh1ain21gfgyl5bfnkfs7rnjdjbz69bvy1k2nmgl3y"; depends=[ape BiocStyle ComplexHeatmap corpcor DESeq2 devtools dplyr DT edgeR ggplot2 glmnet gmodels knitr limma matrixStats phyloseq plotly plyr RColorBrewer rentrez reshape2 ROCR scales shiny shinyjs tidyr vegan webshot XML]; }; + PathwaySplice = derive2 { name="PathwaySplice"; version="1.6.0"; sha256="1z39l1vq188gd2w92xz3baf5n04jzajqknbhc3z4n4761900vscz"; depends=[annotate AnnotationDbi AnnotationHub BiasedUrn Biobase BiocGenerics DOSE dplyr EnrichmentBrowser ensembldb gdata geneLenDataBase GO_db goseq gplots gridExtra htmlwidgets igraph JunctionSeq KEGGREST mgcv org_Hs_eg_db org_Mm_eg_db plotly RColorBrewer reshape2 S4Vectors tibble VennDiagram webshot]; }; + Pbase = derive2 { name="Pbase"; version="0.22.0"; sha256="02h4jhnwf2zgs9in7n70ram7rqkx91f5qmqcpypcrp07hfzmybvl"; depends=[AnnotationFilter Biobase BiocGenerics BiocParallel biomaRt Biostrings cleaver ensembldb GenomicRanges Gviz IRanges MSnbase mzID mzR Pviz Rcpp rtracklayer S4Vectors]; }; + PepsNMR = derive2 { name="PepsNMR"; version="1.0.1"; sha256="1i8k4x6s7isfzxsv7mpzq3gsh434d3z373ghvwljgdq7q89bg7h7"; depends=[ggplot2 gridExtra Matrix matrixStats ptw reshape2]; }; + PharmacoGx = derive2 { name="PharmacoGx"; version="1.12.0"; sha256="1ddh6bmrddbdmqdpmyy5mlkqvhrk39c19lzybrirfclq6cydfh5g"; depends=[Biobase caTools downloader lsa magicaxis piano RColorBrewer reshape2]; }; + PhenStat = derive2 { name="PhenStat"; version="2.18.0"; sha256="1ilsx9fn0aadw0kly5x4lqs88p8lvwidfi38x3h3gpxpf4gygxzx"; depends=[car corrplot ggplot2 graph knitr lme4 logistf MASS msgps nlme nortest pingr reshape SmoothWin]; }; + Pi = derive2 { name="Pi"; version="1.10.0"; sha256="03wzmcz57kdflicjb2wmnxg0fvfmbgizvql5164cf24fsi2lvbgi"; depends=[caret dnet GenomeInfoDb GenomicRanges ggbio ggplot2 ggrepel glmnet Gviz igraph lattice MASS Matrix plot3D randomForest ROCR scales supraHex XGR]; }; + Pigengene = derive2 { name="Pigengene"; version="1.8.0"; sha256="1xj9rxnfbm9py6vlgqfclj6pbry7j8hvwf3395bc1hcvq5ylqnh6"; depends=[bnlearn C50 GO_db graph impute MASS matrixStats partykit pheatmap preprocessCore Rgraphviz WGCNA]; }; + Polyfit = derive2 { name="Polyfit"; version="1.16.0"; sha256="017phfb69sigv8xz1caqghy5671dbrlflw984mw6gc2329miklyl"; depends=[DESeq]; }; + PowerExplorer = derive2 { name="PowerExplorer"; version="1.2.1"; sha256="0624k76ak0zyq3lyga35bmcq488gig7217zkixdspydm1g49zq0h"; depends=[Biobase BiocParallel data_table DESeq2 ggplot2 gridExtra MASS ROTS S4Vectors SummarizedExperiment vsn]; }; + Prize = derive2 { name="Prize"; version="1.12.0"; sha256="1i7v5c9s1y3nfl9655yg7zilsva3hxl53ykawbr48fla7hw27fmq"; depends=[diagram ggplot2 gplots matrixcalc reshape2 stringr]; }; + Prostar = derive2 { name="Prostar"; version="1.14.7"; sha256="1a3wcx9pkwnwpm3ccn84znyqf9qd4i0z531fyd0yp011a5knmxpq"; depends=[BiocManager colourpicker DAPAR DAPARdata data_table DT future highcharter htmlwidgets later promises R_utils rclipboard rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes shinyTree shinyWidgets webshot XML]; }; + ProtGenerics = derive2 { name="ProtGenerics"; version="1.14.0"; sha256="053mmxhzncqgigl2iqjlq56qzimlw2zzw31wpzw19rf7rld1vi3b"; depends=[]; }; + ProteoMM = derive2 { name="ProteoMM"; version="1.0.0"; sha256="0bdw2ayay4assa2pkyx83s3jkpi6laldvphgllsmdd5y4mgcpxpa"; depends=[biomaRt gdata ggplot2 ggrepel gtools matrixStats]; }; + ProteomicsAnnotationHubData = derive2 { name="ProteomicsAnnotationHubData"; version="1.12.0"; sha256="049c0g20kbf12hs3r4il3gpr9chi2w2d2l0s7pkgc1sxyb0aydvs"; depends=[AnnotationHub AnnotationHubData Biobase BiocManager Biostrings GenomeInfoDb MSnbase mzR RCurl]; }; + PureCN = derive2 { name="PureCN"; version="1.12.1"; sha256="1l47iwnv9kqa1vznpdkicx9vcmvh7hb607qczaabjkprqn6131mi"; depends=[BiocGenerics Biostrings data_table DNAcopy futile_logger GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 gridExtra IRanges Matrix RColorBrewer rhdf5 Rsamtools rtracklayer S4Vectors SummarizedExperiment VariantAnnotation VGAM]; }; + Pviz = derive2 { name="Pviz"; version="1.16.0"; sha256="1qgavdwqp2zvixbvpm2mjqcbwcz2gw8kfj6zk9064m7zmh4qg3iz"; depends=[Biostrings biovizBase data_table GenomicRanges Gviz IRanges]; }; + QDNAseq = derive2 { name="QDNAseq"; version="1.18.0"; sha256="04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"; depends=[Biobase BiocParallel CGHbase CGHcall DNAcopy GenomicRanges IRanges matrixStats R_utils Rsamtools]; }; + QSutils = derive2 { name="QSutils"; version="1.0.0"; sha256="1z06c7f2jgr60j9rbarjx310mhy4n91chb3azvw0050z01rgxi02"; depends=[ape BiocGenerics Biostrings psych]; }; + QUALIFIER = derive2 { name="QUALIFIER"; version="1.26.0"; sha256="1w2pyznx5s04c6xrhd96n8im1gcp45qd42arkjmlvxyg8pf9mi7s"; depends=[Biobase data_table flowCore flowViz flowWorkspace hwriter lattice latticeExtra MASS ncdfFlow reshape XML]; }; + QUBIC = derive2 { name="QUBIC"; version="1.10.0"; sha256="08yp8y6rcggrx69326f8gpx3arg9b6hq9fh1f2ngnd409lhlfxdn"; depends=[biclust Matrix Rcpp RcppArmadillo]; }; + QuartPAC = derive2 { name="QuartPAC"; version="1.14.0"; sha256="0bm18r4yfz3z8dr8hhb1a9issggbrw3x3galvmar0wdr1is5mcfk"; depends=[data_table GraphPAC iPAC SpacePAC]; }; + QuasR = derive2 { name="QuasR"; version="1.22.1"; sha256="15lnrj8m8p1ns7iv5f2j0xshma3gpjp3lwry1s0axsxsk9khzrl0"; depends=[Biobase BiocGenerics BiocManager BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges IRanges Rbowtie Rsamtools rtracklayer S4Vectors ShortRead zlibbioc]; }; + QuaternaryProd = derive2 { name="QuaternaryProd"; version="1.16.0"; sha256="0ww0k2akcpzfxq454g3lcr34270pq6kxxngx23lyanbfqqffhzmr"; depends=[dplyr Rcpp yaml]; }; + R3CPET = derive2 { name="R3CPET"; version="1.14.0"; sha256="0ifvifwilpski32pp1z904s97f5g109b8d4l5yds6alpl9663hls"; depends=[BiocGenerics clues clValid data_table GenomeInfoDb GenomicRanges ggbio ggplot2 Hmisc igraph IRanges pheatmap Rcpp RCurl reshape2 S4Vectors]; }; + R453Plus1Toolbox = derive2 { name="R453Plus1Toolbox"; version="1.32.0"; sha256="15a9jfb5c9mnpas3qvq7ca90y8y1yfqbvhgz7k51rzyynzh5nkx8"; depends=[Biobase BiocGenerics biomaRt Biostrings BSgenome GenomicRanges IRanges R2HTML Rsamtools S4Vectors ShortRead SummarizedExperiment TeachingDemos VariantAnnotation xtable XVector]; }; + R4RNA = derive2 { name="R4RNA"; version="1.10.0"; sha256="1n6fhlj0rmk67gdzknx3fysyg46r5lcqrilqq5rhdzrr4gacwx3j"; depends=[Biostrings]; }; + RBGL = derive2 { name="RBGL"; version="1.58.1"; sha256="1l5x2icv9di1lr3gqfi0vjnyd9xc3l77yc42ippqd4cadj3d1pzf"; depends=[graph]; }; + RBM = derive2 { name="RBM"; version="1.14.0"; sha256="1yr1qjc7flgxxjngd55i9xjjc8r7gdhn8j8hwyhd4p5358z2qaqg"; depends=[limma marray]; }; + RBioinf = derive2 { name="RBioinf"; version="1.42.0"; sha256="1l2vqnrc6ilsi50zn9f1p174hwc63qhbn05z1ng3d2va3x3qb9hm"; depends=[graph]; }; + RCAS = derive2 { name="RCAS"; version="1.8.0"; sha256="0ss5hcg2m7gjji6dd23zxa5bd5a7knwcnada4qs5q2l4clgk39ad"; depends=[AnnotationDbi BiocGenerics biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg19 cowplot data_table DBI DT genomation GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggseqlogo knitr motifRG org_Hs_eg_db pbapply pheatmap plotly plotrix proxy rmarkdown RSQLite rtracklayer S4Vectors topGO]; }; + RCASPAR = derive2 { name="RCASPAR"; version="1.28.0"; sha256="1d5mr6j7yfv9amdjyyysw79n4yr57ryxybbccc97jbkmqhijp806"; depends=[]; }; + RCy3 = derive2 { name="RCy3"; version="2.2.6"; sha256="09wsqpzkpxjjdfsy7w9mcrmrw1cva46fbjz42rswsfqrf87xq6mp"; depends=[BiocGenerics graph httr igraph R_utils RJSONIO XML]; }; + RCyjs = derive2 { name="RCyjs"; version="2.4.0"; sha256="1m5zxa5r9kjcfacgv8ny6pa2a5xd94kajmb054074r7av4ymig5z"; depends=[base64enc BiocGenerics BrowserViz graph httpuv]; }; + RDAVIDWebService = derive2 { name="RDAVIDWebService"; version="1.20.0"; sha256="0agdz7r7qcrxmvcm3d6zs36p239ldhc01qa4c4b4dxvlsq5gh6wk"; depends=[Category ggplot2 GO_db GOstats graph RBGL rJava]; }; + RDRToolbox = derive2 { name="RDRToolbox"; version="1.32.0"; sha256="01dpaniy2chd7kim6q9lqq65pfs3y1z05jrhgjmrmc7hg0yp1zb1"; depends=[MASS rgl]; }; + REBET = derive2 { name="REBET"; version="1.0.0"; sha256="1m2czya7af35xqy9cgrdwwwvfqdq2g8s02jbwv5wl6r6lwhcgid2"; depends=[ASSET]; }; + REDseq = derive2 { name="REDseq"; version="1.28.0"; sha256="1kp7nl3z1w27vmcqkvwbyi6d7dsd125zih8zbzlh96axankcqsck"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome BSgenome_Celegans_UCSC_ce2 ChIPpeakAnno IRanges multtest]; }; + REMP = derive2 { name="REMP"; version="1.6.0"; sha256="0ay2ywn3qd4ifbkv878inzlbh4d57rcjli5lfwww4rmimjn751rv"; depends=[AnnotationHub BiocGenerics BiocParallel Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 caret doParallel foreach GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 impute IRanges iterators kernlab minfi org_Hs_eg_db ranger S4Vectors settings SummarizedExperiment]; }; + RGMQL = derive2 { name="RGMQL"; version="1.2.0"; sha256="0rvlsl9acjkpva4x1wxg7pyscr3pzdr9mw2k7yzy429ad0lpk81s"; depends=[BiocGenerics data_table dplyr GenomicRanges glue httr plyr RGMQLlib rJava rtracklayer S4Vectors xml2]; }; + RGSEA = derive2 { name="RGSEA"; version="1.16.0"; sha256="02df90fjqynw4r9jx55na6ky1g814463ipb4ag1f4605hhdnbhmq"; depends=[BiocGenerics]; }; + RGalaxy = derive2 { name="RGalaxy"; version="1.26.0"; sha256="1a0bswfqdv2z7kml32c42h7zv5ayam96ka9frndvkba36zlzysrw"; depends=[Biobase BiocGenerics optparse roxygen2 XML]; }; + RGraph2js = derive2 { name="RGraph2js"; version="1.10.0"; sha256="0c53c4rrpqyna8yxcc0cgyx6b2fhd6fkwi2g7a4a8hsspja1qhcv"; depends=[digest graph rjson whisker]; }; + RIPSeeker = derive2 { name="RIPSeeker"; version="1.22.0"; sha256="1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"; depends=[GenomicAlignments GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + RITAN = derive2 { name="RITAN"; version="1.6.0"; sha256="16w7ypvchhl6ljaq2hga790ycg3hznvr7pc5mf0bah8kk524z6a6"; depends=[BgeeDB dynamicTreeCut ggplot2 gplots gridExtra gsubfn hash igraph knitr linkcomm MCL plotrix png RColorBrewer reshape2 RITANdata sqldf STRINGdb]; }; + RIVER = derive2 { name="RIVER"; version="1.6.0"; sha256="1a7i2zdin9znp9z48wnlj4g9y0bmm6anaphhrihkfqmf0s9lcqwy"; depends=[Biobase ggplot2 glmnet pROC]; }; + RImmPort = derive2 { name="RImmPort"; version="1.10.0"; sha256="1gws1zkh5gzw0drw7c21wp2g8wskaagw0f3g1p41z91sffv8vvrm"; depends=[data_table DBI dplyr plyr reshape2 RSQLite sqldf]; }; + RJMCMCNucleosomes = derive2 { name="RJMCMCNucleosomes"; version="1.6.0"; sha256="1kzsmglxq7lriz5vblprj7g1kbwzgcxjd2l1w12npb6j7vw8s598"; depends=[BiocGenerics BiocParallel consensusSeekeR GenomeInfoDb GenomicRanges IRanges Rcpp S4Vectors]; }; + RLMM = derive2 { name="RLMM"; version="1.44.0"; sha256="17lmjhb0c5w4pp68z4h5ij93n9f31dy7aic40xd958zwxm5gnwyq"; depends=[MASS]; }; + RMassBank = derive2 { name="RMassBank"; version="2.10.0"; sha256="1aa47p0xdmz9mfdnxz2jdyh70szbndj7wqgvh9zvpkqyh7dz1667"; depends=[Biobase digest httr MSnbase mzR rcdk Rcpp RCurl rjson S4Vectors XML yaml]; }; + RNASeqPower = derive2 { name="RNASeqPower"; version="1.22.0"; sha256="1z40lfaxivlrw8f77qf010wkzh7d6x0dp1iq0x6203f03gn9x21c"; depends=[]; }; + RNASeqR = derive2 { name="RNASeqR"; version="1.0.3"; sha256="07nj0iz25czfvywgl8pp1isd5vnskwnhw9w1mjjkn71sk8q5vxdc"; depends=[ballgown Biostrings clusterProfiler corrplot DESeq2 DOSE edgeR factoextra FactoMineR ggplot2 gridExtra org_Hs_eg_db org_Sc_sgd_db pathview PerformanceAnalytics pheatmap rafalib reshape2 reticulate Rsamtools stringr systemPipeR systemPipeRdata]; }; + RNAdecay = derive2 { name="RNAdecay"; version="1.2.0"; sha256="001vdk4b8ya34ik0kxfwn028yhbqsja3lb73h93fw64kfislpci6"; depends=[ggplot2 gplots nloptr TMB]; }; + RNAinteract = derive2 { name="RNAinteract"; version="1.30.0"; sha256="0cnigymdsrv492aicb9wvsiszg8v9axkdza6ksyz0k03ynw3v72l"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; }; + RNAither = derive2 { name="RNAither"; version="2.30.0"; sha256="1ingm1q4achk00jnnf8mfzalsvci5h2q9lg7y9nnnzvg6lqghjr8"; depends=[biomaRt car geneplotter limma prada RankProd splots topGO]; }; + RNAprobR = derive2 { name="RNAprobR"; version="1.14.0"; sha256="0p2cs5ybkj2yjqkcpmrxggm874y05nnz85milx8hix2vdsx6snc7"; depends=[BiocGenerics Biostrings GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr Rsamtools rtracklayer S4Vectors]; }; + ROC = derive2 { name="ROC"; version="1.58.0"; sha256="1qxmxhx5dqnrvp2076512p64rdanaa7cd95zrs783255ifq5jb0v"; depends=[]; }; + ROTS = derive2 { name="ROTS"; version="1.10.0"; sha256="137c06g5w7mjw3b1mly7b7n9iix4fcy23c7a9ym9iz8dazwhzwn5"; depends=[Biobase Rcpp]; }; + ROntoTools = derive2 { name="ROntoTools"; version="2.10.0"; sha256="0v0g4kpz3sc1aikwn59vjy75g0vdblw1nz0qrcwz48glh11qpzdz"; depends=[boot graph KEGGgraph KEGGREST Rgraphviz]; }; + RPA = derive2 { name="RPA"; version="1.38.0"; sha256="04spiv0wp7wm6yx0c4qra148n381k9488j79i91by1qi79zm746z"; depends=[affy BiocGenerics phyloseq]; }; + RProtoBufLib = derive2 { name="RProtoBufLib"; version="1.4.0"; sha256="12r2i9dla3ids1ycfdm670qz61fkf9h5mdzq0q65jaw311dbnspq"; depends=[]; }; + RRHO = derive2 { name="RRHO"; version="1.22.0"; sha256="1p84kgin1vf6vy7la5v0d10l3kv2mnhbjxjykw7yk9faf8xnmsah"; depends=[VennDiagram]; }; + RSVSim = derive2 { name="RSVSim"; version="1.22.0"; sha256="0d99cmazqlsqy58hjs2x9ziyqs7qg084rrp05vnq7ncki7a6bfm1"; depends=[Biostrings GenomicRanges IRanges ShortRead]; }; + RSeqAn = derive2 { name="RSeqAn"; version="1.2.0"; sha256="0jphw3yadhgg0c93sywb7fblv2z54nq6lqrb4p7qx9v2rsv5dvqz"; depends=[]; }; + RTCA = derive2 { name="RTCA"; version="1.34.0"; sha256="1i98g102kw3j36y95f5pjs1frahlx0ibmhv6jpq3gns4da0zcx8j"; depends=[Biobase gtools RColorBrewer]; }; + RTCGA = derive2 { name="RTCGA"; version="1.12.0"; sha256="09gp3g2saizlzfsj8lyl3wz37hfcjjrm0qr4vp3y1lkny3x640dw"; depends=[assertthat data_table dplyr ggplot2 ggthemes knitr purrr rvest scales stringi survival survminer viridis XML xml2]; }; + RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.12.1"; sha256="05gmj49hz4mdpsmp1brzha3swybgm1sqf6jyhnj8w2arwc0bh72y"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges IRanges limma RaggedExperiment RCircos RCurl RJSONIO S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; }; + RTN = derive2 { name="RTN"; version="2.6.0"; sha256="0yyb4747fj44b7x8fk2d0mpxaj9m1wy7jir1vazpynph2nz9qsl4"; depends=[data_table igraph IRanges limma minet mixtools RedeR S4Vectors snow viper]; }; + RTNduals = derive2 { name="RTNduals"; version="1.6.0"; sha256="07lv2papqcihzkkax87fhgayzydygh9r5rp9209qf2rds7m45fa3"; depends=[RTN]; }; + RTNsurvival = derive2 { name="RTNsurvival"; version="1.6.0"; sha256="07kkrgpwd84ai8fpz63gqarz4kyddjqprsqbhjm4zmlhvbfibshq"; depends=[RColorBrewer RTN RTNduals scales survival viper]; }; + RTopper = derive2 { name="RTopper"; version="1.28.0"; sha256="0blpza1kq7qh9yb15hrmkfrc7awljafwxkr5kq368yk2gkvjny91"; depends=[Biobase limma multtest]; }; + RUVSeq = derive2 { name="RUVSeq"; version="1.16.0"; sha256="0xb3bj3n06cb9xddkv77a8svhg4fl1azlfmibwrm9mq9464kgf0m"; depends=[Biobase EDASeq edgeR MASS]; }; + RUVcorr = derive2 { name="RUVcorr"; version="1.14.0"; sha256="05lg37rmf9skqcpnd08v6wnh7sfs449hwwq6nw2hkgy9faip14lz"; depends=[BiocParallel bladderbatch corrplot gridExtra lattice MASS psych reshape2 snowfall]; }; + RUVnormalize = derive2 { name="RUVnormalize"; version="1.16.0"; sha256="1habqdv35v9ypvfmfaxjqpka67bs6hzf4ph9b0gqd67mbfnb49dv"; depends=[Biobase RUVnormalizeData]; }; + RVS = derive2 { name="RVS"; version="1.4.0"; sha256="0v5krr34ihl2ybx9q1jvaiywd58px7406xvmwp7mxkcg96cnyqh1"; depends=[gRain kinship2 snpStats]; }; + RaggedExperiment = derive2 { name="RaggedExperiment"; version="1.6.0"; sha256="1w02nnxpmx05gn6d9kjnahdn9kynbg1szm96c03gh4961zknn3r3"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; + RandomWalkRestartMH = derive2 { name="RandomWalkRestartMH"; version="1.2.0"; sha256="022vckcc46bkhfhi2fzgawhf54hi6y2p5ia4v3x3lj221d7hcaax"; depends=[dnet igraph Matrix]; }; + RankProd = derive2 { name="RankProd"; version="3.8.0"; sha256="0jmpwpmj3y13ylk7riyicywpring14dhq4862jgalsjjwa22zzd0"; depends=[gmp Rmpfr]; }; + RareVariantVis = derive2 { name="RareVariantVis"; version="2.10.0"; sha256="0fb59a5568h0wz92blr6m3w01jnzh3kkil2p82fh2b8n2rv40s66"; depends=[BiocGenerics BSgenome BSgenome_Hsapiens_UCSC_hg19 GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores googleVis gtools IRanges phastCons100way_UCSC_hg19 S4Vectors SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation]; }; + Rariant = derive2 { name="Rariant"; version="1.18.0"; sha256="1wzm0qn8ar6k6fgp8hv79qncc0gca9hks3vzzkqq8ac2ml07zl37"; depends=[BiocGenerics dplyr exomeCopy GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges reshape2 Rsamtools S4Vectors shiny SomaticSignatures VariantAnnotation VGAM]; }; + RbcBook1 = derive2 { name="RbcBook1"; version="1.50.0"; sha256="1900prjqspn5zripf9h9jd5zkdrcc5477rsrflal6n5jdf9lqz3v"; depends=[Biobase graph rpart]; }; + Rbowtie = derive2 { name="Rbowtie"; version="1.22.0"; sha256="00vpszsjkvid25sjrpzw1dylwmgv27z67njvg8h1axnb09a7gnjw"; depends=[]; }; + Rbowtie2 = derive2 { name="Rbowtie2"; version="1.4.0"; sha256="045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr"; depends=[]; }; + Rcade = derive2 { name="Rcade"; version="1.24.0"; sha256="0xx19zxrfjawny75cmp75f1aarngmz8p0vy2ryw0v1qdfm1aby87"; depends=[baySeq GenomeInfoDb GenomicAlignments GenomicRanges IRanges plotrix rgl Rsamtools S4Vectors]; }; + Rchemcpp = derive2 { name="Rchemcpp"; version="2.20.0"; sha256="1g49dndhh8ivz9g67w8gzp2phy94xkdf1h7f309k3ds49bl9df9b"; depends=[ChemmineR Rcpp]; }; + RchyOptimyx = derive2 { name="RchyOptimyx"; version="2.22.0"; sha256="10kk9h1cknpdgbmn5k7aabrfr60n66i5yjxbj81x7ji6yk1ramcg"; depends=[flowType graph Rgraphviz sfsmisc]; }; + RcisTarget = derive2 { name="RcisTarget"; version="1.2.0"; sha256="046gyf1yw14zli2pbnyg10iw579jlaip37d8llajgc8qmfdrln58"; depends=[AUCell BiocGenerics data_table feather GSEABase R_utils SummarizedExperiment]; }; + Rcpi = derive2 { name="Rcpi"; version="1.18.1"; sha256="1fr6wr1w7xyxmqhpmgwcvfxf0m43gxqpfnrpkm35rya2lkk4994h"; depends=[Biostrings ChemmineR doParallel fmcsR foreach GOSemSim rcdk RCurl rjson]; }; + Rdisop = derive2 { name="Rdisop"; version="1.42.0"; sha256="15db2p9z5r1sl99n3afya6xr11hmc9d2fwzwc6zhkizy2mgj3r1m"; depends=[Rcpp RcppClassic]; }; + ReQON = derive2 { name="ReQON"; version="1.28.0"; sha256="1llklca4bz2plkmwgvpw7xrn8hxh1vnf6sk91z1yzld49w1b6rxc"; depends=[rJava Rsamtools seqbias]; }; + ReactomePA = derive2 { name="ReactomePA"; version="1.26.0"; sha256="1kglvgn1sjnx9rm45lxp0ji19vzb8qlvjs01agsdbvkn19im5nkm"; depends=[AnnotationDbi DOSE enrichplot ggplot2 ggraph graphite igraph reactome_db]; }; + ReadqPCR = derive2 { name="ReadqPCR"; version="1.28.0"; sha256="1c1l7nmnv6bcgnamjja423w5lmfsz8wiv4gv0x22ym1mv3293776"; depends=[Biobase]; }; + RedeR = derive2 { name="RedeR"; version="1.30.0"; sha256="1fq3x0sf146pn0ksddachisrd4782d7qyk1vk96dk7h0knvj9jl9"; depends=[igraph]; }; + RefNet = derive2 { name="RefNet"; version="1.18.0"; sha256="0z7k4f38gphmxqjwvwhp2q0l6ljlpzhl69v1yja0c7gfmhr1lq55"; depends=[AnnotationHub BiocGenerics IRanges PSICQUIC RCurl shiny]; }; + RefPlus = derive2 { name="RefPlus"; version="1.52.0"; sha256="1myrgsxh9713hrzzhzln20iabq520xqdmm8narg79wla5rh3vcq7"; depends=[affy affyPLM Biobase preprocessCore]; }; + Repitools = derive2 { name="Repitools"; version="1.28.0"; sha256="1v08fmn4al3rh20zr3afafmxyapdxylbbsf5s8j1wwfz60ysv557"; depends=[aroma_affymetrix BiocGenerics Biostrings BSgenome cluster DNAcopy edgeR GenomeInfoDb GenomicAlignments GenomicRanges gplots gsmoothr IRanges MASS Ringo Rsamtools Rsolnp rtracklayer S4Vectors]; }; + ReportingTools = derive2 { name="ReportingTools"; version="2.22.0"; sha256="0n4vih0j9rsiqwwvwcnk3xfi6dfbiwih11pjinjqcc7q3sbpxyj5"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category DESeq2 edgeR ggbio ggplot2 GOstats GSEABase hwriter IRanges knitr lattice limma PFAM_db R_utils XML]; }; + Rgin = derive2 { name="Rgin"; version="1.2.0"; sha256="0jj8asqp7p45rlag34m0x2lasw6mdj4rdi4ywnm5bk2cim50pji6"; depends=[RcppEigen]; }; + Rgraphviz = derive2 { name="Rgraphviz"; version="2.26.0"; sha256="0bp6517xsih0wng2rgkh9z4r1afqhwl3h04z6ssm7p4cdj0ahm4y"; depends=[graph]; }; + Rhdf5lib = derive2 { name="Rhdf5lib"; version="1.4.2"; sha256="06bxd3wz8lrvh2hzvmjpdv4lvzj5lz9353bw5b3zb98cb8w9r2j5"; depends=[]; }; + Rhtslib = derive2 { name="Rhtslib"; version="1.14.0"; sha256="1h4q54f8za3aaxgy186zf2165sar5c3cgxkk44lq5hzx5pxkl5wn"; depends=[zlibbioc]; }; + RiboProfiling = derive2 { name="RiboProfiling"; version="1.12.0"; sha256="1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr reshape2 Rsamtools rtracklayer S4Vectors sqldf]; }; + Ringo = derive2 { name="Ringo"; version="1.46.0"; sha256="1zg8sq4hqq3yldghfs1m2jn15qmdk6i1pr7c3aq73a6k99qyzihd"; depends=[Biobase BiocGenerics genefilter lattice limma Matrix RColorBrewer vsn]; }; + Risa = derive2 { name="Risa"; version="1.24.0"; sha256="1ln68rxv7wx96b3p2fh70jva07j9hj1cfflxyw34i32qkp2840hm"; depends=[affy Biobase biocViews Rcpp xcms]; }; + Rmagpie = derive2 { name="Rmagpie"; version="1.38.0"; sha256="0di8vf3cj7y2srydjq74r7gmksqhjh3r8wmffq1k96knd68nx0sx"; depends=[Biobase e1071 kernlab pamr]; }; + RmiR = derive2 { name="RmiR"; version="1.38.0"; sha256="0gv6cm5mh54xh2n25mpy6ak849rcppnajq04y7nw9hjv1i66g125"; depends=[DBI RmiR_Hs_miRNA RSVGTipsDevice]; }; + Rmmquant = derive2 { name="Rmmquant"; version="1.0.0"; sha256="08qgk2ap48i6g3cz42ddzj44m5r5zf1ncwwwid7282bv4422j2m3"; depends=[BiocStyle DESeq2 devtools GenomicRanges org_Mm_eg_db Rcpp S4Vectors SummarizedExperiment TBX20BamSubset TxDb_Mmusculus_UCSC_mm9_knownGene]; }; + RnBeads = derive2 { name="RnBeads"; version="2.0.0"; sha256="12rsx6yn7v02rhq5vyhig4rynrac8anp3c2scrvif4j21m7x3rnf"; depends=[BiocGenerics cluster ff fields GenomicRanges ggplot2 gplots gridExtra illuminaio IRanges limma MASS matrixStats methylumi plyr S4Vectors]; }; + RnaSeqSampleSize = derive2 { name="RnaSeqSampleSize"; version="1.14.0"; sha256="1n9hra22aqfdz5clmpw4ikjz9sp6fb0haq7dv1l3jhgz4l2yj8n8"; depends=[biomaRt edgeR heatmap3 KEGGREST matlab Rcpp RnaSeqSampleSizeData]; }; + Rnits = derive2 { name="Rnits"; version="1.16.0"; sha256="1l96jvyq0afkv2k3gasf0420wbhrs1nv1f5xx0h9f4mhcx81hr7q"; depends=[affy Biobase boot ggplot2 impute limma qvalue reshape2]; }; + Roleswitch = derive2 { name="Roleswitch"; version="1.20.0"; sha256="15cb4gbwgkjvidfdlvc2qf62jf3nvddqni9bbymcyi2pnpd1n6lr"; depends=[Biobase biomaRt Biostrings DBI microRNA plotrix pracma reshape]; }; + RpsiXML = derive2 { name="RpsiXML"; version="2.24.0"; sha256="1l9p5mi7b78cwh4pvwqwxx15rr4hms11m5r0vp0d2krfp7ih9m8h"; depends=[annotate AnnotationDbi Biobase graph hypergraph RBGL XML]; }; + Rqc = derive2 { name="Rqc"; version="1.16.2"; sha256="1cxa6c9k9ahcji2c979hr0xz9hv7m8w4l6aiczfdhcnjraa4k2qq"; depends=[BiocGenerics BiocParallel BiocStyle Biostrings biovizBase digest GenomicAlignments GenomicFiles ggplot2 IRanges knitr markdown plyr Rcpp reshape2 Rsamtools S4Vectors shiny ShortRead]; }; + Rsamtools = derive2 { name="Rsamtools"; version="1.34.0"; sha256="01v4bjhj2i126pwyk0v9lvmfp2ih495xsq903k3xa2z24bjxphbi"; depends=[BiocGenerics BiocParallel Biostrings bitops GenomeInfoDb GenomicRanges IRanges S4Vectors XVector zlibbioc]; }; + Rsubread = derive2 { name="Rsubread"; version="1.32.2"; sha256="1kpishka8m9vp0zjmpmmg4g37s0iw8i01sa4zvwd9py18lc1arzd"; depends=[]; }; + Rtreemix = derive2 { name="Rtreemix"; version="1.44.0"; sha256="013x6rdxsxynr8s0x8a1nk7xcanvgkm2lid9bip3v240bg9wwha4"; depends=[Biobase graph Hmisc]; }; + S4Vectors = derive2 { name="S4Vectors"; version="0.20.1"; sha256="18whrw67nxn82xshckl2pjy7d14sa3c27h3n9naqyqwz88lr6dzg"; depends=[BiocGenerics]; }; + SAGx = derive2 { name="SAGx"; version="1.56.0"; sha256="0p81jfm7fr907npbl1qrl4yswbz2a2pgmng5ww68xwmkayxkns79"; depends=[Biobase multtest]; }; + SANTA = derive2 { name="SANTA"; version="2.20.0"; sha256="1x4sq1vxvgrngq5aahbc2sgn1vw8l3d4b24fm0lldvn2b8jprzx7"; depends=[igraph Matrix snow]; }; + SBMLR = derive2 { name="SBMLR"; version="1.78.0"; sha256="02xcsaq2zlsvxj1zs2v4syw0k7fsiq826nny8kazvirkzpqmi446"; depends=[deSolve XML]; }; + SC3 = derive2 { name="SC3"; version="1.10.0"; sha256="0gg0n4xbh7qbqnnyhnciz48ivxz3030hhbrg9zi0d0lm9ivjrvlw"; depends=[BiocGenerics cluster doParallel doRNG e1071 foreach ggplot2 pheatmap Rcpp RcppArmadillo robustbase ROCR rrcov S4Vectors shiny SingleCellExperiment SummarizedExperiment WriteXLS]; }; + SCAN_UPC = derive2 { name="SCAN.UPC"; version="2.24.0"; sha256="0gg7qhzla1fqypasbsdhm3w43gb0gyfa7nm23x0j0kdrwc2i07vz"; depends=[affy affyio Biobase Biostrings foreach GEOquery IRanges MASS oligo sva]; }; + SCBN = derive2 { name="SCBN"; version="1.0.0"; sha256="0cfmpwpp9drz13rrrwg030db1jprxfw2nkxlwlwscaj1vb4q69fv"; depends=[]; }; + SCnorm = derive2 { name="SCnorm"; version="1.4.3"; sha256="15msh1lca3kwqs25pb4mx8278qk8nqv0x5i53r8z81xr6vfkyb0s"; depends=[BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SingleCellExperiment SummarizedExperiment]; }; + SDAMS = derive2 { name="SDAMS"; version="1.2.0"; sha256="0grkkr60hqalsb90w45x65i4wp1d4jqivqmzw4n75081v2nlyj1x"; depends=[qvalue SummarizedExperiment trust]; }; + SELEX = derive2 { name="SELEX"; version="1.14.0"; sha256="1hcsngnxv4q0ig80nr91x1qlxi2swcx9xlvayng25izzjc6yj1k8"; depends=[Biostrings rJava]; }; + SEPA = derive2 { name="SEPA"; version="1.12.0"; sha256="04dl578fm1zdd30q9d5dxhcm1xvkn19ijda07yxdsxifik4297fp"; depends=[ggplot2 org_Hs_eg_db org_Mm_eg_db reshape2 segmented shiny topGO]; }; + SEPIRA = derive2 { name="SEPIRA"; version="1.2.0"; sha256="1lvbx621kspl3ry8hbqgf2chins420vn26x81x5q1skvhk9s6h03"; depends=[corpcor limma]; }; + SGSeq = derive2 { name="SGSeq"; version="1.16.2"; sha256="1s4pipdzppnixqx4x6xcy5pz1ps9mhjjxy1zj5h5dy2wi13mnsfs"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges igraph IRanges Rsamtools rtracklayer RUnit S4Vectors SummarizedExperiment]; }; + SIAMCAT = derive2 { name="SIAMCAT"; version="1.2.0"; sha256="0f3fgcc6lw4mlxjzfi80pkz0hnn377zcw5vgaxg332xpm27iic7h"; depends=[beanplot corrplot glmnet gridBase gridExtra infotheo LiblineaR matrixStats mlr ParamHelpers phyloseq pROC PRROC RColorBrewer scales stringr]; }; + SICtools = derive2 { name="SICtools"; version="1.12.0"; sha256="06ypc7xqn8rpdyp16rlwsaw37gb94z9c980fwadbjvf2bzga5xwd"; depends=[Biostrings doParallel GenomicRanges IRanges matrixStats plyr Rsamtools stringr]; }; + SIM = derive2 { name="SIM"; version="1.52.0"; sha256="16rkh4nnpm1bzq9z85s64fl09ymrwifmdcanwg4q8vnasqdcyp01"; depends=[globaltest quantreg quantsmooth]; }; + SIMAT = derive2 { name="SIMAT"; version="1.14.0"; sha256="1xkbdn06zi3nl6rv3viclisqzkcsd1bca0cxg1mygck2f9fpqih8"; depends=[ggplot2 mzR Rcpp reshape2]; }; + SIMD = derive2 { name="SIMD"; version="1.0.0"; sha256="15ivvgjhsabg9lvdfylqv4640jvmk65kj1lb3z8h7fwc24qhr6aj"; depends=[edgeR methylMnM statmod]; }; + SIMLR = derive2 { name="SIMLR"; version="1.8.0"; sha256="1fxwz2v3wi6wfwqpy45gjvldx3xmnvq42laxxzyzv1lnhmvpmbwi"; depends=[Matrix pracma Rcpp RcppAnnoy RSpectra]; }; + SISPA = derive2 { name="SISPA"; version="1.12.0"; sha256="1vqgm6wiymvy83zj71anqknvya0h03pwcavc0gn6dfmxc2rhhk85"; depends=[changepoint data_table genefilter ggplot2 GSVA plyr]; }; + SLGI = derive2 { name="SLGI"; version="1.42.0"; sha256="09665cxx7rl5aai10pcj5wwq90psygwpj5776vp8fjmv1bq8lgx8"; depends=[AnnotationDbi Biobase BiocGenerics GO_db lattice ScISI]; }; + SLqPCR = derive2 { name="SLqPCR"; version="1.48.0"; sha256="1izzqzn42pzfxx28qj5nviwqd63jicw9gifk1m9w2r3j7asqwpqy"; depends=[]; }; + SMAP = derive2 { name="SMAP"; version="1.46.0"; sha256="0aqlqq0q5f5n9q8xfharzy55gx7p0gzijndbljj656jpy5dq6l9v"; depends=[]; }; + SMITE = derive2 { name="SMITE"; version="1.10.0"; sha256="1gy2331c6rmwpz7rl5g4666f5q7l5h8iby6mazv074vrf3xqzk18"; depends=[AnnotationDbi Biobase BioNet geneLenDataBase GenomicRanges ggplot2 goseq Hmisc igraph IRanges KEGG_db org_Hs_eg_db plyr reactome_db S4Vectors scales]; }; + SNAGEE = derive2 { name="SNAGEE"; version="1.22.0"; sha256="1r9bvjc9l3xs1i9hrfzajhv6yb25qgnjgh1wyxrg0lky0n00z93m"; depends=[SNAGEEdata]; }; + SNPRelate = derive2 { name="SNPRelate"; version="1.16.0"; sha256="0p6lrjj0v63f2y31727my72c4pnqmyb22d6rpi3yk556d21nlbyr"; depends=[gdsfmt]; }; + SNPchip = derive2 { name="SNPchip"; version="2.28.0"; sha256="0vlrgraczyv4si4mrgssh6ijvq02qnb5h186rzqz0ssscjndh111"; depends=[Biobase foreach GenomeInfoDb GenomicRanges IRanges lattice oligoClasses S4Vectors SummarizedExperiment]; }; + SNPediaR = derive2 { name="SNPediaR"; version="1.8.0"; sha256="124nw9ncf2mlkrw11v0azl69hhvj7cc8zyd78i16n8biw8pcphb7"; depends=[jsonlite RCurl]; }; + SNPhood = derive2 { name="SNPhood"; version="1.12.0"; sha256="1f6rhlkisdx8psl7d2anxm03l205aas2iwr2par2q4bl3v10aqky"; depends=[BiocGenerics BiocParallel Biostrings checkmate cluster data_table DESeq2 GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges lattice RColorBrewer reshape2 Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; + SPEM = derive2 { name="SPEM"; version="1.22.0"; sha256="1qy92c8hjlxiji8bwzfmwf2nndnafqfmxpkxxwz3xsa9nvbsy22j"; depends=[Biobase Rsolnp]; }; + SPIA = derive2 { name="SPIA"; version="2.34.0"; sha256="1x9rkhza6wky0wfy5bb4bjlmwlhpap9l7mc2svk15nv6r7dwr0v8"; depends=[KEGGgraph]; }; + SPLINTER = derive2 { name="SPLINTER"; version="1.8.0"; sha256="0v7v4w2jzvrqyrmkxxb4mirrl3x5g5adczs6g3p8c2lfdz2gg36k"; depends=[biomaRt Biostrings BSgenome_Mmusculus_UCSC_mm9 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 googleVis Gviz IRanges plyr S4Vectors seqLogo stringr]; }; + SPONGE = derive2 { name="SPONGE"; version="1.4.0"; sha256="15f7n452nn0avkylvrh49c2s9k2bnfzn4i6d58k8dp71vld0n07i"; depends=[Biobase data_table doRNG expm foreach glmnet gRbase igraph iterators logging MASS ppcor]; }; + SQUADD = derive2 { name="SQUADD"; version="1.32.0"; sha256="02z9mcbwaprjpwbbbyxi50hkhi13zm4sa9qy43bkha98i2r2flkn"; depends=[RColorBrewer]; }; + SRAdb = derive2 { name="SRAdb"; version="1.44.0"; sha256="1d2fbgzz9vrv1z8wj5pgi8f31dbd6zh8kn76qw972b3s3zd9apni"; depends=[GEOquery graph RCurl RSQLite]; }; + SRGnet = derive2 { name="SRGnet"; version="1.8.0"; sha256="0xcnkdnh7ihjay60fig6vq3xs5953m9ar3pysrka8yi1pfk9j4xx"; depends=[DMwR EBcoexpress gbm Hmisc igraph limma MASS matrixStats pvclust]; }; + SSPA = derive2 { name="SSPA"; version="2.22.0"; sha256="0gizdw5l9lnqxsyijbdabbf0xp2zdyfc5hixnw6013484c0dgc7b"; depends=[lattice limma qvalue]; }; + STAN = derive2 { name="STAN"; version="2.10.0"; sha256="0f1aks069z8sh8r05v36vbr6a2bvc34i1byidrq4irgm0dgf2q5r"; depends=[BiocGenerics GenomeInfoDb GenomicRanges Gviz IRanges poilog Rsolnp S4Vectors]; }; + STATegRa = derive2 { name="STATegRa"; version="1.18.0"; sha256="0928yjgaqgx0axiwfrff1dhqcqbjh5hqdsf8607da4ncf58qcglk"; depends=[affy Biobase calibrate edgeR foreach ggplot2 gplots gridExtra limma MASS]; }; + STRINGdb = derive2 { name="STRINGdb"; version="1.22.0"; sha256="0xfcxq1h4c756rfz1pkcq8zigf0lacrskxzid28lzawd047l224h"; depends=[gplots hash igraph plotrix plyr png RColorBrewer RCurl sqldf]; }; + STROMA4 = derive2 { name="STROMA4"; version="1.6.0"; sha256="062w29y2yqqxybhfi8w502064bzsrvfs2fngq8sbn6li8iy6pw3k"; depends=[Biobase BiocParallel cluster matrixStats]; }; + SVAPLSseq = derive2 { name="SVAPLSseq"; version="1.8.0"; sha256="1d3vswkr2rxqvc0v7vax78f1gff04ci7i052csk8hy7i255hxlrw"; depends=[edgeR ggplot2 limma lmtest pls SummarizedExperiment]; }; + SVM2CRM = derive2 { name="SVM2CRM"; version="1.14.0"; sha256="0m8x176kaf7k4zfb7cyxan4if42v4g3w3yr24a35d3a0yhn9lkgb"; depends=[AnnotationDbi GenomicRanges IRanges LiblineaR mclust pls ROCR rtracklayer squash SVM2CRMdata verification zoo]; }; + SWATH2stats = derive2 { name="SWATH2stats"; version="1.12.1"; sha256="1j92121a48lz5bvxa9p3k1h7j1qi0za7z1vqmi683afn15j7cbmb"; depends=[biomaRt data_table ggplot2 reshape2]; }; + SamSPECTRAL = derive2 { name="SamSPECTRAL"; version="1.36.0"; sha256="0rim0hmdd5slxv7mw0vxwnl3jz2gfjq4vwc8hganp8x313p9ry71"; depends=[]; }; + ScISI = derive2 { name="ScISI"; version="1.54.0"; sha256="1xs5vwgvcq72jiir5sl99z9pa4kh28jaidj1h31cvfsz0yjkfsl9"; depends=[annotate AnnotationDbi apComplex GO_db org_Sc_sgd_db RpsiXML]; }; + Scale4C = derive2 { name="Scale4C"; version="1.4.0"; sha256="12d8l6j57gwnrigzyprfw03rzgsni7n75ws2hi1ldybx7bx3nlag"; depends=[GenomicRanges IRanges smoothie SummarizedExperiment]; }; + Sconify = derive2 { name="Sconify"; version="1.2.0"; sha256="0848xx1miilk4hn0nxv6wbydxha48z2lf480hxhaims5wn2ckvrz"; depends=[dplyr flowCore FNN ggplot2 magrittr readr Rtsne tibble]; }; + SemDist = derive2 { name="SemDist"; version="1.16.0"; sha256="086lparkzxssz78dn67x4f7c3pw45y7gj2ldvhmkfqyynfm57giq"; depends=[annotate AnnotationDbi GO_db]; }; + SeqArray = derive2 { name="SeqArray"; version="1.22.3"; sha256="0014pgklkjkrl7k15fln02gwa2k3z7kaaaq7jc7xjpc35s5bbikd"; depends=[Biostrings gdsfmt GenomeInfoDb GenomicRanges IRanges S4Vectors]; }; + SeqGSEA = derive2 { name="SeqGSEA"; version="1.22.0"; sha256="0k55v5i58khgxcghb8z09a2hknlif6wkba4mgfn29q1y02krvpfr"; depends=[Biobase biomaRt DESeq doParallel]; }; + SeqSQC = derive2 { name="SeqSQC"; version="1.4.0"; sha256="1dg4dm45s7l5dgq2cr6g9a5a65jlpf801z3a1x42h36ybgs7gg3j"; depends=[e1071 ExperimentHub gdsfmt GenomicRanges GGally ggplot2 IRanges rbokeh RColorBrewer reshape2 rmarkdown S4Vectors SNPRelate]; }; + SeqVarTools = derive2 { name="SeqVarTools"; version="1.20.0"; sha256="1hngny8zmq631acbc3b26qhhvsji92zw0ww3z3sf8sxkp68g3i9k"; depends=[Biobase dplyr gdsfmt GenomicRanges GWASExactHW IRanges logistf Matrix S4Vectors SeqArray tidyr]; }; + ShortRead = derive2 { name="ShortRead"; version="1.40.0"; sha256="0iks123i1adkb9i2q4wvfqdmmj9dy867jvngj9757y8gj6xbcpy1"; depends=[Biobase BiocGenerics BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges hwriter IRanges lattice latticeExtra Rsamtools S4Vectors XVector zlibbioc]; }; + SigCheck = derive2 { name="SigCheck"; version="2.14.0"; sha256="0k00lrzpjfdcp3yvjbd1bc3710pa0dd884k4yyq43nv0cv9f4szp"; depends=[Biobase BiocParallel e1071 MLInterfaces survival]; }; + SigFuge = derive2 { name="SigFuge"; version="1.20.0"; sha256="0z78yg43wklzrpqawpprgb6nm1wngkd97g09aa9nzv91p05k85dp"; depends=[GenomicRanges ggplot2 matlab reshape sigclust]; }; + SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.20.0"; sha256="0n5awvsjz215g6h0kz6mzhzxw3vnhbf16b1n3bkqb7kv4cdrd4vq"; depends=[Biobase limma mclust Ringo]; }; + SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.4.0"; sha256="19r4r7djrn46qlijkj1g926vcklxzcrxjlxv6cg43m9j9jgfs3dj"; depends=[BiocGenerics S4Vectors SummarizedExperiment]; }; + SomaticSignatures = derive2 { name="SomaticSignatures"; version="2.18.0"; sha256="013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02"; depends=[Biobase Biostrings GenomeInfoDb GenomicRanges ggbio ggplot2 IRanges NMF pcaMethods proxy reshape2 S4Vectors VariantAnnotation]; }; + SpacePAC = derive2 { name="SpacePAC"; version="1.20.0"; sha256="1qm71d11ggwhkfk1rlq8zx2mjz7942ixcda1pgrd9m537zhjy469"; depends=[iPAC]; }; + SparseSignatures = derive2 { name="SparseSignatures"; version="1.2.0"; sha256="0wvlsdr75na5zi92hgj2bnxcxm8z9p8f99nfg6x3jzi39binwfr8"; depends=[Biostrings BSgenome BSgenome_Hsapiens_1000genomes_hs37d5 data_table GenomeInfoDb GenomicRanges ggplot2 gridExtra IRanges NMF nnlasso nnls]; }; + SpeCond = derive2 { name="SpeCond"; version="1.36.0"; sha256="0xx3wdfadw3jgmvvhsd2irdgqdd8pwlprcy07i3j2vja9ji0cx5f"; depends=[Biobase fields hwriter mclust RColorBrewer]; }; + SpidermiR = derive2 { name="SpidermiR"; version="1.12.0"; sha256="1hsf03d8pfwdrh0dwpqgl2wx64wyfp09ashv8sw9byh8xx6czci1"; depends=[AnnotationDbi gdata ggplot2 gplots gridExtra httr igraph lattice latticeExtra miRNAtap miRNAtap_db networkD3 org_Hs_eg_db TCGAbiolinks visNetwork]; }; + SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.22.1"; sha256="0bn7isfjwgyndp5b9afdvlm4ivbdrzna1hvjnzrjsd1h18cas90j"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; }; + StarBioTrek = derive2 { name="StarBioTrek"; version="1.8.1"; sha256="0lhad99k077sknbvlyd1hpgn4swgkq9lg76dxq7hs1aj1lamqx8d"; depends=[AnnotationDbi e1071 igraph KEGGREST org_Hs_eg_db ROCR SpidermiR]; }; + Starr = derive2 { name="Starr"; version="1.38.0"; sha256="1rrs366d8yr02077v34l6yr8w361s94zira2gcf935kkmfrclgij"; depends=[affxparser affy MASS pspline Ringo zlibbioc]; }; + Streamer = derive2 { name="Streamer"; version="1.28.0"; sha256="163rhpr042dk5ch47yrgfjsa5hnbhbz4jcnisvlcmmp0jd12qsrr"; depends=[BiocGenerics graph RBGL]; }; + SummarizedBenchmark = derive2 { name="SummarizedBenchmark"; version="2.0.0"; sha256="0x7m57s4qf57vsphczcfa9w4knrsh6nghmdrp3jzrr3ci2a6pjfw"; depends=[BiocGenerics BiocParallel crayon digest dplyr ggplot2 mclust rlang S4Vectors sessioninfo stringr SummarizedExperiment tibble tidyr UpSetR]; }; + SummarizedExperiment = derive2 { name="SummarizedExperiment"; version="1.12.0"; sha256="07805572xhpj5mfwq6kw1ha21wgalqvhh4ydvafyl1bnf3r20vps"; depends=[Biobase BiocGenerics DelayedArray GenomeInfoDb GenomicRanges IRanges Matrix S4Vectors]; }; + Sushi = derive2 { name="Sushi"; version="1.20.0"; sha256="0dv5di0hgbvk9cxnqhyf18mdjl50k6bk00a89r6zgp83rbxwr1r8"; depends=[biomaRt zoo]; }; + SwathXtend = derive2 { name="SwathXtend"; version="2.4.0"; sha256="0986srxbi3f7pfnhghh9dznwrl9k5qrcmcf1vqa3lg06bwz7pbsc"; depends=[e1071 lattice openxlsx VennDiagram]; }; + SwimR = derive2 { name="SwimR"; version="1.20.0"; sha256="0sgci3rs4kak79yibcvxw3mjb30y9q8hacqykrpav2sjyqc6fcy1"; depends=[gplots heatmap_plus R2HTML signal]; }; + TCC = derive2 { name="TCC"; version="1.22.0"; sha256="1a4r952qplq5kidb6zb2kiza57lrgzlg0f4zfhk2v8x355ymggpy"; depends=[baySeq DESeq DESeq2 edgeR ROC]; }; + TCGAbiolinks = derive2 { name="TCGAbiolinks"; version="2.10.0"; sha256="17d1a00ly4zhhi3zsmha5f72vl45r5ac88gvn9nyffhabkqjrq9l"; depends=[biomaRt circlize ComplexHeatmap ConsensusClusterPlus data_table doParallel downloader dplyr EDASeq edgeR genefilter GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel ggthemes gridExtra httr IRanges jsonlite knitr limma matlab plyr R_utils RColorBrewer readr rvest S4Vectors scales selectr stringr SummarizedExperiment survival survminer sva tibble XML xml2]; }; + TCGAbiolinksGUI = derive2 { name="TCGAbiolinksGUI"; version="1.8.0"; sha256="1af30xy7yk9hqwc4gcr02nprgxgn2ivq6cb2jigzabhi2bjmm70q"; depends=[caret clusterProfiler colourpicker data_table downloader DT ELMER ggplot2 ggrepel IlluminaHumanMethylation27kanno_ilmn12_hg19 IlluminaHumanMethylation27kmanifest IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest maftools minfi pathview plotly readr shiny shinyBS shinydashboard shinyFiles shinyjs stringr SummarizedExperiment TCGAbiolinks TCGAbiolinksGUI_data]; }; + TCGAutils = derive2 { name="TCGAutils"; version="1.2.1"; sha256="1ilvh59qz6bp6pgvcyj51xgmf2kiz416211h8xn8z4kvim5dvpra"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicDataCommons GenomicFeatures GenomicRanges IRanges MultiAssayExperiment RaggedExperiment rvest S4Vectors stringr SummarizedExperiment xml2]; }; + TCseq = derive2 { name="TCseq"; version="1.6.0"; sha256="1h8f1xw20rm8la5g91m1408rq96ib0h6xn6s482m51z54qga5w3v"; depends=[BiocGenerics cluster e1071 edgeR GenomicAlignments GenomicRanges ggplot2 IRanges locfit reshape2 Rsamtools SummarizedExperiment]; }; + TDARACNE = derive2 { name="TDARACNE"; version="1.32.0"; sha256="0b7p7pl9sn2g3f7wv405nwng2xknxqhdwqm2bkr4czxcrmwdal5f"; depends=[Biobase GenKern Rgraphviz]; }; + TEQC = derive2 { name="TEQC"; version="4.4.0"; sha256="16aj8nadcpnv1lqqz7pfss7vc2s5h0k79ahxb4l4405j8yrf16hl"; depends=[Biobase BiocGenerics hwriter IRanges Rsamtools]; }; + TFARM = derive2 { name="TFARM"; version="1.4.0"; sha256="1bi7j7x8libijsf7c144fbf456f5vhaj8b3avdil49qa4k78623w"; depends=[arules fields GenomicRanges stringr]; }; + TFBSTools = derive2 { name="TFBSTools"; version="1.20.0"; sha256="18iqr2xsmgkmm5x4dz1vm9ig13x9vb1kvqxc0gpc4pzanf3w6jrp"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome caTools CNEr DBI DirichletMultinomial GenomeInfoDb GenomicRanges gtools IRanges RSQLite rtracklayer S4Vectors seqLogo TFMPvalue XML XVector]; }; + TFEA_ChIP = derive2 { name="TFEA.ChIP"; version="1.2.1"; sha256="102jb5bh0jhr0244cy96zsc5jrgsjh7amf8kdmfmhx21spq1l59a"; depends=[biomaRt dplyr GenomicFeatures GenomicRanges IRanges org_Hs_eg_db R_utils TxDb_Hsapiens_UCSC_hg19_knownGene]; }; + TFHAZ = derive2 { name="TFHAZ"; version="1.4.0"; sha256="18mfmcbb5vfr2c96gai3hdzvbb3jzfnmmrclcdp9shrpwg6l1ipd"; depends=[GenomicRanges IRanges S4Vectors]; }; + TFutils = derive2 { name="TFutils"; version="1.2.0"; sha256="1gppabscwfbqyvwrnl7mppw9wp528plp3bxq7g73hhgackfwnwkc"; depends=[dplyr magrittr miniUI shiny]; }; + TIN = derive2 { name="TIN"; version="1.14.0"; sha256="0n5lx8pg066z9adjsfnslxw6fv0w0ibv7nk2yz8qaiq6zivvcc1y"; depends=[aroma_affymetrix data_table impute squash stringr WGCNA]; }; + TMixClust = derive2 { name="TMixClust"; version="1.4.0"; sha256="03i9fgq29xr3h72c2scb4fa6305l7bpwj6hgk0j1v7ark6xz5xqz"; depends=[Biobase BiocParallel cluster flexclust gss mvtnorm SPEM zoo]; }; + TPP = derive2 { name="TPP"; version="3.10.0"; sha256="10bd2iihcb51j6wanv9gnrknfh0csc5d4vh9s23w01n8x0vc74hs"; depends=[Biobase biobroom broom data_table doParallel dplyr foreach futile_logger ggplot2 gridExtra knitr limma magrittr MASS mefa nls2 openxlsx plyr purrr RColorBrewer RCurl reshape2 rmarkdown sme stringr tidyr VennDiagram VGAM]; }; + TRONCO = derive2 { name="TRONCO"; version="2.14.2"; sha256="1cqkk6zsfsjpq8iidvmpfvkfak3ryp2bl9p04in0sn8sl9is6nsq"; depends=[bnlearn cgdsr circlize doParallel foreach gridExtra gtable gtools igraph iterators R_matlab RColorBrewer Rgraphviz scales xtable]; }; + TSCAN = derive2 { name="TSCAN"; version="1.20.0"; sha256="1yas32djld4dlsmzi65dflmnrff48m7vb6j7wgr44jip416mh7l1"; depends=[combinat fastICA ggplot2 gplots igraph mclust mgcv plyr shiny]; }; + TSRchitect = derive2 { name="TSRchitect"; version="1.8.9"; sha256="0i5i7m2rfqgnr2n39hfdgbvlhm8aqa6c77i7jvp66lapskww4rgb"; depends=[AnnotationHub BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicRanges gtools IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + TSSi = derive2 { name="TSSi"; version="1.28.0"; sha256="1i0qcp5nygfny8pq6x70miig8gcf0an91rckci602m8il2x66rmp"; depends=[Biobase BiocGenerics Hmisc IRanges minqa plyr S4Vectors]; }; + TTMap = derive2 { name="TTMap"; version="1.4.0"; sha256="0cwajx9kfgs4dz10j88fbg5jlzj3yr6im23972swab58kl2n30vz"; depends=[Biobase colorRamps rgl SummarizedExperiment]; }; + TVTB = derive2 { name="TVTB"; version="1.8.0"; sha256="058h38x6x69jsp8qsdy7mz9wjjvhw4dwbph14qgqvagbaiaj7v19"; depends=[AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz IRanges limma reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation]; }; + TarSeqQC = derive2 { name="TarSeqQC"; version="1.12.0"; sha256="1p1fwmkikh6a6sff3hmdxc3z4ypxz2iv1j544gfmsq47pibn8cgp"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; }; + TargetScore = derive2 { name="TargetScore"; version="1.20.0"; sha256="0kxiv5rghq3fw416gg3z7gfram146hjaf5pjd5hbyvy7rydilvbz"; depends=[Matrix pracma]; }; + TargetSearch = derive2 { name="TargetSearch"; version="1.38.1"; sha256="0gk91i4g5ly6y2xzs8h8f90w3pm6mp3habjjy2bv60jsqxpi3pcb"; depends=[ncdf4]; }; + TimeSeriesExperiment = derive2 { name="TimeSeriesExperiment"; version="1.0.2"; sha256="0ajgy6bkcdxg7qvwibccb438r3dd50w23dwvrcj43vm9zgcf6jay"; depends=[DESeq2 dplyr dynamicTreeCut edgeR ggplot2 Hmisc limma magrittr proxy S4Vectors SummarizedExperiment tibble tidyr vegan viridis]; }; + TissueEnrich = derive2 { name="TissueEnrich"; version="1.2.1"; sha256="13nbcrj441wrbjn8xbrb8fn802bimhnaxjb980bn55l0ix7npy1c"; depends=[dplyr ensurer ggplot2 GSEABase SummarizedExperiment tidyr]; }; + TitanCNA = derive2 { name="TitanCNA"; version="1.20.0"; sha256="1lgqdhi63jimwfhkh07br8jn67xh4yxgfmx79bhvhq0m6gfgqhcn"; depends=[data_table dplyr foreach GenomeInfoDb GenomicRanges IRanges Rsamtools VariantAnnotation]; }; + TnT = derive2 { name="TnT"; version="1.4.0"; sha256="0cza7l550ly35w0c1xjvixgxwdl53v90q0rnb6i7jj6yxgq4ppwq"; depends=[Biobase data_table GenomeInfoDb GenomicRanges htmlwidgets IRanges jsonlite knitr S4Vectors]; }; + ToPASeq = derive2 { name="ToPASeq"; version="1.16.0"; sha256="1k1p9cn5cksc0k4l4hlc0ii3jizdq66a7ira95jdgkzqpnh2ssdh"; depends=[graph graphite Rcpp]; }; + TransView = derive2 { name="TransView"; version="1.26.0"; sha256="0rkfcykfsrgywmp92c4nydvfn8d2adcn24r9g2zv36zm49whmwbh"; depends=[BiocGenerics GenomicRanges gplots IRanges Rsamtools S4Vectors zlibbioc]; }; + Trendy = derive2 { name="Trendy"; version="1.4.4"; sha256="0vmm2gvg3yb5chqj4fg5l0x86zm19vj5zcj32nzgba6c1s38qxhb"; depends=[BiocParallel DT gplots magrittr S4Vectors segmented shiny shinyFiles SummarizedExperiment]; }; + TurboNorm = derive2 { name="TurboNorm"; version="1.30.0"; sha256="0a3f1zgj914rklrdilcnqfcr4g3mhg1bzfzxr6nn2cqin47hlakp"; depends=[affy convert lattice limma marray]; }; + TxRegInfra = derive2 { name="TxRegInfra"; version="1.2.0"; sha256="03bf4bk1gwiy3bqlihczy3fg5vw66nkfi1gg6s6szy2hh8jrd2js"; depends=[BiocParallel GenomeInfoDb GenomicRanges IRanges mongolite RaggedExperiment rjson S4Vectors SummarizedExperiment]; }; + TypeInfo = derive2 { name="TypeInfo"; version="1.48.0"; sha256="0h2jnshr2sgyay3isiapfagjjh4wnff7nw711j4gxw9wg328w24l"; depends=[]; }; + UNDO = derive2 { name="UNDO"; version="1.24.0"; sha256="0yins1aw7gfp5qxmsai4l59nl5i6diq1h2frvdshsg6dbfxkzy67"; depends=[Biobase BiocGenerics boot MASS nnls]; }; + Ularcirc = derive2 { name="Ularcirc"; version="1.0.0"; sha256="1h4pv78x78wlgq0zmdjgdapjp7bxzdkw078pq9h6xzhkwvmyilz3"; depends=[AnnotationHub Biostrings BSgenome data_table DT GenomeInfoDb GenomeInfoDbData GenomicFeatures gsubfn httpuv mirbase_db moments shiny shinyFiles Sushi yaml]; }; + UniProt_ws = derive2 { name="UniProt.ws"; version="2.22.0"; sha256="02rb0ygc3pikb8qbi8134n9hjzza4n3bvqbqfl5dqb2n1ibkknmq"; depends=[AnnotationDbi BiocFileCache BiocGenerics rappdirs RCurl RSQLite]; }; + Uniquorn = derive2 { name="Uniquorn"; version="2.2.0"; sha256="030na1hp7c91svpqc5c3j6hvhrzcqxfb33j7bb05v5gpqnydsc5m"; depends=[data_table doParallel foreach GenomicRanges IRanges R_utils stringr VariantAnnotation WriteXLS]; }; + VanillaICE = derive2 { name="VanillaICE"; version="1.44.0"; sha256="0v4bqcwbbzabmq1pcs55j3jlhqssr2jsr9hxh76p1n7d6fw4dgs6"; depends=[Biobase BiocGenerics BSgenome_Hsapiens_UCSC_hg18 crlmm data_table foreach GenomeInfoDb GenomicRanges IRanges lattice matrixStats oligoClasses S4Vectors SummarizedExperiment]; }; + VariantAnnotation = derive2 { name="VariantAnnotation"; version="1.28.5"; sha256="0k73ax2vjh0mqkfq82nk8cv475hbn9cblsizbf8d0d0gckdw884n"; depends=[AnnotationDbi Biobase BiocGenerics Biostrings BSgenome DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors SummarizedExperiment XVector zlibbioc]; }; + VariantFiltering = derive2 { name="VariantFiltering"; version="1.18.0"; sha256="13z1x1v9xbdzsfn9x66b6sd18pla98cwd5zvxkwaiph8rp8bgvic"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicFeatures GenomicRanges GenomicScores graph Gviz IRanges RBGL Rsamtools S4Vectors shiny shinyjs shinythemes shinyTree SummarizedExperiment VariantAnnotation XVector]; }; + VariantTools = derive2 { name="VariantTools"; version="1.24.0"; sha256="1ml3pl7xnxvzr6zkypr80xzw6nffswk29gzxycn42473sc4ixn7j"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicFeatures GenomicRanges IRanges Matrix Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; + Vega = derive2 { name="Vega"; version="1.30.0"; sha256="035f2ly3y5i4cirwvfham5kpyawg9scfvfvyn7ys4lyjxx59y4dd"; depends=[]; }; + VegaMC = derive2 { name="VegaMC"; version="3.20.0"; sha256="0cgvfmwxrprrzgp0fxhi944y1z83h4mjv89iax2bshpwp1q5d9xr"; depends=[Biobase biomaRt genoset]; }; + Wrench = derive2 { name="Wrench"; version="1.0.0"; sha256="12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg"; depends=[limma locfit matrixStats]; }; + XBSeq = derive2 { name="XBSeq"; version="1.14.0"; sha256="0lva9n2bs5xp7k8is0n8k34q2k3pkvsvg04dav3qbkqzi1xz5ky9"; depends=[Biobase DESeq2 dplyr ggplot2 locfit magrittr matrixStats pracma roar]; }; + XDE = derive2 { name="XDE"; version="2.28.0"; sha256="034474qsc065z85wjlr8g695cpknh9kwbhzqdkh8fab2j06249sr"; depends=[Biobase BiocGenerics genefilter GeneMeta gtools MergeMaid mvtnorm RColorBrewer siggenes]; }; + XINA = derive2 { name="XINA"; version="1.0.0"; sha256="0v5qy3af8q26mkwk5zwkja6pvxdgvif185j6c5ws80lh4kw0h5z8"; depends=[alluvial Biobase ggplot2 gridExtra igraph mclust plyr STRINGdb]; }; + XVector = derive2 { name="XVector"; version="0.22.0"; sha256="01fph1ydd6g0rl5mcw54spx22glq2kqv7wyw8bqw0plmabzcwwdm"; depends=[BiocGenerics IRanges S4Vectors zlibbioc]; }; + YAPSA = derive2 { name="YAPSA"; version="1.8.0"; sha256="1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j"; depends=[circlize ComplexHeatmap corrplot dendextend GenomeInfoDb GenomicRanges GetoptLong ggplot2 gridExtra gtrellis KEGGREST lsei PMCMR reshape2 SomaticSignatures VariantAnnotation]; }; + a4 = derive2 { name="a4"; version="1.30.0"; sha256="1iqjy35rqx3m2y0dm2bk4cnzdm1qvbi608bfmrid88w6wmwz3qlk"; depends=[a4Base a4Classif a4Core a4Preproc a4Reporting]; }; + a4Base = derive2 { name="a4Base"; version="1.30.0"; sha256="0k9k3bv99msbwf2y416cz316ssaha2dxvmaddbl7z9037p8mjr70"; depends=[a4Core a4Preproc annaffy AnnotationDbi Biobase genefilter glmnet gplots limma mpm multtest]; }; + a4Classif = derive2 { name="a4Classif"; version="1.30.0"; sha256="02l77a59865ly3bydv74ff2l2wfb0x5s283g1nx6g1qrw3ly982j"; depends=[a4Core a4Preproc glmnet MLInterfaces pamr ROCR varSelRF]; }; + a4Core = derive2 { name="a4Core"; version="1.30.0"; sha256="1d62afxkfp9zbp59ijcn4wd1gdynygw013av41wq8bfm3cx6f9zr"; depends=[Biobase glmnet]; }; + a4Preproc = derive2 { name="a4Preproc"; version="1.30.0"; sha256="1dd3fqcc7nr2zbi46k0mnqkh42mfxk894ixfpqg7i9np2523p5gp"; depends=[AnnotationDbi]; }; + a4Reporting = derive2 { name="a4Reporting"; version="1.30.0"; sha256="124774z3bfdjgxx2ad40795h92aam21yfx0rw0n01nk2wf6k7xc4"; depends=[annaffy xtable]; }; + aCGH = derive2 { name="aCGH"; version="1.60.0"; sha256="0bmcw2pf4g584vjzagi70bxfasgzbi7nbis638aa5aymqgssclh8"; depends=[Biobase cluster multtest survival]; }; + abseqR = derive2 { name="abseqR"; version="1.0.0"; sha256="0w0ngxnilcrxlixsz7ls3zm99gyabxwn7w1r3r45n96d4aj075ry"; depends=[BiocParallel BiocStyle circlize flexdashboard ggcorrplot ggdendro ggplot2 gridExtra knitr plotly plyr png RColorBrewer reshape2 rmarkdown stringr vegan VennDiagram]; }; + acde = derive2 { name="acde"; version="1.12.0"; sha256="1qlas1fkjwx3x7ylhx4xwgwd3xyyijgsaqprfz3zk32cym67igx2"; depends=[boot]; }; + adSplit = derive2 { name="adSplit"; version="1.52.0"; sha256="0q5h0gizdxmpaz946ynzh1kbx51yd98z23y21bh7a3m2cqhr63gi"; depends=[AnnotationDbi Biobase cluster GO_db KEGG_db multtest]; }; + adaptest = derive2 { name="adaptest"; version="1.2.0"; sha256="1ibrzga0jk5rs6a097gn5ar7hkz8zja54l35xznp72jaradprj2i"; depends=[calibrate origami SummarizedExperiment tmle]; }; + affxparser = derive2 { name="affxparser"; version="1.54.0"; sha256="0cfsab3jih4zbrzfpd2cgi4wry2xmp8hmchpp70z33x0shwcxddx"; depends=[]; }; + affy = derive2 { name="affy"; version="1.60.0"; sha256="0x8h4fk2igv7vykqfvf6v9whmx3344v5rf3gyfajd431xkjldz6k"; depends=[affyio Biobase BiocGenerics BiocManager preprocessCore zlibbioc]; }; + affyContam = derive2 { name="affyContam"; version="1.40.0"; sha256="1qday3swgrgziymmwl2iyz2f8kd610hgpj9i9dsv8x09nks0jxcm"; depends=[affy affydata Biobase]; }; + affyILM = derive2 { name="affyILM"; version="1.34.0"; sha256="1v5spxwfg5vbca6rh2d3zsnsz1rlji02wfxq45pljwqcjr7pk6zy"; depends=[affxparser affy Biobase gcrma]; }; + affyPLM = derive2 { name="affyPLM"; version="1.58.0"; sha256="0n827mshllqj867w137x8qly992rvls9wcygmr09gmpy8f5hr0d2"; depends=[affy Biobase BiocGenerics gcrma preprocessCore zlibbioc]; }; + affyPara = derive2 { name="affyPara"; version="1.42.0"; sha256="0jk2r1v3yq1p9ny9hj46w42aq34m00bfm62a2n38cvql4zjrp6wz"; depends=[affy affyio aplpack snow vsn]; }; + affyQCReport = derive2 { name="affyQCReport"; version="1.60.0"; sha256="0l9znngszbjdwyyc1kpjszy3mrmwx781ww3wq8hs19jwvczgscyc"; depends=[affy affyPLM Biobase genefilter lattice RColorBrewer simpleaffy xtable]; }; + affycomp = derive2 { name="affycomp"; version="1.58.0"; sha256="1hkaa0g6kzmsnhd5vq8qy856rj7l5hcknhl62j47pqvwigfb1adg"; depends=[Biobase]; }; + affycoretools = derive2 { name="affycoretools"; version="1.54.0"; sha256="022pmik9gxpc0j3fcb2gmi8vchjwg3pwp1yn0cg5qfhy4w8mbyzz"; depends=[affy AnnotationDbi Biobase BiocGenerics DBI edgeR gcrma ggplot2 GOstats gplots hwriter lattice limma oligoClasses ReportingTools RSQLite S4Vectors xtable]; }; + affyio = derive2 { name="affyio"; version="1.52.0"; sha256="1s4zp1211vf0krxzch9v3q3r6vs8hihqppq18i2fpvwlknfja7c1"; depends=[zlibbioc]; }; + affylmGUI = derive2 { name="affylmGUI"; version="1.56.0"; sha256="1hpr812jys2d265r6007bh2p1d6hay25dg7ia39xwcycmwjfn9xq"; depends=[affy affyio affyPLM BiocGenerics BiocManager gcrma limma R2HTML tkrplot xtable]; }; + affypdnn = derive2 { name="affypdnn"; version="1.56.0"; sha256="0v8913xw30xf42pvql9m4wk5sqnrvydhn1a13amk7prfr2hhjnjr"; depends=[affy]; }; + agilp = derive2 { name="agilp"; version="3.14.0"; sha256="0jqgd582b9p3dclfs0ps4agj64vxmvqp9a2a9bw12dywschhngq3"; depends=[]; }; + alpine = derive2 { name="alpine"; version="1.8.0"; sha256="1ijh1lxl6w7raw2lvzxf20jx8x20d8p9mci62q3fpkc35i8312m6"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors speedglm stringr SummarizedExperiment]; }; + alsace = derive2 { name="alsace"; version="1.18.0"; sha256="1946iwghbsy0dcdpx7wl284prg5xikr0s7aj8pvv7gcmah8i9i7n"; depends=[ALS ptw]; }; + altcdfenvs = derive2 { name="altcdfenvs"; version="2.44.0"; sha256="1fkly7m4fgah6v7a6fglxqzik2562q6hg6ffq89kbgnzgvab4xsi"; depends=[affy Biobase BiocGenerics Biostrings hypergraph makecdfenv S4Vectors]; }; + ampliQueso = derive2 { name="ampliQueso"; version="1.20.0"; sha256="1dwphzsl45g537ic1m2bbg80dcilvhg1w8c02zlsxlihhid5rwy7"; depends=[DESeq doParallel edgeR foreach genefilter ggplot2 gplots knitr rgl rnaSeqMap samr statmod VariantAnnotation xtable]; }; + amplican = derive2 { name="amplican"; version="1.4.0"; sha256="0wzf1ami896b23bcb3giyahf662c55x8mzhdiywv05n4kqbq7wnp"; depends=[BiocGenerics BiocParallel Biostrings clusterCrit data_table dplyr GenomeInfoDb GenomicRanges ggforce ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats rmarkdown S4Vectors ShortRead stringr waffle]; }; + anamiR = derive2 { name="anamiR"; version="1.10.0"; sha256="0yk56vkibnbfwlnixh5r4a9iw9pnmavl7lv4p0jdmv2wnx85gzgz"; depends=[agricolae DBI DESeq2 gage gplots limma lumi RMySQL S4Vectors SummarizedExperiment]; }; + annaffy = derive2 { name="annaffy"; version="1.54.0"; sha256="16c6allp4vlx0g3nffanrm0mkkf8s2n31dccw4bflnx2pr81bmd5"; depends=[AnnotationDbi Biobase DBI GO_db KEGG_db]; }; + annmap = derive2 { name="annmap"; version="1.24.0"; sha256="12047l7sc3ayvicqnlxc424kbvbiiz1nn4rczd1n50b8kzc25fjs"; depends=[Biobase BiocGenerics DBI digest genefilter GenomicRanges IRanges lattice RMySQL Rsamtools]; }; + annotate = derive2 { name="annotate"; version="1.60.0"; sha256="0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl XML xtable]; }; + annotationTools = derive2 { name="annotationTools"; version="1.56.0"; sha256="0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z"; depends=[Biobase]; }; + annotatr = derive2 { name="annotatr"; version="1.8.0"; sha256="1rknhlndn9fxa68dbkqjphiv50xqp28vf1259k5w7vlm75vvdkdv"; depends=[AnnotationDbi AnnotationHub dplyr GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges readr regioneR reshape2 rtracklayer S4Vectors]; }; + anota = derive2 { name="anota"; version="1.30.0"; sha256="182fp6dpws516y0igvwn6936higfqvy25haa0xs273f8aczr9cf0"; depends=[multtest qvalue]; }; + anota2seq = derive2 { name="anota2seq"; version="1.4.0"; sha256="05p1h6mk4fb8q0k68bzqcs47iwjb0x44f5q7j77phw2n4kzq6ayl"; depends=[DESeq2 edgeR limma multtest qvalue RColorBrewer SummarizedExperiment]; }; + antiProfiles = derive2 { name="antiProfiles"; version="1.22.0"; sha256="1div92hqrri8c0y5g37cc4ysi30gcklf82n6g0p98xwv54ks2y7j"; depends=[locfit matrixStats]; }; + apComplex = derive2 { name="apComplex"; version="2.48.0"; sha256="0f33p7w2kmf7lz8a4j9mg04qnfnn03k3qmvqmfggqm5gb5h7y69l"; depends=[graph org_Sc_sgd_db RBGL Rgraphviz]; }; + apeglm = derive2 { name="apeglm"; version="1.4.1"; sha256="01f4qlhg4xz9mc0gsmmrwxx644f2h1cgwi0f3fhy6srzjdfb6l9v"; depends=[emdbook GenomicRanges Rcpp RcppEigen RcppNumerical SummarizedExperiment]; }; + appreci8R = derive2 { name="appreci8R"; version="1.0.0"; sha256="1ajk6q40dr5il19ffnsfglbh1rfn8ylwv08mw9wfpvc26x4znwak"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 COSMIC_67 DT GenomicFeatures GenomicRanges GenomicScores Homo_sapiens IRanges MafDb_1Kgenomes_phase3_hs37d5 MafDb_ESP6500SI_V2_SSA137_hs37d5 MafDb_ExAC_r1_0_hs37d5 MafDb_gnomADex_r2_0_1_hs37d5 openxlsx PolyPhen_Hsapiens_dbSNP131 rentrez Rsamtools rsnps S4Vectors seqinr shiny shinyjs SIFT_Hsapiens_dbSNP137 SNPlocs_Hsapiens_dbSNP144_GRCh37 stringr SummarizedExperiment TxDb_Hsapiens_UCSC_hg19_knownGene VariantAnnotation XtraSNPlocs_Hsapiens_dbSNP144_GRCh37]; }; + aroma_light = derive2 { name="aroma.light"; version="3.12.0"; sha256="0vfifgpqxjjncbiv6gvlk9jmj14j90r9f30bqk3ks9v1csjnjhrb"; depends=[matrixStats R_methodsS3 R_oo R_utils]; }; + arrayMvout = derive2 { name="arrayMvout"; version="1.40.0"; sha256="1m3n2pqm40wsq7x7acspcq268608pnx58mndqfcbv813685b70p5"; depends=[affy affyContam Biobase lumi mdqc parody simpleaffy]; }; + arrayQuality = derive2 { name="arrayQuality"; version="1.60.0"; sha256="0fbvlilz111ahlm50gmwwjydpasbplr0lpj3dz9apawi0jff4f4a"; depends=[gridBase hexbin limma marray RColorBrewer]; }; + arrayQualityMetrics = derive2 { name="arrayQualityMetrics"; version="3.38.0"; sha256="0xhzz9ixc5mp49cwpi4smdgdc3mrf1ppzhx8dpjahq1f7r3xnbb5"; depends=[affy affyPLM beadarray Biobase Cairo genefilter gridSVG Hmisc hwriter lattice latticeExtra limma RColorBrewer setRNG vsn XML]; }; + artMS = derive2 { name="artMS"; version="1.0.1"; sha256="0gjgpfljrr26b5g6813x84w0s01d9nhr7cw122bzv3jw777gpbvj"; depends=[AnnotationDbi biomaRt bit64 circlize cluster ComplexHeatmap corrplot data_table dplyr factoextra FactoMineR getopt ggdendro ggplot2 ggrepel gplots gProfileR limma MSstats openxlsx org_Hs_eg_db org_Mm_eg_db PerformanceAnalytics pheatmap plotly plyr RColorBrewer reshape2 seqinr stringr tidyr UpSetR VennDiagram yaml]; }; + attract = derive2 { name="attract"; version="1.34.0"; sha256="0s93d6ms4pf2ivl7z602ackbnfwl5956g899ayn65lybikrrhcqa"; depends=[AnnotationDbi Biobase cluster GOstats KEGGREST limma org_Hs_eg_db reactome_db]; }; + bacon = derive2 { name="bacon"; version="1.10.0"; sha256="095z8fpfmam2d6iaq6p4pp2c7agisq9008wd49s7997a8a8rd7vs"; depends=[BiocParallel ellipse ggplot2]; }; + ballgown = derive2 { name="ballgown"; version="2.14.0"; sha256="1vnhw2igd9b8lv4722mrwyv1ffif5jhr6yb5sy1sy122ga1ml4rr"; depends=[Biobase GenomeInfoDb GenomicRanges IRanges limma RColorBrewer rtracklayer S4Vectors sva]; }; + bamsignals = derive2 { name="bamsignals"; version="1.14.0"; sha256="19irfx1y1izf903vq59wxsdbf88g143zy9l89gxqawh7jfxds8w8"; depends=[BiocGenerics GenomicRanges IRanges Rcpp Rhtslib zlibbioc]; }; + banocc = derive2 { name="banocc"; version="1.6.0"; sha256="1549rk72a6alr2swssj2rqhg2zzszb1gz1cy4cz893c3zg14x268"; depends=[coda mvtnorm rstan stringr]; }; + basecallQC = derive2 { name="basecallQC"; version="1.6.0"; sha256="0l2w55lc8aknj3ivma3arp96j46hcfzw20k9js3dgx8k3sgalxmn"; depends=[data_table dplyr DT ggplot2 knitr lazyeval magrittr prettydoc raster rmarkdown ShortRead stringr tidyr XML yaml]; }; + bayNorm = derive2 { name="bayNorm"; version="1.0.6"; sha256="1zlpk76rr95is94l8p06y151w3frv886b9v7mbjvxgsn7rxlkvs9"; depends=[BB BiocParallel doSNOW fitdistrplus foreach iterators locfit MASS Rcpp RcppArmadillo RcppProgress SingleCellExperiment SummarizedExperiment]; }; + baySeq = derive2 { name="baySeq"; version="2.16.0"; sha256="0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"; depends=[abind edgeR GenomicRanges]; }; + bcSeq = derive2 { name="bcSeq"; version="1.4.0"; sha256="11jq77ppagkg4kw1lbp5a2q5rdh3dcqbs12q9ykngjbb0gkjp0s3"; depends=[Biostrings Matrix Rcpp]; }; + beachmat = derive2 { name="beachmat"; version="1.4.0"; sha256="07zgmms0qg8gw7x0js46965bbhpfj2aa1h5ixdz9r332bxv9cdmr"; depends=[BiocGenerics DelayedArray HDF5Array Rcpp rhdf5 Rhdf5lib]; }; + beadarray = derive2 { name="beadarray"; version="2.32.0"; sha256="0xy75h98xkclsi2hxzz8qj21sm8fp3cy7ikmjsryvdbk7jwl6lgg"; depends=[AnnotationDbi BeadDataPackR Biobase BiocGenerics GenomicRanges ggplot2 illuminaio IRanges limma reshape2]; }; + beadarraySNP = derive2 { name="beadarraySNP"; version="1.48.0"; sha256="1s1k5q1mczbnx5gdxa8r1igkmc8jw5dmnp0gl00q862bbsljplk9"; depends=[Biobase quantsmooth]; }; + bgafun = derive2 { name="bgafun"; version="1.44.0"; sha256="1sp3w0g0sxs6g42mjj76sjpi5ybcvhg6a4sp617713a71dab7276"; depends=[ade4 made4 seqinr]; }; + bgx = derive2 { name="bgx"; version="1.48.1"; sha256="0ygqbqpbrp4hy5dp4g7nn7zrfar855a7bp16dxcv7646vp3yrzk4"; depends=[affy Biobase gcrma Rcpp]; }; + bigmelon = derive2 { name="bigmelon"; version="1.8.0"; sha256="1wc5n5cq05a7qv0b46ywbgg1fbz0s8hyf83g861dxw8jhhmnm717"; depends=[Biobase BiocGenerics gdsfmt GEOquery methylumi minfi wateRmelon]; }; + bigmemoryExtras = derive2 { name="bigmemoryExtras"; version="1.30.0"; sha256="0pzqchv9namv73nm2vr6wjny7ghja8bs73s7xp4ixyfg4d1i9h06"; depends=[bigmemory]; }; + bioCancer = derive2 { name="bioCancer"; version="1.10.0"; sha256="17f72vs9h66ny9z0n4fbp6533phrdv60a7ck386rfvpgafdrqh7s"; depends=[AlgDesign AnnotationFuncs Biobase cgdsr clusterProfiler DiagrammeR DOSE dplyr DT geNetClassifier htmlwidgets org_Hs_eg_db plyr r_import radiant_data reactome_db ReactomePA shiny shinythemes tibble visNetwork XML]; }; + bioDist = derive2 { name="bioDist"; version="1.54.0"; sha256="1pl6z8yx1pns19y924x79ky4vqx180hifvy7n4mdhv6mjvhjkijl"; depends=[Biobase KernSmooth]; }; + bioassayR = derive2 { name="bioassayR"; version="1.20.0"; sha256="1wwk00c1lp6a5inna48z2hkb3xni8pcwjhf0qdwf2i70rkls2724"; depends=[BiocGenerics ChemmineR DBI Matrix rjson RSQLite XML]; }; + biobroom = derive2 { name="biobroom"; version="1.14.0"; sha256="1xfqa666n8h65y277a1g56r1z76x9fn0dnj45cqgx3ddaz0v1nil"; depends=[Biobase broom dplyr tidyr]; }; + biocGraph = derive2 { name="biocGraph"; version="1.44.0"; sha256="0nq8wvssikkcrs3vffpy3pj79iydm44ffsx67q38kg51gc4ykipk"; depends=[BiocGenerics geneplotter graph Rgraphviz]; }; + biocViews = derive2 { name="biocViews"; version="1.50.10"; sha256="06ms82pyc5rxbd9crfvqjxcwpafv0c627i83v80d12925mrc51h8"; depends=[Biobase graph RBGL RCurl RUnit XML]; }; + biomaRt = derive2 { name="biomaRt"; version="2.38.0"; sha256="1lshkknp7dmr3p6dd2zbv86cc71h53ggh9ji83jcjym8sgbbspl2"; depends=[AnnotationDbi httr progress RCurl stringr XML]; }; + biomformat = derive2 { name="biomformat"; version="1.10.0"; sha256="1mdxjrza526gn4jli0cjdcilspwb3c07nmjwy1l9mfmnlm7ca0b2"; depends=[jsonlite Matrix plyr rhdf5]; }; + biomvRCNS = derive2 { name="biomvRCNS"; version="1.22.0"; sha256="0bzi8b4g1ki8gslkb2nkrl4fyrl5lj9qipq8lmr6zj924y3pkmnm"; depends=[GenomicRanges Gviz IRanges mvtnorm]; }; + biosigner = derive2 { name="biosigner"; version="1.10.0"; sha256="04mny1lrgmwd1yy07qhim286xvm34802f12rbpsplb0xzwg09y6i"; depends=[Biobase e1071 randomForest ropls]; }; + biosvd = derive2 { name="biosvd"; version="2.18.0"; sha256="1ngmnk4xakpf451lbx9libxwlsqz7xffaj53awkw5iakzmj7szb9"; depends=[Biobase BiocGenerics NMF]; }; + biotmle = derive2 { name="biotmle"; version="1.6.0"; sha256="0vmff5xpcprx1x45fbbm9bx3wygg6r2zb7z9mnkjjshsinf7wwwb"; depends=[BiocGenerics BiocParallel doFuture dplyr future ggplot2 ggsci limma S4Vectors SummarizedExperiment superheat tmle]; }; + biovizBase = derive2 { name="biovizBase"; version="1.30.1"; sha256="0v5gvcx180qn5487i1dph9abadw3ggqwp5yzy41jswzbdc8q6sbm"; depends=[AnnotationDbi AnnotationFilter BiocGenerics Biostrings dichromat ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges Hmisc IRanges RColorBrewer rlang Rsamtools S4Vectors scales SummarizedExperiment VariantAnnotation]; }; + birta = derive2 { name="birta"; version="1.26.0"; sha256="10k6r3g92ksm90gj8z04vs1psgrr1p0yddrjl5zcwrccczcankpb"; depends=[Biobase limma MASS]; }; + birte = derive2 { name="birte"; version="1.18.0"; sha256="036grna913y55qz72npwq6k27wcvaf7swy3y9nrfh0wg327w4y9a"; depends=[Biobase glmnet limma MASS nem Rcpp RcppArmadillo]; }; + blima = derive2 { name="blima"; version="1.16.0"; sha256="1719skygq6mizvr67klja0z1xqbmfhxgjyi90i9p95sbb6mr1n74"; depends=[beadarray Biobase BiocGenerics Rcpp]; }; + bnbc = derive2 { name="bnbc"; version="1.4.0"; sha256="001m8nal3l1ya5w1f9gh7sgvdli9lv0v8ylkdgmdwjy2wrpkqiij"; depends=[BiocGenerics EBImage GenomeInfoDb GenomicRanges IRanges matrixStats preprocessCore Rcpp S4Vectors SummarizedExperiment sva]; }; + brainImageR = derive2 { name="brainImageR"; version="1.0.0"; sha256="1j5axlx12dpl6y58djqbf6dg146zz94ki43nhi9rjl03aw9bg9fc"; depends=[BiocGenerics ExperimentHub ggplot2 gridExtra randomForest RColorBrewer testthat]; }; + branchpointer = derive2 { name="branchpointer"; version="1.8.0"; sha256="1fgfaf7i9f1rr34p38b87wq5qys7r8wqi99xw4yk154bhsahkdlm"; depends=[biomaRt Biostrings BSgenome_Hsapiens_UCSC_hg38 caret cowplot data_table gbm GenomeInfoDb GenomicRanges ggplot2 IRanges kernlab plyr rtracklayer S4Vectors stringr]; }; + breakpointR = derive2 { name="breakpointR"; version="1.0.0"; sha256="19hpwdpj5mqidy0m5q0ilx3p84ry0ym31g2ld3cnihzi2kxcyqzm"; depends=[BiocGenerics breakpointRdata cowplot doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gtools IRanges Rsamtools S4Vectors]; }; + bridge = derive2 { name="bridge"; version="1.46.0"; sha256="0fsf8qcl4p63fgzyk9zsr25krz1a34mi79mnxya0n4fxrf3qcq2f"; depends=[rama]; }; + bsseq = derive2 { name="bsseq"; version="1.18.0"; sha256="0r0l4fwaq09n14bvqy01id569zimxwafs3xnp0zn2089512igis7"; depends=[beachmat Biobase BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats GenomeInfoDb GenomicRanges gtools HDF5Array IRanges limma locfit permute R_utils Rcpp rhdf5 Rhdf5lib S4Vectors scales SummarizedExperiment]; }; + bumphunter = derive2 { name="bumphunter"; version="1.24.5"; sha256="1f9vk3srffbx8jpza40nd18a4y0p0z8q40mx55dlcnddkwrqi19b"; depends=[AnnotationDbi BiocGenerics doRNG foreach GenomeInfoDb GenomicFeatures GenomicRanges IRanges iterators limma locfit matrixStats S4Vectors]; }; + cTRAP = derive2 { name="cTRAP"; version="1.0.3"; sha256="14rfnqmp2mgnkyhgyvlplv4alnwm909pw586n7nc53r82ph4m0f0"; depends=[cowplot data_table fgsea ggplot2 httr limma pbapply piano plyr R_utils readr rhdf5]; }; + caOmicsV = derive2 { name="caOmicsV"; version="1.12.0"; sha256="05zr3z19zzs56gx06r43j6dl59q1z0hba9qfrb0ygvkvfj3h5rk5"; depends=[bc3net igraph]; }; + canceR = derive2 { name="canceR"; version="1.16.0"; sha256="0kfhvkjc6mssp6jphac4p1f2sjc8j08apiwznj621w3wxa2gnkby"; depends=[Biobase cgdsr circlize Formula geNetClassifier GSEABase GSEAlm phenoTest plyr rpart RUnit survival tcltk2 tkrplot]; }; + cancerclass = derive2 { name="cancerclass"; version="1.26.0"; sha256="1fsfxi95iyb2bhy64xdja4231bfs9byzzvdpsf6abd8myqaflcpx"; depends=[binom Biobase]; }; + casper = derive2 { name="casper"; version="2.16.0"; sha256="1l3rp7q2gcs35r8drnwbwmfa922yd810qjmpgc18xjbx12s7hnkf"; depends=[Biobase BiocGenerics coda EBarrays gaga GenomeInfoDb GenomicFeatures GenomicRanges gtools IRanges limma mgcv Rsamtools rtracklayer S4Vectors sqldf survival VGAM]; }; + categoryCompare = derive2 { name="categoryCompare"; version="1.26.0"; sha256="1kb4b833wn5qf3d6vic0jf0p0h6dhgcpjnxnqd6b4bhva0y3jcfd"; depends=[annotate AnnotationDbi Biobase BiocGenerics Category colorspace GOstats graph GSEABase hwriter RCy3]; }; + cbaf = derive2 { name="cbaf"; version="1.4.0"; sha256="10rcph5kk1kdd1idl7wvh766qfg25462sc0airwcsm2w6xw7xgqf"; depends=[BiocFileCache cgdsr genefilter gplots RColorBrewer xlsx]; }; + ccfindR = derive2 { name="ccfindR"; version="1.2.0"; sha256="1z37afhsnf23bygka15jff4awxpc7s3k47biq8z75mxi58xdvmn9"; depends=[ape gtools irlba Matrix RColorBrewer Rcpp RcppEigen Rmpi Rtsne S4Vectors SingleCellExperiment SummarizedExperiment]; }; + ccmap = derive2 { name="ccmap"; version="1.8.0"; sha256="1vkkm455nhhg123jwl2kv3gdf3mvw5zab4whym0vh33rm499hrks"; depends=[AnnotationDbi BiocManager ccdata data_table doParallel foreach lsa xgboost]; }; + ccrepe = derive2 { name="ccrepe"; version="1.18.0"; sha256="0f94bd4iinaajv79bkf2qd6g89qlrznp23l3bv02sgb8yhqxrwq2"; depends=[infotheo]; }; + celaref = derive2 { name="celaref"; version="1.0.0"; sha256="08pddidi2l990n65nan8zsgay3l5c0l9hm8jgjsasc00a008qs0x"; depends=[BiocGenerics dplyr ggplot2 magrittr MAST Matrix readr rlang S4Vectors SummarizedExperiment tibble]; }; + cellGrowth = derive2 { name="cellGrowth"; version="1.26.0"; sha256="1hhxqfpnlhfz5hmmis6pxh1crnjr8yf8zy87zl88h6mzypdc76fh"; depends=[lattice locfit]; }; + cellHTS2 = derive2 { name="cellHTS2"; version="2.46.0"; sha256="10116jg5fx4kp5m2xadb3b8dib623lrazzc62wm19mrghg9y6kzj"; depends=[Biobase BiocGenerics Category genefilter GSEABase hwriter locfit prada RColorBrewer splots vsn]; }; + cellTree = derive2 { name="cellTree"; version="1.12.0"; sha256="1p818hsx2dqnd9x2aym26zm0was3ppnpyxg9si5fjh5h9inkh5mi"; depends=[gplots igraph maptpx slam topGO topicmodels xtable]; }; + cellbaseR = derive2 { name="cellbaseR"; version="1.6.0"; sha256="1jw7pwpn8kpx7js8453rwcajwf8fs3l6yc19vxhw0s96a3c3j5bi"; depends=[BiocParallel data_table doParallel foreach httr jsonlite pbapply R_utils Rsamtools tidyr]; }; + cellity = derive2 { name="cellity"; version="1.10.0"; sha256="0hbh2pi76a5jr7nmvwhgxqsrs8sv6k1m7kn0vgvz67hhx59flncr"; depends=[AnnotationDbi e1071 ggplot2 mvoutlier org_Hs_eg_db org_Mm_eg_db robustbase topGO]; }; + cellscape = derive2 { name="cellscape"; version="1.6.0"; sha256="062x43n5jq8hwlrlgd1ffgbpnifac79j9dzd35f6phb6vc1g63dl"; depends=[dplyr gtools htmlwidgets jsonlite plyr reshape2 stringr]; }; + cghMCR = derive2 { name="cghMCR"; version="1.40.0"; sha256="0h2adfwa6afjik7zi6kn8i7gqbn7x2r7rh8kvi8v8c8y08166d3a"; depends=[BiocGenerics CNTools DNAcopy limma]; }; + charm = derive2 { name="charm"; version="2.28.0"; sha256="1shf9f9b0dl5fskify0lqnqnr9rk4hk5rnrx7b028m83zphizxs8"; depends=[Biobase Biostrings BSgenome ff fields genefilter gtools IRanges limma nor1mix oligo oligoClasses preprocessCore RColorBrewer siggenes SQN sva]; }; + chimera = derive2 { name="chimera"; version="1.24.0"; sha256="1zkwf6zbg1151br9kafbqs4k4d5h70lbzjgy4x3q5pj3iqwg6j8p"; depends=[AnnotationDbi Biobase BSgenome_Hsapiens_UCSC_hg19 GenomicAlignments GenomicRanges Homo_sapiens Rsamtools TxDb_Hsapiens_UCSC_hg19_knownGene]; }; + chimeraviz = derive2 { name="chimeraviz"; version="1.8.0"; sha256="0c337msqk0zvqfr611wm0bdrvf7x2yfxb35rza9gn5bv12hlfzmg"; depends=[AnnotationDbi AnnotationFilter ArgumentCheck BiocStyle Biostrings data_table dplyr DT ensembldb GenomeInfoDb GenomicAlignments GenomicRanges graph Gviz IRanges org_Hs_eg_db org_Mm_eg_db plyr RCircos RColorBrewer Rgraphviz rmarkdown Rsamtools S4Vectors]; }; + chipenrich = derive2 { name="chipenrich"; version="2.6.0"; sha256="1piyp3v42lzm40vvzbcfx0afzgklvp3vcf6i071s8dhjwk8hfa0z"; depends=[AnnotationDbi BiocGenerics chipenrich_data GenomeInfoDb GenomicRanges IRanges lattice latticeExtra mgcv org_Dm_eg_db org_Dr_eg_db org_Hs_eg_db org_Mm_eg_db org_Rn_eg_db plyr rms rtracklayer S4Vectors stringr]; }; + chipseq = derive2 { name="chipseq"; version="1.32.0"; sha256="1pp1rm5fs3hlar5x4dl3a3b4gara7qwf81dbvka6r1n78hrf9x1b"; depends=[BiocGenerics GenomicRanges IRanges lattice S4Vectors ShortRead]; }; + chopsticks = derive2 { name="chopsticks"; version="1.48.0"; sha256="0r52z0hjaxinw11jzg8cyhdpg2g1027vd5aiijwi6bmipdzw4sfk"; depends=[survival]; }; + chroGPS = derive2 { name="chroGPS"; version="2.0.1"; sha256="1bn5s1r927ifhwqifws0wgs7v15fk8922kbm8qdkg5zaqibj5qx7"; depends=[Biobase changepoint cluster DPpackage ellipse GenomicRanges ICSNP IRanges MASS vegan]; }; + chromDraw = derive2 { name="chromDraw"; version="2.12.0"; sha256="0qqam9vklg2cwsvcp9fm3l3c4lmjzf2lnxrv5dci16f8q55z88cl"; depends=[GenomicRanges Rcpp]; }; + chromPlot = derive2 { name="chromPlot"; version="1.10.0"; sha256="15f7wmak0rp0bfzqsjmz6i8zk5g4axsgk7034qg4jw9hlp0nkd6v"; depends=[biomaRt GenomicRanges]; }; + chromVAR = derive2 { name="chromVAR"; version="1.4.0"; sha256="0cg0kjcrqxzclg9whydhd7fbpj2hcxrkl66ilk5y22dsz9wnwq62"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DT GenomeInfoDb GenomicRanges ggplot2 IRanges Matrix miniUI nabor plotly RColorBrewer Rcpp RcppArmadillo Rsamtools Rtsne S4Vectors shiny SummarizedExperiment TFBSTools]; }; + chromstaR = derive2 { name="chromstaR"; version="1.8.0"; sha256="1jpbmh6rjm7484d5blh5ziwn2mq2nkkyyfmwliiyxyjygn5c8bgk"; depends=[bamsignals chromstaRData doParallel foreach GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges mvtnorm reshape2 Rsamtools S4Vectors]; }; + chromswitch = derive2 { name="chromswitch"; version="1.4.0"; sha256="1gbnpk8paydd7liwdws47dqlsgb009l87fdnqvhrldym56ya5kpy"; depends=[Biobase BiocParallel cluster dplyr GenomicRanges gplots IRanges lazyeval magrittr matrixStats NMF rtracklayer S4Vectors tidyr]; }; + cicero = derive2 { name="cicero"; version="1.0.14"; sha256="0n4dl6d5fp989y86lnnhjdlmqcy7qyr5ayb1dp2q05rpa7qkv8cf"; depends=[assertthat Biobase BiocGenerics data_table dplyr FNN GenomicRanges ggplot2 glasso Gviz igraph IRanges Matrix monocle plyr reshape2 S4Vectors stringr tibble VGAM]; }; + cisPath = derive2 { name="cisPath"; version="1.22.0"; sha256="07ym4ma35vngdbv8fdqf755kiafgrn02bizn77pfkzvrf7xsz5c7"; depends=[]; }; + cleanUpdTSeq = derive2 { name="cleanUpdTSeq"; version="1.20.0"; sha256="0lmdrx332p43xw1y3bnq7abr6589rwyirn3kljkzjy8j86v0bgbi"; depends=[BiocGenerics BSgenome BSgenome_Drerio_UCSC_danRer7 e1071 GenomicRanges seqinr]; }; + cleaver = derive2 { name="cleaver"; version="1.20.0"; sha256="0b00a5n87hcssnra9j0qfsq260a83g9p35rnhpg8ywv3kk6z85cc"; depends=[Biostrings IRanges S4Vectors]; }; + clippda = derive2 { name="clippda"; version="1.32.0"; sha256="18jcpcwzf89a29i7qlja4nx9dn8n2r14kpjfl9sy2riaf0v9cmqq"; depends=[Biobase lattice limma rgl scatterplot3d statmod]; }; + clipper = derive2 { name="clipper"; version="1.22.0"; sha256="1gihz3dzii0bf048zbna4yj0fcs8pnhyacpmvyapi70iin03nwng"; depends=[Biobase corpcor graph gRbase igraph KEGGgraph Matrix qpgraph RBGL Rcpp]; }; + clonotypeR = derive2 { name="clonotypeR"; version="1.20.0"; sha256="03k94s5j47mh7hw8m12q7lsyszmf5kpmlc7xsvwbnnazsk15h55v"; depends=[]; }; + clst = derive2 { name="clst"; version="1.30.0"; sha256="1jakdp6ca14n8zc3njwkqibsir6as2nipjsxkanss5rn7s6xvql9"; depends=[lattice ROC]; }; + clstutils = derive2 { name="clstutils"; version="1.30.0"; sha256="0igvcd1dk8njp8fmf8clnx1hjzsbpf6xr7n31qzynzqghdr52660"; depends=[ape clst lattice rjson RSQLite]; }; + clustComp = derive2 { name="clustComp"; version="1.10.0"; sha256="17d86fzadlmv45bxwdnjaw5bcr46zn73y4wqw5xw5rvaawrdc73v"; depends=[sm]; }; + clusterExperiment = derive2 { name="clusterExperiment"; version="2.2.0"; sha256="0r8x21z0clgjbxxdr3iqfmg0nw2pwdidyc41pnbzw9y40lzad4lv"; depends=[ape BiocGenerics cluster DelayedArray dendextend edgeR HDF5Array howmany kernlab limma locfdr matrixStats NMF phylobase RColorBrewer Rcpp RSpectra S4Vectors scales SingleCellExperiment stringr SummarizedExperiment zinbwave]; }; + clusterProfiler = derive2 { name="clusterProfiler"; version="3.10.1"; sha256="1v4fh8ll7zk8yhbaa0nq9xvqrb05kyvbpwkqpnjf07s873805rxm"; depends=[AnnotationDbi DOSE enrichplot ggplot2 GO_db GOSemSim magrittr plyr qvalue rvcheck tidyr]; }; + clusterSeq = derive2 { name="clusterSeq"; version="1.6.0"; sha256="0zq0pah3qk4j5grsj3dyc62n222gacjlhr2xw7frwrrbjlxza7b2"; depends=[baySeq BiocGenerics BiocParallel]; }; + clusterStab = derive2 { name="clusterStab"; version="1.54.0"; sha256="0irwzgayssdnz76k13zf27h9s74x8idi26zfsdd2c3av494d3yl9"; depends=[Biobase]; }; + cn_farms = derive2 { name="cn.farms"; version="1.30.0"; sha256="1lmlixab15xq12dxw04yyxd1p65irwhxkgkxsgvw28f922bkmlsg"; depends=[affxparser Biobase DBI DNAcopy ff lattice oligo oligoClasses preprocessCore snow]; }; + cn_mops = derive2 { name="cn.mops"; version="1.28.0"; sha256="14rrvyfyzva1hpdgsn1df6m4q14mc3zdn1lng6klzrni3ifsidjm"; depends=[Biobase BiocGenerics exomeCopy GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; + cnvGSA = derive2 { name="cnvGSA"; version="1.26.0"; sha256="02p4ba2vy75qfp3nlfvm0dmmihi1k1fbcl6ckxlr5hgimm1q034i"; depends=[brglm doParallel foreach GenomicRanges splitstackshape]; }; + coGPS = derive2 { name="coGPS"; version="1.26.0"; sha256="0jsbgx6xdasqii9wcfn4ilf2dfc790lzzby1bhpzlq94nwlr896h"; depends=[]; }; + coMET = derive2 { name="coMET"; version="1.14.0"; sha256="09r81ag9ix4jh3zvwyzym9g7rc7vkyhagcv934r8i4fzzvpiqsz4"; depends=[biomaRt colortools corrplot GenomicRanges gridExtra Gviz hash IRanges psych rtracklayer S4Vectors]; }; + coRdon = derive2 { name="coRdon"; version="1.0.3"; sha256="1v4zvzff4r54wjgp48l5vazvfy8w0gvvqxxhajm35p6d2bbpfsvd"; depends=[Biobase Biostrings data_table dplyr ggplot2 purrr stringr]; }; + cobindR = derive2 { name="cobindR"; version="1.20.0"; sha256="1bkwjj825srwm3rn3j88p1q35x03f129ca1hk919nnf92psh47nc"; depends=[BiocGenerics biomaRt Biostrings BSgenome gmp gplots IRanges mclust rtfbs seqinr yaml]; }; + codelink = derive2 { name="codelink"; version="1.50.0"; sha256="1nfnb9iz8j31ia9979mjvs9gzdbh9zwfy14qxvjrp3dv8d1gf2rx"; depends=[annotate Biobase BiocGenerics limma]; }; + coexnet = derive2 { name="coexnet"; version="1.4.0"; sha256="0751781vsr46xs3dpq2n29li1zipzad9qv6xnfdm34v62yaggy94"; depends=[acde affy Biobase GEOquery igraph limma minet rmarkdown siggenes STRINGdb SummarizedExperiment vsn]; }; + cogena = derive2 { name="cogena"; version="1.16.0"; sha256="12r86h6fzr6wqvf70jjxf02zm72ks577m6qcv60wiss609c0b0dn"; depends=[amap apcluster Biobase biwt class cluster corrplot devtools doParallel dplyr fastcluster foreach ggplot2 gplots kohonen mclust reshape2]; }; + compEpiTools = derive2 { name="compEpiTools"; version="1.16.0"; sha256="02ygqf2h9bm8vfqjfw0xzd75brcazf1dmhq95l8xqc3gy77cffr6"; depends=[AnnotationDbi BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges GO_db gplots IRanges methylPipe Rsamtools S4Vectors topGO XVector]; }; + compartmap = derive2 { name="compartmap"; version="1.0.2"; sha256="1z0sy4g5p0bagnzqm6j0adx8k0c9gf8a6wz0a84vig182q3wyji2"; depends=[GenomicRanges gtools Homo_sapiens minfi mixOmics SummarizedExperiment]; }; + compcodeR = derive2 { name="compcodeR"; version="1.18.0"; sha256="1wzhabpw6zbf07100vza1lkgmfzwdqwmk1h70ddb1asbs5s2m4qw"; depends=[caTools edgeR gdata ggplot2 gplots gtools KernSmooth knitr lattice limma markdown MASS modeest ROCR sm stringr vioplot]; }; + condcomp = derive2 { name="condcomp"; version="1.0.0"; sha256="1nv3i1r1alpzww6yz4gnic8jjglx8svidcb66kk3gq4pd9fkwafj"; depends=[cluster ggplot2 ggrepel outliers]; }; + consensus = derive2 { name="consensus"; version="1.0.1"; sha256="1hvs97fz95cpfa3ddymkzh186v4wh1hv2jhn72d8pjzx9nlpm230"; depends=[gplots matrixStats RColorBrewer]; }; + consensusDE = derive2 { name="consensusDE"; version="1.0.0"; sha256="1chwwa0jqkby6gs8qmw5hpx8wppfllrhzg5cc1z1jy1xm98853fs"; depends=[airway AnnotationDbi Biobase BiocParallel Biostrings dendextend DESeq2 EDASeq edgeR GenomicAlignments GenomicFeatures limma pcaMethods RColorBrewer Rsamtools RUVSeq S4Vectors SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm3_ensGene]; }; + consensusOV = derive2 { name="consensusOV"; version="1.4.1"; sha256="0bqqbk2mcj1q5bpyv5gykxpjf3c1gszm5irbdhp1hnkvpy5rxdyw"; depends=[Biobase gdata genefu GSVA limma matrixStats randomForest]; }; + consensusSeekeR = derive2 { name="consensusSeekeR"; version="1.10.0"; sha256="1rww42z71x6d7ckjdm6xa4cvvqazbwghq6na3srq5aarp6pyh34w"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges IRanges rtracklayer S4Vectors stringr]; }; + contiBAIT = derive2 { name="contiBAIT"; version="1.10.0"; sha256="0kacksvq3xf077qjab06s4kwj4kx6dcnnml7pw15vlr8af4vdfx7"; depends=[BH BiocParallel clue cluster colorspace data_table diagram DNAcopy exomeCopy GenomicAlignments GenomicFiles GenomicRanges ggplot2 gplots gtools IRanges Rcpp reshape2 Rsamtools rtracklayer S4Vectors TSP]; }; + conumee = derive2 { name="conumee"; version="1.16.0"; sha256="095kzjzvwz5l452arkvrmag7mvqsip14xzbnsfk7wzlr5vpk2765"; depends=[DNAcopy GenomeInfoDb GenomicRanges IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest IRanges minfi rtracklayer]; }; + convert = derive2 { name="convert"; version="1.58.0"; sha256="1z7f4dxlsgknapvwq7dvkhyaq25ns2i53fp085j5yy89aqv12w12"; depends=[Biobase limma marray]; }; + copa = derive2 { name="copa"; version="1.50.0"; sha256="0cl9i2pi0ap9nvhqldsll9vg7k5qlzr0691mp4i7r6qib31xnzpx"; depends=[Biobase]; }; + copynumber = derive2 { name="copynumber"; version="1.22.0"; sha256="0ipwj9i5p1bwhg5d80jdjagm02krpj2v0j47qdgw41h8wncdyal3"; depends=[BiocGenerics GenomicRanges IRanges S4Vectors]; }; + coseq = derive2 { name="coseq"; version="1.6.0"; sha256="1162l198r8m16liv2zj4zz904s4w3yxj75g6jdba3cdf8c4dgs30"; depends=[BiocParallel capushe compositions corrplot DESeq2 e1071 edgeR ggplot2 HTSCluster HTSFilter mvtnorm Rmixmod S4Vectors scales SummarizedExperiment]; }; + cosmiq = derive2 { name="cosmiq"; version="1.16.0"; sha256="1cc6n82zwmzkggi2zgxw3c2h6x6h3wld2bxskkkdf9l4k005bq8v"; depends=[faahKO MassSpecWavelet pracma Rcpp xcms]; }; + countsimQC = derive2 { name="countsimQC"; version="1.0.0"; sha256="17ggp2lsld7r2lbw4akisg4hvkc1sypyh5i9b105hqpcvy0way1l"; depends=[caTools DESeq2 dplyr DT edgeR genefilter GenomeInfoDbData ggplot2 randtests rmarkdown SummarizedExperiment tidyr]; }; + covEB = derive2 { name="covEB"; version="1.8.0"; sha256="16y5ys3n5r2zh4z4sp06b1cphr1nvw8didwrlrkvggrp75501mq9"; depends=[Biobase gsl igraph LaplacesDemon Matrix mvtnorm]; }; + covRNA = derive2 { name="covRNA"; version="1.8.0"; sha256="152yhnq13303wkb4p1bqal7qrg2gxwfqsdpgn84m2sz8gm43dxkc"; depends=[ade4 Biobase genefilter]; }; + cpvSNP = derive2 { name="cpvSNP"; version="1.14.0"; sha256="0g4b4i001z5s5g570cpay61c8b8274cy35gp09mb3hjmg5r6rcxp"; depends=[BiocParallel corpcor GenomicFeatures ggplot2 GSEABase plyr]; }; + cqn = derive2 { name="cqn"; version="1.28.0"; sha256="1y34dy7xza5gqgh883h563w1ycg5s0dc77sza2skszzflw3qp52z"; depends=[mclust nor1mix preprocessCore quantreg]; }; + crisprseekplus = derive2 { name="crisprseekplus"; version="1.8.0"; sha256="125fnm1mrx38bb2c6inw5c45ckh8ryapjvxx7227jj86a3hcljk7"; depends=[AnnotationDbi BiocManager BSgenome CRISPRseek DT GenomicFeatures GenomicRanges GUIDEseq hash shiny shinyjs]; }; + crlmm = derive2 { name="crlmm"; version="1.40.0"; sha256="1j37ff0pp782isnrzfaw0cac8nxcz09yc4z7xgss78ah3af26nwj"; depends=[affyio beanplot Biobase BiocGenerics ellipse ff foreach illuminaio lattice limma matrixStats mvtnorm oligoClasses preprocessCore RcppEigen SNPchip VGAM]; }; + crossmeta = derive2 { name="crossmeta"; version="1.8.0"; sha256="01d8vx016bw4qm3c6pwws1g3s2v7xppsj2v9gzdzwazpk4sfyikk"; depends=[affxparser affy AnnotationDbi Biobase BiocGenerics BiocManager ccmap data_table doParallel doRNG DT fdrtool foreach GEOquery ggplot2 limma matrixStats metaMA metap miniUI oligo pander plotly RColorBrewer rdrop2 reshape shiny stringr sva]; }; + csaw = derive2 { name="csaw"; version="1.16.1"; sha256="0rbmsikhj60np22j84gxinr354b2i892nqic493jhzziiznl51sl"; depends=[AnnotationDbi BiocGenerics BiocParallel edgeR GenomeInfoDb GenomicFeatures GenomicRanges IRanges limma Rcpp Rhtslib Rsamtools S4Vectors SummarizedExperiment zlibbioc]; }; + ctc = derive2 { name="ctc"; version="1.56.0"; sha256="0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"; depends=[amap]; }; + ctsGE = derive2 { name="ctsGE"; version="1.8.0"; sha256="081pi9dqp2pcwpv8zc2mgqqcw4z2q866c15vxrmhmwiz5bwrlfr4"; depends=[ccaPP ggplot2 limma reshape2 shiny stringr]; }; + cummeRbund = derive2 { name="cummeRbund"; version="2.24.0"; sha256="1fl8p63zr1jxif95anhqg56cssi44k5y05g7qxpkf2w3siyv1b91"; depends=[Biobase BiocGenerics fastcluster ggplot2 Gviz plyr reshape2 RSQLite rtracklayer S4Vectors]; }; + customProDB = derive2 { name="customProDB"; version="1.22.0"; sha256="07808bl355gsxgwyd4rqwarrss5rygywh9jn06vavbkgi054z9x5"; depends=[AhoCorasickTrie AnnotationDbi biomaRt Biostrings DBI GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges plyr RCurl Rsamtools RSQLite rtracklayer S4Vectors stringr VariantAnnotation]; }; + cycle = derive2 { name="cycle"; version="1.36.0"; sha256="0kx40mi7dh6k1s3vc32537q8585q8v4applzyw1y2pklap7sxzyl"; depends=[Biobase Mfuzz]; }; + cydar = derive2 { name="cydar"; version="1.6.0"; sha256="00kbnf34chr6nf882fxjav3cflkra9pynj9z0s78k4rc2n3nl4jk"; depends=[Biobase BiocGenerics BiocNeighbors BiocParallel flowCore Rcpp S4Vectors shiny SingleCellExperiment SummarizedExperiment viridis]; }; + cytolib = derive2 { name="cytolib"; version="1.4.0"; sha256="1ls3f1x9kcpqyq25kb0hyx70g68b2r3rb34cw490rjq4ff2568dg"; depends=[BH RProtoBufLib]; }; + dSimer = derive2 { name="dSimer"; version="1.8.0"; sha256="0pcggyimicsyx9wkgjxny8byyhb31phcr8xygi6sfkm17r2nxkwy"; depends=[AnnotationDbi ggplot2 GO_db igraph org_Hs_eg_db Rcpp reshape2]; }; + daMA = derive2 { name="daMA"; version="1.54.0"; sha256="0mgd90hdq0045bvzkvxfm6vd3i1n8fa0zmwnsyz5kmhavcynbvpj"; depends=[MASS]; }; + dada2 = derive2 { name="dada2"; version="1.10.0"; sha256="1rra316yfl039gamrvdpd9p9h190m0a6lisqhmrsja2h2fr22iim"; depends=[BiocGenerics Biostrings data_table ggplot2 IRanges Rcpp RcppParallel reshape2 ShortRead XVector]; }; + dagLogo = derive2 { name="dagLogo"; version="1.20.0"; sha256="1h4mhhnmnfqifa1mxk03j1y7w1azai705q95wdji2nvyhi7gkas2"; depends=[biomaRt Biostrings grImport motifStack pheatmap]; }; + dcGSA = derive2 { name="dcGSA"; version="1.10.0"; sha256="1v3brh473plcysrn1sj9np2vfjcka747xm0myjj15aq3grl2vmwy"; depends=[BiocParallel Matrix]; }; + ddCt = derive2 { name="ddCt"; version="1.38.0"; sha256="1gfxk55f8cgq9bs7rab01qi9093kmjii4833bxcxjhfx1mgsmgzz"; depends=[Biobase BiocGenerics lattice RColorBrewer xtable]; }; + ddPCRclust = derive2 { name="ddPCRclust"; version="1.2.0"; sha256="1s9k86l0jc3jkwc2y85ccmn3jlfcwp985xhjfnv43rlfsi181063"; depends=[clue flowCore flowDensity flowPeaks ggplot2 openxlsx plotrix R_utils SamSPECTRAL]; }; + debrowser = derive2 { name="debrowser"; version="1.10.4"; sha256="1jgp25cph38dmj75hc43npa2s99dcld0rhfi26ajpwld1l69l9bn"; depends=[annotate AnnotationDbi baySeq clusterProfiler colourpicker d3heatmap DESeq2 DOSE DT edgeR enrichplot GenomicRanges ggplot2 googleAuthR gplots Harman heatmaply igraph IRanges jsonlite limma org_Hs_eg_db org_Mm_eg_db pathview plotly RColorBrewer RCurl reshape2 S4Vectors shiny shinyBS shinydashboard shinyjs stringi SummarizedExperiment sva V8]; }; + decontam = derive2 { name="decontam"; version="1.2.0"; sha256="08vvxm5l9x158g2rm2ijmlgia2fq9a1qkx6k1zzvgvzzhzlx7p85"; depends=[ggplot2 reshape2]; }; + deepSNV = derive2 { name="deepSNV"; version="1.28.0"; sha256="0maswzsfv9rw01v9alq9jbifc8lg6g2h65338v9chb05dkj03baj"; depends=[Biostrings GenomicRanges IRanges Rhtslib SummarizedExperiment VariantAnnotation VGAM]; }; + deltaGseg = derive2 { name="deltaGseg"; version="1.22.0"; sha256="02mjlrs3rvlbqdsw9nw03y5ifzkfy1n5r7h4811ghvizy8cdxpqj"; depends=[changepoint fBasics ggplot2 pvclust reshape scales tseries wavethresh]; }; + derfinder = derive2 { name="derfinder"; version="1.16.1"; sha256="1wdig8zfpq1635b83npmram5zwxslgfgv3npswkjjjnbfzngwz2m"; depends=[AnnotationDbi BiocGenerics BiocParallel bumphunter derfinderHelper GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges Hmisc IRanges qvalue Rsamtools rtracklayer S4Vectors]; }; + derfinderHelper = derive2 { name="derfinderHelper"; version="1.16.1"; sha256="1a37q7gkg16wyjznbjgn974kmw0rh2dmknvbf9rpzp9hcibzkcqf"; depends=[IRanges Matrix S4Vectors]; }; + derfinderPlot = derive2 { name="derfinderPlot"; version="1.16.1"; sha256="0pa4ycm3f1bim8byy8ygb8z2r7441rwhmbj7y538scihrsk1q03k"; depends=[derfinder GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 IRanges limma plyr RColorBrewer RefManageR reshape2 S4Vectors scales]; }; + destiny = derive2 { name="destiny"; version="2.12.0"; sha256="1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"; depends=[Biobase BiocGenerics ggplot2 ggthemes igraph Matrix proxy Rcpp RcppEigen scales scatterplot3d smoother SummarizedExperiment VIM]; }; + dexus = derive2 { name="dexus"; version="1.22.0"; sha256="1d4z5icv13hnlv6j03q0l02gi769qp2w4ryb8z6880grgrq45s0j"; depends=[BiocGenerics]; }; + diffGeneAnalysis = derive2 { name="diffGeneAnalysis"; version="1.64.0"; sha256="00f088phbix7wrcjrpf3n2a2ps102sbc85f4fg5sqwdw6bvchk9c"; depends=[minpack_lm]; }; + diffHic = derive2 { name="diffHic"; version="1.14.0"; sha256="1yjsvwwai9jflg743nyksj7krm0f2pdy2y2rwnmd3cpwh73yy6al"; depends=[BiocGenerics Biostrings BSgenome csaw edgeR GenomeInfoDb GenomicRanges InteractionSet IRanges limma locfit Rcpp rhdf5 Rhtslib Rsamtools rtracklayer S4Vectors SummarizedExperiment zlibbioc]; }; + diffcoexp = derive2 { name="diffcoexp"; version="1.2.0"; sha256="1kkm0mw7q81yls750ky9rvx0n9iljgq8j5p9h08yxpr46jc3j8k0"; depends=[BiocGenerics DiffCorr igraph psych SummarizedExperiment WGCNA]; }; + diffcyt = derive2 { name="diffcyt"; version="1.2.0"; sha256="08dwrv6svcdjsz61zk28cximfhwmvpv7a24bvjg77bfpwdmqp3vy"; depends=[circlize ComplexHeatmap dplyr edgeR flowCore FlowSOM limma lme4 magrittr multcomp reshape2 S4Vectors SummarizedExperiment tidyr]; }; + diffloop = derive2 { name="diffloop"; version="1.10.0"; sha256="0fi1vvzfifhdgcnal1axn69dqbgpjqsicjgqw6gj41db50zi1fi6"; depends=[Biobase biomaRt data_table dplyr edgeR foreach GenomeInfoDb GenomicRanges ggplot2 IRanges limma locfit matrixStats pbapply plyr readr reshape2 rtracklayer S4Vectors statmod Sushi]; }; + diffuStats = derive2 { name="diffuStats"; version="1.2.0"; sha256="1hg8scxhndgp0r4m5r7rjliirb4371g9d3lqx2h9mgshadwz5h0r"; depends=[expm igraph MASS Matrix plyr precrec Rcpp RcppArmadillo RcppParallel]; }; + diggit = derive2 { name="diggit"; version="1.14.0"; sha256="1kpi1ahwc90mpfwmy6rsf4argf7fss99lr2v0s99aj39m3lwd2dw"; depends=[Biobase ks viper]; }; + discordant = derive2 { name="discordant"; version="1.6.0"; sha256="18nnclwxzcz14402gizk1mlmwq99fzp0h54klykvjzl884baxz0f"; depends=[Biobase biwt gtools MASS]; }; + dks = derive2 { name="dks"; version="1.28.0"; sha256="0md8x07f117clhxmmrqaki5g5y8r13c4yrw8vk6yvcsf9prybdah"; depends=[cubature]; }; + dmrseq = derive2 { name="dmrseq"; version="1.2.1"; sha256="169qi0bi82hhyhmsb2swssmbx8gwbqyq06gzs3b2l6wfxaqsy2m9"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; }; + doppelgangR = derive2 { name="doppelgangR"; version="1.10.0"; sha256="1x4pmmx74nk84g0f2lf5a9zr85a390qhs75ysddjsq8b01cijp3j"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; }; + drawProteins = derive2 { name="drawProteins"; version="1.2.0"; sha256="13zqpghzpqg92i4mlfmvwx1l1mb7swqmyhisqjp546jzs7vixv25"; depends=[dplyr ggplot2 httr readr stringr]; }; + dualKS = derive2 { name="dualKS"; version="1.42.0"; sha256="0mn0mjzncd53wq0jwq2gfcj3mcsfl81hgsaxnf1dqjwqnw4jy1y3"; depends=[affy Biobase]; }; + dupRadar = derive2 { name="dupRadar"; version="1.12.1"; sha256="1dmkzhdwzw2r0srwi96g0csxcsg2m8xh1446p75byjarvmyzmqh8"; depends=[Rsubread]; }; + dyebias = derive2 { name="dyebias"; version="1.42.0"; sha256="1ml85klh9mwxmz8h2yjagx4sl0dnzg4ijk4pa154njznxr8kqccz"; depends=[Biobase marray]; }; + easyRNASeq = derive2 { name="easyRNASeq"; version="2.18.2"; sha256="0vh245ffjsqf6246d6pj09val43mqhhl5rqw3lrd4sx4kp60bd4s"; depends=[Biobase BiocGenerics BiocParallel biomaRt Biostrings DESeq edgeR GenomeInfoDb genomeIntervals GenomicAlignments GenomicRanges IRanges locfit LSD Rsamtools S4Vectors ShortRead SummarizedExperiment]; }; + ecolitk = derive2 { name="ecolitk"; version="1.54.0"; sha256="0gbw2kdfnyjlq0paqy8hlz8qmaczfa5qx9wzj3ax3vms5v6n58qp"; depends=[Biobase]; }; + edge = derive2 { name="edge"; version="2.14.0"; sha256="0gcwnw9c6qc9b207vlchnw59d025jrdm4b7w5iiw721djwwawdzf"; depends=[Biobase jackstraw MASS qvalue snm sva]; }; + edgeR = derive2 { name="edgeR"; version="3.24.3"; sha256="15yimsbsxmxhlsfmgw5j7fd8qn08zz4xqxrir1c6n2dc103y22xg"; depends=[limma locfit Rcpp]; }; + eegc = derive2 { name="eegc"; version="1.8.1"; sha256="14jjd27hblz1ls1463vd4ymdq58h9as82lj160smy0n8jqpc5nhh"; depends=[AnnotationDbi clusterProfiler DESeq2 DOSE edgeR ggplot2 gplots igraph limma org_Hs_eg_db org_Mm_eg_db pheatmap R_utils S4Vectors sna wordcloud]; }; + eiR = derive2 { name="eiR"; version="1.22.0"; sha256="07lnpgaplw6d63c3wjas5n8rxhgmk75qkq3nvp7w26lmgi4ysz6z"; depends=[BiocGenerics ChemmineR DBI digest gespeR RcppAnnoy RCurl RUnit snow snowfall]; }; + eisa = derive2 { name="eisa"; version="1.34.0"; sha256="1717bpmrr1kmd1a8rqlarhqcrk786vjw55shn5sd8c89f25vspdx"; depends=[AnnotationDbi Biobase BiocGenerics Category DBI genefilter isa2]; }; + enrichplot = derive2 { name="enrichplot"; version="1.2.0"; sha256="0cxqfpy6py4k3z3lnlkiwx89r4ymfpdc4hm25dfpazqgjflz5is7"; depends=[AnnotationDbi cowplot DOSE europepmc ggplot2 ggplotify ggraph ggridges GOSemSim gridExtra igraph purrr RColorBrewer reshape2 UpSetR]; }; + ensemblVEP = derive2 { name="ensemblVEP"; version="1.24.0"; sha256="148phm407clbhp87snazan120bh5hcl90xgbhlwyz0a36i4kjfvc"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicRanges S4Vectors SummarizedExperiment VariantAnnotation]; }; + ensembldb = derive2 { name="ensembldb"; version="2.6.3"; sha256="0kzdsfk6mdwlp57sw4j2cf7lx5nc67v5j0xr3iag9kzmgikaq1lb"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges IRanges ProtGenerics Rsamtools RSQLite rtracklayer S4Vectors]; }; + epiNEM = derive2 { name="epiNEM"; version="1.6.0"; sha256="1pzcajgqsm6mvw8i7aav0918856ghndrdp93831s6zmdkgxzpw2v"; depends=[BoolNet e1071 graph gtools igraph lattice latticeExtra minet nem pcalg RColorBrewer]; }; + epigenomix = derive2 { name="epigenomix"; version="1.22.0"; sha256="0cyf35fygr3rgkcfqhb9p9xgl1lydqprzhn3m189yqm3xqck41il"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; }; + epivizr = derive2 { name="epivizr"; version="2.12.0"; sha256="0ms29c5vl0nn8p4v1l5falmwc8xb6wa8fjbfwrgpz8dphidp7mnm"; depends=[epivizrData epivizrServer GenomicRanges IRanges S4Vectors]; }; + epivizrChart = derive2 { name="epivizrChart"; version="1.4.0"; sha256="03dnkx8zqrhgijipv72ylcrwparqjihzld2ln6dir989kwv75f7l"; depends=[BiocGenerics epivizrData epivizrServer htmltools rjson]; }; + epivizrData = derive2 { name="epivizrData"; version="1.10.0"; sha256="0m7bn9v9j8jsja36x5vj2bs9wg3dw5845r47mw4200j1j4irj9jb"; depends=[Biobase ensembldb epivizrServer GenomeInfoDb GenomicFeatures GenomicRanges IRanges OrganismDbi S4Vectors SummarizedExperiment]; }; + epivizrServer = derive2 { name="epivizrServer"; version="1.10.0"; sha256="17h7cghi9md7yzny07jc0749cpwx5jda78vk9g2db0bf6q91qjq6"; depends=[httpuv mime R6 rjson]; }; + epivizrStandalone = derive2 { name="epivizrStandalone"; version="1.10.0"; sha256="0jvx2kc0wqq7rzi1a3lv94i33cgcqhdpny4563kgjcz9g3qaggsd"; depends=[BiocGenerics epivizr epivizrServer GenomeInfoDb GenomicFeatures git2r S4Vectors]; }; + erccdashboard = derive2 { name="erccdashboard"; version="1.16.0"; sha256="1v5lrbrwgp1r21ii2mpb8adn9q14g5m6hqfvdbi0szrisqq6fhi7"; depends=[edgeR ggplot2 gplots gridExtra gtools limma locfit MASS plyr qvalue reshape2 ROCR scales stringr]; }; + erma = derive2 { name="erma"; version="0.14.0"; sha256="0hj9iz904rr1y66442lkxjywkw1ydyxxlhmjirawbf09ic5ad4g9"; depends=[AnnotationDbi Biobase BiocGenerics BiocParallel GenomeInfoDb GenomicFiles GenomicRanges ggplot2 Homo_sapiens IRanges rtracklayer S4Vectors shiny SummarizedExperiment]; }; + esATAC = derive2 { name="esATAC"; version="1.4.0"; sha256="1a9pizkjrvdnz09vgxkx6flpavkdpmkfzahyc41wbp805mxdym1r"; depends=[AnnotationDbi BiocGenerics BiocManager Biostrings BSgenome ChIPseeker clusterProfiler corrplot DiagrammeR digest GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 igraph IRanges JASPAR2016 knitr magrittr motifmatchr R_utils Rbowtie2 Rcpp rJava rmarkdown Rsamtools rtracklayer S4Vectors ShortRead TFBSTools VennDiagram]; }; + esetVis = derive2 { name="esetVis"; version="1.8.0"; sha256="0n2b7qkgy0gh9jfxi5mgsr8g41141435maq1yniw9mqa3hddwjjp"; depends=[Biobase hexbin MASS MLP mpm Rtsne]; }; + eudysbiome = derive2 { name="eudysbiome"; version="1.12.0"; sha256="09lhzfhlmrw6f50c6d21lmyfh3k4hwrg6waiv1qjg6iavhnbc2a0"; depends=[Biostrings plyr R_utils Rsamtools]; }; + exomeCopy = derive2 { name="exomeCopy"; version="1.28.0"; sha256="1y475ka8lkf3mh4xj0qvgk0nd0gf497dym9bvl5wpss1fqsks6im"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; }; + exomePeak = derive2 { name="exomePeak"; version="2.16.0"; sha256="0i063k0b9d6vvixp52qkg63nlpqzbq2dhf0ylgwchjjk4zsdz5vn"; depends=[GenomicAlignments GenomicFeatures Rsamtools rtracklayer]; }; + explorase = derive2 { name="explorase"; version="1.46.0"; sha256="0h12i2fh7jm0xq0mxy37rcp3pbg18l88l380jsb9jn02rrgkirkd"; depends=[limma rggobi RGtk2]; }; + fCCAC = derive2 { name="fCCAC"; version="1.8.0"; sha256="04mzxvvm1yssdjdibppbl5yv6zpssk3chm222nhs2h7mn4a30rwq"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; }; + fCI = derive2 { name="fCI"; version="1.12.0"; sha256="0wxc6nhl5gcz70i9nbj7caxgif3bpajng8h8pckarflms1va2ic0"; depends=[FNN gtools psych rgl VennDiagram zoo]; }; + fabia = derive2 { name="fabia"; version="2.28.0"; sha256="1ps10cqldbz99rszxqznqc3vlci4fmhyhwcim8bfch197b1pnfl5"; depends=[Biobase]; }; + factDesign = derive2 { name="factDesign"; version="1.58.0"; sha256="113sjbx1r7yzps0mjpka5mf0mx324z4vg0adl7k965p3r0cv3jwm"; depends=[Biobase]; }; + farms = derive2 { name="farms"; version="1.34.0"; sha256="02vb8cy2j53l05naifrafw4pa48ay3hbsxrlm5s3nbmy4cma6rwr"; depends=[affy Biobase MASS]; }; + fastLiquidAssociation = derive2 { name="fastLiquidAssociation"; version="1.18.0"; sha256="109db3kv8rf7dwlsn2cyv5s44b86nmzj746awf28rc03f6ih8f13"; depends=[doParallel Hmisc impute LiquidAssociation preprocessCore WGCNA]; }; + fastseg = derive2 { name="fastseg"; version="1.28.0"; sha256="1l8mdjpfpgwqdss2ywjkb8b4h55wf8v6kmyxdlvy04ds2hj16sb1"; depends=[Biobase BiocGenerics GenomicRanges IRanges S4Vectors]; }; + fdrame = derive2 { name="fdrame"; version="1.54.0"; sha256="1srv11bwyjxlvgv5hky4afwn2bhc8kdvra61jc1dn81qaj5vx41a"; depends=[]; }; + ffpe = derive2 { name="ffpe"; version="1.26.0"; sha256="1bcpdj978wiwfwfbpvnj622wqq4axh82djn17l5vrm20p2hgm74n"; depends=[affy Biobase BiocGenerics lumi methylumi sfsmisc TTR]; }; + fgsea = derive2 { name="fgsea"; version="1.8.0"; sha256="0cxxvlmg340l5l5fz4abbwppiri0ibg4navvq5k3wg511mz8ma2q"; depends=[BiocParallel data_table fastmatch ggplot2 gridExtra Matrix Rcpp]; }; + flagme = derive2 { name="flagme"; version="1.38.0"; sha256="024ph9iydqq0wnxzbv8df6iyn8gbnzqlkgr8nr181j96y4idk0vs"; depends=[CAMERA gcspikelite gplots MASS SparseM xcms]; }; + flipflop = derive2 { name="flipflop"; version="1.20.0"; sha256="100ia0j4ir61ihriyz36jnxpa9s4ivs35fifs4yzfiysf7lma3al"; depends=[GenomicRanges IRanges Matrix]; }; + flowAI = derive2 { name="flowAI"; version="1.12.1"; sha256="0011p73kf3z9gpq9z4rishdwahbh3k01qh35ivv1jcp9hj8ff32x"; depends=[changepoint flowCore ggplot2 knitr plyr RColorBrewer reshape2 rmarkdown scales]; }; + flowBeads = derive2 { name="flowBeads"; version="1.20.0"; sha256="1l3jaqck84al3aqddbsb5hrbv7x7809h0jb5zhsz3zk4z3r9051s"; depends=[Biobase flowCore knitr rrcov xtable]; }; + flowBin = derive2 { name="flowBin"; version="1.18.0"; sha256="14n5zzbipw2iwkk8f88h4jgwjy20df3pqk6xcwycw158fdgwy5fm"; depends=[BiocGenerics class flowCore flowFP limma snow]; }; + flowCHIC = derive2 { name="flowCHIC"; version="1.16.0"; sha256="0bm80b4mn6lj501dvivrz2jam6vv19an4b2f5dy8f63byln8ncw3"; depends=[EBImage flowCore ggplot2 hexbin vegan]; }; + flowCL = derive2 { name="flowCL"; version="1.20.1"; sha256="013b81ab3pmfb3n4430ihwc2qbgqf3iyyykzmqdhqs8llcrpqvph"; depends=[graph Rgraphviz SPARQL]; }; + flowClean = derive2 { name="flowClean"; version="1.20.0"; sha256="0m8n75gkf1dwhs4hyk1jfqvsmb2lymvi0znikb1gi8bkh9224wvk"; depends=[bit changepoint flowCore sfsmisc]; }; + flowClust = derive2 { name="flowClust"; version="3.20.0"; sha256="0ljkgyhcwbgq3d45a9cwahgq1zpycl5d3sl0w4wqwlf8dwfml0s6"; depends=[Biobase BiocGenerics clue corpcor ellipse flowCore flowViz graph mnormt]; }; + flowCore = derive2 { name="flowCore"; version="1.48.0"; sha256="16mh3xlrcxkrqvhv3pry325jzsz97yg84ya8rpvd2lvlpqrz6k3h"; depends=[BH Biobase BiocGenerics corpcor graph MASS matrixStats Rcpp rrcov]; }; + flowCyBar = derive2 { name="flowCyBar"; version="1.18.0"; sha256="065dgb3w7ll6sqaji93vdhva9zhx64375pgk7ip4rpc3i4aa2dyx"; depends=[gplots vegan]; }; + flowDensity = derive2 { name="flowDensity"; version="1.16.0"; sha256="19db67h85c02iqwc9fkln9f50b1jisq6qd98g947rf5a7hfifk13"; depends=[car flowCore flowWorkspace gplots RFOC rgeos sp]; }; + flowFP = derive2 { name="flowFP"; version="1.40.0"; sha256="0i8kyvsrb3mrhb36mvj2a62clw4avrbchmr5k3byxndd63x67xwr"; depends=[Biobase BiocGenerics flowCore flowViz]; }; + flowFit = derive2 { name="flowFit"; version="1.20.0"; sha256="06kdrm4wi3qw8ikkx18j1ss9asl9h62g5p4rw3a8i5jrxpjzwbcm"; depends=[flowCore flowViz gplots kza minpack_lm]; }; + flowMap = derive2 { name="flowMap"; version="1.20.0"; sha256="1lfdia0s2spdxgkqfpwbhvk2xdwsgax23zjzp594f0b4k7rphpmn"; depends=[abind ade4 doParallel Matrix reshape2 scales]; }; + flowMatch = derive2 { name="flowMatch"; version="1.18.0"; sha256="1gc54jy9kdhrya9kmhilqwvrl7l42q2hq6iczxy6kl872hd984l9"; depends=[Biobase flowCore Rcpp]; }; + flowMeans = derive2 { name="flowMeans"; version="1.42.0"; sha256="03zli85xjr7761ib476lza6il48fh1nmnraqsncc3w9l3xayhv7m"; depends=[Biobase feature flowCore rrcov]; }; + flowMerge = derive2 { name="flowMerge"; version="2.30.0"; sha256="13ds10b8mfarrnw3xqw66pm0rjzqvd7cmg8b1ayik68cp28kz6dw"; depends=[feature flowClust flowCore foreach graph Rgraphviz rrcov snow]; }; + flowPeaks = derive2 { name="flowPeaks"; version="1.28.0"; sha256="0g0xaafr351w1ij1nic14kv7rpk9qlhgx8ibiqivjcg0ygj7nls5"; depends=[]; }; + flowPloidy = derive2 { name="flowPloidy"; version="1.8.0"; sha256="0s2d541id8mf3igidn5n7v6d3g21yaskzc7kx9zvywx9391sd9qx"; depends=[car caTools flowCore knitr minpack_lm rmarkdown shiny]; }; + flowPlots = derive2 { name="flowPlots"; version="1.30.0"; sha256="1i9yniihhc3qfyk897cf148mpj718fzicgfrz25825g6f5p1f7cd"; depends=[]; }; + flowQB = derive2 { name="flowQB"; version="2.10.0"; sha256="00i8kdwkz1h79d1r8iv7mipiw2wcf3vzfgwyyqy4dimzppkmpg3x"; depends=[extremevalues flowCore]; }; + flowStats = derive2 { name="flowStats"; version="3.40.0"; sha256="0d2q4d9aih4rgjrn0cyfawsli1473rwh315yx20hb8dhi68gx8c7"; depends=[Biobase BiocGenerics cluster fda flowCore flowViz flowWorkspace KernSmooth ks lattice MASS ncdfFlow RColorBrewer]; }; + flowTime = derive2 { name="flowTime"; version="1.6.0"; sha256="1jjjg1a9drpx726rv6gxiniczi09an24pl3bjspaizyggy9nvdlw"; depends=[flowCore plyr]; }; + flowTrans = derive2 { name="flowTrans"; version="1.34.0"; sha256="11s6f3cfqj1yn5z0r09xpnl9n6l3kiarsrxsa58zad0792sq8dfw"; depends=[flowClust flowCore flowViz]; }; + flowType = derive2 { name="flowType"; version="2.20.0"; sha256="14rs8i21gn0fa2viwnal1c2xagjpvmm0nbiqnhilqz5g6cpr9z1j"; depends=[BH Biobase flowClust flowCore flowMeans flowMerge Rcpp rrcov sfsmisc]; }; + flowUtils = derive2 { name="flowUtils"; version="1.46.0"; sha256="10y809p3figzp1vn92jmb0zwql9bmiicxmh3bwn4wf69xslcsvqg"; depends=[Biobase corpcor flowCore graph RUnit XML]; }; + flowVS = derive2 { name="flowVS"; version="1.14.0"; sha256="1261xy1q1gbr9yfm47bgahs32rnji2c2apyisgbg1c1ic7kcq8fx"; depends=[flowCore flowStats flowViz]; }; + flowViz = derive2 { name="flowViz"; version="1.46.0"; sha256="050anps4hzi107cgcnr98hj2ac86cf7gm84qjfsghq26yqgand3a"; depends=[Biobase flowCore hexbin IDPmisc KernSmooth lattice latticeExtra MASS RColorBrewer]; }; + flowWorkspace = derive2 { name="flowWorkspace"; version="3.30.1"; sha256="06dky6dl6ykzab1fi2g6a7060f2rhc5gwncq7spx57nrcpmx0pdl"; depends=[BH Biobase BiocGenerics cytolib data_table dplyr flowCore flowViz graph gridExtra lattice latticeExtra matrixStats ncdfFlow RBGL RColorBrewer Rcpp Rgraphviz RProtoBufLib scales stringr XML]; }; + flowcatchR = derive2 { name="flowcatchR"; version="1.16.0"; sha256="0cwfm8d3s7nvkfm0zfx84mcamyszc8cwwy7b9rn9m27rj3q80f1z"; depends=[abind BiocParallel colorRamps EBImage plotly shiny]; }; + fmcsR = derive2 { name="fmcsR"; version="1.24.0"; sha256="0dl39066y0s391hczpi3482dwwpsp1767f6n881n00sv7pb4znxy"; depends=[BiocGenerics ChemmineR RUnit]; }; + focalCall = derive2 { name="focalCall"; version="1.16.0"; sha256="06x6d5j17wabdy03r4h9clmdp69wbxgzpsvalrmg8l4yyj9z7lrc"; depends=[CGHcall]; }; + frma = derive2 { name="frma"; version="1.34.0"; sha256="1g48s0kji9ln4z80h704j1rc5vji9g8kx8mgngi95k7vj744firg"; depends=[affy Biobase BiocGenerics DBI MASS oligo oligoClasses preprocessCore]; }; + frmaTools = derive2 { name="frmaTools"; version="1.34.0"; sha256="1n1i5xsn38ml7h34pkv4xlx8yvrf4vpcjrz92sfzmrff531gf3a2"; depends=[affy Biobase DBI preprocessCore]; }; + funtooNorm = derive2 { name="funtooNorm"; version="1.6.0"; sha256="0s4vafjskzyc6hf616cbi7g9prf6lh7fmi7zywr97pr11390n7qg"; depends=[GenomeInfoDb IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest matrixStats minfi pls]; }; + gCMAP = derive2 { name="gCMAP"; version="1.26.0"; sha256="1ql9nxlj4wgc22g699lxsn57iam7k3w33v3cinhywsy9zfswawh9"; depends=[annotate AnnotationDbi bigmemory bigmemoryExtras Biobase Category DESeq genefilter GSEABase GSEAlm limma Matrix]; }; + gCMAPWeb = derive2 { name="gCMAPWeb"; version="1.22.0"; sha256="0jvn3h3hn2b8av0c901gbidhrkgkhhm4027qymn5dhg4xsg2dayg"; depends=[annotate AnnotationDbi Biobase BiocGenerics brew gCMAP GSEABase hwriter Rook yaml]; }; + gCrisprTools = derive2 { name="gCrisprTools"; version="1.10.0"; sha256="1y91pan4wdj2xfwgkpvbaispl98wxp97f7vm9n8rmk8f58w10s3m"; depends=[Biobase ggplot2 limma PANTHER_db rmarkdown RobustRankAggreg]; }; + gQTLBase = derive2 { name="gQTLBase"; version="1.14.0"; sha256="1lbk1m1mkvbk30flk5pf3pcrnm2s0sj5r48kbjgad39dsvd8zgqx"; depends=[BatchJobs BBmisc BiocGenerics bit doParallel ff ffbase foreach GenomicFiles GenomicRanges rtracklayer S4Vectors SummarizedExperiment]; }; + gQTLstats = derive2 { name="gQTLstats"; version="1.14.0"; sha256="1sg9kw59dlayj7qxql9pd93d4hmml504sa3kkfpzfh3xri7m5pxf"; depends=[AnnotationDbi BatchJobs BBmisc beeswarm Biobase BiocGenerics doParallel dplyr erma ffbase foreach GenomeInfoDb GenomicFeatures GenomicFiles GenomicRanges ggbeeswarm ggplot2 gQTLBase HardyWeinberg Homo_sapiens IRanges limma mgcv plotly reshape2 S4Vectors shiny snpStats SummarizedExperiment VariantAnnotation]; }; + gaga = derive2 { name="gaga"; version="2.28.0"; sha256="13kqrqc8fskr53mhhg55k1sld03h94wk1fq0aj8jkl3xfjr0i6fi"; depends=[Biobase coda EBarrays mgcv]; }; + gage = derive2 { name="gage"; version="2.32.0"; sha256="07b098wvryxf0zd423nk6h52s3gyngwjcx2vplqybpbpgl8h2931"; depends=[AnnotationDbi graph KEGGREST]; }; + gaggle = derive2 { name="gaggle"; version="1.50.0"; sha256="1yj10aahr1pmn7kspiplczalr1awmybr320y49cadh17l3p3i224"; depends=[graph rJava RUnit]; }; + gaia = derive2 { name="gaia"; version="2.26.0"; sha256="1a3lmazx5dlb484llfvwk6b4g89r3dcbmkjz7wah44kpyp0k5lrv"; depends=[]; }; + garfield = derive2 { name="garfield"; version="1.10.0"; sha256="1hcb4dvhir20ldfr7zrd0b3xcdpkafb0sc3gwns4651a9hs2cx8j"; depends=[]; }; + gcapc = derive2 { name="gcapc"; version="1.6.0"; sha256="00jv9c231s4zr02nl11qcs8qlbwklyc0iis1c4n2ifkp8kcd1c34"; depends=[BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS matrixStats Rsamtools S4Vectors]; }; + gcatest = derive2 { name="gcatest"; version="1.12.0"; sha256="14902mc3vnnj64xxhj5dzd787r59wj0dryn074n4yyw0lyzfydwk"; depends=[lfa]; }; + gcrma = derive2 { name="gcrma"; version="2.54.0"; sha256="1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim"; depends=[affy affyio Biobase BiocManager Biostrings XVector]; }; + gdsfmt = derive2 { name="gdsfmt"; version="1.18.1"; sha256="1axbs23armc8r4nmfnhv6ripxzh551lgwd0580nknif4jj1a98ga"; depends=[]; }; + geNetClassifier = derive2 { name="geNetClassifier"; version="1.22.0"; sha256="079v4jrscq93kapv4676d4zsy3rk7j547pn9hsj7fi0sypv9sg4h"; depends=[Biobase e1071 EBarrays minet]; }; + geecc = derive2 { name="geecc"; version="1.16.0"; sha256="1lmc52532ibdzhwkyrx20rnjd11fqp1gwy7i9d9a5zbr17b0y91q"; depends=[gplots hypergea MASS Rcpp]; }; + genArise = derive2 { name="genArise"; version="1.58.0"; sha256="0drncw83b214w8fk11z3dilshd9p9z4irb23gbvkq67xm62nbkxn"; depends=[locfit tkrplot xtable]; }; + genbankr = derive2 { name="genbankr"; version="1.10.0"; sha256="18pw66ilh7mnlar94885k182hay05vana7pjki38bb2jbifk4m2f"; depends=[Biobase BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges IRanges rtracklayer S4Vectors VariantAnnotation]; }; + geneAttribution = derive2 { name="geneAttribution"; version="1.8.0"; sha256="1wngaq654gzp2llk8zk8z3gmnpb3lwx4l6sfi9dn8n551q6lbbcg"; depends=[BiocGenerics GenomeInfoDb GenomicFeatures GenomicRanges IRanges org_Hs_eg_db rtracklayer]; }; + geneClassifiers = derive2 { name="geneClassifiers"; version="1.6.0"; sha256="0nxp2jmrq3fyhvgys4gxycqc7v2nixsa3mk57fq3339xilcxzycp"; depends=[Biobase BiocGenerics]; }; + geneRecommender = derive2 { name="geneRecommender"; version="1.54.0"; sha256="1b6y5ilz1ffsqsb5y667sa9fi4h6hpwk4wgdiy13lq2vry9x7j0w"; depends=[Biobase]; }; + geneRxCluster = derive2 { name="geneRxCluster"; version="1.18.0"; sha256="0kg42vy1asv5gak2d9h3fm679yfai7d7n56nqig3dny5a0g04fmc"; depends=[GenomicRanges IRanges]; }; + geneXtendeR = derive2 { name="geneXtendeR"; version="1.8.0"; sha256="1nkaxzw8vdxafb9nb39lwdb6qj8z54p19l8rw1rdjy8dxlia262n"; depends=[AnnotationDbi BiocStyle data_table dplyr GO_db networkD3 org_Rn_eg_db RColorBrewer rtracklayer SnowballC tm wordcloud]; }; + genefilter = derive2 { name="genefilter"; version="1.64.0"; sha256="0p64s1n1627yafnp25wjr4b22p34lqw574fx2qg4s1m0lffh1z6i"; depends=[annotate AnnotationDbi Biobase S4Vectors survival]; }; + genefu = derive2 { name="genefu"; version="2.14.0"; sha256="1dapkgmjwxr6c62l72h217xrjnycnc3sc7qclmbrbwjl42c6ma1f"; depends=[AIMS amap biomaRt iC10 limma mclust survcomp]; }; + geneplast = derive2 { name="geneplast"; version="1.8.0"; sha256="06xvdsfjqg8jx8b1g8i829i8x8p2bxv57hzflh08nd6n91fys6qn"; depends=[ape igraph snow]; }; + geneplotter = derive2 { name="geneplotter"; version="1.60.0"; sha256="10khr0pznxf3m0f5gzck9ymljrwcv3vamfmpskd51yjh36lhllqz"; depends=[annotate AnnotationDbi Biobase BiocGenerics lattice RColorBrewer]; }; + genoCN = derive2 { name="genoCN"; version="1.34.0"; sha256="164d9cwp6mngmmvk1lc7xs03w9sqqx7b3w4mrx94xg5f4k2jzv3m"; depends=[]; }; + genomation = derive2 { name="genomation"; version="1.14.0"; sha256="0g0v4alfpqlinqinjnyzl3mrjnpbdx9ri34mcaiqbvbvg8ic8wvg"; depends=[Biostrings BSgenome data_table GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridBase impute IRanges matrixStats plotrix plyr Rcpp readr reshape2 Rsamtools rtracklayer RUnit S4Vectors seqPattern]; }; + genomeIntervals = derive2 { name="genomeIntervals"; version="1.38.0"; sha256="09ck7d1lklxh5rr8k4rfswlyi41a94siqpqfp6byf34qjhv9mxvv"; depends=[BiocGenerics GenomeInfoDb GenomicRanges intervals IRanges S4Vectors]; }; + genomes = derive2 { name="genomes"; version="3.12.0"; sha256="18pwqjr01qwjn93vyf2pfp5n88djyb0vln78m8kl598pcxr7ifkh"; depends=[curl readr]; }; + genoset = derive2 { name="genoset"; version="1.38.0"; sha256="1z0iwp5pp3655kd63p3jf5fficd61p1i0g06p2n6pw4q38dp2h28"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges S4Vectors SummarizedExperiment]; }; + genotypeeval = derive2 { name="genotypeeval"; version="1.14.0"; sha256="0xi0n87g5qh1yswr3whv8wvmxswd66j6g8662qsfgy3cs69hxl3m"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicRanges ggplot2 IRanges rtracklayer VariantAnnotation]; }; + genphen = derive2 { name="genphen"; version="1.10.0"; sha256="184iys5x8pwikrvkn7wh4fcclkcnx5s0pk0s3vhwq6kvi6bhgi8w"; depends=[Biostrings doParallel e1071 foreach ranger rstan]; }; + gep2pep = derive2 { name="gep2pep"; version="1.2.0"; sha256="1sxkps92hf85svngd5511j3sbwn8904nn9ijn168v7xzzmld3z5y"; depends=[Biobase digest foreach GSEABase iterators repo rhdf5 XML]; }; + gespeR = derive2 { name="gespeR"; version="1.14.0"; sha256="0qknix99j5q45l3yamczdv32w1mnqwxv4ndhlcjw1xck0bzvy4p9"; depends=[Biobase biomaRt cellHTS2 doParallel dplyr foreach ggplot2 glmnet Matrix reshape2]; }; + ggbio = derive2 { name="ggbio"; version="1.30.0"; sha256="0wq49qqzkcn8s19xgaxf2s1j1a563d7pbhhvris6fhxfdjsz4934"; depends=[AnnotationDbi AnnotationFilter Biobase BiocGenerics Biostrings biovizBase BSgenome ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GGally ggplot2 gridExtra gtable Hmisc IRanges OrganismDbi reshape2 rlang Rsamtools rtracklayer S4Vectors scales SummarizedExperiment VariantAnnotation]; }; + ggcyto = derive2 { name="ggcyto"; version="1.10.0"; sha256="1p1hcd8a779902aq12438qyj708vf4vnnmlf61ishs7blrwb8qq7"; depends=[data_table flowCore flowWorkspace ggplot2 gridExtra ncdfFlow plyr RColorBrewer rlang scales]; }; + ggtree = derive2 { name="ggtree"; version="1.14.4"; sha256="0ysw7yw5s3lbfr3pyaqg3xcvfbslcdyja5mk1yq78sqwyss5vs8y"; depends=[ape dplyr ggplot2 magrittr purrr rlang rvcheck scales tibble tidyr tidytree treeio]; }; + girafe = derive2 { name="girafe"; version="1.34.0"; sha256="13hk8rfldbwadqhy5mqcdzggili3ib6whwqcf85pl72x627iif5j"; depends=[Biobase BiocGenerics Biostrings genomeIntervals intervals IRanges Rsamtools S4Vectors ShortRead]; }; + glmSparseNet = derive2 { name="glmSparseNet"; version="1.0.0"; sha256="0aqcnqmnl977yc7lp9gb8a4hqaxdh2pjw2lhiw3vly933xzd78sc"; depends=[biomaRt dplyr forcats futile_logger ggplot2 glmnet loose_rock Matrix MultiAssayExperiment readr reshape2 rlang sparsebn sparsebnUtils STRINGdb stringr SummarizedExperiment survminer]; }; + globalSeq = derive2 { name="globalSeq"; version="1.10.0"; sha256="11vnfj4nkfwijsi6ax0algimi58zs3ixnb98b7ijrqi09l095rc1"; depends=[]; }; + globaltest = derive2 { name="globaltest"; version="5.36.0"; sha256="16v8rn25n87kk892c3yvmqdv03csqdrzp7krcr8w2y0wznys2cqn"; depends=[annotate AnnotationDbi Biobase survival]; }; + gmapR = derive2 { name="gmapR"; version="1.24.1"; sha256="19b55ng508n5iwws67n0z6mxnnwmmnq6cy2wvvh8gp0f94n8bzf9"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; }; + goProfiles = derive2 { name="goProfiles"; version="1.44.0"; sha256="0rpks421g0rbdcfnkfqpd5l22cysdcfljnmngq9pbgh04wpwi8f1"; depends=[AnnotationDbi Biobase CompQuadForm GO_db stringr]; }; + goSTAG = derive2 { name="goSTAG"; version="1.6.1"; sha256="0ib9a1v9zblysmk7a6wrg6cj1q6is2s9mranb28nn2r067kfx77l"; depends=[AnnotationDbi biomaRt GO_db memoise]; }; + goTools = derive2 { name="goTools"; version="1.56.0"; sha256="0w2mb8g5fnn7vm35cqw437f2sdiba4c72ay1n7frh0z1xc7hqc3r"; depends=[AnnotationDbi GO_db]; }; + goseq = derive2 { name="goseq"; version="1.34.0"; sha256="1401x0jn5f8hqc12r3gd1wammp1nxir3is1k5ldd03ln97x00i7a"; depends=[AnnotationDbi BiasedUrn BiocGenerics geneLenDataBase GO_db mgcv]; }; + gpart = derive2 { name="gpart"; version="1.0.0"; sha256="0dgv8g5vxzab4ax1aqvs7bjrd52i299jvxrdfxrswxdrsl7jj0ad"; depends=[AnnotationDbi biomaRt data_table GenomicRanges Homo_sapiens igraph IRanges OrganismDbi Rcpp TxDb_Hsapiens_UCSC_hg38_knownGene]; }; + gpls = derive2 { name="gpls"; version="1.54.0"; sha256="14sffq2h6hqlzaq1nzw34rkg7nnshfp6k5r3wyvavq6k25384jr0"; depends=[]; }; + gprege = derive2 { name="gprege"; version="1.26.0"; sha256="0b2zrxggljfgr8w2ns7h80ymqrvfi8kaliy32k2najm089kpv8dy"; depends=[gptk]; }; + graph = derive2 { name="graph"; version="1.60.0"; sha256="1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"; depends=[BiocGenerics]; }; + graphite = derive2 { name="graphite"; version="1.28.1"; sha256="04mw63c9qw0p3bf4zzv5mmsdrxzm0066pb03r7rpgishn3cyj7kb"; depends=[AnnotationDbi checkmate graph httr rappdirs]; }; + groHMM = derive2 { name="groHMM"; version="1.16.0"; sha256="1ph92fv44b90v7mk4b1mjvv0dlrhl8ba01klxbnd0vs4qn9zxplh"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS rtracklayer S4Vectors]; }; + gsean = derive2 { name="gsean"; version="1.2.0"; sha256="01f3wlv2gr28hd9cmyaf7z7pd08hf7i3849blxmy04b9k9a35md3"; depends=[fgsea PPInfer]; }; + gtrellis = derive2 { name="gtrellis"; version="1.14.0"; sha256="17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v"; depends=[circlize GenomicRanges GetoptLong IRanges]; }; + gwascat = derive2 { name="gwascat"; version="2.14.0"; sha256="1fnyjydhicq4ayrv0lqjv48h9bd72h40s6l82g1h2ng0icwz38g0"; depends=[AnnotationDbi AnnotationHub BiocGenerics Biostrings GenomeInfoDb GenomicFeatures GenomicRanges ggbio ggplot2 gQTLstats graph Gviz Homo_sapiens IRanges Rsamtools rtracklayer S4Vectors snpStats SummarizedExperiment VariantAnnotation]; }; + gwasurvivr = derive2 { name="gwasurvivr"; version="1.0.0"; sha256="0f1p2l6ypbrnaqlmqsjz5rfa6afd4kqhkrniqi7hfwjza7myrcvp"; depends=[GWASTools matrixStats SNPRelate SummarizedExperiment survival VariantAnnotation]; }; + h5vc = derive2 { name="h5vc"; version="2.16.0"; sha256="1jhl2cv8rd9sfw5adm81ncpz3ysyb9wdvjzqg7k48rh5ycgi9whz"; depends=[abind BatchJobs BiocParallel Biostrings GenomeInfoDb GenomicRanges ggplot2 gridExtra h5vcData IRanges reshape rhdf5 Rsamtools S4Vectors]; }; + hapFabia = derive2 { name="hapFabia"; version="1.24.0"; sha256="1y14gmm4vj5qvnkbssqr4scqrl86v949kd6y0ic48p5rlqcgsjj3"; depends=[Biobase fabia]; }; + heatmaps = derive2 { name="heatmaps"; version="1.6.0"; sha256="1srppr0y50y2j9ajscc93778jk2s7pnaqnf4h7yf12cx8185izsj"; depends=[BiocGenerics Biostrings EBImage GenomeInfoDb GenomicRanges IRanges KernSmooth Matrix plotrix RColorBrewer]; }; + hiAnnotator = derive2 { name="hiAnnotator"; version="1.16.0"; sha256="0hbrrvdl41nidsihyalnqridg87gidpnzdb6scf07jyfqmdym862"; depends=[BSgenome dplyr foreach GenomicRanges ggplot2 iterators rtracklayer scales]; }; + hiReadsProcessor = derive2 { name="hiReadsProcessor"; version="1.18.0"; sha256="0azmgzczkbjhg8fpl7js4g3s44lna3jzsdccchfv715smykxs24n"; depends=[BiocGenerics BiocParallel Biostrings dplyr GenomicAlignments GenomicRanges hiAnnotator readxl rSFFreader sonicLength]; }; + hicrep = derive2 { name="hicrep"; version="1.6.0"; sha256="0j92hg6qk9rd84lkl63zirwyydvnsrsgwibyv8ndrap4nw9hiswv"; depends=[]; }; + hierGWAS = derive2 { name="hierGWAS"; version="1.12.0"; sha256="0fsp5zyaz7kdgyyfnzvzcvsscxh69skvkn245sw41svq3gyswpcl"; depends=[fastcluster fmsb glmnet]; }; + hierinf = derive2 { name="hierinf"; version="1.0.0"; sha256="0p0kxqap5qdrfgh6jcn94c7hdk9k3xp178wz5ip1c3x3pqj30ndh"; depends=[fmsb glmnet]; }; + hipathia = derive2 { name="hipathia"; version="1.3.1"; sha256="10j4152vikdx6jfnspgd7sgw28k4jzrhf8qb3avsjm45677j2ckb"; depends=[AnnotationHub coin DelayedArray igraph limma matrixStats MultiAssayExperiment preprocessCore S4Vectors servr SummarizedExperiment]; }; + hmdbQuery = derive2 { name="hmdbQuery"; version="1.2.0"; sha256="0wliaddym62p9gf57y349q854jsng5chh5jd0gh3j3pdg5nlb7c0"; depends=[S4Vectors XML]; }; + hopach = derive2 { name="hopach"; version="2.42.0"; sha256="0mrc9yw1gwk6nx0bdcckphd5n13si3yvf3brn5yyg6xnl1b019c3"; depends=[Biobase BiocGenerics cluster]; }; + hpar = derive2 { name="hpar"; version="1.24.0"; sha256="1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"; depends=[]; }; + htSeqTools = derive2 { name="htSeqTools"; version="1.30.0"; sha256="11lywvkgl07fd2f82j00lw8zbvdg4g2aaa2w670vhh24v5w38xng"; depends=[Biobase BiocGenerics BSgenome GenomeInfoDb GenomicRanges IRanges MASS S4Vectors]; }; + hyperdraw = derive2 { name="hyperdraw"; version="1.34.0"; sha256="0widxxs8rk9xmpzwj4pmxg5px2ym2g2psqiwnqnhvd0pqhfpssvr"; depends=[graph hypergraph Rgraphviz]; }; + hypergraph = derive2 { name="hypergraph"; version="1.54.0"; sha256="1qhn3y3wvh2azbcabi95zbpdlv0y1fhrw3l8w7qgi78asiq5b3jp"; depends=[graph]; }; + iASeq = derive2 { name="iASeq"; version="1.26.0"; sha256="138ahl3l2vghnbm7ck9yg6yr8yilrnv12xi8j8bqzyxavaszf122"; depends=[]; }; + iBBiG = derive2 { name="iBBiG"; version="1.26.0"; sha256="02pw4v01ck6kfpylbymy46wsavcpf1q9xmrz1fywb1z5rday2kdb"; depends=[ade4 biclust xtable]; }; + iBMQ = derive2 { name="iBMQ"; version="1.22.0"; sha256="08lw0a4c9gp3vx6ggrxmsr2lgikfzw5gdw3ri08f89cqqmb6cazi"; depends=[Biobase ggplot2]; }; + iCARE = derive2 { name="iCARE"; version="1.10.3"; sha256="1m58fprg00ns55cgbd63dn9276hx3351r69cwskrrsl68kza3i2r"; depends=[gtools Hmisc plotrix]; }; + iCNV = derive2 { name="iCNV"; version="1.2.0"; sha256="1pmqz15j665qd9yyif6kjkpv26xaw6d9cfw17alnhvsnhwfs1xpb"; depends=[CODEX data_table dplyr fields ggplot2 rlang tidyr truncnorm]; }; + iCOBRA = derive2 { name="iCOBRA"; version="1.10.0"; sha256="0i1swrm31g0zffi5pm48bfvdfqpd32d0zdchkbyipz96al46jnld"; depends=[dplyr DT ggplot2 limma reshape2 ROCR scales shiny shinyBS shinydashboard UpSetR]; }; + iCheck = derive2 { name="iCheck"; version="1.12.0"; sha256="0wsgplym9kf1v7lvnnkxxgs9d9ahhb456vs9kgxydik94hyxpiz4"; depends=[affy Biobase GeneSelectMMD gplots limma lmtest lumi MASS preprocessCore randomForest rgl scatterplot3d]; }; + iChip = derive2 { name="iChip"; version="1.36.0"; sha256="1ak11v8xywgqximfy99g3d2lyci7pj0r4p1yy6g77j8bwf1frz5d"; depends=[limma]; }; + iClusterPlus = derive2 { name="iClusterPlus"; version="1.18.0"; sha256="08w6f1ad1mc05ws7jdq1j6sn3rflbdp1q5nii09a6qjx83micr4n"; depends=[]; }; + iGC = derive2 { name="iGC"; version="1.12.0"; sha256="1m3mhxkvxsswmk6sqd78brx94pwyzc3z71kv2dzxj1409g6s1h25"; depends=[data_table plyr]; }; + iPAC = derive2 { name="iPAC"; version="1.26.0"; sha256="01s5sgkid33jhzkjk7mdkdn48asp4ibj8b9r5cx5f3ngmkbfpdql"; depends=[Biostrings gdata multtest scatterplot3d]; }; + iSEE = derive2 { name="iSEE"; version="1.2.0"; sha256="1fhhsy07gy73yfc0pbx3jv92a8fzfmg38fzywryzga997wqyip2h"; depends=[AnnotationDbi BiocGenerics colourpicker cowplot dplyr DT ggplot2 igraph mgcv rentrez reshape2 rintrojs S4Vectors scales shiny shinyAce shinydashboard shinyjs SingleCellExperiment SummarizedExperiment vipor viridisLite]; }; + iSeq = derive2 { name="iSeq"; version="1.34.0"; sha256="0hlslyypijb4w9m01xkn6r8svs0kkp4nbv4xdz844pvyyxcn4afc"; depends=[]; }; + iasva = derive2 { name="iasva"; version="1.0.0"; sha256="1v6jx309m0ar4pb1zvh2wlipqhfbcmb1028c2syg7avbv41h4zbp"; depends=[BiocParallel cluster irlba SummarizedExperiment]; }; + ibh = derive2 { name="ibh"; version="1.30.0"; sha256="0wghj4qbnfg7zy1pbz580x9m1wszlhiyc34s9sd4q5spviz8dxh5"; depends=[simpIntLists]; }; + icetea = derive2 { name="icetea"; version="1.0.0"; sha256="01scc2vcfnifqrdk9bngw47ifpq87dhj659h1ndrwqqxv2drb67r"; depends=[BiocGenerics BiocParallel Biostrings csaw edgeR GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges limma Rsamtools rtracklayer S4Vectors ShortRead SummarizedExperiment TxDb_Dmelanogaster_UCSC_dm6_ensGene VariantAnnotation]; }; + ideal = derive2 { name="ideal"; version="1.6.0"; sha256="173nlxmilmaz792jz3nv7dm98icl38gbidmcwbj7zhsl5q7wd8z5"; depends=[AnnotationDbi BiocParallel d3heatmap DESeq2 dplyr DT GenomicRanges ggplot2 GO_db goseq GOstats gplots IHW IRanges knitr limma pcaExplorer pheatmap rentrez rintrojs rmarkdown S4Vectors shiny shinyAce shinyBS shinydashboard stringr SummarizedExperiment topGO UpSetR]; }; + idiogram = derive2 { name="idiogram"; version="1.58.0"; sha256="0m4p1ar2z7wj8zk24kiazwr8i55b0b6i7j03skqzcgy5jdv3jzyp"; depends=[annotate Biobase plotrix]; }; + igvR = derive2 { name="igvR"; version="1.2.0"; sha256="1g5q877hpwckf3m2qvgysvwa9ggxg99mbmk0vkqsyamqxh74pwx6"; depends=[BiocGenerics BrowserViz GenomicRanges httpuv rtracklayer VariantAnnotation]; }; + illuminaio = derive2 { name="illuminaio"; version="0.24.0"; sha256="1rdp9b4xlv91yzba7pd7k50s3nkljfxmdmyz5jl0j8ybhmpl6rns"; depends=[base64]; }; + imageHTS = derive2 { name="imageHTS"; version="1.32.0"; sha256="0d0wc48vr4p8yqzb68xrfxi5zlimzmss1da2apv1cbrcavzs2392"; depends=[Biobase cellHTS2 e1071 EBImage hwriter vsn]; }; + immunoClust = derive2 { name="immunoClust"; version="1.14.1"; sha256="0ncb6szwd5ghh5x3bi9d3dqmfgyjawhflsc1rxbmyf3qs67796my"; depends=[flowCore lattice]; }; + impute = derive2 { name="impute"; version="1.56.0"; sha256="08z0pj1dz5iq967nwj67qyka7ir7m5an2ggv7bsrlz3apzfsla33"; depends=[]; }; + intansv = derive2 { name="intansv"; version="1.22.0"; sha256="1gj6sxh84v5g7nriskyg7jx0z3kqmicymv53651cgr66wc86z2lm"; depends=[BiocGenerics GenomicRanges ggbio IRanges plyr]; }; + interactiveDisplay = derive2 { name="interactiveDisplay"; version="1.20.0"; sha256="1zlxmj8wwn916xf7qkvpapsqg9i53bywn2z3xny3yj6jp9xmibff"; depends=[AnnotationDbi BiocGenerics Category ggplot2 gridSVG interactiveDisplayBase plyr RColorBrewer reshape2 shiny XML]; }; + interactiveDisplayBase = derive2 { name="interactiveDisplayBase"; version="1.20.0"; sha256="04xz3dkwan2s5ic1mwkdfnggm0l41mgqfagx160bcsrpkw6z7ark"; depends=[BiocGenerics shiny]; }; + inveRsion = derive2 { name="inveRsion"; version="1.30.0"; sha256="0qaxl6arlx2zki5gkic52b575ickh7mzwls70xyqj8342hyxhi30"; depends=[haplo_stats]; }; + ipdDb = derive2 { name="ipdDb"; version="1.0.0"; sha256="049hzzj2x7wwd4ybjbq6vrc4kg21fcx7yxj501lyyp1qddvvrmvs"; depends=[AnnotationDbi AnnotationHub assertthat Biostrings DBI GenomicRanges IRanges RSQLite]; }; + isobar = derive2 { name="isobar"; version="1.28.0"; sha256="0bs7xskx8q366sij7n2ga2spryzpknsdfh2xfv70gvb6ysqknksm"; depends=[Biobase biomaRt distr ggplot2 plyr]; }; + isomiRs = derive2 { name="isomiRs"; version="1.10.0"; sha256="0a2yjkgnfkw0vr4n7n8d8v36zdcwkxdc5ldgrl6fz25y5hrpwiyg"; depends=[AnnotationDbi assertive_sets Biobase BiocGenerics cluster cowplot DEGreport DESeq2 DiscriMiner dplyr GenomicRanges GGally ggplot2 gplots gridExtra gtools IRanges limma RColorBrewer readr reshape rlang S4Vectors SummarizedExperiment tibble tidyr]; }; + iterClust = derive2 { name="iterClust"; version="1.4.0"; sha256="12nm79j67ls330lnld1wf4xdjxnfi15yjd8x5ibppv9ccsq6vlrn"; depends=[Biobase cluster]; }; + iterativeBMA = derive2 { name="iterativeBMA"; version="1.40.0"; sha256="0x3fk3faslrcc24wrchdy57ip2nq49dr0l5yf99ihr1gnkfzjrsr"; depends=[Biobase BMA leaps]; }; + iterativeBMAsurv = derive2 { name="iterativeBMAsurv"; version="1.40.0"; sha256="1k6pivwa69n1ppwvfdr90nlm7lw2kji2p1s6s35dc9463a6qyh7r"; depends=[BMA leaps survival]; }; + iteremoval = derive2 { name="iteremoval"; version="1.2.0"; sha256="0xmx4k6h8ii2mfqik5kkx7gwmhn4br8a7pnqv4bk9dbvphaqknk8"; depends=[GenomicRanges ggplot2 magrittr SummarizedExperiment]; }; + ivygapSE = derive2 { name="ivygapSE"; version="1.4.0"; sha256="0r9j2r0n5hw75ylbc8scq070p4kazc4m9vrjcbxvfkyv22qppjr2"; depends=[ggplot2 hwriter plotly S4Vectors shiny SummarizedExperiment survival survminer UpSetR]; }; + joda = derive2 { name="joda"; version="1.30.0"; sha256="1v21j6maydhfxixfa27napp1k59f1jngz7p9hidijmm4nqbg4w60"; depends=[bgmm RBGL]; }; + karyoploteR = derive2 { name="karyoploteR"; version="1.8.5"; sha256="00qxhnwhrj0w35jqhh2j1pmlh9kcm6xjfb20py8ixyxh4bvblr1k"; depends=[bamsignals bezier biovizBase digest GenomeInfoDb GenomicFeatures GenomicRanges IRanges memoise regioneR Rsamtools rtracklayer S4Vectors]; }; + kebabs = derive2 { name="kebabs"; version="1.16.0"; sha256="1ibxymqpiq85a5zs5wrngkyjqvwb4n5k2jxiics4mqv28pg34023"; depends=[apcluster Biostrings e1071 IRanges kernlab LiblineaR Matrix Rcpp S4Vectors XVector]; }; + keggorthology = derive2 { name="keggorthology"; version="2.34.0"; sha256="107wi6mlrz15pgwg7jrlb3q771v0yhxqph5i5c0h6v3yzr47xx15"; depends=[AnnotationDbi DBI graph hgu95av2_db]; }; + kimod = derive2 { name="kimod"; version="1.10.0"; sha256="081vanahyk3figp6jc9cjvq9lrn1mchc08wbw79f6k5sind4ic7z"; depends=[Biobase cluster]; }; + kissDE = derive2 { name="kissDE"; version="1.2.0"; sha256="0vqg7gjcj6z0v5ngj3z6zrmh5kdyk7hghj38yv7vp36miiqzrlw6"; depends=[aod Biobase DESeq2 doParallel DSS foreach ggplot2 gplots matrixStats]; }; + lapmix = derive2 { name="lapmix"; version="1.48.0"; sha256="12s3k81bysmmqc6r524jsx9yv0vyd5ppw1xs7myk2y7067355wxc"; depends=[Biobase]; }; + ldblock = derive2 { name="ldblock"; version="1.12.0"; sha256="0xbf4pmhrk5fnd1iz5wzjvdr75v114bwpznhcig4wiqmxc27sips"; depends=[BiocGenerics erma GenomeInfoDb GenomicFiles GO_db Homo_sapiens Matrix Rsamtools snpStats VariantAnnotation]; }; + les = derive2 { name="les"; version="1.32.0"; sha256="0iv4srhkirw2ix0a2bv44byydwxgihy027wahcskamm6dzk0k9lz"; depends=[boot fdrtool gplots RColorBrewer]; }; + levi = derive2 { name="levi"; version="1.0.0"; sha256="177zjvijca57f0hr4wb3zr83is3bgag5yfc07p9azic64ilwfqdb"; depends=[colorspace dplyr DT ggplot2 httr igraph knitr RColorBrewer Rcpp reshape2 shiny shinydashboard shinyjs testthat xml2]; }; + lfa = derive2 { name="lfa"; version="1.12.0"; sha256="1lvkycg4d7grqj7x5s3bcq2h4936kvd75r029zsa9mxdakc94kld"; depends=[corpcor]; }; + limma = derive2 { name="limma"; version="3.38.3"; sha256="08va8jggmv61wym955mnb1n31mgikrmjys7dl1kp5hp3yia8jg7l"; depends=[]; }; + limmaGUI = derive2 { name="limmaGUI"; version="1.58.0"; sha256="0fjq8qr5f6cv0bx4sfinnjiy0jc3dymlzhfkrxbd0c24fw35m3f4"; depends=[limma R2HTML tkrplot xtable]; }; + lmdme = derive2 { name="lmdme"; version="1.24.0"; sha256="069s419q5ca4py0c5r392kl08pmb6fnm76vsznqkbbl4g1yclyp3"; depends=[limma pls stemHypoxia]; }; + loci2path = derive2 { name="loci2path"; version="1.2.0"; sha256="1aps0yq7wg5gi9nacg5znfa5bf9i8ijf0qv5xn03s4rbzbwxwlfz"; depends=[BiocParallel data_table GenomicRanges pheatmap RColorBrewer S4Vectors wordcloud]; }; + logicFS = derive2 { name="logicFS"; version="2.2.0"; sha256="1kvwcm2b66hqlpf693s0cy8sr7sgxqvcdg1czwj7f77hf9ys3x40"; depends=[LogicReg mcbiopi survival]; }; + logitT = derive2 { name="logitT"; version="1.40.0"; sha256="1xmyixzihnv6svxhk76f695fs641p3zwj3k6xk5ds2989p6zkymy"; depends=[affy]; }; + lol = derive2 { name="lol"; version="1.30.0"; sha256="0z78jddb3cv5w26rm3bh27b3qqc2fbf3lv57xj8aq8fvya2w4ma2"; depends=[Matrix penalized]; }; + lpNet = derive2 { name="lpNet"; version="2.14.0"; sha256="1b3xsaq8ibsiz5895q6qqa632wlg08ca5sxm82ppm70fddpy26fd"; depends=[lpSolve nem]; }; + lpsymphony = derive2 { name="lpsymphony"; version="1.10.0"; sha256="0vnsf5x6gvd1k8h89al7r6xbgbxsjbxphr675czzwggz79zbvq7y"; depends=[]; }; + lumi = derive2 { name="lumi"; version="2.34.0"; sha256="1fpmjpgcy5n0hx9whn9m3jhjmciqq0l59nvy5addbq0a4wnjhx8q"; depends=[affy annotate AnnotationDbi Biobase DBI GenomicFeatures GenomicRanges KernSmooth lattice MASS methylumi mgcv nleqslv preprocessCore RSQLite]; }; + mAPKL = derive2 { name="mAPKL"; version="1.12.0"; sha256="1bp8xpcrz7d76lazp72p25rzp3gcmr2z4cyhcgbg678gpsp61lj9"; depends=[AnnotationDbi apcluster Biobase clusterSim e1071 igraph limma multtest parmigene reactome_db]; }; + mBPCR = derive2 { name="mBPCR"; version="1.36.0"; sha256="0vsb87518x770li85jdkns1qsabmixsn8mvh96hamr0adcwvgzrz"; depends=[Biobase oligoClasses SNPchip]; }; + mCSEA = derive2 { name="mCSEA"; version="1.2.0"; sha256="0vc7jbx43493znbvy9576sk0qfc5lac92bal3ihyvl5bz4vr046b"; depends=[fgsea GenomicFeatures GenomicRanges ggplot2 Gviz Homo_sapiens IRanges limma mCSEAdata S4Vectors SummarizedExperiment]; }; + maCorrPlot = derive2 { name="maCorrPlot"; version="1.52.0"; sha256="11gg32sj2iyd3l7hxlqlhgd8adcgsfdz7n5lypsz1d7d3y760f7y"; depends=[lattice]; }; + maPredictDSC = derive2 { name="maPredictDSC"; version="1.20.0"; sha256="00m792cgx3v6gp81axpqf48bdxkl8l2gnl6fvsx3xbsk4akm33p2"; depends=[affy AnnotationDbi caret class e1071 gcrma hgu133plus2_db limma LungCancerACvsSCCGEO MASS ROC ROCR]; }; + maSigPro = derive2 { name="maSigPro"; version="1.54.0"; sha256="15bndkrwafj1vg2ik0s5003dzs65ibyhgz79ya5gry0b5h365qri"; depends=[Biobase MASS mclust venn]; }; + maanova = derive2 { name="maanova"; version="1.52.0"; sha256="1p1g5p2qflcgk24h1ww0nj4nnfas5pyg1caw2bgxrqyb161rl90x"; depends=[Biobase]; }; + macat = derive2 { name="macat"; version="1.56.0"; sha256="11jvvs3w1kiv2lvjwgzcxr5xy3m7c6b56bvhs8kiwf5lkqrqw6kn"; depends=[annotate Biobase]; }; + made4 = derive2 { name="made4"; version="1.56.0"; sha256="05bk877d81jjifj6rgrx0j2fhlsnmy8s093fnpqp7khrjwqh3zhn"; depends=[ade4 gplots RColorBrewer scatterplot3d]; }; + maftools = derive2 { name="maftools"; version="1.8.0"; sha256="1l7jnwb54zwag0xzz1j08zk5mwyghza5w27v1annfyxbfa3hd9xd"; depends=[Biostrings BSgenome cometExactTest ComplexHeatmap cowplot data_table ggplot2 ggrepel gridExtra mclust NMF RColorBrewer rjson survival wordcloud]; }; + maigesPack = derive2 { name="maigesPack"; version="1.46.0"; sha256="07rd63lifw4vmf2cxb7lwmnwpynv39ac0h2dd97dvjwqzj6kq1cs"; depends=[convert graph limma marray]; }; + makecdfenv = derive2 { name="makecdfenv"; version="1.58.0"; sha256="0djhh5kj4ymxjk1qhpx8kcy8cjzx3syx6na7v52aqhys0zssdbip"; depends=[affy affyio Biobase zlibbioc]; }; + manta = derive2 { name="manta"; version="1.28.0"; sha256="1hgy4vrklxmnxsggaby8r793953ih4k6asdcxdyxwjmikcghj1hc"; depends=[caroline edgeR Hmisc]; }; + mapscape = derive2 { name="mapscape"; version="1.6.0"; sha256="148b7g4qiczc215x9nrggjqzjbsd4wxwydjxsfbsmy51db7n4gp2"; depends=[base64enc htmlwidgets jsonlite stringr]; }; + marray = derive2 { name="marray"; version="1.60.0"; sha256="1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"; depends=[limma]; }; + martini = derive2 { name="martini"; version="1.2.0"; sha256="072k0wphk4nl096wvbfrn0v1sgryg74ay6r9jqci7pzmninc0kci"; depends=[igraph Matrix Rcpp RcppEigen Rgin S4Vectors snpStats]; }; + maser = derive2 { name="maser"; version="1.0.0"; sha256="08zfqzbryir2sf5a5bmdy63a9ix983kkn281flfbwm81694wx7pg"; depends=[BiocGenerics data_table dplyr DT GenomeInfoDb GenomicRanges ggplot2 Gviz IRanges reshape2 rtracklayer]; }; + maskBAD = derive2 { name="maskBAD"; version="1.26.0"; sha256="0nkc7s219b9vhc3fl01ji94pxls0r8li042k8lrq8jx1g940smh4"; depends=[affy gcrma]; }; + massiR = derive2 { name="massiR"; version="1.18.0"; sha256="1fsic9w4bkkmi177f1f8lk4835cs2y4r5dy5vf71nc89y4jg7h67"; depends=[Biobase cluster diptest gplots]; }; + matchBox = derive2 { name="matchBox"; version="1.24.0"; sha256="0whhbp49imvrl0a4xdmmbz8fz8vv9i19168smm7xq2p7wa1am364"; depends=[]; }; + matter = derive2 { name="matter"; version="1.8.3"; sha256="03hsgl0k48j458aa20s4xxrpslypllg74qf6yr9irx9h939hszwm"; depends=[biglm BiocGenerics digest irlba]; }; + mcaGUI = derive2 { name="mcaGUI"; version="1.30.0"; sha256="0id5zlpk8zdim8gmmh61dabirg52kmbi63dx316838idk4i06a5h"; depends=[bpca foreign gWidgets gWidgetsRGtk2 lattice MASS OTUbase proto vegan]; }; + mdgsa = derive2 { name="mdgsa"; version="1.14.0"; sha256="01yh036hy3jn1q76bz2whfdf2qjs5xra7570rf25fff824cbszdk"; depends=[AnnotationDbi cluster DBI GO_db KEGG_db Matrix]; }; + mdp = derive2 { name="mdp"; version="1.2.0"; sha256="0mvpziy476wq9yniwyvpmbcmhsvgafhc4k6c5hi8k85rkaczip4q"; depends=[ggplot2]; }; + mdqc = derive2 { name="mdqc"; version="1.44.0"; sha256="0w4455xqkwwz8bhac36sxkqziq9pacp8n81zc3b1wwcwf95m2r6q"; depends=[cluster MASS]; }; + meshes = derive2 { name="meshes"; version="1.8.0"; sha256="0lc0mmvmrfzirqc0ydhzwdpq7d6rb8ffi8ka52qs6wc6nfqb6qg8"; depends=[AnnotationDbi DOSE enrichplot GOSemSim MeSH_db rvcheck]; }; + meshr = derive2 { name="meshr"; version="1.18.0"; sha256="12rwfqjpa9bzgrm3yqfz7h8v22icps8dr709lmp7k1jx9jbzp3gs"; depends=[BiocGenerics Category cummeRbund fdrtool MeSH_Aca_eg_db MeSH_AOR_db MeSH_Bsu_168_eg_db MeSH_db MeSH_Hsa_eg_db MeSH_PCR_db MeSH_Syn_eg_db MeSHDbi org_Hs_eg_db RSQLite S4Vectors]; }; + messina = derive2 { name="messina"; version="1.18.0"; sha256="1dhl6l5ids2ffsfbc9jk36ihrpsd161w9c1j93jvdvpa6130jl6f"; depends=[foreach ggplot2 plyr Rcpp survival]; }; + metaArray = derive2 { name="metaArray"; version="1.60.0"; sha256="049xwhycw2czzshvy5rc4plngaylwrj3ilk7dzynksn7av6sz4zd"; depends=[Biobase MergeMaid]; }; + metaCCA = derive2 { name="metaCCA"; version="1.10.0"; sha256="1h3xnrnlpbrjvrjpifm6i4kzyfgc2a0gnzpxya9lj105m9svpvca"; depends=[]; }; + metaMS = derive2 { name="metaMS"; version="1.18.0"; sha256="1f98hpx2mmygxfyrcccy9408qfm2gpcz4k9j6afw0irb4lsfpysj"; depends=[BiocGenerics CAMERA Matrix robustbase xcms]; }; + metaSeq = derive2 { name="metaSeq"; version="1.22.1"; sha256="00jwcgcx250v9glqxc1d0cvydn2jqzxxq62jmwskv87av68ppqbs"; depends=[NOISeq Rcpp snow]; }; + metabomxtr = derive2 { name="metabomxtr"; version="1.16.0"; sha256="0xcmfsy6ilggal6l9x05yz431jb2bs4qs0nlf5jq52xwvqz10q0d"; depends=[Biobase BiocParallel Formula ggplot2 multtest optimx plyr]; }; + metagene = derive2 { name="metagene"; version="2.14.0"; sha256="09krnp862jz8mgjyp6v5ynvsrl4asfvzsvi21rj8af5b0ywkwvwg"; depends=[BiocParallel data_table DBChIP EnsDb_Hsapiens_v86 ensembldb GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges magrittr matrixStats muStat purrr R6 Rsamtools rtracklayer stringr]; }; + metagenomeFeatures = derive2 { name="metagenomeFeatures"; version="2.2.0"; sha256="04kw9lpig17b2l1z3qnr56wglasij5bzcxyzvkv9zar63l4acrv8"; depends=[ape Biobase Biostrings dbplyr DECIPHER dplyr lattice lazyeval magrittr purrr RSQLite S4Vectors stringr]; }; + metagenomeSeq = derive2 { name="metagenomeSeq"; version="1.24.0"; sha256="1cbryqcfv5f3jvs9f4zjf5zf834jv12n2a2jj2h94z7zaql8zpqq"; depends=[Biobase foreach glmnet gplots limma Matrix matrixStats RColorBrewer]; }; + metahdep = derive2 { name="metahdep"; version="1.40.0"; sha256="02xw6pb6688hhgq3213s55sb73qmd6xjfaqk7bz4ci7m4ilf6c2k"; depends=[]; }; + metaseqR = derive2 { name="metaseqR"; version="1.22.0"; sha256="1plqlhwy595y7scqzz2vjygjscdn0gdp3vhrdkhc0vk63li66z7a"; depends=[baySeq biomaRt brew corrplot DESeq EDASeq edgeR gplots limma log4r NBPSeq NOISeq qvalue rjson vsn]; }; + metavizr = derive2 { name="metavizr"; version="1.6.1"; sha256="0gkmfial3m1q46dnja1irk2jiib0rcg6h1vzq1wa2pxfsg4sa0sx"; depends=[Biobase data_table digest epivizr epivizrData epivizrServer epivizrStandalone GenomeInfoDb httr metagenomeSeq phyloseq vegan]; }; + methInheritSim = derive2 { name="methInheritSim"; version="1.4.1"; sha256="0cshckvhrvlq9wgcjk3z2bi1qfq1my947rwvdma5la8ydf3x1i5w"; depends=[BiocGenerics GenomeInfoDb GenomicRanges IRanges methylKit msm S4Vectors]; }; + methVisual = derive2 { name="methVisual"; version="1.34.0"; sha256="09ss0s5z950m6v2y037v8qwsp238w73302ls1xh9ps8gkz05a800"; depends=[Biostrings ca gridBase gsubfn IRanges plotrix sqldf]; }; + methimpute = derive2 { name="methimpute"; version="1.4.0"; sha256="0z16bx2lb0g5sp0arc2s1zs3s87c62pgz6wy1b7a491cpplpxmlx"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges ggplot2 IRanges minpack_lm Rcpp reshape2]; }; + methyAnalysis = derive2 { name="methyAnalysis"; version="1.24.0"; sha256="0afgaf3xl2dnpl86agbx44fiq4i5i96535p3hd9y845xdq5ymvnp"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges genoset Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; }; + methylGSA = derive2 { name="methylGSA"; version="1.0.2"; sha256="11wrks3fc9fyrchcc41203d6yfkd8cvigi5w4di2hxdzijg8qlm2"; depends=[AnnotationDbi clusterProfiler ggplot2 GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylationEPICanno_ilm10b2_hg19 missMethyl org_Hs_eg_db reactome_db RobustRankAggreg stringr]; }; + methylInheritance = derive2 { name="methylInheritance"; version="1.6.1"; sha256="0n11jkka37aqmirn73hl8kabilb220i1pv10i62jzq623sqpdsz9"; depends=[BiocParallel GenomicRanges ggplot2 gridExtra IRanges methylKit rebus S4Vectors]; }; + methylKit = derive2 { name="methylKit"; version="1.8.1"; sha256="1zcfwy7i10aqgnf7r0c41hakb5aai3s3n9y8pc6a98vimz51ly2z"; depends=[data_table emdbook fastseg GenomeInfoDb GenomicRanges gtools IRanges KernSmooth limma mclust qvalue R_utils Rcpp Rhtslib Rsamtools rtracklayer S4Vectors zlibbioc]; }; + methylMnM = derive2 { name="methylMnM"; version="1.20.0"; sha256="0sd3vj58yfscngpcl9hys2nys3siq1h2ask5r8j6jx6yz3qs91xd"; depends=[edgeR statmod]; }; + methylPipe = derive2 { name="methylPipe"; version="1.16.0"; sha256="1qrvf0kf1948v2bhkxv979p6cr8mknmqkb04hz30bm8fqpmn1wfw"; depends=[BiocGenerics Biostrings data_table GenomeInfoDb GenomicAlignments GenomicRanges gplots Gviz IRanges marray Rsamtools S4Vectors SummarizedExperiment]; }; + methylumi = derive2 { name="methylumi"; version="2.28.0"; sha256="14p2qi18cprfvb2gxng1vm48c7zwh23h88q9qjgipj9xl5axsgw2"; depends=[annotate AnnotationDbi Biobase BiocGenerics FDb_InfiniumMethylation_hg19 genefilter GenomeInfoDb GenomicRanges ggplot2 illuminaio IRanges lattice matrixStats minfi reshape2 S4Vectors scales SummarizedExperiment]; }; + methyvim = derive2 { name="methyvim"; version="1.4.0"; sha256="1scybf1hdzyvjmcbfbqpbwph38alp594lj3ggxcdgfxvjapq3rsb"; depends=[BiocGenerics BiocParallel bumphunter cluster doFuture dplyr future GenomeInfoDb ggplot2 ggsci gridExtra gtools IRanges limma minfi S4Vectors SummarizedExperiment superheat tmle]; }; + mfa = derive2 { name="mfa"; version="1.4.0"; sha256="0kp314rshiidi3zp78a5wlbsrnqrcaa5bqz5qs5nkrzlvz5w6y11"; depends=[Biobase coda dplyr ggmcmc ggplot2 magrittr MCMCglmm MCMCpack Rcpp tibble]; }; + mgsa = derive2 { name="mgsa"; version="1.30.0"; sha256="0b30hlqyx8aw8a9naln2m5k8lgkr9f9fgv1mwnww5xiwqdnbqfcw"; depends=[gplots]; }; + miRBaseConverter = derive2 { name="miRBaseConverter"; version="1.6.0"; sha256="0gb7vg35wff0kckb6dqkggvshdy43q04f07niiqamnl71h59wjh7"; depends=[]; }; + miRLAB = derive2 { name="miRLAB"; version="1.12.0"; sha256="0vpvd93zrz4ihcinpwppc954585vjafmcpj1rpamqkyi2giyxldm"; depends=[Category ctc dplyr energy entropy glmnet GOstats gplots heatmap_plus Hmisc httr impute InvariantCausalPrediction limma org_Hs_eg_db pcalg RCurl Roleswitch stringr SummarizedExperiment TCGAbiolinks]; }; + miRNAmeConverter = derive2 { name="miRNAmeConverter"; version="1.10.0"; sha256="0wkkgqki7sv92adwzxay6xjyfx921ll8yh6aw2yp0mdgk9021zr8"; depends=[AnnotationDbi DBI miRBaseVersions_db reshape2]; }; + miRNApath = derive2 { name="miRNApath"; version="1.42.0"; sha256="1hrnnvp3y2q8ldmlq2pdyd3dpkqpyrhhgzqms3mc7djnv6ybv3cd"; depends=[]; }; + miRNAtap = derive2 { name="miRNAtap"; version="1.16.0"; sha256="1iy4gks0c0alg5bl1l40fdja6wffm0hjv40xvny9s1g036zmqca6"; depends=[AnnotationDbi DBI plyr RSQLite sqldf stringr]; }; + miRSM = derive2 { name="miRSM"; version="1.0.0"; sha256="09z2ca1qpf2m3s5cc59y4xzcixlbl847c17lx1kmrakabqpsxy8i"; depends=[BiBitR BicARE biclust Biobase dynamicTreeCut fabia flashClust GFA GSEABase iBBiG igraph isa2 linkcomm MCL miRsponge NMF PMA Rcpp rqubic runibic s4vd SummarizedExperiment WGCNA]; }; + miRcomp = derive2 { name="miRcomp"; version="1.12.0"; sha256="17b6bq70d6ly09vma5mdlk54620jdxw6k4bwdyxgghyk7kwmd753"; depends=[Biobase KernSmooth miRcompData]; }; + miRmine = derive2 { name="miRmine"; version="1.4.0"; sha256="0zfdm5d6ifkq55v38xcjwzq19ifh6jgbg1pjp298mn15yjsjzfj1"; depends=[SummarizedExperiment]; }; + miRsponge = derive2 { name="miRsponge"; version="1.8.0"; sha256="0j1ab8pw9sa8pm53b1z8kx5pj3jkiw6lncv8cj77g0zcwg3f7xpw"; depends=[clusterProfiler corpcor DOSE igraph linkcomm MCL Rcpp ReactomePA survival varhandle]; }; + microRNA = derive2 { name="microRNA"; version="1.40.0"; sha256="1asrjljh4bxgzvbgnp72sqyqv13kvzbfdn3jy01v3l98dppjnwsf"; depends=[Biostrings]; }; + microbiome = derive2 { name="microbiome"; version="1.4.2"; sha256="0amla1m69axhlslbg1pbvl61qyxb6qjpdfd5g2j8b116h8xrmyab"; depends=[dplyr ggplot2 phyloseq reshape2 tidyr vegan]; }; + mimager = derive2 { name="mimager"; version="1.6.0"; sha256="097fv7wfj0wj0chijcl5v52lf35pc48va1ddsq6qii5xzi626cpd"; depends=[affy affyPLM Biobase BiocGenerics DBI gtable oligo oligoClasses preprocessCore S4Vectors scales]; }; + minet = derive2 { name="minet"; version="3.40.0"; sha256="0hb1k3p750qykmqjz59yjak5h8vmnln8zcp2dffjnqvwgn78i23w"; depends=[infotheo]; }; + minfi = derive2 { name="minfi"; version="1.28.0"; sha256="0bdbrk0rlh1sg38yjs92rjxdzj11m9fww4jyvcfjydps8amil952"; depends=[beanplot Biobase BiocGenerics BiocParallel Biostrings bumphunter data_table DelayedArray DelayedMatrixStats genefilter GenomeInfoDb GenomicRanges GEOquery HDF5Array illuminaio IRanges lattice limma MASS mclust nlme nor1mix preprocessCore quadprog RColorBrewer reshape S4Vectors siggenes SummarizedExperiment]; }; + mirIntegrator = derive2 { name="mirIntegrator"; version="1.12.0"; sha256="1vgl2kz4jahrw885gib7yaxwliij1ric9mmsad8v4zravw7d9knj"; depends=[AnnotationDbi ggplot2 graph org_Hs_eg_db Rgraphviz ROntoTools]; }; + missMethyl = derive2 { name="missMethyl"; version="1.16.0"; sha256="0axssdkyvdfpq7r47sckbbp7w8wa06j1ncskcn2w9f95nl1dbya5"; depends=[AnnotationDbi BiasedUrn GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest limma methylumi minfi org_Hs_eg_db ruv statmod stringr]; }; + missRows = derive2 { name="missRows"; version="1.2.0"; sha256="0fgw36358z0lc0ppkpy49vw1p2k2w3ji01apff8gpkfb310zipwc"; depends=[ggplot2 gtools MultiAssayExperiment plyr S4Vectors]; }; + mitoODE = derive2 { name="mitoODE"; version="1.20.0"; sha256="1gf6isnf83x6sxmdankb2l63ms60lrpwhjnd8c3cpq2kalmj9dy1"; depends=[KernSmooth MASS minpack_lm mitoODEdata]; }; + mixOmics = derive2 { name="mixOmics"; version="6.6.0"; sha256="186v3md70g8i54d93yjvdn973l0jq082jj1gymx2z79v5nv33kf2"; depends=[corpcor dplyr ellipse ggplot2 gridExtra igraph lattice MASS matrixStats rARPACK RColorBrewer reshape2 tidyr]; }; + mogsa = derive2 { name="mogsa"; version="1.16.0"; sha256="14rl7md4bdpb24cxj5pmr196dy0amih8l4611kgwbrvdm9k13d3s"; depends=[Biobase BiocGenerics cluster corpcor genefilter gplots graphite GSEABase svd]; }; + monocle = derive2 { name="monocle"; version="2.10.0"; sha256="1rwd1qk82bx5dzqm12z8nya1bdikwm4mpwqyhwlfd018yqf99nhv"; depends=[Biobase BiocGenerics biocViews cluster combinat DDRTree densityClust dplyr fastICA ggplot2 HSMMSingleCell igraph irlba limma MASS Matrix matrixStats pheatmap plyr proxy qlcMatrix RANN Rcpp reshape2 Rtsne slam stringr tibble VGAM viridis]; }; + mosaics = derive2 { name="mosaics"; version="2.20.0"; sha256="1536y2fizmi7jafq7bhbv8bzpf5b97dfskpg9a7v4c9xv6isagnx"; depends=[GenomeInfoDb GenomicAlignments GenomicRanges IRanges lattice MASS Rcpp Rsamtools S4Vectors]; }; + motifRG = derive2 { name="motifRG"; version="1.26.0"; sha256="1wxww6i0jgyapqclcwy0zzf9kqjvrvylr89z7yhg1izi7jnw2fka"; depends=[Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 IRanges seqLogo XVector]; }; + motifStack = derive2 { name="motifStack"; version="1.26.0"; sha256="1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf"; depends=[ade4 Biostrings grImport htmlwidgets MotIV scales XML]; }; + motifbreakR = derive2 { name="motifbreakR"; version="1.12.0"; sha256="191w8nzjm1lkgbzlhixnfvpgadq2mlhmwk7ai8xaadmxckrf494a"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges grImport Gviz IRanges matrixStats MotifDb motifStack rtracklayer S4Vectors stringr TFMPvalue VariantAnnotation]; }; + motifcounter = derive2 { name="motifcounter"; version="1.6.0"; sha256="04i8s6r26kir9fcqbvy1wfxrav5imwj4r0sqvsf4vq2jxkwb4brr"; depends=[Biostrings]; }; + motifmatchr = derive2 { name="motifmatchr"; version="1.4.0"; sha256="1s65gr15iil1y8sa7wggrj5sb0mgw6vgs2qrmk1xka9zqjx957kv"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp RcppArmadillo Rsamtools S4Vectors SummarizedExperiment TFBSTools]; }; + mpra = derive2 { name="mpra"; version="1.4.1"; sha256="0wwn5cix0npk8lhsmk9dzagnfrqcn9x22wzgf5kq3xk4gwaraqdw"; depends=[BiocGenerics limma S4Vectors scales statmod SummarizedExperiment]; }; + msPurity = derive2 { name="msPurity"; version="1.8.0"; sha256="13r16568c5zdl1gc5r1np91vqcr5vw14g3n21c1s43f5ia0nmwjv"; depends=[DBI doSNOW fastcluster foreach ggplot2 mzR plyr Rcpp reshape2 RSQLite stringr]; }; + msa = derive2 { name="msa"; version="1.14.0"; sha256="1g0ny0hjnzwqh9kbp6n770vfdvxsl95vhiydjqasma2hz205plf9"; depends=[BiocGenerics Biostrings IRanges Rcpp S4Vectors]; }; + msgbsR = derive2 { name="msgbsR"; version="1.6.0"; sha256="19gwfx682fqrnp43jrvdmdlhww8lmknnxzdxzszifzass7vgqp1q"; depends=[BSgenome easyRNASeq edgeR GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr R_utils Rsamtools S4Vectors SummarizedExperiment]; }; + msmsEDA = derive2 { name="msmsEDA"; version="1.20.0"; sha256="1gyqnmw63xgi1zd3578g5hlnq5b6hlv0dkm7dz6mka1pqc5gdlqh"; depends=[gplots MASS MSnbase RColorBrewer]; }; + msmsTests = derive2 { name="msmsTests"; version="1.20.0"; sha256="1fvvs5963104iwwvds8ipzf298dbkg4gb6bn98a8zd1z4c2lma03"; depends=[edgeR msmsEDA MSnbase qvalue]; }; + multiClust = derive2 { name="multiClust"; version="1.12.0"; sha256="0ddk1sl9zsc4dgrxasnqa2h341blirpwzygl89wh2k4ga0wsmw6q"; depends=[amap cluster ctc dendextend mclust survival]; }; + multiHiCcompare = derive2 { name="multiHiCcompare"; version="1.0.0"; sha256="0aixi21zmj2lc54cmkqc9k596nll01nyxhpkkzx40lv7jihw6p1c"; depends=[BiocParallel BLMA data_table dplyr edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges HiCcompare metap pbapply pheatmap qqman]; }; + multiMiR = derive2 { name="multiMiR"; version="1.4.0"; sha256="1mip48rcqk47sj5sdqi2rxcwsd6l6v3nssnnkx41mpx8amn3cigb"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; }; + multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.6.0"; sha256="0h7spx39c079mzpbnbg4fv7bfnrdqz95101zxd4cdsffjk5zrly8"; depends=[doParallel foreach SummarizedExperiment]; }; + multiscan = derive2 { name="multiscan"; version="1.42.0"; sha256="1h5b55j0m4znp9gpzqdv974vvxhlbskxy9m474g8y72q0zbri4gk"; depends=[Biobase]; }; + multtest = derive2 { name="multtest"; version="2.38.0"; sha256="0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"; depends=[Biobase BiocGenerics MASS survival]; }; + muscle = derive2 { name="muscle"; version="3.24.0"; sha256="1v0n6ncq467kpfli498gddz0r6ilkhjfw0q9srl1gcknz5y2frsw"; depends=[Biostrings]; }; + mygene = derive2 { name="mygene"; version="1.18.0"; sha256="03knrfbqm9hr30l3s58jkqyl6sl83p1vf4zyahr1ld0qrw81pvx7"; depends=[GenomicFeatures Hmisc httr jsonlite plyr S4Vectors sqldf]; }; + myvariant = derive2 { name="myvariant"; version="1.12.0"; sha256="1vsp8m6rwyk09i0rg5j8w29vgn5hzz7fh8gc2fbjbg3icls26gn8"; depends=[GenomeInfoDb Hmisc httr jsonlite magrittr plyr S4Vectors VariantAnnotation]; }; + mzID = derive2 { name="mzID"; version="1.20.0"; sha256="08jbq223viwknsmsi30hyxyxslvmb0l4wx3vmqlkl6qk4vfmxzjz"; depends=[doParallel foreach iterators plyr ProtGenerics XML]; }; + mzR = derive2 { name="mzR"; version="2.16.0"; sha256="0li1y6p95ljiva4lvfmql9sipn4dq42sknbh60b36ycjppnf8lj5"; depends=[Biobase BiocGenerics ncdf4 ProtGenerics Rcpp Rhdf5lib zlibbioc]; }; + ncdfFlow = derive2 { name="ncdfFlow"; version="2.28.0"; sha256="001nrbhzdm1vjprn0w4qrgbkq6cxvzfymvviqp0fkcvjfwiwxax5"; depends=[BH Biobase BiocGenerics flowCore flowViz Rcpp RcppArmadillo Rhdf5lib zlibbioc]; }; + ndexr = derive2 { name="ndexr"; version="1.4.0"; sha256="10f4jm1dar67kiya19qcn04virb1jn4zafllp370jcqn7flm6abs"; depends=[httr igraph jsonlite plyr tidyr]; }; + nem = derive2 { name="nem"; version="2.56.0"; sha256="02j5rm0h9bjghgba244k0acshbnhrr38ghvx6cmf8za8fw19k3v2"; depends=[boot e1071 graph limma plotrix RBGL RColorBrewer Rgraphviz statmod]; }; + netReg = derive2 { name="netReg"; version="1.6.0"; sha256="01qxq7zlbmvh0mazw069fm6bjw0ks90baj8y5i0jc7m101dsm2qi"; depends=[Rcpp RcppArmadillo]; }; + netSmooth = derive2 { name="netSmooth"; version="1.2.0"; sha256="1cz3rca9ig9jl8ddcadbij129v5rpb86ncfrdmfj4m9qy0krlyac"; depends=[cluster clusterExperiment data_table entropy Matrix scater SingleCellExperiment SummarizedExperiment]; }; + netbenchmark = derive2 { name="netbenchmark"; version="1.14.0"; sha256="1gc8dnma4pr1j9wq422x8xh89mvb15kyvjvv86fhhshvdisihngw"; depends=[c3net corpcor fdrtool GeneNet GENIE3 grndata Matrix minet PCIT pracma Rcpp]; }; + netbiov = derive2 { name="netbiov"; version="1.16.0"; sha256="0zg4wkf4z6yi84sdp4h8dg8cq5sm6m04abg15hm68y27vw42prs2"; depends=[igraph]; }; + nethet = derive2 { name="nethet"; version="1.14.0"; sha256="1xp08ad4lsmrjgvqydr85k4y0b57hcaxicndh4hz4plqswzl7qpf"; depends=[CompQuadForm GeneNet ggm ggplot2 glasso glmnet GSA huge ICSNP limma mclust multtest mvtnorm network parcor]; }; + netprioR = derive2 { name="netprioR"; version="1.8.0"; sha256="0yw9rpyflk6kcw6w5gm2n2wxqf45mjk7scf4cl616kkr7h4jgkaz"; depends=[doParallel dplyr foreach ggplot2 gridExtra Matrix pROC sparseMVN]; }; + netresponse = derive2 { name="netresponse"; version="1.42.0"; sha256="16hgcjzvbsx1lj2aq8jkam926ykb06im06rr62z705x6hna8k4g0"; depends=[dmt ggplot2 graph igraph mclust minet plyr qvalue RColorBrewer reshape2 Rgraphviz]; }; + networkBMA = derive2 { name="networkBMA"; version="2.22.0"; sha256="12pl1hl1r2j3kvbr061xzzv5fmkh1g60j5ihvzi14gy8chvjk7wk"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; }; + nnNorm = derive2 { name="nnNorm"; version="2.46.0"; sha256="0fslid2ywqbx4d3c2gvhhsmkkkidgjnlr8jsd61qralcdln494wv"; depends=[marray nnet]; }; + nondetects = derive2 { name="nondetects"; version="2.12.0"; sha256="1wsckq31y6cxlgyg579zh6yk1sa1s0lczkvx29dbvy11hjnsgkm6"; depends=[arm Biobase HTqPCR limma mvtnorm]; }; + normalize450K = derive2 { name="normalize450K"; version="1.10.0"; sha256="0ab9g0k0y8lzqx8vvfwxy8yjmal4lgxf64fnz0923jss98czvk21"; depends=[Biobase illuminaio quadprog]; }; + normr = derive2 { name="normr"; version="1.8.0"; sha256="1yj9nnfzj522yr5nw0sm9l6cvk21w4vpxn0bayggs2wx5g03pbsj"; depends=[bamsignals GenomeInfoDb GenomicRanges IRanges qvalue Rcpp rtracklayer]; }; + npGSEA = derive2 { name="npGSEA"; version="1.18.0"; sha256="199n898qn6799p6zk46vlz192zj0z10f9q0xfc129ickfa7zk6gf"; depends=[Biobase BiocGenerics GSEABase]; }; + nuCpos = derive2 { name="nuCpos"; version="1.0.0"; sha256="1ibw5z9p02smbbv2p8spsrdapjy29675h0app3y08m8gdyvbrix8"; depends=[]; }; + nucleR = derive2 { name="nucleR"; version="2.14.0"; sha256="19y2ars61gbzglqvfzj2xq08iw34vnjm3fzn4dx67r0ivnxncs34"; depends=[Biobase BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr Rsamtools S4Vectors ShortRead]; }; + nucleoSim = derive2 { name="nucleoSim"; version="1.10.0"; sha256="09mls6rv9qw9w1g3avgj57pi2avg4pnlbcbg29da0szz0dbbb7yn"; depends=[IRanges S4Vectors]; }; + occugene = derive2 { name="occugene"; version="1.42.0"; sha256="0sqmnr571rx18mh9m9ivjp79bqn6dydzhh3h4xc7xxwqwwp0l4fa"; depends=[]; }; + odseq = derive2 { name="odseq"; version="1.10.0"; sha256="0936n8qzxcaxlqwpzh3dc2gnzh7q5cyrk4cif3vxb4hrlix8b1bv"; depends=[kebabs mclust msa]; }; + oligo = derive2 { name="oligo"; version="1.46.0"; sha256="1j9p22chnb09fp26xnlx5zmrxccg0q56ywgxfvbmm0s2jnr02nam"; depends=[affxparser affyio Biobase BiocGenerics Biostrings DBI ff oligoClasses preprocessCore RSQLite zlibbioc]; }; + oligoClasses = derive2 { name="oligoClasses"; version="1.44.0"; sha256="03kdxgrznx204y7pma1ca4bjgrhhhwfz2ia9radgkl70m447hz13"; depends=[affyio Biobase BiocGenerics BiocManager Biostrings DBI ff foreach GenomicRanges IRanges RSQLite S4Vectors SummarizedExperiment]; }; + omicRexposome = derive2 { name="omicRexposome"; version="1.4.0"; sha256="0hbnh85iqjhmjz2h3lxiks947nahcs4c7nryy3h686kay40v5f5c"; depends=[Biobase ggplot2 ggrepel gridExtra isva limma MultiDataSet omicade4 PMA rexposome SmartSVA stringr SummarizedExperiment sva]; }; + omicade4 = derive2 { name="omicade4"; version="1.22.0"; sha256="1bwfbzkq7p9h1njgaj15hk69cw9649kq5hwf2k8jf3spnbirp114"; depends=[ade4 made4]; }; + omicplotR = derive2 { name="omicplotR"; version="1.2.0"; sha256="1v77lijpzg7k12v48dcyzsdgh02klhcnlj0xj7ab670v407iy0y0"; depends=[ALDEx2 compositions knitr matrixStats rmarkdown shiny vegan zCompositions]; }; + omicsPrint = derive2 { name="omicsPrint"; version="1.2.0"; sha256="0yxcx787nq1kw2cd8ybic2yqknk2g46zgh89sr2y0wavsmqjv026"; depends=[MASS matrixStats MultiAssayExperiment RaggedExperiment SummarizedExperiment]; }; + oncomix = derive2 { name="oncomix"; version="1.4.0"; sha256="00pwd0nbbdlv35p85h5kqybvvzz2833qx2jgprffg2bhmxvaky8w"; depends=[ggplot2 ggrepel mclust RColorBrewer SummarizedExperiment]; }; + oneSENSE = derive2 { name="oneSENSE"; version="1.4.0"; sha256="0f2m7xnv9kfzx36dav0g2hh24rfgrd7hzcm1drfrcqp1qw6g19an"; depends=[flowCore gplots plotly Rtsne scatterplot3d shiny shinyFiles webshot]; }; + onlineFDR = derive2 { name="onlineFDR"; version="1.0.0"; sha256="1738wy4px32jzinj9311hvng887ys61dqqs3m3zi5cqkpwcs19hd"; depends=[]; }; + ontoProc = derive2 { name="ontoProc"; version="1.4.0"; sha256="08sgf142b8l4gdsap44b75jcxvwlcz19saqjrw9sg0307h509n77"; depends=[AnnotationDbi Biobase ontologyIndex S4Vectors shiny]; }; + openCyto = derive2 { name="openCyto"; version="1.20.0"; sha256="1z45r91fyih0jyj5a02bb0z6l3n2f6h039mzl2kn0wbykd63b3l8"; depends=[Biobase BiocGenerics clue data_table flowClust flowCore flowStats flowViz flowWorkspace graph gtools ks lattice MASS ncdfFlow plyr R_utils RBGL RColorBrewer Rcpp rrcov]; }; + openPrimeR = derive2 { name="openPrimeR"; version="1.4.1"; sha256="0cmixmj1mnalr89c32ih5hf4v73qf4x73hzvbiw0mnz8niizaqgz"; depends=[ape BiocGenerics Biostrings DECIPHER digest distr distrEx dplyr fitdistrplus foreach GenomicRanges ggplot2 Hmisc IRanges lpSolveAPI magrittr openxlsx plyr RColorBrewer reshape2 S4Vectors scales seqinr stringdist stringr tinytex uniqtag XML]; }; + openPrimeRui = derive2 { name="openPrimeRui"; version="1.4.1"; sha256="163a8frs637yvm6vqhi7sxashkbdc61m8mb5lc6n0i98zicmaj4p"; depends=[DT openPrimeR rmarkdown shiny shinyBS shinyjs]; }; + oposSOM = derive2 { name="oposSOM"; version="2.0.0"; sha256="190sg040nxjja0phmw9k81s139756qsnk1pac3cby21ml6hwbr0j"; depends=[ape Biobase biomaRt fastICA fdrtool igraph pixmap Rcpp RcppParallel scatterplot3d tsne]; }; + oppar = derive2 { name="oppar"; version="1.10.0"; sha256="012ypy3z2dgm6ddmbrq3vyyf5yk9ac18gs733s70jv61z2bd1rlw"; depends=[Biobase GSEABase GSVA]; }; + pRoloc = derive2 { name="pRoloc"; version="1.22.0"; sha256="1wqr85igb023bjxg2j2298lk0bd712gx345ypcdywl2infk92viv"; depends=[Biobase BiocGenerics BiocParallel biomaRt caret class coda dendextend e1071 FNN ggplot2 gtools hexbin kernlab knitr LaplacesDemon lattice MASS mclust mixtools MLInterfaces MSnbase mvtnorm nnet plyr proxy randomForest RColorBrewer Rcpp RcppArmadillo sampling scales]; }; + pRolocGUI = derive2 { name="pRolocGUI"; version="1.16.0"; sha256="13z6zd7m7hsjvm52lgy9v8ypkr6gs190c26qs0yzq7s4vfq48db2"; depends=[Biobase dplyr DT ggplot2 MSnbase pRoloc scales shiny]; }; + paircompviz = derive2 { name="paircompviz"; version="1.20.0"; sha256="1iraq8n5q24zz3xdv15wiyhd5avz0yr6hh1mzygypp8bmhkgcixv"; depends=[Rgraphviz]; }; + pandaR = derive2 { name="pandaR"; version="1.14.0"; sha256="0jm5xxxynrh08l0iz0wj7jl120a6vsglppryjhl4mgv7cs5pdx9w"; depends=[Biobase BiocGenerics ggplot2 hexbin igraph matrixStats plyr reshape RUnit]; }; + panelcn_mops = derive2 { name="panelcn.mops"; version="1.4.0"; sha256="1ib6v4zkgj7qc5ncnjgsx0rwb7awbisd64p7zxah175zds33gxph"; depends=[cn_mops GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors]; }; + panp = derive2 { name="panp"; version="1.52.0"; sha256="1vv7i3zykv48s0v4nvxaziixkkdl660166cg9fgvbxb8689c2cw7"; depends=[affy Biobase]; }; + parglms = derive2 { name="parglms"; version="1.14.0"; sha256="0mzd1x8xj6sjjm98dahip663zq3k3bm9jn2j60hsyvr18win2bkx"; depends=[BatchJobs BiocGenerics doParallel foreach]; }; + parody = derive2 { name="parody"; version="1.40.0"; sha256="14rzpmmcdq9j19ydb9qksga6l06zdnb29qn13wjxlbn9l7mbfzy4"; depends=[]; }; + pathRender = derive2 { name="pathRender"; version="1.50.0"; sha256="17q2vs878nmjs1k2f11l66wmkjz8zxy9wbhsyg8aal83yzr65hkc"; depends=[AnnotationDbi cMAP graph RColorBrewer Rgraphviz]; }; + pathVar = derive2 { name="pathVar"; version="1.12.0"; sha256="09ncdyamlhs24yyg7fnb77vchqxpxh6asmj32pxhpvkkkgq106p4"; depends=[data_table EMT ggplot2 gridExtra Matching mclust]; }; + pathifier = derive2 { name="pathifier"; version="1.20.0"; sha256="064q5nbxgyz4hx6h4f92w7vyd77pndmxadwa8cw9y5qzh9g29a5m"; depends=[princurve R_oo]; }; + pathprint = derive2 { name="pathprint"; version="1.12.0"; sha256="06lv35nx0d098idjnlcr5bziilwnpapbbcsdfrwglcibgqis9hzh"; depends=[]; }; + pathview = derive2 { name="pathview"; version="1.22.0"; sha256="13gzl8kvmj3pvi09634kigxch055i5vw6l7b0r0ivnj84ff9y4b7"; depends=[AnnotationDbi graph KEGGgraph KEGGREST org_Hs_eg_db png Rgraphviz XML]; }; + paxtoolsr = derive2 { name="paxtoolsr"; version="1.16.0"; sha256="0sa680x51kcsbmlrb54z8m1qn1pjyzx7k26pni17mfdzaw1q9jki"; depends=[httr igraph jsonlite plyr R_utils readr rJava rjson XML]; }; + pcaExplorer = derive2 { name="pcaExplorer"; version="2.8.0"; sha256="0g26dmzx3h7wlr1zy1vij41vir0zzwgfrdx5w7brrgsfinqvbimi"; depends=[AnnotationDbi biomaRt d3heatmap DESeq2 DT genefilter GenomicRanges ggplot2 ggrepel GO_db GOstats IRanges knitr limma NMF pheatmap plyr rmarkdown S4Vectors scales shiny shinyAce shinyBS shinydashboard SummarizedExperiment threejs tidyr topGO]; }; + pcaGoPromoter = derive2 { name="pcaGoPromoter"; version="1.26.0"; sha256="0rdj9043zdvfh2gwas13i6787kw01m1cr998prgf12n9l107v68s"; depends=[AnnotationDbi Biostrings ellipse]; }; + pcaMethods = derive2 { name="pcaMethods"; version="1.74.0"; sha256="0ik82s9bsdj4a1mmv0a3k6yisa92mxx7maf3dvip1r8gqlm3dyng"; depends=[Biobase BiocGenerics MASS Rcpp]; }; + pcot2 = derive2 { name="pcot2"; version="1.50.0"; sha256="0rj3wd9a917p20kr28cc8si7yjqdh9ddc3n58aih7f96v6qxzq4i"; depends=[amap Biobase]; }; + pcxn = derive2 { name="pcxn"; version="2.4.0"; sha256="0a4hs1rc3p3lx9r188fgfhly60l570qna5ydmkixci5pjvnijv4b"; depends=[pcxnData pheatmap]; }; + pdInfoBuilder = derive2 { name="pdInfoBuilder"; version="1.46.0"; sha256="1fwkfyazqq9i51fq965xvxqmidmnzg9xxfk74abfaz8y0w4jamak"; depends=[affxparser Biobase BiocGenerics Biostrings DBI IRanges oligo oligoClasses RSQLite S4Vectors]; }; + pepStat = derive2 { name="pepStat"; version="1.16.0"; sha256="1msy1wcvp1d2sdddygnqkgzgldgpb6481wj0q0qvb8f2g47lghb7"; depends=[Biobase data_table fields GenomicRanges ggplot2 IRanges limma plyr]; }; + pepXMLTab = derive2 { name="pepXMLTab"; version="1.16.0"; sha256="16g92abqcfwdv7x0bmanizz44g322nyrl15sg9g74j4sp47zamdm"; depends=[XML]; }; + perturbatr = derive2 { name="perturbatr"; version="1.2.0"; sha256="080naijyl2nq8zbvfsrj4vwsw63fw9l4535akddyzh40i5bwpn4a"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; }; + pgca = derive2 { name="pgca"; version="1.6.0"; sha256="1sgwmlbjj52nymcapmid3473qxzg6yxisq304ns2xzi5aq4pxfgb"; depends=[]; }; + phantasus = derive2 { name="phantasus"; version="1.2.1"; sha256="0nd4zfazkbny94s7jnvj8flnxdvhlv4878w0hklf0fnsyzgc9am9"; depends=[assertthat Biobase ccaPP fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix Matrix_utils opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; }; + phenoTest = derive2 { name="phenoTest"; version="1.30.0"; sha256="0m9ginyg2jda48ihkvalzs89xpn3bshnyli26s0mb91hhdjcn55c"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach HTSanalyzeR limma mgcv SNPchip survival xtable]; }; + phenopath = derive2 { name="phenopath"; version="1.6.0"; sha256="01xh4yf2h63p1zgh7a68wl7yyfyg50kixii2bcckvhvlw7ywsq1d"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; }; + philr = derive2 { name="philr"; version="1.8.0"; sha256="171xk27psjhyhb1pw0l6s93vf6clkcs63bzkqx4pfrkwmdw418is"; depends=[ape ggplot2 ggtree phangorn tidyr]; }; + phosphonormalizer = derive2 { name="phosphonormalizer"; version="1.6.0"; sha256="186580zsbbvjz1nck1nrnp81yfyll0rzpbfij127h26ghq49lccc"; depends=[matrixStats plyr]; }; + phyloseq = derive2 { name="phyloseq"; version="1.26.0"; sha256="11k6pibnqj3fdf4bi6628cbygjkm0jlr6l4amzpq1k70qsnpi730"; depends=[ade4 ape Biobase BiocGenerics biomformat Biostrings cluster data_table foreach ggplot2 igraph multtest plyr reshape2 scales vegan]; }; + piano = derive2 { name="piano"; version="1.22.0"; sha256="0fkimnbgmsh3x1r138855glml876al9fbzzz03xw5cybh0rk1ghx"; depends=[Biobase BiocGenerics fgsea gplots igraph marray relations]; }; + pickgene = derive2 { name="pickgene"; version="1.54.0"; sha256="0lsyh1hlpnn7vxqh3ga69qs72wlsrn8hxnzvlv03ga9124kfmnr9"; depends=[MASS]; }; + pint = derive2 { name="pint"; version="1.32.0"; sha256="0ppb7hghv0152qs6zac4i69r0sjckl9hyw8skbb0ksqv785yxpxh"; depends=[dmt Matrix mvtnorm]; }; + pkgDepTools = derive2 { name="pkgDepTools"; version="1.48.0"; sha256="0bsrr3jya1nn694znbsq3zi4h099ak1jsak9fyyccd3icmcmk2x2"; depends=[graph RBGL]; }; + plateCore = derive2 { name="plateCore"; version="1.40.0"; sha256="1z6zyjzvj8igpl87wfxxsabvm0c2h8skgw1fy7hb22dlrsx9bx2w"; depends=[Biobase flowCore flowStats flowViz lattice latticeExtra MASS robustbase]; }; + plethy = derive2 { name="plethy"; version="1.20.0"; sha256="1018bn55hppwrvj6i5yyzy7fscy1w5v616smpghmplbbycxv3gpi"; depends=[Biobase BiocGenerics DBI ggplot2 IRanges plyr RColorBrewer reshape2 RSQLite S4Vectors Streamer]; }; + plgem = derive2 { name="plgem"; version="1.54.0"; sha256="1bwz9pflvk5vyczb3gbb2cl5k7srpzjh64sjcabkjvdcj69jwhn0"; depends=[Biobase MASS]; }; + plier = derive2 { name="plier"; version="1.52.0"; sha256="1xg9c232z3vlaa356g1c7b4ysx2bkck5ywb57kim9d5bgbvbk83p"; depends=[affy Biobase]; }; + plotGrouper = derive2 { name="plotGrouper"; version="1.0.0"; sha256="02xzjsdljy7yvi0cf9qjggsk6s61xqkhfg948d1pc0pzqhc2mrw7"; depends=[colourpicker dplyr egg ggplot2 ggpubr gridExtra gtable Hmisc magrittr readr readxl rlang scales shiny shinythemes stringr tibble tidyr]; }; + plrs = derive2 { name="plrs"; version="1.22.0"; sha256="1xr6z9fdbdj8qyjlr1fw2mx30iqz1bcxcqs7snarc34qdzr088m5"; depends=[Biobase BiocGenerics CGHbase ic_infer marray quadprog Rcsdp]; }; + plw = derive2 { name="plw"; version="1.42.0"; sha256="1kbn1hhqnf2cmqxjvq4whaj4h7i4v7cbcybcspafy4wvmysjsjvd"; depends=[affy MASS]; }; + plyranges = derive2 { name="plyranges"; version="1.2.0"; sha256="12cc8pnlq1rq01dwia0994chflm184mp2yb983lz973fp0kpbhd2"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges IRanges magrittr rlang Rsamtools rtracklayer S4Vectors tidyr tidyselect]; }; + pmm = derive2 { name="pmm"; version="1.14.0"; sha256="1ld7bcw6vphm48k8sy07j3j02pxfz6wiwqbz94jblc93s121b3z7"; depends=[lme4]; }; + podkat = derive2 { name="podkat"; version="1.14.0"; sha256="0df21vdia2zl70niajwqfswbicwb2agarak7dyd7arp29xz9ivvf"; depends=[Biobase BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges Matrix Rcpp Rsamtools]; }; + pogos = derive2 { name="pogos"; version="1.2.0"; sha256="0s1wkagy4fi2mr65frzx890i3i0lmymlb2ygq7cw64b9kq0gihnx"; depends=[ggplot2 httr ontoProc rjson S4Vectors shiny]; }; + polyester = derive2 { name="polyester"; version="1.18.0"; sha256="0acwamzwhqbavv0pxah20230mlanncc71lwbbxwki948j1qvg3rp"; depends=[Biostrings IRanges limma logspline S4Vectors zlibbioc]; }; + powerTCR = derive2 { name="powerTCR"; version="1.2.0"; sha256="16x8kzidv6d2zm61jw47dgr047ijfkm18xddkk70qxgkrqc0gdpa"; depends=[cubature doParallel evmix foreach magrittr purrr tcR truncdist vegan VGAM]; }; + ppiStats = derive2 { name="ppiStats"; version="1.48.0"; sha256="1aclxj5y32rca97qv5gqfgsq2aly35gs12jxbvwikwbw6hwvi6pn"; depends=[Biobase Category graph lattice ppiData RColorBrewer ScISI]; }; + pqsfinder = derive2 { name="pqsfinder"; version="1.10.0"; sha256="0f0q4vcrwghzv9lg9s4zf46b201nr3ny1b1l56xgd1mw5n7p3mqw"; depends=[BH Biostrings GenomicRanges IRanges Rcpp S4Vectors]; }; + prada = derive2 { name="prada"; version="1.58.0"; sha256="005raxhmk17k6k4liiik7msqislr3hm6vdii48bf5kpqk900kzz7"; depends=[Biobase BiocGenerics MASS RColorBrewer rrcov]; }; + prebs = derive2 { name="prebs"; version="1.22.0"; sha256="0bbc15zzcinwl3svf5mggzfck0ivzm4wlm30n18vi882h2j6cqnv"; depends=[affy Biobase GenomeInfoDb GenomicAlignments GenomicRanges IRanges RPA S4Vectors]; }; + predictionet = derive2 { name="predictionet"; version="1.28.0"; sha256="0hhxdvc30pdrpc96i4jvdn4q8gycdlk6hi9p8xdgmfin6pp375rk"; depends=[catnet igraph MASS penalized RBGL]; }; + preprocessCore = derive2 { name="preprocessCore"; version="1.44.0"; sha256="0ijyjqi8mxxf350dhvgp36swwww5ag7ac9a6r6ymihc5syjr4w4j"; depends=[]; }; + primirTSS = derive2 { name="primirTSS"; version="1.0.0"; sha256="0bkysms6qxkcwd839a4l3ksrksfp163xi343yp3i1wgy3fx1yn5q"; depends=[BiocGenerics Biostrings BSgenome_Hsapiens_UCSC_hg38 dplyr GenomicRanges GenomicScores Gviz IRanges JASPAR2018 phastCons100way_UCSC_hg38 purrr R_utils rtracklayer S4Vectors shiny stringr TFBSTools tibble tidyr]; }; + proBAMr = derive2 { name="proBAMr"; version="1.16.0"; sha256="11403f1z77wafpmhi58nl06lrvnpwbnchyyv5hvnwn4wpxax89jq"; depends=[AnnotationDbi Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer]; }; + proFIA = derive2 { name="proFIA"; version="1.8.0"; sha256="107f2lkx3vcjw8x827mzgn8qgc284wpld4d2chz18kgax3lwbk22"; depends=[Biobase BiocParallel minpack_lm missForest pracma ropls xcms]; }; + procoil = derive2 { name="procoil"; version="2.10.0"; sha256="0bv9kq1jsviyxvnclsc47lfjpxwlvsk479bk65zg0qbi397a3cwl"; depends=[Biostrings kebabs S4Vectors]; }; + profileScoreDist = derive2 { name="profileScoreDist"; version="1.10.0"; sha256="0xfnava0bqpsqwzzw5nkwqkcajzacvifd3b2jm3qg5579myjprx4"; depends=[BiocGenerics Rcpp]; }; + progeny = derive2 { name="progeny"; version="1.4.0"; sha256="061d2gszqwzx77dslcijz2jisfd6k49cimjbby7g55y27zgg920z"; depends=[Biobase]; }; + prot2D = derive2 { name="prot2D"; version="1.20.0"; sha256="0ljggyj557zmbf51cgvq3sl42xqgqh3a2wayyd6s8501ww1xk7fg"; depends=[Biobase fdrtool impute limma MASS Mulcom qvalue samr st]; }; + proteinProfiles = derive2 { name="proteinProfiles"; version="1.22.0"; sha256="1jjricjdc9l2lk7m48x3isrzmn8jxsy8x865ijnmqz9zlzgzz8zs"; depends=[]; }; + proteoQC = derive2 { name="proteoQC"; version="1.18.0"; sha256="1jk95lvggcjfnnpcapqiwh0q7h0zyfda9p4aakh4fibz5f1x6r23"; depends=[dplyr ggplot2 MSnbase Nozzle_R1 plotly plyr reshape2 rmarkdown rpx rTANDEM seqinr tidyr VennDiagram XML]; }; + psichomics = derive2 { name="psichomics"; version="1.8.1"; sha256="1y8yzbjv947kccfzgxka2df5zl58n0wndimhvpffyx8r361dj824"; depends=[AnnotationHub cluster colourpicker data_table digest dplyr DT edgeR fastICA fastmatch ggplot2 ggrepel highcharter htmltools httr jsonlite limma miscTools pairsD3 plyr R_utils Rcpp recount shiny shinyBS shinyjs stringr SummarizedExperiment survival XML xtable]; }; + psygenet2r = derive2 { name="psygenet2r"; version="1.14.0"; sha256="11vsh96pmbf4ypyszgz3yqr0y3q7rxxd61hx2xhwy4v82fq8il2f"; depends=[BgeeDB Biobase BiocManager biomaRt ggplot2 GO_db igraph labeling RCurl reshape2 stringr topGO]; }; + puma = derive2 { name="puma"; version="3.24.0"; sha256="1mjl2zkf6kxcadb0pcp157hhq4dgrxzjvs5i5s8mfxx54d7i80ih"; depends=[affy affyio Biobase mclust oligo oligoClasses]; }; + pvac = derive2 { name="pvac"; version="1.30.0"; sha256="0r92vrsbvbmyqajcldnjfnyigq5ppsh3bgm5h1i299sr4q7m85iv"; depends=[affy Biobase]; }; + pvca = derive2 { name="pvca"; version="1.22.0"; sha256="0s45j854parwwp5f173p5m8f58n18fqdn4z4z7x2ap5f733fr483"; depends=[Biobase lme4 Matrix vsn]; }; + pwOmics = derive2 { name="pwOmics"; version="1.14.0"; sha256="0v5gsk82899i98b8kv95mj4qry0j8plbj7qb1qsl5k51hz79i5pz"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics biomaRt data_table GenomicRanges gplots graph igraph rBiopaxParser STRINGdb]; }; + qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.0.2"; sha256="00skq2rxrxcc51j46jqinrrcvx6c9ldshmbxqy0v5l57p5wybf14"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr GenomicRanges ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer statmod stringr tibble tidyr]; }; + qcmetrics = derive2 { name="qcmetrics"; version="1.20.0"; sha256="1wysijshlh0hvpka3im5cfgz7z5k18cy271drrcz58lyzwk424rl"; depends=[Biobase knitr Nozzle_R1 pander S4Vectors xtable]; }; + qpcrNorm = derive2 { name="qpcrNorm"; version="1.40.0"; sha256="0m67a0b3i5nmd2lxx9ga0p6223y9x0bpz2j8gvqzsjnkh4ix1z0g"; depends=[affy Biobase limma]; }; + qpgraph = derive2 { name="qpgraph"; version="2.16.0"; sha256="110krd6sf87qai60qf9ixgkc43i51xvfiqnzdmwk1na2qhda2sp8"; depends=[annotate AnnotationDbi Biobase BiocParallel GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges Matrix mvtnorm qtl Rgraphviz S4Vectors]; }; + qrqc = derive2 { name="qrqc"; version="1.36.0"; sha256="1pdadzlfx5kbsyp79iqxdliilsnhvx1d9j4dj89pl8hgz4n1zyvz"; depends=[Biostrings biovizBase brew ggplot2 plyr reshape Rsamtools testthat xtable]; }; + qsea = derive2 { name="qsea"; version="1.8.0"; sha256="0m6h75fvzg7chi2sasaqrddxgl27qymxim7j7j3wg0gizhm2w59l"; depends=[BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicRanges gtools HMMcopy IRanges limma Rsamtools rtracklayer zoo]; }; + quantro = derive2 { name="quantro"; version="1.16.0"; sha256="1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib"; depends=[Biobase doParallel foreach ggplot2 iterators minfi RColorBrewer]; }; + quantsmooth = derive2 { name="quantsmooth"; version="1.48.0"; sha256="0s7dwf4xkj6ab12ra0ibkn9myif174s476s8nkaz8x8a8yxlzmjn"; depends=[quantreg]; }; + qusage = derive2 { name="qusage"; version="2.16.0"; sha256="0027bg7ri17fv7f1aypg2vlvffbh4c3p4fa3snwgjmiv86d1g51b"; depends=[Biobase limma lsmeans nlme]; }; + qvalue = derive2 { name="qvalue"; version="2.14.0"; sha256="03qxshqwwq1rj23p6pjrz08jm3ziikvy9badi4mz2rcwy2nz783a"; depends=[ggplot2 reshape2]; }; + r3Cseq = derive2 { name="r3Cseq"; version="1.28.0"; sha256="00gx50wlnq3dxybsj8fiwb0qmlyk9f9fddya7wckgs4yjb0y9lv4"; depends=[Biostrings data_table GenomeInfoDb GenomicRanges IRanges qvalue RColorBrewer Rsamtools rtracklayer sqldf VGAM]; }; + rBiopaxParser = derive2 { name="rBiopaxParser"; version="2.22.0"; sha256="1zy72y9wiskwr4nymka3p9cw0zbgg0883422ysiijqkywz5cvawn"; depends=[data_table XML]; }; + rCGH = derive2 { name="rCGH"; version="1.12.0"; sha256="0ydd8685ly3kgvry09d0dc8lm6zl9355361bi7y6ra2v7sz4rvbj"; depends=[aCGH affy AnnotationDbi DNAcopy GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 IRanges lattice limma mclust org_Hs_eg_db plyr shiny TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; }; + rDGIdb = derive2 { name="rDGIdb"; version="1.8.0"; sha256="0rwgcra484hpbch4pxnqa7x0vw5kzabilr308w1f4vdi6ydrz3gk"; depends=[httr jsonlite]; }; + rGADEM = derive2 { name="rGADEM"; version="2.30.0"; sha256="1a3mvxabp7yb275cv1wr0rzyvjhnsaysk2hnmll4z4cci171z2j2"; depends=[Biostrings BSgenome IRanges seqLogo]; }; + rGREAT = derive2 { name="rGREAT"; version="1.14.0"; sha256="0fpi797byvplg73hinsnm07nqgknwb4cbcn0wdw3q178jmksb5j0"; depends=[GenomicRanges GetoptLong IRanges RCurl rjson]; }; + rHVDM = derive2 { name="rHVDM"; version="1.48.0"; sha256="0mf74pi9p7kfl9c2hjkmvfzsdfq7sp6gpbxlinj3k3vlbavpkgyg"; depends=[affy Biobase minpack_lm R2HTML]; }; + rMAT = derive2 { name="rMAT"; version="3.32.0"; sha256="1305v5gsbwvy2z7r0gg4gq48xn9yxgbyk4jpjfxaqza49l5sf283"; depends=[affxparser Biobase BiocGenerics IRanges]; }; + rRDP = derive2 { name="rRDP"; version="1.16.0"; sha256="1idrm7d2rsjnlhfyqf8klihcbg1p8byzsx4kjm3l5f4a64407cd7"; depends=[Biostrings]; }; + rSFFreader = derive2 { name="rSFFreader"; version="0.30.0"; sha256="14x6xdhdavfrz3ylkys3dlzr8hwshc6v43lccvl4lfhc3jq8xhj5"; depends=[Biostrings IRanges S4Vectors ShortRead XVector]; }; + rTANDEM = derive2 { name="rTANDEM"; version="1.22.0"; sha256="1a4rildmvvxd9h5s969sjnf959zkhw6qxq37zxzcpgckx69bb8mm"; depends=[data_table Rcpp XML]; }; + rTRM = derive2 { name="rTRM"; version="1.20.0"; sha256="1alz54x6vxsm7mhsasn1cviad0gbg3vlrzm3m5mf9rj61nlz6zgd"; depends=[AnnotationDbi DBI igraph RSQLite]; }; + rTRMui = derive2 { name="rTRMui"; version="1.20.0"; sha256="09rc2kvcpi7c0b0dmq07byrd5208szwm4nvisdr8xhnhcsxq8f51"; depends=[MotifDb org_Hs_eg_db org_Mm_eg_db rTRM shiny]; }; + rWikiPathways = derive2 { name="rWikiPathways"; version="1.2.0"; sha256="19sndn705580cg6idwnw9rbr92cgl83lv0zbvdaxnrvly22i9242"; depends=[caTools httr RJSONIO]; }; + rain = derive2 { name="rain"; version="1.16.0"; sha256="02grbm9c8q34np24218myzv0zgkq4p37mynpkm6c6xncywijgcsi"; depends=[gmp multtest]; }; + rama = derive2 { name="rama"; version="1.56.0"; sha256="0ns6dczyj8zglrfni1i0sfiqhpcii5h6hdv8yjg0hkm29g2qjzd0"; depends=[]; }; + ramwas = derive2 { name="ramwas"; version="1.6.0"; sha256="19iqh994x28mninyfay6rkjib947w9wjhsz1ac528w9paqjyk0ha"; depends=[BiocGenerics biomaRt Biostrings digest filematrix GenomicAlignments glmnet KernSmooth Rsamtools]; }; + randPack = derive2 { name="randPack"; version="1.28.0"; sha256="03vi35c3mglpiqrkzgnspgxj42bz952ms9bq0cvy5sp6lh9f6l3l"; depends=[Biobase]; }; + rbsurv = derive2 { name="rbsurv"; version="2.40.0"; sha256="08sd8i68zgbbd8anh828yjdl9j19l7m66wdrpqsmgns4n2gwpg80"; depends=[Biobase survival]; }; + rcellminer = derive2 { name="rcellminer"; version="2.4.0"; sha256="1r627fhzzjvjzdj8y0cxr65csj023c1jwl04jnj2i3g2g4pzcicl"; depends=[Biobase fingerprint ggplot2 gplots rcdk rcellminerData shiny stringr]; }; + readat = derive2 { name="readat"; version="1.8.0"; sha256="0sg4dccxkyl7arlfhd0qmq1kx5f1sykvi822ssh0brp8yjj1hx53"; depends=[assertive_base assertive_files assertive_numbers assertive_properties assertive_sets assertive_types Biobase data_table dplyr magrittr openxlsx pathological reshape2 stringi SummarizedExperiment testthat tidyr]; }; + reb = derive2 { name="reb"; version="1.60.0"; sha256="1a62sfl0hw9nqw25b7hv76m9bn5l56d0sin1ii9s4qa2hj67nwxy"; depends=[Biobase idiogram]; }; + recount = derive2 { name="recount"; version="1.8.1"; sha256="1aziihmg3jq3qrkvg39fmx4wawmpdgvcp8f4zxnl6fq1p2p2rfw3"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; }; + recoup = derive2 { name="recoup"; version="1.10.0"; sha256="1vlprf6sv3cq8yvs2xbvnqs5kg60j2mj1hm2a60pax2mx6qzrddz"; depends=[BiocGenerics biomaRt circlize ComplexHeatmap GenomicAlignments GenomicRanges ggplot2 plyr rtracklayer]; }; + regionReport = derive2 { name="regionReport"; version="1.16.1"; sha256="1c4yf6nda4i9h4mapskfnxrrzgv5ic8bkbwyssd650vx840agj99"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitcitations knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; }; + regioneR = derive2 { name="regioneR"; version="1.14.0"; sha256="19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; }; + regsplice = derive2 { name="regsplice"; version="1.8.0"; sha256="122dxmaxs5kvd8baqsc0jsywxyl2wx7g0fvn38xfv9c3q018jb42"; depends=[edgeR glmnet limma pbapply S4Vectors SummarizedExperiment]; }; + restfulSE = derive2 { name="restfulSE"; version="1.4.0"; sha256="0r4f34lg5f3fl4lcfkjx0lqkvdyc07s1pxf29365is9jayaa2v5l"; depends=[AnnotationDbi AnnotationHub bigrquery Biobase DBI DelayedArray dplyr ExperimentHub GO_db magrittr reshape2 rhdf5client rlang S4Vectors SummarizedExperiment]; }; + rexposome = derive2 { name="rexposome"; version="1.4.0"; sha256="1i0c97lfl18s647l36y0wpjd516viysfcybyp6fpkn8j04v7zxg6"; depends=[Biobase circlize corrplot FactoMineR ggplot2 ggrepel glmnet gplots gridExtra gtools Hmisc imputeLCMD lme4 lsr mice pryr reshape2 S4Vectors scales scatterplot3d stringr]; }; + rfPred = derive2 { name="rfPred"; version="1.20.0"; sha256="07fw3y7jsk6yzqsq521r2d7mckyn7b167y9sc9r6zqsixj9g3fa1"; depends=[data_table GenomicRanges IRanges Rsamtools]; }; + rgsepd = derive2 { name="rgsepd"; version="1.14.0"; sha256="1v7bbdwxizy7dbkyid55v8xvpwq6dmrsaw580acllrg7p9f3dfah"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots hash org_Hs_eg_db SummarizedExperiment]; }; + rhdf5 = derive2 { name="rhdf5"; version="2.26.2"; sha256="10zkw3k13wmvyif417gplyf6rwp2gpkjasw97lhwv2f9i32rry9l"; depends=[Rhdf5lib]; }; + rhdf5client = derive2 { name="rhdf5client"; version="1.4.1"; sha256="1pbdwrzwa7r65wkcw821khnvcjy1rbx4vm8rln5srkra5zgmjjhx"; depends=[DelayedArray httr R6 rjson S4Vectors]; }; + riboSeqR = derive2 { name="riboSeqR"; version="1.16.0"; sha256="1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools seqLogo]; }; + rnaSeqMap = derive2 { name="rnaSeqMap"; version="2.40.0"; sha256="0ryc2693zhnsppc2f48hmj0g56acms24g96b97vmkcimddvlp7x3"; depends=[Biobase DBI DESeq edgeR GenomicAlignments GenomicRanges IRanges Rsamtools]; }; + rnaseqcomp = derive2 { name="rnaseqcomp"; version="1.12.0"; sha256="0n4jpd9aqbc14wsi8k1vqhdaz7gp6nn7qr3nk3s783q293rjq1m1"; depends=[RColorBrewer]; }; + roar = derive2 { name="roar"; version="1.18.0"; sha256="15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw"; depends=[BiocGenerics GenomeInfoDb GenomicAlignments GenomicRanges IRanges rtracklayer S4Vectors SummarizedExperiment]; }; + rols = derive2 { name="rols"; version="2.10.0"; sha256="0gfkz6lbgwqsbnhgsilqpbag66p4c5yl8ha0md5za0688krwv11d"; depends=[Biobase BiocGenerics httr jsonlite progress]; }; + ropls = derive2 { name="ropls"; version="1.14.0"; sha256="06rh4j0prsmph4qsp8054yvmvmh5byqnfxw9ab9clabqf7kwxnc4"; depends=[Biobase]; }; + rpx = derive2 { name="rpx"; version="1.18.0"; sha256="1l6r69i6ji8yaa21zdw4idhisf01ixbb1zvm0cf46dqhymgcqlm4"; depends=[RCurl xml2]; }; + rqt = derive2 { name="rqt"; version="1.8.0"; sha256="08kics4hq4y23ydilafylm2rmbnh88hj02rrd5bbl5685as724vn"; depends=[car CompQuadForm glmnet Matrix metap pls ropls RUnit SummarizedExperiment]; }; + rqubic = derive2 { name="rqubic"; version="1.28.0"; sha256="0va7263mxij13qyjmqrv9hxbgxig17hjw1617v0gzrcprs978735"; depends=[biclust Biobase BiocGenerics]; }; + rsbml = derive2 { name="rsbml"; version="2.40.0"; sha256="04brk985cdf6psr8ixkqahg9nmb7lrv1jfy0j1c84l2znskya77f"; depends=[BiocGenerics graph]; }; + rtracklayer = derive2 { name="rtracklayer"; version="1.42.1"; sha256="1ycmcxvgvszvjv75hlmg0i6pq8i7r8720vgmfayb905s9l6j82x6"; depends=[BiocGenerics Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl Rsamtools S4Vectors XML XVector zlibbioc]; }; + runibic = derive2 { name="runibic"; version="1.4.0"; sha256="1s1zbcbfxbchrh8h9602n5gh8ji8zqll9kfd4wg3w3668ckv7vx3"; depends=[biclust Rcpp SummarizedExperiment testthat]; }; + sRAP = derive2 { name="sRAP"; version="1.22.0"; sha256="0qgskdizjh8z15qx4lvrdy5rg7h20hdg454n2wqvpmrk6wvp0ylp"; depends=[gplots pls qvalue ROCR WriteXLS]; }; + sSeq = derive2 { name="sSeq"; version="1.20.0"; sha256="0kqlyaj8cbjh1l7ngpq4xshj4g60dnsfbsrxhj3ijh3ci8iwpp8g"; depends=[caTools RColorBrewer]; }; + safe = derive2 { name="safe"; version="3.22.0"; sha256="0is94jnljq0lsqiyvy91bzkv7xig35q97cjwziszxr9gacizyqay"; depends=[AnnotationDbi Biobase SparseM]; }; + sagenhaft = derive2 { name="sagenhaft"; version="1.52.0"; sha256="0rx7vkm19m18wvyawypp20m1ib7wi8yrmrpj1fg0f15yf9nfiwjg"; depends=[SparseM]; }; + samExploreR = derive2 { name="samExploreR"; version="1.6.0"; sha256="12lhjrbv8b32gwwzmwhm793m1bv7lbma459q5zg1x2ixmqq7aaiv"; depends=[edgeR ggplot2 RNAseqData_HNRNPC_bam_chr14 Rsubread]; }; + sampleClassifier = derive2 { name="sampleClassifier"; version="1.6.0"; sha256="1bq202dmzyiw6ydksm2yb41zj55zrxl0y4b6ph19xjadgs21wy17"; depends=[annotate e1071 ggplot2 MGFM MGFR]; }; + sangerseqR = derive2 { name="sangerseqR"; version="1.18.0"; sha256="1dw3s011w0pir3i9zz3b62qx4frwkw541k569w1qhl0z66qidmgz"; depends=[Biostrings shiny]; }; + sapFinder = derive2 { name="sapFinder"; version="1.20.0"; sha256="14s9iavhw3bjvmpnkmvwvzfgg7gppjlhp908nrhnjhswz9fpiaa0"; depends=[pheatmap Rcpp rTANDEM]; }; + savR = derive2 { name="savR"; version="1.20.0"; sha256="13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"; depends=[ggplot2 gridExtra reshape2 scales XML]; }; + scDD = derive2 { name="scDD"; version="1.6.0"; sha256="12wg94cb5rhlzwhq1lkkmypcwpj57b59s62in1g1n5mrdza5h16d"; depends=[arm BiocParallel EBSeq fields ggplot2 mclust outliers S4Vectors scran SingleCellExperiment SummarizedExperiment]; }; + scFeatureFilter = derive2 { name="scFeatureFilter"; version="1.2.0"; sha256="1bqywn234c5dmqlminkrzl9sj95vh5aw37zl2x5z4jcz0dn812f2"; depends=[dplyr ggplot2 magrittr rlang tibble]; }; + scPipe = derive2 { name="scPipe"; version="1.4.0"; sha256="1qkjfpvl6j385hal7chjh97aaqk2khja430g87h5a2hblqzjqg0v"; depends=[AnnotationDbi BiocGenerics biomaRt dplyr GenomicRanges GGally ggplot2 glue hashmap magrittr MASS mclust org_Hs_eg_db org_Mm_eg_db Rcpp reshape Rhtslib robustbase rtracklayer S4Vectors scales SingleCellExperiment stringr SummarizedExperiment testthat zlibbioc]; }; + scater = derive2 { name="scater"; version="1.10.0"; sha256="1kwa9n70c5j0xcj6nkmlkzjr63cnj78mp8nhg58n07fq1ijm4ns3"; depends=[beachmat BiocGenerics BiocParallel DelayedArray DelayedMatrixStats dplyr ggbeeswarm ggplot2 Matrix plyr Rcpp reshape2 Rhdf5lib S4Vectors SingleCellExperiment SummarizedExperiment viridis]; }; + scde = derive2 { name="scde"; version="2.10.0"; sha256="1h0qvvlzd597a2k4ppxqzj9n8zq9w22cgba2qw7v225azvwalimx"; depends=[BiocParallel Cairo edgeR extRemes flexmix MASS mgcv nnet pcaMethods quantreg RColorBrewer Rcpp RcppArmadillo rjson RMTstat Rook]; }; + scfind = derive2 { name="scfind"; version="1.4.0"; sha256="0g9jx38b7gpv226f4mhhbhikiw4pmy8k014yr3yj10612yc9wpai"; depends=[bit dplyr hash Rcpp reshape2 SingleCellExperiment SummarizedExperiment]; }; + scmap = derive2 { name="scmap"; version="1.4.0"; sha256="1hd2b0dkn2d4wvnxb2cw3kq48d11a06c0d26mgzhfzvsy9cc8qzf"; depends=[Biobase BiocGenerics dplyr e1071 ggplot2 googleVis matrixStats proxy randomForest Rcpp RcppArmadillo reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; }; + scmeth = derive2 { name="scmeth"; version="1.2.1"; sha256="1l5gw0zxy9vhvqqknnaakawbnhzz8rdanw9nkz02qdbqph39vqqw"; depends=[AnnotationHub annotatr Biostrings BSgenome bsseq DelayedArray DT GenomeInfoDb GenomicRanges HDF5Array knitr reshape2 rmarkdown SummarizedExperiment]; }; + scone = derive2 { name="scone"; version="1.6.0"; sha256="1347gwwn8952lf9ham2b77x033wqbb7dlcgdn6pmix3563bdkcw6"; depends=[aroma_light BiocParallel boot class cluster compositions diptest edgeR fpc gplots hexbin limma matrixStats mixtools rARPACK RColorBrewer rhdf5 RUVSeq SummarizedExperiment]; }; + scoreInvHap = derive2 { name="scoreInvHap"; version="1.4.0"; sha256="03d7pny3qkcs279869yry8rkw7js3xyrc8b7p4i7hlpzd44x25a3"; depends=[BiocParallel Biostrings GenomicRanges snpStats SummarizedExperiment VariantAnnotation]; }; + scran = derive2 { name="scran"; version="1.10.1"; sha256="1viyzrwfm9vccsf54c6g7k1dn7skkfx4ml1jy12q67wa20sx8l03"; depends=[beachmat BiocGenerics BiocNeighbors BiocParallel DelayedArray DelayedMatrixStats dynamicTreeCut edgeR igraph limma Matrix Rcpp Rhdf5lib S4Vectors scater SingleCellExperiment statmod SummarizedExperiment]; }; + scruff = derive2 { name="scruff"; version="1.0.1"; sha256="0m7lab7ac1jvp4y092rsyrr4l40gdrqi92khhkq30261f2fm6cf6"; depends=[AnnotationDbi BiocGenerics BiocParallel Biostrings data_table GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 ggthemes plyr refGenome Rsamtools S4Vectors scales ShortRead SingleCellExperiment stringdist SummarizedExperiment]; }; + scsR = derive2 { name="scsR"; version="1.18.0"; sha256="11mf5kv8mk1nlfxd081a7dx1v60yf94cg46b5bjflidp3qhrsi9g"; depends=[BiocGenerics Biostrings ggplot2 hash IRanges plyr RColorBrewer sqldf STRINGdb]; }; + segmentSeq = derive2 { name="segmentSeq"; version="2.16.0"; sha256="0pljd8hn2vxcsh22wmv53a7wkw3cdxpdv8q4ksfj5mvasa2mmkvi"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools S4Vectors ShortRead]; }; + semisup = derive2 { name="semisup"; version="1.6.0"; sha256="0lizf5x3abv4g8j4jxmsbbdiqj4f4gybc3jvw7zz12bd3fsj3c1i"; depends=[SummarizedExperiment VGAM]; }; + seq2pathway = derive2 { name="seq2pathway"; version="1.14.0"; sha256="1zr6z9kgsvlcvb6fw2r39kx4jm3dxlyv7z5l9p0lkdykfnm313y8"; depends=[biomaRt GenomicRanges GSA nnet seq2pathway_data WGCNA]; }; + seqCAT = derive2 { name="seqCAT"; version="1.4.0"; sha256="1g4nh95h9njihxjxga2bnn9bhzmwxd17zk6cjdv3b818zs93h2yr"; depends=[dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges lazyeval S4Vectors scales SummarizedExperiment tidyr VariantAnnotation]; }; + seqCNA = derive2 { name="seqCNA"; version="1.28.0"; sha256="1qf76zslj54g6bxll5bi9kqkph1hb5b1b2yg9qr34ywiq4cw7i8i"; depends=[adehabitatLT doSNOW GLAD seqCNA_annot]; }; + seqLogo = derive2 { name="seqLogo"; version="1.48.0"; sha256="022vr9ydwcivs7rw7kwj73gfk5gc7ckwa1q66vhd4kw9ylh70v68"; depends=[]; }; + seqPattern = derive2 { name="seqPattern"; version="1.14.0"; sha256="0di83qi83mrlw7i12khsq55d03hlazcywaa9m9pki1sfhafpq733"; depends=[Biostrings GenomicRanges IRanges KernSmooth plotrix]; }; + seqTools = derive2 { name="seqTools"; version="1.16.0"; sha256="0dcql2pmgpaa5vin1zzhx472qm90rw962pd3pw32ispn02yw0f2l"; depends=[zlibbioc]; }; + seqbias = derive2 { name="seqbias"; version="1.30.0"; sha256="0jwlwqa1z2scnaqkrz5hmmakrjaajf4dwd875s7pswvacygiy859"; depends=[Biostrings GenomicRanges Rsamtools zlibbioc]; }; + seqcombo = derive2 { name="seqcombo"; version="1.4.1"; sha256="0046www9rl5lswcjn6friijd5plj0p7bfg0y0qzqsz7gqpm3nj58"; depends=[Biostrings cowplot dplyr ggplot2 igraph magrittr rvcheck]; }; + seqplots = derive2 { name="seqplots"; version="1.20.0"; sha256="08aa5ms9rdkca20yzrj4a45q4ns7qc8s068rf8k9xrhkknc8f06h"; depends=[BiocManager Biostrings BSgenome class DBI digest DT fields GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges jsonlite kohonen plotrix RColorBrewer reshape2 Rsamtools RSQLite rtracklayer S4Vectors shiny]; }; + seqsetvis = derive2 { name="seqsetvis"; version="1.2.0"; sha256="0wzgka604d6dgfqxmgqbc99441xnmywfcbnl22mx9r332y1wkasr"; depends=[data_table eulerr GenomicRanges ggplot2 IRanges limma png RColorBrewer Rsamtools rtracklayer S4Vectors]; }; + sesame = derive2 { name="sesame"; version="1.0.0"; sha256="01qxdnpkilxv18fpl3rizxri2l7crs62z8nd7ywhxfm6g4ch5l1z"; depends=[DNAcopy GenomicRanges ggplot2 illuminaio IRanges MASS preprocessCore R6 randomForest S4Vectors sesameData wheatmap]; }; + sevenC = derive2 { name="sevenC"; version="1.2.0"; sha256="1p2xkv0n8hl9s4dlg54wgry73vnnlzylwximhan2ymnp3hgbg4j0"; depends=[BiocGenerics boot data_table GenomeInfoDb GenomicRanges InteractionSet IRanges purrr readr rtracklayer S4Vectors]; }; + sevenbridges = derive2 { name="sevenbridges"; version="1.12.3"; sha256="1cwrqgixm6l83737fsdycqqyrap7xph8xp9m45hpcgh35z4d9r1y"; depends=[curl docopt dplyr httr jsonlite objectProperties S4Vectors stringr uuid yaml]; }; + shinyMethyl = derive2 { name="shinyMethyl"; version="1.18.0"; sha256="0dzg1idkdy4x9h3z5yashrb03ad8ncjxz5j05jlaxx6k4aa7z8j8"; depends=[BiocGenerics IlluminaHumanMethylation450kmanifest matrixStats minfi RColorBrewer shiny]; }; + shinyTANDEM = derive2 { name="shinyTANDEM"; version="1.20.0"; sha256="1asi5v38xfyq58nyamgjqhizylv3k67rx3sv7mgiz8x22b6b4526"; depends=[mixtools rTANDEM shiny xtable]; }; + sigFeature = derive2 { name="sigFeature"; version="1.0.0"; sha256="0kjf4ss0baq4p7nn305szpvpdssagndxjmggdgfm6mfjsgfi5nj1"; depends=[BiocParallel biocViews e1071 Matrix nlme openxlsx pheatmap RColorBrewer SparseM SummarizedExperiment]; }; + sigPathway = derive2 { name="sigPathway"; version="1.50.0"; sha256="0pygrla2q2151981gshzv51jnj60h1df3vby5gsxqvxn2pdr4bv3"; depends=[]; }; + sigaR = derive2 { name="sigaR"; version="1.30.0"; sha256="1vlmd6rqdhz9vzvjidxrq7k9vbbp1c82qspkmdxd9nkycyjjp5cg"; depends=[Biobase CGHbase corpcor igraph limma marray MASS mvtnorm penalized quadprog snowfall]; }; + siggenes = derive2 { name="siggenes"; version="1.56.0"; sha256="0cjlb5r04x15xkhk00i3wvpx21kj0k29pn0mj3whwqk31zznnk1b"; depends=[Biobase multtest]; }; + sights = derive2 { name="sights"; version="1.8.0"; sha256="1yvncmk7hq3ws0c24dmbygi0amprw0n6agy350yzlkcdlis9p0b7"; depends=[ggplot2 lattice MASS qvalue reshape2]; }; + signeR = derive2 { name="signeR"; version="1.8.0"; sha256="1qpaa8ag8lv9s7340fdk3k3qc2jyq4r8268rvxb038zdrv7nzvv4"; depends=[BiocGenerics Biostrings class GenomicRanges nloptr NMF PMCMR Rcpp RcppArmadillo VariantAnnotation]; }; + signet = derive2 { name="signet"; version="1.2.2"; sha256="18v5j9bdpyh1krmbpw6byhyq49cj8msq2mibq50nksmsr648h86z"; depends=[graph igraph RBGL]; }; + sigsquared = derive2 { name="sigsquared"; version="1.14.0"; sha256="1y6h3z5mnww2f26hw4a09qiwpgij89bixf3ak5b253apkwd4bpi9"; depends=[Biobase survival]; }; + similaRpeak = derive2 { name="similaRpeak"; version="1.14.0"; sha256="0wf24nk2vibspqdkgw1a55xhnxs1ygshi548ms0lswkprrqcllg2"; depends=[R6]; }; + simpleaffy = derive2 { name="simpleaffy"; version="2.58.0"; sha256="0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s"; depends=[affy Biobase BiocGenerics gcrma genefilter]; }; + simulatorZ = derive2 { name="simulatorZ"; version="1.16.0"; sha256="19xjhrjwxlpygvv7xs752jsvdnqwzj742jkwzsz2nzwkixkw41hf"; depends=[Biobase BiocGenerics CoxBoost gbm GenomicRanges Hmisc SummarizedExperiment survival]; }; + sincell = derive2 { name="sincell"; version="1.14.0"; sha256="1526qjpbd7rqjjicyii18f2psqqcllbc85i5zrg7r8vx2fmr4p85"; depends=[cluster entropy fastICA fields ggplot2 igraph MASS proxy Rcpp reshape2 Rtsne scatterplot3d statmod TSP]; }; + singleCellTK = derive2 { name="singleCellTK"; version="1.2.3"; sha256="1n0gxrj7wshzxpqwsmsicrhdf4q45afywqdc59yy2fxm440s0w50"; depends=[AnnotationDbi ape Biobase circlize cluster colourpicker ComplexHeatmap data_table DelayedArray DESeq2 DT enrichR ggplot2 ggtree gridExtra GSVA GSVAdata limma MAST matrixStats multtest plotly RColorBrewer reshape2 Rtsne S4Vectors shiny shinyalert shinycssloaders shinyjs SingleCellExperiment SummarizedExperiment sva]; }; + singscore = derive2 { name="singscore"; version="1.2.2"; sha256="0a32k23l26vjgag7vgv21n9vl8qjy6asrq7ms22wiw9lmg2qkyyc"; depends=[Biobase BiocParallel edgeR ggplot2 ggrepel ggsci GSEABase magrittr matrixStats plotly plyr RColorBrewer reshape SummarizedExperiment tidyr]; }; + sizepower = derive2 { name="sizepower"; version="1.52.0"; sha256="082hfzw8348fra6fr1gli5cqjnrg3bgyx28ccy66jzxvrijm2qfl"; depends=[]; }; + skewr = derive2 { name="skewr"; version="1.14.0"; sha256="09132dwp8h3wdrf0agyc0vmby5z7c2hd3px4jrp9vgi2x1849mvn"; depends=[IlluminaHumanMethylation450kmanifest methylumi minfi mixsmsn RColorBrewer S4Vectors wateRmelon]; }; + slalom = derive2 { name="slalom"; version="1.4.0"; sha256="1481kx3xiyl7rzd27dd9mh8jqvnalk54bwbw2yvlvmdrih64p8i4"; depends=[BH ggplot2 GSEABase Rcpp RcppArmadillo rsvd SingleCellExperiment SummarizedExperiment]; }; + slingshot = derive2 { name="slingshot"; version="1.0.0"; sha256="0nrqzsjwyk78cahw21x4i5lqac7h85k6nrq045nq4jmxyc977li3"; depends=[ape clusterExperiment igraph matrixStats princurve rgl SingleCellExperiment SummarizedExperiment]; }; + slinky = derive2 { name="slinky"; version="1.0.0"; sha256="1b4pam8ajcc1zz1gxdz1gcjxrv75b60mwwhhvcfin3g9xfmgnkc3"; depends=[curl dplyr foreach httr jsonlite readr rhdf5 SummarizedExperiment tidyr]; }; + snapCGH = derive2 { name="snapCGH"; version="1.52.0"; sha256="15fx1ryc6ab1aia768wpp8zhggfz2l9vildhkjh8chwaam1qd610"; depends=[aCGH cluster DNAcopy GLAD limma tilingArray]; }; + snm = derive2 { name="snm"; version="1.30.0"; sha256="1qjd7g6c03rygp95cpry1m3yi83lyd57zp94whaymfriz39dx2i9"; depends=[corpcor lme4]; }; + snpStats = derive2 { name="snpStats"; version="1.32.0"; sha256="1pplx4pf9bqi7v5v1l74yknc1s61carvbqkf327ky7vbvp0bck33"; depends=[BiocGenerics Matrix survival zlibbioc]; }; + soGGi = derive2 { name="soGGi"; version="1.14.0"; sha256="0v0hvxadqsmscb8h0zy8xi4336pxha2vj5xk03ms81734jaj6adj"; depends=[BiocGenerics BiocParallel Biostrings chipseq GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges preprocessCore reshape2 Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + sparseDOSSA = derive2 { name="sparseDOSSA"; version="1.6.0"; sha256="05ymzk72h4ff5sr80mcsjkhybvcam3d873hp5a12k2k5xw4ll0l9"; depends=[MASS MCMCpack optparse tmvtnorm]; }; + sparsenetgls = derive2 { name="sparsenetgls"; version="1.0.0"; sha256="1c41fzisd42972kz4wh8vcwxxq00l32ahv5gmsj2qnrqq0j0x01i"; depends=[glmnet huge MASS Matrix parcor]; }; + specL = derive2 { name="specL"; version="1.16.0"; sha256="1dgnnrdmpxwjvf30ayfbvgk905j6da9i32qz2fii0mpm6h5d8imm"; depends=[DBI protViz RSQLite seqinr]; }; + spikeLI = derive2 { name="spikeLI"; version="2.42.0"; sha256="055zbrbh6wf3vvnc9p8px2ffz9wdhdg0h96260r7c72ax3v6wi5g"; depends=[]; }; + spkTools = derive2 { name="spkTools"; version="1.38.0"; sha256="0rm2vlzid3wjm1g1kzmjklga1gcf852aznhxb1xr50v8drivkkz9"; depends=[Biobase gtools RColorBrewer]; }; + splatter = derive2 { name="splatter"; version="1.6.1"; sha256="1kw9shzqwph44q2fksgp79mrjq23j3806clc4xydw3ys2w4kspj8"; depends=[akima BiocGenerics BiocParallel checkmate crayon edgeR fitdistrplus ggplot2 locfit matrixStats scales scater SingleCellExperiment SummarizedExperiment]; }; + spliceSites = derive2 { name="spliceSites"; version="1.30.0"; sha256="1j40awy9irx53d1cdsx52pnxirjrrvgsj9zx5qhl2556ca65l26n"; depends=[Biobase BiocGenerics Biostrings doBy IRanges rbamtools refGenome seqLogo]; }; + splicegear = derive2 { name="splicegear"; version="1.54.0"; sha256="0phpkgjkc4c8lfr8xsciqyz7imsjpc3sxwsh95glxhrsm7i2mnip"; depends=[annotate Biobase XML]; }; + splineTimeR = derive2 { name="splineTimeR"; version="1.10.0"; sha256="15dzhijkhpy7d8hwif59bic83fk6fnyjpp4qi7y7vwq139j6yaj2"; depends=[Biobase FIs GeneNet GSEABase gtools igraph limma longitudinal]; }; + splots = derive2 { name="splots"; version="1.48.0"; sha256="0s10ha17p4yf6id0h0r0a2fk992jp4ah7v8ani689zy6pcc0w34d"; depends=[RColorBrewer]; }; + spotSegmentation = derive2 { name="spotSegmentation"; version="1.56.0"; sha256="06b4dwjll21i13ag5f2si5499gc6h63b5rnlz372pg95idwxsqbh"; depends=[mclust]; }; + srnadiff = derive2 { name="srnadiff"; version="1.2.0"; sha256="09gqa8z9s8md8nrdgff1a252nfw4ssn937rms4cj7k66zdxgwdqc"; depends=[BiocParallel BiocStyle DESeq2 devtools GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges Rcpp Rsamtools rtracklayer S4Vectors SummarizedExperiment]; }; + sscore = derive2 { name="sscore"; version="1.54.0"; sha256="0anpfqvv6as5i28bb0i2h86p51m42ch4gzap5lcxia97lzvxh210"; depends=[affy affyio]; }; + sscu = derive2 { name="sscu"; version="2.12.0"; sha256="0y41krw0r0kmlp32b7cmlwf5qpncha8j357mx9sr3zvm52dphlpp"; depends=[BiocGenerics Biostrings seqinr]; }; + ssize = derive2 { name="ssize"; version="1.56.0"; sha256="13bc5hbnqqxr16pqw0waq29mpgrf4sys4kg63np2a4hpc6l2nrqk"; depends=[gdata xtable]; }; + ssviz = derive2 { name="ssviz"; version="1.16.0"; sha256="1hpvpiainfg382wbm0zz8libs9vfqdi5c1wa17wi75aah1in6c6p"; depends=[Biostrings ggplot2 RColorBrewer reshape Rsamtools]; }; + staRank = derive2 { name="staRank"; version="1.24.0"; sha256="0zbrsbdfca7y87cii5iyipf0g7rn7f3h8blzbn4n1ir8khrl8qs1"; depends=[cellHTS2]; }; + stageR = derive2 { name="stageR"; version="1.4.0"; sha256="063mprdjjvys09cxlgrd930r96i470z30h00pf0h15g5h4w02jak"; depends=[SummarizedExperiment]; }; + statTarget = derive2 { name="statTarget"; version="1.12.0"; sha256="0fxy1s1d9l7jrhj7rs1hvam5r85y608143sb2d17fhm0x77bs78f"; depends=[impute pdist pls plyr randomForest ROC rrcov]; }; + stepNorm = derive2 { name="stepNorm"; version="1.54.0"; sha256="16sn793zj06dh69cwzx3vfjkx4gs3dy6x0apyh01vwhnqkani4vl"; depends=[marray MASS]; }; + strandCheckR = derive2 { name="strandCheckR"; version="1.0.0"; sha256="0pmw6iwynpy6mdfh8mb939100715mpwy458i6w6sw1pjghlykrzq"; depends=[BiocGenerics dplyr GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges magrittr reshape2 Rsamtools S4Vectors stringr TxDb_Hsapiens_UCSC_hg38_knownGene]; }; + subSeq = derive2 { name="subSeq"; version="1.12.0"; sha256="065r2856lrdp43z3lhzr5cp445g7r68yjfxrwxr05dic3yln4fq6"; depends=[Biobase data_table digest dplyr ggplot2 magrittr qvalue tidyr]; }; + supraHex = derive2 { name="supraHex"; version="1.20.0"; sha256="0p27h8xg104ip8lwasvac74hjj9582xc85q06q0n8lr660chfx2b"; depends=[ape hexbin MASS]; }; + survcomp = derive2 { name="survcomp"; version="1.32.0"; sha256="1f6vz8fbifa5lsywxcqdak5gb7fvz6rvds5a7bvdginjy1zindw9"; depends=[bootstrap ipred KernSmooth prodlim rmeta SuppDists survival survivalROC]; }; + sva = derive2 { name="sva"; version="3.30.0"; sha256="1xf0hlrqjxl0y3x13mrkxghiv39fd9v2g8gq3qzbf1wj7il6bph3"; depends=[BiocParallel genefilter limma matrixStats mgcv]; }; + swfdr = derive2 { name="swfdr"; version="1.8.0"; sha256="0hib9mb1yrfl3hqddkqws32ninyc8ylzw8gd4a0sv06l16ks8b4m"; depends=[dplyr ggplot2 reshape2]; }; + switchBox = derive2 { name="switchBox"; version="1.18.0"; sha256="1s49vi0vyh0bmrc6marn69hi9ln12j3kyjkkm2z5fpvv3rvxhgw7"; depends=[gplots pROC]; }; + switchde = derive2 { name="switchde"; version="1.8.0"; sha256="0vcypblf3d3sfsklmk88pdjyinim7vqwbgp0rqgz4whyi9c4m2i3"; depends=[dplyr ggplot2 SingleCellExperiment SummarizedExperiment]; }; + synapter = derive2 { name="synapter"; version="2.6.0"; sha256="0l1lmrn4ilp990675msgs96kcgb3gjwbx9g7jiffaprgs3dpwkgj"; depends=[Biobase Biostrings cleaver knitr lattice MSnbase multtest qvalue RColorBrewer readr rmarkdown]; }; + synergyfinder = derive2 { name="synergyfinder"; version="1.8.0"; sha256="1idc0lnjw8zx6nih1hrzfq9h40zkbdv0iv9si214wx4ynf0w18iv"; depends=[drc ggplot2 gplots gridBase lattice nleqslv reshape2 SpatialExtremes]; }; + synlet = derive2 { name="synlet"; version="1.12.0"; sha256="07rz4jx6n8cmzzp3j0zfah1z0l0r5xd7raclzvwh0gvhg97bqlz8"; depends=[doBy dplyr ggplot2 magrittr RankProd RColorBrewer reshape2]; }; + systemPipeR = derive2 { name="systemPipeR"; version="1.16.0"; sha256="0l26q8zjdmzg84g7f25gv9z60sykybahlpg5bg9bmpbg5lzcsx04"; depends=[annotate BatchJobs BiocGenerics Biostrings DESeq2 edgeR GenomicFeatures GenomicRanges ggplot2 GO_db GOstats limma pheatmap rjson Rsamtools ShortRead SummarizedExperiment VariantAnnotation]; }; + tRNA = derive2 { name="tRNA"; version="1.0.0"; sha256="1kzl79q0zim9y7px0dirk41qay96nl2bz8sw76nx56pr1d5jh245"; depends=[assertive BiocGenerics Biostrings GenomicRanges ggplot2 IRanges S4Vectors scales stringr XVector]; }; + tRNAdbImport = derive2 { name="tRNAdbImport"; version="1.0.0"; sha256="0b6h2xzxyl3kh1h8fijm5l0cqy7364p5l0s604fvhnaxa6n3y1ds"; depends=[assertive Biostrings GenomicRanges httr IRanges S4Vectors stringr tRNA xml2]; }; + tRNAscanImport = derive2 { name="tRNAscanImport"; version="1.2.0"; sha256="1pcnwlxbw2g4398y4q94m6z7xsl492hik4z57xgjcri35y3ma06x"; depends=[assertive BiocGenerics Biostrings GenomeInfoDb GenomicRanges rtracklayer S4Vectors stringr tRNA]; }; + tRanslatome = derive2 { name="tRanslatome"; version="1.20.0"; sha256="0aa2gd1mp5lzp62vl0556i7q761jyi02ls04nw175fbq6381l2vy"; depends=[anota Biobase DESeq edgeR GOSemSim gplots Heatplus limma org_Hs_eg_db plotrix RankProd sigPathway topGO]; }; + tenXplore = derive2 { name="tenXplore"; version="1.4.0"; sha256="1914n0sdx9nvrja6mpx4hm5x9wzp1c1n0v4a43p4xwigj8qvgrvz"; depends=[AnnotationDbi matrixStats ontoProc org_Mm_eg_db restfulSE shiny SummarizedExperiment]; }; + ternarynet = derive2 { name="ternarynet"; version="1.26.0"; sha256="0xar386wy1viks44s2gyiakmvy5d1k2qc422zn74nc0wwgky0jmc"; depends=[igraph]; }; + tigre = derive2 { name="tigre"; version="1.36.0"; sha256="1hyl4d1111bs6bgjpy3dwkfj9yi11r07hwsf2jn4iqcmr9l6g0rz"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; }; + tilingArray = derive2 { name="tilingArray"; version="1.60.0"; sha256="0ak32w49adrrh6xaf20g48xnsxr33d3irng3lbv03y2al812wpha"; depends=[affy Biobase genefilter pixmap RColorBrewer strucchange vsn]; }; + timecourse = derive2 { name="timecourse"; version="1.54.0"; sha256="1cpmcbjwsh2mn4c0bgpvcq5da4cngsznfvz7r6cpma7iivqam1jz"; depends=[Biobase limma marray MASS]; }; + timescape = derive2 { name="timescape"; version="1.6.0"; sha256="0wnk4iwy8ji4xn1cyh257byxfvh5njd9z08hl5f74k1ni94llkp6"; depends=[dplyr gtools htmlwidgets jsonlite stringr]; }; + tkWidgets = derive2 { name="tkWidgets"; version="1.60.0"; sha256="17z04pqys4nhs0c6phffkwj2yw34cajpfbgx70jsd0dba125pzh7"; depends=[DynDoc widgetTools]; }; + tofsims = derive2 { name="tofsims"; version="1.10.0"; sha256="0fxgfvgfpssw160bmbb34xaz3123rxi7wzf9bpiml7yrdvqxk2wd"; depends=[ALS ChemometricsWithR KernSmooth ProtGenerics Rcpp RcppArmadillo signal]; }; + topGO = derive2 { name="topGO"; version="2.34.0"; sha256="1j1jcd16j564kr6qz28140fzmnh9xasi84v1c1fi98sqv30zq9bh"; depends=[AnnotationDbi Biobase BiocGenerics DBI GO_db graph lattice matrixStats SparseM]; }; + topdownr = derive2 { name="topdownr"; version="1.4.0"; sha256="03vpg0f4h8jff6p9p06lp76fiyhhishly023x9aqbjgrr463d6pl"; depends=[Biobase BiocGenerics Biostrings ggplot2 Matrix MSnbase mzR ProtGenerics S4Vectors]; }; + trackViewer = derive2 { name="trackViewer"; version="1.18.0"; sha256="031bamc10gfwdk0vxcrb75yv9qxrk2n5sfwnmsfvbv7n9pdkg7lp"; depends=[AnnotationDbi BiocGenerics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph grImport Gviz htmlwidgets InteractionSet IRanges plotrix Rgraphviz Rsamtools rtracklayer S4Vectors scales]; }; + tracktables = derive2 { name="tracktables"; version="1.16.0"; sha256="160zh73yripvd150jfwm1xpk1amrg1qqjcyl8wwclpss0ks04ayb"; depends=[GenomicRanges IRanges RColorBrewer Rsamtools stringr tractor_base XML XVector]; }; + transcriptR = derive2 { name="transcriptR"; version="1.10.0"; sha256="0hxgh054kfygq9dfaq94sbzbssrd1sarag9ribdvxby7r2r1818s"; depends=[BiocGenerics caret chipseq e1071 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges pROC reshape2 Rsamtools rtracklayer S4Vectors]; }; + transcriptogramer = derive2 { name="transcriptogramer"; version="1.4.1"; sha256="1qd447glnwk3ysxnfjyn5i2smyq79mn6qgsa0klrgr3v1909ib57"; depends=[biomaRt data_table doSNOW foreach ggplot2 igraph limma progress RedeR snow tidyr topGO]; }; + transite = derive2 { name="transite"; version="1.0.1"; sha256="09dwlgysgiyz8svfhfap17q3j7y8nh1bq5grq199dvrrs8ai8k80"; depends=[BiocGenerics Biostrings dplyr GenomicRanges ggplot2 ggseqlogo gridExtra Rcpp scales TFMPvalue]; }; + traseR = derive2 { name="traseR"; version="1.12.0"; sha256="1bf2cblagqkwsc66l9820kb7yh05bk62k0rplnqznnl36i5fw428"; depends=[BSgenome_Hsapiens_UCSC_hg19 GenomicRanges IRanges]; }; + treeio = derive2 { name="treeio"; version="1.6.1"; sha256="013kvbjkc508vmd7qnq1adl5bgw2j9l685fyl2w22hngwixc8qjg"; depends=[ape dplyr jsonlite magrittr rlang rvcheck tibble tidytree]; }; + trena = derive2 { name="trena"; version="1.4.2"; sha256="1rrbkjizc4glp4ql30wn6ijmym4vxl3xda3ffy02maab1vg07mjp"; depends=[AnnotationDbi BiocParallel biomaRt Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 BSgenome_Mmusculus_UCSC_mm10 DBI flare GenomicRanges glmnet lassopv MotifDb org_Hs_eg_db randomForest RMariaDB RPostgreSQL RSQLite SNPlocs_Hsapiens_dbSNP150_GRCh38 vbsr]; }; + triform = derive2 { name="triform"; version="1.24.0"; sha256="12ca24pv1r5vbw3rq345jqg7x3prrbsxk6445zikpzfblwmw0b4s"; depends=[BiocGenerics IRanges yaml]; }; + trigger = derive2 { name="trigger"; version="1.28.0"; sha256="0wi8lk1ld21h1i0i31c858a0sgisg4ak11kyxjmsh9lyhfzayvwq"; depends=[corpcor qtl qvalue sva]; }; + trio = derive2 { name="trio"; version="3.20.0"; sha256="0fz74p4xj19mp2bbrlcrn2gr0yg7hhk0d1a2dy2k2shg7vwr15lj"; depends=[]; }; + triplex = derive2 { name="triplex"; version="1.22.0"; sha256="1fh7446v07bdhj7babj3gjq4n4zk1y7r37fs30r2cgc9lhqyccr9"; depends=[Biostrings GenomicRanges IRanges S4Vectors XVector]; }; + tspair = derive2 { name="tspair"; version="1.40.0"; sha256="1anz7by0hg51ywk9q49xjaqm8agiqdwd6rnf1mp6axph1wjfhkjm"; depends=[Biobase]; }; + tweeDEseq = derive2 { name="tweeDEseq"; version="1.28.0"; sha256="0gygl2pv25ar2psqdb5vdksj8f4d8kqim7wl68lh2ab8mp92cpwd"; depends=[cqn edgeR limma MASS]; }; + twilight = derive2 { name="twilight"; version="1.58.0"; sha256="16vj02kxlfii0r8cdvbd4q6yqm54znn2i0697dmdfmrqbvn9rjky"; depends=[Biobase]; }; + twoddpcr = derive2 { name="twoddpcr"; version="1.6.0"; sha256="1j4xb6y2hnrvaspv7lpirx62801rq0y0gkqdgy87qkphqsf4n44z"; depends=[class ggplot2 hexbin RColorBrewer S4Vectors scales shiny]; }; + tximeta = derive2 { name="tximeta"; version="1.0.1"; sha256="02h2bc5ram7lmhpmv1m3lpir3zs18kp2gpiz9akpg7bf0l628y9d"; depends=[AnnotationDbi BiocFileCache ensembldb GenomeInfoDb GenomicFeatures jsonlite rappdirs S4Vectors SummarizedExperiment tibble tximport]; }; + tximport = derive2 { name="tximport"; version="1.10.0"; sha256="0za2js8hqjgz8ria09cglynffj4w9vrzg85nmn1xgpvmc1xk813h"; depends=[]; }; + uSORT = derive2 { name="uSORT"; version="1.8.0"; sha256="11fn71njy6fphn9by5m41hjhqcwmv223fy0xrwabgy5389c7y9lh"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; }; + unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.18.0"; sha256="110kb1g1kkfgk3nw099wyaww8l2jk3kk41bsz3gmbb2jni9v0ykx"; depends=[BiocGenerics HTqPCR]; }; + universalmotif = derive2 { name="universalmotif"; version="1.0.1"; sha256="0xix65wr4m2vq45kmdkphpzx7mfw43i7xbd5s5da2mz1a0fzcg3k"; depends=[ape BiocGenerics Biostrings ggplot2 ggseqlogo ggtree gtools processx Rcpp Rdpack]; }; + variancePartition = derive2 { name="variancePartition"; version="1.12.0"; sha256="15nryf165w0wjvfjprp3raxz2r7cq8j0jhcldavnr2x5jzc4df49"; depends=[Biobase colorRamps doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS pbkrtest reshape2 scales]; }; + vbmp = derive2 { name="vbmp"; version="1.50.0"; sha256="08iyryhmahmm1p93c0kgvknf9gkd7i4l4jd3b9a234vwx5xy0zx2"; depends=[]; }; + vidger = derive2 { name="vidger"; version="1.2.0"; sha256="1b0r9wm7sibhs34my4zmwhfim0p8iv7izjv4hp1mlyxsjk30bp7a"; depends=[Biobase DESeq2 edgeR GGally ggplot2 ggrepel knitr RColorBrewer rmarkdown scales SummarizedExperiment tidyr]; }; + viper = derive2 { name="viper"; version="1.16.0"; sha256="0pi9s37xw03pkqmsyqnigzfjmq9llk0gwh92ply07mbppldssrwc"; depends=[Biobase e1071 KernSmooth mixtools]; }; + vsn = derive2 { name="vsn"; version="3.50.0"; sha256="1g6qkpykw99jm2wv2i61dg2ffwk0n8fm4s5pm2q4c024vw5c9b69"; depends=[affy Biobase ggplot2 lattice limma]; }; + vtpnet = derive2 { name="vtpnet"; version="0.22.0"; sha256="03f96286lvhy7wlpi39awf5fjx1b40jzjp5mslfgpwx9gvk0kzdw"; depends=[doParallel foreach GenomicRanges graph gwascat]; }; + vulcan = derive2 { name="vulcan"; version="1.4.0"; sha256="0w9cmfn7m2yn98jrgf1ixkchd2jmfinpbxhcycdfmq2yihla3l3v"; depends=[Biobase caTools ChIPpeakAnno csaw DESeq DiffBind GenomicRanges gplots locfit S4Vectors TxDb_Hsapiens_UCSC_hg19_knownGene viper wordcloud zoo]; }; + wateRmelon = derive2 { name="wateRmelon"; version="1.26.0"; sha256="0ymchg3nk89dm92hqksq7cmvwr2a7fxr7z4ymfigj6ifw2r4575s"; depends=[Biobase IlluminaHumanMethylation450kanno_ilmn12_hg19 illuminaio limma lumi matrixStats methylumi ROC]; }; + wavClusteR = derive2 { name="wavClusteR"; version="2.16.0"; sha256="1vzikjs86p0gw0xhcygjv3c5adyyvqnys6g9xqd6519zzp14v4hs"; depends=[BiocGenerics Biostrings foreach GenomicFeatures GenomicRanges ggplot2 Hmisc IRanges mclust Rsamtools rtracklayer S4Vectors seqinr stringr wmtsa]; }; + waveTiling = derive2 { name="waveTiling"; version="1.24.0"; sha256="023d329nk0w7wm8zplhqw7qwc8jwlscxkf8kbafjljrzpzwvh8an"; depends=[affy Biobase Biostrings GenomeGraphs GenomicRanges IRanges oligo oligoClasses preprocessCore waveslim]; }; + weaver = derive2 { name="weaver"; version="1.48.0"; sha256="1hys2gjr353lb798anamfg6mhv8hadh90qs9sc99zi96ps6c24hf"; depends=[codetools digest]; }; + webbioc = derive2 { name="webbioc"; version="1.54.0"; sha256="16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi"; depends=[affy annaffy Biobase BiocManager gcrma multtest qvalue vsn]; }; + widgetTools = derive2 { name="widgetTools"; version="1.60.0"; sha256="0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf"; depends=[]; }; + wiggleplotr = derive2 { name="wiggleplotr"; version="1.6.0"; sha256="1xbn8ifqbb19ba9x3m6ir1ajqq890mv8jwfbm62zgdr1crs572fg"; depends=[assertthat cowplot dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges purrr rtracklayer S4Vectors]; }; + xcms = derive2 { name="xcms"; version="3.4.1"; sha256="1gmmnmxnzzzn502zcav4najxb9bd4fhk3d53bfgjvkibbnxyikl9"; depends=[Biobase BiocGenerics BiocParallel lattice MassSpecWavelet MSnbase multtest mzR plyr ProtGenerics RANN RColorBrewer robustbase S4Vectors]; }; + xmapbridge = derive2 { name="xmapbridge"; version="1.40.0"; sha256="1a93vxrv9brfwv64wpiriwak1chlz6rg25dhcb9hyk2b8j8ky3ag"; depends=[]; }; + xps = derive2 { name="xps"; version="1.42.0"; sha256="0x391j5rlihp64k5wslghlrw6vi4xwwjphskvl1k3iffda5yqknb"; depends=[]; }; + yamss = derive2 { name="yamss"; version="1.8.1"; sha256="13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9"; depends=[BiocGenerics data_table EBImage IRanges limma Matrix mzR S4Vectors SummarizedExperiment]; }; + yaqcaffy = derive2 { name="yaqcaffy"; version="1.42.0"; sha256="192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk"; depends=[simpleaffy]; }; + yarn = derive2 { name="yarn"; version="1.8.0"; sha256="1vy8ilnp62bckq587ls42mp1lhkxq9if2l7jlqh12a8bf1848mrg"; depends=[Biobase biomaRt downloader edgeR gplots limma matrixStats preprocessCore quantro RColorBrewer readr]; }; + zFPKM = derive2 { name="zFPKM"; version="1.4.0"; sha256="12g9q9yxyrjldlhr6n7g66n8mlflvhfyadb8sc1qdwp9y6prvxbk"; depends=[checkmate dplyr ggplot2 SummarizedExperiment tidyr]; }; + zinbwave = derive2 { name="zinbwave"; version="1.4.0"; sha256="1w5j8f4py6yfalihkzbssy6rk5kdm2gkhpghnz9wlsczbvh6cnh8"; depends=[BiocParallel copula edgeR genefilter glmnet Matrix SingleCellExperiment softImpute SummarizedExperiment]; }; + zlibbioc = derive2 { name="zlibbioc"; version="1.28.0"; sha256="0bjvzy24kab7ank02cc1qk2ikcz4dllgf66wpsdl0d3zp4gn3l2h"; depends=[]; }; } diff --git a/pkgs/development/r-modules/cran-packages.nix b/pkgs/development/r-modules/cran-packages.nix index 7d988014da49..6d3a455ca5fc 100644 --- a/pkgs/development/r-modules/cran-packages.nix +++ b/pkgs/development/r-modules/cran-packages.nix @@ -4,7 +4,7 @@ # Rscript generate-r-packages.R cran >new && mv new cran-packages.nix { self, derive }: -let derive2 = derive { snapshot = "2018-12-11"; }; +let derive2 = derive { snapshot = "2019-01-03"; }; in with self; { A3 = derive2 { name="A3"; version="1.0.0"; sha256="017hq9pjsv1h9i7cqk5cfx27as54shlhdsdvr6jkhb8jfkpdb6cw"; depends=[pbapply xtable]; }; ABC_RAP = derive2 { name="ABC.RAP"; version="0.9.0"; sha256="1kdspln17v0krvahcd55vib4dv5azp60b3r1zf489x10qqbp1mxk"; depends=[]; }; @@ -32,7 +32,7 @@ in with self; { ADPF = derive2 { name="ADPF"; version="0.0.1"; sha256="1n7302xx77ngvp9i2h582i1mqslzllcdr0bn3pl2zk9jd8k97p7n"; depends=[]; }; ADPclust = derive2 { name="ADPclust"; version="0.7"; sha256="0s47cpsjykn7imsssa9w9b6g9d1sz2yah78yqzxmh0i3lqd757c1"; depends=[cluster dplyr fields knitr]; }; AEDForecasting = derive2 { name="AEDForecasting"; version="0.20.0"; sha256="16q2sn5zzvysyy3r32jnr21pbdkkn0k0sbarni6fdkx7pj27yijn"; depends=[changepoint forecast signal]; }; - AER = derive2 { name="AER"; version="1.2-5"; sha256="0qksj91h1c5kaci0w7q1n6780669di146ll5wnbjppnkz57z237g"; depends=[car Formula lmtest sandwich survival zoo]; }; + AER = derive2 { name="AER"; version="1.2-6"; sha256="0x4l8ridghxlqjvq5wyv34yvy8mj5bzjrw9cik7f069q4lnklg35"; depends=[car Formula lmtest sandwich survival zoo]; }; AF = derive2 { name="AF"; version="0.1.4"; sha256="1ych5b2bin65lk415l8rhql2cpma3djnxvdi8ja1hgd9absm7j04"; depends=[data_table drgee stdReg survival]; }; AFM = derive2 { name="AFM"; version="1.2.4"; sha256="12k0rx7mi45anyg31gbi8ni9jrfh6asp3cbpwvbhl6kv7ypip9ww"; depends=[data_table dbscan fftwtools fractaldim ggplot2 gridExtra gstat igraph mixtools moments plyr png pracma rgl scales shiny shinyjs sp stringr]; }; AGD = derive2 { name="AGD"; version="0.39"; sha256="0hmq684snnffc2v7vmns4ky200a6zh1ggiap03n5cvpb3nlqc6lr"; depends=[gamlss gamlss_dist]; }; @@ -62,7 +62,7 @@ in with self; { AMOEBA = derive2 { name="AMOEBA"; version="1.1"; sha256="1npzh3rpfnxd4r1pj1hm214sfgbw4wmq4ws093lnl7pvsl0q37xn"; depends=[rlecuyer snowfall spdep]; }; AMORE = derive2 { name="AMORE"; version="0.2-15"; sha256="00zfqcsah2353mrhqkv8bbh24l8gaxk4y78icr9kxy4pqb2988yz"; depends=[]; }; AMR = derive2 { name="AMR"; version="0.5.0"; sha256="1y1fnbxmrfz04y4lfqszav0m1nr4szqrmpz1a2gbri0c1hqfwygf"; depends=[backports crayon curl data_table dplyr hms knitr rlang rvest tidyr xml2]; }; - ANN2 = derive2 { name="ANN2"; version="1.5"; sha256="17b0dv1dl4kni7yvrrwk65cadk6f7qk7505r27j9v530pffyv1k3"; depends=[Rcpp RcppArmadillo robustbase]; }; + ANN2 = derive2 { name="ANN2"; version="2.0"; sha256="16g8v16q48qp71wm92asm8c5lw692s3y8ancb1w57r77zgvrj17g"; depends=[ggplot2 Rcereal Rcpp RcppArmadillo reshape2 viridisLite]; }; ANOM = derive2 { name="ANOM"; version="0.5"; sha256="14nfy9xplbabfprwxz5fvx26nmqhp657vr6d90dc8vk8ds63ckiz"; depends=[ggplot2 MCPAN multcomp nparcomp SimComp]; }; ANOVA_TFNs = derive2 { name="ANOVA.TFNs"; version="1.0"; sha256="0dwspvxj2gzyvxsd9xyhv47n1hjlqa7z9qza4h3hn1xda12vkjly"; depends=[FuzzyNumbers]; }; ANOVAreplication = derive2 { name="ANOVAreplication"; version="1.1.3"; sha256="1cmps21lrmk6lh6gx0q9fz2736q7cibfcisvir6hnik3ablv70bn"; depends=[quadprog shiny]; }; @@ -111,6 +111,7 @@ in with self; { Actigraphy = derive2 { name="Actigraphy"; version="1.3.2"; sha256="0y0ccmxhdfhdmi4k6pbfvnqknkqbgvfsf2qf7z7rc4xpfgym6574"; depends=[fda SDMTools]; }; ActisoftR = derive2 { name="ActisoftR"; version="0.0.2"; sha256="07nq31r71kg94zlyzshcnsfl99cc3x03fw5q8qgsfkpc92ridikr"; depends=[data_table dplyr ggplot2 lubridate magrittr RColorBrewer scales tibble tidyr]; }; ActiveDriver = derive2 { name="ActiveDriver"; version="1.0.0"; sha256="10c7ga48fwvpd5mc4dqiyw4kc2l0iz5qn4hg7xk15r1qmm5rsipa"; depends=[MASS]; }; + ActivityIndex = derive2 { name="ActivityIndex"; version="0.3.6"; sha256="14k6d78s15j7kb7jhixf4msrdjdl28d0r264cbvy41p8dkq7ysvk"; depends=[data_table matrixStats R_utils]; }; AcuityView = derive2 { name="AcuityView"; version="0.1"; sha256="0f0iclmnwdc8ixiiai4svk4x1g3pjy7dhm3cm58fv6ckx12d3d2l"; depends=[fftwtools imager plotrix]; }; AdMit = derive2 { name="AdMit"; version="2.1.3"; sha256="150zjxl56axhpgm25hzyhwwc5g77pkgi291d2v56zbjjqycfz2v8"; depends=[mvtnorm]; }; AdaSampling = derive2 { name="AdaSampling"; version="1.1"; sha256="1n3kcxmhzllnj2cac5jx400k85n20dgjmgma9r6wva43j49sag05"; depends=[caret class e1071 MASS]; }; @@ -124,7 +125,8 @@ in with self; { AdhereR = derive2 { name="AdhereR"; version="0.3.1"; sha256="1yggn5bmdblr7d5gy9as1jv9vvis37rcad72w2w4dhm6clfchx79"; depends=[data_table lubridate manipulate shiny]; }; AdjBQR = derive2 { name="AdjBQR"; version="1.0"; sha256="14437pyz9v09ighwqvy1lcw0vfp2gaqzs9nzrb1gkfbb8ndzjw7k"; depends=[coda MHadaptive quantreg survival]; }; AdvBinomApps = derive2 { name="AdvBinomApps"; version="1.0"; sha256="1cnmn6c2dyl8qfl7g5sqwbjb52psqxzrj1mbm06zak2y1j7j8f49"; depends=[GenBinomApps rootSolve]; }; - AdvDif4 = derive2 { name="AdvDif4"; version="0.3.18"; sha256="0a7yjz9qsyacwb620pcgax9dxmr1qy7a0vypsr5dw2baxm9y4k6z"; depends=[]; }; + AdvDif4 = derive2 { name="AdvDif4"; version="0.4.18"; sha256="1zcia5n8vb01j6m2hjh5jviyqpzk5f1zk69fryy8jlf5ammmr34f"; depends=[]; }; + AeRobiology = derive2 { name="AeRobiology"; version="1.0.0"; sha256="0mbbm4x9l3wr0lam818xxy7gxm0iqlcvr1lkpiz7x7dfwsdxk62a"; depends=[circular devtools dplyr ggplot2 ggvis imager lubridate plotly plyr reshape2 scales tidyr writexl zoo]; }; AggregateR = derive2 { name="AggregateR"; version="0.0.2"; sha256="15gxzs3baa6f1rqwv7s7k6zybx0za1mpzc7db1n47jy9rbh2yxb2"; depends=[dummy]; }; AgreementInterval = derive2 { name="AgreementInterval"; version="0.1.1"; sha256="1bvinzylvsaipa8mq15f45b6h37znavlrdl0rbrx1pqw52r7z8kv"; depends=[psych]; }; AhoCorasickTrie = derive2 { name="AhoCorasickTrie"; version="0.1.0"; sha256="0k2lcyxfsavis9g1g5293f0mw7f6jakkr11wkkjvxdlnba9c80r8"; depends=[Rcpp]; }; @@ -164,7 +166,7 @@ in with self; { ArCo = derive2 { name="ArCo"; version="0.3-1"; sha256="1afjdmcalx3m19jlvqs83fg5qlds59l5zzg3pzk13qk31r0hz7mk"; depends=[boot glmnet Matrix]; }; ArDec = derive2 { name="ArDec"; version="2.0"; sha256="14niggcq7xlvpdhxhy8j870gb11cpk4rwn9gwsfmcfvh49g58i80"; depends=[]; }; ArchaeoChron = derive2 { name="ArchaeoChron"; version="0.1"; sha256="1qma2432mm73h72g9ah1k02wlcb6yrhc6mpai9nj7v58s126ffxn"; depends=[ArchaeoPhases Bchron coda rjags]; }; - ArchaeoPhases = derive2 { name="ArchaeoPhases"; version="1.3"; sha256="0012rjbk3bxf6j7p0skp02yrgqzl903dclnmm7c038f941krjcfq"; depends=[coda DT ggalt ggplot2 ggthemes hdrcde readr shiny shinythemes toOrdinal]; }; + ArchaeoPhases = derive2 { name="ArchaeoPhases"; version="1.4"; sha256="1wdr72w0qfh165v5prgxx0py7344v8rw03rhnh7pi5rwd5nyxvhv"; depends=[coda DT ggalt ggplot2 ggthemes hdrcde readr shiny shinythemes toOrdinal]; }; ArfimaMLM = derive2 { name="ArfimaMLM"; version="1.3"; sha256="0s5igf703zzvagsbdxf5yv4gn0vdq51b7fvbc8xkgvlmv91yy372"; depends=[fracdiff fractal lme4]; }; ArgumentCheck = derive2 { name="ArgumentCheck"; version="0.10.2"; sha256="0mgx7mzbg2wynixcf9hvs0i9p4zka7c3chrfvjmvvvwwgsy24hkc"; depends=[]; }; Arothron = derive2 { name="Arothron"; version="1.0.2"; sha256="1nfdy0gwxm0xw0lp6245zz0ma481yf0yw4giisqpkkkg56snjjmx"; depends=[compositions doParallel foreach geometry Morpho rgl Rvcg stringr vegan]; }; @@ -186,8 +188,11 @@ in with self; { AutoStepwiseGLM = derive2 { name="AutoStepwiseGLM"; version="0.2.0"; sha256="0wwi8hg2q1zkf28rq7bj0f9fcxc5hj59hkmk0gl9p8i3rghlyrms"; depends=[caret formula_tools]; }; Autoplotprotein = derive2 { name="Autoplotprotein"; version="1.1"; sha256="13mxqmhhdiq7mz4m6nx39dsq7x3bm8fsgskswx48vsq6x2k6byxa"; depends=[ade4 plotrix plyr seqinr XML]; }; AutoregressionMDE = derive2 { name="AutoregressionMDE"; version="1.0"; sha256="1dmg0q4sp2d2anzhw2my8xjhpyjsx0kf7r202q5bkw8yr57jnhvr"; depends=[]; }; + AzureContainers = derive2 { name="AzureContainers"; version="1.0.0"; sha256="01x0w4lr2ixjnid1l54czgfq2cfzcjcmhsyhqjl7n6aar16mkmdd"; depends=[AzureRMR httr openssl R6]; }; AzureML = derive2 { name="AzureML"; version="0.2.14"; sha256="1jhlbgfm3mr772hdkfi8jbv5lw8a08yb49sqaa14m1nz4ar9rckv"; depends=[base64enc codetools curl foreign jsonlite miniCRAN uuid]; }; AzureRMR = derive2 { name="AzureRMR"; version="1.0.0"; sha256="1ak7xjy2mwzffhyzf6x3v9lv5h1y2aqvg43wjywyqpwisni3fad7"; depends=[httr jsonlite R6]; }; + AzureStor = derive2 { name="AzureStor"; version="1.0.0"; sha256="1h448psnw2545dlc7pzs9csf4vba1hd69mvnaflg2vf6lx9iz4ih"; depends=[AzureRMR httr mime openssl R6 xml2]; }; + AzureVM = derive2 { name="AzureVM"; version="1.0.0"; sha256="0gx3qvml07siz3x81xlbax3wqnwffpjxhdv1i5cnb2w4vccxsg3b"; depends=[AzureRMR R6]; }; B2Z = derive2 { name="B2Z"; version="1.4"; sha256="0w7394vs883vb32gs6yhrc1kh5406rs851yb2gs8hqzxad1alvpn"; depends=[coda mvtnorm numDeriv]; }; BACA = derive2 { name="BACA"; version="1.3"; sha256="1vbip7wbzix1s2izbm4058wmwar7w5rv3q8bmj9pm7hcapfi19k0"; depends=[ggplot2 RDAVIDWebService rJava]; }; BACCO = derive2 { name="BACCO"; version="2.0-9"; sha256="0i1dnk0g3miyv3b60rzgjjm60180wxzv6v2q477r71q74b0v0r1y"; depends=[approximator calibrator emulator]; }; @@ -250,7 +255,7 @@ in with self; { BHTSpack = derive2 { name="BHTSpack"; version="0.5"; sha256="1sz99sgxhiajxca5bx2ns9g9qs9ymsvh8i5882nlp7c78qxmqc4g"; depends=[R2HTML xtable]; }; BICORN = derive2 { name="BICORN"; version="0.1.0"; sha256="0mqk8vgp6jdk7f0paa06yqlibkd1y3vs69pg7i9mkvxmda7p4nkq"; depends=[]; }; BIEN = derive2 { name="BIEN"; version="1.2.3"; sha256="0p23kahba55gkk6wx10ii6vrni3b7ia2a4jb64ww4kwp86bknx3d"; depends=[ape DBI rgdal rgeos RPostgreSQL sp]; }; - BIFIEsurvey = derive2 { name="BIFIEsurvey"; version="2.191-12"; sha256="13my1yz7q40fg79m1klfqi0ngbfmkj0k6p8a1fvzl11xcwiszn44"; depends=[miceadds mitools Rcpp RcppArmadillo survey TAM]; }; + BIFIEsurvey = derive2 { name="BIFIEsurvey"; version="3.0-14"; sha256="14d9pab2wafg0r7i2p3jk0shlfs4cqkp15kipspvbbnvds8pqgbg"; depends=[miceadds mitools Rcpp RcppArmadillo survey TAM]; }; BIGDAWG = derive2 { name="BIGDAWG"; version="2.1"; sha256="0zvy5sl94qi20gdrnxb2lmadfy7p0wqfngjsf6jc2cgwyzk4gnrj"; depends=[haplo_stats httr knitr rmarkdown XML]; }; BIGL = derive2 { name="BIGL"; version="1.2.3"; sha256="0r1la9bxczblpcmr09drp5740bclxzi7zp0nl7hgd2h4chc40iq4"; depends=[ggplot2 MASS minpack_lm numDeriv progress rgl robustbase scales]; }; BINCOR = derive2 { name="BINCOR"; version="0.2.0"; sha256="0x2s82jql429shk70bhjdy9kamz8dz5ymsxj6kp8ga1711bpwyq6"; depends=[pracma]; }; @@ -300,6 +305,7 @@ in with self; { BSagri = derive2 { name="BSagri"; version="0.1-10"; sha256="096l2ilr4x2fbjxchkksxkbiyaf7wwdmzn4xyjx001w873x9dgf6"; depends=[boot gamlss MCPAN mratios multcomp mvtnorm]; }; BSquare = derive2 { name="BSquare"; version="1.1"; sha256="1s16307m5gj60nv4m652iisyqi3jw5pmnvar6f52rw1sypfp5n49"; depends=[quadprog quantreg VGAM]; }; BTLLasso = derive2 { name="BTLLasso"; version="0.1-7"; sha256="1lhi3dlg37g4r7nrj46w1yc8jkrzi9159ansapnqdi15jrjpx9p9"; depends=[Matrix psychotools Rcpp RcppArmadillo stringr TeachingDemos]; }; + BTM = derive2 { name="BTM"; version="0.2"; sha256="0cd9yjfip05l3bgp8qvflnaggwl4pw7p9jbj3pflqan8f9gpma5x"; depends=[Rcpp]; }; BTR = derive2 { name="BTR"; version="1.2.4"; sha256="0vf71a36id6zgx0phb0kyry7y9xcdhnincxh3fryzhdigxkahg4h"; depends=[diptest doParallel entropy foreach igraph infotheo poweRlaw Rcpp]; }; BTSPAS = derive2 { name="BTSPAS"; version="2014.0901"; sha256="0ankkhm38rvq06g0jnbvjbja4jv8lg21dsc0rxsy174b1i6vjhwi"; depends=[actuar coda ggplot2 plyr R2OpenBUGS rjags]; }; BTYD = derive2 { name="BTYD"; version="2.4"; sha256="13szcsgsrd7mwc4f47xrfrmsm2sg5sf7pfm21ly4cbvqcz8m0147"; depends=[hypergeo Matrix]; }; @@ -311,14 +317,14 @@ in with self; { BWStest = derive2 { name="BWStest"; version="0.2.2"; sha256="02amzlfprmw5pyis0dg0kg0x8xqh50a4vfdcxxmklrzik3b1vzzs"; depends=[memoise Rcpp]; }; BaBooN = derive2 { name="BaBooN"; version="0.2-0"; sha256="145q2kabjks2ql3m48sfjis5y35l8rcqnr5s176viv9yhfafn351"; depends=[coda Hmisc MASS nnet Rcpp RcppArmadillo]; }; BaM = derive2 { name="BaM"; version="1.0.1"; sha256="0y8m6mhghlrp379swj9cfrzqcdr3a7y29mx4d6zld4is00wdw16b"; depends=[coda dlm MASS mice nnet]; }; - BaMORC = derive2 { name="BaMORC"; version="1.0"; sha256="1slwawpsqgqd1705inbzyiwx9vlr58k556lw1f952n0hz204f58i"; depends=[BMRBr data_table DEoptim devtools docopt httr jsonlite RBMRB readr stringr tidyr]; }; + BaMORC = derive2 { name="BaMORC"; version="1.0.1"; sha256="133j1rhfvsq1qxr7hxp7gfarbj8lfimirr73gyyrpfkq1vjxmhc9"; depends=[BMRBr data_table DEoptim devtools docopt httr jsonlite RBMRB readr stringr tidyr]; }; BaPreStoPro = derive2 { name="BaPreStoPro"; version="0.1"; sha256="0zyyyrr5h8dhjsmgaii8jmb8ignvixpc9nzbfishw9yymjswvm57"; depends=[]; }; BaSTA = derive2 { name="BaSTA"; version="1.9.4"; sha256="1j092gsdip7rpw0g74ha0kjsrqpp5swi7wd4sxlmx6zarcqnxlal"; depends=[snowfall]; }; BaTFLED3D = derive2 { name="BaTFLED3D"; version="0.2.11"; sha256="0gab9iz1ra72hw8j31n97ysyr3cclhgvdxriyjk8wwv2nrmbw12h"; depends=[foreach iterators R6 RColorBrewer rTensor]; }; BacArena = derive2 { name="BacArena"; version="1.7"; sha256="137n3nyz68v912c5nhq1qslgifb7k797f5sz567smhimzjhx842f"; depends=[deSolve ggplot2 glpkAPI igraph Matrix plyr Rcpp RcppArmadillo RcppEigen ReacTran reshape2 sybil]; }; BalanceCheck = derive2 { name="BalanceCheck"; version="0.1"; sha256="09mkssic173glgcn592cb6zmz80kndggqc4hc800f91xnfql0332"; depends=[ade4 mvtnorm]; }; BalancedSampling = derive2 { name="BalancedSampling"; version="1.5.4"; sha256="01vnq8n0w9h7p5xpvfdhipdqcj82in0zhj61kvcmz7jx9grx22vi"; depends=[Rcpp SamplingBigData]; }; - Ball = derive2 { name="Ball"; version="1.3.6"; sha256="184jbprl497lmhwhaaw7zm21dqa3pg4ch3w07536fmcr092bx2f0"; depends=[gam mvtnorm survival]; }; + Ball = derive2 { name="Ball"; version="1.3.7"; sha256="0bf19zvcylx6rjql59gcc561rzj040c4jbi5blz9lykh1fg0z1km"; depends=[gam mvtnorm survival]; }; BarBorGradient = derive2 { name="BarBorGradient"; version="1.0.5"; sha256="0g2g7hrm23as1xbj79g48r8sj3gsj66fmi895jqlqfbqrl2fl7a5"; depends=[]; }; BarcodingR = derive2 { name="BarcodingR"; version="1.0-2"; sha256="1mn5rdax8v1s2z3apk9z0kzy4hw19m8ql6j91l6wd29g2n2bjqxx"; depends=[ape class nnet sp]; }; Barnard = derive2 { name="Barnard"; version="1.8"; sha256="1ki58hjs5kpmp76kwj1qi6hwmdvjphqb1lvrlhnmkgqxg4hw4vqg"; depends=[]; }; @@ -465,6 +471,7 @@ in with self; { Brq = derive2 { name="Brq"; version="2.1"; sha256="0my9sb0761nq1ivx31k7nwpg8xidqvd0zv3lan57hnsmn7d1i7a9"; depends=[]; }; Brundle = derive2 { name="Brundle"; version="1.0.8"; sha256="1yj196x6xb75qgi16pgg3dyjmxmjklfjcpxymaki32drhmylf24z"; depends=[DESeq2 DiffBind lattice Rsamtools]; }; BsMD = derive2 { name="BsMD"; version="2013.0718-1"; sha256="06w1dl5zp1cgjhk3m2zz6xsmcfwdk6ar3gmxdn96v71mqnhv81v1"; depends=[]; }; + Buddle = derive2 { name="Buddle"; version="1.0"; sha256="1aw0xmdw4m778vk9wqxy90dv9rkkb17d51f0sdwypb3l7d4d897b"; depends=[Rcpp RcppArmadillo]; }; BullsEyeR = derive2 { name="BullsEyeR"; version="0.2.0"; sha256="1p8b5w818zi7zs0n13cc3sw8z0z9mfr5cn5y5icsx1jam5amppci"; depends=[Matrix NLP slam tm topicmodels]; }; BurStFin = derive2 { name="BurStFin"; version="1.02"; sha256="16w2s0bg73swdps9r0i8lwvf1najiqyx7w7f91xrsfhmnqkkjzka"; depends=[]; }; BurStMisc = derive2 { name="BurStMisc"; version="1.1"; sha256="0cyi42zkn2dby162x9f95b3hpqxbzx25s7nahb4p86r60xj3a5c0"; depends=[]; }; @@ -510,7 +517,7 @@ in with self; { CDECRetrieve = derive2 { name="CDECRetrieve"; version="0.1.2"; sha256="1p8d9rwkcd2bxma9h3ccg2k4795v3ycihwh9hblymfis8ncfhr19"; depends=[dplyr glue httr lazyeval lubridate magrittr purrr readr roxygen2 rvest stringr tibble tidyr xml2]; }; CDFt = derive2 { name="CDFt"; version="1.0.1"; sha256="0sc8ga48l3vvqfjq3ak5j1y27hgr5dw61wp0w5jpwzjz22jzqbap"; depends=[]; }; CDLasso = derive2 { name="CDLasso"; version="1.1"; sha256="0n699y18ia2yqpk78mszgggy7jz5dybwsi2y56kdyblddcmz1yv7"; depends=[]; }; - CDM = derive2 { name="CDM"; version="7.0-12"; sha256="1bykyivhkiz50gqanidjlqka13gly0i58rvh5gw8q3srm464h356"; depends=[MASS mvtnorm polycor Rcpp RcppArmadillo sfsmisc]; }; + CDM = derive2 { name="CDM"; version="7.1-20"; sha256="1y4ni4nm75dsz7nqrp5a9yhlnrmkj1ffn4qkpyspyc5fc1iskdcv"; depends=[MASS mvtnorm polycor Rcpp RcppArmadillo sfsmisc]; }; CDNmoney = derive2 { name="CDNmoney"; version="2012.4-2"; sha256="1isbvfq0lygs75y1hn3klqms8q7g1xbkcr8fgj75h1c99d4khvm6"; depends=[]; }; CDROM = derive2 { name="CDROM"; version="1.1"; sha256="0mvhqs4m8jp39x1rk31a1sqqmfq1avcnasgh8bizlyxx62igmi1b"; depends=[]; }; CDVine = derive2 { name="CDVine"; version="1.4"; sha256="0cp78pb6yny4n5q2j9k6xdql588536572gbphnw8zkdmrg65qyz7"; depends=[igraph MASS mvtnorm]; }; @@ -530,6 +537,7 @@ in with self; { CIAAWconsensus = derive2 { name="CIAAWconsensus"; version="1.3"; sha256="0yhay4fp5lyf0sdcf807yvys17qz9cr5f5ikim25mq336p7fp03x"; depends=[Matrix mvtnorm numDeriv stringr]; }; CIEE = derive2 { name="CIEE"; version="0.1.1"; sha256="03kq9cp0v41y0r2l9j5imcrsail2xsvlzhhhsrw454d4s9gqdql9"; depends=[survival]; }; CIFsmry = derive2 { name="CIFsmry"; version="1.0.1.1"; sha256="1m2m2zvg9ghy3bm2sll7jp4xm2vw58kc5xaxd2c9k82771m3a4j0"; depends=[]; }; + CIM = derive2 { name="CIM"; version="1.0.0"; sha256="02l8rspiiv6vj6k0q6wpiazny3f2s4dsivsm7zb9cm90qh1rv2d7"; depends=[]; }; CINID = derive2 { name="CINID"; version="1.2"; sha256="0pkgzi2j0045p10kjvnq8f4j1agzrqfw0czvvfrzj9yjfpj8xc99"; depends=[]; }; CINNA = derive2 { name="CINNA"; version="1.1.50"; sha256="19xh2n73b0qbnj9pihbwxkvaq96d459mj4wrkcnzbh93dj6841an"; depends=[centiserve circlize corrplot dendextend factoextra FactoMineR GGally ggplot2 igraph intergraph network pheatmap plyr qdapTools Rtsne sna viridis]; }; CISE = derive2 { name="CISE"; version="0.1.0"; sha256="10mbi4v8dfdc9ngnrrmxpng8fnig5m8nv7799jksbcf6pnj8yv51"; depends=[far gdata glmnet MASS Matrix rARPACK]; }; @@ -550,7 +558,6 @@ in with self; { CNLTtsa = derive2 { name="CNLTtsa"; version="0.1-2"; sha256="1vy0jjg6s8yvsvkx4pin183y5bnikm5cmjcpa9znz9dj1w6hwr5r"; depends=[adlift CNLTreg fields nlt]; }; CNOGpro = derive2 { name="CNOGpro"; version="1.1"; sha256="1frsmhfqrlg1vsa06cabqmrzngq4p5gqwyb9qgnsgg81a9ybm6l8"; depends=[seqinr]; }; CNVScope = derive2 { name="CNVScope"; version="1.9.7"; sha256="1xj82nwkv27wfwrks9rckdgmhlqfl4n0zmcqqa3f9ryx79jm7zbl"; depends=[BiocManager biomaRt blockseg BSgenome_Hsapiens_UCSC_hg19 circlize ComplexHeatmap data_table doParallel dplyr DT foreach GenomicFeatures GenomicInteractions GenomicRanges ggplot2 heatmaply HiCseg htmltools htmlwidgets igraph InteractionSet IRanges jointseg logging magrittr Matrix matrixStats numbers OpenImageR plotly plyr RCurl readr reshape2 rslurm rtracklayer S4Vectors shiny shinycssloaders shinyjs shinythemes spatialfil tidyr visNetwork]; }; - CNVassocData = derive2 { name="CNVassocData"; version="1.0"; sha256="17r3b1w9i9v6llawnjnrjns6jkd82m2cn9c90aif8j0bf4dmgdli"; depends=[]; }; CNprep = derive2 { name="CNprep"; version="2.0"; sha256="08dpjikx3ldqzw2kwb12q0kbw15qzl09srjdfs0sz9si0x6bfxs6"; depends=[mclust rlecuyer]; }; CNull = derive2 { name="CNull"; version="1.0"; sha256="14hy86zg18hqxi63bfzrpkz70yrzfxp2v2pva5xnrvx9dmlyz820"; depends=[ape Matrix PhyloMeasures Rcpp]; }; COBRA = derive2 { name="COBRA"; version="0.99.4"; sha256="1r1cw12d7c148pcgcg08bfsr1q1s736kfpyyss6b4d7ny7wgmqy4"; depends=[]; }; @@ -567,6 +574,7 @@ in with self; { COUNT = derive2 { name="COUNT"; version="1.3.4"; sha256="02f7779fy0d2bql88x5v9csbxljhnyvl8wb8h83xrmwl7kaxsdpy"; depends=[MASS msme sandwich]; }; COUSCOus = derive2 { name="COUSCOus"; version="1.0.0"; sha256="1ykqi72v8v1b3g9qy6h34dvk5fynzf1rl2mby65p08axmaba5798"; depends=[bio3d matrixcalc]; }; CP = derive2 { name="CP"; version="1.6"; sha256="18zblf13riiz3mq3hkvg6vhiwjzpsn6mvgc2p0bqyldy98v4aisd"; depends=[survival]; }; + CPAT = derive2 { name="CPAT"; version="0.1.0"; sha256="0zygncwww3cazwmx06bhzq0g41xcqfpw307azdhygc8jmcy6qj71"; depends=[purrr Rcpp RcppArmadillo Rdpack]; }; CPBayes = derive2 { name="CPBayes"; version="0.3.0"; sha256="1vzh9sgij194j7kiwjgba7xsqffiif9zamj9gdv2lk91wdcqaxid"; depends=[forestplot MASS]; }; CPE = derive2 { name="CPE"; version="1.5.1"; sha256="0n3pd6daj0mzhh547syh7nz8iys6q27igqngldb8zd4ib4778603"; depends=[rms survival]; }; CPMCGLM = derive2 { name="CPMCGLM"; version="1.2"; sha256="07hx2ik5zg05w1h6i94398mp54q958phws9ydgp6syjqlp9dpf1p"; depends=[abind mvtnorm plyr]; }; @@ -576,7 +584,7 @@ in with self; { CRAC = derive2 { name="CRAC"; version="1.0"; sha256="0vnqmmmwakx5jnzqp20dng35p7rvmz3ypm2m7bs41m8nhh2wq1xa"; depends=[]; }; CRANsearcher = derive2 { name="CRANsearcher"; version="1.0.0"; sha256="09gw1s28gb0l2cn4w3asl6zlr7wfacxwafbdrayajwckyfkjl5dl"; depends=[curl dplyr DT lubridate miniUI shiny shinyjs stringr]; }; CREAM = derive2 { name="CREAM"; version="1.1.1"; sha256="1lccpwn6c5pmykgf689gvvpqdcilkys4vclpxjhllhanjrfhcs3q"; depends=[]; }; - CRF = derive2 { name="CRF"; version="0.3-16"; sha256="1vw8gkrhymqi7x3p257k8vvn4df4s16w8hhm1myzhcp6bf44jqg4"; depends=[Matrix]; }; + CRF = derive2 { name="CRF"; version="0.4-1"; sha256="08bahabgp5dw93j1ikmlr0pdmw5h7s78gbmd0296qx7malsih1b5"; depends=[Matrix]; }; CRM = derive2 { name="CRM"; version="1.2.4"; sha256="0jv2z1y3zyj1m86p4pmqww58hj8pvid1ss6ym67y46n9srzxsmj5"; depends=[]; }; CRPClustering = derive2 { name="CRPClustering"; version="1.2"; sha256="19m7jg6ck2gqmry2p35h3vv8msm4w1x7qwwmm746r646q7w9ylml"; depends=[dplyr lucid MASS mvtnorm png randomcoloR]; }; CRTSize = derive2 { name="CRTSize"; version="1.0"; sha256="1d45zx26bf0zk0piham69gvb8djqf48g6iisbldv0ds3s2hhcsin"; depends=[]; }; @@ -611,7 +619,7 @@ in with self; { Canopy = derive2 { name="Canopy"; version="1.3.0"; sha256="0979hpphzhf4v71jx0shh3l8nffmpsn9l6f8ip2wxzcyx571i1wd"; depends=[ape fields pheatmap scatterplot3d]; }; CarletonStats = derive2 { name="CarletonStats"; version="2.0"; sha256="0pgzvw6gf8kjv8ndprwp4wlgdgh5sb75ga8z5syfw57fb05v7ac3"; depends=[]; }; CaseBasedReasoning = derive2 { name="CaseBasedReasoning"; version="0.1"; sha256="0hwll17j0br8sr0ci3bfa5rx4r36hr7myq7b5fav664zjxdh9wr4"; depends=[cowplot data_table dplyr magrittr R6 ranger Rcpp RcppArmadillo RcppParallel rms survival tidyverse]; }; - CatDyn = derive2 { name="CatDyn"; version="1.1-0"; sha256="0bdixcf1iwbmjd2axi6csrzms25ghdj4r6223qhk2b54wlmbzaiz"; depends=[BB optimx]; }; + CatDyn = derive2 { name="CatDyn"; version="1.1-1"; sha256="0gkaxs7apqhq7mp3chjsyhrnk3qkk11f8p7smmyj6h73888ry8jn"; depends=[BB optimx]; }; CatEncoders = derive2 { name="CatEncoders"; version="0.1.1"; sha256="1q9wzq06lac8z9y8b65alsxpb48bw8wqmifd893kknk51xq6r9kl"; depends=[data_table Matrix]; }; CatPredi = derive2 { name="CatPredi"; version="1.1"; sha256="1fqz2mb3xhpzvamf0bpqfql3vd86vq6fq7n6p8xq7lraj1w77lys"; depends=[CPE mgcv rgenoud rms survival]; }; CateSelection = derive2 { name="CateSelection"; version="1.0"; sha256="194lk6anrb05gaarwdg8lj5wm6k61b4r702cja3nf3z91i8paqi7"; depends=[]; }; @@ -633,13 +641,13 @@ in with self; { ChannelAttribution = derive2 { name="ChannelAttribution"; version="1.14"; sha256="1rasn1ghk4k0crdvxs9l8xjajdxvjsy7rwx9gz0nf41rw8pm16qa"; depends=[Rcpp RcppArmadillo]; }; ChannelAttributionApp = derive2 { name="ChannelAttributionApp"; version="1.1"; sha256="0qy92ij1riynz7dhri3z85pafww5w9j1gx1bcgr8phlr32a7had7"; depends=[ChannelAttribution data_table ggplot2 shiny]; }; Chaos01 = derive2 { name="Chaos01"; version="1.1.1"; sha256="0ibxibmlyc6wkhqj2achwkwdkniin60y8xh8b80nq6ggmm7w9crw"; depends=[]; }; - ChaosGame = derive2 { name="ChaosGame"; version="0.3"; sha256="0nfp2qnhzpncs0yd5rknspin6c4hidqhxdd973ysiivg63wxwz8d"; depends=[colorRamps ggplot2 gridExtra plot3D RColorBrewer rgl sphereplot]; }; + ChaosGame = derive2 { name="ChaosGame"; version="0.4"; sha256="10bq8i6b6zkg8nzq5np998xabyvijizxfbvw1m2nvfh74vxspj4p"; depends=[colorRamps ggplot2 gridExtra plot3D RColorBrewer rgl sphereplot]; }; CharFun = derive2 { name="CharFun"; version="0.1.0"; sha256="0cqy1na1lh9w3nspy68yylali9y5b64jlgh4fyzas556239dnyk7"; depends=[Bessel]; }; ChargeTransport = derive2 { name="ChargeTransport"; version="1.0.2"; sha256="0mq06ckp3yyj5g1z2sla79fiqdk2nlbclm618frhqcgmq93h0vha"; depends=[]; }; CheckDigit = derive2 { name="CheckDigit"; version="0.1-1"; sha256="0091q9f77a0n701n668zaghi6b2k3n2jlb1y91nghijkv32a7d0j"; depends=[]; }; - ChemoSpec = derive2 { name="ChemoSpec"; version="5.0.207"; sha256="1gd97qy3brnngdqwrifkcy1jfar2rmfh4i5ic7aqcy1scsqspfdn"; depends=[ChemoSpecUtils plyr]; }; + ChemoSpec = derive2 { name="ChemoSpec"; version="5.0.225"; sha256="1my7klhx20cyn0r3k49ryrizlnf17q9pmrsnh0jjmzq4zc96wy11"; depends=[ChemoSpecUtils plyr]; }; ChemoSpec2D = derive2 { name="ChemoSpec2D"; version="0.2.0"; sha256="1zhq5bg8alm9ys75x9839nvwgg1g36vckyqa5gx51by643p6wm4m"; depends=[ChemoSpecUtils matrixStats multiway plyr R_utils ThreeWay]; }; - ChemoSpecUtils = derive2 { name="ChemoSpecUtils"; version="0.2.163"; sha256="1sx10cxrm0mh51rxflrdpyg9w8g6abx8bm4r6hbzdwbxlh532yk2"; depends=[amap plyr RColorBrewer robustbase]; }; + ChemoSpecUtils = derive2 { name="ChemoSpecUtils"; version="0.2.204"; sha256="0j43hi3z2lyqcnj4ani3y310bzma367fqrz3rh0y79zyl683spx0"; depends=[amap plyr RColorBrewer robustbase]; }; ChemometricsWithR = derive2 { name="ChemometricsWithR"; version="0.1.11"; sha256="00z09bplm5qvd31y7m4b4knsrl0n27j9635m1gdak6lg4db4nxrd"; depends=[devtools kohonen MASS pls]; }; ChoR = derive2 { name="ChoR"; version="0.0-4"; sha256="08mildsx542zfm0kcdakcv7c71hb4jgbcq1lhidf0fz76zj1pzk1"; depends=[commonsMath rJava]; }; ChocoLattes = derive2 { name="ChocoLattes"; version="0.1.0"; sha256="0ircdar4fswaf34969gzgn83ia891jvwl29jn4s9a87cc4qagzgr"; depends=[ggplot2 knitr plotly R_utils rmarkdown WriteXLS XML]; }; @@ -663,7 +671,7 @@ in with self; { ClimClass = derive2 { name="ClimClass"; version="2.1.0"; sha256="1r836md31z2r5d9xckkbalzbhm4kf5paljv71kxpy53q92k7yi91"; depends=[geosphere ggplot2 reshape2]; }; ClimDown = derive2 { name="ClimDown"; version="1.0.2"; sha256="0dbv5vn985bi9nqxhq7jcj6k38s8dlbqnln3adgd0ih2fwilvalg"; depends=[abind fields foreach ncdf4 PCICt seas udunits2]; }; ClimProjDiags = derive2 { name="ClimProjDiags"; version="0.0.2"; sha256="178jsjhz3c2aq8bix34rs569qv6l0c8428zi10aadvzkip4xxbk7"; depends=[climdex_pcic multiApply PCICt plyr]; }; - ClinicalTrialSummary = derive2 { name="ClinicalTrialSummary"; version="0.1.0"; sha256="1lqf2ksgchl1j5hfkz7r5yczvkjgi3238k8nkfkd70nyil9vjq06"; depends=[Rcpp]; }; + ClinicalTrialSummary = derive2 { name="ClinicalTrialSummary"; version="1.0.0"; sha256="00k1mcfb38bpsipq5v3ra322j9whbr4br36438lm8x05q220slp8"; depends=[Rcpp]; }; ClueR = derive2 { name="ClueR"; version="1.4"; sha256="0awl3ag48idg0396hcgqrh5f16mbgximr5xbxjiimib5zysdc558"; depends=[e1071]; }; ClusVis = derive2 { name="ClusVis"; version="1.1.0"; sha256="17cn3hm37jv10aybaidy89kch6814hdi8g44s94xa9li7nixzass"; depends=[MASS mgcv mvtnorm Rcpp RcppArmadillo Rmixmod VarSelLCM]; }; ClustGeo = derive2 { name="ClustGeo"; version="2.0"; sha256="1p5k2w1k7hnacbazzj2yhxh4z2jngnsl4v5a9b3c8z1dr4nhcwxc"; depends=[sp spdep]; }; @@ -708,7 +716,7 @@ in with self; { CompareCausalNetworks = derive2 { name="CompareCausalNetworks"; version="0.2.2"; sha256="0zyawv3kh3hxp771bh01jck2cvy3mz92nkv454lk70h35qm4sgrb"; depends=[data_table expm Matrix]; }; CompareTests = derive2 { name="CompareTests"; version="1.2"; sha256="1z96kh851bpr2szgyjszkpv6m5ma6abz7hrm50fgvfpgxkj7f4yi"; depends=[]; }; Compind = derive2 { name="Compind"; version="2.0"; sha256="1qadyl96c9cmk1i763gc055hgv414ha59418lqk183kwl5sgbqy5"; depends=[Benchmarking boot GPArotation Hmisc lpSolve MASS nonparaeff np psych smaa spdep]; }; - Compositional = derive2 { name="Compositional"; version="3.1"; sha256="0xy9b1gvxpr3k2351yax5yq6iijk3yws2fa07wmjykkl0y7m85zc"; depends=[doParallel emplik fields foreach MASS mixture Rfast sn]; }; + Compositional = derive2 { name="Compositional"; version="3.2"; sha256="0x18k02q159wr6c0nir0b3j7y0l1jwcx37qny5jpqqb82lxpncsb"; depends=[doParallel emplik fields foreach MASS mixture Rfast sn]; }; Compounding = derive2 { name="Compounding"; version="1.0.2"; sha256="1xlb3ylwjv70850agir0mx79kcvs43h0n1sm22zcny3509s2r7lf"; depends=[hypergeo]; }; ConConPiWiFun = derive2 { name="ConConPiWiFun"; version="0.4.6"; sha256="1kkc4xp5b6q54b76wk4ga28wl668psbpyivl6bnh3xm21276yx5k"; depends=[Rcpp]; }; ConR = derive2 { name="ConR"; version="1.2.2"; sha256="0my9cb7psm0zinyfr1p8a53lbfbqf6hx7lfyxkqszckpj7gsg3hr"; depends=[doParallel fields geosphere maptools plyr raster rgdal rgeos sp spatstat spatstat_utils tibble writexl]; }; @@ -724,7 +732,7 @@ in with self; { ConsRank = derive2 { name="ConsRank"; version="2.0.1"; sha256="18f1gqa46f8jrcf2zj4njyy78cl0scjs9k8s9mvg0f9dpr44xnan"; depends=[gtools proxy rgl]; }; ContaminatedMixt = derive2 { name="ContaminatedMixt"; version="1.3.3"; sha256="16pkpgvg46xscp6z2xlhlnfzc9048jlgqxxbqa4c90z7dclcmrqk"; depends=[caret mclust mixture mnormt mvtnorm]; }; ContourFunctions = derive2 { name="ContourFunctions"; version="0.1.0"; sha256="1hlff3wx8r1wpkhrz0n27wjnzy6z2q8s9smyb906gwwa9xga7njy"; depends=[]; }; - ConvergenceClubs = derive2 { name="ConvergenceClubs"; version="1.4.2"; sha256="14fgbz0fhaqqp55bh577bhb4gs2adbvldf52xjn663vdg99rwvaf"; depends=[lmtest sandwich]; }; + ConvergenceClubs = derive2 { name="ConvergenceClubs"; version="1.4.3"; sha256="0glfnwmfs6xv4d1h5y0859srvj3y68192589mdjcx0jgkgk2c9np"; depends=[lmtest sandwich]; }; ConvergenceConcepts = derive2 { name="ConvergenceConcepts"; version="1.2.1"; sha256="0kl67ds6369mxl2i93h43r00ji12qkg0k9m4jhcxsb0ydd8rfqgp"; depends=[lattice tkrplot]; }; CoordinateCleaner = derive2 { name="CoordinateCleaner"; version="2.0-3"; sha256="1kb21a8mp3blgnvyzqcwh1zz1mkdq6c759g9dlw3dzp2gnpzl5zp"; depends=[dplyr geosphere ggplot2 raster rgdal rgeos rnaturalearth sp tidyselect]; }; CopCTS = derive2 { name="CopCTS"; version="1.0.0"; sha256="1j0bhkjk181y9k69442diswgwax5whmh5vfqydhf3b1r5ll1wkm3"; depends=[copBasic copula msm]; }; @@ -737,7 +745,8 @@ in with self; { CorDiff = derive2 { name="CorDiff"; version="1.0"; sha256="12rgfhygrdq1ign4ybr8g171wxic8zbp83n1xdsnqpj910k5jdr5"; depends=[mcc]; }; CorReg = derive2 { name="CorReg"; version="1.2.8"; sha256="18l9aiv2ipvs14ycnzq99yvnkws38wnj42zbk5jqgv33kn37qbx2"; depends=[corrplot elasticnet glmnet lars MASS Matrix mclust mvtnorm Rcpp RcppEigen Rmixmod rpart]; }; CorShrink = derive2 { name="CorShrink"; version="0.1-6"; sha256="15ay6ws9216lv15mpgldank3klw3zz5j4nwvv1s88jjfn2ln5c1l"; depends=[ashr corpcor corrplot glmnet gridExtra MASS Matrix reshape2 SQUAREM]; }; - Corbi = derive2 { name="Corbi"; version="0.4-2"; sha256="0h088iplryaipnfp8svw3djh016z23lv66q51gfbqpvchvjdwypw"; depends=[CRF Matrix mpmi]; }; + Corbi = derive2 { name="Corbi"; version="0.4-3"; sha256="00fjw7jn7syxnczc31m3nmafz6pjyidkr81vrck2ma50m6zx9mwv"; depends=[CRF Matrix mpmi]; }; + CornerstoneR = derive2 { name="CornerstoneR"; version="1.0.1"; sha256="129f537pqiw1hbagnk5203jy8w2nhpw852qfcwg4nklw7mj1phnj"; depends=[checkmate data_table ranger vcd]; }; CorporaCoCo = derive2 { name="CorporaCoCo"; version="1.1-0"; sha256="1s3wlcy6mnw9riivw5lc4gd6bjbsd77m15ipr95g46isdcrli8zb"; depends=[data_table RColorBrewer rlist]; }; CorrBin = derive2 { name="CorrBin"; version="1.5"; sha256="1kg8kms76z127j2vmf7v162n0sh2jqylw4i7c35x5sig4q22m9gy"; depends=[boot combinat dirmult geepack mvtnorm]; }; CorrMixed = derive2 { name="CorrMixed"; version="0.1-13"; sha256="02zg5kmv5qxnasnz872r3z7x7dmdcniq1x5xyfnnb3niwkdjgxzx"; depends=[nlme psych]; }; @@ -756,7 +765,6 @@ in with self; { CoxPhLb = derive2 { name="CoxPhLb"; version="1.0.0"; sha256="1j8dvbjv4h0zdjvwvpswdlsb9pf3gxixh2rhl0m1kxm6f6h5ig0z"; depends=[survival]; }; CoxPlus = derive2 { name="CoxPlus"; version="1.1.1"; sha256="038wsz206bgc0pnzx403b5ihcwhxpkrpxmwvrvqcxf8333pb62l5"; depends=[Rcpp RcppArmadillo]; }; CoxRidge = derive2 { name="CoxRidge"; version="0.9.2"; sha256="0p65mg4hzdgks03k1lj90yj6qbk50s94rwvcwzkb5xxxwrijd10r"; depends=[survival]; }; - CpDyna = derive2 { name="CpDyna"; version="1.0"; sha256="0a8b58nxp0pik03kh3lb02gm6z21lqw6y62z11jjllmrycbmc68j"; depends=[igraph mclust RColorBrewer Rcpp RcppArmadillo RcppProgress]; }; CpGFilter = derive2 { name="CpGFilter"; version="1.1"; sha256="0ccvk7lawmay0wqdyhs6ww7396dcfzazn72sq6zwyw7dl45k2j0i"; depends=[matrixStats]; }; CpGassoc = derive2 { name="CpGassoc"; version="2.60"; sha256="1zx18x8pxjl2ajnj7a7lb8383m75ysg17f4mzz0vkgl5mnf617ny"; depends=[nlme]; }; Cprob = derive2 { name="Cprob"; version="1.4.1"; sha256="1m4ys8xpj1jbn3lf8fym935y94dxipiimsf9zxwyw5sy71y7skgq"; depends=[geepack lattice lgtdl prodlim tpr]; }; @@ -764,12 +772,12 @@ in with self; { CreditRisk = derive2 { name="CreditRisk"; version="0.1.3"; sha256="09ks8xlsrbp3an1drcwmmd6df4fsfz61z21ma2p62a1pk0bnc86c"; depends=[fOptions]; }; CrossClustering = derive2 { name="CrossClustering"; version="4.0.3"; sha256="05lbdmblwmmv24h46ixxabbrp7mpajyv7raw1p5h0dmsbfbq9hi5"; depends=[assertive cli cluster crayon dplyr flip glue magrittr mclust purrr]; }; CrossScreening = derive2 { name="CrossScreening"; version="0.1.1"; sha256="1gig80r8p611ysn35ajx7xdjj5wnkcf1vspcf0i06dmh75xpm3w9"; depends=[plyr tables]; }; - CrossVA = derive2 { name="CrossVA"; version="0.9.3"; sha256="1nagbgcih6ix21js91vfpr4yjkhnirblgdmf04nn7ipv2ins8kw6"; depends=[lubridate stringi]; }; + CrossVA = derive2 { name="CrossVA"; version="0.9.4"; sha256="199k3mys56asiih5x1mp2cmpr2hdivf7wq82rzjllrrg8284gmbm"; depends=[lubridate stringi]; }; CrossValidate = derive2 { name="CrossValidate"; version="2.3.2"; sha256="1dlvkv712rz3gw03c04qlk0l0mqjyds3m3pnbszk4848zby5ac6r"; depends=[Modeler oompaBase]; }; Crossover = derive2 { name="Crossover"; version="0.1-17"; sha256="168j8fl6h7x1pia5f5c18yrf0y1lvznib8clq1mv0imb7cjzkkhi"; depends=[CommonJavaJars crossdes digest ggplot2 JavaGD MASS Matrix multcomp Rcpp RcppArmadillo rJava xtable]; }; CryptRndTest = derive2 { name="CryptRndTest"; version="1.2.2"; sha256="1cg0agwqp1f7pgxdf9wilwparklyfsv900r47fpihnqw3ycvbdai"; depends=[gmp kSamples LambertW MissMech Rmpfr sfsmisc tseries]; }; CrypticIBDcheck = derive2 { name="CrypticIBDcheck"; version="0.3-3"; sha256="1c7n020i9lxp0fam05k9v4az4rvx8fakhzi9fkma82smpl709x8q"; depends=[car chopsticks ellipse rJPSGCS]; }; - CsChange = derive2 { name="CsChange"; version="0.1.4"; sha256="1lpi8igwfdmsgm26qy4qi5cikilb0xpaajl1fd6vn696bwm1ljc2"; depends=[boot Hmisc rms survival]; }; + CsChange = derive2 { name="CsChange"; version="0.1.5"; sha256="1xsbysjcqlky8lsgk2rbaby49zgipp3wzj5navm7kcnk04sg90f6"; depends=[boot Hmisc rms survival]; }; CuCubes = derive2 { name="CuCubes"; version="0.1.0"; sha256="1cpazar85rp8xfjvy0vxivr61grzvxz7a9mirxvhynln964by6ns"; depends=[]; }; Cubist = derive2 { name="Cubist"; version="0.2.2"; sha256="1m45dpnr5djsfgqlinng6z0f2wbig2vbidlg19r3zcraqwn1agnd"; depends=[lattice reshape2]; }; CustomerScoringMetrics = derive2 { name="CustomerScoringMetrics"; version="1.0.0"; sha256="166v0hbxy4xgbfqh7sx6zsrv4pghqpimx5xry3h2qwynnvr4ng1a"; depends=[]; }; @@ -788,7 +796,8 @@ in with self; { DACF = derive2 { name="DACF"; version="1.0.0"; sha256="0hv7c9lk6ivj4iz953yn11iy5p611q4si4ghn9d5a9i229s5hig8"; depends=[]; }; DAISIE = derive2 { name="DAISIE"; version="1.4"; sha256="16653wwz20lhf3bpzflpj5d1h7j3cqyfaqk5gn24aifga2jc0wbb"; depends=[DDD deSolve Matrix subplex tensor]; }; DAKS = derive2 { name="DAKS"; version="2.1-3"; sha256="0vmpwxvksnmyq40faimbgpj0y3zbk519986n38ipwdfzllcg0zs4"; depends=[relations sets]; }; - DALEX = derive2 { name="DALEX"; version="0.2.4"; sha256="0zrgp266bmn0b87bf0gvi4yc2ngj4pvhw9qbmvnhqlifrqb55ir6"; depends=[ALEPlot breakDown factorMerger ggplot2 ggpubr pdp]; }; + DALEX = derive2 { name="DALEX"; version="0.2.5"; sha256="0iv9wfl77mq7j2w7x78kpbkq7v8q4ixdj515lrifw7hvwpr8iy68"; depends=[ALEPlot breakDown factorMerger ggplot2 ggpubr pdp]; }; + DALEX2 = derive2 { name="DALEX2"; version="0.9"; sha256="1k39gswksicrb60nx7zzna3mqdm36ckg590iw511ga7frnb8fjl9"; depends=[]; }; DALY = derive2 { name="DALY"; version="1.5.0"; sha256="1v7ld01xcn5jiygl1c3xhd5h71ip90lks87fs9gmpnivp8jz5cr5"; depends=[]; }; DAMOCLES = derive2 { name="DAMOCLES"; version="1.1"; sha256="07z8mynhqnk1zcvm84w09xzkiy2dfxwhmnpi6gaddr3p0waql4gj"; depends=[ape caper deSolve expm geiger matrixStats picante]; }; DAMisc = derive2 { name="DAMisc"; version="1.4-3"; sha256="1hic53vi7mj4fvggxjl4d3j4zw8wwczh6pldyi8idrhm45hw2nh4"; depends=[boot car effects gdata lattice MASS nnet pscl QRM sm VGAM xtable]; }; @@ -837,7 +846,7 @@ in with self; { DHS_rates = derive2 { name="DHS.rates"; version="0.4.0"; sha256="12q5qn9k9svabqsya039axx1lnafcq4mlnnb0nyfdjhklnh7k870"; depends=[haven matrixStats reshape survey]; }; DIFboost = derive2 { name="DIFboost"; version="0.2"; sha256="0wyjk870n18lq0dwhm9ndsh5vv0d8wkrbcky68w454vzrrw1q9h8"; depends=[mboost penalized stabs]; }; DIFlasso = derive2 { name="DIFlasso"; version="1.0-3"; sha256="195wiy0jjkq6bh2b6wrjmr5l34pzx0i2qqvwp4pzv77sx737ds0v"; depends=[grplasso miscTools penalized]; }; - DIFtree = derive2 { name="DIFtree"; version="2.1.4"; sha256="16cyd634jflaszpfq0ymwlbv57ci1iyffwai641jczn8cny504zl"; depends=[penalized plotrix]; }; + DIFtree = derive2 { name="DIFtree"; version="3.1.4"; sha256="1q02229vlmyxqasbxiscxvqpcip1r0sbwbp7ja909ljhc5b76pr8"; depends=[gridBase penalized plotrix VGAM]; }; DIME = derive2 { name="DIME"; version="1.2"; sha256="11l6mk6i3kqphrnq4iwk4b0ridbbpg2pr4pyqaqbsb06ng899xw0"; depends=[]; }; DIMORA = derive2 { name="DIMORA"; version="0.1.0"; sha256="0qcy2pqpx7za4ckf6wvmbhz5a52j44ksn81f8j1lj0z90idj6psn"; depends=[minpack_lm numDeriv]; }; DIRECT = derive2 { name="DIRECT"; version="1.0.1"; sha256="00z4xlc9kxn19lw2b8xq6krsf5v3wfbr1ghl5ah5shr9dnv84lc1"; depends=[]; }; @@ -999,6 +1008,7 @@ in with self; { DrBats = derive2 { name="DrBats"; version="0.1.4"; sha256="0jzl1jklxsbqf5hv3a71lckk51jxi1lnbk5zmvd4x3y9b9azl2cq"; depends=[ade4 coda MASS Matrix rstan sde]; }; DrImpute = derive2 { name="DrImpute"; version="1.0"; sha256="1adzarrwqb282pqgx2yqswp9rpwd1naxsmar54kddr6qyd6b923b"; depends=[Rcpp RcppArmadillo]; }; DrInsight = derive2 { name="DrInsight"; version="0.1.1"; sha256="02lqf6bwbgcgyg5zx16nvnzpagmcmbsngnhmyv47256vsd9vppjd"; depends=[igraph qusage]; }; + DriftBurstHypothesis = derive2 { name="DriftBurstHypothesis"; version="0.1"; sha256="1459l5bq4yz79qrxqqm7svd4swcxghk4mjkv98nmxwxaasg9srhc"; depends=[Rcpp RcppArmadillo]; }; DrillR = derive2 { name="DrillR"; version="0.1"; sha256="0n7pim5kk0wfdjcc67v4vvdb7wyhn5bcgi2a12nbyfyydss7pk1g"; depends=[httr]; }; DrugClust = derive2 { name="DrugClust"; version="0.2"; sha256="0acvjqwzkbjmy101m501l7fkfxzkp6zflwvn56li5307xv9ggnfg"; depends=[cclust cluster e1071 MESS ROCR]; }; DstarM = derive2 { name="DstarM"; version="0.3.0"; sha256="16vcv21dgnymhsy9j5x5pblnipf4hdyscajx6pr8kl6i95hs3hmj"; depends=[DEoptim ggplot2 Rcpp RcppArmadillo rtdists RWiener]; }; @@ -1088,7 +1098,7 @@ in with self; { EWGoF = derive2 { name="EWGoF"; version="2.2.1"; sha256="0n1fx6k9ndb2s9ybzizbqz662c9s1f48q6v697pqhnfy9si1nplz"; depends=[Rcpp]; }; EXRQ = derive2 { name="EXRQ"; version="1.0"; sha256="1iqsr52sl2j5q03122a7rsp6n6a2bkysk2r908c89l36gk4sj2i5"; depends=[mnormt quantreg]; }; EZtune = derive2 { name="EZtune"; version="1.0.0"; sha256="0a74wnmxbvnm1zil0slg4kphvqc1n03y26zp1a0gpawpkfxcmbch"; depends=[ada doParallel e1071 GA gbm mlbench]; }; - Eagle = derive2 { name="Eagle"; version="1.1.0"; sha256="1n2aqp6pd7cglhmnhf8g086xv4468hhqx6qvlwjbvj6diwhym35c"; depends=[data_table matrixcalc Rcpp RcppEigen shiny shinyBS shinyFiles shinyjs shinythemes]; }; + Eagle = derive2 { name="Eagle"; version="1.2.0"; sha256="1h0i4qxww3cnnmbyyg0lmzsqj8rq4v8sva7x8s2x7cm59qzwhin7"; depends=[data_table matrixcalc Rcpp RcppEigen shiny shinyBS shinyFiles shinyjs shinythemes]; }; EasyABC = derive2 { name="EasyABC"; version="1.5"; sha256="17qv6y8sf2iwwqcv5wfg6sii259gv5jyr72dnfpir2bw78wb3mqx"; depends=[abc lhs MASS mnormt pls tensorA]; }; EasyHTMLReport = derive2 { name="EasyHTMLReport"; version="0.1.1"; sha256="1hgg8i7py7bx48cldyc7yydf0bggmbj3fx3kwiv9jh1x5wyh929z"; depends=[base64enc ggplot2 knitr markdown reshape2 scales xtable]; }; EasyMARK = derive2 { name="EasyMARK"; version="1.0"; sha256="10slkblbyxq98c3sxgs194dnkx996khfcpxj6jhz355dp35z7c9d"; depends=[coda doParallel foreach MASS random rjags stringr]; }; @@ -1145,7 +1155,7 @@ in with self; { EpiEstim = derive2 { name="EpiEstim"; version="1.1-2"; sha256="0r56iglhkrqvlsf3gbahd544h944fmbyn6jdc113rhjscf6dl605"; depends=[]; }; EpiILM = derive2 { name="EpiILM"; version="1.4.2"; sha256="16vml2p7c4nv0lfis661x7b9wimrni1ncpa256dh99cps9508j28"; depends=[coda]; }; EpiILMCT = derive2 { name="EpiILMCT"; version="1.1.2"; sha256="1rxq9z5lhcgzn02d9k6vgl2cb5x0s9gsly63byx4gg1h91bsvmp6"; depends=[coda]; }; - EpiModel = derive2 { name="EpiModel"; version="1.7.0"; sha256="0jg3l9bcvjxvazxzpcdmzw3ybprpvm4saka14c1mynzsg1ab70wg"; depends=[ape deSolve doParallel ergm foreach ggplot2 lazyeval network networkDynamic RColorBrewer tergm]; }; + EpiModel = derive2 { name="EpiModel"; version="1.7.2"; sha256="0zkj17kvssn4y2rglasx2s0ks1ha6bf1lzbj809pmf2m4gvyc4gb"; depends=[ape deSolve doParallel ergm foreach ggplot2 lazyeval network networkDynamic RColorBrewer tergm]; }; EpiReport = derive2 { name="EpiReport"; version="0.1.0"; sha256="1bfh7nrwmplsk7whvmsf0wxg795xrwvarxw974v58mjb282yp87s"; depends=[dplyr extrafont flextable ggplot2 knitr officer png rmarkdown tidyr zoo]; }; EpiSignalDetection = derive2 { name="EpiSignalDetection"; version="0.1.1"; sha256="04bagnx9fs0r3167hmwgc389fl5hq7l4j6kdjjmi360vcaimx9qi"; depends=[dplyr DT ggplot2 ISOweek knitr pander rmarkdown shiny surveillance]; }; EpiStats = derive2 { name="EpiStats"; version="1.2"; sha256="102s7637afm3scif20r75wcfkz9g8k4w55qxv1gqqc1kcmn2zqar"; depends=[dplyr epiR]; }; @@ -1217,6 +1227,7 @@ in with self; { FIT = derive2 { name="FIT"; version="0.0.5"; sha256="1hky7m5b7n0d7lm79b7l7p055f8zfl7gsjdvbq09c4iwdli8h33n"; depends=[gglasso MASS Rcpp RcppEigen XML]; }; FITSio = derive2 { name="FITSio"; version="2.1-0"; sha256="021xmbavigg70m96xw1bvsdasi5yj2wmafgb6xw4b09fmyv9hvjp"; depends=[]; }; FKF = derive2 { name="FKF"; version="0.1.5"; sha256="1qzf7y3f4xfirjkm795rcxckjbw6sn7xpilhkyvayqm2vyhf7518"; depends=[RUnit]; }; + FLAME = derive2 { name="FLAME"; version="1.0.0"; sha256="0va9mbwlnvr64hii203rmq4x3izpix0x36kpsns43yb9wdqq70hv"; depends=[dplyr gmp lattice latticeExtra reticulate rlang RPostgreSQL RSQLite]; }; FLLat = derive2 { name="FLLat"; version="1.2-1"; sha256="0306bpwp2az4x4m5sv88hlh7vs0y5isfby7lxrn2gjnk76gg6mw1"; depends=[gplots]; }; FLR = derive2 { name="FLR"; version="1.0"; sha256="0k50vi73qj7sjps0s6b2hq1cmpa4qr2vwkpd2wv2w1hhhrj8lm0n"; depends=[combinat]; }; FLSSS = derive2 { name="FLSSS"; version="7.7"; sha256="09zinc1z4k3vdk7qyrsya8l1zlwg04d1v7n3wmal6c75vdgam6x3"; depends=[Rcpp RcppParallel]; }; @@ -1248,7 +1259,6 @@ in with self; { FSelectorRcpp = derive2 { name="FSelectorRcpp"; version="0.3.0"; sha256="1isvihpiy4bkkaxcyk9b3q2293wgs4m7r5g5pnksrw61r2f26mvl"; depends=[BH foreach iterators Rcpp RcppArmadillo testthat]; }; FTICRMS = derive2 { name="FTICRMS"; version="0.8"; sha256="0kv02mdmwflhqdrkhzb55si5qnqqgdadgyabqc2hwr6iccn7aq8c"; depends=[lattice Matrix]; }; FTRLProximal = derive2 { name="FTRLProximal"; version="0.3.0"; sha256="0wnlswvxiw7gvmn9yq1v8jixwspfbvcg3rklqcd0ib38d72ww7w0"; depends=[Matrix]; }; - FUNLDA = derive2 { name="FUNLDA"; version="1.1"; sha256="1qqwpics63qab43mvpm275rk9iywawr4gap0qa832i6iy3jp1h3c"; depends=[Rcpp RcppArmadillo]; }; FUNTA = derive2 { name="FUNTA"; version="0.1.0"; sha256="02yxz95s2hs26mfmgwhv5d54yyjz0aczjpnay8b4gpzbpd6aci61"; depends=[]; }; FWDselect = derive2 { name="FWDselect"; version="2.1.0"; sha256="0w0hkmhcz7h1lixk7p3yffbbalgxwh2lv463vqz361k80sri6wz7"; depends=[cvTools mgcv]; }; FacPad = derive2 { name="FacPad"; version="3.0"; sha256="0h7knzin0rfk25li127zwjsyz223w7nx959cs328p6b2azhgn59b"; depends=[MASS Rlab]; }; @@ -1269,6 +1279,7 @@ in with self; { FastImputation = derive2 { name="FastImputation"; version="2.0"; sha256="0zhin8000c78kba6zly9mvpxdxx68kcsh2hn697pxkl73wqsz3p5"; depends=[Matrix]; }; FastKM = derive2 { name="FastKM"; version="1.0"; sha256="0sqxd2pg9y6yn1lnxni32ca3bgbmz04k9z37q9pzgijvf9qvik3f"; depends=[rARPACK]; }; FastKNN = derive2 { name="FastKNN"; version="0.0.1"; sha256="1iz8ybzkvbyqwb00s7cp1zvy9xlmyjid441mf62dq08a0zncnyss"; depends=[assertthat pdist]; }; + FastLZeroSpikeInference = derive2 { name="FastLZeroSpikeInference"; version="2018.12.10"; sha256="0ybpmns7bc1j5xzqjl7734grihmvvpa3h52gixv3h70l0r89d8ys"; depends=[]; }; FastPCS = derive2 { name="FastPCS"; version="0.1.3"; sha256="152fy5hq675n1mjdsi31a77rmi3vylvvbfgywrh62chy5xa1bf34"; depends=[matrixStats Rcpp RcppEigen]; }; FastRCS = derive2 { name="FastRCS"; version="0.0.8"; sha256="11kqd8aii9sy65m5inxiqggyajb41iy6w92zp5wggx7pbg9m6lmy"; depends=[matrixStats Rcpp RcppEigen]; }; FastRWeb = derive2 { name="FastRWeb"; version="1.1-1"; sha256="0xh3710kvnc60pz9rl5m3ym2cxf0mag9gi29y7j3fl4dh2k7zf74"; depends=[base64enc Cairo]; }; @@ -1280,6 +1291,7 @@ in with self; { FedData = derive2 { name="FedData"; version="2.5.5"; sha256="0krfz76mxw0dybm4adqf5mg53g8gpypp5sk2z99s7b54w196cmqh"; depends=[curl data_table devtools dplyr foreach Hmisc httr igraph lubridate magrittr ncdf4 raster readr rgdal rgeos sf soilDB sp stringr]; }; FeedbackTS = derive2 { name="FeedbackTS"; version="1.4"; sha256="1mcsr48hvrpfnk2f0z1bc8556jf848bpd8prm3y46gqdj452wpmm"; depends=[geoR mapdata maps proj4 sp]; }; Fgmutils = derive2 { name="Fgmutils"; version="0.9.5"; sha256="05n8lvx3cs1ckliaj7ni2rbfcrdl7d0pzf9bkwlyd1779h684cxz"; depends=[data_table devEMF ggplot2 gridExtra plyr png sqldf stringr]; }; + FiRE = derive2 { name="FiRE"; version="1.0"; sha256="0biy53i10yj261p3y55q7mdkd8g20smszd2dx36z1jkkfr61hy84"; depends=[BH Rcpp]; }; FieldSim = derive2 { name="FieldSim"; version="3.2.1"; sha256="1snz2wja3lsgxys0mdlrjjvk5575cyd64mjipafibwcs97bva5x1"; depends=[RColorBrewer rgl]; }; FinAna = derive2 { name="FinAna"; version="0.1.2"; sha256="09svg5z52vv90ih85awgh6ns3pqi789qjm2wi1gb9hbg9v5g7pdv"; depends=[]; }; FinAsym = derive2 { name="FinAsym"; version="1.0"; sha256="0v15ydz4sq9djwcdcfp90mk8l951rry7h91d7asgg53mddbxjj6f"; depends=[]; }; @@ -1311,6 +1323,7 @@ in with self; { ForecastComb = derive2 { name="ForecastComb"; version="1.3.1"; sha256="07cbiv172mpkwvg6svhwgavlfy2144ir3y1l7w37wbd0ygs514id"; depends=[forecast ggplot2 Matrix mtsdi psych quadprog quantreg]; }; ForecastCombinations = derive2 { name="ForecastCombinations"; version="1.1"; sha256="07vzgm2jy992p1l9b8rsv2lbc8cbfzvql85n5ah4p4l3zjxdxgk9"; depends=[quadprog quantreg]; }; ForecastFramework = derive2 { name="ForecastFramework"; version="0.9.0"; sha256="131h9f148wn89znzsnym43amlvf4s7jzg4f2p7ld9ns7727sf56q"; depends=[abind dplyr lubridate magrittr R6 reshape2]; }; + ForestGapR = derive2 { name="ForestGapR"; version="0.0.1"; sha256="0dm7jv9zgw5wsqllah9im2nm1grvmf2d9g6z8fcjvbc1rh7admz0"; depends=[igraph raster sp VGAM viridis]; }; ForestTools = derive2 { name="ForestTools"; version="0.2.0"; sha256="0q9nk9n001bnz5hd8cxj6wmaf8c7g0kwfkpa0hk6ap42666rrrah"; depends=[APfun imager raster rgeos sp]; }; FormalSeries = derive2 { name="FormalSeries"; version="1.0"; sha256="09m4ifinasww0xfprs29xsrqhxxkw9zffb3919xnkkjkwp0nax4v"; depends=[]; }; Formula = derive2 { name="Formula"; version="1.2-3"; sha256="0wiqh8rr9d5ciy80wj8f5fnmiiw0ywanvvnhkwd622dx42dk848l"; depends=[]; }; @@ -1325,6 +1338,7 @@ in with self; { Frames2 = derive2 { name="Frames2"; version="0.2.1"; sha256="0xbz19v5r1h15p8mf94vacw04h3kvmm88ayy4b1aqxrd925n63mw"; depends=[MASS nnet sampling]; }; FreeSortR = derive2 { name="FreeSortR"; version="1.3"; sha256="1m6ahhixbbizzn09pz71zvinrdshn3j6gmy05jdxa9d932agqk0w"; depends=[ellipse smacof vegan]; }; FreqProf = derive2 { name="FreqProf"; version="0.0.1"; sha256="1yqn2435l2sghfcv5mma0rv9yqvpa69z8cqqsjlrlbih9gib82d4"; depends=[ggplot2 reshape2 shiny]; }; + Fstability = derive2 { name="Fstability"; version="0.1.2"; sha256="0kscdmrs5namvhi112b47c811w0bg9s3xg48mfa566pxwxz1nv45"; depends=[]; }; FunChisq = derive2 { name="FunChisq"; version="2.4.5-3"; sha256="0ic912ygjj5gm1s6cn32di5hqxdh9pdn9xhs3wngd92s8anm3axl"; depends=[BH Rcpp]; }; FunCluster = derive2 { name="FunCluster"; version="1.09"; sha256="0i73asn1w4s6ydf2ddn5wpr0mwbbxzgmaly1pslarzkx71wk03fz"; depends=[cluster Hmisc]; }; FuncMap = derive2 { name="FuncMap"; version="1.0.10"; sha256="0iaay6qz9a2s77xjfpp7wm37y7xwnvmlw6s5k5riccmqzc6dcjs7"; depends=[mvbutils]; }; @@ -1413,7 +1427,7 @@ in with self; { GLSE = derive2 { name="GLSE"; version="0.1.0"; sha256="1snzcz637ppz3lkg1575ln3shfidkrnynqh1d8b5rk0z0974bpm1"; depends=[gRbase igraph mvtnorm]; }; GLSME = derive2 { name="GLSME"; version="1.0.4"; sha256="1bh56dv4czl89dm9b6syfpsbds4wni03d5vamvjbp6wblhysxnpm"; depends=[corpcor mvtnorm]; }; GMAC = derive2 { name="GMAC"; version="3.0"; sha256="0c2cfpr8dik7j5br87hkvswrhqzj5vcna54gw6ffdf1rk9rz9j22"; depends=[]; }; - GMCM = derive2 { name="GMCM"; version="1.2.4"; sha256="1y0yr6i4l28qw22drca7r4mzqjfbpm3jdssfb7p8pc664g6vmm81"; depends=[Rcpp RcppArmadillo]; }; + GMCM = derive2 { name="GMCM"; version="1.3.0"; sha256="0yb7zvw0a1qaa3j7f5pfix66barhkc1s4x8b8hdhfmi8cggcdisn"; depends=[ellipse Rcpp RcppArmadillo]; }; GMDH = derive2 { name="GMDH"; version="1.6"; sha256="093glyz73246m5f2xb2xgbgi80haj4fanmr325byr99dnf4x35yn"; depends=[MASS]; }; GMDH2 = derive2 { name="GMDH2"; version="1.4"; sha256="13vbzqxmqvp39rbxw41nqfrmk0w6w8qc9nzgfbfpc07h3gcwva41"; depends=[e1071 glmnet magrittr MASS nnet plotly randomForest xtable]; }; GMMBoost = derive2 { name="GMMBoost"; version="1.1.2"; sha256="01q165vkdiv4qh96lha0g2g94jpnzdclbby6q43ghh9j1yrd4qzj"; depends=[magic minqa]; }; @@ -1454,7 +1468,7 @@ in with self; { GSIF = derive2 { name="GSIF"; version="0.5-4"; sha256="1vh3dffi5hakk32rwaabw9k34wigd0n5bhzcyqhadl6fxjsaz6b6"; depends=[aqp dismo gstat plotKML plyr raster rgdal RSAGA scales sp]; }; GSM = derive2 { name="GSM"; version="1.3.2"; sha256="04xjs9w4gaszwzxmsr7657ry2ywa9pvpwpczpvinxi8vpj347jbb"; depends=[gtools]; }; GSMX = derive2 { name="GSMX"; version="1.3"; sha256="1n1d7rixj14ari46snsmi48qfmy00ihmzvayk3hkrp2d2d0xi2gh"; depends=[MASS]; }; - GSODR = derive2 { name="GSODR"; version="1.3.0"; sha256="1iwa7s5qwv4bjccsi03h2dpwfcj2ky8n68ppzhhq2zbbwxiyqrq0"; depends=[curl dplyr future_apply magrittr purrr R_utils readr rlang tibble]; }; + GSODR = derive2 { name="GSODR"; version="1.3.1"; sha256="1kqkq1dqb9q2cq6wfkpfpwm26smq9x7k78qzpjyxdg0iwzwazcwr"; depends=[curl dplyr future_apply magrittr purrr R_utils readr rlang tibble]; }; GSSE = derive2 { name="GSSE"; version="0.1"; sha256="034mmxa6kjq5kgikhb5q75viagz5ck9irrjbxm26zq9099qxm13b"; depends=[Iso zoo]; }; GSparO = derive2 { name="GSparO"; version="1.0"; sha256="0xna2crxqwy8fj0s79rxbdcaz9x912rp1vdwqv1557fsnmfv2yf0"; depends=[ggplot2 ThreeWay]; }; GUIDE = derive2 { name="GUIDE"; version="1.2.7"; sha256="0klaczmn3jnlzyh45yaqlc897irjfk467f4w03awmflaiwan3h6v"; depends=[rpanel tkrplot]; }; @@ -1481,7 +1495,7 @@ in with self; { GeNetIt = derive2 { name="GeNetIt"; version="0.1-1"; sha256="1xjz22m4yn642m0bqa33w4m2rygpxjwg43c54lw168jck9zzgv1f"; depends=[nlme raster rgeos sp spatialEco spdep]; }; GenAlgo = derive2 { name="GenAlgo"; version="2.1.5"; sha256="0d3y9kc2njsbzdngv67d4qrdsnn7nsxph5acc09vmwxpv1cyhxiw"; depends=[ClassDiscovery MASS oompaBase]; }; GenBinomApps = derive2 { name="GenBinomApps"; version="1.0-2"; sha256="1ps1rq8cjlwh658mysdh3xbn5fihanzcwxb38xvg4031vnwv80in"; depends=[]; }; - GenEst = derive2 { name="GenEst"; version="1.2.0"; sha256="0ida037y2bzykr2s1569gwr0c46cfmkkyywd41jfx586kqchlska"; depends=[cbinom corpus DT gsl gtools htmltools lubridate matrixStats mvtnorm Rcpp shiny shinyjs sticky survival zip]; }; + GenEst = derive2 { name="GenEst"; version="1.2.1"; sha256="037630akjvnzcgjdkqvz6dav4yxx4xs7plg4va4x9rdh0rkw6bax"; depends=[cbinom corpus DT gsl gtools htmltools lubridate matrixStats mvtnorm Rcpp shiny shinyjs sticky survival]; }; GenForImp = derive2 { name="GenForImp"; version="1.0"; sha256="1wcvi52fclcm6kknbjh4r9bpkc2rg8nk6cddnf5j8zqbvrwf4k5x"; depends=[mvtnorm sn]; }; GenKern = derive2 { name="GenKern"; version="1.2-60"; sha256="12qmd9ydizl7h178ndn25i4xscjnrssl5k7bifwv94m0wrgj4x6c"; depends=[KernSmooth]; }; GenOrd = derive2 { name="GenOrd"; version="1.4.0"; sha256="17mfrj1fwj8mri1w0bl2pw1rqriidmd67i7gpn9v56g9dzw5rzms"; depends=[MASS Matrix mvtnorm]; }; @@ -1496,6 +1510,7 @@ in with self; { GeneralizedHyperbolic = derive2 { name="GeneralizedHyperbolic"; version="0.8-4"; sha256="01gqfvmzfslhxdnigzbl3rd55hk6r0kgd8fm9xjl0kb9vmb735lm"; depends=[DistributionUtils MASS]; }; GeneralizedUmatrix = derive2 { name="GeneralizedUmatrix"; version="1.1.2"; sha256="13dyzd2xspiw709iq1xw8lsik8q7abz327x11cdn02zalizvw5ip"; depends=[ggplot2 Rcpp RcppArmadillo]; }; GeneticSubsetter = derive2 { name="GeneticSubsetter"; version="0.8"; sha256="0bd4snv3dwabc7mknmd2rjmffj67xq535x0bycajhd83d1jhjars"; depends=[]; }; + GenoScan = derive2 { name="GenoScan"; version="0.1"; sha256="0p98imfvvz7l94kim3pxypyjs2pbxng4a2nagbafbady82ylr2vi"; depends=[data_table MASS Matrix seqminer SKAT]; }; GenomicMating = derive2 { name="GenomicMating"; version="2.0"; sha256="02v1pkarmardf7g8hf2n4jj4cq4707g5lcc7gnwsiyyh7pknd1y6"; depends=[dplyr emoa kohonen LowRankQP magrittr plotly qtl Rcpp RcppArmadillo scatterplot3d SOMbrero]; }; GenomicTools = derive2 { name="GenomicTools"; version="0.2.6"; sha256="19illcfcm34vr90kh4cbdwf7k8hy700dlzylsaicv3h4xi7iydgs"; depends=[circlize data_table gMWT Rcpp RcppArmadillo snpStats stringr]; }; GenomicTools_fileHandler = derive2 { name="GenomicTools.fileHandler"; version="0.1.2"; sha256="1snv2z95v7lyvzpssjsjpy4163k6imfjbb0svm8icsb85mpyj7af"; depends=[data_table snpStats]; }; @@ -1562,7 +1577,7 @@ in with self; { HBglm = derive2 { name="HBglm"; version="0.1"; sha256="1sral7lh5qw5mn31n8459pk52frgw1bjq0z5ckpsnbc4qf3xxcjn"; depends=[bayesm Formula MfUSampler sns]; }; HCR = derive2 { name="HCR"; version="0.1.1"; sha256="14s46dyw3ifp3pwwlcwbbl47i6hy2whjj1n65i28am5a33nycgha"; depends=[data_table]; }; HCT = derive2 { name="HCT"; version="0.1.0"; sha256="0p1bj0spqff8m27lvxdfhk8z1r1z04v1dsv7mqbjyzl07w005hk3"; depends=[rstan]; }; - HCmodelSets = derive2 { name="HCmodelSets"; version="0.2.1"; sha256="18996hvhwnf1w9kslprr18x78r9ldi09yxg5adi1s9y2nykv3l18"; depends=[ggplot2 mvtnorm survival]; }; + HCmodelSets = derive2 { name="HCmodelSets"; version="1.0.2"; sha256="0nwr36jgmrfvr7kn71yyah80qv55dwj8zd2hpc4ixhi4kvpr372f"; depends=[ggplot2 mvtnorm survival]; }; HDCI = derive2 { name="HDCI"; version="1.0-2"; sha256="0wxbv54kbygymhh4r7052vnbj603c1kya01ykvmqzzkjyyfzidkz"; depends=[doParallel foreach glmnet iterators lattice Matrix mvtnorm slam]; }; HDDesign = derive2 { name="HDDesign"; version="1.1"; sha256="1jim4h9bwn8r637va7m81kwwsfwyzs9pzn5a9i7c8xz8b1x191bj"; depends=[]; }; HDGLM = derive2 { name="HDGLM"; version="0.1"; sha256="0a5lnh3780lsczj8339sp97c5y64a2gsdf77i56fvpxpphq0dnf8"; depends=[]; }; @@ -1659,6 +1674,7 @@ in with self; { HotDeckImputation = derive2 { name="HotDeckImputation"; version="1.1.0"; sha256="1mqfn6yw5846ynrcgzka0m6ikfppa5civjkhj42rhp2v2xk25li7"; depends=[Rglpk]; }; Hotelling = derive2 { name="Hotelling"; version="1.0-5"; sha256="1ism2lzi2kmi62gp319qsi64pj2kj5sfh50f1qnv8vgdkb76bdx5"; depends=[corpcor]; }; HyPhy = derive2 { name="HyPhy"; version="1.0"; sha256="0994ymv7sswbp8qw3pay34s926cflw2hq2gnchw7rknybvlsrinq"; depends=[ape R_utils]; }; + HyRiM = derive2 { name="HyRiM"; version="1.0.0"; sha256="1fh7y1abwz2cmdxviribfmdvkmd706p4mmf5myl84z7dbgqh6mgp"; depends=[compare orthopolynom]; }; HybridFS = derive2 { name="HybridFS"; version="0.1.2"; sha256="05skml3v2zm5hmd6slpmx3lfwi6x5wfgbx7cnhc6l077b11jpdd9"; depends=[caTools FSelector InformationValue ROCR woeBinning]; }; HybridMC = derive2 { name="HybridMC"; version="0.2"; sha256="1wgzfyk0scwq9s2sdmc91fj7r4d7zlgwgnj6mdiia8w88ja8kzqy"; depends=[coda]; }; HydeNet = derive2 { name="HydeNet"; version="0.10.8"; sha256="0rb456rfx3jgvjkbn50v38aq7chi6482wxk4mm26l9n537rhdpjz"; depends=[checkmate DiagrammeR dplyr magrittr nnet pixiedust plyr rjags stringr]; }; @@ -1688,7 +1704,7 @@ in with self; { ICEinfer = derive2 { name="ICEinfer"; version="1.1"; sha256="0q07npgnssia7assvl1084080w3w434viyz5r1lj5slrx9gfdh8b"; depends=[lattice]; }; ICGE = derive2 { name="ICGE"; version="0.3"; sha256="0xin7zml1nbygyi08hhg3wwr2jr1zcsvrlgia89zp4xanxlzgaqa"; depends=[cluster MASS]; }; ICGOR = derive2 { name="ICGOR"; version="2.0"; sha256="18fn10f5nqqbrfibqmp602nqpx794fy3gpxp1bd10xn48llhqfc4"; depends=[ICsurv MASS pracma survival]; }; - ICRanks = derive2 { name="ICRanks"; version="1.3"; sha256="0n8gyqlwx38v2lfx7r49h43k2f4z4ml78x3lq0sc952n4rckzgiv"; depends=[multcomp Rcpp]; }; + ICRanks = derive2 { name="ICRanks"; version="2.0"; sha256="1zgnb66rizsihxwqw3m9vvbdia051jn0zmvjy8hryccw3qkxsa06"; depends=[multcomp Rcpp]; }; ICS = derive2 { name="ICS"; version="1.3-1"; sha256="0x3cwhvzcibgyb8gqy6dc6lgnvbf6x8425zai57g8yn5i6zzc1li"; depends=[mvtnorm survey]; }; ICSNP = derive2 { name="ICSNP"; version="1.1-1"; sha256="1zf0k1kwdmjjqsbiiy3r2l47vjsrg09fj65p6zfld3j4gjbp17fd"; depends=[ICS mvtnorm]; }; ICSOutlier = derive2 { name="ICSOutlier"; version="0.3-0"; sha256="1vj1y4zw8pkghkg4qnmx0yk1yw4zzl9075n5czrna9ckk2p29fmh"; depends=[ICS moments mvtnorm]; }; @@ -1729,6 +1745,7 @@ in with self; { IPMRF = derive2 { name="IPMRF"; version="1.2"; sha256="1zvwwhiy0p134zvm5ldc92pdd1ap72bhbrlf02rz9m2hlsxmwy67"; depends=[gbm party randomForest]; }; IPMpack = derive2 { name="IPMpack"; version="2.1"; sha256="08b79g5a9maxnxladvc2x2dgcmm427i8p6hhgda3mw2h5qmch2q3"; depends=[MASS Matrix nlme]; }; IPSUR = derive2 { name="IPSUR"; version="3.0"; sha256="0nlxlmp2vjj17pxvx9nly85wnwgv19qs1a3fsw7p1c5jrk6daqqi"; depends=[actuar aplpack binom boot coin distrEx e1071 HH Hmisc lmtest mvtnorm prob qcc RcmdrPlugin_IPSUR reshape scatterplot3d TeachingDemos vcd]; }; + IPWboxplot = derive2 { name="IPWboxplot"; version="0.1.0"; sha256="0lyqcjnbissick5hzwrx21pykq4pww9j0i03j0gy43awl1cq5qq8"; depends=[isotone]; }; IPWsurvival = derive2 { name="IPWsurvival"; version="0.5"; sha256="0lmw0ifj8cds8lzyjkkv0i0zim23p0a3pawlhmhdm3nfvwawb853"; depends=[survival]; }; IPtoCountry = derive2 { name="IPtoCountry"; version="0.0.1"; sha256="1b10z93mc31cr1c5wxp9xz9cr3jm4n4g5kav09dyallpgw60rskp"; depends=[data_table devtools dtables ggplot2 install_load maps scales]; }; IQCC = derive2 { name="IQCC"; version="0.7"; sha256="1zalpmyywkrnci0jd8irakjhiqmr52zhj1sbxf9pz5c7wks2rdbc"; depends=[MASS miscTools qcc]; }; @@ -1737,7 +1754,6 @@ in with self; { IRISSeismic = derive2 { name="IRISSeismic"; version="1.4.9"; sha256="1732056jcq06wb65648vx4h80dfk0brd8igm6ssk5hgfjxzy221n"; depends=[pracma RCurl seismicRoll signal stringr XML]; }; IROmiss = derive2 { name="IROmiss"; version="1.0.1"; sha256="01l08s1g7h8cki372daa61pw3wac3pbv5d4yqnphg5p8ihsmrc5d"; depends=[equSA huge mvtnorm ncvreg]; }; IRTShiny = derive2 { name="IRTShiny"; version="1.2"; sha256="094ax94y6k5z4vlxfla2w19f57q0z32nwwd5npjbgmnkhvfhhl9v"; depends=[beeswarm CTT ltm psych shiny shinyAce]; }; - IRTpp = derive2 { name="IRTpp"; version="0.2.6.1"; sha256="10shzyiawk65pikawvhg58kx6fpvs1dazqmfjf3rfvly1lc0px1q"; depends=[FactoMineR MASS mvtnorm numDeriv Rcpp]; }; IRdisplay = derive2 { name="IRdisplay"; version="0.7.0"; sha256="12chk53nf4zckgc4yl7gbvd7m5dvli52inp5b3f0zvcjvfncksli"; depends=[repr]; }; IRkernel = derive2 { name="IRkernel"; version="0.8.14"; sha256="0p0fkclvcgcgswn030nclsl28g2waakgixqzfvy6326ji5li6mvr"; depends=[crayon digest evaluate IRdisplay jsonlite pbdZMQ repr uuid]; }; ISAT = derive2 { name="ISAT"; version="1.0.5"; sha256="0xlq568spfz527jxbqamrn1j87hnasg0kp2bcyjycaghmhsc6zmg"; depends=[gtools stringr]; }; @@ -1842,6 +1858,7 @@ in with self; { Johnson = derive2 { name="Johnson"; version="1.4"; sha256="12ajcfz5mwxvimv8nq683a2x3590gz0gnyviviyzf5x066a4q0lj"; depends=[]; }; JointAI = derive2 { name="JointAI"; version="0.4.0"; sha256="0nl6zgzmdw3wg9r3xqwh93hlyg379r8apc25k4k0fjgv446cl39l"; depends=[coda MASS mcmcse rjags]; }; JointModel = derive2 { name="JointModel"; version="1.0"; sha256="1zgs5c7saqyqxvxmhw5sxy5w67abq344aid6igw1da05bfy2az6h"; depends=[lme4 statmod survival]; }; + JointNets = derive2 { name="JointNets"; version="1.0.0"; sha256="1kvpx1xmpw1pns8x9wk4s27vf8wq6bq3r5bv1w9kbdd7130bpspz"; depends=[brainR igraph lpSolve MASS misc3d oro_nifti pcaPP rgl shiny]; }; Julia = derive2 { name="Julia"; version="1.1"; sha256="0i1n150d89pkds7qyr0xycz6h07zikb2y07d5fcpaqs4446a8prg"; depends=[]; }; JuliaCall = derive2 { name="JuliaCall"; version="0.16.1"; sha256="11ganlkc65i4vljdjzhr419p1rw3dr4pw2jk6gvb8jk8pasfs36h"; depends=[Rcpp]; }; JumpTest = derive2 { name="JumpTest"; version="0.0.1"; sha256="1d5zmjwmajzdg5d1ws40zchx9wiaav01fby1v3irym2mx30jgbqn"; depends=[MASS Rcpp RcppEigen]; }; @@ -1918,7 +1935,7 @@ in with self; { LINselect = derive2 { name="LINselect"; version="1.1"; sha256="1dx97pnfwlv6w00qp8b2ah8jl1arfh39x1vzry8zrxgxisq407wq"; depends=[elasticnet gtools MASS mvtnorm pls randomForest]; }; LIStest = derive2 { name="LIStest"; version="2.1"; sha256="1gk253v3f1jcr4z5ps8nrqf1n7isjhbynxsi9jq729w7h725806a"; depends=[]; }; LLM = derive2 { name="LLM"; version="1.0.0"; sha256="0x4488mg8q4nhyjhqlzkwmh51frkkjn0gir22rk8rfzg4r6d18d6"; depends=[partykit RWeka stringr]; }; - LLSR = derive2 { name="LLSR"; version="0.0.2.4"; sha256="0r3d3cr86ilx0vm8xxqlmmsix1zivm4g11xsg2n7gyg8bcg8qf86"; depends=[digest dplyr ggplot2 minpack_lm rootSolve svDialogs svglite XLConnect]; }; + LLSR = derive2 { name="LLSR"; version="0.0.2.5"; sha256="0m8pikszldclhjbdpd6jvf5yaxr7hbv54fpj768rlvz2df4ylgys"; depends=[digest dplyr ggplot2 minpack_lm rootSolve svDialogs svglite XLConnect]; }; LMERConvenienceFunctions = derive2 { name="LMERConvenienceFunctions"; version="2.10"; sha256="08jz0i7sv7gn3bqckphbmnx0kc6yjnfvi06iyf7pcdzjaybxhj06"; depends=[fields LCFdata lme4 Matrix mgcv rgl]; }; LMest = derive2 { name="LMest"; version="2.4.3"; sha256="0ynkm4f1ri80h5fraywyvwhrm6f6sa7hp95rzl29zc91904yycx1"; depends=[MASS mmm MultiLCIRT mvtnorm]; }; LMfilteR = derive2 { name="LMfilteR"; version="0.1.2"; sha256="10agjrljnqw689nn9af9ihhb9sq2gmsx7l3zfmrizkavjjk67mcd"; depends=[MASS]; }; @@ -1954,17 +1971,19 @@ in with self; { LTPDvar = derive2 { name="LTPDvar"; version="1.2"; sha256="0r9v5g5y9n85jdcvm7zpapm73ism48m3mmybpcmgcs028h2ndv7v"; depends=[]; }; LTR = derive2 { name="LTR"; version="1.0.0"; sha256="15g5hbrwhab80sarbjgwzvsn6c4fl18h014kz5fpzf0n1rijybik"; depends=[]; }; LTRCtrees = derive2 { name="LTRCtrees"; version="1.1.0"; sha256="07mvbk3hwl240r46ahha0a4fzq96awk963zl8dhky51b6abp83gz"; depends=[icenReg inum partykit rpart survival]; }; + LUCIDus = derive2 { name="LUCIDus"; version="0.9.0"; sha256="08z7ikvql40zwnh2sxn9fkzyjyn7gvq2pljff6iyqwvah01fd5ih"; depends=[doParallel foreach glasso glmnet lbfgs Matrix mvtnorm networkD3 nnet]; }; LVGP = derive2 { name="LVGP"; version="2.1.4"; sha256="05krn48q0zz578862jjb4x5wma86blzlpf8cbqdimgkzbysryyy2"; depends=[lhs randtoolbox]; }; LW1949 = derive2 { name="LW1949"; version="1.1.0"; sha256="147ymp7j98ihp1dcz3p5v9ar6h767phjdnga5q5vf1wwa2mxawg7"; depends=[MASS mgcv plotrix]; }; LZeroSpikeInference = derive2 { name="LZeroSpikeInference"; version="1.0.3"; sha256="15x29afaq13iwlj66h97k3kczg9rfgp6i9d76rji58hfgh8i8by6"; depends=[]; }; LaF = derive2 { name="LaF"; version="0.8.0"; sha256="1nasj0502i0dbzqgm1pdvmc0wj1hk2q5fzanpcsh7zslsikiqxyq"; depends=[Rcpp]; }; + LabRS = derive2 { name="LabRS"; version="0.1.0"; sha256="1a9qafimia83qldsif5wfqx273mvqbx22p5i0hg8n4jvj4vzpy2w"; depends=[knitr]; }; LabourMarketAreas = derive2 { name="LabourMarketAreas"; version="3.2.2"; sha256="16v9vwy7g7vj38pbikrinvhx2b5xdl0vd9i6yr9hhdrgqls0c243"; depends=[data_table maptools rgdal rgeos sp spdep]; }; - LadR = derive2 { name="LadR"; version="1.0.4"; sha256="04wg7p9whjna1szdkqhy5m2nbqxllwfd9q2s6h85diby7r3akglz"; depends=[L1pack]; }; + LadR = derive2 { name="LadR"; version="1.0.5"; sha256="0ali0lfsw3f5snsdrv2kawxlj0jg2avlrp31h307nx5mbh6in7zz"; depends=[L1pack]; }; Lahman = derive2 { name="Lahman"; version="6.0-0"; sha256="1616iaa28z6wrxcvvmnic5awj33b7km9yxnn8bnll9yw99ks6qk6"; depends=[dplyr]; }; LakeMetabolizer = derive2 { name="LakeMetabolizer"; version="1.5.0"; sha256="06mvdrdyl0rh9rwd0jxww0sycadcp7cj08hq35q6vyzq0jkxn2xf"; depends=[plyr rLakeAnalyzer]; }; Lambda4 = derive2 { name="Lambda4"; version="3.0"; sha256="04ikkflfr0nmy1gr3gfldlh2v8mpl82k1wwnzp57d2kn75m9vbxz"; depends=[]; }; LambertW = derive2 { name="LambertW"; version="0.6.4"; sha256="09ygalklv0d767nwziqwaxa7h517rzqgaznmb04q43122x2gwb3k"; depends=[ggplot2 lamW MASS RColorBrewer Rcpp reshape2]; }; - Langevin = derive2 { name="Langevin"; version="1.2"; sha256="0iy1nh4wzipw8spmfr0kscdnpaz3cq4idkbl5khiia2jid0kimvl"; depends=[Rcpp RcppArmadillo]; }; + Langevin = derive2 { name="Langevin"; version="1.2.1"; sha256="1bl7145585z173jv8y6f36ba29q1iq29anm44bdq9hcpql235ihy"; depends=[Rcpp RcppArmadillo]; }; LaplaceDeconv = derive2 { name="LaplaceDeconv"; version="1.0.4"; sha256="0n56cmrb536j1vmfizzag1x8wm68c2znpclwbdl8qraqzp8rmffx"; depends=[orthopolynom polynom]; }; LaplacesDemon = derive2 { name="LaplacesDemon"; version="16.1.1"; sha256="0xxx8967v015fy56m0hqfnr1mwgisj8ximdl05bs28ymzvdx37kp"; depends=[]; }; LassoBacktracking = derive2 { name="LassoBacktracking"; version="0.1.2"; sha256="1z1cnj6r6cq3b8xa9qck3ijfmzsr70r2p9m1ndakijb36pgwrzcs"; depends=[Matrix Rcpp]; }; @@ -2070,7 +2089,7 @@ in with self; { MCMCglmm = derive2 { name="MCMCglmm"; version="2.26"; sha256="0dx3464mihnm8pf2vwr409ca5m7mvm2054x9jigazg66zsd3fxyj"; depends=[ape coda corpcor cubature Matrix tensorA]; }; MCMCpack = derive2 { name="MCMCpack"; version="1.4-4"; sha256="1xzrgib2mjz0xpqranhdyc5m4fmg2fir9mcf51ciw5pp53b97qcp"; depends=[coda lattice MASS mcmc quantreg]; }; MCMCprecision = derive2 { name="MCMCprecision"; version="0.3.9"; sha256="1zmlz2kwrp1qiyvq3v5vv1rsy3s2idlifmckmgznk4nkqds5ifwh"; depends=[combinat Matrix Rcpp RcppArmadillo RcppEigen RcppProgress]; }; - MCMCvis = derive2 { name="MCMCvis"; version="0.11.2"; sha256="1b81sqvmnqmbm363llgrm61zm2yy0d0myzvv28sf6pibjijdznq8"; depends=[coda overlapping rstan]; }; + MCMCvis = derive2 { name="MCMCvis"; version="0.12.0"; sha256="12wypcbf5sh2r1pk2qd9wxw36xiz6wrzi1nsxgwaj5vm0ld6qc24"; depends=[coda overlapping rstan]; }; MCPAN = derive2 { name="MCPAN"; version="1.1-21"; sha256="0q1m0xg8825q9zjwxcz2h2n0dyr21q5bk29qbqpdhirlwm6f1a51"; depends=[magic MCMCpack multcomp mvtnorm plyr]; }; MCPMod = derive2 { name="MCPMod"; version="1.0-10"; sha256="0ns74qhm9bzi70m9bn61zs4mmqmmxxi77f49pdrcnr8wrrnn1kdn"; depends=[lattice mvtnorm]; }; MCPerm = derive2 { name="MCPerm"; version="1.1.4"; sha256="0g65vzn43k6qrsglxd2kz245f662gl3c2gdz6qvvxa96v6q9lhh1"; depends=[metafor]; }; @@ -2090,7 +2109,7 @@ in with self; { MEGENA = derive2 { name="MEGENA"; version="1.3.7"; sha256="0cr10pmj1n831scz5kgaq3nkglr3imwgc62cxng2dvdxr9991g21"; depends=[BH cluster doParallel foreach fpc ggplot2 ggraph ggrepel igraph Matrix Rcpp reshape]; }; MEMSS = derive2 { name="MEMSS"; version="0.9-2"; sha256="0wyw8yjs4miwgwdfcnfbzvkxrgv5r3jlg3cg8q2vy7s69wvhksmy"; depends=[lme4]; }; MEPDF = derive2 { name="MEPDF"; version="3.0"; sha256="15hbp7g5dsdpvi239jm6jn11fn371ir6la31g0flqkilq6sr1sqd"; depends=[gtools mvtnorm plyr pracma]; }; - MESS = derive2 { name="MESS"; version="0.5.3"; sha256="0m2pb1n7nhwhpygxqhxhi9qyiqjqspz607anli1qrhhwymhhis2i"; depends=[geeM geepack glmnet kinship2 MASS Matrix mvtnorm Rcpp RcppArmadillo]; }; + MESS = derive2 { name="MESS"; version="0.5.4"; sha256="11092snwwj94fcfxsdqmqvlp2z9f1d5aqzrgczzla283543qg7zl"; depends=[geeM geepack glmnet kinship2 MASS Matrix mvtnorm Rcpp RcppArmadillo]; }; MEclustnet = derive2 { name="MEclustnet"; version="1.2.1"; sha256="1pznisvvgshqbixyj8jya35yhmmpxxa1ivh48c9iafgapwc4yn4s"; depends=[e1071 ellipse latentnet MASS mclust mvtnorm nnet vegan]; }; MExPosition = derive2 { name="MExPosition"; version="2.0.3"; sha256="1l27wp0psfvlkk79fhb8ypf8awardjljg1f37yj42friy9pdfksz"; depends=[ExPosition prettyGraphs]; }; MF = derive2 { name="MF"; version="4.3.2"; sha256="1arnhyqf1cjvngygcpqk2g4d52949rhkjmclbaskyxcrvp62qln0"; depends=[]; }; @@ -2106,7 +2125,7 @@ in with self; { MGSDA = derive2 { name="MGSDA"; version="1.4"; sha256="0grwl740yvz2av5nkvmyyrr8ji5f39sjs1c5gxp6lp9p36i2wc32"; depends=[MASS]; }; MHCtools = derive2 { name="MHCtools"; version="1.1.0"; sha256="03y6m3a46bzazxkrxdrii2p1fyc26il09z5676c63rk8wz9wcxa0"; depends=[rlist]; }; MHTcop = derive2 { name="MHTcop"; version="0.1.0"; sha256="1fhi7inv8zf3ygj4pf8am445ldq9qpwzi3ll4xqwz8d4s6ajx405"; depends=[copula matrixStats MCMCpack mvtnorm stabledist]; }; - MHTdiscrete = derive2 { name="MHTdiscrete"; version="1.0.0"; sha256="0w1hxa3qk8glijhc4h1wrl5xw54zflibgilhs1w872w9wrkxs5ih"; depends=[]; }; + MHTdiscrete = derive2 { name="MHTdiscrete"; version="1.0.1"; sha256="0czpsk4jiwbzd6g2dwssmggsdhwchikmc1skv48d9j4xvglns7yw"; depends=[]; }; MHTmult = derive2 { name="MHTmult"; version="0.1.0"; sha256="1y3vh2kab6nfkiz4nzdhrpy9h6drk1ibfd2h62hpr3y09z9a2yld"; depends=[]; }; MHTrajectoryR = derive2 { name="MHTrajectoryR"; version="1.0.1"; sha256="13idcjx7pjpwvr4c52938yqhhaj1gprb8hjhaim3jx4062wf9pla"; depends=[mgcv]; }; MHadaptive = derive2 { name="MHadaptive"; version="1.1-8"; sha256="1w3bm82v8ahxrf0vqn0pznv7dqn212drinkz8y5kr1flx423l9ws"; depends=[MASS]; }; @@ -2121,7 +2140,7 @@ in with self; { MImix = derive2 { name="MImix"; version="1.0"; sha256="033gxr0z2xba0pgckiigblb1xa94wrfmpgv3j122cdynjch44j4r"; depends=[]; }; MInt = derive2 { name="MInt"; version="1.0.1"; sha256="1nk02baainxk7z083yyajxrnadg2y1dnhr51fianibvph1pjjkl6"; depends=[glasso MASS testthat trust]; }; MKLE = derive2 { name="MKLE"; version="0.05"; sha256="00hcihjn3xfkzy0lvb70hl2acjkwk6s3y7l4gprix24shnblvxzi"; depends=[]; }; - MKmisc = derive2 { name="MKmisc"; version="1.1"; sha256="1di9dbfnbi69psk3qnrfnc62amx3ifvirw2bb783y775zpg07gz7"; depends=[ggplot2 RColorBrewer robustbase scales]; }; + MKmisc = derive2 { name="MKmisc"; version="1.2"; sha256="01797n3sfab384v1dpa2pj5xrwj1w4y8rwwr0qmjkl3gv0ibp7i4"; depends=[ggplot2 RColorBrewer robustbase scales]; }; ML_MSBD = derive2 { name="ML.MSBD"; version="1.1.0"; sha256="0r9v6dkfarwzryai53c4z5i5isdh8clgwfpzmjsh430zbf9vkdk2"; depends=[ape]; }; MLCIRTwithin = derive2 { name="MLCIRTwithin"; version="2.1"; sha256="07fhbhfnlmllxxdpdqiaz6d72y4pj3vrz6lw5rnlb2m7vknx51ik"; depends=[limSolve MASS MultiLCIRT]; }; MLDS = derive2 { name="MLDS"; version="0.4.5"; sha256="1a5y031kd6zx0zqlk6dvxzsv3isbvg9jap4gqad2jwryh0a9x3c1"; depends=[MASS]; }; @@ -2133,7 +2152,7 @@ in with self; { MLZ = derive2 { name="MLZ"; version="0.1.1"; sha256="1x2mmd7rb6rk2qb84i7k71w8l14m5dvkwg1xpjqgy9lzqnwhxi45"; depends=[dplyr ggplot2 gplots RcppEigen reshape2 TMB]; }; MLmetrics = derive2 { name="MLmetrics"; version="1.1.1"; sha256="061129b36h7xqw4zsznik694n8yy9qq6aaqfhdxkhdv8n5v1nzvp"; depends=[ROCR]; }; MM = derive2 { name="MM"; version="1.6-5"; sha256="0vi6wp6p48jjfmnspdsnmw0yqz39sjk6nrkxdw7kan5h17h4rwd7"; depends=[abind emulator magic Oarray partitions]; }; - MM4LMM = derive2 { name="MM4LMM"; version="1.0.5"; sha256="1kj0kq98fqsfaj2gahn16jnfj86jq1v6jnmcs5ml944yvhmwx5n3"; depends=[Matrix Rcpp RcppEigen]; }; + MM4LMM = derive2 { name="MM4LMM"; version="1.1.4"; sha256="0hx73vc1jcmzrvchni7v4br2ckwbnwy7ra3aakrgv2ca2lx0j8q7"; depends=[Matrix Rcpp RcppEigen]; }; MMAC = derive2 { name="MMAC"; version="0.1.2"; sha256="1xwz48iizf0lvmhc7krsraabc49ky85qvgr23w4ip6jzfv4sn1jr"; depends=[]; }; MMDai = derive2 { name="MMDai"; version="1.4.0"; sha256="0bb7hg8fkmzg87xr1b2hxhy75xi461ks6w12z85k4c77kswfpx3b"; depends=[DirichletReg]; }; MMDvariance = derive2 { name="MMDvariance"; version="0.0.9"; sha256="1yiqabifym7gdknqrhfnql6qc8p163npzrrckbyqjry3yvkqr5wi"; depends=[Biobase lawstat MASS]; }; @@ -2193,13 +2212,14 @@ in with self; { MSQC = derive2 { name="MSQC"; version="1.0.2"; sha256="11wcy04cpjlnc71s2svs4lm1cp718dz1p4a1603x6zwpbf22bygn"; depends=[rgl]; }; MST = derive2 { name="MST"; version="2.1"; sha256="16mnsn2an02k4jrqb6yj0n1i563zny5v10ngfq1y28fqaw6h8yyq"; depends=[Formula MASS partykit survival]; }; MSbox = derive2 { name="MSbox"; version="1.1.1"; sha256="1bw1c6yf3lnvd0rb3nwcrq3yckwnnrvck96mdq64njjldap8i152"; depends=[magick stringr xml2]; }; - MScombine = derive2 { name="MScombine"; version="1.1"; sha256="0kgz1l4jlhcada3fp02dscf4zx6a22cjxj251838lfz65f512hrn"; depends=[plyr]; }; + MScombine = derive2 { name="MScombine"; version="1.2"; sha256="1cidhksv0a1lgz173ry8y3m5z1zqsqn74fy1fjmdw2k8rxqs8pi8"; depends=[plyr]; }; MSeasy = derive2 { name="MSeasy"; version="5.3.3"; sha256="191mvg1imxfjlnd808ypn4lsjx7n6ydf16flax79hv01z7rcjylh"; depends=[amap cluster clValid fpc mzR xcms]; }; MSeasyTkGUI = derive2 { name="MSeasyTkGUI"; version="5.3.3"; sha256="0ihz8vr2wbgy88bzssilgvlhkbr13jznfjvnqy73wpchqgwy0wy6"; depends=[MSeasy]; }; MSwM = derive2 { name="MSwM"; version="1.4"; sha256="1zhfar02s7hm4gjs1flkh9a4526d98hik8bqrksy75758baiqg7l"; depends=[nlme]; }; MTA = derive2 { name="MTA"; version="0.1.2"; sha256="1149xjq6ybjv6llzlq67j5xc6dspb4mvd72n62nlbq3zz80x7f84"; depends=[igraph rgeos sp]; }; MTDrh = derive2 { name="MTDrh"; version="0.1.0"; sha256="0ass3b90nr4i0y7v30hk8xhq3hj9bxaxcsr4f8wfi0lnvzfv6aaa"; depends=[]; }; MTE = derive2 { name="MTE"; version="1.0.0"; sha256="009mrl9dgxafl4hrgfzvsfvgx3dljb0rbbs74j2cxc5ray87kp55"; depends=[parcor quantreg]; }; + MTLR = derive2 { name="MTLR"; version="0.1.0"; sha256="1dp1b6w3nqhchl0mqyc4q25lnr4g8xpdkzjf0lgn0jzm2f0ywf1x"; depends=[Rcpp RcppArmadillo survival]; }; MTS = derive2 { name="MTS"; version="1.0"; sha256="09pypanjmqrvxbrrckydxyyswsgjx4nhb052x4llk7va9w4lbcjs"; depends=[fBasics fGarch mvtnorm Rcpp]; }; MTSYS = derive2 { name="MTSYS"; version="1.2.0"; sha256="04dkan3hxl3difflskp7d1lw1bvxhg4s28ssy2v4m7z7wbpj3v1m"; depends=[]; }; MTurkR = derive2 { name="MTurkR"; version="0.8.0"; sha256="0q498chr2s67ai7lfxi6kdficqbs5sxj9asyv69z2a37fmsr4va7"; depends=[base64enc curl digest XML]; }; @@ -2213,14 +2233,16 @@ in with self; { MVNBayesian = derive2 { name="MVNBayesian"; version="0.0.8-11"; sha256="1iaxyp480v91887cn4w3l74907wvbzs3ay4cjgzd8xk2dp47w8bg"; depends=[mvtnorm plyr]; }; MVR = derive2 { name="MVR"; version="1.33.0"; sha256="1ygz47a2p5r5axql5zsxvsn25pcqyxz6mpw50zfmzrcqdrfa3bg8"; depends=[statmod]; }; MVT = derive2 { name="MVT"; version="0.3"; sha256="0vinlv3d5daf8q7pd9xgs51nxz2njgdba5750vygmv883srlzi9d"; depends=[]; }; - MVar = derive2 { name="MVar"; version="2.0.2"; sha256="0h1sm2vzjg86v3sv43pbf9fxjx5d6bxx519aa25y0r27nh9fif5y"; depends=[]; }; - MVar_pt = derive2 { name="MVar.pt"; version="2.0.2"; sha256="0b7qgfa180vv2m6l5vqxqc96700srdzzix2kwccfvjimby522a1b"; depends=[]; }; + MVTests = derive2 { name="MVTests"; version="1.0"; sha256="1d6vwh8zb13207yn92fi81h9f925ldd8xcgpi825sxv9lwbnabs7"; depends=[matrixcalc]; }; + MVar = derive2 { name="MVar"; version="2.0.3"; sha256="168ffwvwcj5hv6mmg6a223x86rzl1a5bm3jj5czi2gh4vqg13wv9"; depends=[]; }; + MVar_pt = derive2 { name="MVar.pt"; version="2.0.3"; sha256="1z7mfrgk17i5x9d65w6aszvnybj7s95lrrgfvic29km3snwfr9my"; depends=[]; }; MVisAGe = derive2 { name="MVisAGe"; version="0.2.1"; sha256="1plrzzj7cr2hxk1npadvjnk7sanhilh99l5vrkjjh3l6li2ym09b"; depends=[]; }; MWLasso = derive2 { name="MWLasso"; version="1.3.1"; sha256="11lyk46lmjcd60q0mixi41b8ybjgyp1xi18g3ag4450xyhw3r17s"; depends=[]; }; MWRidge = derive2 { name="MWRidge"; version="1.0.0"; sha256="17kvs9npr1ff24z3pv9x2qnfwyy6w3hc7hm60ynzbjlk2rr11xr9"; depends=[glmnet]; }; MXM = derive2 { name="MXM"; version="1.4.1"; sha256="0vcw518h80i49csrg5n5s35w8gsc7lxcsf85b9rdmmq277s2qzvy"; depends=[bigmemory coxme doParallel dplyr energy foreach geepack knitr lme4 MASS nnet ordinal quantreg relations Rfast survival visNetwork]; }; MaXact = derive2 { name="MaXact"; version="0.2.1"; sha256="1n7af7kg54jbr09qk2a8gb9cjh25cnxzj2snscpn8sr8cmcrij0i"; depends=[mnormt]; }; - MachineShop = derive2 { name="MachineShop"; version="0.3.0"; sha256="190ivyq3c04lz08dq6pv57cs9p21f3h7wrg1hb0j03x5m9mjia2p"; depends=[abind foreach ggplot2 Hmisc irr kernlab magrittr MLmetrics ModelMetrics party recipes rsample Rsolnp survival survivalROC]; }; + MachineLearning = derive2 { name="MachineLearning"; version="0.0.2"; sha256="07dpvfmgqidpzvdskrrgbjy5b64w7bg64mia0jipxblxacg8kbnd"; depends=[arules crayon dplyr formula_tools FSelectorRcpp ggplot2 magrittr NbClust rpart rpart_plot]; }; + MachineShop = derive2 { name="MachineShop"; version="1.0.0"; sha256="12afv40fzn82qy2mg5wfcrvqyaica8szdgvk1czagdr1c1zh9fyd"; depends=[abind foreach ggplot2 Hmisc kernlab magrittr party polspline recipes ROCR rsample Rsolnp survival survivalROC]; }; Maeswrap = derive2 { name="Maeswrap"; version="1.7"; sha256="0cnnr5zq7ax1j7dx7ira7iccqppc6qpdjghjarvdb2zj0lf69yyb"; depends=[geometry lattice rgl stringr]; }; MakefileR = derive2 { name="MakefileR"; version="1.0"; sha256="1pfjic2lsar8ghbb6byr4rqrs30qrgfih092z4rxdpsiwkk3y7l1"; depends=[magrittr]; }; Mangrove = derive2 { name="Mangrove"; version="1.21"; sha256="1qf3fjzf0sb6fqbfdbxwbw6wah3gg2qran4mgg13hcmk4n3j0hxp"; depends=[]; }; @@ -2333,7 +2355,7 @@ in with self; { MixtureRegLTIC = derive2 { name="MixtureRegLTIC"; version="1.0.0"; sha256="052gyk4gqv49fa2rxbxnib29f1vjxiw4q8llkfhsv8kw5pw38699"; depends=[]; }; MlBayesOpt = derive2 { name="MlBayesOpt"; version="0.3.3"; sha256="0aazcf94gckgxd51r21hv3msa18br5xcq8xp03w448di546qzbnn"; depends=[data_table dplyr e1071 foreach Matrix ranger rBayesianOptimization rlang xgboost]; }; MmgraphR = derive2 { name="MmgraphR"; version="0.3-1"; sha256="0nfv2cax2v2zhsbprwykngq5n6i5qcf8189rci9d48d5k9qm4a5r"; depends=[colorspace march msm TraMineR]; }; - MoEClust = derive2 { name="MoEClust"; version="1.2.0"; sha256="1is0k96czjqfr9z9kajz1qfqpa7b38pi1lyngzrj6y1hhgfrxywk"; depends=[lattice matrixStats mclust mvnfast nnet vcd]; }; + MoEClust = derive2 { name="MoEClust"; version="1.2.1"; sha256="14gzcgga8471k8nm9ix1d3kibakf0kxk4hpwdh74nvac04phnacf"; depends=[lattice matrixStats mclust mvnfast nnet vcd]; }; MoLE = derive2 { name="MoLE"; version="1.0.1"; sha256="0bq19vwqjn5hl4mw5imkydbp39gal992vnh2dwrq8bb8cmj3qh91"; depends=[]; }; Mobilize = derive2 { name="Mobilize"; version="2.16-4"; sha256="16vdvpwspa0igb52zvzyk0if9l4wq1hm8y42572i8sh1m82wyyfs"; depends=[ggplot2 Ohmage reshape2 wordcloud]; }; Modalclust = derive2 { name="Modalclust"; version="0.7"; sha256="0ymzdxp6rh6baih1xm6kj8l8jxjclvnmq0gfp38cl8lpskspb26x"; depends=[class mvtnorm zoo]; }; @@ -2480,10 +2502,11 @@ in with self; { NetWeaver = derive2 { name="NetWeaver"; version="0.0.2"; sha256="0wsmz7db8q2fycz6rfbbfs67ccj857y9zs4d80k1gnqazgj5whkn"; depends=[]; }; NetworkChange = derive2 { name="NetworkChange"; version="0.4"; sha256="0vl0w7f34fxh32gi521hzyd0a47q7l9fyn53d1g5bsl5w5l9bym1"; depends=[abind ggplot2 ggvis LaplacesDemon MASS MCMCpack mvtnorm plyr RColorBrewer Rmpfr tidyr]; }; NetworkComparisonTest = derive2 { name="NetworkComparisonTest"; version="2.0.1"; sha256="09fqlnpdibf9jr5mw2pzmwi66f6cjz8rmm8jay0cv2bami7jhy2a"; depends=[IsingFit IsingSampler qgraph reshape2]; }; - NetworkDistance = derive2 { name="NetworkDistance"; version="0.3.0"; sha256="1s406jj0hg7aijacwcvp5li5lvdsiiba2vg5qmkdlgmvxw8zb3q8"; depends=[doParallel foreach igraph Matrix network pracma Rcpp RcppArmadillo Rdpack RSpectra]; }; + NetworkDistance = derive2 { name="NetworkDistance"; version="0.3.1"; sha256="17x0is591580zqc2p5v8nwsd6n35mfwalyd15mlgirdcpz1s9wrs"; depends=[CovTools doParallel foreach igraph Matrix network pracma Rcpp RcppArmadillo Rdpack RSpectra]; }; NetworkExtinction = derive2 { name="NetworkExtinction"; version="0.1.0"; sha256="1scza639kf3zzz2yd9q31wsvxpvpq8hbx82a206jkxlxb4dq6vxr"; depends=[broom dplyr ggplot2 magrittr network scales sna tidyr]; }; NetworkInference = derive2 { name="NetworkInference"; version="1.2.3"; sha256="1l30xs7342cyczk7vnnhrz8ngbl1j7y9icvyfabvi9zj87rw788q"; depends=[assertthat checkmate ggplot2 ggrepel Rcpp RcppProgress]; }; NetworkRiskMeasures = derive2 { name="NetworkRiskMeasures"; version="0.1.2"; sha256="0c10nahybjd1n0yr78ynbsdnkfa0p7kz6dx3rbwxwsp3x4mrcd6y"; depends=[dplyr expm ggplot2 Matrix]; }; + NetworkSim = derive2 { name="NetworkSim"; version="0.1.0"; sha256="1gvhzlmq46p99wald4pjnv9wxxqdympjkh3bzi98qa7qi84lny7y"; depends=[igraph incgraph]; }; NetworkToolbox = derive2 { name="NetworkToolbox"; version="1.2.2"; sha256="0rdpq6wxh220lc46ww6bkf6fcc8izlq4k8d0svhc6gmgnscp80gz"; depends=[corrplot doParallel fdrtool foreach igraph MASS Matrix ppcor psych pwr qgraph R_matlab]; }; NeuralNetTools = derive2 { name="NeuralNetTools"; version="1.5.2"; sha256="0d73rbp8v0k0j8dp4yigan7krhglx6qfbadvyg7nsj67xc00vbfd"; depends=[ggplot2 nnet reshape2 scales tidyr]; }; Newdistns = derive2 { name="Newdistns"; version="2.1"; sha256="1b5njkzj8b0wrvvfv904di0933k9d320gadmfm5zl6pzdp34bh1i"; depends=[AdequacyModel]; }; @@ -2537,7 +2560,7 @@ in with self; { ORIClust = derive2 { name="ORIClust"; version="1.0-1"; sha256="1biddddyls2zsg71w4innxl0ckfb80q2j9pmd56wvbc0qnbm0w3q"; depends=[]; }; ORMDR = derive2 { name="ORMDR"; version="1.3-2"; sha256="0y7b2aja3zvsd6lm7jal9pabcfxv16r2wh0kyzjkdfanvvgk3wmm"; depends=[]; }; OSCV = derive2 { name="OSCV"; version="1.0"; sha256="17wrfak6b6m2l3iqbhdwcfh0rlqb14rkvrbari7v46gya9v7hq20"; depends=[mc2d]; }; - OSDR = derive2 { name="OSDR"; version="1.1.2"; sha256="0p7kfmby9fbg3x61khfxf0381830gph82yadl2f9da494ysc1l0l"; depends=[]; }; + OSDR = derive2 { name="OSDR"; version="1.1.3"; sha256="059sj003zsrabmjfhwvvpi599ssrckcqpiw2b3vz405ljnhjmlap"; depends=[]; }; OSMscale = derive2 { name="OSMscale"; version="0.5.1"; sha256="0rjhyhh1iafgd9h1pbd2clyg2sh0gg7y1aqmiislqyn6h6jrvgqn"; depends=[berryFunctions OpenStreetMap sp]; }; OSTSC = derive2 { name="OSTSC"; version="0.0.1"; sha256="0p92w25xvajsn44rd5hg1m7l9l4m0rpmw175nnqr438432hqh7cc"; depends=[doParallel doSNOW fields foreach MASS]; }; OTE = derive2 { name="OTE"; version="1.0"; sha256="18w483syhs523yfib9sibzmj16bypqxk4sc4771kfr1958h3igai"; depends=[randomForest]; }; @@ -2556,6 +2579,7 @@ in with self; { OmicKriging = derive2 { name="OmicKriging"; version="1.4.0"; sha256="08frr38yf5d0l3zwkbq9465xrbyzsn8sx9icqc3yvfnxrkhrpzig"; depends=[doParallel foreach irlba ROCR]; }; OmicsPLS = derive2 { name="OmicsPLS"; version="1.1.0"; sha256="16q226y8wshjdry538w6zk116rip97hr5bfjyz8g960gy40pjn6j"; depends=[ggplot2]; }; Omisc = derive2 { name="Omisc"; version="0.1.0"; sha256="1dii0hr9sbza0vgxqgr3mzsbmx8b5189x9qi4is8zkn5nsl78pk8"; depends=[MASS psych]; }; + OmnibusFisher = derive2 { name="OmnibusFisher"; version="1.0"; sha256="0x3q04g45nixgsrl4biqqi6bk4kx79spq5whm3n4ppr0nkv8dw4h"; depends=[CompQuadForm stringr survey]; }; OnAge = derive2 { name="OnAge"; version="1.0.1"; sha256="1zby5sf92c185b5m19jv4ndgbv6mz107nc47zn1d6bijrypzpc20"; depends=[]; }; Oncotree = derive2 { name="Oncotree"; version="0.3.3"; sha256="147rc9ci66lxbb91ys2ig40sgmldi15p604yysrd4ccbxpbk2zwf"; depends=[boot]; }; OneArmPhaseTwoStudy = derive2 { name="OneArmPhaseTwoStudy"; version="1.0.3"; sha256="0q8g33s1jq0ipvwq83xhrly8idsh68licgyivxc628zbm1id5p38"; depends=[Rcpp]; }; @@ -2647,7 +2671,7 @@ in with self; { PDShiny = derive2 { name="PDShiny"; version="0.1.0"; sha256="0s09sywvy83dj06rkxzyi06wfymwnfpgf3lpgjbb8ps8q3byd4vs"; depends=[shiny]; }; PEGroupTesting = derive2 { name="PEGroupTesting"; version="1.0"; sha256="1z863ard0cc2g8ibxnmxhiqhvs53r6b8gpnavnfchm9432ifcbwi"; depends=[]; }; PEIP = derive2 { name="PEIP"; version="2.2-1"; sha256="0bzynmd7azs33994dlsabxp29lncs1v2njp6iy5l62rwrnxj9y0a"; depends=[bvls fields geigen Matrix pracma RSEIS]; }; - PELVIS = derive2 { name="PELVIS"; version="1.0.4"; sha256="0gw4bxck9fvkpbqls3rj0lwjcnw7i2x3f5whiglhd712j2m63ayq"; depends=[MASS shiny]; }; + PELVIS = derive2 { name="PELVIS"; version="1.0.5"; sha256="02v5ni33jlz3v25v3d5za9jwv8r80n5swvayfjrq9p8443cxv99h"; depends=[DT MASS shiny]; }; PEMM = derive2 { name="PEMM"; version="1.0"; sha256="18dd9hsbdrnhrrff7gpdqrw2jv44j8lg0v3lkcdpbd4pppcaq84h"; depends=[]; }; PET = derive2 { name="PET"; version="0.5.1"; sha256="1gdq7ai8hgl9h53b72j7sfk09l7yr2b84pdy9bl1z3x8zxbsp8br"; depends=[adimpro]; }; PGEE = derive2 { name="PGEE"; version="1.5"; sha256="1qcxbqnbpplnfjy83nm9fj9y4abzgbxnsggzx7ix3vb9qs18cdwh"; depends=[MASS mvtnorm]; }; @@ -2751,7 +2775,7 @@ in with self; { ParentOffspring = derive2 { name="ParentOffspring"; version="1.0"; sha256="117g8h0k65f2cjffigl8n4x37y41rr2kz33qn2awyi876nd3mh93"; depends=[]; }; ParetoPosStable = derive2 { name="ParetoPosStable"; version="1.1"; sha256="1fwji5wrhbxr089dll812csamvb5q2pxn1607rpirarifgfbj28m"; depends=[ADGofTest doParallel foreach lmom]; }; PartCensReg = derive2 { name="PartCensReg"; version="1.39"; sha256="0blzv57cbxqghkz4fc3plvrcw80g0kx17dzmajkfv598m1wm6hc8"; depends=[Matrix optimx ssym]; }; - Partiallyoverlapping = derive2 { name="Partiallyoverlapping"; version="1.1"; sha256="1js7rfzy3qiv2prp398rw7b4mv6n8dk7n2chvc1mc3fgwfgz1c3x"; depends=[]; }; + Partiallyoverlapping = derive2 { name="Partiallyoverlapping"; version="2.0"; sha256="0pb0digyigqyzb0zqikgz002kqf1xprcjhxr62a7iqbzy1yycayf"; depends=[]; }; PathSelectMP = derive2 { name="PathSelectMP"; version="1.1"; sha256="036b70bpylmibny6dny79f7gdzn78arqgl2hfs031vygw63yyh9b"; depends=[mice MplusAutomation]; }; PatternClass = derive2 { name="PatternClass"; version="1.7.1"; sha256="11r4p4s2pm0c4fmnpijzz5srhpai444mbx5nszhkssfsp9rh7cm9"; depends=[SDMTools]; }; PdPDB = derive2 { name="PdPDB"; version="2.0.1"; sha256="05aqg0rqrnlmvjxa32ms1vywgwhw5zlfkyf2ij0fn06rp8l2z3lv"; depends=[dendextend plyr tseries]; }; @@ -2814,7 +2838,6 @@ in with self; { PoisNonNor = derive2 { name="PoisNonNor"; version="1.5"; sha256="1078lfq8y5gsklmgj0jharqpgw7w0yqhc0l4xvkjhr0ifvigmd0h"; depends=[BB corpcor MASS Matrix]; }; PoisNor = derive2 { name="PoisNor"; version="1.2"; sha256="0jpndpxajv598lpk2bx0np0yzfh1k903hpdadr4labpbjmr4pfrr"; depends=[corpcor Matrix mvtnorm]; }; PoissonSeq = derive2 { name="PoissonSeq"; version="1.1.2"; sha256="1hhx0gv06cp6hm6h36mqy411qn9x15y45crpzbyf8crfs85c6gbg"; depends=[combinat]; }; - PoloniexR = derive2 { name="PoloniexR"; version="0.0.1"; sha256="1qik272z5lmzv9k1kfr5v0m8sydbdhbrc732n1zpwnqc1spfqb20"; depends=[anytime digest httr jsonlite RApiDatetime xts zoo]; }; PolyPatEx = derive2 { name="PolyPatEx"; version="0.9.2"; sha256="1z1hwvsw7b6cz5xfy35a5ldrzb3fhp3swiyz56v1zqblpsaz8n9g"; depends=[gtools]; }; PolyTrend = derive2 { name="PolyTrend"; version="1.2"; sha256="17n6phkzgaqrlzs8x1l5smnij1gxfklr0zj9pqfy5n8xqnpwssm5"; depends=[]; }; Polychrome = derive2 { name="Polychrome"; version="1.1.1"; sha256="100hxrzgyxxnwm2y2f0y740x9qk7dhxnrvya6hyg3kgg0mmr3nq3"; depends=[colorspace scatterplot3d]; }; @@ -2836,7 +2859,7 @@ in with self; { Power2Stage = derive2 { name="Power2Stage"; version="0.5-1"; sha256="155w5yp0pdq4g3638m0c54i81lfk0g0f339hzbxpkxhs8ds7g2zv"; depends=[cubature mvtnorm PowerTOST]; }; PowerNormal = derive2 { name="PowerNormal"; version="1.2.0"; sha256="1kryqcjvgwk0l4z3gqxdiz47mha3jw5583jlb9z7ml6v7cam06sm"; depends=[]; }; PowerTOST = derive2 { name="PowerTOST"; version="1.4-7"; sha256="02k6jn5dw70518g55bchax0l5gkci827lqwwyxwnn6rzs3mx4ybs"; depends=[cubature mvtnorm TeachingDemos]; }; - PowerUpR = derive2 { name="PowerUpR"; version="1.0.1"; sha256="1m7w3851kpnf7nnajh9w427cjpyiz18gmqhqvd4gz4gdwqpl6chz"; depends=[]; }; + PowerUpR = derive2 { name="PowerUpR"; version="1.0.2"; sha256="1kzxvya7ql4x2ddr57gy59zvd0jwg9n2lx2fqqap6yz09bkkmgxh"; depends=[]; }; PracTools = derive2 { name="PracTools"; version="1.1"; sha256="19yyhri8wr7ki62zhl9bhpf0wbx9fhrfph44j4l65kx68aphl22d"; depends=[]; }; PreKnitPostHTMLRender = derive2 { name="PreKnitPostHTMLRender"; version="0.1.0"; sha256="1749cd734f4bf0n4068s2m617k6as8h9bwp44mm3la2xy3vjf5g1"; depends=[knitr rmarkdown XML]; }; PreProcess = derive2 { name="PreProcess"; version="3.1.5"; sha256="049gdrp4kwvsid2bn12f61557qgpfv8cpzrd1b4ml47jpw8w0xdk"; depends=[oompaBase]; }; @@ -2918,7 +2941,7 @@ in with self; { QuantifQuantile = derive2 { name="QuantifQuantile"; version="2.2"; sha256="01bdz8a6nhjil6n2z62x5g41v3d6md5v16g0ladsl5zc8raivqdq"; depends=[rgl]; }; QuantileGradeR = derive2 { name="QuantileGradeR"; version="0.1.1"; sha256="1zwc6bg636gk8zll7wpznd3pzl611hcj2fmzp8b9505rra13p0g2"; depends=[]; }; QuantumClone = derive2 { name="QuantumClone"; version="1.0.0.6"; sha256="1520jgkzp8g7gv7ggqhvlrdnpdyhygqjgsd1my5jq30afdqj6qmp"; depends=[DEoptim doParallel foreach fpc ggplot2 gridExtra NbClust optimx]; }; - QuantumOps = derive2 { name="QuantumOps"; version="1.0"; sha256="0jhq8kr3dpwi2dm4n44ljyzr6bd0n7wjg3b2mcbaid8r1dpn87pa"; depends=[]; }; + QuantumOps = derive2 { name="QuantumOps"; version="2.0"; sha256="01j0a0ml0b42i3p39rgk73jsbnv9z2njvlaryy7pj02rmj1bbx66"; depends=[]; }; QuasiSeq = derive2 { name="QuasiSeq"; version="1.0-10-2"; sha256="1mr43vys9l1n859lzlcakjrvjllybgrwl0p8mc28h7m87yjkj670"; depends=[edgeR mgcv pracma]; }; R_cache = derive2 { name="R.cache"; version="0.13.0"; sha256="1hf5cb7xvnca5zlh9245b5g62sgsaxwdhiv7x59yld37cydakm6k"; depends=[digest R_methodsS3 R_oo R_utils]; }; R_devices = derive2 { name="R.devices"; version="2.16.0"; sha256="1f4jsa7b425rm1a0d00njx0pgvrvnhzf0xz2asq4yjhm4rhz0pbz"; depends=[base64enc R_methodsS3 R_oo R_utils]; }; @@ -2935,6 +2958,7 @@ in with self; { R2BayesX = derive2 { name="R2BayesX"; version="1.1-1"; sha256="1ff8cscl839ykp7l34sscc8zqp516mh64igk7dfv9n02l40w8ypf"; depends=[BayesXsrc colorspace mgcv]; }; R2DGC = derive2 { name="R2DGC"; version="1.0.3"; sha256="0f84fmpf3m2s2p6bllvjs8rgnhwjy54adblv02dq8gakwvb4j2aw"; depends=[]; }; R2DT = derive2 { name="R2DT"; version="0.1"; sha256="0zydrdx6xdlacq6s01jwv4rv6ydmbwmiif40rilp8h76bim0kdbr"; depends=[data_table devFunc plyr]; }; + R2GUESS = derive2 { name="R2GUESS"; version="2.0"; sha256="16spx5wq755ar5fvkncikaabrw75hbgnxi7j32vjg8qk4knjiwj9"; depends=[fields MCMCpack mixOmics mvtnorm snowfall]; }; R2HTML = derive2 { name="R2HTML"; version="2.3.2"; sha256="00kxny7hajs9r2kw63qk7d03ggdxx2j1g8vbrmzp806y8aczvik9"; depends=[]; }; R2MLwiN = derive2 { name="R2MLwiN"; version="0.8-5"; sha256="09p8xrxhcf6biy1mffv31p2hlr19s51f3n67az52f3xv5lyp9wm8"; depends=[coda digest doParallel foreach foreign lattice Matrix memisc rbugs texreg]; }; R2OpenBUGS = derive2 { name="R2OpenBUGS"; version="3.2-3.2"; sha256="1cxr93g0fkdv3lqdh63l2gcp7qn3q42pm1r6nzf35550k9ahkhnv"; depends=[boot coda]; }; @@ -2999,11 +3023,11 @@ in with self; { RDSTK = derive2 { name="RDSTK"; version="1.1"; sha256="07vfhsyah8vpvgfxfnmp5py1pxf4vvfzy8jk7zp1x2gl6dz2g7hq"; depends=[plyr RCurl rjson]; }; RDStreeboot = derive2 { name="RDStreeboot"; version="1.0"; sha256="10ry8rna450j389cplvyvgwljxa8lli7licwdin64b1kyzy2cdn7"; depends=[]; }; RDataCanvas = derive2 { name="RDataCanvas"; version="0.1"; sha256="1aw19lmdphxwva5cs3f4fb8hllirzfkk48nqdgrarz32l11y5z5j"; depends=[jsonlite]; }; - RDieHarder = derive2 { name="RDieHarder"; version="0.1.4"; sha256="0p37r45fy75a0is2mycvhrz705707acdb2858yd9qx70n6sg3jph"; depends=[]; }; + RDieHarder = derive2 { name="RDieHarder"; version="0.2.0"; sha256="0yy17vn7m0042ykrlvlvhd2fbz0hw60nra5zmnc822r2f13h2acg"; depends=[]; }; RDocumentation = derive2 { name="RDocumentation"; version="0.8.2"; sha256="0qdn3c5xbjyrhk56wfch50xpyyfd4f79hs0v00cqk9iwsnjlwmb5"; depends=[httr proto rjson]; }; RDota2 = derive2 { name="RDota2"; version="0.1.6"; sha256="0fjsgg4dmzw2xwrf8jxq0f2d7f78bf67bl3ms5qcjk9kskfnymag"; depends=[httr jsonlite]; }; REAT = derive2 { name="REAT"; version="2.2.0"; sha256="1i6pj76k497wvl3a0x0klilyplnnqgizfbqxlyrdyhs5qyh5qq4c"; depends=[]; }; - REBayes = derive2 { name="REBayes"; version="1.3"; sha256="0byd7587vddffplzp8kc2aakab61pck2r25rajxfn0rsvl5yvxyx"; depends=[Matrix reliaR Rmosek]; }; + REBayes = derive2 { name="REBayes"; version="1.4"; sha256="1a5npj0bnabs1p22yahk9644p2ymymy0v0asamviaw2qn4zp9c7p"; depends=[Matrix reliaR Rmosek]; }; RECA = derive2 { name="RECA"; version="1.6"; sha256="0bb6phd7f8rrz7754bn6sp53jrvcl6xg6lkj330945xwia1dhpxi"; depends=[]; }; REDCapR = derive2 { name="REDCapR"; version="0.9.8"; sha256="14psw0sxlyig4nf968n997djwf80hgy5ia2g0bp8rdpn8lrj01g6"; depends=[data_table dplyr httr magrittr readr tibble tidyr]; }; REEMtree = derive2 { name="REEMtree"; version="0.90.3"; sha256="01sp36p12ky8vgsz6aik80w4abs70idr9sn4627lf94r92wwwsbc"; depends=[nlme rpart]; }; @@ -3025,7 +3049,7 @@ in with self; { RFOC = derive2 { name="RFOC"; version="3.4-6"; sha256="0cs5wmpvrlag9aisbfiwkvwcb3skv5z4sawl30krmsq49mzj7yhd"; depends=[GEOmap MASS RPMG RSEIS splancs]; }; RFgroove = derive2 { name="RFgroove"; version="1.1"; sha256="1ank7jvmn83w0xzylf7i0fjb60mbrzzydspksfzcy16rkl6f5dvb"; depends=[fda randomForest wmtsa]; }; RFinanceYJ = derive2 { name="RFinanceYJ"; version="0.3.1"; sha256="0qhmzsch7c2p0zckjkspsajzh8m10cf75ixjlgd0nj8rm41fngm3"; depends=[XML xts]; }; - RFishBC = derive2 { name="RFishBC"; version="0.1.1"; sha256="0fc8b5wiyj8gxvzvak9p2vj5whfw0m64aj8yfq24gb7704iv8m89"; depends=[clisymbols crayon readbitmap rlang settings stringr tidyr withr]; }; + RFishBC = derive2 { name="RFishBC"; version="0.2.0"; sha256="0xs0dg49b07clc8wkbbi8k3xnilvhqcy9zlp6mx7x455z17cr1nj"; depends=[cli clisymbols crayon readbitmap rlang settings stringr tidyr withr]; }; RFmarkerDetector = derive2 { name="RFmarkerDetector"; version="1.0.1"; sha256="1zd0sbcji620pka5600ilj4bq9gzdnk5kf82qfd5k5dcx7q9x7rk"; depends=[AUCRF ggplot2 randomForest ROCR UsingR WilcoxCV]; }; RForcecom = derive2 { name="RForcecom"; version="1.1"; sha256="1ch1pwpnqagzb9n4qbgr804bmnz819kp36r5a4zhijmq8xpv3qr2"; depends=[httr plyr RCurl XML]; }; RFormatter = derive2 { name="RFormatter"; version="0.1.1"; sha256="0jmzdc2cl4vvffsyfwp493fiygh9xinhv970qxp1667rw8wlap8l"; depends=[formatR]; }; @@ -3072,9 +3096,9 @@ in with self; { RJafroc = derive2 { name="RJafroc"; version="1.1.0"; sha256="0qqilj5fpqjx6m6xc5xg0mhqvl801n40vmsccxal7h5wp7c3aazl"; depends=[bbmle binom ggplot2 mvtnorm numDeriv openxlsx Rcpp stringr]; }; RKEA = derive2 { name="RKEA"; version="0.0-6"; sha256="1dncplg83b4zznh1zh90wr8jv5259cy93imrry86c5kqdijmhrrp"; depends=[rJava RKEAjars tm]; }; RKEAjars = derive2 { name="RKEAjars"; version="5.0-3"; sha256="0sm7dkdprmqh319jc43ra7qbk4qq0b2kdj9zs9mjcjz58gcrkl7s"; depends=[rJava]; }; - RKEEL = derive2 { name="RKEEL"; version="1.2.3"; sha256="0w4ahialryzazla0xdfy6ci9v60sn57rmafhcpjp6vdjsy2r27r2"; depends=[arules doParallel foreach gdata Matrix pmml R6 rJava RKEELdata RKEELjars XML]; }; + RKEEL = derive2 { name="RKEEL"; version="1.2.5"; sha256="1939ywx2q61vaphs8i0fpmanwf493ssgdwa0ac6ysdl8h26ks22v"; depends=[arules doParallel foreach gdata Matrix pmml R6 rJava RKEELdata RKEELjars XML]; }; RKEELdata = derive2 { name="RKEELdata"; version="1.0.5"; sha256="1swzqw6j006ya48ahg6n1g8faxhqiv9v5q1zrnihpzj6868lf7y3"; depends=[]; }; - RKEELjars = derive2 { name="RKEELjars"; version="1.0.18"; sha256="0gnjpqkm0bl6wpy9fhma6gfm6ngw786jv01kkbxz072hp1swrgmx"; depends=[downloader]; }; + RKEELjars = derive2 { name="RKEELjars"; version="1.0.19"; sha256="1a879b0xq5jk7r2pf4n41nm0c4himl4yqw083xh2ha4qdhab5kq0"; depends=[downloader]; }; RKlout = derive2 { name="RKlout"; version="1.0"; sha256="17mx099393b1m9dl3l5xjcpzmb9n3cpjghb90m9nidccxkhacmqf"; depends=[RCurl]; }; RLRsim = derive2 { name="RLRsim"; version="3.1-3"; sha256="1r0xqay3jfg435dh9fqc6yy73wjffp658da194rx63vpfhshgz8w"; depends=[lme4 mgcv nlme Rcpp]; }; RLT = derive2 { name="RLT"; version="3.2.2"; sha256="1a8cip975z99g8ljng4y86wv1gf1xwg0sqnxz79wj6zxpw8fk37c"; depends=[]; }; @@ -3100,7 +3124,7 @@ in with self; { RMixpanel = derive2 { name="RMixpanel"; version="0.7-1"; sha256="1xwmmfvky49n1l0w3kwcyaf2h4rhzz4k5icjwvpc90fqk8sxib6a"; depends=[base64enc jsonlite RCurl uuid]; }; RMySQL = derive2 { name="RMySQL"; version="0.10.15"; sha256="0bmc7w5fnkjaf333sgc0hskiy332m9gmfaxg0yzkjxscpizdw43n"; depends=[DBI]; }; RNAseqNet = derive2 { name="RNAseqNet"; version="0.1.2"; sha256="07wk0i8iz3cvkiqawxhm61g3nka8adw0zrrv60zx329gg49w0ycl"; depends=[ggplot2 glmnet hot_deck igraph PoiClaClu]; }; - RNAsmc = derive2 { name="RNAsmc"; version="0.3.0"; sha256="15k88skwqcd0m4m502fipdl1iind4mzizqdz4h63izpqfxijl3iz"; depends=[RRNA]; }; + RNAsmc = derive2 { name="RNAsmc"; version="0.4.0"; sha256="17gkhmnrxa1zwh6qhc0x48smgyq35g5gdb4wv0m5pnbyhkqzs7sq"; depends=[RRNA]; }; RNAstructureModuleMiner = derive2 { name="RNAstructureModuleMiner"; version="0.1.0"; sha256="026r1h4z1jdfww0ay9iixa77ax6b19pgp589bbn77xg1vwjjlbsk"; depends=[RRNA]; }; RNCBIEUtilsLibs = derive2 { name="RNCBIEUtilsLibs"; version="0.9"; sha256="1h1ywx8wxy6n2rbpmjbqw4c0djz29pbncisd0mlbshj1fw226jba"; depends=[rJava]; }; RNCEP = derive2 { name="RNCEP"; version="1.0.8"; sha256="0nkx33997c5rgc3ch5a2bb6rrw5xw1y71rliygw5k1ldi335rsm7"; depends=[abind fields fossil maps RColorBrewer sp tgp]; }; @@ -3138,12 +3162,12 @@ in with self; { ROI_plugin_ecos = derive2 { name="ROI.plugin.ecos"; version="0.3-1"; sha256="1d409hc4cnd1q9d5ldylygis82a4ha1hfbqq36vn7n4xx89wf0k3"; depends=[ECOSolveR Matrix ROI slam]; }; ROI_plugin_glpk = derive2 { name="ROI.plugin.glpk"; version="0.3-0"; sha256="1a1vag47lfhiqmplrbkp95k36angpi9nvh0jd4cgy5y2416w22hn"; depends=[Rglpk ROI]; }; ROI_plugin_ipop = derive2 { name="ROI.plugin.ipop"; version="0.2-5"; sha256="0xampxba8s9kigxv4xj6nb8a7a02w1aj4ansj99z8m7qg0bg2ivv"; depends=[kernlab ROI slam]; }; - ROI_plugin_lpsolve = derive2 { name="ROI.plugin.lpsolve"; version="0.3-1"; sha256="0i1skxk88s8cgxbr2hl5z8h88aqchrfs3206dfb92libw3yi1vas"; depends=[lpSolveAPI ROI]; }; + ROI_plugin_lpsolve = derive2 { name="ROI.plugin.lpsolve"; version="0.3-2"; sha256="0jc6v5xx50gl86ard34k1r32mjqr4hi8ribqm6jkfz68csmzgy6n"; depends=[lpSolveAPI ROI]; }; ROI_plugin_msbinlp = derive2 { name="ROI.plugin.msbinlp"; version="0.3-0"; sha256="00zvjqq2sj7iaymc0lrf5lmqfbqilwh8llmq841lvsmbps45w41k"; depends=[ROI slam]; }; ROI_plugin_neos = derive2 { name="ROI.plugin.neos"; version="0.3-0"; sha256="0hs64qbna8ggmn83g903kbxiyv5ghh2454xca0caf14x9lszv02j"; depends=[ROI xml2 xmlrpc2]; }; ROI_plugin_nloptr = derive2 { name="ROI.plugin.nloptr"; version="0.3-1"; sha256="1cy6q0cchd4rqmd2gxmg83q7cg93w6nnafjqsjxlj13773jr46f0"; depends=[nloptr ROI]; }; ROI_plugin_optimx = derive2 { name="ROI.plugin.optimx"; version="0.3-0"; sha256="0hwjgwmaclq6y5mfmykjrchpyb632qzwcvvs1nnanmrh3yhfmpg9"; depends=[optimx ROI]; }; - ROI_plugin_qpoases = derive2 { name="ROI.plugin.qpoases"; version="0.3-1"; sha256="0ph6l85hrsc40wl443kkxywb2i0cjyh38g20000rnzhygl8kd7db"; depends=[Matrix Rcpp ROI slam]; }; + ROI_plugin_qpoases = derive2 { name="ROI.plugin.qpoases"; version="0.3-2"; sha256="1mclf6nf9ci331pgf3mw2fci502991vfzkiqx4l2l6n662jpxpqy"; depends=[checkmate Rcpp ROI slam]; }; ROI_plugin_quadprog = derive2 { name="ROI.plugin.quadprog"; version="0.2-5"; sha256="1c4fd16kgg60gfs52xc64ii4kzl8fb8qz3rpy69d08avb4q6grir"; depends=[quadprog ROI slam]; }; ROI_plugin_scs = derive2 { name="ROI.plugin.scs"; version="0.3-0"; sha256="0krlrmw85j1g35pvh4ig10djb6y6akyrfymkfk4dqg751w7mb4fm"; depends=[Matrix ROI scs slam]; }; ROI_plugin_symphony = derive2 { name="ROI.plugin.symphony"; version="0.2-5"; sha256="1kpa82g33i2fdcnkpcqdpslj14ilrl7cp0fq1jmp4vj8ddz1s9g5"; depends=[ROI Rsymphony slam]; }; @@ -3190,7 +3214,7 @@ in with self; { RRedshiftSQL = derive2 { name="RRedshiftSQL"; version="0.1.2"; sha256="03jbml8d19hcg6achnyc4hcnl5j10yvsx59j80r46zyn0flsnizq"; depends=[DBI RPostgreSQL]; }; RRphylo = derive2 { name="RRphylo"; version="1.0.0"; sha256="1h167w16lky8aa18fc90rgclx1by3qa9d69n72dxmjzy0d14zjc6"; depends=[ape doParallel foreach geiger lmtest mvMORPH phangorn phytools pvclust R_utils rlist scales smatr]; }; RRreg = derive2 { name="RRreg"; version="0.7.0"; sha256="023yfx5mvpzdhns897ibijc7hbr1771c2k6h1yhiy4b7pnaxl0n6"; depends=[doParallel foreach lme4]; }; - RSA = derive2 { name="RSA"; version="0.9.12"; sha256="0ii7isrk6c1wb3clbwqzr37v2kypwszi4rjf4caip96bmh7jg3kq"; depends=[aplpack ggplot2 lattice lavaan plyr RColorBrewer tkrplot]; }; + RSA = derive2 { name="RSA"; version="0.9.13"; sha256="19xkziixmwwmf7fxkzbsmp9bjii6mznnxyzghbw64kx0kq8bc1ll"; depends=[aplpack ggplot2 lattice lavaan plyr RColorBrewer tkrplot]; }; RSADBE = derive2 { name="RSADBE"; version="1.0"; sha256="1nzpm88rrzavk0n8iflsx8r3s1xcry15n80zqdw6jijjycz10w1q"; depends=[]; }; RSAGA = derive2 { name="RSAGA"; version="1.3.0"; sha256="1y1zhy2bxkfsv8vmnxjdg9i5rqkvs32kw8h5z1mclv953srgkpn9"; depends=[gstat magrittr plyr rgdal shapefiles stringr]; }; RSAlgaeR = derive2 { name="RSAlgaeR"; version="1.0.0"; sha256="1hp0v2vkj9ixiv541d53kyl0ph3jsdc5w98r81gv5ck5ixrp6bxp"; depends=[cvTools ggplot2 hydroGOF lubridate mblm plyr]; }; @@ -3225,15 +3249,16 @@ in with self; { RStoolbox = derive2 { name="RStoolbox"; version="0.2.3"; sha256="06b54g186bwgl5g8wkbj6q05bdy6sqvx433xwwvj7az1qxpa5kwr"; depends=[caret codetools doParallel foreach geosphere ggplot2 raster Rcpp RcppArmadillo reshape2 rgdal rgeos sp XML]; }; RStorm = derive2 { name="RStorm"; version="1.0"; sha256="1n2kiy9b8w6rnv2zmzbl22grwibf619hadf2cjq1ch7rmbr7qb65"; depends=[plyr]; }; RStripe = derive2 { name="RStripe"; version="0.1"; sha256="0vp7zsd5xm8rf7196fivb76kkmxfx3gawxlyjhn9xqv92vawivra"; depends=[httr jsonlite RCurl]; }; - RSuite = derive2 { name="RSuite"; version="0.33-246"; sha256="0npaafcz4afpcyvwp7bjyc7vlsypid03rspwb00sf0z3v8k6k1r9"; depends=[devtools git2r httr jsonlite logging processx roxygen2]; }; - RSurveillance = derive2 { name="RSurveillance"; version="0.2.0"; sha256="1lvl9msnd8l9svd9nyivx1cqfmcxirxvfjfj0xv7yjklza8af7w3"; depends=[epiR epitools mc2d]; }; + RSuite = derive2 { name="RSuite"; version="0.34-248"; sha256="0a34zlpnc79f2rv1bi5xx69bg3zkk4xrwg3dh0dyzkrhdn47dd3d"; depends=[devtools git2r httr jsonlite logging processx roxygen2]; }; RSurvey = derive2 { name="RSurvey"; version="0.9.3"; sha256="0yk969jdvpgv01zbmk4zyxcmrbdizh37bddj1k128ndyf191z37x"; depends=[colorspace inlmisc MBA raster rgdal rgeos sp]; }; RSvgDevice = derive2 { name="RSvgDevice"; version="0.6.4.4"; sha256="0vplac5jzg6bmvbpmj4nhiiimsr9jlbk8mzyifnnndk9iyf2lcmz"; depends=[]; }; RSwissMaps = derive2 { name="RSwissMaps"; version="0.1.0"; sha256="0p57pb3p6j0g4ngzikys9i4d02p4dc4k0s8k7r1wgdmdy2rak3k2"; depends=[downloader dplyr ggplot2]; }; RTConnect = derive2 { name="RTConnect"; version="0.1.4"; sha256="1000jmmqzyhl6vh1ii75jdh88s9inaz52gvfwcin2k2zr7bi91ba"; depends=[]; }; + RTD = derive2 { name="RTD"; version="0.1.1"; sha256="1f36wn9f7wjadvll234m97wqfj4adpvif4x0ywn4wfk91cwa5zib"; depends=[httr jsonlite openssl readr urltools]; }; RTDE = derive2 { name="RTDE"; version="0.2-0"; sha256="1dj7dsj4256z9m70y2fpcgprxpqbgqxz0dqwn0jl80sj2325f66s"; depends=[]; }; RTOMO = derive2 { name="RTOMO"; version="1.1-6"; sha256="03jb96ahzgp662vj2v65giv8ss61vad5w26kvq8hg9q06z879jza"; depends=[GEOmap RPMG RSEIS splancs]; }; RTaxometrics = derive2 { name="RTaxometrics"; version="2.3"; sha256="02446y86g21i37ycavg0xc1ggxk0k93d38n71fis9fav06lywxx3"; depends=[]; }; + RTest = derive2 { name="RTest"; version="1.2.3"; sha256="1npk1n770b17rnh69srsng3y64skwkyzdsizficz79dhiq3axrbk"; depends=[base64 glue jsonlite magick magrittr rlang stringr testthat XML]; }; RTextTools = derive2 { name="RTextTools"; version="1.4.2"; sha256="1j3zfywq8xgax51mbizxz704i3ys4vzp8hyi5kkjzq6g2lw7ywq2"; depends=[caTools e1071 glmnet ipred maxent nnet randomForest SparseM tau tm tree]; }; RTextureMetrics = derive2 { name="RTextureMetrics"; version="1.1"; sha256="0d0mvpmcpd62cvqlajrqp32lnvpflyf9bqvdzly2v8v1kb8274fc"; depends=[]; }; RTransProb = derive2 { name="RTransProb"; version="0.3.3"; sha256="1fl8ag7aizj7k7j5ypx632qa98jp3wp8z3mp5z490n1277ajzrkb"; depends=[caret chron e1071 expm MASS Matrix matrixStats neuralnet nnet pracma Rcpp RcppArmadillo zoo]; }; @@ -3287,12 +3312,13 @@ in with self; { RaschSampler = derive2 { name="RaschSampler"; version="0.8-8"; sha256="0y7dkgv1cy6r1mbmyqm27qwl10rl12g1svpx9jkzq5hq0hnm2xhw"; depends=[]; }; RateDistortion = derive2 { name="RateDistortion"; version="1.01"; sha256="1micjlbir1v5ar51g1x7bgkqw9m8217qi82ii6ysgjkhwdvpm075"; depends=[]; }; RatingScaleReduction = derive2 { name="RatingScaleReduction"; version="1.2.2"; sha256="15xkfjp0bkx9wjp8y27vs0iq2ir4qxjdl8405ix59sjb6lkvv3l2"; depends=[ggplot2 pROC]; }; + RationalExp = derive2 { name="RationalExp"; version="0.2.1"; sha256="0zc2bxjqck9qb8s035rj4w76hwzdif7m98qxpsaynniv5857iyz9"; depends=[snowfall]; }; Rbent = derive2 { name="Rbent"; version="0.1.0"; sha256="0xkb57dhhfd3342rv0xwbhbhn4zp5fbfch84fbh0sickm09l9vrj"; depends=[Rfit]; }; Rbgs = derive2 { name="Rbgs"; version="0.2"; sha256="1q0dnbcpgx7x9klr6z33z6g2p9p8mrmhnsqjy6qw15ch720rrgn3"; depends=[imager magrittr rJava]; }; Rbitcoin = derive2 { name="Rbitcoin"; version="0.9.2"; sha256="0ndq4kg1jq6h0jxwhpdp8sw1n5shg53lwa1x0bi7rifmy0gnh66f"; depends=[data_table digest RCurl RJSONIO]; }; Rblpapi = derive2 { name="Rblpapi"; version="0.3.8"; sha256="1d1b3rdp9zqz9x6xb7zmbs4yrz339qjvlhif7s8ifcz1zdpzzhal"; depends=[BH Rcpp]; }; Rborist = derive2 { name="Rborist"; version="0.1-8"; sha256="0zr8vfbv11ascng7n2zv5xbqv7h0r0bycwn8bqlq8q10y2lyxg70"; depends=[Rcpp RcppArmadillo]; }; - Rcan = derive2 { name="Rcan"; version="1.3.62"; sha256="1kvi2ks6y493qxrrlgzyh8az6d5iv820sblybn8k78ixvdam2iv4"; depends=[data_table ggplot2 scales]; }; + Rcan = derive2 { name="Rcan"; version="1.3.64"; sha256="1mngfkjksk7jw7gs16c7b736qmw72vkk7k9vlgqhfixwj0ckbvwb"; depends=[data_table ggplot2 scales]; }; Rcapture = derive2 { name="Rcapture"; version="1.4-2"; sha256="1nsxy5vpfv7fj03i6l5pgzjm0cldwqxxycnvqkfkshbryjcyl0ps"; depends=[]; }; RcellData = derive2 { name="RcellData"; version="1.3-2"; sha256="1zzkgpj2pc42xzz5pspyj981a04gjpna4br3lxna255366ijgz4l"; depends=[]; }; Rcereal = derive2 { name="Rcereal"; version="1.2.1"; sha256="0nl4p0wqpni16z62610sqcxsz1x6kannl2s1zakpmjkk80pyxlk6"; depends=[]; }; @@ -3326,8 +3352,9 @@ in with self; { RcmdrPlugin_RiskDemo = derive2 { name="RcmdrPlugin.RiskDemo"; version="2.0"; sha256="1mclhcb138f13p7ghiggdm8zjrgxqrn3zn8biygfy6yvhw2j396p"; depends=[demography ftsa Rcmdr rgl]; }; RcmdrPlugin_SCDA = derive2 { name="RcmdrPlugin.SCDA"; version="1.1.1"; sha256="0lky4vmia97vcpwsvzprgmkwkdwjwnmi8bdjx3r3w6rrc2lqb6a8"; depends=[Rcmdr SCMA SCRT SCVA]; }; RcmdrPlugin_SLC = derive2 { name="RcmdrPlugin.SLC"; version="0.2"; sha256="1nwpzmgfla1y05dxf81w0wmvvmvcq5jn5k8phlq30920ia7ybs8g"; depends=[Rcmdr SLC]; }; + RcmdrPlugin_TeachStat = derive2 { name="RcmdrPlugin.TeachStat"; version="1.0.10"; sha256="0kbbvwjyfmd14d2nxiyin934vz3n3fgbp04bb8hxpcff3sp3wbxk"; depends=[Hmisc randtests Rcmdr tcltk2 tseries]; }; RcmdrPlugin_TeachingDemos = derive2 { name="RcmdrPlugin.TeachingDemos"; version="1.1-0"; sha256="0fgl1v1g74ca14pf3mmbv26j09v7jy6ddyap5qavgiy9s8qrwrh8"; depends=[Rcmdr rgl TeachingDemos tkrplot]; }; - RcmdrPlugin_UCA = derive2 { name="RcmdrPlugin.UCA"; version="4.2-5"; sha256="1skqqkii44ajdwqj6svk19n4z2vi9lp36j7bdhasd9ay3k8f9wgh"; depends=[randtests Rcmdr TeachingDemos tseries]; }; + RcmdrPlugin_UCA = derive2 { name="RcmdrPlugin.UCA"; version="4.2-6"; sha256="1fdy1xvrfjy2yz9ihhayj3d0avyx8xqlblb2wv73fmqvnvihag49"; depends=[randtests Rcmdr rmarkdown TeachingDemos tseries]; }; RcmdrPlugin_aRnova = derive2 { name="RcmdrPlugin.aRnova"; version="0.0.5"; sha256="0ys3565pcbr554yb1gi2h149vhvwc0gdfmh7mz8zzd4367hqn553"; depends=[Rcmdr]; }; RcmdrPlugin_coin = derive2 { name="RcmdrPlugin.coin"; version="1.0-22"; sha256="0qmdjnjmgq52wgl4llg69q9x7hvwd73mz3swv0sv88v8zqg7xj93"; depends=[coin multcomp Rcmdr survival]; }; RcmdrPlugin_depthTools = derive2 { name="RcmdrPlugin.depthTools"; version="1.3"; sha256="09mjn5jn4rdj1lh515vr3xlnk615flg13kcwbpk0an2si4xkgm9h"; depends=[depthTools Rcmdr]; }; @@ -3376,7 +3403,7 @@ in with self; { RcppMsgPack = derive2 { name="RcppMsgPack"; version="0.2.3"; sha256="0ffdw5ckkax8j87q0ykjhyp45l7gvxjppdi73kc4r5qxvijll2g3"; depends=[BH Rcpp]; }; RcppNLoptExample = derive2 { name="RcppNLoptExample"; version="0.0.1"; sha256="1fml6hpa12q0lgg5fg6fi9lz6mckwh345pbh95mld2qagzvmg01n"; depends=[nloptr Rcpp]; }; RcppNumerical = derive2 { name="RcppNumerical"; version="0.3-2"; sha256="0j0hvwsbidahk2zx3zk7fhc6m9cca27iq3ivx7vdvggz8iqzszrz"; depends=[Rcpp RcppEigen]; }; - RcppParallel = derive2 { name="RcppParallel"; version="4.4.1"; sha256="1y37bpn6ifvlh8ilp78qx518dmal6s0lc16gk029hvy1rdlkr2ga"; depends=[BH]; }; + RcppParallel = derive2 { name="RcppParallel"; version="4.4.2"; sha256="116rd0cxpp92ymj6v275jdf35rx8xpw5l0b6r53cvfc8z97kywr8"; depends=[]; }; RcppProgress = derive2 { name="RcppProgress"; version="0.4.1"; sha256="0yk01hfv961zyp569682k9igvhnwqyg5j0n5fm63sxigj82l2xhi"; depends=[]; }; RcppQuantuccia = derive2 { name="RcppQuantuccia"; version="0.0.2"; sha256="1si5njb8g4g6fjrkqbp3y6z23yxs901nq9kmiwwbqs8di6svc5q3"; depends=[BH Rcpp]; }; RcppRedis = derive2 { name="RcppRedis"; version="0.1.9"; sha256="08c2c5d3rn3z89yhlymbr8w145y85hlz1bq3g6kz0kwkjfnkbs1x"; depends=[BH RApiSerialize Rcpp]; }; @@ -3396,8 +3423,8 @@ in with self; { Rd2md = derive2 { name="Rd2md"; version="0.0.2"; sha256="07j1nnsk5nyl8kvgvh9f684g6bhc01jiq1fcmq2pnpx57jdzfbpi"; depends=[knitr]; }; Rd2roxygen = derive2 { name="Rd2roxygen"; version="1.7"; sha256="0rfhhqibgxapbc9jrv08fnm3p5fqkhj7s9yj7kbcck0lygy1kpx4"; depends=[formatR roxygen2]; }; Rdice = derive2 { name="Rdice"; version="1.0.0"; sha256="1xibvm690808p2g3jch7rh1825yrpgln2hjfclgxjwn822qvs4xr"; depends=[data_table]; }; - Rdimtools = derive2 { name="Rdimtools"; version="0.4.1"; sha256="1yjcplr79f6d6pr5cypkmsjrkazj648l48iigz9i37ldlxygw2qw"; depends=[ADMM CVXR Matrix Rcpp RcppArmadillo RcppDE Rcsdp Rdpack RSpectra Rtsne]; }; - Rdistance = derive2 { name="Rdistance"; version="2.1.2"; sha256="1c9vil4pjd49jmcv7vib98dv31gh794zcxhm30nbv8kx8n16xi0f"; depends=[]; }; + Rdimtools = derive2 { name="Rdimtools"; version="0.4.2"; sha256="1pklnvg3qrlhskhk2vra38nnqcfdi3fncddm39w9mpxzbzmb62k7"; depends=[ADMM CVXR Matrix Rcpp RcppArmadillo RcppDE Rcsdp Rdpack RSpectra Rtsne]; }; + Rdistance = derive2 { name="Rdistance"; version="2.1.3"; sha256="03wh6y9h5jgfc6xdncpgyz0v7lqavikp3pf5wwfmm2rqfj7yjr8c"; depends=[]; }; Rdpack = derive2 { name="Rdpack"; version="0.10-1"; sha256="0bbjnw88h54v40hzim00i8yd3p4rk9i84zfdmgcbnylscwvsf0av"; depends=[bibtex gbRd]; }; Rdrools = derive2 { name="Rdrools"; version="1.1.1"; sha256="0awdj1q9ysrhwli16izi0lb6pppqxs1lb6wlv40111q483p41fj7"; depends=[dplyr magrittr purrr Rdroolsjars rJava rlang tibble]; }; Rdroolsjars = derive2 { name="Rdroolsjars"; version="1.0.1"; sha256="1l9bc1bwpj10irr973hzkhr04i1f3g998n8hcl2k2i9kgv1naqmz"; depends=[rJava]; }; @@ -3414,7 +3441,7 @@ in with self; { Records = derive2 { name="Records"; version="1.0"; sha256="08y1g2m6bdrvv4rpkhd5v2lh7vprxy9bcx9ahp1f7p062bn2lwji"; depends=[]; }; RedditExtractoR = derive2 { name="RedditExtractoR"; version="2.1.2"; sha256="0qbgamqkwh31ybk6a0jrd2r7jfvzprm6s90fiwpld8rzimgnh4f9"; depends=[dplyr igraph magrittr RJSONIO rlang visNetwork]; }; Redmonder = derive2 { name="Redmonder"; version="0.2.0"; sha256="02qrz1b0g7hdacj2s2bks5gfwnypkbiwlmn0bv7im1zz1swg9cp8"; depends=[]; }; - RefFreeEWAS = derive2 { name="RefFreeEWAS"; version="2.1"; sha256="1w0cx988ixl10d8ylfsblmk1mdd9dhzxdhp9z4n1643dkd2xzr02"; depends=[isva quadprog]; }; + RefFreeEWAS = derive2 { name="RefFreeEWAS"; version="2.2"; sha256="1aya34iz5v3xfpj86x9ab998m7fdwl138ly007mgdayacvqi4a6y"; depends=[quadprog]; }; RefManageR = derive2 { name="RefManageR"; version="1.2.0"; sha256="09l17mj9m4v1hhc71smqbk566axycwb0f5np2z11y4waqf09dwkc"; depends=[bibtex httr jsonlite lubridate plyr stringr xml2]; }; RegClust = derive2 { name="RegClust"; version="1.0"; sha256="1d9w74phw4fgafglc18j7dpmln96fvxnf1kdc9zddgj90p8yfx63"; depends=[]; }; RegressionFactory = derive2 { name="RegressionFactory"; version="0.7.2"; sha256="1g23paq42xiiqavikbrflwmr8ikls9z97v1xpgg16pb88svdyayc"; depends=[]; }; @@ -3466,8 +3493,8 @@ in with self; { Rknots = derive2 { name="Rknots"; version="1.3.2"; sha256="1krhma8hy3l5lbm6d8rxjlj9jw1zrd16h4wy4p1clfa5vlhh3bwi"; depends=[bio3d rgl rSymPy]; }; Rlab = derive2 { name="Rlab"; version="2.15.1"; sha256="1pb0pj84i1s4ckdmcglqxa8brhjha4y4rfm9x0na15n7d9lzi9ag"; depends=[]; }; Rlabkey = derive2 { name="Rlabkey"; version="2.2.4"; sha256="003qr7j38wlr1lwd4cpqxrkd3s7bdiy2da59b9024abs4y43g14n"; depends=[httr jsonlite Rcpp]; }; - Rlda = derive2 { name="Rlda"; version="0.2.5"; sha256="1wv5n1r7m9jimmv4dcih967hy6lmmgmywvch716rqdpayngp399h"; depends=[coda doParallel foreach gtools Rcpp RcppArmadillo RcppProgress]; }; - Rlibeemd = derive2 { name="Rlibeemd"; version="1.4.0"; sha256="0nnkblrgycvfwn0lb9j92f5wpln69kk54z4irwi35rrfl31f689m"; depends=[Rcpp]; }; + Rlda = derive2 { name="Rlda"; version="0.2.6"; sha256="0i8n01h9072q339p1kiqhcpwphw0d2x6bsszbhgfqc2b160dk2bl"; depends=[coda doParallel foreach gtools Rcpp RcppArmadillo RcppProgress]; }; + Rlibeemd = derive2 { name="Rlibeemd"; version="1.4.1"; sha256="06bb939awawpwn4g63b9jzq5b658lsznzy272zl0fy19x62c6bwr"; depends=[Rcpp]; }; Rlinkedin = derive2 { name="Rlinkedin"; version="0.2"; sha256="15sbiis1d0s466nqk1adjhflb01sb9kn25f4y6sagkdggvyz6b56"; depends=[httpuv httr XML]; }; Rlinsolve = derive2 { name="Rlinsolve"; version="0.3.0"; sha256="1kvlpfrw4w2dykpdym9sg6h2ghavnm7lwxn6bzqldwg53wlinvxk"; depends=[BH bigmemory Matrix Rcpp RcppArmadillo Rdpack]; }; Rlof = derive2 { name="Rlof"; version="1.1.1"; sha256="1px6ax2mr2agbhv41akccrjdrvp8a9lmhymp0cn8fjrib0ig8vql"; depends=[doParallel foreach]; }; @@ -3522,6 +3549,7 @@ in with self; { Rrdrand = derive2 { name="Rrdrand"; version="0.1-16"; sha256="0j9yyvq8r1cgwj3kw1ak6hyazr67f2q0c1m651wdm0wcvm1ajx7f"; depends=[]; }; Rsampletrees = derive2 { name="Rsampletrees"; version="1.0.2"; sha256="1wz3dp1myjkxzf9l5mfli3dfbkc2fwg70xx7m9cxa06vq0a4w5pv"; depends=[ape haplo_stats Rcpp]; }; Rsampling = derive2 { name="Rsampling"; version="0.1.1"; sha256="14rp3j7iaii4rc3jkbijmbgvlagxxqjkz3vvfwwpxix43rsi8zsk"; depends=[]; }; + Rsconctdply = derive2 { name="Rsconctdply"; version="0.1.3"; sha256="12xc1laxgivv4szp8341pvhmxnzzzzc2s4jhnqsqrbx71lbd9szg"; depends=[dplyr rjson rsconnect]; }; Rserve = derive2 { name="Rserve"; version="1.7-3"; sha256="09rha4p86vak7ss721mwp5bm5ig09xam8zlqv63n9wf36v3kdmpn"; depends=[]; }; RsimMosaic = derive2 { name="RsimMosaic"; version="1.0.3"; sha256="0jlzrs9xxlpazvq3iw8znk0bd00bzlry7bgxsxq7xl23akizj0ji"; depends=[fields jpeg RANN]; }; Rsmlx = derive2 { name="Rsmlx"; version="1.1.0"; sha256="1ljw8xnzr9asv1vxim86prm8wana6gy72388f273hv36vpr2h3w5"; depends=[ggplot2 gridExtra MASS RJSONIO]; }; @@ -3622,7 +3650,7 @@ in with self; { SFS = derive2 { name="SFS"; version="0.1.2"; sha256="119dh1pyvjna4k0m7nk601kyvm57jijqsr5aphzvgywhkmk9yzh9"; depends=[Rcpp RcppArmadillo]; }; SFtools = derive2 { name="SFtools"; version="0.1.0"; sha256="08k2ywkpk1pzp0qcwm7qx9gnv9hglspl9hrsrrfblagdpkw6rm2x"; depends=[doParallel ff wordspace]; }; SGCS = derive2 { name="SGCS"; version="2.6"; sha256="09czgfc0mg64qcigp36kjaf52zlmrpz3m2d1dp42d9hhlciliqf5"; depends=[spatstat]; }; - SGL = derive2 { name="SGL"; version="1.1"; sha256="1wc430jqn3li102zpfmyyavfbab7x7ww9p89clxsndyigrrbjdr7"; depends=[]; }; + SGL = derive2 { name="SGL"; version="1.2"; sha256="13lpziwkxw2qj4496lvh76d59nfnmrd371jbgz78dhy8dpzyd7c3"; depends=[]; }; SGP = derive2 { name="SGP"; version="1.8-0.0"; sha256="02yh6kvc34gn33cbnhc5b86pmir1zbl6s875hangwb3qx7r13dx0"; depends=[Cairo colorspace crayon data_table digest doParallel doRNG equate foreach gridBase gtools iterators jsonlite matrixStats plotly quantreg randomNames RSQLite sn toOrdinal]; }; SGPdata = derive2 { name="SGPdata"; version="20.0-0.0"; sha256="0fxv7nnxiaq6z9wii9x5qiy0vd2z8jw3gcwl5fj9m29ja7j3900g"; depends=[crayon data_table]; }; SHELF = derive2 { name="SHELF"; version="1.4.0"; sha256="1lc8f19dvnpv1mg32q3vrg96pwcsapkb30fqis6q58v434v42x89"; depends=[ggExtra ggplot2 gridExtra MASS rmarkdown scales shiny tidyr]; }; @@ -3632,6 +3660,7 @@ in with self; { SIBERG = derive2 { name="SIBERG"; version="2.0.2"; sha256="0wfx1dpjd09gb736sm2xhrkba26nwnzn5x575h39n2g33jwqqy2r"; depends=[mclust]; }; SID = derive2 { name="SID"; version="1.0"; sha256="1446zy4rqbw0lpyhnhyd06dzv238dxpdxgmsk34hqv7g3j7q5h1w"; depends=[igraph Matrix pcalg RBGL]; }; SIDES = derive2 { name="SIDES"; version="1.13"; sha256="10759nx2x3gy6zacn37fpr2dgx8j8ap8ic4infljfk0048f9in8w"; depends=[doParallel foreach MASS memoise multicool nnet survival]; }; + SIGN = derive2 { name="SIGN"; version="0.1.0"; sha256="1ak4zv5a50iknrxpfw1iffn8gv8mc0rz2gk96nzky9zx6li5drhk"; depends=[GSVA survcomp survival]; }; SII = derive2 { name="SII"; version="1.0.3.1"; sha256="1xvk04b7725ksfd7h4p7px5zanbf6s7xlmjpb7w0nvbi6km2f7ri"; depends=[]; }; SILGGM = derive2 { name="SILGGM"; version="1.0.0"; sha256="1lhmisgg2zbfksl7czz0fqag3732gkjc44n615ipxbdi2pvnc7m0"; depends=[glasso MASS Rcpp reshape]; }; SIMMS = derive2 { name="SIMMS"; version="1.1.1"; sha256="1wgqz8zgijv5psz5r5zj9k63ikq5sr1dxqxvh48n2041slj6jdap"; depends=[doParallel foreach glmnet MASS survival xtable]; }; @@ -3653,7 +3682,7 @@ in with self; { SMCP = derive2 { name="SMCP"; version="1.1.3"; sha256="0ksx2ibz849vhrz2px9p7z8hlgvspz7kxhadvhk5mhkfbhrnpdf0"; depends=[]; }; SMCRM = derive2 { name="SMCRM"; version="0.0-3"; sha256="1x06w00sdijhg5h1s61q4ym5wgk97pw9md6api7if2cxjv7h5zcy"; depends=[]; }; SMFI5 = derive2 { name="SMFI5"; version="1.0"; sha256="10qp33l0dig00y9gfhpzqig6dbkjw76ch9pfq64dn4xrdkpq1kx5"; depends=[corpcor ggplot2 reshape]; }; - SMFilter = derive2 { name="SMFilter"; version="1.0.2"; sha256="0a2fj7l46n90ws95xg9y84n336s1n2pzl0gqvf87frr97f3g7vrc"; depends=[]; }; + SMFilter = derive2 { name="SMFilter"; version="1.0.3"; sha256="1islyqg9w08mvs2kf0ddmdlp885arzp0jy7mqvixjm4ayi5zfrri"; depends=[]; }; SMLoutliers = derive2 { name="SMLoutliers"; version="0.1"; sha256="10frs7wcyn368m7fvw2f1cyd0xqr6sv5jziixnyvr8q5fadyl2p0"; depends=[]; }; SMM = derive2 { name="SMM"; version="1.0.1"; sha256="0g2blwcir0sxvqrivcyn9a8ssx34834lgcwrjwb6kcrq224dchws"; depends=[DiscreteWeibull seqinr]; }; SMMA = derive2 { name="SMMA"; version="1.0.2"; sha256="13psgrpljnaxpcq4amiyg5mqhpzmb2hyb7jzh3h8wyq18rvs3s4d"; depends=[Rcpp RcppArmadillo]; }; @@ -3722,7 +3751,7 @@ in with self; { SSsimple = derive2 { name="SSsimple"; version="0.6.4"; sha256="0p7d4hx7mhn5myq8ajcij6hhg79rjxigk5v8z93yfdw4gjcb5wad"; depends=[mvtnorm]; }; STAND = derive2 { name="STAND"; version="2.0"; sha256="07wrpmvk0jjlghvrb37xyai48vgzj0fby8y09qdxsxdlgwqg1f3s"; depends=[survival]; }; STAR = derive2 { name="STAR"; version="0.3-7"; sha256="1g78j4iyh78li1jaa3zz5qv4p41cg0imhmvbfakd34l32ppih4ll"; depends=[codetools gss mgcv R2HTML survival]; }; - STARTS = derive2 { name="STARTS"; version="0.5-28"; sha256="14iby34ngn6i6dj7rhg5ykkd4kg06966qpn31lakqpxj41lnxfvy"; depends=[CDM LAM Rcpp RcppArmadillo sirt]; }; + STARTS = derive2 { name="STARTS"; version="1.1-6"; sha256="0c1pcknigqbzplcmykr0214kylrl3rjjsnxv4by06icbbj5dscll"; depends=[CDM LAM Rcpp RcppArmadillo sirt]; }; STARTdesign = derive2 { name="STARTdesign"; version="1.0"; sha256="1q61l3v8ishzax3ppy0pz4ky4l46472l6j36hjlsa8cl01ik1zjf"; depends=[Rcpp]; }; STB = derive2 { name="STB"; version="0.6.3.1"; sha256="0fj1cfxqhijpxl41z799zd7id95jsb84ylrbqzrd1jlp80plyw83"; depends=[Matrix VCA]; }; STEPCAM = derive2 { name="STEPCAM"; version="1.2"; sha256="03crbc7hag8w333j9c7k0q7zy7xmfid4lq773p74r55jmac5xpjf"; depends=[ade4 ape FD geometry gtools MASS vcd]; }; @@ -3748,7 +3777,7 @@ in with self; { SampleSizeProportions = derive2 { name="SampleSizeProportions"; version="1.0"; sha256="0mvkvx3nni0l8ys68sq3h2zlbjvksdcdzxqlf03k0ca5bbcmdf9l"; depends=[]; }; SamplerCompare = derive2 { name="SamplerCompare"; version="1.3.0"; sha256="1lqnkgbg1naa3crk3rakrf37vvxj6mbilbpxrv0k5iifdmh0b7k1"; depends=[mvtnorm]; }; SamplingBigData = derive2 { name="SamplingBigData"; version="1.0.0"; sha256="0khrh7vfqqzpfp16x0ic5ml854wr2fj28cx95s6c0pz91hzlxkns"; depends=[]; }; - SamplingStrata = derive2 { name="SamplingStrata"; version="1.3"; sha256="0x4qppi3pbxmlcpcp62yxjia3nk3iy2f1rl6wqm0jsjp4rbn2mn9"; depends=[doParallel memoise pbapply]; }; + SamplingStrata = derive2 { name="SamplingStrata"; version="1.4"; sha256="1ci0imzdxaakbfi2yy7jcach5k4n1swlcrq8w4jcmapw1g517fib"; depends=[doParallel formattable memoise pbapply]; }; SanFranBeachWater = derive2 { name="SanFranBeachWater"; version="0.1.0"; sha256="18w2q3hzcrbmagnjyrn1ikwiyjh723mjb2vy0d8p1a6za0460p9w"; depends=[dplyr lubridate magrittr readr rvest tibble xml2]; }; SanzCircos = derive2 { name="SanzCircos"; version="0.1.0"; sha256="0vw41qldp1gsj4mx2hdd5jfhx9r8pv62i8gvs86p6bvfzy2l1lq4"; depends=[dplyr pbapply purrr randomcoloR readr tibble tidyr]; }; Scale = derive2 { name="Scale"; version="1.0.4"; sha256="1fa3840kji34qpbw6mxfavk8wq0vq0vx2w6ya71idbkxnvwc3y06"; depends=[Hmisc MASS psych]; }; @@ -3932,7 +3961,7 @@ in with self; { Stack = derive2 { name="Stack"; version="2.0-1"; sha256="09fgfhw9grxnpl5yg05p9gvlz38iw4prns1jn14nj3qx01k5rnxb"; depends=[bit ff ffbase plyr stringr]; }; StagedChoiceSplineMix = derive2 { name="StagedChoiceSplineMix"; version="1.0.0"; sha256="1008gm6zv5k8lpv0qg42qjriajmx0n4kshjh76mvx91dpi788ivh"; depends=[plyr]; }; StakeholderAnalysis = derive2 { name="StakeholderAnalysis"; version="1.2"; sha256="164mah8h8izxaqp8hc43l6mlnf95pydkcx2laqrlqr9b0bybadxb"; depends=[]; }; - StanHeaders = derive2 { name="StanHeaders"; version="2.18.0"; sha256="1h2g4j3ja71szvmwxp5c38s64zf1iamxpjlhkbc40jvw9fhbfc15"; depends=[]; }; + StanHeaders = derive2 { name="StanHeaders"; version="2.18.0-1"; sha256="12kfsci52j29q0ihqdf2v2mz76zj3vx4j80d0py6haxyd5f05bj6"; depends=[]; }; StandardizeText = derive2 { name="StandardizeText"; version="1.0"; sha256="0s267k2b109pcdiyd26gm4ag5afikrnnb55d3cs6g2fvzp744hfp"; depends=[]; }; Stat2Data = derive2 { name="Stat2Data"; version="1.6"; sha256="0pk68ffc6ffpddfpf9wi8ch39h6k3r80kldld3z5pnql18rc8nvx"; depends=[]; }; StatCharrms = derive2 { name="StatCharrms"; version="0.90.91"; sha256="0gjxp6jz8j2kz87g17gax1pyrd498vcswrmv9az5dj52dvyxbwxf"; depends=[cairoDevice car clinfun coxme gWidgets gWidgetsRGtk2 lattice multcomp nlme R2HTML RGtk2 RSCABS survival]; }; @@ -3956,6 +3985,7 @@ in with self; { Strategy = derive2 { name="Strategy"; version="1.0.1"; sha256="0phja1r0qfvcswvw5w1x6ny86p84wkqb029fdqgw10djdm9xp0f2"; depends=[xts zoo]; }; StratifiedBalancing = derive2 { name="StratifiedBalancing"; version="0.2.0"; sha256="0iwzvschncb2vrmsawb6i94shn2cjbkph854x1z4ykr6ddw411g2"; depends=[plyr]; }; StratifiedRF = derive2 { name="StratifiedRF"; version="0.2.2"; sha256="0a5djia6xacs17nnr5knr1acwzicrffz73q9nvnhdmihazq8v27d"; depends=[C50 dplyr]; }; + StratigrapheR = derive2 { name="StratigrapheR"; version="0.0.1"; sha256="1f0kbwymgj05dkak2cizz3jii94y883mxccvdgsayr2kjhrsvw1v"; depends=[diagram dplyr GGally ggplot2 hexbin shiny stringr]; }; StreamMetabolism = derive2 { name="StreamMetabolism"; version="1.1.2"; sha256="1sv30i7armk7jhxg5x9lh0r9qq3xixn1k2h0q89halkh1yraal8a"; depends=[chron maptools zoo]; }; StressStrength = derive2 { name="StressStrength"; version="1.0.2"; sha256="1fq26bzmwsk4nzz9bgasyxz9alw8x2ssahz67mham7vw483w79pd"; depends=[]; }; String2AdjMatrix = derive2 { name="String2AdjMatrix"; version="0.1.0"; sha256="058r30kjjna02nmd6ngqfcnn1yk5390i20xvl6qb5qk3bcp2wmxn"; depends=[stringr]; }; @@ -3977,6 +4007,7 @@ in with self; { SuperLearner = derive2 { name="SuperLearner"; version="2.0-24"; sha256="0hzgqhkj638dcrd4rwi1m37i0rjap2llz6zvf32jbcc5r2i5ixmd"; depends=[cvAUC nnls]; }; SuperPCA = derive2 { name="SuperPCA"; version="0.1.0"; sha256="02kn3gvmlnn89pk054pmyxgkh5h1qf78fym0j3xagl3cq97h1js8"; depends=[fBasics glmnet MASS matlab matlabr Matrix matrixStats pracma psych R_matlab RSpectra spls timeSeries]; }; SuperRanker = derive2 { name="SuperRanker"; version="1.1.1"; sha256="1yiklw9zk7yw0xz5g3lmyl5lv325fnysimdwbxa37nyj6qdfv0ls"; depends=[prodlim Rcpp]; }; + SuperpixelImageSegmentation = derive2 { name="SuperpixelImageSegmentation"; version="1.0.0"; sha256="1jfv0ql58kcczyy44pb51z8w7pj4kk406dnxh2lanc5c9kwj2fk2"; depends=[ClusterR OpenImageR R6 Rcpp RcppArmadillo]; }; SuppDists = derive2 { name="SuppDists"; version="1.1-9.4"; sha256="1ffx8wigqqvz2pnh06jjc0fnf4vq9z2rhwk2y3f9aszn18ap3dgw"; depends=[]; }; SurfaceTortoise = derive2 { name="SurfaceTortoise"; version="0.1.0"; sha256="0cw2nsqc9dx36svb49pqkmrxwk5hhbih206mwwkzfyavswxd2lpv"; depends=[gstat gtools raster rgdal rgeos sp]; }; Surrogate = derive2 { name="Surrogate"; version="1.1"; sha256="1wmvr0wmhb0pfgn5rjq7v0zvkcy0bn01bqylbimkfrp5qlc2nf65"; depends=[extraDistr ks lattice latticeExtra lme4 logistf MASS mixtools msm nlme OrdinalLogisticBiplot rgl rms rootSolve survival]; }; @@ -4037,7 +4068,7 @@ in with self; { TInPosition = derive2 { name="TInPosition"; version="0.13.6"; sha256="1cxxrfpbiyknaivv6gyp79lz0rxwhrndcd054smksxq8zcfz0v7c"; depends=[ExPosition InPosition prettyGraphs TExPosition]; }; TKF = derive2 { name="TKF"; version="0.0.8"; sha256="1db87lwx26ayv1x2k8qd9dfr6j3jkvdl9ykisaxr42l6akqy21nr"; depends=[ape expm numDeriv phangorn phytools]; }; TLBC = derive2 { name="TLBC"; version="1.0"; sha256="08w187akbhfbz6nrrf7avf02lrhgj7bbrjmim9gkh4wlbjhzvw67"; depends=[caret HMM randomForest signal stringr]; }; - TLMoments = derive2 { name="TLMoments"; version="0.7.4"; sha256="0p3d4ydz22k5ardk8qr7sgfhg9qw655bjlbjckvzwps8cbxgnag3"; depends=[ggplot2 hypergeo Rcpp]; }; + TLMoments = derive2 { name="TLMoments"; version="0.7.4.1"; sha256="1miw28mv425i8q5zrdd5xf23glbzlrmgldkmv3w2x35lkh9a1ini"; depends=[ggplot2 hypergeo Rcpp]; }; TLdating = derive2 { name="TLdating"; version="0.1.3"; sha256="12lmakk1zd6wqh1318pnl14i7km2hynjn4ymchfjr2bwmp45c1ra"; depends=[gplots Luminescence]; }; TMB = derive2 { name="TMB"; version="1.7.15"; sha256="1r2d8c5iazihba42sn33yarv0dcfiy989sx64zcf14zr8k6cgjzs"; depends=[Matrix RcppEigen]; }; TMDb = derive2 { name="TMDb"; version="1.0"; sha256="0bbcmsv7b3vvskhdjww03gbcgql44vsvyjz2fajy9w2vgkr6ga90"; depends=[httr jsonlite]; }; @@ -4047,7 +4078,7 @@ in with self; { TP_idm = derive2 { name="TP.idm"; version="1.5"; sha256="07rxn0mpar3p6blg8fd3kbvdngyz9h9n0r0lcljnfdajfzbysv7h"; depends=[]; }; TPD = derive2 { name="TPD"; version="1.0.0"; sha256="1fwj5l519mwsffm2pw2nbpm1mnlxkxzl53i7sqy810fccw47hgag"; depends=[ggplot2 gridExtra ks mvtnorm]; }; TPEA = derive2 { name="TPEA"; version="3.1.0"; sha256="1yyc3q4dyf4d8m7wi851dnxf3xnvvfnvj28kl8z8py4r4jsb2hfy"; depends=[foreach igraph Matrix MESS RCurl XML]; }; - TPMplt = derive2 { name="TPMplt"; version="0.1.1"; sha256="0acxig6b77d7d4slmd27wxvi17q0hkdcifxx90pdxgll068b4kx2"; depends=[directlabels e1071 ggplot2 RColorBrewer rgl rowr VBTree]; }; + TPMplt = derive2 { name="TPMplt"; version="0.1.2"; sha256="1sq72b0n0bskd488z2cag6hz9p48xgkwvp43hfc2gzs5x6ca7pmn"; depends=[directlabels e1071 ggplot2 RColorBrewer rgl rowr VBTree]; }; TPmsm = derive2 { name="TPmsm"; version="1.2.1"; sha256="1vynzb6qpp8785rdjyarhvwbkasviamhljjlnp4i0dds96wwdgx1"; depends=[KernSmooth]; }; TR8 = derive2 { name="TR8"; version="0.9.19"; sha256="1vqjjhyx7igrkdmxbgypds6qq7al6hznv4s5mhspg833mzjhz92c"; depends=[gWidgets gWidgetstcltk plyr rappdirs RCurl readxl reshape taxize XML]; }; TRADER = derive2 { name="TRADER"; version="1.2-3"; sha256="1w9m2b866dyj82s118m64q8j9a1chpq2km2pnn9mfwwj8sivgdgn"; depends=[dplR]; }; @@ -4155,7 +4186,7 @@ in with self; { TopKLists = derive2 { name="TopKLists"; version="1.0.6"; sha256="1hmm9g68scq8sqdb9axqn51p00mx6p6lw0fdgjljfi2q72xcqhq3"; depends=[gplots Hmisc]; }; TotalCopheneticIndex = derive2 { name="TotalCopheneticIndex"; version="1.0.0"; sha256="1w8irl49cxg0rsbk57cl443gmy4i3vrh3ialx9c9d08wc7d2zisa"; depends=[]; }; TraMineR = derive2 { name="TraMineR"; version="2.0-10"; sha256="1zzszc6hnqwlqdmbpg6yphpqd5dflx384hd0dpwdgcy50r04xjgg"; depends=[boot cluster Hmisc RColorBrewer]; }; - TraMineRextras = derive2 { name="TraMineRextras"; version="0.4.3"; sha256="1dmhq5fk2a7vj8s1cvmm7p9pc77z6m46hh7nqp0vkvm811l16v02"; depends=[cluster RColorBrewer survival TraMineR]; }; + TraMineRextras = derive2 { name="TraMineRextras"; version="0.4.4"; sha256="0dx4j1pvd5i3r0yfd9acjm89k47lzyyjbkgpds66q539g24v3q50"; depends=[cluster RColorBrewer survival TraMineR]; }; TrackReconstruction = derive2 { name="TrackReconstruction"; version="1.1"; sha256="1f2l3nshb6qrhyczw5rxqqzmsjxf0rvv3y78j8d9lv1nnd9kxzq5"; depends=[fields RColorBrewer]; }; Trading = derive2 { name="Trading"; version="1.1"; sha256="1mzqck9n14xp16vflx1sx8lry0wjmx37hqv76ldj21xnk5zbrgil"; depends=[]; }; TrafficBDE = derive2 { name="TrafficBDE"; version="0.1.0"; sha256="1lnh9lbjxaradivnd1dkd2szggjh2r4v7klpyxb862dxsmdxxrqw"; depends=[caret data_table dplyr lubridate neuralnet RCurl zoo]; }; @@ -4164,10 +4195,10 @@ in with self; { TransModel = derive2 { name="TransModel"; version="2.1"; sha256="0brlr4w5k8xsgbrizm7ha0cmq0kqzd2fcjpszq7gym844jj93csi"; depends=[MASS survival]; }; TransP = derive2 { name="TransP"; version="0.1"; sha256="0p6pfcp8qjdah0lfhx0a396nxjzp3ckpda9hl3snpppx79iyww55"; depends=[]; }; TreatmentSelection = derive2 { name="TreatmentSelection"; version="2.1.1"; sha256="1pw64hx697jg2f1r2zd8y98g3ivj2gm8fnixcjfn4drsd0xixb4p"; depends=[binom ggplot2 survival]; }; - TreeBUGS = derive2 { name="TreeBUGS"; version="1.4.0"; sha256="0xcipsfwghnf2x2x0i77vr79xs646v354skwxxw6m72ff6arbfz4"; depends=[coda hypergeo logspline MASS Rcpp RcppArmadillo rjags runjags]; }; + TreeBUGS = derive2 { name="TreeBUGS"; version="1.4.1"; sha256="06mmz6aazrwcxfnwhhk1zg3083s319qrwx6rrn8ma8ay156y67v4"; depends=[coda hypergeo logspline MASS Rcpp RcppArmadillo rjags runjags]; }; TreeDep = derive2 { name="TreeDep"; version="0.1.3"; sha256="0ja2hp9sxzybac6dqdsns5q1rj12swl240znsnsffg9mkvzhq6rl"; depends=[ggplot2 lubridate]; }; TreePar = derive2 { name="TreePar"; version="3.3"; sha256="1sm518b1b4b1p0n5979qzvi2nacxpp3znbg9n75pf2a8z8wy6p4l"; depends=[ape deSolve Matrix subplex TreeSim]; }; - TreeSearch = derive2 { name="TreeSearch"; version="0.2.1"; sha256="13ii1192qc2b3kn3l6mpfmrpw5g4bfm30ic79kc1a32wph26z27g"; depends=[ape colorspace gmp memoise phangorn R_cache Rcpp Rdpack]; }; + TreeSearch = derive2 { name="TreeSearch"; version="0.2.2"; sha256="1q9cd0kp78d8gx33mcgbwks085i3rsb2lilsrxyn120ikkzs7gck"; depends=[ape colorspace gmp memoise phangorn R_cache Rcpp Rdpack]; }; TreeSim = derive2 { name="TreeSim"; version="2.3"; sha256="1y98m2whpx9kssgklw2d6prs6af9vcn8yva1l7lm1l509py1fn6h"; depends=[ape geiger]; }; TreeSimGM = derive2 { name="TreeSimGM"; version="2.3"; sha256="0qwqvmmdn290llz5hmmx2q24jjmd1bxssrslzv31kzi1yq5h6w0b"; depends=[ape TreeSim]; }; TrendInTrend = derive2 { name="TrendInTrend"; version="1.1.2"; sha256="1kdjrzv2s5vpyg1lx6qkxj3dyi84qwhrvz17mx731f9pp70cz29j"; depends=[pROC rms]; }; @@ -4231,6 +4262,7 @@ in with self; { VCA = derive2 { name="VCA"; version="1.3.4"; sha256="1qyf20i6bgjg3lxivhx4kgr66m63wkzw8r26aqhz0cs1j0w741dk"; depends=[lme4 Matrix numDeriv]; }; VDA = derive2 { name="VDA"; version="1.3"; sha256="063mpwbyykx4f46wzfvrgnlq73ar7i06gxr4mjzbhqcfrsybi72b"; depends=[rgl]; }; VDAP = derive2 { name="VDAP"; version="2.0.0"; sha256="134x4aisaim72xkyzb1vb8vhl2m4i12yzh6cj858a1ag7b0ing3n"; depends=[drc ggplot2 reshape2 stringr]; }; + VDJgermlines = derive2 { name="VDJgermlines"; version="0.1"; sha256="1aqjhkcj3bd5hk7iz0f2cy5nfp23gvhqsmg6nzlxd9klwc6xpq2h"; depends=[ape stringdist]; }; VDSPCalibration = derive2 { name="VDSPCalibration"; version="1.0"; sha256="1hrmmhvk3mhd3bdl0msnm5shcj4cjgd3pn1rkfkv8fh4llqvz7w8"; depends=[]; }; VFP = derive2 { name="VFP"; version="1.0"; sha256="1gkpqxmxyv1hdaxk5yi3cd1k9q246q5gj9xhfnc87dp60rfg8p8f"; depends=[gnm MASS]; }; VFS = derive2 { name="VFS"; version="1.0.2"; sha256="1b8sl8id2gj4iqkpjzd3giybbix2jvskwsbw1kqj3zqr77hygxwg"; depends=[e1071 nleqslv]; }; @@ -4295,7 +4327,7 @@ in with self; { WRS2 = derive2 { name="WRS2"; version="0.10-0"; sha256="17iriwkng75iy93mp99ihzmvgpgbrg0sgwxs2yx1d3ss7h0k1x3j"; depends=[MASS mc2d plyr reshape]; }; WRSS = derive2 { name="WRSS"; version="2.0"; sha256="0a6k6c9xpxglw2ph90i8kb1d1kpai82caqkkdy2si6zihs3ih87i"; depends=[GGally ggplot2 Hmisc network nloptr]; }; WRTDStidal = derive2 { name="WRTDStidal"; version="1.1.1"; sha256="0q2rdzbz3cbgr19sh9j3fqdn0lvwrq93qq2rjmnhx6ia9avkywa8"; depends=[caret dplyr fields foreach forecast ggplot2 gridExtra lubridate purrr quantreg RColorBrewer survival tidyr]; }; - WVPlots = derive2 { name="WVPlots"; version="1.0.6"; sha256="13ps401z1c9qyhqh18qkc7isnq4kjc928h001dkhsrd684a0lkly"; depends=[cdata ggplot2 gridExtra mgcv sigr wrapr]; }; + WVPlots = derive2 { name="WVPlots"; version="1.0.7"; sha256="011jknqzrfgk1kqb4k6w5yb6vgcvzjmn9cq7r0snwsfn1zbzs63y"; depends=[cdata ggplot2 gridExtra mgcv sigr wrapr]; }; WWGbook = derive2 { name="WWGbook"; version="1.0.1"; sha256="0q8lnd1fp4rmz715x0lf61py3xw8wg55yq3gvswaqwy68dlqrzjc"; depends=[]; }; WWR = derive2 { name="WWR"; version="1.2.2"; sha256="0ia1dd12r1l08s9nhgvk55jmqwv58jawm25gd2ni6wpa3mcmq02g"; depends=[inline]; }; WaterML = derive2 { name="WaterML"; version="1.7.1"; sha256="0aqcanq2l3m9w1kglmkbqshs80wx9inmjp0c1i2j901g4k35ss5j"; depends=[httr RJSONIO XML]; }; @@ -4325,7 +4357,7 @@ in with self; { WikipediaR = derive2 { name="WikipediaR"; version="1.1"; sha256="0fxk247jb82g0f3nmwraa4kvdpjxy5s4dcyzj9vkjw2lq8by3l0h"; depends=[httr XML]; }; WilcoxCV = derive2 { name="WilcoxCV"; version="1.0-2"; sha256="1kbb7ikgnlxybmvqrbn4cd8xnqrkwipk4xd6yja1xsi39a109xzl"; depends=[]; }; WindCurves = derive2 { name="WindCurves"; version="0.1.3"; sha256="0bvbnrkdk0g0radgcw4zbhq6czpvq3f7f34x83qk09i8ngmwd28c"; depends=[drc imputeTestbench readbitmap]; }; - WordPools = derive2 { name="WordPools"; version="1.0-2"; sha256="1izs4cymf2xy1lax85rvsgsgi05ygf0ibi9gzxc96sbgvy4m78kf"; depends=[]; }; + WordPools = derive2 { name="WordPools"; version="1.1-1"; sha256="081qnsq7wn1vczgf6ipz8wjmyg4vwhj1s5nrzh0dw4p9yz28dxv2"; depends=[]; }; WordR = derive2 { name="WordR"; version="0.3.1"; sha256="17g8v3xhdy57y0b95zrakhi0zamqi35v0zcmjpy47xyqyk4b2grs"; depends=[dplyr flextable officer]; }; Wrapped = derive2 { name="Wrapped"; version="2.0"; sha256="1z5kypsd39z9arsw57axckvl8b4jnr5wv60s9z58f5s89gn5vxxg"; depends=[AdequacyModel ald cubfits evd fBasics gamlss_dist GeneralizedHyperbolic GEVStableGarch glogis irtProb LCA lqmm metRology NormalLaplace normalp ordinal sgt SkewHyperbolic sld sn VarianceGamma VGAM]; }; WrightMap = derive2 { name="WrightMap"; version="1.2.1"; sha256="16zp7h28fap5hq5xzvkb4lc217yhfmwzfbvw2lsni0gf9qxqkgqd"; depends=[]; }; @@ -4350,6 +4382,7 @@ in with self; { Xplortext = derive2 { name="Xplortext"; version="1.1.1"; sha256="18a8qqpakwgv60gm89cmil18q35mlir3xl4yl5j5fswcj5qpdkdx"; depends=[FactoMineR ggplot2 gridExtra slam stringr tm]; }; YPInterimTesting = derive2 { name="YPInterimTesting"; version="1.0.0"; sha256="1ah58dqz277sc99932wln9jqhm63dqg9f7xakaiwh7fhgbq3mpax"; depends=[MASS Rcpp]; }; YPmodel = derive2 { name="YPmodel"; version="1.3"; sha256="1vll33nm7xynnbq15wksk9c38jhjfd6l1bbzijn5skqc5yik1r5x"; depends=[]; }; + YRmisc = derive2 { name="YRmisc"; version="0.1.3"; sha256="13835qlvcv8m0r9iagbln0lzrd03qa8xr4gwg7b3ailjk5lz44hx"; depends=[ggplot2 gridExtra robust]; }; YaleToolkit = derive2 { name="YaleToolkit"; version="4.2.2"; sha256="12wggdyz0wgnmxnqhp8bypyy1x1p50g49fwdzl2l43il44cdyv0g"; depends=[foreach iterators]; }; YieldCurve = derive2 { name="YieldCurve"; version="4.1"; sha256="0w47j8v2lvarrclnixwzaq98nv1xh2m48q5xvnmk7j9nsv2l3p68"; depends=[xts]; }; YuGene = derive2 { name="YuGene"; version="1.1.6"; sha256="1kv9n82wrms0c4y5fz9ckzhm1a609mnqp0pwvd0fpyscp8krmlpp"; depends=[mixOmics]; }; @@ -4397,7 +4430,7 @@ in with self; { accelmissing = derive2 { name="accelmissing"; version="1.4"; sha256="1nql9inx6azdzi3z4sfm2vdml2mms6krl8wzlf1dn1c97ahn57fy"; depends=[mice pscl]; }; accrual = derive2 { name="accrual"; version="1.3"; sha256="11clm9s5c5518nmp6hd6pjnp0s28y92b2i2x0xgj4j5g816p4j3z"; depends=[fgui SMPracticals tcltk2]; }; accrued = derive2 { name="accrued"; version="1.4.1"; sha256="05g1jb5914z18rcai1ahn7nihn27vr2rnadwv94gc1j7ivvikvs5"; depends=[]; }; - acebayes = derive2 { name="acebayes"; version="1.5.2"; sha256="0xdakqh9f0vazyqr044w4gcn1qbv4a5yjdfxpf1ys2nscyky6z7w"; depends=[compare lhs randtoolbox Rcpp RcppArmadillo]; }; + acebayes = derive2 { name="acebayes"; version="1.6.0"; sha256="19bf3swcpr13a3mw767p2wadsmfh8sbj2nw8if4m4ykmnk66r7a2"; depends=[compare lhs randtoolbox Rcpp RcppArmadillo]; }; acepack = derive2 { name="acepack"; version="1.4.1"; sha256="1f98rpfjmhd92rdc3j004plyfpjailz6j0ycysbac0kgj83haxc2"; depends=[]; }; acid = derive2 { name="acid"; version="1.1"; sha256="030i0y8s283ivbsmjccpbv9v7mgbcg2jk9df7vgcbbns74swf9hd"; depends=[gamlss gamlss_dist Hmisc]; }; acm4r = derive2 { name="acm4r"; version="1.0"; sha256="1wqzc35i1rshx0zlmas8y4qkkvy6h9r4i4apscjjv1xg2wjflzxa"; depends=[MASS]; }; @@ -4435,7 +4468,7 @@ in with self; { ade4TkGUI = derive2 { name="ade4TkGUI"; version="0.2-9"; sha256="0kfnikkzhyfxskrphr65b8amjhdfq35x6dda4kivdhn7ak07s3ll"; depends=[ade4 adegraphics lattice tkrplot]; }; adeba = derive2 { name="adeba"; version="1.1.2"; sha256="1z1law3qh6l902g62y8yapk4nypdmb20jmpwhxp9jbglalw9lm73"; depends=[mixtools pdist Rcpp]; }; adegenet = derive2 { name="adegenet"; version="2.1.1"; sha256="0ynfblp0hbd3dp3k86fn1wyhqr28lk6hs2bg4q7gyf0sfdfzwhrh"; depends=[ade4 ape boot dplyr ggplot2 igraph MASS reshape2 seqinr shiny spdep vegan]; }; - adegraphics = derive2 { name="adegraphics"; version="1.0-12"; sha256="0rq1v9fp6nh181y8v8nxch2f8507hz5z2kaxy95ybp4bhp0jj37r"; depends=[ade4 KernSmooth lattice latticeExtra RColorBrewer sp]; }; + adegraphics = derive2 { name="adegraphics"; version="1.0-15"; sha256="12k77x6vnjz9s9dvz1r81ajqcl1nh9g33r7dymaqk2cs5q3wvfw7"; depends=[ade4 KernSmooth lattice latticeExtra RColorBrewer sp]; }; adehabitatHR = derive2 { name="adehabitatHR"; version="0.4.15"; sha256="1bwx2mfkzfknr6fjjkbx2xnm4gksd78i8fz0bcizqyi1zhg5hd0c"; depends=[ade4 adehabitatLT adehabitatMA deldir sp]; }; adehabitatHS = derive2 { name="adehabitatHS"; version="0.3.13"; sha256="158a6qzks0hml6hk4f1vr66gvwdn09792i2ca3k23061i3j3xp75"; depends=[ade4 adehabitatHR adehabitatMA sp]; }; adehabitatLT = derive2 { name="adehabitatLT"; version="0.3.23"; sha256="0hf6wpwhsvfp906xk5sadfnvz524zmm05d0h2zxpx6089c6hnw3j"; depends=[ade4 adehabitatMA CircStats sp]; }; @@ -4477,7 +4510,7 @@ in with self; { ahaz = derive2 { name="ahaz"; version="1.14"; sha256="1z7w5rxd5cya7kxhgxqvn72k87y33ginxra9g7j9wrfs5jgx6kvx"; depends=[Matrix survival]; }; ahnr = derive2 { name="ahnr"; version="0.3.1"; sha256="1g8m3q108ricfyn4fjjaihpr93xz7fm2sfzg3i0fz1n1i703jwm8"; depends=[ggplot2 magrittr matrixcalc pdist pracma purrr visNetwork]; }; ahp = derive2 { name="ahp"; version="0.2.12"; sha256="0zjhgl0smzx4bkhmdm4rmpyrq4hmxy1nkxvwqjr40pz7vm69icqx"; depends=[data_tree DiagrammeR formattable yaml]; }; - ahpsurvey = derive2 { name="ahpsurvey"; version="0.2.2"; sha256="0y1afsxakfx6zfv4vjl54zgp5yqfl2haga08qbz9shjwsm28jw0p"; depends=[dplyr knitr magrittr Rdpack tidyr]; }; + ahpsurvey = derive2 { name="ahpsurvey"; version="0.3.0"; sha256="0w6b5rmq00fs2n45xhw33mnsqj4pfqpdf5ppdysngjkg45z45b5s"; depends=[dplyr knitr magrittr Rdpack tidyr]; }; aiRthermo = derive2 { name="aiRthermo"; version="1.2.1"; sha256="058082qdfi1pbdgf26vbfahri1kbc8b2l816q4dq89j5aj5is0a2"; depends=[]; }; aidar = derive2 { name="aidar"; version="1.0.5"; sha256="1q2iz2qzh2yl0v0sc537xq4vbx2nblym3kv419vr7jvrghdpx3vj"; depends=[XML]; }; aimPlot = derive2 { name="aimPlot"; version="1.0.0"; sha256="1d52b7kccxba6j7n0gbd7pzs0p87zn32vv8gdf2f7lyr75qzgz7x"; depends=[ggplot2]; }; @@ -4541,7 +4574,7 @@ in with self; { aniDom = derive2 { name="aniDom"; version="0.1.3"; sha256="1xjbj9d6kv5nprsh1z58gbi338f7sj7dimgvy92j6n1xbrlh83p5"; depends=[rptR]; }; anim_plots = derive2 { name="anim.plots"; version="0.2"; sha256="1plpi90qzk4ng0sm77fvqyv1063w67axvdc29q5nvz4h6v4j7ks3"; depends=[animation]; }; animalTrack = derive2 { name="animalTrack"; version="1.0.0"; sha256="0jlvfflpaq64s48sblzh1n1vx8g3870iss97whigri29s6hn79ry"; depends=[rgl]; }; - animation = derive2 { name="animation"; version="2.5"; sha256="0pxmihfr3q1hh4cdnzf7wbzqak5spa3kv4p1wl89giqqngqzwcmj"; depends=[]; }; + animation = derive2 { name="animation"; version="2.6"; sha256="02jv4h9hpp8niw9656r5n36kqr71jbyynxnywkkkdi0aj8w3cach"; depends=[magick]; }; anipaths = derive2 { name="anipaths"; version="0.9.6"; sha256="0wqpnn85gqsy0m40allx0mngnq5lqz5qhl9g8v0kh0073xq4mvvc"; depends=[animation knitr mgcv RColorBrewer rgdal scales sp]; }; anocva = derive2 { name="anocva"; version="0.1.1"; sha256="1byg40jla71k1901js5h9yq89j63d00vkm60id1fxlpv95c4wdrr"; depends=[cluster]; }; anoint = derive2 { name="anoint"; version="1.4"; sha256="10gdqgag9pddvxh80h458gagvv1474g4pcpa71cg3h7g62rqvmv5"; depends=[glmnet MASS survival]; }; @@ -4550,6 +4583,7 @@ in with self; { anomalyDetection = derive2 { name="anomalyDetection"; version="0.2.5"; sha256="132wb0xz04zib3x7802b2q546rkf097rsxyi9mi86g6vv7yyw9z1"; depends=[caret dplyr ggplot2 gmp magrittr MASS plyr purrr Rcpp RcppArmadillo tibble tidyr]; }; anominate = derive2 { name="anominate"; version="0.6"; sha256="01p2qkqf88bzhwywyass5r8dwg2ycflmkbzmsps7fzy0kv3xyb02"; depends=[coda MCMCpack pscl wnominate]; }; anonymizer = derive2 { name="anonymizer"; version="0.2.0"; sha256="0zlzxcqy8fjhh6ab58a1pi0k686dzgap58d160ms6bsr5mgn3fbf"; depends=[]; }; + antaresEditObject = derive2 { name="antaresEditObject"; version="0.1.5"; sha256="0bh5p7lbmjq2ycxhf4ckc6g89gx0d5wv2qv64y89nbil9ydmcpvd"; depends=[antaresRead assertthat data_table whisker]; }; antaresProcessing = derive2 { name="antaresProcessing"; version="0.17.0"; sha256="0mq2b1dkkgli8d53mpcllilh72gf8189f5mf0dxjcv4qinnhrrvm"; depends=[antaresRead data_table stringi]; }; antaresRead = derive2 { name="antaresRead"; version="2.2.1"; sha256="0j94waw0pq9fni4kpmcry354fwpqg64k9si5p3zgcrxhx3ah2dp5"; depends=[bit64 data_table lubridate plyr shiny stringr]; }; antaresViz = derive2 { name="antaresViz"; version="0.15.0"; sha256="16gf5spgx56rgf2d25zv5dihhbbgvfxryswfqa4gjlpjc2827zar"; depends=[antaresProcessing antaresRead assertthat data_table dygraphs geojsonio htmltools htmlwidgets leaflet leaflet_minicharts lubridate manipulateWidget plotly rAmCharts raster rgeos shiny sp spMaps webshot]; }; @@ -4599,8 +4633,9 @@ in with self; { archdata = derive2 { name="archdata"; version="1.2"; sha256="0igh6qy3yv5hzprj9izpkqp3f6jkb7pydqzmnl8sqhqjqvb3lnij"; depends=[]; }; archetypes = derive2 { name="archetypes"; version="2.2-0"; sha256="1djzlnl1pjb0ndgpfj905kf9kpgf9yizrcvh4i1p6f043qiy0axf"; depends=[modeltools nnls]; }; archiDART = derive2 { name="archiDART"; version="3.2"; sha256="08jam0nbqvrgrxjqj24k7f0dybyi935w977yi1qk34q1p48462ph"; depends=[rgl sp XML]; }; - archivist = derive2 { name="archivist"; version="2.3.1"; sha256="04f1f9fczibda2a4wivmgwzh5p9xblm9hk8wkgd6xqrvxgv5z8mn"; depends=[DBI digest flock httr lubridate magrittr RCurl RSQLite]; }; + archivist = derive2 { name="archivist"; version="2.3.2"; sha256="0v3l9k0g4ddzqm1aghic4mmnzdbz8hyi2c4zjyv2d34iy58032p3"; depends=[DBI digest flock httr lubridate magrittr RCurl RSQLite]; }; archivist_github = derive2 { name="archivist.github"; version="0.2.6"; sha256="092fzi505vx9xbk41m86d0isxna42iflp7q2kjiqa6z1ccvim2yx"; depends=[archivist digest git2r httr jsonlite]; }; + areal = derive2 { name="areal"; version="0.1.2"; sha256="1015c6hikdwjpiffw0fkgi03f4kvq0wl789yjqn13iwhn06jhpn0"; depends=[dplyr glue lwgeom purrr rlang sf tibble]; }; areaplot = derive2 { name="areaplot"; version="1.2-0"; sha256="0xzfgbnzqsvnq46nsxwyqrwldbaqns3h5np0f5wxpjda9cy2rna1"; depends=[]; }; arena2r = derive2 { name="arena2r"; version="1.0.0"; sha256="14zjpglp389pldi436935fz6mgi4jdgfii1m035nsvihrms9gqkh"; depends=[dplyr ggplot2 magrittr purrr rlang shiny shinyBS shinydashboard shinyjs tidyr]; }; arf3DS4 = derive2 { name="arf3DS4"; version="2.5-10"; sha256="12cbrk57c9m7fj1x7nfmcj1vp28wj0wymsjdz8ylxhm3jblbgmxc"; depends=[corpcor]; }; @@ -4627,7 +4662,7 @@ in with self; { arsenal = derive2 { name="arsenal"; version="1.5.0"; sha256="0yljqa643maa64zq2jig6yiqn1pwhn8sjpmynqfrq5r8pv7xggb3"; depends=[testthat]; }; artfima = derive2 { name="artfima"; version="1.5"; sha256="1nqsq9fsqk9kag9n7i2r9yvf578nkdfrkkv7qy8650prka0jca2p"; depends=[gsl ltsa]; }; arules = derive2 { name="arules"; version="1.6-2"; sha256="0vnss6akk3564kbci3h5rq8ylpckz77cgmflly3gn6fki66f7g96"; depends=[Matrix]; }; - arulesCBA = derive2 { name="arulesCBA"; version="1.1.3-1"; sha256="0k41m966m2x8xjzvpy6xn4whn9l2dpvidyh39kmhyvya87ibhyg8"; depends=[arules discretization Matrix testthat]; }; + arulesCBA = derive2 { name="arulesCBA"; version="1.1.4"; sha256="1d0ln8mislns7ix1rch63ry4856b2cnpx99rmw9d967dmvyrm8vs"; depends=[arules discretization Matrix testthat]; }; arulesNBMiner = derive2 { name="arulesNBMiner"; version="0.1-5"; sha256="1q4sx6c9637kc927d0ylmrh29cmn4mv5jxxpl09yaclzfihjlk9a"; depends=[arules rJava]; }; arulesSequences = derive2 { name="arulesSequences"; version="0.2-20"; sha256="0qgsf1wbdw4yqcnbczi2kcvb6vg9f4gy403qds1qh4129yrjyvy9"; depends=[arules]; }; arulesViz = derive2 { name="arulesViz"; version="1.3-2"; sha256="14cv63kgxjks789gjlxsag5ih146wx0g1pgfgnv12pax022kmwxw"; depends=[arules colorspace DT igraph plotly scatterplot3d seriation vcd visNetwork]; }; @@ -4642,6 +4677,7 @@ in with self; { ash = derive2 { name="ash"; version="1.0-15"; sha256="1ay2a2agdmiz7zzvn26mli0x0iwk09g5pp4yy1r23knhkp1pn2lb"; depends=[]; }; ashr = derive2 { name="ashr"; version="2.2-7"; sha256="1bgkzab7f7fqi259vxrpkxq8yzhh1sl3mqdzc73dk54c5849b2pz"; depends=[assertthat doParallel etrunct foreach Matrix pscl Rcpp SQUAREM truncnorm]; }; asht = derive2 { name="asht"; version="0.9.4"; sha256="1aq384vgf26ig3isyp99z09glcjhl2qd43kp8qdcwk75dcrmxd7z"; depends=[bpcp coin exact2x2 exactci perm ssanv]; }; + askpass = derive2 { name="askpass"; version="1.0"; sha256="0smk5i16di0x3him3v48sh17jqm1zxmy5vdi3d48gfvxsfz323gi"; depends=[sys]; }; aslib = derive2 { name="aslib"; version="0.1"; sha256="0dkb6bb6dqavjklbciqxqhi3fdqib9asdnhiap2gp9b9wfnkyq7k"; depends=[BatchExperiments BatchJobs BBmisc checkmate corrplot ggplot2 llama mlr parallelMap ParamHelpers plyr reshape2 RWeka stringr yaml]; }; asnipe = derive2 { name="asnipe"; version="1.1.11"; sha256="06bjw99rssna1pgxq8yrsp3mbwgs2x3wxf86him1766gvcs9yawq"; depends=[MASS Matrix]; }; aspace = derive2 { name="aspace"; version="3.2"; sha256="1g51mrzb6amafky2kg2mx63g6n327f505ndhna6s488xlsr1sl49"; depends=[Hmisc shapefiles splancs]; }; @@ -4755,7 +4791,7 @@ in with self; { backShift = derive2 { name="backShift"; version="0.1.4.2"; sha256="1nj7mcdpzfzq68qg86rrys752gzw69n99yyb0jzg6r8qrgpcxj49"; depends=[clue ggplot2 igraph MASS matrixcalc mvnmle reshape2]; }; backblazer = derive2 { name="backblazer"; version="0.1.0"; sha256="020kdydksm0brnxsa00blf5sylxd4hz49wmngk1x1fx43kdlyc41"; depends=[httr jsonlite openssl]; }; backpipe = derive2 { name="backpipe"; version="0.2.3"; sha256="12k2cv9x8h0b002m9c8g4vj5a7chp4b8jqz377ia0diqw89dydpm"; depends=[]; }; - backports = derive2 { name="backports"; version="1.1.2"; sha256="0mml9h3xagi7144pyb3jj9zbh9qzns7izkhdg7df20v7bikr6nz8"; depends=[]; }; + backports = derive2 { name="backports"; version="1.1.3"; sha256="1hac46xaawnqajlsfb5k7pfkc2ya9h76s5qv9ycj3jafh93d26z4"; depends=[]; }; backtest = derive2 { name="backtest"; version="0.3-4"; sha256="1s0mf247dz2vvyf4m3sp9xiqhv7xcs4rphyg9gdcy73060sah2ad"; depends=[lattice]; }; bacr = derive2 { name="bacr"; version="1.0.1"; sha256="14zr1v4rihx0ra3x0vsb81vsz0g8gzskkdxkg7nhiz835hp2fiy8"; depends=[MCMCpack]; }; badgecreatr = derive2 { name="badgecreatr"; version="0.1.0"; sha256="070zb5jw817s9ykqc3dvzjqk48612gydkdc31svc0ji01s1y1545"; depends=[stringr]; }; @@ -4768,7 +4804,7 @@ in with self; { bamboo = derive2 { name="bamboo"; version="0.9.23"; sha256="02mvj78kkcpa0bszf8jd0s7nvjwhgbxhgazqssw0fjifs2iqr2zn"; depends=[rscala]; }; bamdit = derive2 { name="bamdit"; version="3.2.1"; sha256="18l9kd3a0d4y6z38k9nm18j32g6dxmwylv8cv1wp3fzffv51lm1s"; depends=[ggExtra ggplot2 gridExtra MASS R2jags rjags]; }; bamlss = derive2 { name="bamlss"; version="1.0-1"; sha256="1nxy8a075dhdwz9jhyicqj1naz95w0mns64c6j59gpzwp03nvml4"; depends=[coda colorspace Formula Matrix MBA mgcv mvtnorm sp survival]; }; - bamp = derive2 { name="bamp"; version="2.0.4"; sha256="02nlz4yqrz6alhf0np1l9kaqmjsh8ni2inbzbf6m37h45sq5ix4c"; depends=[abind coda]; }; + bamp = derive2 { name="bamp"; version="2.0.5"; sha256="0z8gv9py6ismvphxfm75h4hxzc44183kvd7hsiq47k5c5sb63wl9"; depends=[abind coda]; }; banR = derive2 { name="banR"; version="0.2.0"; sha256="0m71m99f8f4wckylry6z16gw6r2cc4wxbd9287ns00jr6s13x6c8"; depends=[dplyr httr magrittr purrr readr rlang stringr tibble]; }; bandit = derive2 { name="bandit"; version="0.5.0"; sha256="03mv4vbn9g4mqikd9map33gmw2fl9xvb62p7gpxs1240w5r4w3fp"; depends=[boot gam]; }; bang = derive2 { name="bang"; version="1.0.0"; sha256="16wy2imrdvhpdzi6ix9k69afqdyc44d1xr655yd3q1cl12x1nr04"; depends=[bayesplot rust]; }; @@ -4788,7 +4824,7 @@ in with self; { baseballDBR = derive2 { name="baseballDBR"; version="0.1.2"; sha256="0w54g1avcqamc12lmvjchlqbqck9jfjccm441k03nsql460mpydq"; depends=[dplyr magrittr rvest xml2]; }; basefun = derive2 { name="basefun"; version="1.0-2"; sha256="16j7lzpyiw9iw3zb1cw2l685303dljv93kdxgfdzajzgcmmmpr6m"; depends=[Matrix orthopolynom polynom variables]; }; baseline = derive2 { name="baseline"; version="1.2-1"; sha256="1vk0vf8p080ainhv09fjwfspqckr0123qlzb9dadqk2601bsivgy"; depends=[SparseM]; }; - basicMCMCplots = derive2 { name="basicMCMCplots"; version="0.1.1"; sha256="08z5bhjk2iiksz62xz6133lsmczkqvza9iyvilq6mrvw5wwy0i7a"; depends=[]; }; + basicMCMCplots = derive2 { name="basicMCMCplots"; version="0.1.2"; sha256="121aiac2n6fxsmgspnj14y0m1xm2aryswq1v9a0bi97dfl251mna"; depends=[]; }; basicTrendline = derive2 { name="basicTrendline"; version="2.0.3"; sha256="10rq9hriyn50b28ikvl0vsvchbkrc0pjzxamq4ix1xd04n4drkl9"; depends=[investr scales]; }; basicspace = derive2 { name="basicspace"; version="0.20"; sha256="0nyljk8ydasirgv7ijxplyhk10s8m9k3rw5qmgf0z81dm7p257wc"; depends=[]; }; basictabler = derive2 { name="basictabler"; version="0.1.0"; sha256="1m4cgghfh3aixsnwjlbaj3prnnqxhij60bakz9vdr5dvnqg92an9"; depends=[dplyr htmltools htmlwidgets jsonlite R6]; }; @@ -4821,7 +4857,7 @@ in with self; { bayeslm = derive2 { name="bayeslm"; version="0.8.0"; sha256="1gvqkbz1wmqkxjwkdgj5pir5j1qy5dzjm4jv6mz3mplm16z5vzbl"; depends=[coda Rcpp RcppArmadillo RcppParallel]; }; bayesloglin = derive2 { name="bayesloglin"; version="1.0.1"; sha256="0j2ziahf6mwsz2gvb1azvdzlmszlpqgr5zqcqa68pxgq947sa2cs"; depends=[igraph]; }; bayeslongitudinal = derive2 { name="bayeslongitudinal"; version="0.1.0"; sha256="0g45ikpnbry1albb3asrzab5z3sy98yf74c64qn02d65xgafifwg"; depends=[LearnBayes MASS mvtnorm]; }; - bayesm = derive2 { name="bayesm"; version="3.1-0.1"; sha256="04b4s8clxrmdyhnhd2arnsdi992422yam3z91w6dzrmngwxq4yaq"; depends=[Rcpp RcppArmadillo]; }; + bayesm = derive2 { name="bayesm"; version="3.1-1"; sha256="0y30cza92s6kgvmxjpr6f5g0qbcck7hslqp89ncprarhxiym2m28"; depends=[Rcpp RcppArmadillo]; }; bayesmeta = derive2 { name="bayesmeta"; version="2.3"; sha256="12rljnlr7wv0q95ild7vrsbgkpg7zw1lmh6gx4kpip1ckax04360"; depends=[forestplot metafor]; }; bayesmix = derive2 { name="bayesmix"; version="0.7-4"; sha256="1qms1nnk2nq3gqr8zf2b9ri4wv8jrxv5i8s087k1rwdvya3k5r9a"; depends=[coda rjags]; }; bayesplot = derive2 { name="bayesplot"; version="1.6.0"; sha256="0in9cq2ybpa7njrwqx4l6nc8i01cjswsvzwlyiw465pi74aapr57"; depends=[dplyr ggplot2 ggridges reshape2 rlang]; }; @@ -4884,7 +4920,7 @@ in with self; { benchmarkme = derive2 { name="benchmarkme"; version="0.6.0"; sha256="0w98q4b814bz3q0vqdfnwqrgfrky3ggsyyzmdiz17kv6xk17qds8"; depends=[benchmarkmeData doParallel foreach httr Matrix]; }; benchmarkmeData = derive2 { name="benchmarkmeData"; version="0.5.1"; sha256="0vv5d90qv81lwrgi5d3zbwlwxwjqlx70xi4ljhcc0ljv50x2rvv4"; depends=[]; }; benchr = derive2 { name="benchr"; version="0.2.2"; sha256="1ls75pmhvj6d4wc9knifv6d1dfr0avfhry370m636mhfpw4z2ybf"; depends=[Rcpp RcppProgress]; }; - benford_analysis = derive2 { name="benford.analysis"; version="0.1.4.1"; sha256="0acbjjavbvsaigy78b5k9qhj8011751116lqln8j0v8w1k3vqwqm"; depends=[data_table]; }; + benford_analysis = derive2 { name="benford.analysis"; version="0.1.5"; sha256="0y0c7l2r9s7lg9bw4ndcqwisa5l6a2cpydn1vmz88h3yva0l68cg"; depends=[data_table]; }; bentcableAR = derive2 { name="bentcableAR"; version="0.3.0"; sha256="1gjrlv94av9955jqhicaiqm36rrgmy0avxn9y7wbp2s1sbg7fyg7"; depends=[]; }; benthos = derive2 { name="benthos"; version="1.3-5"; sha256="1mzhqqy4dblwv70v1ky5gzrr3jyky9k4wibbp589jjjrga2vhq2a"; depends=[dplyr lazyeval readr]; }; ber = derive2 { name="ber"; version="4.0"; sha256="0gl7rms92qpa5ksn8h3ppykmxk5lzbcs13kf2sjiy0r2535n8ydi"; depends=[MASS]; }; @@ -4902,15 +4938,16 @@ in with self; { betategarch = derive2 { name="betategarch"; version="3.3"; sha256="0hqvyps3lwix2fkzk18wrkhxpqhgardvib9sq1ip8gn8sn1dsi8y"; depends=[zoo]; }; bethel = derive2 { name="bethel"; version="0.2"; sha256="1zlkw672k1c5px47bpa2vk3w2906vkhvifz20h6xm7s51gmm64i0"; depends=[]; }; beyondWhittle = derive2 { name="beyondWhittle"; version="1.1"; sha256="178bhy2plkahklgwyhk2rlamjzyi8md612z58wi1mrbryzv4lsy1"; depends=[BH forecast ltsa MASS MTS Rcpp RcppArmadillo]; }; - bezier = derive2 { name="bezier"; version="1.1"; sha256="1bhqf1zbshkf1x8mgqp4mkgdxk9jxi51xj6i47kqkyn9gbdzch0c"; depends=[]; }; + bezier = derive2 { name="bezier"; version="1.1.2"; sha256="1vw5128v8h973xwa1fdm9cw2jvrldj87nd55lddlp3qsz3ag4br6"; depends=[]; }; bfa = derive2 { name="bfa"; version="0.4"; sha256="08n6446xl2w8z0rsqi6v2hp9cp744frxw6vrbxg5cpybhyyfzr36"; depends=[coda Rcpp RcppArmadillo]; }; bfast = derive2 { name="bfast"; version="1.5.7"; sha256="0n75minka55rxpvs3qkj0c65ydn1gc3i8lkr2gdyn1adjkl5yn01"; depends=[forecast raster sp strucchange zoo]; }; bfp = derive2 { name="bfp"; version="0.0-39"; sha256="1g3sbmi1yl7ai8v6a2ri54jqv64wzfy580s8i1w9xwbqjcrpj77m"; depends=[Rcpp]; }; + bfsl = derive2 { name="bfsl"; version="0.1.0"; sha256="1hl53nis8bb1ffgkx91ij9vh680cpkb80y548y67y9w18iyd4aw4"; depends=[]; }; bfw = derive2 { name="bfw"; version="0.3.0"; sha256="0kmyr77hp5vs41f8w7arcyxvhwhkbhdiq4v88ch7h822byfiwlzq"; depends=[coda MASS runjags]; }; bgeva = derive2 { name="bgeva"; version="0.3-1"; sha256="0qm4xknyab8hdyn3in2hsvm8s062cnmqqf41b5jvax1mi5hs0z8c"; depends=[magic mgcv trust]; }; bgmfiles = derive2 { name="bgmfiles"; version="0.0.6"; sha256="10qldfjjq5fx5jrrakdxc8k2pf0vp8ifg18nq56lvx9n28mqigim"; depends=[]; }; bgmm = derive2 { name="bgmm"; version="1.8.3"; sha256="09hsqjjyzlpl0fqb7832j5ydrr0yc42zb1c9q1y5hbrms7yp00p8"; depends=[car combinat lattice mvtnorm]; }; - bgsmtr = derive2 { name="bgsmtr"; version="0.2"; sha256="05d4bd350parb3nfwb2arb1z2g24l6pr81z9m5q76rhhsxp6rzn8"; depends=[coda EDISON inline LaplacesDemon Matrix matrixcalc miscTools mnormt mvtnorm Rcpp sparseMVN statmod TargetScore]; }; + bgsmtr = derive2 { name="bgsmtr"; version="0.3"; sha256="01v40mla6ly1g4yfzc6vn1i62psabsj0dzvypc8a5va9sz96x2vy"; depends=[coda EDISON inline LaplacesDemon Matrix matrixcalc miscTools mnormt mvtnorm Rcpp sparseMVN statmod TargetScore]; }; bhm = derive2 { name="bhm"; version="1.13"; sha256="1iq1hjc7xn2kmmxgzv6mzcvvf48kqp5b8lavmzrqykak3v4z02nz"; depends=[coda survival]; }; bhrcr = derive2 { name="bhrcr"; version="1.0.2"; sha256="15c04vknhm8350xylixapb8nw5va0i02a5s5832fsfcndlqr4cpj"; depends=[AER Cairo MASS MCMCpack msm mvtnorm survival]; }; biasbetareg = derive2 { name="biasbetareg"; version="1.0"; sha256="1562zdin0y5mrp36ih11ir3h9cv49cx1l98chxd89fkj8x3c1fbg"; depends=[betareg]; }; @@ -4924,7 +4961,7 @@ in with self; { bigKRLS = derive2 { name="bigKRLS"; version="3.0.0"; sha256="043lm32cams2hc0fg1mvq08r4ippy4s5z62n1616vndfmqsn41v8"; depends=[BH bigalgebra biganalytics bigmemory ggplot2 Rcpp RcppArmadillo shiny]; }; bigQueryR = derive2 { name="bigQueryR"; version="0.4.0"; sha256="1b89yfa0gwd3frdh1z6ygxv2dfncb6g4lp67nh7hkm6r9xamfrxr"; depends=[assertthat googleAuthR googleCloudStorageR httr jsonlite]; }; bigReg = derive2 { name="bigReg"; version="0.1.2"; sha256="1hmvh5j40zpzz6c88hmikphps8rb741yvkg60dxmkfl8gxqsrp3w"; depends=[MASS Rcpp RcppArmadillo uuid]; }; - bigalgebra = derive2 { name="bigalgebra"; version="0.8.4"; sha256="19rv552ac0q9djc1yvpldkc0lipdf6q143m9dnndpsqs7ayqlr4g"; depends=[BH bigmemory]; }; + bigalgebra = derive2 { name="bigalgebra"; version="0.8.4.1"; sha256="19j5f7d6yf9g0glybdwahj7n0mrgbxrbdajh7s30v25fkmm36r2z"; depends=[BH bigmemory]; }; biganalytics = derive2 { name="biganalytics"; version="1.1.14"; sha256="1hsqdg5hkhs6z9pwvn055q02hzpksjwrf33q5zdnkm387g188ca6"; depends=[BH biglm bigmemory foreach Rcpp]; }; bigchess = derive2 { name="bigchess"; version="1.2.0"; sha256="0c5g4hd5wm51w4grdhl6jhd3lm4m3x4jndhwnlvnnfmpsl0y3902"; depends=[ff ffbase]; }; bigdatadist = derive2 { name="bigdatadist"; version="1.1"; sha256="16gkybwcp9sxqb0iic2fhmc4gndr44ayg14wrfcjvjaj4g5r6xs2"; depends=[FNN MASS pdist rrcov]; }; @@ -4933,7 +4970,7 @@ in with self; { bigleaf = derive2 { name="bigleaf"; version="0.6.5"; sha256="0l2a4xi9jyx9sd79fvva9rqqxb4mld99k0gycn07fb81m8lkf690"; depends=[robustbase]; }; biglm = derive2 { name="biglm"; version="0.9-1"; sha256="1z7h4by457z93k5i6qf5rq7xmd1y2kcd1rq4pv465cd32d4mb2g1"; depends=[DBI]; }; biglmm = derive2 { name="biglmm"; version="0.9-1"; sha256="1f4w59jvq7lq0bh5fs41czw0yc8h56iijbj0hlcq47zyqx6gll9a"; depends=[DBI]; }; - bigmatch = derive2 { name="bigmatch"; version="0.5.1"; sha256="00v60cy0j9h8r69b8r2xrarqa5y9sn170m1550g27pxgmyn3y371"; depends=[liqueueR mvnfast plyr rcbalance]; }; + bigmatch = derive2 { name="bigmatch"; version="0.6.1"; sha256="1s9i42h82cdp4qqdpw11dmymvrz0f9vj14ibyrlqjkg18lpz0m5y"; depends=[liqueueR mvnfast plyr rcbalance]; }; bigmemory = derive2 { name="bigmemory"; version="4.5.33"; sha256="0ycl9dzm3drpyas625h34rir5bnbjlncxlvawfsfmqwcbmwdjdvj"; depends=[BH bigmemory_sri Rcpp]; }; bigmemory_sri = derive2 { name="bigmemory.sri"; version="0.1.3"; sha256="0mg14ilwdkd64q2ri9jdwnk7mp55dqim7xfifrs65sdsv1934h2m"; depends=[]; }; bigml = derive2 { name="bigml"; version="0.1.2"; sha256="0vl5krjbgckknxwl26b2hn63jhb80zbn7abpckhxzxfxzncpnfz9"; depends=[plyr RCurl RJSONIO]; }; @@ -4966,7 +5003,7 @@ in with self; { bingat = derive2 { name="bingat"; version="1.3"; sha256="1y68rgafipfad78yrzcygdszgy1d5q739kap06pzr78bn3i8hiwa"; depends=[doParallel foreach gplots matrixStats network vegan]; }; binhf = derive2 { name="binhf"; version="1.0-3"; sha256="1vdw2s8zddp7gad8l3c4jpmnjcc0f5wpqbrp6gp9lgp1c3qa505y"; depends=[adlift EbayesThresh wavethresh]; }; binman = derive2 { name="binman"; version="0.1.1"; sha256="0hm0h285p4v9lhrqjy8s22f1s1vmfpfla5iaycpj8vw3qb3632az"; depends=[assertthat httr jsonlite rappdirs semver xml2 yaml]; }; - binneR = derive2 { name="binneR"; version="1.1.1"; sha256="07cfcp9jj5bks8kmxvir9y9z7fj44hvy1wyrg4jy029dvkz8g2ki"; depends=[dplyr magrittr mzR plyr tidyr]; }; + binneR = derive2 { name="binneR"; version="2.0.5"; sha256="0vmfj9fwpscfakjl5dz4089k24y5qw2a7i0sdgg85ggyil5d2rb3"; depends=[cli crayon dplyr ggplot2 ggthemes lubridate magrittr mzR plyr purrr stringr tibble tidyr]; }; binnednp = derive2 { name="binnednp"; version="0.2.0"; sha256="1dklymwsz0l0xklmvq34mf11chd2hm91r5qa031zjf1hsm3gplh8"; depends=[fitdistrplus kedd mclust nor1mix Rcpp Rdpack]; }; binom = derive2 { name="binom"; version="1.1-1"; sha256="0mjj92dqf5q69jxzqya4izb1mly3mkydbnmlm4wb3zqqg82a324c"; depends=[]; }; binomSamSize = derive2 { name="binomSamSize"; version="0.1-5"; sha256="1an6dcqsjh5r0w4kc3n6yfvvha5qhrb2i4bpf7g5ykhl3i60zfcc"; depends=[binom]; }; @@ -4980,6 +5017,7 @@ in with self; { bio3d = derive2 { name="bio3d"; version="2.3-4"; sha256="1zmswa9xs81lbrlkkgi8dvv9xpf0ynqjqwy1k36szvfb8ar9mczr"; depends=[Rcpp]; }; bioOED = derive2 { name="bioOED"; version="0.1.4"; sha256="1rjcqrni5xag97pxfsf40isr2c8pkqsvihf86phak8ngwl7qdgmc"; depends=[bioinactivation corrplot dplyr FME ggplot2 MEIGOR]; }; bioPN = derive2 { name="bioPN"; version="1.2.0"; sha256="0mvqgsfc7d4h6npgg728chyp5jcsf49xhnq8cgjxfzmdayr1fwr8"; depends=[]; }; + bioRad = derive2 { name="bioRad"; version="0.4.0"; sha256="100b1fz7dxpvsc452r4yvd4g6gmzz80pvw1l0sp6g4310gyzs2fb"; depends=[curl fields ggmap ggplot2 maptools raster rgdal rhdf5 sp]; }; bioacoustics = derive2 { name="bioacoustics"; version="0.1.6"; sha256="1q3sddqbx75hwncrzl3bfx6kagmcf3kqki5k8dig1gj3zk9bmqyl"; depends=[htmltools moments Rcpp stringr tuneR]; }; biofiles = derive2 { name="biofiles"; version="1.0.0"; sha256="1bglgl2jcp6jy3f7xwndil56i98xx4kn518s3fqdixw7n5ibmqd2"; depends=[assertthat BiocGenerics Biostrings foreach GenomeInfoDb GenomicRanges IRanges iterators Rcpp RCurl reutils S4Vectors XVector]; }; biogas = derive2 { name="biogas"; version="1.10.3"; sha256="1qfidjwhaxg5zplzkldhj4zqg81xrcqmvh9x5km5yhyymzr6y4vs"; depends=[]; }; @@ -5036,6 +5074,7 @@ in with self; { blme = derive2 { name="blme"; version="1.0-4"; sha256="1ca2b0248k0fj3lczn9shfjplz1sl4ay4v6djldizp2ch2vwdgy2"; depends=[lme4]; }; blmeco = derive2 { name="blmeco"; version="1.2"; sha256="1kc9sf3j12kwzq58x07nfrxxg0hcxhgms7ddm97dnlmwxpjns9jm"; depends=[arm lme4 MASS MuMIn]; }; blob = derive2 { name="blob"; version="1.1.1"; sha256="0lsg91hk508dd95ivig2lwg62qafwnarjw68110kx63cfk4zkjxc"; depends=[prettyunits]; }; + blockForest = derive2 { name="blockForest"; version="0.1.7"; sha256="16x107ipk2nqhzj6aiwkpvl24h5g4vzmk6i1mp1drnjmabkaxnp3"; depends=[Matrix Rcpp RcppEigen survival]; }; blockTools = derive2 { name="blockTools"; version="0.6-3"; sha256="0023p0msfmp8swq4f5aff40m976np7y051x8hjizzw91hrfa4w2n"; depends=[MASS tibble]; }; blockcluster = derive2 { name="blockcluster"; version="4.3.2"; sha256="15xp4navipxcr2pqxnxc47b0ifdazcsdkn5kmay883vzqj8c1nrb"; depends=[Rcpp rtkore]; }; blockingChallenge = derive2 { name="blockingChallenge"; version="1.0"; sha256="0zj649gj4djdl0wly3gh99ayk1i1rk5dawcrrlzxxh56xqf4l19i"; depends=[]; }; @@ -5043,10 +5082,10 @@ in with self; { blockmodeling = derive2 { name="blockmodeling"; version="0.3.1"; sha256="0cbx44mg5b9w1sz32wsgjprbss4mfx79sn6m42lvminf0023ds1r"; depends=[doParallel doRNG foreach Matrix]; }; blockmodels = derive2 { name="blockmodels"; version="1.1.1"; sha256="088629i4g63m8rnqmrv50dgpqbnxd1a4zl5wr3ga0pdpqhmd53wp"; depends=[digest Rcpp RcppArmadillo]; }; blockrand = derive2 { name="blockrand"; version="1.3"; sha256="1090vb26w6s7iqjcal0xbb3qb6p6j46a5w25f1wjdppd1spvh7f9"; depends=[]; }; - blocksdesign = derive2 { name="blocksdesign"; version="3.1"; sha256="1ykh0clj5fwli40cj4jvdkmvn4i4n4iba5sbasbaqdk45dlka5sf"; depends=[crossdes lme4]; }; + blocksdesign = derive2 { name="blocksdesign"; version="3.2"; sha256="1a9aa1jvh0i5106w5hkx5h285cgx1kd6vf96fqxfvn3daaps14kl"; depends=[crossdes lme4 plyr]; }; blockseg = derive2 { name="blockseg"; version="0.5.0"; sha256="1zc6mvkdwjz7n0yj46c610gz2d3rwsjchbzdcg7k56j06vc9w4lp"; depends=[ggplot2 Matrix Rcpp RcppArmadillo reshape2 shiny]; }; blogdown = derive2 { name="blogdown"; version="0.9"; sha256="1ps07zrr0zzp763hrfhqrmc927cl97v7l1r617s1lqhxwcji1fkx"; depends=[bookdown htmltools httpuv knitr rmarkdown servr xfun yaml]; }; - blorr = derive2 { name="blorr"; version="0.1.0"; sha256="148x2ns7l9s7pb4ksg7h8ayn2lkr18gpfskvjasycccw1q44l8bk"; depends=[car caret checkmate cli clisymbols crayon descriptr dplyr e1071 ggplot2 glue gridExtra magrittr purrr Rcpp rlang scales shiny tibble]; }; + blorr = derive2 { name="blorr"; version="0.2.0"; sha256="1jnhkqja0wn5f9mx6mzmx65zb2ablbq1902vfxv810q8igxaikvl"; depends=[car caret checkmate cli clisymbols crayon dplyr e1071 ggplot2 glue gridExtra magrittr purrr Rcpp rlang scales shiny tibble]; }; blsAPI = derive2 { name="blsAPI"; version="0.2.1"; sha256="0p45g4qqaialh5m9bxgrvnc7nqmm0429syw0bml8h4h8vy4014a7"; depends=[httr rjson]; }; bmd = derive2 { name="bmd"; version="0.5"; sha256="0d4wxyymycb416sdn272292l70s1h2m5kv568vakx3rbvb8y6agy"; depends=[drc]; }; bmem = derive2 { name="bmem"; version="1.5"; sha256="1miiki743rraralk9dp12dsjjajj3iizcrfwmplf6xas6pl8sfk6"; depends=[Amelia lavaan MASS sem snowfall]; }; @@ -5070,10 +5109,10 @@ in with self; { boa = derive2 { name="boa"; version="1.1.8-2"; sha256="04lhqk5qfvaz1jk90glr2yi5vq7cdy0w8m6g2lnzk359l9y41zhp"; depends=[]; }; bodenmiller = derive2 { name="bodenmiller"; version="0.1"; sha256="0gqrjscgq4qgk7yl32w0965yscc1py9klr49s8q8hkzyihlwzim2"; depends=[]; }; boilerpipeR = derive2 { name="boilerpipeR"; version="1.3"; sha256="0467bjqhdmi3p02fp0r7rgm00x9ry464f2hniav990qzsw8i16q6"; depends=[rJava]; }; - bold = derive2 { name="bold"; version="0.8.0"; sha256="16w623k83xydgj2m0qyxc2s08226nvqrlfj242ix4lb51kghxy3j"; depends=[crul data_table jsonlite plyr reshape stringr tibble xml2]; }; + bold = derive2 { name="bold"; version="0.8.6"; sha256="0ph1a6gnw10yccvv8cn3rq32nch3wa6w6a7k2h46qin0fsps55y6"; depends=[crul data_table jsonlite plyr reshape stringr tibble xml2]; }; bomrang = derive2 { name="bomrang"; version="0.4.0"; sha256="16rc60pzphbxmijff5rk3vp8ara9vy1bk48m55drpqqdc3sbc0g3"; depends=[curl data_table dplyr foreign hoardr httr janitor jsonlite lubridate magrittr raster readr rgdal rvest tidyr xml2]; }; - bookdown = derive2 { name="bookdown"; version="0.8"; sha256="08485nb6ncymxs502rsxs8l92fi481isiqnwzhanyyimxxgy06ss"; depends=[htmltools knitr rmarkdown tinytex xfun yaml]; }; - bookdownplus = derive2 { name="bookdownplus"; version="1.5.2"; sha256="09h45h9dry7ask3pg15c7zc9pghd8rdcp1cnaqgcrs6q6jgscld4"; depends=[bookdown]; }; + bookdown = derive2 { name="bookdown"; version="0.9"; sha256="0vg1s1w0l9pm95asqb21yf39mfk1nc9rdhmlys9xwr7p7i7rsz32"; depends=[htmltools knitr rmarkdown tinytex xfun yaml]; }; + bookdownplus = derive2 { name="bookdownplus"; version="1.5.4"; sha256="17jkrrc5m34gnhv0zvbdw82mqv3gna6g1z530gc2cwjc27sa7sza"; depends=[bookdown]; }; boostSeq = derive2 { name="boostSeq"; version="1.0"; sha256="0sikyzhn1i6f6n7jnk1kb82j0x72rj8g5cimp2qx3fxz33i0asx6"; depends=[genetics lpSolveAPI]; }; boostmtree = derive2 { name="boostmtree"; version="1.3.0"; sha256="0q1lgjvbc15m2gygnmh63m0wy2c6x25iwrh9cbn0baq598hnr7j9"; depends=[nlme randomForestSRC]; }; boostr = derive2 { name="boostr"; version="1.0.0"; sha256="123ag8m042i1dhd4i5pqayqxbkfdj4z0kq2fyhxfy92a7550gib2"; depends=[foreach iterators stringr]; }; @@ -5095,11 +5134,11 @@ in with self; { bossMaps = derive2 { name="bossMaps"; version="0.1.0"; sha256="0w4ks1xicvfm8ari4fr18wjm0qj2nxdsapl6lpfjz8l1id0y78cg"; depends=[doParallel foreach ggplot2 raster rgdal rgeos scales sp tidyr]; }; boussinesq = derive2 { name="boussinesq"; version="1.0.3"; sha256="1j1jarc3j5rby1wvj1raj779c1ka5w68z7v3q8xhzjcaccrjhzxk"; depends=[]; }; boxcoxmix = derive2 { name="boxcoxmix"; version="0.21"; sha256="0pav4nksh1zbic11l38jyyq8i58hfvwzkp88ra6nny3jn2axzipl"; depends=[npmlreg qicharts statmod]; }; - boxoffice = derive2 { name="boxoffice"; version="1.1.0"; sha256="08b897dp5cfv6f30k2pdvh8y5n1981msnjr6lfs4dzfc1i6y2zfy"; depends=[httr rvest]; }; + boxoffice = derive2 { name="boxoffice"; version="1.2.0"; sha256="13w167swn9dgbmpb5j2db6b67lvrplzk4jqk13skc4wqc7jf9hp8"; depends=[httr rvest]; }; boxplotdbl = derive2 { name="boxplotdbl"; version="1.3.0"; sha256="1y1b45q69sxbszd83s8ch10z4i55h34ixm8q7yxr7byx3px8y65n"; depends=[]; }; boxr = derive2 { name="boxr"; version="0.3.4"; sha256="0wx3x65rk1ma8bw5h4yskr7ii95ynkm7il22l1bj34kv9f4bfyj3"; depends=[assertthat bit64 digest dplyr httpuv httr mime rio stringr]; }; bpa = derive2 { name="bpa"; version="0.1.1"; sha256="0np7q1nasrq4j7ssaipvbjgrsi9n612p9lp96frq1dgix95mcgf0"; depends=[magrittr plyr]; }; - bpbounds = derive2 { name="bpbounds"; version="0.1.0"; sha256="1ydx0sbxcgrqpwvbjx88radsqiyv6vyzbqv7fyyvbaf1655h9244"; depends=[]; }; + bpbounds = derive2 { name="bpbounds"; version="0.1.1"; sha256="1b4mlm3pj77n978zzqaiba4xd6l3ssx6p5v981147z8bnri4y1cw"; depends=[]; }; bpca = derive2 { name="bpca"; version="1.3-0"; sha256="16a7b94nk5psnm435vrwilcsria9mhr5d31fwzxy53pzp8n78kcr"; depends=[rgl scatterplot3d]; }; bpcp = derive2 { name="bpcp"; version="1.3.4"; sha256="0l4x3n7lcwinnrh2sy386grisj1x7k1d5hll1k4bljg01p7lb475"; depends=[]; }; bpkde = derive2 { name="bpkde"; version="1.0-7"; sha256="1ls6rwmbgb2vzsjn34r87ab8rnz3ls61g6f4x3jpglbk0j91f0h8"; depends=[]; }; @@ -5122,7 +5161,7 @@ in with self; { breakaway = derive2 { name="breakaway"; version="3.0"; sha256="0y3h7gifv279z3x77jmr97c0i3vy58m5wsr8pa2vyn26m02rbkpc"; depends=[]; }; breakfast = derive2 { name="breakfast"; version="1.0.0"; sha256="0p0svsqphd5w99pf5c5jmak1xxl8md881lapa8aps9xr73m4x6lf"; depends=[plyr]; }; breakpoint = derive2 { name="breakpoint"; version="1.2"; sha256="004vi1qr7iib8ykg6sp7xzv0bb841h4vsz2x0cyrhkdp41frglx9"; depends=[doParallel foreach ggplot2 MASS msm]; }; - breathtestcore = derive2 { name="breathtestcore"; version="0.4.5"; sha256="121s88q4gfc576gixilgahhv0dqwzwa0k5drwh344vgi033x1nhm"; depends=[assertthat broom dplyr ggfittext ggplot2 MASS multcomp nlme purrr readr readxl signal stringr tibble tidyr xml2]; }; + breathtestcore = derive2 { name="breathtestcore"; version="0.4.6"; sha256="1d175pwph88nqd3i5nvs4csga9jnlzqxnsimlm63mnbnbxyzbf2q"; depends=[assertthat broom dplyr ggfittext ggplot2 MASS multcomp nlme purrr readr readxl signal stringr tibble tidyr xml2]; }; breathteststan = derive2 { name="breathteststan"; version="0.4.7"; sha256="0lvyp3524cha6ckfx2c25829ys1g97xhjc3mi5cmdbfg8zfgcy58"; depends=[BH dplyr purrr Rcpp RcppEigen rstan rstantools StanHeaders stringr tibble tidyr]; }; brew = derive2 { name="brew"; version="1.0-6"; sha256="1vghazbcha8gvkwwcdagjvzx6yl8zm7kgr0i9wxr4jng06d1l3fp"; depends=[]; }; brglm = derive2 { name="brglm"; version="0.6.1"; sha256="17r3az6za98v2r06aak77kypdaqssc9wxcc6m6vb20y7xm8dp1mp"; depends=[profileModel]; }; @@ -5133,7 +5172,7 @@ in with self; { briskaR = derive2 { name="briskaR"; version="0.1.2"; sha256="1y9sabj7pfgyvv6s3bbvrb0xhjhwc4pcfsfx847kqdajid92qx8w"; depends=[deldir fftwtools fields MASS mvtnorm pracma raster rgdal rgeos sp]; }; brlrmr = derive2 { name="brlrmr"; version="0.1.5"; sha256="14dnmh062fw11bm236ilaqs6ss4ywajvsk3sxj0zwqk2bjf7y7vh"; depends=[boot brglm MASS profileModel Rcpp]; }; brm = derive2 { name="brm"; version="1.0"; sha256="0h4kgig28hkqv1amadznc0n9256dx613rxbn8s8si11ygx79x2dd"; depends=[]; }; - brms = derive2 { name="brms"; version="2.6.0"; sha256="0zahc6p5k6sji172a148j8bcz8bzg7wbdzmaard4wr07dxqpinhj"; depends=[abind backports bayesplot bridgesampling coda ggplot2 loo Matrix matrixStats mgcv nleqslv nlme Rcpp rstan rstantools shinystan]; }; + brms = derive2 { name="brms"; version="2.7.0"; sha256="1a7rmkwvns5lb6jj94q1jr07mj9pdc27q28hh7039wzm7yd9nddp"; depends=[abind backports bayesplot bridgesampling coda ggplot2 loo Matrix matrixStats mgcv nleqslv nlme Rcpp rstan rstantools shinystan]; }; brnn = derive2 { name="brnn"; version="0.7"; sha256="1bfqr21szlpn1izjwlzih9j7f34x31zrapckk184rvynbsbgg7g6"; depends=[Formula]; }; broman = derive2 { name="broman"; version="0.68-2"; sha256="0h6lrxrcjggrkv1dnbqsancjj69072nacaaazibl1v99rawanghi"; depends=[assertthat ggplot2 jsonlite RPushbullet]; }; broom = derive2 { name="broom"; version="0.5.1"; sha256="0bmf38yvwalqf5j5yrr48nsk5k3n75s0gwcw621hp5lgrgvnp7ns"; depends=[backports dplyr generics nlme purrr reshape2 stringr tibble tidyr]; }; @@ -5197,7 +5236,7 @@ in with self; { calibrate = derive2 { name="calibrate"; version="1.7.2"; sha256="010nb1nb9y7zhw2k6d2i2drwy5brp7b83mjj2w7i3wjp9xb6l1kq"; depends=[MASS]; }; calibrateBinary = derive2 { name="calibrateBinary"; version="0.1"; sha256="1k6sl4bg05piyczpk6wsva914gcmy8viyz4423gx9i6ddflb7xdb"; depends=[gelnet GPfit kernlab randtoolbox]; }; calibrator = derive2 { name="calibrator"; version="1.2-6"; sha256="1arprrqmczbhc1gl85fh37cwpcky8vvqdh6zfza3hy21pn21i4kh"; depends=[cubature emulator]; }; - callr = derive2 { name="callr"; version="3.1.0"; sha256="1srsm6dndnxjvzb8xz4m90j2sw2yrkhyn1a7iiiarxybmihmz4xd"; depends=[processx R6]; }; + callr = derive2 { name="callr"; version="3.1.1"; sha256="15l1qfa3aigba2ghgr2gwcjjy7anagrwg8khsd36fymwkmqj5g69"; depends=[processx R6]; }; calmate = derive2 { name="calmate"; version="0.12.1"; sha256="07sjbq7bcrhal52pdzsb5pfmk6a8a44wg8xn79sv4y5v74c5xaqz"; depends=[aroma_core MASS matrixStats R_filesets R_methodsS3 R_oo R_utils]; }; calpassapi = derive2 { name="calpassapi"; version="0.0.2"; sha256="0i81ffdfw3m15cfbag3l9s245dyhapqhy7adb3228vam3qp3n59b"; depends=[digest dplyr httr jsonlite stringr]; }; camsRad = derive2 { name="camsRad"; version="0.3.0"; sha256="06gar6qan1ka01ngjvbpcv649yvfga697mplwn1x6qnfr4ngb7cs"; depends=[httr xml2]; }; @@ -5207,6 +5246,7 @@ in with self; { cancerTiming = derive2 { name="cancerTiming"; version="3.1.8"; sha256="1sfi8q2f5ag7iak0sf9pmqncb89w3gnxdiwjwpivkwhr28ais4mq"; depends=[gplots LearnBayes]; }; candisc = derive2 { name="candisc"; version="0.8-0"; sha256="0hq5bwvq791rhff2c29xdjbbkcyydii1lbsy05c1fapyn88ir0mi"; depends=[car heplots]; }; canprot = derive2 { name="canprot"; version="0.1.1"; sha256="14g7wl4p9bgwf5jm48mp676z0pwlsd2xgxjwzixri7mxxh0ivfh1"; depends=[CHNOSZ xtable]; }; + cansim = derive2 { name="cansim"; version="0.2.2"; sha256="1id6kcjls5w4lsqid8vlsp1pp927cvfhnjdaxq8xl1ww87a18xxl"; depends=[dplyr httr jsonlite purrr readr rlang rvest stringr tibble xml2]; }; canvasXpress = derive2 { name="canvasXpress"; version="1.21.6"; sha256="1sv3vz08nfn69iymr99gsyn9si8w701s0qwqhh3bv4f4kyd9vmby"; depends=[htmlwidgets httr]; }; cap = derive2 { name="cap"; version="1.0"; sha256="1pv8hskxjbp589dn7rx80yaa1ld76x1w37bss2fyrys1p3qr78aa"; depends=[MASS multigroup]; }; cape = derive2 { name="cape"; version="2.0.2"; sha256="0ngm9scd3f2zcy7gy0lqk05cgbfrhhcss3mj5g6bj0byhgwd7msn"; depends=[corpcor doParallel evd fdrtool foreach HardyWeinberg igraph Matrix qpcR RColorBrewer regress shape]; }; @@ -5246,6 +5286,7 @@ in with self; { catR = derive2 { name="catR"; version="3.16"; sha256="1w39dxfzqk065v64qzmfamx8p1njsv13a461s6clagbqmhysmzbx"; depends=[]; }; catSurv = derive2 { name="catSurv"; version="1.0.3"; sha256="1qjmjdmc81inim5kpwh4k2r3cffmkyp2wpcqqzv731hciqrad8a8"; depends=[BH ltm Rcpp RcppArmadillo RcppGSL RcppParallel]; }; catch = derive2 { name="catch"; version="1.0"; sha256="16gdjrmlsnpyc38fihggj6c7wpgpmf4phcwrimnncdhwlk038yn8"; depends=[MASS Matrix tensr]; }; + catchr = derive2 { name="catchr"; version="0.1.0"; sha256="1rz8m8f934y3ksjrkapmzpc2jp03g0vaimi3hs9ky2axzs85idki"; depends=[]; }; catcont = derive2 { name="catcont"; version="0.5.0"; sha256="0ix6ipm3nn9aq5vxirjga2kwwfnxn4v8ggfjlg5v9027v2r8rb96"; depends=[dplyr]; }; catdap = derive2 { name="catdap"; version="1.3.4"; sha256="0i877l61f6c75pczi235rzci67w29zv1d7z5zn5p5ymndclvlpl2"; depends=[]; }; catdata = derive2 { name="catdata"; version="1.2.1"; sha256="0fjylb55iw8w9sd3hbg895pzasliy68wcq95mgrh7af116ss637w"; depends=[MASS]; }; @@ -5320,7 +5361,7 @@ in with self; { cetcolor = derive2 { name="cetcolor"; version="0.2.0"; sha256="0kygdcr9ldanr0z4qpygwh0padki7s2ad0j6myky601g4228z79q"; depends=[]; }; ceterisParibus = derive2 { name="ceterisParibus"; version="0.3.0"; sha256="1ajc5irn9b0ww58vp09pi5bkgx5qdfs5nih9zyayb3nka3jnrkpz"; depends=[DALEX ggplot2 gower knitr]; }; cfa = derive2 { name="cfa"; version="0.10-0"; sha256="12z58y4ls9m58wpj1xa4ir2p2apzxaskps05sxy2946m24i71zfk"; depends=[]; }; - cffdrs = derive2 { name="cffdrs"; version="1.8.1"; sha256="1l3iihqp5yqr7215ahpb80mdd0qr68xfbhskh7ypl9aq6aw4flzd"; depends=[data_table doParallel foreach geosphere raster rgdal spatial_tools]; }; + cffdrs = derive2 { name="cffdrs"; version="1.8.4"; sha256="0fycmkqclv1j1hjq80mrcrgc7z6cjvx108wr9wcnyab9v1404d0x"; depends=[data_table doParallel foreach geosphere raster rgdal spatial_tools]; }; cfma = derive2 { name="cfma"; version="1.0"; sha256="006z5g3rqpg44jqdf6ivyxr47sxm5cd9cqhayfi8qk73xx5w4lv9"; depends=[]; }; cg = derive2 { name="cg"; version="1.0-3"; sha256="1kbyal1sicbr10yvxpwgcij710kqpi23vmndp9kyfzn3k8zfird3"; depends=[Hmisc lattice MASS multcomp nlme rms survival VGAM]; }; cgAUC = derive2 { name="cgAUC"; version="1.2.1"; sha256="172f9rkfhv4xzwpw8izsnsdbcw9p3hvxhh0fd8hzlkil7vskr3k8"; depends=[Rcpp]; }; @@ -5330,7 +5371,7 @@ in with self; { cghRA = derive2 { name="cghRA"; version="1.6.0"; sha256="16dlw27s8wckc75xcwc2g74pw6bar0y0ii3h53w1hql05d4f7sb8"; depends=[DNAcopy Rgb]; }; cglasso = derive2 { name="cglasso"; version="1.1.0"; sha256="0qr6y06aablncj4ja4xjp4dhykqy15qmbigi4px9snpwssrqhwl2"; depends=[igraph MASS]; }; cglm = derive2 { name="cglm"; version="1.0"; sha256="1539n1q1zz1888d143w6vva9465viwcnb49frcsb74j3zvk6j4zp"; depends=[data_table nleqslv Rcpp RcppArmadillo]; }; - cgmanalysis = derive2 { name="cgmanalysis"; version="2.0"; sha256="0j8nl0r69hm5niq7bhjc4rh9sjy5x6pd2dxrsqifj9zv7kz4w4yq"; depends=[gdata ggplot2 lubridate pastecs pracma readr zoo]; }; + cgmanalysis = derive2 { name="cgmanalysis"; version="2.1"; sha256="16m5r1k3brsq0c6i2xqsjxmi3dqxpr78gwkakfv0jifzx2rckxnx"; depends=[gdata ggplot2 lubridate pastecs pracma readr zoo]; }; cgraph = derive2 { name="cgraph"; version="3.0.1"; sha256="0il92x41ifjrl6v9k719xcawdz7zw6bzi326pkzbhw79n2as9jmi"; depends=[R6]; }; chandwich = derive2 { name="chandwich"; version="1.1.1"; sha256="0dpd1b9bq9i8a9wlmid6rvhpmvxj8dilv9xppmzr0jrh0nrcj9yx"; depends=[numDeriv]; }; changepoint = derive2 { name="changepoint"; version="2.2.2"; sha256="1jbki95pck10phpxna0b4i79hhl912zqi5ii9mjqb673y64dszkj"; depends=[zoo]; }; @@ -5358,7 +5399,7 @@ in with self; { childesr = derive2 { name="childesr"; version="0.1.0"; sha256="14jca7lxyn0fip794l70mznhz4ld6iix995wrmiqynxdms6j80np"; depends=[DBI dbplyr dplyr jsonlite magrittr purrr RMySQL]; }; childhoodmortality = derive2 { name="childhoodmortality"; version="0.3.0"; sha256="1ixd10jyzgr1ssnjas35kngpsqyjzl73wwpvcspv06cn12sv2b8d"; depends=[dplyr matrixStats plyr]; }; childsds = derive2 { name="childsds"; version="0.6.7"; sha256="1m5w0wbdk032b6d6h1704wji84yckyl427bja0mb4vqp28m99z48"; depends=[boot class dplyr gamlss gamlss_dist magrittr purrr reshape2 tibble tidyr]; }; - chillR = derive2 { name="chillR"; version="0.70.6"; sha256="0vkw9r2k8xdshwb3v90bp93mgbp3vj04c7hjxcmaxpsqkhxwda04"; depends=[fields httr jsonlite Kendall pls R_utils raster RCurl readxl RMAWGEN sp XML]; }; + chillR = derive2 { name="chillR"; version="0.70.12"; sha256="1slg9fy1n0fxmbc2w0qg4zrfylbmyqgca9j3hjx93lha78i7r631"; depends=[fields httr jsonlite Kendall pls R_utils raster RCurl readxl RMAWGEN sp XML]; }; chinese_misc = derive2 { name="chinese.misc"; version="0.1.9"; sha256="1rs16a5rqp0yq1c5j4yl6yji7hf9x76v6x7qmxppshjii5r8055h"; depends=[jiebaR Matrix NLP purrr Ruchardet slam stringi tm]; }; chipPCR = derive2 { name="chipPCR"; version="0.0.8-10"; sha256="1mff7n7ga4sfwvcq7zkjkrl68nybnm2zkn37hmxvnw9yl3ls9lnw"; depends=[lmtest MASS outliers ptw quantreg Rfit robustbase shiny signal]; }; chngpt = derive2 { name="chngpt"; version="2018.10-17"; sha256="0vj6n3q96li9agh2axq5nd5ybgi504nyavcigmgmglbhcjv25zbz"; depends=[boot kyotil MASS rgl survival]; }; @@ -5388,7 +5429,7 @@ in with self; { cit = derive2 { name="cit"; version="2.2"; sha256="1lf8r3r4zwvs08vl4byhw6rvf54nb7vg83558pi0b5866m7in4sc"; depends=[]; }; citbcmst = derive2 { name="citbcmst"; version="1.0.4"; sha256="1zkd117h9nahwbg5z6byw2grg5n3l0kyvv2ifrkww7ar30a2yikl"; depends=[]; }; citccmst = derive2 { name="citccmst"; version="1.0.2"; sha256="1b7awn1hjckxisfdi4ck697hwd4a5sqklwi7xzh6kgqhk9pv7vjn"; depends=[]; }; - citr = derive2 { name="citr"; version="0.2.0"; sha256="1nzn0yw74k6zkwzb6spfzqkj3cbx6ry6ypbsnhy6w2flabnnvy4v"; depends=[assertthat curl miniUI RefManageR rstudioapi shiny yaml]; }; + citr = derive2 { name="citr"; version="0.3.0"; sha256="0pik6s6xk5768s3kkppw2192dj455py53gsn6k2b7xgg96ircy0g"; depends=[assertthat bibtex curl httr miniUI RefManageR rstudioapi shiny shinyjs yaml]; }; ciuupi = derive2 { name="ciuupi"; version="1.0.0"; sha256="1c72crf0his7vzmh86isvcvi0ahxnqdq4i6ms84hk20jmlz2hxin"; depends=[functional nloptr pracma statmod]; }; civis = derive2 { name="civis"; version="1.5.1"; sha256="13zc0p63i2iqnc27xcnkvhfz0bxyv4grqg4qi8ah7a1n7d2jq2ks"; depends=[DBI dbplyr devtools dplyr feather future ggplot2 httr jsonlite lubridate memoise purrr roxygen2 stringr testthat]; }; cjoint = derive2 { name="cjoint"; version="2.1.0"; sha256="1bs380ji9vsc1d77wqhl0ij9xblww3g9x3hiwpcpz26wihqcx7ac"; depends=[DT ggplot2 lmtest Matrix sandwich shiny shinyBS shinyjs survey]; }; @@ -5399,9 +5440,9 @@ in with self; { clam = derive2 { name="clam"; version="2.3.1"; sha256="1n30fvx4macyawhzv17bzvc1s4qdn51p9mx28apfjbf80qck24g9"; depends=[]; }; clampSeg = derive2 { name="clampSeg"; version="1.0-4"; sha256="0clmv53wz7shawg6mp4q3qp0z0gmd8jmd6flgzn2q1m8j2i62vq0"; depends=[Rcpp stepR]; }; clarifai = derive2 { name="clarifai"; version="0.4.2"; sha256="0igi4xl27nz0r85hpws2zfc2gn5z2nmywp3saxgp74mh2y99lg6s"; depends=[curl jsonlite]; }; - class = derive2 { name="class"; version="7.3-14"; sha256="173b8a16lh1i0zjmr784l0xr0azp9v8bgslh12hfdswbq7dpdf0q"; depends=[MASS]; }; + class = derive2 { name="class"; version="7.3-15"; sha256="1x1hqz8xyhbpq4krsh02glqnlzcch25agkmn4a3da9n723b37gzn"; depends=[MASS]; }; classGraph = derive2 { name="classGraph"; version="0.7-5"; sha256="19jb9jr1gfg4karymrbilh0zjrlsczhy2q03x5b0jxnh4ykhxfj8"; depends=[graph Rgraphviz]; }; - classInt = derive2 { name="classInt"; version="0.2-3"; sha256="1afiw3d5vpxky5scngj63095453xr95wrjj8kw36zsz71hrlgx11"; depends=[class e1071 spData]; }; + classInt = derive2 { name="classInt"; version="0.3-1"; sha256="1fcjrb593bzvx1z57hq1sjs2gp6g7sm4d4xrhasfrps4nmbzirp2"; depends=[class e1071]; }; classiFunc = derive2 { name="classiFunc"; version="0.1.1"; sha256="1qaima3sii394741p5n06lcqkk4fiv9apb7qqnpi6srx5h02lfl5"; depends=[BBmisc checkmate dtw fda fda_usc fdasrvf proxy rucrdtw zoo]; }; classifierplots = derive2 { name="classifierplots"; version="1.3.3"; sha256="01rvn0jwliyxj7q4cmyv8an5g7fzn6y3sccp8mj6bcqjyblfcfaa"; depends=[caret data_table ggplot2 gridExtra png Rcpp ROCR]; }; classifly = derive2 { name="classifly"; version="0.4"; sha256="0mw1vcas0gr1r4yvh0j02zhk7kp5342r0bhhg776hqgqdczgh5zj"; depends=[class plyr]; }; @@ -5419,6 +5460,7 @@ in with self; { clespr = derive2 { name="clespr"; version="1.1.2"; sha256="1993kd70w48a110im47vcpll0c6nfrm7m33r6l8rzgwnpsmcls8g"; depends=[AER clordr doParallel foreach magic MASS pbivnorm survival]; }; clhs = derive2 { name="clhs"; version="0.7-0"; sha256="0wliffs16misvlsxcng89a6yasq9blrlic88n59334vj60p42l3m"; depends=[cluster ggplot2 plyr raster reshape2 scales sp]; }; cli = derive2 { name="cli"; version="1.0.1"; sha256="1r2yih4c0bdmbx0qrarlf0m1p5z30sri755zmdazsq2pw76zp07g"; depends=[assertthat crayon]; }; + cliapp = derive2 { name="cliapp"; version="0.1.0"; sha256="152hllp4iiva2qib79700v1mx1biy8bg4sy496vwq6mi4afvswjy"; depends=[cli crayon fansi glue prettycode progress R6 selectr withr xml2]; }; clickR = derive2 { name="clickR"; version="0.4.20"; sha256="140ncl7iv48yxnwf55rf8cwcyznzw7kslkjzymslyqmhvvw43q6p"; depends=[beeswarm boot flextable lme4 lmerTest officer xtable]; }; clickstream = derive2 { name="clickstream"; version="1.3.0"; sha256="01bii527xy7hdph1pm6f1g4qnwa5yf3mwz01rjg1h2gc12s5vzgg"; depends=[arules ClickClust data_table ggplot2 igraph linprog MASS plyr reshape2 Rsolnp]; }; clifro = derive2 { name="clifro"; version="3.2-0"; sha256="1pq66wg19dvmacqj5pdh8ngxq1irihg76g0hnfy16gxsz7snvnkh"; depends=[ggplot2 lubridate magrittr RColorBrewer RCurl reshape2 scales xml2]; }; @@ -5511,7 +5553,7 @@ in with self; { codebook = derive2 { name="codebook"; version="0.7.5"; sha256="02mh4g82v56x13wk28ddvwqcibf2dymha7db3f2a7k9297vxlbfz"; depends=[dplyr DT future ggplot2 glue haven htmltools knitr labeling labelled likert miniUI pander psych purrr rio rlang rmarkdown rstudioapi shiny skimr stringr tibble tidyr]; }; codemetar = derive2 { name="codemetar"; version="0.1.6"; sha256="1jjm1c7fkrzyhb57ckdf3d808im5j6c20ykkjsnddh220jy4sgss"; depends=[crul curl desc devtools gh git2r jsonld jsonlite memoise purrr readr sessioninfo stringi stringr tibble usethis whisker]; }; codep = derive2 { name="codep"; version="0.9-1"; sha256="17jziwm56icswa4ngp51ah8w1ma7ij3cksbdaipk0ikqvb5kinkb"; depends=[]; }; - codetools = derive2 { name="codetools"; version="0.2-15"; sha256="0h7sjmvvsi35041jp47cxhsqzgf1y8jrw6fxii7n26i8g7nrh1sf"; depends=[]; }; + codetools = derive2 { name="codetools"; version="0.2-16"; sha256="00bmhzqprqfn3w6ghx7sakai6s7il8gbksfiawj8in5mbhbncypn"; depends=[]; }; codified = derive2 { name="codified"; version="0.2.0"; sha256="1hmw7yrw4qx8v9rkqqvqf4013s9whq5qlgwz7v882j4slpvm6gb1"; depends=[checkmate dplyr kableExtra knitr magrittr readr rlang tibble tidyr]; }; codingMatrices = derive2 { name="codingMatrices"; version="0.3.2"; sha256="0kldx2h3mksw4644d0ask6ij7i63rrwk0njlsvkbdjz3bf7pdv1b"; depends=[fractional Matrix]; }; codyn = derive2 { name="codyn"; version="2.0.0"; sha256="1h58w4hb5m8qy7i5h1r7306c5aac1j887aig0imgsjhinj48pi5l"; depends=[assertthat permute vegan]; }; @@ -5553,7 +5595,7 @@ in with self; { colortools = derive2 { name="colortools"; version="0.1.5"; sha256="0z9sx0xzfyb5ii6bzhpii10vmmd2vy9vk4wr7cj9a3mkadlyjl63"; depends=[]; }; colourlovers = derive2 { name="colourlovers"; version="0.2.2"; sha256="0fgxs73l4g1lnmc2q613ykxxrbmvq6w66zpidccqg64wa9cy5yhm"; depends=[jsonlite png XML]; }; colourpicker = derive2 { name="colourpicker"; version="1.0"; sha256="0z3v2083g7kwdp21x9s2n1crfh24agpdq3yxkcdzc2awn2pwpnpi"; depends=[ggplot2 htmltools htmlwidgets jsonlite miniUI shiny shinyjs]; }; - colourvalues = derive2 { name="colourvalues"; version="0.2.0"; sha256="18qvmingga3n8s4mz0mlx1nl4nswhjl44hivnb9p228qxw43j77j"; depends=[BH Rcpp]; }; + colourvalues = derive2 { name="colourvalues"; version="0.2.1"; sha256="1s3fqm3xyxb4qkj0pb52np6ics83mxs8kvkgc87g51nx479pxz13"; depends=[BH Rcpp]; }; colourvision = derive2 { name="colourvision"; version="2.0.2"; sha256="15ndhqpp5fi9jgiri9ysl68nf4rdamh9c25svf5nvh2wvv8shrd9"; depends=[Matrix rgl]; }; colr = derive2 { name="colr"; version="0.1.900"; sha256="0ilz1y0jd2vgyh81g3dwx2l64sir6z6sgmqx7lnvr1hafsqnwfc8"; depends=[]; }; colt = derive2 { name="colt"; version="0.1.1"; sha256="028jqvgr14ig8jxp8h2lrf7mainzppgqh6v1479qfv4l9is3bnwy"; depends=[crayon]; }; @@ -5611,7 +5653,7 @@ in with self; { condusco = derive2 { name="condusco"; version="0.1.0"; sha256="0zydinzlksynkz4r712rzv9qqdx8dkdz3h1ygi9cfmd6hya3580s"; depends=[assertthat bigrquery DBI jsonlite]; }; condvis = derive2 { name="condvis"; version="0.5-1"; sha256="1ngxqfa0mr86cv610da4ljypxpdvx0n5pfgj3zfksnwxlwc0dvbj"; depends=[MASS]; }; coneproj = derive2 { name="coneproj"; version="1.14"; sha256="0km7njsxjgrv4d8bx709nci59ngm00jg1r55702yapyjl0f2zg93"; depends=[Rcpp RcppArmadillo]; }; - conf = derive2 { name="conf"; version="1.4.0"; sha256="1xhnil3cm3a72hngpxp7kxvh98l2017yidk7qp7lgb5aggcslc9c"; depends=[fitdistrplus SDMTools STAR statmod]; }; + conf = derive2 { name="conf"; version="1.5.0"; sha256="17w8vslppp1f88vz9f4m85x2zyw65mjxd5h0r8s8l9ckbbykv5fg"; depends=[fitdistrplus SDMTools STAR statmod]; }; conf_design = derive2 { name="conf.design"; version="2.0.0"; sha256="06vdxljkjq1x56xkg041l271an1xv9wq79swxvzzk64dqqnmay51"; depends=[]; }; confSAM = derive2 { name="confSAM"; version="0.2"; sha256="1l67ndya07hh0yqfbabfhsvp3hryklx0022grpr0cb7ff88d1zam"; depends=[]; }; confidence = derive2 { name="confidence"; version="1.1-2"; sha256="0m6iz59n5jpi0ig3za3nir4d4bdsysf5g47d2nakfmaz03wk520z"; depends=[ggplot2 knitr markdown plyr xtable]; }; @@ -5621,6 +5663,7 @@ in with self; { conflicted = derive2 { name="conflicted"; version="1.0.1"; sha256="0hj9dvyi59y917cac1d3g1bgaghs40nr71z3y2msr29q01d1sqkp"; depends=[memoise rlang]; }; conformalClassification = derive2 { name="conformalClassification"; version="1.0.0"; sha256="03v6xbgipb97byarqj0d38z9yb2g54mkkw343jxmi2j058z26yw7"; depends=[doParallel foreach mlbench randomForest]; }; confreq = derive2 { name="confreq"; version="1.5.1"; sha256="0gy6d1kffb1w86ifldswb9krxyc2p646g9yjlfm1h243qlp52sfa"; depends=[gmp]; }; + congressbr = derive2 { name="congressbr"; version="0.1.7"; sha256="0n5zq31n0mfx4wwpi6jsjayiybpzhkxyz9laljpvnlpk0g3vzrad"; depends=[dplyr glue httr janitor lubridate magrittr progress pscl purrr stringi stringr tibble tidyr xml2]; }; conicfit = derive2 { name="conicfit"; version="1.0.4"; sha256="1d704xgiyqmbwfxnsmhqg885x10q8yqxmrk4khqpg3lh696bw97d"; depends=[geigen pracma]; }; conics = derive2 { name="conics"; version="0.3"; sha256="06p6dj5dkkcy7hg1aa7spi9py45296dk0m6n8s2n3bzh3aal5nzq"; depends=[]; }; conjoint = derive2 { name="conjoint"; version="1.41"; sha256="1iq3226a6fn1gddmh2nxlzvjcvbj7502r9520g9d4xdmk8smfx33"; depends=[AlgDesign broom cluster fpc ggfortify ggplot2]; }; @@ -5639,7 +5682,7 @@ in with self; { convertGraph = derive2 { name="convertGraph"; version="0.1"; sha256="1jsrygj6ydzc0nzyzaq95j4blqavj7dqz182vgm1ckv8an3if0jx"; depends=[]; }; convertr = derive2 { name="convertr"; version="0.1"; sha256="1y9aq5in2qv1323amblmq3g22flpqvpkgkrw12kahg56mqf2b3iq"; depends=[DT miniUI rstudioapi shiny]; }; convevol = derive2 { name="convevol"; version="1.3"; sha256="1b0lygbrdm6rqascck5iwjnm248lklc4cxr71qlgand5jsblpcnn"; depends=[ape cluster geiger MASS phytools]; }; - convexjlr = derive2 { name="convexjlr"; version="0.7.0"; sha256="1dxvz5jnflswqh7iqc4fw7gbp8s6qn7rfy2b5qx4jklrvfj696yj"; depends=[JuliaCall magrittr XRJulia]; }; + convexjlr = derive2 { name="convexjlr"; version="0.8.1"; sha256="1x2ra1xcyd7bvc7wq49wpihh0g9ygh1bq5214vvrhfrjfjifvlaw"; depends=[JuliaCall magrittr]; }; convey = derive2 { name="convey"; version="0.2.1"; sha256="1fcfzcpiy35xr2i81q002h07zf8gvbv1m5is7j475bi13666ynzh"; depends=[survey]; }; convoSPAT = derive2 { name="convoSPAT"; version="1.2.4"; sha256="0by1z2z7gzycwrll1agkqnpn5h5cjr6b62gpwy11wl4lh48p4213"; depends=[ellipse fields geoR MASS plotrix StatMatch]; }; cooccur = derive2 { name="cooccur"; version="1.3"; sha256="1wlaghhi4f3v8kzwhcgq3c6as7v3zlpkzhb232qz1amr7f0058kv"; depends=[ggplot2 gmp reshape2]; }; @@ -5652,7 +5695,7 @@ in with self; { cope = derive2 { name="cope"; version="0.2.3"; sha256="1r02nb6wy25ixhdcbqqz167s7ny3hydpxfxry5ar4136qvcamgyy"; depends=[abind fields maps MASS Matrix mvtnorm nlme]; }; coppeCosenzaR = derive2 { name="coppeCosenzaR"; version="0.1.3"; sha256="1chwsfyaf5rmlsypr43n7px8b2220dfa5mzcriq1swylgbx4181l"; depends=[]; }; coprimary = derive2 { name="coprimary"; version="1.0"; sha256="0pjln9p5lzv6wl5xrz0kb90hnjlnp7ch2kvh054nxdbmlxv5akc3"; depends=[digest gsDesign plyr proto]; }; - copula = derive2 { name="copula"; version="0.999-18"; sha256="1xdjnp8zgla2hixyp524nvgbji0jcrmqc4j99hr8xp9365xb6z86"; depends=[ADGofTest colorspace gsl lattice Matrix mvtnorm numDeriv pcaPP pspline stabledist]; }; + copula = derive2 { name="copula"; version="0.999-19"; sha256="16ikz5ffxay5y38kgyz8ahcnxaw092ciygk4zcml3z57niqpw55l"; depends=[ADGofTest colorspace gsl lattice Matrix mvtnorm numDeriv pcaPP pspline stabledist]; }; copulaData = derive2 { name="copulaData"; version="0.0-1"; sha256="1s917g8wasxndg1xq4b4fjaq29nyzzigpflgqcy4rxdb7r54dl0z"; depends=[]; }; copulaedas = derive2 { name="copulaedas"; version="1.4.3"; sha256="01wp8jnz7kndknj7lh9ia7mm41k1vbaksalyy9v19bb77yhgzmba"; depends=[copula mvtnorm truncnorm vines]; }; corHMM = derive2 { name="corHMM"; version="1.22"; sha256="03di9250hjn5fiwn47f0pr4zprmsza4if3xpmy3j1czahc8zlqnj"; depends=[ape corpcor expm GenSA nloptr nnet numDeriv phangorn Rmpfr]; }; @@ -5668,6 +5711,7 @@ in with self; { corehunter = derive2 { name="corehunter"; version="3.2.1"; sha256="0cxvhmi768kz3q8hydb6y9nqvc8hvkmq8nc5yfry4k94whk12wax"; depends=[naturalsort rJava]; }; corkscrew = derive2 { name="corkscrew"; version="1.1"; sha256="1nb81r4lsrajcj3xz3f7p6xznnb38yg3rnnh44rd3kabca4d8r1s"; depends=[ggplot2 gplots igraph RColorBrewer]; }; corlink = derive2 { name="corlink"; version="1.0.0"; sha256="06n9pcvbn8y9gy0mn9c0sw05424ss8smpaw3ly6a785cmj3d9b6m"; depends=[]; }; + coroICA = derive2 { name="coroICA"; version="1.0.1"; sha256="0hjy1sdii8kk859bj1xv3vh1hzxznhymhgdb583z57i0hqxnijiv"; depends=[MASS]; }; corpcor = derive2 { name="corpcor"; version="1.6.9"; sha256="1hi3i9d3841snppq1ks5pd8cliq1b4rm4dpsczmfqvwksg8snkrf"; depends=[]; }; corpora = derive2 { name="corpora"; version="0.5"; sha256="0b4yw37msx9h8hf5mjs4h10gdmc1qc2gv5bzyj1r90n4gcli042d"; depends=[]; }; corpus = derive2 { name="corpus"; version="0.10.0"; sha256="0c984rsnbai2qrm2s10lkdfgx31m0ax46zhl74bns2bxfmagcn3l"; depends=[utf8]; }; @@ -5682,7 +5726,7 @@ in with self; { corrr = derive2 { name="corrr"; version="0.3.0"; sha256="1l5157m4k5zvxnkgndvkxc0ghcsgxvm5jr6hpbpdc6s1nnz7s027"; depends=[dplyr ggplot2 ggrepel lazyeval magrittr purrr rlang seriation tibble tidyr]; }; corrsieve = derive2 { name="corrsieve"; version="1.6-8"; sha256="0ak3j9khcwv5rxbicck2sr260wpmd3xj254y7pdavx2fk0b72yxs"; depends=[]; }; corset = derive2 { name="corset"; version="0.1-4"; sha256="0ladyqvkys4cldvbhkii9jwn1k5p1ym2g5bgdlz1hq1sv30ixn2f"; depends=[]; }; - cosa = derive2 { name="cosa"; version="1.2.0"; sha256="1g2n9l79bi6pr5m9f4c0byw2ls9nhykkaaivssxbx4m6qpqlqg54"; depends=[nloptr]; }; + cosa = derive2 { name="cosa"; version="1.2.1"; sha256="0v8hscvl59inb9kd283n92x86r1nv3n0f2d3g7br8vnniah97frz"; depends=[nloptr]; }; cosinor = derive2 { name="cosinor"; version="1.1"; sha256="02nnqg51vq48lzk667cyarnmhcf5mifnsdij7dlgqvz2k4fdq4pl"; depends=[ggplot2 shiny]; }; cosinor2 = derive2 { name="cosinor2"; version="0.2.1"; sha256="1pp0z86fflqkkllfrzx3vj98kzxjwnawr4a2d8z5q6zhq6v5qrvf"; depends=[cosinor cowplot ggplot2 Hmisc magrittr matrixStats purrr scales stringr]; }; cosmoFns = derive2 { name="cosmoFns"; version="1.0-1"; sha256="0a6xhbgxxnymlvicg99yhgny2lscxcbmvqmy17kxmahdi797dsg6"; depends=[]; }; @@ -5758,7 +5802,7 @@ in with self; { crimedata = derive2 { name="crimedata"; version="0.1.0"; sha256="006wz4nvfq10dppkg8kqp2bmllcc7zpwdqkp3nqwm4qgw7pllyvz"; depends=[digest dplyr httr magrittr purrr readr stringr tibble]; }; crimelinkage = derive2 { name="crimelinkage"; version="0.0.4"; sha256="1zzk50kyccvnp51vzp28c9yi23hsp25arrgdn88lwfwa0m43rlar"; depends=[geosphere igraph]; }; crisp = derive2 { name="crisp"; version="1.0.0"; sha256="1gs8jnd9y9pd55w6kwv9mvmg3wd8hjiw3lwx7k242pxccsxklfxq"; depends=[MASS Matrix]; }; - crmPack = derive2 { name="crmPack"; version="0.2.7"; sha256="1d0ydllcbykwip9dw3arvn6lv4h88n5nkm3ms122gfrf44f6h2c0"; depends=[GenSA ggplot2 gridExtra MASS mvtnorm rjags]; }; + crmPack = derive2 { name="crmPack"; version="0.2.9"; sha256="1w9xrfhhxkirxh36y8jym9v1wc2y0x7mfajl55635r0ll1j99cxi"; depends=[GenSA ggplot2 gridExtra MASS mvtnorm rjags]; }; crminer = derive2 { name="crminer"; version="0.2.0"; sha256="1rlh7bxk8bry2v9fnqzy0ph62dda1pzifksr7v4pmdyhji9mjw33"; depends=[crul hoardr jsonlite pdftools xml2]; }; crmn = derive2 { name="crmn"; version="0.0.20"; sha256="1kl1k1s2gm63f9768cg8w4j6y1gq4hws3i7hdfhj7k9015s0a25p"; depends=[Biobase pcaMethods]; }; crn = derive2 { name="crn"; version="1.1"; sha256="1fw0cwx478bs6hxidisykz444jj5g136zld1i8cv859lf44fvx2d"; depends=[chron RCurl]; }; @@ -5793,7 +5837,7 @@ in with self; { crunch = derive2 { name="crunch"; version="1.24.0"; sha256="0jydmicc4c4vkf6r3krybbrdf96059nx6q611lyd2qj32irlr49j"; depends=[crayon curl httpcache httr jsonlite]; }; crunchy = derive2 { name="crunchy"; version="0.2.0"; sha256="1q9mqpkg5ljb798922fmvjjp36kyjr1rrm6jf3s2fwjrhq186y3z"; depends=[crunch shiny]; }; cruts = derive2 { name="cruts"; version="0.5"; sha256="08mklbmwgaq6cf3hd40mingplwjss5im30l5j6nmy7lijp15nq7k"; depends=[lubridate ncdf4 raster sp stringr]; }; - crypto = derive2 { name="crypto"; version="1.0.3"; sha256="19d245sq8xhxmq252cjcymc86n6q6yq2b1liy2mm62agkyjxznrd"; depends=[curl doSNOW dplyr foreach jsonlite lubridate magrittr rvest tibble tidyr xml2 xts yaml]; }; + crypto = derive2 { name="crypto"; version="1.1.0"; sha256="0z1zyjidpl7sk9vk278jljrbyfhhzv4wq195spyd63xwj2p33fgc"; depends=[cli crayon curl dplyr httr jsonlite keyring lubridate progress rstudioapi rvest tibble tidyr xml2 xts]; }; cryst = derive2 { name="cryst"; version="0.1.0"; sha256="04da19dy3mkngd3ma44cd8cdkb5acjy9lbhfipa9flp339j1pp57"; depends=[flux pracma]; }; csSAM = derive2 { name="csSAM"; version="1.2.4"; sha256="1ms8w4v5m9cxs9amqyljc2hr1178cz6pbhmv7iiq9yj1ijnl4r1x"; depends=[]; }; csabounds = derive2 { name="csabounds"; version="1.0.0"; sha256="15l7i15w5jk4h3148dlk8v2i4awns5vxvv6m59qcv0hzns6jhx9j"; depends=[BMisc ggplot2 pbapply progress qte]; }; @@ -5810,7 +5854,7 @@ in with self; { csvy = derive2 { name="csvy"; version="0.3.0"; sha256="0id015szw1c63vd1h0515jsqdhyn32sxpxm89f3sb1qkgq3yynmy"; depends=[data_table jsonlite yaml]; }; cthreshER = derive2 { name="cthreshER"; version="1.1.0"; sha256="18b66d08dq8pvnixmm4ir4r800b37z5yillaa88l317mdilbci9s"; depends=[Matrix]; }; ctl = derive2 { name="ctl"; version="1.0.0-2"; sha256="1gpb43zn411l476dby2g38qkcvh2fsdcvbkr9jb274l1154km1xm"; depends=[MASS qtl]; }; - ctmcd = derive2 { name="ctmcd"; version="1.4.0"; sha256="1b4bf2j3gdzm417pimn9m365y7x11ddinq9mb5mixwsbf77dqagm"; depends=[coda expm numDeriv Rcpp RcppArmadillo]; }; + ctmcd = derive2 { name="ctmcd"; version="1.4.1"; sha256="01nflgdyb70kh4f8bnxpavr31fz4fh02kgz2nlx3zzblnm2idbcx"; depends=[coda expm numDeriv Rcpp RcppArmadillo]; }; ctmcmove = derive2 { name="ctmcmove"; version="1.2.9"; sha256="1pxyxbbhfa8arqfb7qw10ya1b8hy9ylqbqqzys6d9dsixvdk98h0"; depends=[fda gdistance Matrix raster sp]; }; ctmle = derive2 { name="ctmle"; version="0.1.1"; sha256="1k9nr2xbaqrbpp31vdcnmpwyazcw79k0r3gbcbinva4pgv2psp29"; depends=[glmnet SuperLearner tmle]; }; ctmm = derive2 { name="ctmm"; version="0.5.2"; sha256="1x8nzmhdby0nwm18l6b3y4x4b7pihfkpnhakykh23rfnr7d6ajj3"; depends=[data_table expm fasttime Gmedian manipulate MASS numDeriv pbivnorm pracma raster rgdal scales shape]; }; @@ -5819,7 +5863,7 @@ in with self; { cts = derive2 { name="cts"; version="1.0-21"; sha256="0wagxqb8msjc8z33qp7sc92l53f56d9bzz9160bmgpjxlj6cnqcj"; depends=[]; }; ctsem = derive2 { name="ctsem"; version="2.7.6"; sha256="1k435f2miq44m95wwbz4r9zxz20mgyynkkbdjwfxkbz15srci9f5"; depends=[BH corrplot data_table DEoptim KernSmooth MASS Matrix mvtnorm OpenMx plyr Rcpp RcppEigen rstan rstantools shiny StanHeaders]; }; ctv = derive2 { name="ctv"; version="0.8-5"; sha256="0kl6z8dbbjgm29q0c5xy6lihjgf5cdihrllm27x0zbcvy8lyl51p"; depends=[]; }; - cubature = derive2 { name="cubature"; version="2.0.1"; sha256="01zc7n3xqnqp9ll1spixaadjzw604nvn3vf1m89ydd870kswybf6"; depends=[Rcpp]; }; + cubature = derive2 { name="cubature"; version="2.0.3"; sha256="0wvs80i4axj7pdcy9gjl08qzjbcjkldha94xy4gdxc34vgmh7gvr"; depends=[Rcpp]; }; cubfits = derive2 { name="cubfits"; version="0.1-3"; sha256="0i2iybm9vpyqnahzka66yms1namdd36bz1i1yjy74qsc1h995rga"; depends=[coda foreach]; }; cubing = derive2 { name="cubing"; version="1.0-5"; sha256="1q23fplvklaaldicqic0zpnh301m08zb9k21l47zj47g9m9pj4bc"; depends=[rgl]; }; cultevo = derive2 { name="cultevo"; version="1.0.2"; sha256="0rmncp4mrdpf3izhhqn9406i36j3d3d7i8cglip04lkfbypl9jvy"; depends=[combinat Hmisc pspearman stringi]; }; @@ -5901,7 +5945,7 @@ in with self; { dataCompareR = derive2 { name="dataCompareR"; version="0.1.2"; sha256="0n10dqnrlpwafxys68b3ly156235lhqby71qay0vb0r6bvl2g349"; depends=[dplyr knitr markdown stringi]; }; dataMaid = derive2 { name="dataMaid"; version="1.2.0"; sha256="0w2dslyzr35y6mjg46sq7cc3mar6v29md1i716hiix9kzy7b5782"; depends=[DT ggplot2 gridExtra haven htmltools magrittr pander robustbase stringi whoami]; }; dataMeta = derive2 { name="dataMeta"; version="0.1.1"; sha256="13xxayqxbps07h0xr5b7sb7q30gy5zm7jzzaq4k20fskkjrzhzcm"; depends=[dplyr]; }; - dataPreparation = derive2 { name="dataPreparation"; version="0.3.8"; sha256="1k4lww4n57zqf5lk2gwrjjk9qfv3b4zvb18591mnq5bbvylkw2c4"; depends=[data_table lubridate Matrix progress stringr]; }; + dataPreparation = derive2 { name="dataPreparation"; version="0.3.9"; sha256="1ap25xk0lvb94d79zz7dqc0y1f53fdxmhs2ij44qkjxzzd34ik30"; depends=[data_table lubridate Matrix progress stringr]; }; dataQualityR = derive2 { name="dataQualityR"; version="1.0"; sha256="0f2410sd6kldv7zkqsmbz1js0p5iq7zwlnfwmmnlbrd303p35p3j"; depends=[]; }; dataRetrieval = derive2 { name="dataRetrieval"; version="2.7.3"; sha256="0lrv6fyqi7k079wdpqilgjlb4j2qfs3r02d9ip8s9yznfwqsl826"; depends=[curl dplyr httr jsonlite lubridate readr reshape2 xml2]; }; datacheck = derive2 { name="datacheck"; version="1.2.2"; sha256="1i3n5g1b6ix8gpn4c74s7ll1dbrllrzgpb1f3hk449d6p4kmisq6"; depends=[Hmisc shiny stringr]; }; @@ -5922,13 +5966,13 @@ in with self; { dataseries = derive2 { name="dataseries"; version="0.2.0"; sha256="11wc2p5m8qbdmkpbd21lpwl28a1dpab88c3gqyrhsn0298lpnip4"; depends=[]; }; datasets_load = derive2 { name="datasets.load"; version="0.3.0"; sha256="13ywnqln831i5hlf1cpqcyc77blg99w8jvy8jic17z86fjxh4gim"; depends=[DT miniUI shiny]; }; datastepr = derive2 { name="datastepr"; version="0.0.2"; sha256="039yggdj8jdici7hwmkjwgix45lvwjl7rw5h2rfzsm9xaq6vw1z2"; depends=[dplyr lazyeval magrittr R6 tibble]; }; - datastructures = derive2 { name="datastructures"; version="0.2.7"; sha256="0lvm2n056msbmx3aw3a2wkn8vcyjhb5m9iaqdirpcvbzdpigfj80"; depends=[BH purrr Rcpp]; }; + datastructures = derive2 { name="datastructures"; version="0.2.8"; sha256="1lf48c77z4br1sv8kdbxadn30v5ygn9shjgsf8g37rci7nngpx1k"; depends=[BH purrr Rcpp]; }; datasus = derive2 { name="datasus"; version="0.4.1"; sha256="175bzhjigri49p4v9v3kwdc233w0l3v35220m05qsbpn6in7gw67"; depends=[dplyr httr magrittr RCurl readr rvest stringi stringr xml2]; }; datautils = derive2 { name="datautils"; version="0.1.5"; sha256="1yy25a84zmfh54jvxwa7mv4j296rmjgd40m4p81mrsswlqvncmfn"; depends=[deldir gplots gtools]; }; dataverse = derive2 { name="dataverse"; version="0.2.0"; sha256="0lyga8rdsir2yr1n9nr10iiaf6a7dxp1nb04bx8mq8ljrvpkgr8n"; depends=[httr jsonlite xml2]; }; dataview = derive2 { name="dataview"; version="2.1.1"; sha256="1nn33h5c1h4a3zm1xm7sdz4s6sy0f3r53jhm7bv6qk7aiylwqf6v"; depends=[data_table xtermStyle]; }; date = derive2 { name="date"; version="1.2-38"; sha256="1ziy17kz02j7lals14s43rs9lmxxfn2ppfi55q4b3m4gfj9pr4jc"; depends=[]; }; - datetime = derive2 { name="datetime"; version="0.1.3"; sha256="1grl6ygfwmi8a307fibdlkqv4mnzixjfzmi1vl0svx1w4d527bv9"; depends=[]; }; + datetime = derive2 { name="datetime"; version="0.1.4"; sha256="0nn1yxknsn3crmwbkws5kvfjhd65dw0fkfbg67gba0dyaqp1jg37"; depends=[]; }; datetimeutils = derive2 { name="datetimeutils"; version="0.2-12"; sha256="023jxsih2zlfv9yldn68cbrdl7jw5rpbz4cc9y0z530bb1fs8d1k"; depends=[]; }; datoramar = derive2 { name="datoramar"; version="0.1.0"; sha256="0zq6vhq6dmsyagmqrmb85z6fy9qhwra3s3iasr3jgc4ryr009pml"; depends=[httr jsonlite tibble]; }; datr = derive2 { name="datr"; version="0.1.0"; sha256="0sqwhn6zdaq8i45ry207mpbda1djjaxp9mcn13hi5wkry6z0bmlr"; depends=[devtools]; }; @@ -5938,12 +5982,13 @@ in with self; { dbConnect = derive2 { name="dbConnect"; version="1.0"; sha256="1vab5l4cah5vgq6a1b9ywx7abwlsk0kjx8vb3ha03hylcx546w42"; depends=[gWidgets RMySQL]; }; dbEmpLikeGOF = derive2 { name="dbEmpLikeGOF"; version="1.2.4"; sha256="0vhpcxy702cp3lvlif2fzmvccys8iy7bv1fbg6ki2l8bvn2f7c5p"; depends=[]; }; dbEmpLikeNorm = derive2 { name="dbEmpLikeNorm"; version="1.0.0"; sha256="0h5r2mqgallxf9hin64771qqn9ilgk1kpsjsdj2dqfl3m8zg967l"; depends=[dbEmpLikeGOF]; }; - dbarts = derive2 { name="dbarts"; version="0.9-5"; sha256="0pjw5fljn3fzsimsyfc21xq6klrxmav8snjjjp8myn19viikv1rg"; depends=[]; }; + dbarts = derive2 { name="dbarts"; version="0.9-8"; sha256="1advv5k2m6fryz87wa2375kh2iwpgacm4qfnhn258xhbpynnk46s"; depends=[]; }; dbfaker = derive2 { name="dbfaker"; version="0.1.0"; sha256="00n2z4q5drpg26pw826i16rg07m7w66a0r466q2lrl14hxs4rcaq"; depends=[assertive DBI dplyr foreach parsedate RPostgreSQL tidyr]; }; dbhydroR = derive2 { name="dbhydroR"; version="0.2-6"; sha256="0pmd6bakifacmdk2zwlsg2zfdqc5jibc5jbd1mvnmllh5d0wwcqm"; depends=[httr reshape2 XML]; }; dblcens = derive2 { name="dblcens"; version="1.1.7"; sha256="02639vyaqg7jpxih8cljc8snijb78bb084f4j3ns6byd09xbdwcw"; depends=[]; }; dblr = derive2 { name="dblr"; version="0.1.0"; sha256="0wzmhmp706mw0pkh81nsb7qzclwyhm6f2mjvpvz043ng5xrxwvvw"; depends=[CatEncoders data_table Metrics xgboost]; }; dbmss = derive2 { name="dbmss"; version="2.6-3"; sha256="0b3vbsb01rz46mspfk8v9dgwqkxnjkv5d6152zg1zsvyv0z9wvqd"; depends=[cubature Rcpp RcppParallel spatstat spatstat_utils]; }; + dbparser = derive2 { name="dbparser"; version="1.0.0"; sha256="060hmnwhindwlk7xjcz1nbr4lazd4v4918zs6q13ba9gp9ydi98c"; depends=[DBI dplyr ggplot2 odbc purrr tibble XML]; }; dbplot = derive2 { name="dbplot"; version="0.3.0"; sha256="1sdhw73a518pj81p4xzfkyk5qnfvv7pmizqgwypmkmr3j87klkdx"; depends=[dplyr ggplot2 purrr rlang]; }; dbplyr = derive2 { name="dbplyr"; version="1.2.2"; sha256="0j5w6a1qim972kv4vmvinp3j50yr4idmm9cd3w7y3zsz0nq0nhcx"; depends=[assertthat DBI dplyr glue purrr R6 rlang tibble tidyselect]; }; dbscan = derive2 { name="dbscan"; version="1.1-3"; sha256="1q0vlrp0abzci2zsjgh7jp3sk1wflcvwjmy9fp0gsay8sgdcixgk"; depends=[Rcpp]; }; @@ -5961,13 +6006,13 @@ in with self; { ddalpha = derive2 { name="ddalpha"; version="1.3.7"; sha256="1fjxky9wdy2f3qch3z97gd930mpialilish2jwhffz2n2c32hlk4"; depends=[BH class geometry MASS Rcpp robustbase sfsmisc]; }; ddeploy = derive2 { name="ddeploy"; version="1.0.4"; sha256="06s4mn93sl33gldda9qab8l3nqig8zq0fh1s2f98igsysmn31br5"; depends=[httr jsonlite]; }; ddiv = derive2 { name="ddiv"; version="0.1.0"; sha256="1r2sxlkw1vxf2svdi1nary3hb7c5k1b4j820mj268r9swmy632ch"; depends=[MASS segmented]; }; - ddpcr = derive2 { name="ddpcr"; version="1.9"; sha256="0xdy36wdl972xgzs3chzs7x1n4z1xvj1vahcz2pxa1wrr4sd9z8q"; depends=[dplyr DT ggplot2 lazyeval magrittr mixtools plyr readr shiny shinyjs]; }; ddsPLS = derive2 { name="ddsPLS"; version="1.0.5"; sha256="00pcpdqkihcvqj6w52kr00rf6m19dh3ql6xhazk865gk9g5phgy5"; depends=[doParallel foreach MASS RColorBrewer Rdpack]; }; ddst = derive2 { name="ddst"; version="1.4"; sha256="1y0immm337adkd2bjx8c5pf02w9wysv3gj26f4qf0jiba0f2wk8n"; depends=[evd orthopolynom]; }; deBInfer = derive2 { name="deBInfer"; version="0.4.2"; sha256="108vijk71sgsj14hwfv78r4lnn68cybvnpr92zvrvl0d82b7qxfd"; depends=[coda deSolve MASS mvtnorm PBSddesolve plyr RColorBrewer truncdist]; }; deGradInfer = derive2 { name="deGradInfer"; version="1.0.0"; sha256="1wl1pw1rwins4gr47a8ii4diw6wd6cx8ib4l5bhri5f3crbw7l86"; depends=[deSolve gdata gptk]; }; deSolve = derive2 { name="deSolve"; version="1.21"; sha256="0qqc4mknw1jblzcmph1dg3k1p6w42yal0k1xjh8pqk7yb3a75hs5"; depends=[]; }; deTestSet = derive2 { name="deTestSet"; version="1.1.5"; sha256="07wbgniwkpp0yry6wvchvszr8isxs1i9k6km951r5c009w1iviwk"; depends=[deSolve]; }; + deaR = derive2 { name="deaR"; version="1.0"; sha256="0wmkqcv4cwlfrwzr4j4g8myhq0lj0p742p2w6h5w6y0bjxzkf9aj"; depends=[dplyr ggplot2 gridExtra igraph lpSolve plotly tidyr writexl]; }; deadband = derive2 { name="deadband"; version="0.1.0"; sha256="02pq3d0l0wy8bdlyfir3zf46j1ascx4qajyq5cf28yl62q6ngq5d"; depends=[TTR]; }; deal = derive2 { name="deal"; version="1.2-39"; sha256="0sw0v1mm004ky1gjw3dmvf2vb7nf2j9s9386bhqxijw63j7xnjd3"; depends=[]; }; deamer = derive2 { name="deamer"; version="1.0"; sha256="1xbxr78n6s1yhf192ab4syi1naqlwl9z4cxzchrkw80q7bxqfiz8"; depends=[]; }; @@ -6046,7 +6091,7 @@ in with self; { detect = derive2 { name="detect"; version="0.4-2"; sha256="03xzv13y2l15afyp00lgvbh51vxg1jaakxjcbnsxzdgb11039x2g"; depends=[Formula Matrix pbapply]; }; detectRUNS = derive2 { name="detectRUNS"; version="0.9.5"; sha256="0w4pz7waaabgsb47xcmgiz8bzlrs2a83y3v6j7bqb5125y1wn8hw"; depends=[data_table ggplot2 gridExtra iterators itertools plyr Rcpp reshape2]; }; detector = derive2 { name="detector"; version="0.1.0"; sha256="010i063b94hzx7qac8gpl67gmk7hzgqm9i1c7pbbw4la3wcd9lz7"; depends=[stringr]; }; - detpack = derive2 { name="detpack"; version="1.1.1"; sha256="0q7c01bjrvrlbrhb8vhkjw2f43jp46ny3jdyay0j760cfdaqb5zk"; depends=[]; }; + detpack = derive2 { name="detpack"; version="1.1.2"; sha256="0vrzg4h80jkkghgm86jfqxshfb4pwqv66d7sndkxh3ji9gfd7d84"; depends=[]; }; detrendeR = derive2 { name="detrendeR"; version="1.0.4"; sha256="1z10gf6mgqybb9ml6z3drq65n7g28h2pqpilc2h84l6y76sy909c"; depends=[dplR]; }; detrendr = derive2 { name="detrendr"; version="0.6.0"; sha256="0dlkhyxdxzxlbnw3wa05rykfczmkm45ymfhz1qgad7vzikzd4472"; depends=[assertthat autothresholdr checkmate doParallel dplyr filesstrings foreach glue ijtiff iterators magrittr matrixStats plyr purrr Rcpp RcppParallel rlang sigmoid stringi stringr]; }; detzrcr = derive2 { name="detzrcr"; version="0.2.3"; sha256="09a8x7zphsk06n64qqbh840vrp89sza9vfnz08il6jdy77j02974"; depends=[ggplot2 MASS shiny]; }; @@ -6054,7 +6099,7 @@ in with self; { devFunc = derive2 { name="devFunc"; version="0.1"; sha256="0f2s5gssk9napmah7zcss1rnh7pzlq90gzwcnvyr9rrq6k118n8q"; depends=[plyr stringr]; }; devRate = derive2 { name="devRate"; version="0.1.9"; sha256="1dy9hfhhlxj5sim69870dkwrarrl5pvmfvls8ys43h300my331gp"; depends=[]; }; devtools = derive2 { name="devtools"; version="2.0.1"; sha256="1nyspqicn9zd1rgq3k07b3179i8w5ys6jbd65g9q8qczrb7z3x8f"; depends=[callr cli digest git2r httr jsonlite memoise pkgbuild pkgload rcmdcheck remotes rstudioapi sessioninfo usethis withr]; }; - dexter = derive2 { name="dexter"; version="0.8.3"; sha256="0zlqybm27cimyhfys878p2rsk9x5kyxmnjf61c6bbda9fy9mn3x0"; depends=[colorspace DBI dbplyr dplyr DT fastmatch RColorBrewer rlang rprintf RSQLite shiny shinyBS shinydashboard tibble tidyr]; }; + dexter = derive2 { name="dexter"; version="0.8.4"; sha256="1jsq4qisz1k1vyf8cf204aram75zj8z933ggw2sf86zzsx7w15vk"; depends=[colorspace DBI dbplyr dplyr DT fastmatch RColorBrewer rlang rprintf RSQLite shiny shinyBS shinydashboard tibble tidyr]; }; dexterMST = derive2 { name="dexterMST"; version="0.1.1"; sha256="0i9y5qngg85x6h9zm4rf8p7fydl3s72rmc2bh3qpb9vc8js99m35"; depends=[crayon DBI dbplyr dexter dplyr fastmatch igraph Rcpp rlang RSQLite tibble tidyr]; }; dextergui = derive2 { name="dextergui"; version="0.1.5"; sha256="0k6m977jkhapcdy9gyrq2gx3lynr5796ka9pd4yjna89v45cz6qc"; depends=[Cairo DBI dexter dplyr DT ggExtra ggplot2 ggridges htmltools htmlwidgets igraph jsonlite networkD3 RColorBrewer RCurl readODS readxl rlang shiny shinyBS shinyFiles shinyjs tibble tidyr writexl]; }; df2json = derive2 { name="df2json"; version="0.0.2"; sha256="10m7xn7rm4aql1bzpckjcx5kvdw44m1pxgzqkgkd40lzqb1cwk18"; depends=[rjson]; }; @@ -6081,7 +6126,7 @@ in with self; { dhh = derive2 { name="dhh"; version="0.0.1"; sha256="00kg2x1was85aq2vr15bak8y5p4mymbs8pbriijlbw64401djmb0"; depends=[]; }; di = derive2 { name="di"; version="1.1.4"; sha256="1w2gjhyi410z98d8wnhbd69jxm69nz4pmnr4fb09i70a90f53s25"; depends=[scales]; }; diagis = derive2 { name="diagis"; version="0.1.3-1"; sha256="1cagcr5znhrg4fp96d79ly0z7bs3hhh3zfspclyfc88p2p3qsd96"; depends=[coda ggplot2 gridExtra Rcpp RcppArmadillo]; }; - diagmeta = derive2 { name="diagmeta"; version="0.2-0"; sha256="1qdpsn0c4g459p8p90p2a9fghiwjqqmmanz3zsa5a3lv7zxmk496"; depends=[lme4 meta]; }; + diagmeta = derive2 { name="diagmeta"; version="0.3-0"; sha256="1h1hc56540z14ldy15wf079ibnwb4myjd231i1zw94ciai3p06jd"; depends=[lme4 meta]; }; diagonals = derive2 { name="diagonals"; version="0.4.0"; sha256="03n6lm0hkgylswgj1qlgrjigm7basl5frip99mxx19mvaqa3bhqy"; depends=[]; }; diagram = derive2 { name="diagram"; version="1.6.4"; sha256="0f6ffprn5k0ir1s7m9s7izc64aa17r3gnygagz5bihrlsvawaavw"; depends=[shape]; }; dials = derive2 { name="dials"; version="0.0.2"; sha256="1ip8hdv293lcj0jiycinc66fib1q1vsnb3px26zsmlw49nb32q5h"; depends=[dplyr glue purrr rlang scales tibble withr]; }; @@ -6138,6 +6183,7 @@ in with self; { disclapmix = derive2 { name="disclapmix"; version="1.7"; sha256="11qkk5bl5x3axyfdzm1hw522g643mmvk5qg7g3sc3licfvsn32i1"; depends=[cluster disclap MASS Rcpp RcppProgress]; }; disco = derive2 { name="disco"; version="0.6"; sha256="1abvhf0yb4mw02j1krjb7q68jpwdnl2narcalf3vkjcbflcp76z3"; depends=[ggplot2 RColorBrewer tmod]; }; discord = derive2 { name="discord"; version="0.1"; sha256="0nrjpl7l9lzkn92fwzaj3vh8zv2b6706gnh5c4zalkld0xac3c23"; depends=[dplyr]; }; + discoveR = derive2 { name="discoveR"; version="1.0.1"; sha256="01gv2hsff3zvhmmqy91dnyr51ks325dmmcd7gjm2vxkkk8cj5i7v"; depends=[colourpicker corrplot dendextend DT factoextra FactoMineR future ggdendro ggplot2 knitr promises raster reshape rgdal rmarkdown rstudioapi scatterplot3d shiny shinyAce shinydashboard shinydashboardPlus shinyjs shinyWidgets stringi stringr zip]; }; discreteMTP = derive2 { name="discreteMTP"; version="0.1-2"; sha256="13qsf1kc3rph0kkdkz31qj072www5dwjyk73lfpy141rzhcn1v1x"; depends=[]; }; discreteRV = derive2 { name="discreteRV"; version="1.2.2"; sha256="1lhf67cccr96zl3j1sysh2bv0pbgvkbgjdzm35fvrdm7k74ypjsi"; depends=[MASS plyr]; }; discretecdAlgorithm = derive2 { name="discretecdAlgorithm"; version="0.0.5"; sha256="1q4g455jjg293yxdwdppw04ah15idk5j233x2kbqv0jni4v0l2bf"; depends=[igraph Rcpp RcppEigen sparsebnUtils]; }; @@ -6154,7 +6200,7 @@ in with self; { dissUtils = derive2 { name="dissUtils"; version="1.0"; sha256="00fzlmkdfw2s3k824wp2pk3v7cvxnywi1hfp86g4mm95z2qlw9br"; depends=[]; }; dissever = derive2 { name="dissever"; version="0.2-3"; sha256="1lgs5nmv3lpm4gsryxvcwiwibvvg9flv23q8maisp77x49c18qcp"; depends=[boot caret dplyr foreach magrittr plyr raster sp viridis]; }; distance_sample_size = derive2 { name="distance.sample.size"; version="0.0"; sha256="0hlf3kp34rg1gnkxp4k3rnv0shv4fpgb0rhx3a6x5692lhyigbcs"; depends=[MASS]; }; - distances = derive2 { name="distances"; version="0.1.4"; sha256="0axh75s0l478nlgd2sd1nxbmpx0iw1wi5aaa6b24hy1v3bizazbn"; depends=[]; }; + distances = derive2 { name="distances"; version="0.1.6"; sha256="1n21klp81bcixfr54051qizmw597wk6bq45yb59s5fkz0s1rf0xg"; depends=[]; }; distcomp = derive2 { name="distcomp"; version="1.0-1"; sha256="0f69bxw52ai39dmkmfvrs0lbibcgmv6n849xa9xgd2jm5mvbc58f"; depends=[digest httr jsonlite R6 shiny stringr survival]; }; distcrete = derive2 { name="distcrete"; version="1.0.3"; sha256="0sa6z2mpmk51ig1r7bmpbyv2jd8z6z7mixki2vlq1kybg8cx3wmi"; depends=[]; }; distdichoR = derive2 { name="distdichoR"; version="0.1-1"; sha256="0v19m3n1jgipg65yrv75rm4v27b5aq58cbsmbp7lxvfxmj5ra328"; depends=[boot emmeans nlme sn]; }; @@ -6239,6 +6285,7 @@ in with self; { downsize = derive2 { name="downsize"; version="0.2.2"; sha256="18b9shd79z0bsdnp0apqqwv6c73j4wnfiv41ywqz761nmxbldxbn"; depends=[magrittr R_utils]; }; dpa = derive2 { name="dpa"; version="1.0-3"; sha256="0dmwi68riddi1q4b10c12wx6n7pqfmv30ix5x72zpdbgm72v343h"; depends=[igraph sem]; }; dparser = derive2 { name="dparser"; version="0.1.8"; sha256="1yx425s3iq03j043g41pyfp3cgmajb4qh50zirhd0qpplzwy8xj5"; depends=[digest]; }; + dpcid = derive2 { name="dpcid"; version="1.0"; sha256="1gx8gyrxvm07mjiasl0b80y0x3crq6gy170v6s817d11jw44n86z"; depends=[]; }; dpglasso = derive2 { name="dpglasso"; version="1.0"; sha256="1mx28xbm2z2bxyp33wv2v6vgn1yfsdsa0bzjjdxasgd6lvr51myf"; depends=[]; }; dplR = derive2 { name="dplR"; version="1.6.9"; sha256="0pb2f0f09qwi6az7c0pp28jhv5cgdfy4wqwfsqgkq5nlzlbkbnri"; depends=[animation digest lattice Matrix matrixStats plyr png R_utils signal stringi stringr XML]; }; dplRCon = derive2 { name="dplRCon"; version="1.0"; sha256="10xnawgnhxp5y949fxs1vvadc1qz2ldy0s9w9w7kf6iqh59d35sw"; depends=[]; }; @@ -6267,13 +6314,13 @@ in with self; { dropR = derive2 { name="dropR"; version="0.1"; sha256="0sw5lqlfdn64dbykxdhk1pz18f83if871vkapa2nxgcfiy79b0vs"; depends=[plyr shiny]; }; droptest = derive2 { name="droptest"; version="0.1.3"; sha256="1wlfhj6c4pb5mcybyd2bcn55y3azk7dv7d7il97qwbhl8kf59csl"; depends=[data_table]; }; drsmooth = derive2 { name="drsmooth"; version="1.9.0"; sha256="1wgi961bvbsnq4bygxbpy4sy5fy34lrrkaaj0r2rxcahwa1sc38n"; depends=[boot car DTK lubridate mgcv multcomp pgirmess segmented]; }; - drtmle = derive2 { name="drtmle"; version="1.0.3"; sha256="1b2nlkmx7park79pkmnjnkckli89zh3klfamxkqndgd1s5p0aa11"; depends=[doFuture future future_apply future_batchtools np plyr SuperLearner]; }; + drtmle = derive2 { name="drtmle"; version="1.0.4"; sha256="0k8cps3kpfrlv33a0czjp327qzdj69lwbpv4k5q7qjcv0878yypg"; depends=[doFuture future future_apply future_batchtools np plyr SuperLearner]; }; drugCombo = derive2 { name="drugCombo"; version="1.0.3"; sha256="03hlv6alhjd84liixb7nqcfgyhcr59bjni049h71jpicqzci2qk9"; depends=[BIGL Deriv ggplot2 minpack_lm nlme rgl]; }; ds = derive2 { name="ds"; version="3.0"; sha256="10xp575l0wh85wg32k3as02kgqm9ax9nx9i5kd5bkimfwg4qv745"; depends=[]; }; dsa = derive2 { name="dsa"; version="0.60.32"; sha256="0jl21a81i047igmwxxalflfcvkmsl6gh61balkyj50vxv4v4l8x8"; depends=[dygraphs extrafont forecast ggplot2 gridExtra htmlwidgets R2HTML reshape2 rJava timeDate tsoutliers xtable xts zoo]; }; dsample = derive2 { name="dsample"; version="0.91.2.2"; sha256="18c0zxaqwgbn9kmkwlnicwd74ljy2sxj0b9ksif13pdlj3zn57h1"; depends=[MASS]; }; dse = derive2 { name="dse"; version="2015.12-1"; sha256="1976h57zallhzq43nshg77bsykcvkfwnasha1w59c44fjpl1gs9w"; depends=[setRNG tfplot tframe]; }; - dslabs = derive2 { name="dslabs"; version="0.5.1"; sha256="1pzpvgwzgnr3hi9idkkx6ik80bralg5bgnz4b5p24ab5fcr45gy5"; depends=[ggplot2]; }; + dslabs = derive2 { name="dslabs"; version="0.5.2"; sha256="1igzn6g9sgbmvqbqq588573618ii9ki3gda9b2hi9r8ljpgys8h6"; depends=[ggplot2]; }; dslice = derive2 { name="dslice"; version="1.2.0"; sha256="1k9hxpmr563p8bpd9m991lx5ig366mzk9j1lzldci9pq4jiayin1"; depends=[ggplot2 Rcpp scales]; }; dsm = derive2 { name="dsm"; version="2.2.16"; sha256="1glw3pwgar9qadjya615n5n10lg7xvclcnr3k9vn8y3fgid22f80"; depends=[ggplot2 mgcv mrds nlme numDeriv plyr statmod]; }; dsmodels = derive2 { name="dsmodels"; version="1.1.0"; sha256="0gidxi4ph49mjm2hdf9flphfb9916al4cpdkiig504n7ms2sbpbg"; depends=[latex2exp pryr shape]; }; @@ -6282,7 +6329,7 @@ in with self; { dst = derive2 { name="dst"; version="1.3.0"; sha256="1pck09g2430d08x2f72zc2zxx6yaybcpzramjvjldwj1kmz32l1w"; depends=[]; }; dtables = derive2 { name="dtables"; version="0.2.0"; sha256="0ikgip3p4b7q97b2dshlx0fq09xsk304gfk5prw4rk95w9wck3qs"; depends=[psych]; }; dtangle = derive2 { name="dtangle"; version="0.3.1"; sha256="0kvds49gx850rmrcja0xr3j9nja5zqnsg1q2zjb07qp425jc3j46"; depends=[]; }; - dti = derive2 { name="dti"; version="1.2-6.1"; sha256="1p88k7qkmas49niq618jhddc0h4mwh5gd267v6rlzzpmv5f98fkb"; depends=[adimpro awsMethods gsl oro_dicom oro_nifti quadprog rgl]; }; + dti = derive2 { name="dti"; version="1.3-0.3"; sha256="01dpmjbaizf64s2icqs825vi23gsllnwa3lhblpwzp8q31hsm5h4"; depends=[adimpro awsMethods gsl oro_dicom oro_nifti quadprog rgl]; }; dtp = derive2 { name="dtp"; version="0.1.0"; sha256="0qy8nrbq22bfbajkxq6blkq7583pc5mb392gmqb3c9daxmqn42vb"; depends=[Formula gtools plyr]; }; dtplyr = derive2 { name="dtplyr"; version="0.0.2"; sha256="1q75xnk52zfxnphj095dppcqdmk9v1n32069rffpnvr39nnik565"; depends=[data_table dplyr lazyeval]; }; dtree = derive2 { name="dtree"; version="0.4.2"; sha256="1cpv0pyf515610djxzfw1c83p3alk5a93clg4x9gk7a7qy4cyhr1"; depends=[caret evtree party partykit rpart]; }; @@ -6305,9 +6352,9 @@ in with self; { dynBiplotGUI = derive2 { name="dynBiplotGUI"; version="1.1.5"; sha256="0fvyn33mzjcc3sis05phc6412y25m406il2wzdfw8caa8dafj0yw"; depends=[tcltk2 tkrplot]; }; dynCorr = derive2 { name="dynCorr"; version="1.1.0"; sha256="0l5k764j1zhsqpgp0ndihah63hsk3zv9hviixfmh4h3i0sr0q52p"; depends=[lpridge]; }; dynOmics = derive2 { name="dynOmics"; version="1.2"; sha256="0fsck5wx4rcfckjr6xg0s3a6cvh4881cqzy0af91icqg0p3zjj2l"; depends=[ggplot2 gplots]; }; - dynRB = derive2 { name="dynRB"; version="0.13"; sha256="04axc6hzwaclgdyl5lplihgbg6ip8irpiyanghfhhid3c4jm03r7"; depends=[corrplot ggplot2 RColorBrewer reshape2 vegan]; }; + dynRB = derive2 { name="dynRB"; version="0.15"; sha256="0fa6g4aj2cncg6mi0yc2yn6321qi7fz9d9cvqrnxhcnbbghdyzq9"; depends=[corrplot dplyr foreign ggplot2 RColorBrewer reshape2 vegan]; }; dynaTree = derive2 { name="dynaTree"; version="1.2-10"; sha256="1ng672mlv98xnsbd4xq70hxc8j158la4n63y46rw74granaz29ya"; depends=[]; }; - dynamac = derive2 { name="dynamac"; version="0.1.5"; sha256="1s44lk8qbcb3gndik3fbl897mmaxqzp8bl0c8slq8avib80jyb9i"; depends=[lmtest MASS]; }; + dynamac = derive2 { name="dynamac"; version="0.1.6"; sha256="1awi9rq4kgxmvwwq9n6vxkjpcqy563h99ran0gzgvb0k6bri5pp3"; depends=[lmtest MASS]; }; dynamicGraph = derive2 { name="dynamicGraph"; version="0.2.2.6"; sha256="1xnsp8mr3is4yyn0pyrvqhl893gdx2y1zv8d2d55aah2xbfk0fjj"; depends=[ggm]; }; dynamicTreeCut = derive2 { name="dynamicTreeCut"; version="1.63-1"; sha256="1fadbql7g5r2vvlkr89nlrjxwp4yx4xrdqmv077qvmnx9vv0f4w3"; depends=[]; }; dynamichazard = derive2 { name="dynamichazard"; version="0.6.1"; sha256="0xwvfpw0djnzi4igim8g32s233f5xf53pskg5w4xwnqja7x6w8v2"; depends=[boot Rcpp RcppArmadillo survival]; }; @@ -6349,6 +6396,7 @@ in with self; { easySVG = derive2 { name="easySVG"; version="0.1.0"; sha256="03gl5gl0yqgpygd4kna79wrhflbnq3zrz3iq2i8hk9xqd83mszh3"; depends=[]; }; easySdcTable = derive2 { name="easySdcTable"; version="0.3.1"; sha256="0z0fq73m7vjc8wry633lvz58r2c6a6zz6w867hij1627c74mjhs4"; depends=[sdcTable shiny SSBtools]; }; easyVerification = derive2 { name="easyVerification"; version="0.4.4"; sha256="08mih1arx01vj7cs1jsln644pcvslpyw1rgr6jmv2czr6xd8qb7d"; depends=[pbapply Rcpp SpecsVerification]; }; + easyalluvial = derive2 { name="easyalluvial"; version="0.1.7"; sha256="0856lrb5lq6m3bj33yjf6lj6sk36a91wp4r4j7j4nl84ix0701g6"; depends=[dplyr forcats ggalluvial ggplot2 magrittr purrr RColorBrewer recipes rlang stringr tibble tidyr]; }; easyanova = derive2 { name="easyanova"; version="6.0"; sha256="16cypapzrsf70wrpd0rq00kks96rx3kiqnxswd410l6ss2gnni7h"; depends=[car emmeans lme4 lmerTest]; }; easycsv = derive2 { name="easycsv"; version="1.0.8"; sha256="1i2k5372b6a5pypk6m0rsvvkcy0y51pvh57a60rpgqk8q0yq8pig"; depends=[data_table]; }; easyformatr = derive2 { name="easyformatr"; version="0.1.2"; sha256="0mrpd21hyafn82apclxmhs2jbd87sdw0g6lwc3h6gl5cbm213nxb"; depends=[dplyr knitr lazyeval magrittr stringi tibble tidyr]; }; @@ -6427,7 +6475,7 @@ in with self; { effects = derive2 { name="effects"; version="4.1-0"; sha256="01c970619y27w4w8bq7i8f7sb324rk2jds229x0vb5r5827bpqb3"; depends=[carData colorspace estimability lattice lme4 nnet survey]; }; effectsizescr = derive2 { name="effectsizescr"; version="0.1.0"; sha256="0shfjk6r3bz04jakrn5nwgymjx60lk83i0akcx7zqfxp3k8yncs5"; depends=[Kendall]; }; efflog = derive2 { name="efflog"; version="1.0"; sha256="1sfmq7xrr6psa6hwi05m44prjcpixnrl7la03k33n0bksj8r1w6b"; depends=[]; }; - effsize = derive2 { name="effsize"; version="0.7.1"; sha256="0l0ja7qcknn8r5hf7nrjk5cy0ajw0z60ggbyj8qvjzf8qah4mlss"; depends=[]; }; + effsize = derive2 { name="effsize"; version="0.7.4"; sha256="0m9qbcvisrf1d95b9rjj7f63s37wmmzldl05l9l77jws7vxql1hf"; depends=[]; }; efreadr = derive2 { name="efreadr"; version="0.2.2"; sha256="1h27by1m451wrnw017005avs5yj3fjzrm2lq5153aqm1mbbxxwvs"; depends=[dplyr ensurer magrittr readr]; }; efts = derive2 { name="efts"; version="0.9-0"; sha256="1cdn37sij3q73z9gal6x3nnnds55whfj5ywyww119hx092xcb2h4"; depends=[lubridate magrittr ncdf4 plyr stringr udunits2 xts]; }; ega = derive2 { name="ega"; version="2.0.0"; sha256="04kwh24aap22yclmcrix3vi553qb30hd43mgfzpdl0cw3ibrh7xg"; depends=[ggplot2 mgcv]; }; @@ -6481,7 +6529,7 @@ in with self; { emil = derive2 { name="emil"; version="2.2.10"; sha256="05f0i33rd9pp7kkpry1v1ysgny3bwi712glxlcj6qm4fmi0ciik6"; depends=[data_table dplyr ggplot2 lazyeval magrittr Rcpp tidyr]; }; emma = derive2 { name="emma"; version="0.1-0"; sha256="0psd8lrbcqla8mkhp0wlassaaimgwlmqy5yv2wwcq59mc5k1v27f"; depends=[clusterSim earth]; }; emme2 = derive2 { name="emme2"; version="0.9"; sha256="035s4h95ychqb14wib0dqbg4sjy9q01fsryr0ri25g1hsi5f8lpm"; depends=[reshape]; }; - emmeans = derive2 { name="emmeans"; version="1.3.0"; sha256="0kdyy4qp332c4yyvp1cnh48h6ks6ffir5rjcv0py0vm3m8c3hh61"; depends=[estimability mvtnorm plyr xtable]; }; + emmeans = derive2 { name="emmeans"; version="1.3.1"; sha256="1sf7gmdb7aqhdpx489vg693ivc5677n4yjx27ixv8v7pjh8mlwwx"; depends=[estimability mvtnorm plyr xtable]; }; emoa = derive2 { name="emoa"; version="0.5-0"; sha256="1wcnsnkdmpcn21dyql5dmj728n794bmfr6g9hgh9apzbhn4cri8p"; depends=[]; }; emojifont = derive2 { name="emojifont"; version="0.5.2"; sha256="0s1as6i5dz2rbd1aashn99fji2iksjzrkdkfi7wqnnxxpmkha3yx"; depends=[ggplot2 proto showtext sysfonts]; }; emon = derive2 { name="emon"; version="1.3.2"; sha256="19khjjpyxvzhzihqq15w02l5v5ryyvxlklz1ch2gkmqcpnvyga32"; depends=[MASS mgcv]; }; @@ -6532,6 +6580,7 @@ in with self; { epanet2toolkit = derive2 { name="epanet2toolkit"; version="0.3.2"; sha256="0j64riiy7b2v1m8ki6d43jm61s7yjwlx4kxxdvlz3fx1xw7qf522"; depends=[]; }; epanetReader = derive2 { name="epanetReader"; version="0.7.3"; sha256="05pwa6z03qsjwr9pxpbxycsd21p7mf5j5ajyg4yaas5g100s1k8c"; depends=[]; }; epiDisplay = derive2 { name="epiDisplay"; version="3.5.0.1"; sha256="08ym6hcbmajzr4rasdb35fxk79vgpzfc16rmcm34f7f3zzz09dyl"; depends=[foreign MASS nnet survival]; }; + epiGWAS = derive2 { name="epiGWAS"; version="1.0.0"; sha256="1nyc9mibvdj1rmykw1zsgrha5zvw6z2dihafqfpg2ssaqqz0ls67"; depends=[DescTools glmnet matrixStats SNPknock]; }; epiR = derive2 { name="epiR"; version="0.9-99"; sha256="1x7r8nm636x1innbzhpihyi43b2dqlys9qw7b621jnqni3shlv9j"; depends=[BiasedUrn survival]; }; epibasix = derive2 { name="epibasix"; version="1.5"; sha256="0ivr51x37cbdryli9b4p4iq9v2c90zwmywrwdmg7ryq5vprvvbp0"; depends=[]; }; epicontacts = derive2 { name="epicontacts"; version="1.1.0"; sha256="0f4a1y311z3fxw7ygj6fgsq6d2qn0ivxsjlh742pkmg3jb63s0f3"; depends=[colorspace dplyr igraph magrittr threejs visNetwork]; }; @@ -6653,7 +6702,7 @@ in with self; { excerptr = derive2 { name="excerptr"; version="1.4.1"; sha256="0z5gayf7kkhdg7ad2w4ycar5dd42jdjybrhzfmkqb3xr9pdrnijg"; depends=[git2r rprojroot rPython]; }; excursions = derive2 { name="excursions"; version="2.4.4"; sha256="140p0vks40vsj1bi89rhdqih5jh7795pxzzqm9140vfiv8b0aya5"; depends=[Matrix sp]; }; exif = derive2 { name="exif"; version="0.1.0"; sha256="12phqn5x1x0xs2xczl3064q983dalm261vqpyafhdcndm1y3gwbc"; depends=[Rcpp]; }; - exifr = derive2 { name="exifr"; version="0.2.2"; sha256="1na5d28x2s6lgwydfnhjvkya8kwsf4nh894f1inhzchk7g5cj475"; depends=[curl dplyr jsonlite purrr tibble]; }; + exifr = derive2 { name="exifr"; version="0.3.0"; sha256="00hixxc14wswn26s66443dkah67l498arnvwhya9cm5ybnc96h4k"; depends=[curl jsonlite plyr rappdirs tibble]; }; exiftoolr = derive2 { name="exiftoolr"; version="0.1.1"; sha256="0qip3r2vvxj0ax2pf150hmka70yiv9k2vlfj5pxyminri7scvf39"; depends=[curl jsonlite]; }; exp2flux = derive2 { name="exp2flux"; version="0.1"; sha256="1b3ychb4wcf6dbccx2ddms5xygdgc296cnw4474fm81yrfjznplv"; depends=[gage igraph sybil]; }; expandFunctions = derive2 { name="expandFunctions"; version="0.1.0"; sha256="0661l4ab0xhjidmh8ycvymhp3wgxafm7nd1c59bfpxhyhz76n1p4"; depends=[glmnet orthopolynom plyr polynom]; }; @@ -6668,9 +6717,9 @@ in with self; { expoTree = derive2 { name="expoTree"; version="1.0.1"; sha256="0hj1x4niqp0ghqik3mz733nc3zpnhyknrdpzpj6y2rfia2ysdiz8"; depends=[ape deSolve]; }; export = derive2 { name="export"; version="0.2.2"; sha256="03i3jk4b9q1sak6m36p349bzqcwfq3bw6y8sgrw65475mrwipm4m"; depends=[broom flextable officer openxlsx rgl rvg stargazer xml2 xtable]; }; expp = derive2 { name="expp"; version="1.2.2"; sha256="0xr24xzplgamj8dkjk9n9jmrbyw056z57hkm9h4j43g63vxrinlj"; depends=[deldir rgeos sp spatstat spdep]; }; - exprso = derive2 { name="exprso"; version="0.4.0"; sha256="122bh96hhn2wbwjlrnrb9s9bkfd2wp43vsyr8glxrd47mdvm2i9v"; depends=[cluster e1071 frbs kernlab lattice MASS nnet plyr randomForest ROCR rpart sampling]; }; + exprso = derive2 { name="exprso"; version="0.4.7"; sha256="066cqzbmdbrprqxd5dx9220k20pgidc49rqvksznadsxnrbzhq61"; depends=[cluster e1071 frbs glmnet kernlab lattice MASS nnet plyr randomForest ROCR rpart sampling]; }; expsmooth = derive2 { name="expsmooth"; version="2.3"; sha256="0alqg777g7zzbjbg86f00p2jzzlp4zyswpbif7ndd0zr8xis6zdc"; depends=[forecast]; }; - expss = derive2 { name="expss"; version="0.8.8"; sha256="1swq1wgbv28624rjbmpl4176cyhngr0bgmgv6d1j1fhj8r1aa2n6"; depends=[data_table foreign htmlTable magrittr matrixStats]; }; + expss = derive2 { name="expss"; version="0.8.10"; sha256="00h68pni8z1mnwzvjyr7zlxnp2b8rm6qbv5kjwa2a2q7fs3nswl7"; depends=[data_table foreign htmlTable magrittr matrixStats]; }; exptest = derive2 { name="exptest"; version="1.2"; sha256="0wgjg62rjhnr206hkg5h2923q8dq151wyv54pi369hzy3lp8qrvq"; depends=[]; }; exreport = derive2 { name="exreport"; version="0.4.1"; sha256="0vj60rchhrc5q6x1kv7b95fcmh2a5qynli2w54rrrw1nx54xm8c2"; depends=[ggplot2 reshape2]; }; exsic = derive2 { name="exsic"; version="1.1.1"; sha256="1k6nqs9i4iivxnk4nkimp6zvdly274wibkmx9n0wz01gnzxqil0p"; depends=[markdown stringr]; }; @@ -6687,7 +6736,7 @@ in with self; { extrafont = derive2 { name="extrafont"; version="0.17"; sha256="0b9k2n9sk23bh45hjgnkxpjyvpdrz1hx7kmxvmb4nhlhm1wpsv9g"; depends=[extrafontdb Rttf2pt1]; }; extrafontdb = derive2 { name="extrafontdb"; version="1.0"; sha256="115n42hfvv5h4nn4cfkfmkmn968py4lpy8zd0d6w5yylwpzbm8gs"; depends=[]; }; extremeStat = derive2 { name="extremeStat"; version="1.4.0"; sha256="0fvkvlm47ri05w9h5qa937ijsc5lg51jc825wq9pmn7aiv58yxzm"; depends=[berryFunctions evd evir extRemes fExtremes ismev lmomco pbapply RColorBrewer Renext]; }; - extremefit = derive2 { name="extremefit"; version="0.2.4"; sha256="0r21qx4kl6mcjp8mx9pcrmwhchyd7jggkm8bqid2czhd3y29j8yh"; depends=[]; }; + extremefit = derive2 { name="extremefit"; version="1.0.0"; sha256="064cb0xzpl3akvzg155pfppkkwalmdr06xi7h9pq9s5icrznyzdf"; depends=[]; }; extremevalues = derive2 { name="extremevalues"; version="2.3.2"; sha256="0pyngxljdnjwnbwcb0gmxcirv70r1s1wyq4m1wm5rprpdj8v9xil"; depends=[gWidgets gWidgetstcltk]; }; extremis = derive2 { name="extremis"; version="0.90"; sha256="1cnwn70d9swks5b2y915l18gky9v23vaqlaaggshi0ghn3snb4sm"; depends=[emplik]; }; extremogram = derive2 { name="extremogram"; version="1.0.2"; sha256="13k869v6j4ik9p8w0gf1absvb45xbd3nnwghsz0ix7y0vyvry358"; depends=[boot MASS]; }; @@ -6746,6 +6795,7 @@ in with self; { fakemake = derive2 { name="fakemake"; version="1.4.0"; sha256="0ncwdy66975argnghp8kkd9f571pphk6wj572wp8nhl5qkrfi7rk"; depends=[callr igraph MakefileR pkgbuild withr]; }; falcon = derive2 { name="falcon"; version="0.2"; sha256="09hlvwwj3k3nhcsxijjvv8x74a9m200ayjjplrp4baxvczwyq341"; depends=[]; }; falconx = derive2 { name="falconx"; version="0.2"; sha256="0648mvbc7ga7vr2xqzyln3dgd11h5s4bqhv3p55mj7smr4qv7hv9"; depends=[]; }; + fam_recrisk = derive2 { name="fam.recrisk"; version="0.1"; sha256="1lyrq7bq7p7ijc2vf545nazw4akncz08548ya1dv3lsc5jmkgfzj"; depends=[]; }; fam2r = derive2 { name="fam2r"; version="1.2"; sha256="0pq5cmzwk3s8cz5x8dsfb2d6qfpapkrwbzvkqmqkhcwhwryy40mm"; depends=[Familias paramlink]; }; famSKATRC = derive2 { name="famSKATRC"; version="1.1.0"; sha256="1xbh0by4sjxrmy00v1svcj3lb98p9krpncbhpjbli1jd2p47yk60"; depends=[bdsmatrix CompQuadForm coxme kinship2]; }; fame = derive2 { name="fame"; version="2.21"; sha256="15pcgc67qcg6qkgssbfissicic317v60jsybp86ryqvzqg70cqx3"; depends=[tis]; }; @@ -6828,7 +6878,6 @@ in with self; { features = derive2 { name="features"; version="2015.12-1"; sha256="0rd8r1dxzddb6718hcm8ck7531c9wdrjfy8n67875bbxgzcvds61"; depends=[lokern]; }; featurizer = derive2 { name="featurizer"; version="0.2"; sha256="05jvwsvpbdj94q3wl7ld6xmfc9p7ff9zsmryd3mmxz0hzbq2cnkc"; depends=[]; }; febr = derive2 { name="febr"; version="1.0.1"; sha256="0wlanldcz8xdr1hng7ixhssvihdymv91icxn3qjcpm5cajnpnr7a"; depends=[dplyr glue googlesheets knitr pedometrics readr sp stringr xlsx]; }; - fecR = derive2 { name="fecR"; version="0.0.2"; sha256="1p4166cxajapm158aqbz9p7m8c8dqga1infl6y6wazjnayaib3cb"; depends=[lubridate plyr]; }; fechner = derive2 { name="fechner"; version="1.0-3"; sha256="0bassigcipwlr2g8cdjh8jyhmb903k3hla9gnigcbz7qwzlfwa86"; depends=[]; }; federalregister = derive2 { name="federalregister"; version="0.2.0"; sha256="0qr8nd3ylnwcv1wxspw5i7ray5sh30zr648spg0lpqq8dp2b8p7b"; depends=[curl httr jsonlite]; }; fedregs = derive2 { name="fedregs"; version="0.1.0"; sha256="1ydkw1090n8kw26d89wrzs86xq47mahdj41pgf8x1m292xcffvjm"; depends=[dplyr httr magrittr purrr rvest stringi tidytext xml2]; }; @@ -6849,7 +6898,7 @@ in with self; { fgof = derive2 { name="fgof"; version="0.2-1"; sha256="0bclkb3as0fl2gyggqxczndfyj9pfnni5pa3inpn5msrnjg4g2j2"; depends=[mvtnorm numDeriv]; }; fgpt = derive2 { name="fgpt"; version="2.3"; sha256="1d0qzsn4b68jhk07k97iv765jpmzzh1gwqpid0r76vg4cwqfs3n7"; depends=[]; }; fgui = derive2 { name="fgui"; version="1.0-8"; sha256="024fzd1c7iwqprn26hwjb9l2qlvvyzl449d7iixy0x69djwsrysv"; depends=[]; }; - fieldRS = derive2 { name="fieldRS"; version="0.1.1"; sha256="1zyi1qnyn9wi2rcf1d512dyrlkws2adp2wamzbrcbcgv8l4kysz7"; depends=[caret ggplot2 raster rgeos sp spatialEco]; }; + fieldRS = derive2 { name="fieldRS"; version="0.2.1"; sha256="04h6jwlpar5s0rv35379qr0f64ca3hg510qh62k896rn38z2265d"; depends=[caret concaveman ggplot2 raster rgeos sp spatialEco stringdist]; }; fields = derive2 { name="fields"; version="9.6"; sha256="1v7z48a8jmdcil28rj8c3455k6rssr5v9qi6dyhhpbb193bj8121"; depends=[maps spam]; }; fiery = derive2 { name="fiery"; version="1.1.1"; sha256="07cfrzajr5knmz5ngczkdd2kzjfdnn1y4b0z73daxwhk4dq8j6ji"; depends=[assertthat crayon future glue httpuv later R6 reqres stringi uuid]; }; filehash = derive2 { name="filehash"; version="2.4-1"; sha256="1x7an7rsy5pz2qr86m511rsv297vacxwk3y1a71754yq739qgq6h"; depends=[]; }; @@ -6861,7 +6910,7 @@ in with self; { files = derive2 { name="files"; version="0.0.1"; sha256="1vhhawqjjbb6fadkn3l10mvz63w3vmcwvl93fk0q9mhkifzlj9kc"; depends=[]; }; filesstrings = derive2 { name="filesstrings"; version="3.0.0"; sha256="1r32z9xlid9pj8sapb73iwzq6cczz96f1ipdbszwb6x9vlq2nw7l"; depends=[checkmate magrittr matrixStats ore purrr Rcpp rlang strex stringr tibble]; }; filling = derive2 { name="filling"; version="0.2.0"; sha256="0yxixwgvn7jq09j4r3q33mmdda9a4anfi7y0xqscbdjz6p9bx48w"; depends=[CVXR nabor Rcpp RcppArmadillo Rdpack ROptSpace RSpectra]; }; - finalfit = derive2 { name="finalfit"; version="0.8.8"; sha256="0km8qh7dx54msn48sgr4x7f22alk2wdpxjv5dvb1r4lxz0fhdq6y"; depends=[boot broom dplyr forcats GGally ggplot2 gridExtra Hmisc lme4 mice plyr pROC purrr scales stringr survival survminer tidyr]; }; + finalfit = derive2 { name="finalfit"; version="0.8.9"; sha256="1sxmvs40nwijnjkv2ispj6vnv81ra6vm3ny9spmpnns3987dhdqm"; depends=[boot broom dplyr forcats GGally ggplot2 gridExtra Hmisc lme4 magrittr mice pillar plyr pROC purrr scales stringr survival survminer tidyr]; }; finch = derive2 { name="finch"; version="0.2.0"; sha256="1vganbkz2d96xfz2jf1q0kqarc575w3nswss2igynsbbd0y53mjm"; depends=[data_table digest EML hoardr plyr rappdirs xml2]; }; findR = derive2 { name="findR"; version="0.2.1"; sha256="1a7cf6kd7i2l4ffr2b17nb9xnpsjhf6fcwpjy06r0qgcapnfp54b"; depends=[pdftools stringr]; }; findpython = derive2 { name="findpython"; version="1.0.4"; sha256="1zfcdcp4d48d2pzf5n59kqrfk2z9nnyzkx5j00gfmgfkadnv93x5"; depends=[]; }; @@ -6869,7 +6918,7 @@ in with self; { fingerPro = derive2 { name="fingerPro"; version="1.1"; sha256="1a1lj8gyrbgcg8hr03cj2bjzlaafddspri7abc83ys1raqwd4j68"; depends=[car GGally ggplot2 gridExtra klaR MASS plyr Rcmdr Rcpp RcppGSL RcppProgress reshape rgl scales]; }; fingerprint = derive2 { name="fingerprint"; version="3.5.7"; sha256="04jcwkydjrs31pia6kq8z2n9s54im950q08hs2ay15xjxxkmb8ic"; depends=[]; }; fingertipsR = derive2 { name="fingertipsR"; version="0.2.0"; sha256="1zgazqa7mxajgcf9pfq3kvr9qmfy0pncwdlq9g9vi5qasm2ix6g1"; depends=[curl dplyr DT httr jsonlite miniUI purrr readr shiny shinycssloaders]; }; - fingertipscharts = derive2 { name="fingertipscharts"; version="0.0.2"; sha256="12izvrmjdwy212zxgl54cbry53fv351g3vxmjw5vimqmdd991fxw"; depends=[dplyr fingertipsR geojsonio ggplot2 leaflet lemon mapproj purrr rlang scales sf stringr tibble tidyr]; }; + fingertipscharts = derive2 { name="fingertipscharts"; version="0.0.3"; sha256="0b0pivm2k3db4hkd65dfxdq13682hakkkrcx0y4s6lly70a3cf7z"; depends=[dplyr fingertipsR geojsonio ggplot2 leaflet lemon mapproj purrr rlang scales sf stringr tibble tidyr]; }; finiteruinprob = derive2 { name="finiteruinprob"; version="0.6"; sha256="0z4l0crymh58chxniqq70fqmvi6f5jkgvz72vbc7s3l9lrrapgr3"; depends=[numDeriv sdprisk]; }; finreportr = derive2 { name="finreportr"; version="1.0.1"; sha256="1mansiyl4p4zqc1h2aw9zgzb3fy4mppgmshdm8mcf4nbm340g4vk"; depends=[curl dplyr httr rvest XBRL xml2]; }; firebehavioR = derive2 { name="firebehavioR"; version="0.1.1"; sha256="1hf7j9nqqa2i92y73c1yniw6lgmjrl8fag9r4xnkd8vpiw453ck4"; depends=[ggplot2]; }; @@ -6929,6 +6978,7 @@ in with self; { flows = derive2 { name="flows"; version="1.1.1"; sha256="0l152p17plkrbnrlis8rfr9ij406agckdxvnjsciilv6qwcync29"; depends=[igraph reshape2 sp]; }; flsa = derive2 { name="flsa"; version="1.05"; sha256="07z2b1pnpnimgbzkjgjl2b074pl9mml7nac2p8qvdgv7aj070cmh"; depends=[]; }; fluoSurv = derive2 { name="fluoSurv"; version="1.0.0"; sha256="1dv4lf7k28bih2qqkpy15f7d14ibxk48p3z6sj3dj5yvh25mhv81"; depends=[]; }; + fluspect = derive2 { name="fluspect"; version="1.0.0"; sha256="0j80wx00s8ljqg1qaqw66rj7kxhhk438hb0syv0lr9vld03cxy2w"; depends=[pracma]; }; flux = derive2 { name="flux"; version="0.3-0"; sha256="0pc9cab2pwrfl0fnz29wp7a398r49hvbi50jp8i2fk2rfvck21a7"; depends=[caTools]; }; fluxweb = derive2 { name="fluxweb"; version="0.2.0"; sha256="1ssq90fqm4p0j4g171mx208lmgz3hkxs8hgsffkawpmxgacs0gh1"; depends=[]; }; fma = derive2 { name="fma"; version="2.3"; sha256="1z7shh9ng3q7ax22cwg86y79jzz5gbchdny2rppzzm0lkvvyy5pm"; depends=[forecast]; }; @@ -6950,23 +7000,24 @@ in with self; { fontcm = derive2 { name="fontcm"; version="1.1"; sha256="1z6b4qdgj5vhvjqj90sm1hp0fffi1vxzvq71p0flxybzyb7d15la"; depends=[]; }; fontquiver = derive2 { name="fontquiver"; version="0.2.1"; sha256="0qv3i9hch7cygl9983s3w68wfh5qvym2jkm52pp06p6mq8a1i1wm"; depends=[fontBitstreamVera fontLiberation]; }; foodweb = derive2 { name="foodweb"; version="1-0"; sha256="1zm2a87g9bkpz90j9lax28s5hq1w7ia28qqb6vnvr1d7a47g9zi9"; depends=[rgl]; }; - foolbox = derive2 { name="foolbox"; version="0.1.0"; sha256="1wqswfsanak9p0hpgbblva4b90pamlq1hcjf4xzwd3awjicsp56y"; depends=[magrittr rlang]; }; + foolbox = derive2 { name="foolbox"; version="0.1.1"; sha256="06lcr5v6bcqqxskrwdm16b46zq4h67x8bwqya88jxs5bgi5w0hj3"; depends=[magrittr rlang]; }; forams = derive2 { name="forams"; version="2.0-5"; sha256="1fh3m9896ksv1h7b027yb955bzyv70yafhqvn5crkzalzk3jpb0s"; depends=[vegan]; }; forcats = derive2 { name="forcats"; version="0.3.0"; sha256="0mxn1hng43zdjh1v8shd80hrszrqahcpaqxs1s1sif0qxh84d0cm"; depends=[magrittr rlang tibble]; }; foreSIGHT = derive2 { name="foreSIGHT"; version="0.9.6"; sha256="0vz80p227fvw18rrar5d1ikz42j47jsly0h1wmiy9gww14rcnncd"; depends=[cowplot directlabels doParallel GA ggplot2 moments zoo]; }; foreach = derive2 { name="foreach"; version="1.4.4"; sha256="0j2yj0rn0d5nbzz9nq5rqqgnxhp9pbd92q4klsarl2xpsn8119y0"; depends=[codetools iterators]; }; forecTheta = derive2 { name="forecTheta"; version="2.2"; sha256="1a7ip3czm8k82kb8dx95m8q47kjhifdj51gzavd1zj9ni3vwbhfn"; depends=[forecast tseries]; }; forecast = derive2 { name="forecast"; version="8.4"; sha256="13qq25b4r4fl18yl1wb441pqk98yqhi2gidy6si1kxgifq1xyp39"; depends=[colorspace fracdiff ggplot2 lmtest magrittr nnet Rcpp RcppArmadillo timeDate tseries urca uroot zoo]; }; - forecastHybrid = derive2 { name="forecastHybrid"; version="3.0.14"; sha256="0n97lw1hhi9qkdp37nn66b073v0sn67i4d1aqx0rwwqz6643sqib"; depends=[doParallel foreach forecast ggplot2 zoo]; }; + forecastHybrid = derive2 { name="forecastHybrid"; version="4.1.16"; sha256="1srli1s96bamagqvga8qkbiyxap256bdb3hrq63nix10cv35iv61"; depends=[doParallel foreach forecast ggplot2 purrr zoo]; }; forecastSNSTS = derive2 { name="forecastSNSTS"; version="1.2-0"; sha256="1rnf2a7sri52sm976iicab660qk07pmz8jmd3q71dg4hmc30yf9j"; depends=[Rcpp]; }; foreign = derive2 { name="foreign"; version="0.8-71"; sha256="1mv04w3ycz0ymsszn8aa87k6k5sb8mg8lhf1b8w4zpfrphpkkliv"; depends=[]; }; forensic = derive2 { name="forensic"; version="0.2"; sha256="0kn8wn6p3fm67w88fbarg467vfnb42pc2cdgibs0vlgzw8l2dmig"; depends=[combinat genetics]; }; forensim = derive2 { name="forensim"; version="4.3"; sha256="1jhlv9jv832qxxw39zsfgsf4gbkpyvywg11djldlr9vav7dlh3iw"; depends=[tcltk2 tkrplot]; }; + forestChange = derive2 { name="forestChange"; version="0.3"; sha256="1kjibqy8prpbakxficxdx9kqn4qyh3nfpzfcvg19djpnh8p04h78"; depends=[raster rgdal rmarkdown SDMTools]; }; forestControl = derive2 { name="forestControl"; version="0.2.0"; sha256="1w1x7i57dqlrm6zzgx4k0p1zs83nrg2w2jhhvjjk9s6y1ba3whyg"; depends=[dplyr magrittr purrr Rcpp tibble]; }; forestFloor = derive2 { name="forestFloor"; version="1.11.1"; sha256="1sslxq44qmmmdhr7800bz8lj9w2l7f7x1vly3w2z7j1qdijc7nw7"; depends=[kknn randomForest Rcpp rgl]; }; forestHES = derive2 { name="forestHES"; version="1.0-1"; sha256="05l04ly3l8xkdz3rnnrfa4y0wfmh1am2ixbz1vfarnqkc0zppwpj"; depends=[]; }; forestinventory = derive2 { name="forestinventory"; version="0.3.1"; sha256="0brbg0q8j9ymvm527db7063kgs6i6flja7mxqk7yvaf3dh8wsi46"; depends=[ggplot2 plyr tidyr]; }; - forestmangr = derive2 { name="forestmangr"; version="0.9.0"; sha256="1k3n6k7jf1b5pd1vp51z47hbln3cfwdb1nl2dv28jv1ba5lb7ja6"; depends=[broom car covr curl dplyr ggplot2 ggpmisc ggthemes htmltools magrittr minpack_lm plyr psych purrr rlang rmarkdown scales systemfit tibble tidyr]; }; + forestmangr = derive2 { name="forestmangr"; version="0.9.1"; sha256="1b0yijc1yzgwkypyxb6v03sw32r3zz9rfjw63xiwzspq7hkbpinx"; depends=[broom car dplyr FinCal formattable ggdendro ggplot2 ggpmisc ggthemes gridExtra magrittr minpack_lm plyr purrr rlang scales systemfit tibble tidyr]; }; forestmodel = derive2 { name="forestmodel"; version="0.5.0"; sha256="09gwgsh42gkmhs8ijq5xfbbkb1hk6sjb0q32mw2ymc6x9ycr1a9j"; depends=[broom dplyr ggplot2 lazyeval tibble]; }; forestplot = derive2 { name="forestplot"; version="1.7.2"; sha256="1cqk0fwpbn4an6xn28kpvqmcp3mgv8isg8dy755sv5fkqzzjz1dg"; depends=[checkmate magrittr]; }; forestr = derive2 { name="forestr"; version="1.0.1"; sha256="0m26x7ngl89ngk1qhg50npmwli2npmjs9pfb9rg5hmx4fzr8k63i"; depends=[dplyr ggplot2 plyr]; }; @@ -7036,7 +7087,7 @@ in with self; { fsia = derive2 { name="fsia"; version="1.1.1"; sha256="0id7cnswrqylgpwjil1zfn89ryrdpl20fim8x1srl8s1hm5bg35r"; depends=[]; }; fslr = derive2 { name="fslr"; version="2.22.0"; sha256="1a3sclwhmalp4g05yr8gw80zgcbqvgpbppj1pyw4x846ahk1wikd"; depends=[neurobase oro_nifti R_utils]; }; fso = derive2 { name="fso"; version="2.1-1"; sha256="0hn2ypm0nwfbmnh9il78pi30x7gfmayfangqyh0d63ngyz40bvma"; depends=[labdsv]; }; - fst = derive2 { name="fst"; version="0.8.8"; sha256="0yhkpq54msr0620456gzyg5c47n8cjvnpc3iyvj24cvyar2l9vwp"; depends=[Rcpp]; }; + fst = derive2 { name="fst"; version="0.8.10"; sha256="1wlrkky5anjv7a1ma3kvrbq0pzv6mff2fvp5rkgrwzp9cqmms997"; depends=[Rcpp]; }; fsthet = derive2 { name="fsthet"; version="1.0.1"; sha256="0z6az1jcvdahgn97r6cpj1s6fn0lvr7j12gcw2r7wbpajrvyl5j6"; depends=[]; }; ftDK = derive2 { name="ftDK"; version="1.0"; sha256="1xs2rr2afjza97kpym5zkas3k78pilxjlh7lp1gc66banldr71g2"; depends=[dplyr httr pbapply purrr tibble]; }; ftnonpar = derive2 { name="ftnonpar"; version="0.1-88"; sha256="0df9zxwjpfc939ccnm1iipwhpf76b34v0x74nsi1mm1g927dfl0i"; depends=[]; }; @@ -7083,6 +7134,7 @@ in with self; { fuzzr = derive2 { name="fuzzr"; version="0.2.2"; sha256="1cwq7a5j6lzrlz9dw3hsfap988rh1kkgf03yni7c33zl69xp5w77"; depends=[assertthat progress purrr]; }; fuzzyFDR = derive2 { name="fuzzyFDR"; version="1.0"; sha256="0zd8i9did0d9gp42xjmwrccm32glabvvy08kl8phhwb1yaq53h7w"; depends=[]; }; fuzzyRankTests = derive2 { name="fuzzyRankTests"; version="0.3-10"; sha256="1xj5xsm2s4ylv3b8v80qny201iddjym07h8d50asas7xy1k7945z"; depends=[]; }; + fuzzySim = derive2 { name="fuzzySim"; version="2.0"; sha256="00rl5npz656hwpd1ah8bgh9baqpa9z2lgxc44amm5w3pb9pqjkbs"; depends=[]; }; fuzzyforest = derive2 { name="fuzzyforest"; version="1.0.5"; sha256="1ifhvdzn0rs8gxqmpz8w1prxg3pxs5jqx5lh0r4i5rai49qjy3sb"; depends=[doParallel doRNG foreach ggplot2 mvtnorm randomForest]; }; fuzzyjoin = derive2 { name="fuzzyjoin"; version="0.1.4"; sha256="06r103hshc6xcjllv5qfiw3i1ddz4c8svy0i4j0avnffaarlc2wa"; depends=[dplyr geosphere purrr stringdist stringr tidyr]; }; fuzzyreg = derive2 { name="fuzzyreg"; version="0.4.1"; sha256="1n1hc9br70rpg6r7cchgyj9xg1fm0fi8jnfj74yyvkpf39b0cj25"; depends=[limSolve quadprog]; }; @@ -7132,6 +7184,7 @@ in with self; { gamboostLSS = derive2 { name="gamboostLSS"; version="2.0-1"; sha256="06n2xk7k24gz95jy1cr6shpfd89ylispq6mn3fvxblqdf8vhdixj"; depends=[mboost stabs]; }; gamboostMSM = derive2 { name="gamboostMSM"; version="1.1.87"; sha256="0if0x92lch57ksll8d5i3jzk0kh40593b20c17g3hvc33920c7r0"; depends=[mboost]; }; gamclass = derive2 { name="gamclass"; version="0.58"; sha256="0dldqnbdgrafkm1a9kb0gyyfs0s2g31iv4ndlnnm2rd63ga4xxsn"; depends=[ape car DAAG KernSmooth lattice latticeExtra MASS mgcv randomForest rpart]; }; + gameofthrones = derive2 { name="gameofthrones"; version="1.0.0"; sha256="15jgpv197aqb56iyp4afjajx2rcxz21dhigx9mxipa0b8g2h0s6k"; depends=[ggplot2 gridExtra MASS]; }; games = derive2 { name="games"; version="1.1.2"; sha256="01hbbr2hsxi5j9axpdl0jihpd55pa9hacjxmab8p7cixk3xqqqbf"; depends=[Formula MASS maxLik stringr]; }; gamesGA = derive2 { name="gamesGA"; version="1.1.3.5"; sha256="1xvy0azyjcr077lwpnh6083ypv0j8qjd0frkc6z6vs6fgbv2lv5p"; depends=[shiny]; }; gamlr = derive2 { name="gamlr"; version="1.13-5"; sha256="0fc27b6qcm01drb7pb14wri2hlb464jig3x7sb8njwrxcqqia14n"; depends=[Matrix]; }; @@ -7161,7 +7214,7 @@ in with self; { gapminder = derive2 { name="gapminder"; version="0.3.0"; sha256="067cra1ca4ngwjx8d1y9pyzwcpsfi1wcal0glzyy6ghd1k6jflpv"; depends=[tibble]; }; garray = derive2 { name="garray"; version="1.1.2"; sha256="0s2dgi556x9jnhafvzz4qkxdbq9dm12gsvsqd2g9iy3468fx9flq"; depends=[]; }; gaselect = derive2 { name="gaselect"; version="1.0.5"; sha256="0xzx00n46x6x7w1xbx8nvabkkrna45pv1i70787m8h05q1yrjjij"; depends=[Rcpp RcppArmadillo]; }; - gasfluxes = derive2 { name="gasfluxes"; version="0.4"; sha256="1shjyksnqq2sjv8k2qidx9k1s6clh3lfvffdwxqbm3lp7wqzlmg6"; depends=[AICcmodavg data_table MASS sfsmisc]; }; + gasfluxes = derive2 { name="gasfluxes"; version="0.4-1"; sha256="0x1ckb72xkfcm0aidj5m7d2aavqij0qdfclsm3gf3dp7rdm9ymw1"; depends=[AICcmodavg data_table MASS sfsmisc]; }; gastempt = derive2 { name="gastempt"; version="0.4.3"; sha256="009g6w22yjybjhdpphc2gqn3lqng6vqr0n2myp3y02s6zxl9h7qj"; depends=[assertthat BH dplyr ggplot2 nlme Rcpp RcppEigen rstan rstantools shiny StanHeaders stringr tibble]; }; gaston = derive2 { name="gaston"; version="1.5.4"; sha256="1yjl100z6cakpfd1gqryigpclyslygzvhps7w6gyrp85yipj5i0r"; depends=[Rcpp RcppEigen RcppParallel]; }; gatepoints = derive2 { name="gatepoints"; version="0.1.3"; sha256="02qxxf4a6rl3l0jdgqxmzxfnqd9lh5i0q2knaxxsiz0nd74c1jg5"; depends=[]; }; @@ -7179,7 +7232,7 @@ in with self; { gbts = derive2 { name="gbts"; version="1.2.0"; sha256="1v8x4dnja8va28rjznyqa6js9wazndijasb95lfj2qwhxhgf5h65"; depends=[doParallel doRNG earth foreach gbm]; }; gbutils = derive2 { name="gbutils"; version="0.4-0"; sha256="01ka10k599c8q7l55jzkrvqlxhzdanc4xnmsh6js5ji5yr7v385f"; depends=[Rdpack]; }; gcForest = derive2 { name="gcForest"; version="0.2.7"; sha256="10fjha76sgnrkhwjm0rm4hrbn0643p9dsyb5ahw43x8m5kmw2ydq"; depends=[cli crayon pkgdown reticulate]; }; - gcKrig = derive2 { name="gcKrig"; version="1.1.2"; sha256="1wqmw56805bny8w6zdj5zn4c89p3x39d5pkp4xslpd5f623zvf6x"; depends=[Rcpp RcppArmadillo]; }; + gcKrig = derive2 { name="gcKrig"; version="1.1.3"; sha256="18rnmvq7kgjysic24hwc39ay4yjnhn7zs6pg05q8hz7wsq8xlvjx"; depends=[Rcpp RcppArmadillo]; }; gcbd = derive2 { name="gcbd"; version="0.2.6"; sha256="1dvnly0aljv2c4x7sn3q55ncvfdfjfgp7w0k2900p77h4w8nixia"; depends=[DBI lattice Matrix plyr reshape RSQLite]; }; gcdnet = derive2 { name="gcdnet"; version="1.0.5"; sha256="159dl8v1n7s9wnfrjb6f0b3ssblkqgbfzs15vjxhc8xkz0jp9z1c"; depends=[Matrix]; }; gcerisk = derive2 { name="gcerisk"; version="18.02.22"; sha256="1wy9l4s17ji5xj1cxjnb59qz3242yjs4zp76fy3rg1m0k7ib52vg"; depends=[cmprsk ggplot2 survival]; }; @@ -7265,7 +7318,8 @@ in with self; { geoelectrics = derive2 { name="geoelectrics"; version="0.2.0"; sha256="1dmpaf16750ni4yr36cglfz9pv9jax8jxb3kwn47kxgnx3l8qq98"; depends=[fields lattice rgl]; }; geofacet = derive2 { name="geofacet"; version="0.1.9"; sha256="0z9xd24hn9j8azd4kal81lz72zy6vv9rvwx1jsmkq7z7f1wwly48"; depends=[geogrid ggplot2 ggrepel gridExtra gtable imguR rnaturalearth sp]; }; geofd = derive2 { name="geofd"; version="1.0"; sha256="16312g9mgw52mpsfky1j20zcqkkv91ihl0xhvv1bl80diffzf0zi"; depends=[fda geoR]; }; - geogrid = derive2 { name="geogrid"; version="0.1.0.1"; sha256="1skklrv2k0a0wi86q5d5mn7ma028ggl1pby7gpl3jssh7bgxw8wp"; depends=[Rcpp RcppArmadillo rgeos sf sp]; }; + geogrid = derive2 { name="geogrid"; version="0.1.1"; sha256="0b8afwgj9x56z6zh525y7qkiwbv77mjcw3v19kfba0426jn4vi87"; depends=[Rcpp RcppArmadillo rgeos sf sp]; }; + geohashTools = derive2 { name="geohashTools"; version="0.2.0"; sha256="1jc6kghs2lpjvn1zrw635fyf5vhs9r570hyrdyqcxpv77lixs4gg"; depends=[Rcpp]; }; geojson = derive2 { name="geojson"; version="0.2.0"; sha256="1xvbkdaaf55x015pflvcdy06ayrmhqi3my0sdqb48z129rdbr3i7"; depends=[jqr jsonlite lazyeval magrittr protolite sp]; }; geojsonR = derive2 { name="geojsonR"; version="1.0.6"; sha256="17zcrkazcnn1507m5cpphzp14m40w1wzrhrb77rl5hn1jrxqvhh5"; depends=[R6 Rcpp RcppArmadillo]; }; geojsonio = derive2 { name="geojsonio"; version="0.6.0"; sha256="10vi40ppy65yg655xy0j8zl6icn7d7icwfj4a84wpp28pd1bwic8"; depends=[geojson httr jqr jsonlite magrittr maptools readr rgdal rgeos sf sp V8]; }; @@ -7275,7 +7329,7 @@ in with self; { geomapdata = derive2 { name="geomapdata"; version="1.0-4"; sha256="1g89msnav87kim32xxbayqcx1v4439x4fsmc8xhlvq4jwlhd5xxw"; depends=[]; }; geomedb = derive2 { name="geomedb"; version="0.2"; sha256="1nsf7xzqayk8zbw3b6xpgiqk2w2kzc896gjswzxq128xw05cia0a"; depends=[ape httr]; }; geomerge = derive2 { name="geomerge"; version="0.3.1"; sha256="0pvyhpv4vq8mvvlybxhviq8rbazw29dgf9m0xnldaxg9r6lqdp4d"; depends=[geosphere ggplot2 gridExtra inlmisc lubridate raster scales sp spdep]; }; - geometa = derive2 { name="geometa"; version="0.3-0"; sha256="0cw29a4zsqvqyj4zmvk92752k65yhxxjqmqp0kl0pnidl18vbp46"; depends=[R6 XML]; }; + geometa = derive2 { name="geometa"; version="0.4-0"; sha256="0lcm5ndgx0y1d83813xxfp06j1x1lnh388v6npv4a3n0ln4kczwn"; depends=[httr R6 XML]; }; geometry = derive2 { name="geometry"; version="0.3-6"; sha256="0s09vi0rr0smys3an83mz6fk41bplxyz4myrbiinf4qpk6n33qib"; depends=[magic]; }; geomnet = derive2 { name="geomnet"; version="0.2.0"; sha256="0xanzx8p34bac4zcf9j69nivwhllvsrw7x70mzgl95jhg3gvv96a"; depends=[dplyr ggplot2 network plotly readr sna tidyr]; }; geomorph = derive2 { name="geomorph"; version="3.0.7"; sha256="1q9qdpb08kfs1xs5s9xjxh98wb3hqilqynwzihlz1hsv38p99y38"; depends=[ape geiger jpeg Matrix rgl RRPP]; }; @@ -7327,6 +7381,7 @@ in with self; { ggallin = derive2 { name="ggallin"; version="0.1.1"; sha256="0hrxa7m07ppvnndivxcgxksdyblb6fw17aw46maqavlvcrz3fjgm"; depends=[ggplot2 scales]; }; ggalluvial = derive2 { name="ggalluvial"; version="0.9.1"; sha256="0np4dwhxz9q3p9y1w45fyvs4cphi50mbgi9wrinpi3k5i3anv6zf"; depends=[dplyr ggplot2 lazyeval rlang tidyr tidyselect]; }; ggalt = derive2 { name="ggalt"; version="0.4.0"; sha256="0ssa274d41vhd6crzjz7jqzbwgnjimxwxl23p2cx35aqs5wdfjpc"; depends=[ash dplyr extrafont ggplot2 gtable KernSmooth maps MASS plotly proj4 RColorBrewer scales tibble]; }; + gganimate = derive2 { name="gganimate"; version="1.0.0"; sha256="1lbabyraklkd4l6128kw96xhrc7c8plsk3sdbvkh9waz0jfgixak"; depends=[ggplot2 glue plyr progress rlang scales stringi tweenr]; }; ggbeeswarm = derive2 { name="ggbeeswarm"; version="0.6.0"; sha256="0crk29p5vi1r3a988kms4y7r0iqwgwzsikgvh18r9wbzyr98bb5v"; depends=[beeswarm ggplot2 vipor]; }; ggbuildr = derive2 { name="ggbuildr"; version="0.1.0"; sha256="0pld635v6fv46ky7s4icwxlcnr7z6bp5ikf20adpkljwhy0wwxak"; depends=[ggplot2 purrr readr]; }; ggconf = derive2 { name="ggconf"; version="0.1.3"; sha256="0g4xasqhdiqfqahakv6p5npl56f2iakx4bnc9v9zcjr077kdda4n"; depends=[ggplot2 rly]; }; @@ -7396,12 +7451,12 @@ in with self; { ggsn = derive2 { name="ggsn"; version="0.4.0"; sha256="0si3llqlb0dg482cqxhv5lm6raawqwpcd5ymjicw3780xq7d7mrk"; depends=[ggplot2 maptools png]; }; ggsolvencyii = derive2 { name="ggsolvencyii"; version="0.1.1"; sha256="0qk1219waymg8czr7vgdr0i31gzfr46zr0qjv8zgx5ba7ngdq12b"; depends=[dplyr ggplot2 magrittr tidyr]; }; ggsom = derive2 { name="ggsom"; version="0.2.1"; sha256="0gycd3yzdy58m22r62my5v0s00mr7ga7mcfa6i300arp47lzdwq1"; depends=[dplyr ggplot2 ggthemes kohonen tidyr tidyverse]; }; - ggspatial = derive2 { name="ggspatial"; version="1.0.2"; sha256="0j22s3icqxd1qv38cbznnrdfsprma9mbakfb49hfqbf9m22f2lkn"; depends=[abind ggplot2 plyr raster reshape2 rosm scales sf tibble tidyr]; }; + ggspatial = derive2 { name="ggspatial"; version="1.0.3"; sha256="0ka15qj3f0yq9nfkgk77wp490nz9ymi80918apv9zp6x39kcprj9"; depends=[abind ggplot2 plyr raster reshape2 rlang rosm scales sf tibble tidyr]; }; ggspectra = derive2 { name="ggspectra"; version="0.3.1"; sha256="0w9hrqxyrcds47g46bfccprrv0gykrmgqklmlig50zbnzssd3ac8"; depends=[dplyr ggplot2 ggrepel lubridate photobiology photobiologyWavebands scales tidyr]; }; ggstance = derive2 { name="ggstance"; version="0.3.1"; sha256="0v7f3xdaaridw6d4jvnsfwxmpjrasvx5vl555wsrn50aah17fkvh"; depends=[ggplot2 plyr rlang withr]; }; ggstatsplot = derive2 { name="ggstatsplot"; version="0.0.7"; sha256="0rg38yhmaya18zl24scpdhzkla13z6r4526m6afmy6pnkfiplyrc"; depends=[BayesFactor boot broom broom_mixed coin cowplot crayon dplyr effsize exact2x2 ggcorrplot ggExtra ggplot2 ggrepel ggsignif glmmTMB glue groupedstats jmv magrittr paletteer PMCMRplus psych purrr purrrlyr rlang scales sjstats tibble tidyr WRS2]; }; ggswissmaps = derive2 { name="ggswissmaps"; version="0.1.1"; sha256="0is48x6k2p5dgj9q4km0dv33a9pcpfhlai9vz295y3acpyrkmnn4"; depends=[ggplot2]; }; - ggtern = derive2 { name="ggtern"; version="3.0.0.1"; sha256="12b5swg55d4f9iwr5cf3fvdazrgd2jvm187w3gx9n84h26i5jnlp"; depends=[compositions ggplot2 gridExtra gtable latex2exp lattice MASS plyr proto scales]; }; + ggtern = derive2 { name="ggtern"; version="3.1.0"; sha256="1fhs5s3sxhb46abzni7cyymyknk9z7ff8fanln41pkih76s5i18j"; depends=[compositions ggplot2 gridExtra gtable latex2exp lattice MASS plyr proto scales]; }; ggthemes = derive2 { name="ggthemes"; version="4.0.1"; sha256="0y6570wv135sf7pv57l7bqilzw47rziaqx4vsk45pf1w4lmj0w8b"; depends=[ggplot2 purrr scales stringr tibble]; }; ggversa = derive2 { name="ggversa"; version="0.0.1"; sha256="0xqn8iznrm8q30pxwka88wi1z7lndi6lm12rq6ngcaxf294fbz01"; depends=[]; }; ggvis = derive2 { name="ggvis"; version="0.4.4"; sha256="1bxggjr2313kfy895j0fvrv4bg7yh2z87907lk48i1kn5c9flchk"; depends=[assertthat dplyr htmltools jsonlite lazyeval magrittr shiny]; }; @@ -7441,18 +7496,18 @@ in with self; { gldrm = derive2 { name="gldrm"; version="1.5"; sha256="1mbdxqjw6sa47kigwrjq1gn6vi36zhg9j2lck144iwa10ms0y9xp"; depends=[]; }; glinternet = derive2 { name="glinternet"; version="1.0.8"; sha256="06ak80j01cbrr6s8hmcc734z476rrqzib0xqjgv7c3jbw0api71y"; depends=[]; }; gllm = derive2 { name="gllm"; version="0.37"; sha256="169y3yz947d8qdphqv2a6yrdash6v2h9jfvj2fk7rcpmz0r45kl6"; depends=[]; }; - gllvm = derive2 { name="gllvm"; version="1.1.0"; sha256="06djkb46c4r2fjzgz7zpjdj9irmxy50k8b2zpx1d7g33n29pw6km"; depends=[fishMod MASS Matrix mvabund mvtnorm RcppEigen statmod TMB]; }; + gllvm = derive2 { name="gllvm"; version="1.1.2"; sha256="1ndd7zsy2czcr2rmbmwpvv8hvw3qi6zcmcljb879dd5h5z7n36v2"; depends=[fishMod MASS Matrix mvabund mvtnorm RcppEigen statmod TMB]; }; glm_deploy = derive2 { name="glm.deploy"; version="1.0.4"; sha256="1akklvbhz2pp0sv1hax1jq0s9ajbfv1597z643gh5l9hwizj2h9m"; depends=[Rcpp]; }; glm_predict = derive2 { name="glm.predict"; version="3.0-1"; sha256="0miba0xha99rmriqs7ifriq86ykn04j04f3ywk29bpph4iwc5faq"; depends=[MASS nnet]; }; glm2 = derive2 { name="glm2"; version="1.2.1"; sha256="1byqlvpls23gzy7xlbs1kgfr4bsrmsrpc8rzzacf9czap1nlw39y"; depends=[]; }; glmBfp = derive2 { name="glmBfp"; version="0.0-51"; sha256="15jm450j1f0nl7vqvpb2mwapdlvn7kq2kxf5s96x21siwsz7sssv"; depends=[coda Rcpp RcppArmadillo rms Runuran statmod survival]; }; glmbb = derive2 { name="glmbb"; version="0.3"; sha256="12yabwswps0fmprh8nb9jdny9xrm13jvc0d9m3w04ppmsvalrmwl"; depends=[digest]; }; - glmc = derive2 { name="glmc"; version="0.2-4"; sha256="03m1ym9w0b0gqib13pnh1yrjijlcwsn5lijg0nsr4hd6gxw29cla"; depends=[emplik]; }; + glmc = derive2 { name="glmc"; version="0.3-1"; sha256="0x6jk2l5rpjkp5x815gpiwv8maa7mhmy6m8gaxbv1cbn3zyccynn"; depends=[emplik]; }; glmdm = derive2 { name="glmdm"; version="2.60"; sha256="09vljki24fccqkvxkmg2i6a8pxqhfwm155b41m2q51lqaq29bfw7"; depends=[]; }; glmertree = derive2 { name="glmertree"; version="0.1-1"; sha256="0wfpx7y6x9ll86av399i7vaycjjbgmmmh78wy77cbq0gkp1rzb47"; depends=[Formula lme4 partykit]; }; glmgraph = derive2 { name="glmgraph"; version="1.0.3"; sha256="16sq6i7kbw20nvwikpa02z3pb7wqw3270j6ss7f8sgf548skhmx0"; depends=[Rcpp RcppArmadillo]; }; glmlep = derive2 { name="glmlep"; version="0.1"; sha256="0jnm3cf2r9fyncxzpk87g4pnxbryqcxxrc5y2a80pv48al3sxlzk"; depends=[]; }; - glmm = derive2 { name="glmm"; version="1.2.3"; sha256="0cxlcx09a5vypv6kkcfvfjdpz2rnxhay0pjv6q53hdmbshmchbmj"; depends=[digest Matrix mvtnorm trust]; }; + glmm = derive2 { name="glmm"; version="1.3.0"; sha256="088m626c2f75ij457mskdyi927y6g01m5rgfsjaxpm7xbywk51sw"; depends=[doParallel foreach itertools Matrix mvtnorm trust]; }; glmmBUGS = derive2 { name="glmmBUGS"; version="2.4.2"; sha256="1c4nxm6hv2x9acjss9psnh87ldsrxidnrxn01rjxbmihziyirp0y"; depends=[abind MASS sp]; }; glmmEP = derive2 { name="glmmEP"; version="1.0-1"; sha256="0w6q504map1frx7ch2gb7557xmc361lngsw2f80bnrlchj43rdgg"; depends=[lme4 matrixcalc]; }; glmmLasso = derive2 { name="glmmLasso"; version="1.5.1"; sha256="1az9vdnyqyrfn1q7zrn6x4ywx77b0vg65cni45x37b0ybkwpis39"; depends=[Matrix minqa]; }; @@ -7513,7 +7568,7 @@ in with self; { goldi = derive2 { name="goldi"; version="1.0.1"; sha256="191ac02bwrxr3khq6qirhxzfhv7pqfhqyg7jb473p5vwygpvc53l"; depends=[dplyr futile_logger magrittr Rcpp RcppArmadillo SnowballC tm]; }; gomms = derive2 { name="gomms"; version="1.0"; sha256="1i9d5y28wrhal990x7xxy99v3z9y2pzlakj7wnynd3dpx5pqr0jj"; depends=[]; }; goodpractice = derive2 { name="goodpractice"; version="1.0.2"; sha256="08rnm8z0pry5mwpc7p37r6f2rd56dry9djpcvvs9yl170w56psx0"; depends=[clisymbols covr crayon cyclocomp desc jsonlite lintr praise rcmdcheck rstudioapi whoami withr xml2 xmlparsedata]; }; - googleAnalyticsR = derive2 { name="googleAnalyticsR"; version="0.5.0"; sha256="183wywvsfq58yn8hj6kz83c3by36w8knckndwbih2xhxqqqj3cf0"; depends=[assertthat dplyr googleAuthR httr magrittr memoise purrr rlang tidyr]; }; + googleAnalyticsR = derive2 { name="googleAnalyticsR"; version="0.6.0"; sha256="0amhhp7h7f6a2qmmbxjg5rqhj6jdvmjv9rsvcx83ql3b6vbaxrpz"; depends=[assertthat dplyr googleAuthR httr jsonlite magrittr memoise purrr rlang tidyr]; }; googleAuthR = derive2 { name="googleAuthR"; version="0.7.0"; sha256="05y2y4z09in7af4lffpjlcvz51qbyzh93fhcjwdjmh80n1f4q8h9"; depends=[assertthat digest httr jsonlite memoise R6]; }; googleCloudStorageR = derive2 { name="googleCloudStorageR"; version="0.4.0"; sha256="1iwn0qjyxyg1xr1s492h7z2g5yzcfw8kasd4ghxmghnqvhzzf7vn"; depends=[assertthat curl googleAuthR httr jsonlite openssl yaml zip]; }; googleComputeEngineR = derive2 { name="googleComputeEngineR"; version="0.2.0"; sha256="1kslsi7gc4na8pm8dyizswf9pfpdq1rprn08rd7kbxsisclbzc7y"; depends=[assertthat future googleAuthR httr jsonlite]; }; @@ -7656,7 +7711,7 @@ in with self; { h2o = derive2 { name="h2o"; version="3.20.0.8"; sha256="17piklf91fmpf7bl4sk300bwnvsxljad925whs2h12xhqgw3amgv"; depends=[jsonlite RCurl]; }; h2o4gpu = derive2 { name="h2o4gpu"; version="0.2.0"; sha256="06d2rrr27xvnsai6zjiaiw0jjfzdza1cc39c03d6pjkvnh0mqh2c"; depends=[magrittr reticulate]; }; h5 = derive2 { name="h5"; version="0.9.9"; sha256="14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx"; depends=[Rcpp]; }; - hBayesDM = derive2 { name="hBayesDM"; version="0.6.0"; sha256="0il3w1vlw8p02lq5svymv5qafmal784c037dbjk1f6j96lg7i69f"; depends=[ggplot2 loo Rcpp rstan rstantools]; }; + hBayesDM = derive2 { name="hBayesDM"; version="0.7.0"; sha256="0j4q7q44x407b973s7jz5zvfp3k8rnnpm558pfbygmakqv1cwz35"; depends=[BH data_table ggplot2 loo Rcpp RcppEigen rstan StanHeaders]; }; hIRT = derive2 { name="hIRT"; version="0.1.3"; sha256="12rg4srh9s6a72gvb5f7qn9zar6yaqa7p0mfmazfqj353icrannd"; depends=[pryr rms]; }; hNMF = derive2 { name="hNMF"; version="0.9"; sha256="0qavavgiqah4dv0gz8v5ssz637sd341n9s0pyc232n2jhqpzl0cz"; depends=[MASS NMF nnls oro_nifti R_matlab rasterImage spatialfil]; }; hR = derive2 { name="hR"; version="0.1.4"; sha256="0ylqn7fv8dbhiqa6q41ajvh59yjmw18gpwvnm4fsna67q5wj98ql"; depends=[data_table data_tree]; }; @@ -7678,7 +7733,7 @@ in with self; { hapsim = derive2 { name="hapsim"; version="0.31"; sha256="0jw6iw89d4y8wjy58biv40szp123ql7frz1mmdjdxljmwaby963h"; depends=[MASS]; }; harmonicmeanp = derive2 { name="harmonicmeanp"; version="1.0"; sha256="071ysgyi8daq8q1vqzgypkz4bgaxr0iw4djv906vkfx5ywihr768"; depends=[FMStable]; }; harrietr = derive2 { name="harrietr"; version="0.2.3"; sha256="0n6vsqysj4ijh06z6nqmj8x1z4w9711dxhbfp8p8fwi0l75pj0cj"; depends=[ape dplyr ggtree lazyeval magrittr rlang tidyr]; }; - harrypotter = derive2 { name="harrypotter"; version="0.1.0"; sha256="0h02rli2l42a2vjgrw7fqxib31pyqcyhqam499bpybk5crqnpffx"; depends=[ggplot2 gridExtra MASS]; }; + harrypotter = derive2 { name="harrypotter"; version="2.0.0"; sha256="0q7b20f2l7d1ljbfw3kg8qqq78ccp4n7wj4dacd28ab1hgzwm7yr"; depends=[ggplot2 gridExtra]; }; harvestr = derive2 { name="harvestr"; version="0.7.1"; sha256="0xgxzbfbc33asfm8sl2y60ki6bwgd6vdh9nz466crkx7m9lsvll8"; depends=[digest foreach plyr]; }; hash = derive2 { name="hash"; version="2.2.6"; sha256="0mkx59bmni3b283znvbndnkbar85fzavzdfgmwrhskidsqcz34yz"; depends=[]; }; hashFunction = derive2 { name="hashFunction"; version="1.0"; sha256="1v57xj8xwv6xhxvgp0zxgvs5vcjw8z5k2ciwbn0jxf4ilyd66cgj"; depends=[]; }; @@ -7698,6 +7753,7 @@ in with self; { hcc = derive2 { name="hcc"; version="0.54"; sha256="14b3pamkywb0wsjpbm0wpflcds0b5mfymvgk92rmf6ngz1bkpdbq"; depends=[]; }; hcci = derive2 { name="hcci"; version="1.0.0"; sha256="11piy1ajg3j3dbh66szzf7lhc3x28fz75ai39vlx0gl5nc2v5zs5"; depends=[]; }; hcp = derive2 { name="hcp"; version="0.1"; sha256="0hhcy70g13kclxv733kgiys7qn5bi28abpkli5n2vj0a58ac333m"; depends=[]; }; + hctrial = derive2 { name="hctrial"; version="0.1.0"; sha256="19li8i8hx0r3b63q80cnj6pr72rdbmykxq0kcfbn4azq3sdd046y"; depends=[clinfun GenBinomApps]; }; hda = derive2 { name="hda"; version="0.2-14"; sha256="0azfxyws7yslcqplfddmdp5ngk91j5h7llvrg77yh5z0kkd09j1b"; depends=[e1071]; }; hdbinseg = derive2 { name="hdbinseg"; version="1.0.1"; sha256="0fy9cqrygsnxkb3nxg56md19svrvkbijpxkqfk9p18cj5ibwrq94"; depends=[doParallel foreach iterators Rcpp RcppArmadillo]; }; hddplot = derive2 { name="hddplot"; version="0.59"; sha256="18llkpawm12cjxlcrlra60m16virfpjqiaqkvy9mb3wq1zif61rh"; depends=[MASS multtest]; }; @@ -7709,9 +7765,9 @@ in with self; { hdme = derive2 { name="hdme"; version="0.2.1"; sha256="0kcpc0ygjk8d6v099x1m5hi6dbapjcc0lzjsg9779i6bbf43mls2"; depends=[ggplot2 glmnet Rcpp RcppArmadillo Rdpack]; }; hdnom = derive2 { name="hdnom"; version="5.0"; sha256="0g7l5km18j11qfw8iq9ybl8lzdq6fk2g7cjc2yjsm3ava60n4xqh"; depends=[foreach ggplot2 glmnet gridExtra ncvreg penalized rms survAUC survival]; }; hdpca = derive2 { name="hdpca"; version="1.0.0"; sha256="1sv7caw4nhpcvsb7fxpvf2b5zskvfsv004hrqc51b5jx4fsc7y92"; depends=[boot lpSolve]; }; - hdrcde = derive2 { name="hdrcde"; version="3.2"; sha256="1901mg2k2ch9fzn1n9k0kmxkgd1m4pxvrda7mv0mp64nf4mx43xw"; depends=[ash ggplot2 KernSmooth ks locfit RColorBrewer]; }; + hdrcde = derive2 { name="hdrcde"; version="3.3"; sha256="0c2qbw4c3mq1cb068kjs72rxlbibz8svwcrx853jyr8ybs23z7ab"; depends=[ash ggplot2 KernSmooth ks locfit RColorBrewer]; }; hds = derive2 { name="hds"; version="0.8.1"; sha256="1smg5ixrl7f2x3wn7s5i26dyadn5sigpf4jsk236z1bhnz617ax4"; depends=[survival tensor]; }; - healthcareai = derive2 { name="healthcareai"; version="2.2.0"; sha256="1i1xnxd2v8qbv8pqn7w3ivh1yv4nvxm5llwhxd24gfzqkxck7c3w"; depends=[broom caret cowplot data_table dbplyr dplyr e1071 ggplot2 glmnet lubridate MLmetrics purrr ranger recipes rlang ROCR stringr tibble tidyr xgboost]; }; + healthcareai = derive2 { name="healthcareai"; version="2.3.0"; sha256="0lyx9fldw28gx2lr2cpi7lyrwf5qz549v2vqxjx83ih5kxm6mlnp"; depends=[caret cowplot data_table dbplyr dplyr e1071 forcats generics ggplot2 glmnet lubridate MLmetrics purrr ranger recipes rlang ROCR stringr tibble tidyr xgboost]; }; heatex = derive2 { name="heatex"; version="1.0"; sha256="0c7bxblq24m80yi24gmrqqlcw8jh0lb749adsh51yr6nzpap6i9n"; depends=[]; }; heatmap_plus = derive2 { name="heatmap.plus"; version="1.3"; sha256="0rzffm15a51b7l55k0krk6w7v8czy3vpwz1qmbybr7av0pln7wn3"; depends=[]; }; heatmap3 = derive2 { name="heatmap3"; version="1.1.1"; sha256="14zkij0gr9awzic71k2j7pniamkywfvwrifdk7jbds70zsi30ph5"; depends=[fastcluster]; }; @@ -7790,8 +7846,8 @@ in with self; { hkclustering = derive2 { name="hkclustering"; version="1.0.1"; sha256="19syq06y5dl0mcwyaxr7w1hj8ffp5s140j72djcz0lljhskzmp6f"; depends=[cluster]; }; hkevp = derive2 { name="hkevp"; version="1.1.4"; sha256="01m5yywi4vjnwhdayaqaqcp5lz70mllj5ifnwdb4c60wm9aby9pm"; depends=[Rcpp RcppArmadillo]; }; hkex_api = derive2 { name="hkex.api"; version="0.1"; sha256="0hqwihlrppchpaz2yaq92gf779yi5k8n7sxy1kbpjxs2qc18xvj2"; depends=[httr RCurl XML]; }; - hmeasure = derive2 { name="hmeasure"; version="1.0"; sha256="0wr0xq956glmhvy4yis3qq7cfqv9x82ci9fzx3wjvaykd16h0sx9"; depends=[]; }; - hmi = derive2 { name="hmi"; version="0.9.13"; sha256="0rxxrx5ckjzj2wqdx05mihj86v0npj99q2n7zz9d44wncvnzz9g9"; depends=[boot coda linLIR lme4 MASS Matrix MCMCglmm mice msm mvtnorm nlme nnet ordinal pbivnorm tmvtnorm VGAM]; }; + hmeasure = derive2 { name="hmeasure"; version="1.0-1"; sha256="1hj2a0v6sc6hnxk5yv5bilk5s11q3vih1ikh1xa4hd1kd59cfy8z"; depends=[]; }; + hmi = derive2 { name="hmi"; version="0.9.15"; sha256="0n716ng4a246vwqz7wf28k7nx8bh1cdby41wyz5qqi2qbmff2j7x"; depends=[boot coda linLIR lme4 MASS Matrix MCMCglmm mice msm mvtnorm nlme nnet ordinal pbivnorm rlang tmvtnorm VGAM]; }; hmm_discnp = derive2 { name="hmm.discnp"; version="2.1-5"; sha256="1nawdj5rxh54gxyrr9xw1zw1k1b20ds397mz07x6n7nyjmj4lak2"; depends=[nnet]; }; hmmm = derive2 { name="hmmm"; version="1.0-4"; sha256="1sbr85lcmcw3lv0ygqwfbarr91dp3br1xnlygy49145cvl93nfci"; depends=[MASS mvtnorm nleqslv quadprog]; }; hms = derive2 { name="hms"; version="0.4.2"; sha256="1g6hslk3z0xga38r71irxq802wskg6nv804mp8y9f7i2wfrj0y55"; depends=[pkgconfig rlang]; }; @@ -7831,7 +7887,7 @@ in with self; { hsphase = derive2 { name="hsphase"; version="2.0.2"; sha256="1b62k9sc6604djy37anslvqjpbrj9wsc9mvnfbrnmhqf4g0nnpdq"; depends=[Rcpp RcppArmadillo snowfall]; }; htdp = derive2 { name="htdp"; version="0.1.4"; sha256="0w579qp0p544xryb5r08m1nhqf7rmgv9q0lyx6my4av62l70ka5w"; depends=[Rcpp]; }; htm2txt = derive2 { name="htm2txt"; version="2.1.1"; sha256="09q026yy8qm1fb3a4bf9vsp4j09kayl7xmk0p58ikar5l3bmfdjv"; depends=[]; }; - htmlTable = derive2 { name="htmlTable"; version="1.12"; sha256="1n5136vb7mi4rxl5jgwdmdhn4mwv2pcqyw2mrj406ih4hy6hpxa2"; depends=[checkmate htmltools htmlwidgets knitr magrittr rstudioapi stringr]; }; + htmlTable = derive2 { name="htmlTable"; version="1.13"; sha256="03fhzd5600m2bssz6xjagklhk1d22gxamr408x8h3q7k1qwdxw71"; depends=[checkmate htmltools htmlwidgets knitr magrittr rstudioapi stringr]; }; htmltab = derive2 { name="htmltab"; version="0.7.1"; sha256="0lymagm7z6zn0ddygqxi831ikk74112lkqkbvs5j1djhmr359ajc"; depends=[httr XML]; }; htmltidy = derive2 { name="htmltidy"; version="0.4.0"; sha256="090rj1fzdsa8m4g33d4mx92dm8afh173i4hqa4zym8c909jwh9qn"; depends=[htmltools htmlwidgets Rcpp XML xml2]; }; htmltools = derive2 { name="htmltools"; version="0.3.6"; sha256="18k8r1s8sz1jy7dkz35n69wj20xhmllr53xmwb4pdzf2z61gpbs4"; depends=[digest Rcpp]; }; @@ -7844,8 +7900,8 @@ in with self; { httpcode = derive2 { name="httpcode"; version="0.2.0"; sha256="06k853ihwzkcx4z3jzazpb03p91frqkwz18jy4fwr8j2nwyqbhgv"; depends=[]; }; httping = derive2 { name="httping"; version="0.2.0"; sha256="0hdcf51yak8yagy4xj9cyck934lgmvpkd08jvlql33ir5mqvvv3i"; depends=[httpcode httr jsonlite magrittr pryr]; }; httptest = derive2 { name="httptest"; version="3.2.2"; sha256="1q2lhqi5lhdc15wjrcr4z2yxjrfhjkgn0wwxr0mawsfz8cy3703q"; depends=[digest httr jsonlite testthat]; }; - httpuv = derive2 { name="httpuv"; version="1.4.5"; sha256="1ddpcarzf694h0gy5pdz7l5glqfv4hr9dmxb4vw7yqd0bga174gi"; depends=[BH later promises Rcpp]; }; - httr = derive2 { name="httr"; version="1.3.1"; sha256="0n7jz2digbgv48rbr9vmzv4vmf4rahl9jjy31izs7sxj4rs4s4r2"; depends=[curl jsonlite mime openssl R6]; }; + httpuv = derive2 { name="httpuv"; version="1.4.5.1"; sha256="0mqd40jckdpkjw1jjd860cdwkb03l6dkh931maijfdaqr1w9hwvn"; depends=[BH later promises Rcpp]; }; + httr = derive2 { name="httr"; version="1.4.0"; sha256="0j6vknwyvkjpjsxwch4q02aik4dnm3h4l0wc7dgzc555bm1g2cyn"; depends=[curl jsonlite mime openssl R6]; }; hues = derive2 { name="hues"; version="0.1"; sha256="0b6y4ld242fqzx4ccxzk4i4zbx7myk7v3a03r0klgbh2mmw3ixm0"; depends=[colorspace]; }; huge = derive2 { name="huge"; version="1.2.7"; sha256="134d951x42vy9dcmf155fbvik2934nh6qm2w5jlx3x2c6cf7faq4"; depends=[igraph lattice MASS Matrix]; }; humanFormat = derive2 { name="humanFormat"; version="1.0"; sha256="0zwjbl8s5dx5d57sfmq6myc6snximc56zl88h8y1s1jqphyn9sir"; depends=[testthat]; }; @@ -7853,7 +7909,7 @@ in with self; { humanize = derive2 { name="humanize"; version="0.2.0"; sha256="0hhhd640n77s8xaa2gbd9fckdk2yjg68gdb7wjy56a2khzqfssxr"; depends=[assertthat glue lubridate]; }; humanleague = derive2 { name="humanleague"; version="2.1.0"; sha256="1mp7lqwx97r60amllz9cjsixw21zspgs4zkp0nc63z315vgfzwrx"; depends=[Rcpp]; }; humidity = derive2 { name="humidity"; version="0.1.4"; sha256="1nnrjk9wjvp28s615xd9wllnwv4js3kg7rj2f6al3sk3vhiqljsk"; depends=[]; }; - hunspell = derive2 { name="hunspell"; version="2.9"; sha256="10186544s6nyd2ba470idxrxsl788dkmr1g1ri8x2n1lky9zmrik"; depends=[digest Rcpp]; }; + hunspell = derive2 { name="hunspell"; version="3.0"; sha256="0mwqw5p0ph083plm2hr2hqr50bjg2dw862dpsfm4l2fgyy3rryq1"; depends=[digest Rcpp]; }; hurdlr = derive2 { name="hurdlr"; version="0.1"; sha256="1ryrqsxa07isxv2zx156bcn36d4yjvwpirb8jqcmqm97q7rmihmq"; depends=[]; }; hurricaneexposure = derive2 { name="hurricaneexposure"; version="0.0.1"; sha256="1j6srqnmdhmg1yg06nqxapdrd9p3yrfs01z0sk43dvjq4dmwmrjr"; depends=[data_table dplyr ggmap ggplot2 lazyeval lubridate maps purrr RColorBrewer stringr tidyr]; }; hutils = derive2 { name="hutils"; version="1.3.0"; sha256="03czrdrwpqjvghh8396fx9884l24ag1wrkfkvvr6n743qb60k1p8"; depends=[data_table fastmatch magrittr]; }; @@ -7903,7 +7959,7 @@ in with self; { iGasso = derive2 { name="iGasso"; version="1.4"; sha256="17xxqncl5xcphdqclghcazygcgibf8ijdf4kkl3ga11xf70sahj2"; depends=[CompQuadForm lattice]; }; iMRMC = derive2 { name="iMRMC"; version="1.1.0"; sha256="04wpqdds5vfqvl8n5g64vnyh4a40dxjh8l1bgw1vdz1372n0421g"; depends=[]; }; iMediate = derive2 { name="iMediate"; version="0.5"; sha256="0gr0nibfdmiyxz8n7pfcl1d2gxhl5g2pi9yhnmsvqzry4j3x27yw"; depends=[mvtnorm plotly]; }; - iNEXT = derive2 { name="iNEXT"; version="2.0.17"; sha256="1gg9zzcfjn70scz9kmn37rvz3lnbkbd4a59xmfy56x9xgs3wrxwp"; depends=[ggplot2 reshape2]; }; + iNEXT = derive2 { name="iNEXT"; version="2.0.18"; sha256="0gmzs4d1lc2bq0b072ljg1hpxz19dcz3dv2fd16d06305s5kbhz9"; depends=[ggplot2 reshape2]; }; iNOTE = derive2 { name="iNOTE"; version="1.0"; sha256="1969xmgfv9405r09zpd2icvjd9vvzw4dx5qaqxk1a0jvbvhp3h88"; depends=[CompQuadForm mixtools plyr]; }; iNextPD = derive2 { name="iNextPD"; version="0.3.2"; sha256="06wka2qr1jm3hvi8j0b19fr21v72gmqknz8dg0l5wl91m0prqns3"; depends=[ade4 ggplot2 iNEXT Rcpp]; }; iRF = derive2 { name="iRF"; version="2.0.0"; sha256="1ll4lxg743p2zipxcq13yjsc7j7dk766dcyixwxilllbisg0dh8y"; depends=[AUC data_table doParallel dplyr foreach Matrix RColorBrewer Rcpp]; }; @@ -7996,7 +8052,7 @@ in with self; { imdbapi = derive2 { name="imdbapi"; version="0.1.0"; sha256="11v7c0s7qqf02b186md5lhgkgmywkn8lmmanlz3gfcxca26g047y"; depends=[dplyr httr stringr]; }; imfr = derive2 { name="imfr"; version="0.1.5"; sha256="1f4zynra79h42dmd9qhg67wwvs7c640f5is98bq30fdphiybihgz"; depends=[dplyr httr jsonlite]; }; imguR = derive2 { name="imguR"; version="1.0.3"; sha256="14f7ghgc8rbrpqb21rinfbrj1wh80i6ii0awwi814152v5qzj4b3"; depends=[httr jpeg png]; }; - iml = derive2 { name="iml"; version="0.7.1"; sha256="1wiylfd83p4wzccp0r3ydxy14zvw81q368h61gimrcm7110fdpx9"; depends=[checkmate data_table foreach ggplot2 glmnet Metrics partykit R6 yaImpute]; }; + iml = derive2 { name="iml"; version="0.8.1"; sha256="1cz7gk37wfzbvfh6mlz4vz0dsl5dd9fcszvcljpbwh59lylhzz94"; depends=[checkmate data_table foreach Formula ggplot2 glmnet Metrics partykit prediction R6 yaImpute]; }; immer = derive2 { name="immer"; version="1.1-35"; sha256="1nmf9wxxyq3p8b5kikpsr8b0v4s84zjpahg1rxvcrhc8blg26hjq"; depends=[CDM coda MASS psychotools Rcpp RcppArmadillo sirt TAM]; }; imp4p = derive2 { name="imp4p"; version="0.7"; sha256="1hpxx1jpwd4v19xnpjjbwcvfzvb63jfd0jq3vcq000w7am9pwwba"; depends=[Iso norm Rcpp truncnorm]; }; impimp = derive2 { name="impimp"; version="0.3.0"; sha256="0zv4rs5c80rvwwr4gk6zlphvyf0drkfrdqpcw0p2i7kig8ynq4qx"; depends=[]; }; @@ -8035,6 +8091,7 @@ in with self; { inference = derive2 { name="inference"; version="0.1.0"; sha256="0j92isfkbhk13yx2hd3a5dd7ikcbgjc04zisd1n5kmg6ajw2aj6r"; depends=[sandwich]; }; inferference = derive2 { name="inferference"; version="1.0.0"; sha256="1x6i8ycba9z57m1n143p1j9pmlfrhjhi4iw0fsny8xmcvqrlr85p"; depends=[Formula lme4 numDeriv]; }; inferr = derive2 { name="inferr"; version="0.3.0"; sha256="1z5bfq0gv1h6iw8nwc19ar6f2sgsvgs3ghq52s09wclqk2yy4azz"; depends=[dplyr magrittr purrr Rcpp rlang shiny tibble tidyr]; }; + infix = derive2 { name="infix"; version="0.1.0"; sha256="1zgy8f8b9pmpvpgqh3niczkr94xkc53xcjim73djmd10azw3kgrk"; depends=[magrittr]; }; inflection = derive2 { name="inflection"; version="1.3"; sha256="168ms6hfakr6wql45r9qvk7hpas6sgpaiqyxicihsq0j3dpzvys4"; depends=[]; }; influence_ME = derive2 { name="influence.ME"; version="0.9-9"; sha256="0f6d2hvs9qllyfpsp2cgh7w8yjxafclbk47n8av7j9zpp7s5yg9v"; depends=[lattice lme4 Matrix]; }; influence_SEM = derive2 { name="influence.SEM"; version="2.2"; sha256="1cabl6486mlrmk0418s18wii3n6nl1ckv6w9281wdk4fy27y9qk2"; depends=[lavaan]; }; @@ -8133,7 +8190,6 @@ in with self; { irregulAR1 = derive2 { name="irregulAR1"; version="1.0.0"; sha256="0pccasqcya99j4n0qdcjjnvmigj53axji9ddxbpmrgvzsyamb8ja"; depends=[Matrix Rcpp RcppArmadillo]; }; irtDemo = derive2 { name="irtDemo"; version="0.1.4"; sha256="0rpwryybnj7b4bxn0mn1m496y85s2fpqdd78lmdl6jg1ck4j4pb3"; depends=[fGarch shiny]; }; irtProb = derive2 { name="irtProb"; version="1.2"; sha256="12wnvbzkh0mx9i3iyh1v2n2f2wjsjj7ad3dgv9xj949x4nbz16j0"; depends=[lattice moments]; }; - irteQ = derive2 { name="irteQ"; version="1.0.0"; sha256="0d1xfgk0spdkfbvwyqi99hwsj9p46q71b8v79rr51bw88rx17shp"; depends=[dplyr ggplot2 ggrepel purrr reshape2 rlang statmod tidyr]; }; irtoys = derive2 { name="irtoys"; version="0.2.1"; sha256="0h6iiaxikhbxhbyksbjnb09qdxinlkwr2v9yzs5wslbni14paq5q"; depends=[ltm sm]; }; irtrees = derive2 { name="irtrees"; version="0.1.0"; sha256="03jmfyx1ia987zhi74fmmcdz70wnm8c7z5z30rwzd1cs11dijjwv"; depends=[]; }; irtreliability = derive2 { name="irtreliability"; version="0.1-1"; sha256="15qs8bvgrwajj5kfd57rd34l1p2805ilyd7w60ngrqc14d6az9d2"; depends=[fastGHQuad ltm mirt]; }; @@ -8174,7 +8230,7 @@ in with self; { ivpanel = derive2 { name="ivpanel"; version="1.0"; sha256="0irjmkw3nnd8ssidvj23lr0hihlhd9acsbaznh88lknx53ijc2qv"; depends=[Formula]; }; ivprobit = derive2 { name="ivprobit"; version="1.1"; sha256="05b5gf5gmi2yrkg61n7w12qlgpnjakd1z8hhqxy6py8hahsf84gm"; depends=[Formula]; }; ivregEX = derive2 { name="ivregEX"; version="1.0"; sha256="0zh3rqvhn8ald6lxv9kywy2v1p0nr9ijv6plhpbxc6k51zzsgyl8"; depends=[AER Formula lmtest sandwich]; }; - ivtools = derive2 { name="ivtools"; version="2.0.0"; sha256="0nslq40q5vdsfn1p2y85q1f9gpc2ziixilvgrwkq6vcwl2bwl0kp"; depends=[ahaz data_table nleqslv numDeriv Rcpp survival]; }; + ivtools = derive2 { name="ivtools"; version="2.1.0"; sha256="13zzayarsc38c4w90ilvcz0896sr4zaz47f3vwxxkp6c2pbcv2z0"; depends=[ahaz data_table nleqslv numDeriv Rcpp survival]; }; jSonarR = derive2 { name="jSonarR"; version="1.1.1"; sha256="054q3ly471xa64yyz2as6vkr440ip1y8n5wl6s3zbhqy3bqkdqif"; depends=[jsonlite RCurl]; }; jaatha = derive2 { name="jaatha"; version="3.2.0"; sha256="00886j0cabrq6a69w8s1gsfkmx1wqs1vpxjafpm71msk54r0dj55"; depends=[assertthat R6]; }; jaccard = derive2 { name="jaccard"; version="0.1.0"; sha256="1dmla6qc1k8iw2d7zfjqhf13gqd2lpsrj09yh47ljf994fpab936"; depends=[dplyr magrittr qvalue Rcpp]; }; @@ -8197,13 +8253,14 @@ in with self; { jiebaRD = derive2 { name="jiebaRD"; version="0.1"; sha256="1wadpcdca4pm56r8q22y4axmqdbb2dazsh2vlhjy73rpymqfcph4"; depends=[]; }; jipApprox = derive2 { name="jipApprox"; version="0.1.1"; sha256="0kgx7v8fyfdh8kdz8jnh6y6zrf7ivgqjgagpddxnynldzcrc2ml7"; depends=[sampling]; }; jjb = derive2 { name="jjb"; version="0.1.0"; sha256="0izpvban8v85g6w2mnmimhdh4yg6kcaf046v3jjba368nsj67q9n"; depends=[]; }; + jlctree = derive2 { name="jlctree"; version="0.0.1"; sha256="17n39jc7cwv6hiayy7h1859prdwy2j3pz1vhi6jqnzm4wy6p8a9a"; depends=[lme4 rpart survival]; }; jmcm = derive2 { name="jmcm"; version="0.2.1"; sha256="1giyd0agjz1qpgj7q55maxk7jjmpwc3mrj02ailvwl44rdvhl90v"; depends=[Formula lattice Rcpp RcppArmadillo roptim]; }; jmdem = derive2 { name="jmdem"; version="1.0"; sha256="1qz2l02m4gnxrm1ankr5qqlskl8amphzj8r763yas218fvzfa34q"; depends=[statmod VGAM]; }; jmdl = derive2 { name="jmdl"; version="0.3.0"; sha256="0167yj368lh1n79jwbqs4g2asb67hfmgh97519linmfpx0n6xdpa"; depends=[boot Formula MASS minqa mnormt mvtnorm]; }; jmetrik = derive2 { name="jmetrik"; version="1.1"; sha256="1if1kxx8apgkbxpkjnlj2lpsfnyj2splsg1p3j5vxa7q6wx70f9j"; depends=[]; }; jmotif = derive2 { name="jmotif"; version="1.0.3"; sha256="1llmrksajrd35kfdzq2vqfm17yv5kwark6gz3rvyzcmbrqk5spqv"; depends=[Rcpp RcppArmadillo]; }; jmuOutlier = derive2 { name="jmuOutlier"; version="1.4"; sha256="1vrihjvq8l2q7d3z80fkzzzwg6xmnfi8sipsgwic1lcbv6vnqndp"; depends=[]; }; - jmv = derive2 { name="jmv"; version="0.9.5"; sha256="0xk3lsddpxwynviarcwisbbwy04jlrj9pwlwp06l7n9g0kxkcpxs"; depends=[afex BayesFactor car emmeans GGally ggplot2 ggridges GPArotation jmvcore lavaan MASS multcomp mvnormtest nnet PMCMR psych R6 ROCR vcd vcdExtra]; }; + jmv = derive2 { name="jmv"; version="0.9.6"; sha256="10i6l6wg6348hsyl238in4im2b1spb1qanb5v65h5y9p9smwn60p"; depends=[afex BayesFactor car emmeans GGally ggplot2 ggridges GPArotation jmvcore lavaan MASS multcomp mvnormtest nnet PMCMR psych R6 ROCR vcd vcdExtra]; }; jmvconnect = derive2 { name="jmvconnect"; version="1.0.7"; sha256="1sy7xa2k1ilbl0gmxgqkgyhigmzngk03nrk5p7b3dxw9vr867wdi"; depends=[BH evaluate httr jmvcore rappdirs Rcpp]; }; jmvcore = derive2 { name="jmvcore"; version="0.9.5.2"; sha256="0npzy2qmyxsjkkxwz08d6w42npfn0aryycwq6xaw3ldncjakk1yr"; depends=[base64enc R6 rjson rlang stringi]; }; jocre = derive2 { name="jocre"; version="0.3.3"; sha256="1i9n3r16pq6r4sy3fc1rxpil5ws8v2is0xdxafinvwr1hzkv1gz6"; depends=[boot KernSmooth plyr TSP]; }; @@ -8231,8 +8288,8 @@ in with self; { jsonlite = derive2 { name="jsonlite"; version="1.6"; sha256="0lyvhnr6n57h3a89bvipii7x17nvfaycm9j5j50bfrlr48jv9ic8"; depends=[]; }; jsonstat = derive2 { name="jsonstat"; version="0.0.2"; sha256="0p0d3snl1971p5ikrkmwqrjjh4fy0b89qk3rnd1dayfb0r80xnnj"; depends=[cli dplyr jsonlite rlang]; }; jsonvalidate = derive2 { name="jsonvalidate"; version="1.0.0"; sha256="08c1s8fk95np4l6km077dmd1nibhhggi80f5465hhbq521gm0awl"; depends=[V8]; }; - jsr223 = derive2 { name="jsr223"; version="0.3.2"; sha256="00i90b37811sva8f9bd50xxvjcn7rag9hq5ya953v6whm370r737"; depends=[curl jdx R6 rJava]; }; - jstor = derive2 { name="jstor"; version="0.3.5"; sha256="0h8llh9kgmix5yicq1vmphcmn3mrbp4lw9zasvdj6f0fgnd4jn3g"; depends=[cli crayon dplyr furrr magrittr pryr purrr readr rlang stringr tibble tidyr xml2]; }; + jsr223 = derive2 { name="jsr223"; version="0.3.3"; sha256="0i00nbsj6b4mx9pgp5rana1kj57hi4lz3lsiniv7baz5avmhp65n"; depends=[curl jdx R6 rJava]; }; + jstor = derive2 { name="jstor"; version="0.3.6"; sha256="00sd4mq21al8f8ixgy8f65xbgp90if1jpp7mcm50jrbajdwwflmk"; depends=[cli crayon dplyr furrr magrittr pryr purrr readr rlang stringr tibble tidyr xml2]; }; jtGWAS = derive2 { name="jtGWAS"; version="1.5.1"; sha256="06cgsncgrqslxcc7s0lb3zwa85bhzkmjzz3f04716xpzwa186vxq"; depends=[Rcpp]; }; jtools = derive2 { name="jtools"; version="1.1.1"; sha256="0c7ygllgq5vyb4w188l44f5q8bn1jn2kw3yvc1f1zi0ni1ngsf7g"; depends=[cli crayon ggplot2 magrittr]; }; jtrans = derive2 { name="jtrans"; version="0.2.1"; sha256="18zggqdjzjhjwmsmdhl6kf35w9rdajpc2nffag4rs6134gn81i3m"; depends=[]; }; @@ -8240,6 +8297,7 @@ in with self; { jug = derive2 { name="jug"; version="0.1.7"; sha256="01m6hyr26f6zih49pz2bmmr8ypdl1qiz0wv3padcy68kaccf44a4"; depends=[base64enc httpuv infuser jsonlite magrittr mime R6 webutils]; }; junctions = derive2 { name="junctions"; version="1.1"; sha256="1v5jx4mw6x4q3fivsvidd49b8czzbvv5icj39h6jrpmqvrnc8w32"; depends=[Rcpp]; }; junr = derive2 { name="junr"; version="0.1.3"; sha256="0wcglpziyi6z4n7w70srziljba3jkb27iqxbxz4kk6774c7valbf"; depends=[httr jsonlite]; }; + jvcoords = derive2 { name="jvcoords"; version="1.0.2"; sha256="1mlamzg0qz5l23v2w08imrlbnzc3b3amr6yz5hbaf8vc3k3cff5f"; depends=[]; }; jvnVaR = derive2 { name="jvnVaR"; version="1.0"; sha256="0zh0dc6wqlrxn5r2yv9vkpyfb8xsbdidkjv9g6qr94fyxlbs4yci"; depends=[]; }; jwutil = derive2 { name="jwutil"; version="1.2.1"; sha256="1n9q2p167cmp134p8qpknfg4avi4nzxqmazyr1gs63sk5x51yk48"; depends=[Rcpp testthat]; }; kSamples = derive2 { name="kSamples"; version="1.2-8"; sha256="15d5q5vpp4wx5rk5kjxjdxpwc8mkq5sbdz8gi07iscrvhzb5rzfr"; depends=[SuppDists]; }; @@ -8259,7 +8317,7 @@ in with self; { kdecopula = derive2 { name="kdecopula"; version="0.9.2"; sha256="0g5c12wm3byd4chd8i9mxv599gsf4ip4qghx83j3mmhsmn05zf4y"; depends=[lattice locfit qrng quadprog Rcpp RcppArmadillo]; }; kdensity = derive2 { name="kdensity"; version="1.0.0"; sha256="0di027xjcd8xllkbygmkmpvp9wchh3haf15vrw7sjck3yvh68k5f"; depends=[assertthat EQL knitr rmarkdown]; }; kdetrees = derive2 { name="kdetrees"; version="0.1.5"; sha256="1plf2yp2vl3r5znp5j92l6hx1kgj0pzs7ffqgvz2nap5nf1c6rdg"; depends=[ape distory ggplot2]; }; - kdevine = derive2 { name="kdevine"; version="0.4.1"; sha256="0ci51dn7jhz9swlywiqj3inkk4329argm63lhkyvcbj2kd2rjay1"; depends=[cctools doParallel foreach kdecopula KernSmooth MASS qrng Rcpp VineCopula]; }; + kdevine = derive2 { name="kdevine"; version="0.4.2"; sha256="15hw27y4rlifz3kyirm7yacca38xqdwr42k21gg67dhmbdplbnz0"; depends=[cctools doParallel foreach kdecopula KernSmooth MASS qrng Rcpp VineCopula]; }; kdist = derive2 { name="kdist"; version="0.2"; sha256="18q7njvsb9sbm412c6ms4b4nxg768z9qahws5rnin06gvb25nfcx"; depends=[]; }; kdtools = derive2 { name="kdtools"; version="0.3.1"; sha256="1c04rfnnbkh6d8435hjgnq3q42rsfyvf36ypxjsax39spynip457"; depends=[BH Rcpp strider]; }; kedd = derive2 { name="kedd"; version="1.0.3"; sha256="17rwz3yia95xccbxwn43wr6c9b3062094yfahnnnk3wfijyhlxiq"; depends=[]; }; @@ -8277,6 +8335,7 @@ in with self; { kerndwd = derive2 { name="kerndwd"; version="2.0.2"; sha256="0nf5hyb274gn02n4lygwryv1jaqff77i040bd8gs1xykgvy6jxny"; depends=[]; }; kernelFactory = derive2 { name="kernelFactory"; version="0.3.0"; sha256="001kw9k3ivd4drd4mwqapkkk3f4jgljiaprhg2630hmll064s89j"; depends=[AUC genalg kernlab randomForest]; }; kernelboot = derive2 { name="kernelboot"; version="0.1.5"; sha256="0m31akhya7390lbkw0cjxcrzw28njbz4smd35m93aarb2lgpcj4k"; depends=[future future_apply Rcpp]; }; + kernhaz = derive2 { name="kernhaz"; version="0.1.0"; sha256="1cxwjnfyhxfjdbhs21airycs704jic21pdpsbxsx37wkl11cxpai"; depends=[doParallel foreach GA rgl]; }; kernlab = derive2 { name="kernlab"; version="0.9-27"; sha256="1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"; depends=[]; }; kernplus = derive2 { name="kernplus"; version="0.1.1"; sha256="1dxw1qk5gx7g05kgsbh5436r7mbv77631zjs0c4ibpscaw77g475"; depends=[circular KernSmooth mixtools]; }; kernscr = derive2 { name="kernscr"; version="1.0.3"; sha256="0h3xv76dxch8kv4z7cgx60iaikk6906n75c4kc1mccpw0jvyxrvb"; depends=[MASS mvtnorm]; }; @@ -8310,7 +8369,7 @@ in with self; { kmconfband = derive2 { name="kmconfband"; version="0.1"; sha256="10n5w8k57faqcclwshs4m66i2i5b70i6f3xq5nqlgsi2ldkysbc9"; depends=[survival]; }; kmcudaR = derive2 { name="kmcudaR"; version="1.0.0"; sha256="1adixf4nsgnk8rgvcv37aznh8gxrfwn19ihh3c6siss51hlmhln2"; depends=[Rcpp RcppEigen]; }; kmeRs = derive2 { name="kmeRs"; version="1.1.0"; sha256="1wafa9wgqlwrk6jwmbn34n3rmvbc9s6s235z8mscbqgw67snwcq6"; depends=[Biostrings rDNAse tcR]; }; - kmed = derive2 { name="kmed"; version="0.1.0"; sha256="1sqcrl75hjxpvaz1m40h7z3xzxkda8mnmq90jd6igvpbznixq2yc"; depends=[ggplot2]; }; + kmed = derive2 { name="kmed"; version="0.2.0"; sha256="1y09a6l8zmxnp0xq5y8b2nbdswcyb3a9ms5a1j96sb0c500n2285"; depends=[ggplot2]; }; kmer = derive2 { name="kmer"; version="1.1.0"; sha256="0c96rz75qggqfb0zccn0v92jx9ws2nlw8pk6j5jghllcgm99qbdc"; depends=[openssl phylogram Rcpp]; }; kmi = derive2 { name="kmi"; version="0.5.4"; sha256="07h4gn69r4zxm00alj74fd0qdyp7g9x38gpi1v7yzy806wlg93fr"; depends=[mitools survival]; }; kml = derive2 { name="kml"; version="2.4.1"; sha256="1my9gcripiqc6iphycjr3srj8qxy05yvd0648vblygrx2qym5hy2"; depends=[clv longitudinalData]; }; @@ -8335,7 +8394,7 @@ in with self; { koRpus_lang_en = derive2 { name="koRpus.lang.en"; version="0.1-2"; sha256="0v3cjzcpa24n479xi2lkj3yhjrgbd14iq9rz1bvywbj3shixs0bn"; depends=[koRpus sylly_en]; }; kofdata = derive2 { name="kofdata"; version="0.1.3.2"; sha256="0s7y1djmiz598bx0ppabb5pc1cssaavr67yf4zk9aai90xs2p2v1"; depends=[httr jsonlite xts zoo]; }; kofnGA = derive2 { name="kofnGA"; version="1.3"; sha256="0w0881ydnqdah04sifi25ypzxdwnsiqxfq1xam4yhr670bdak1vm"; depends=[bigmemory]; }; - kohonen = derive2 { name="kohonen"; version="3.0.7"; sha256="1rxx5ssfpmjvy1a5a57ikp97gbkq134yyagwl5qm78yzfmnnhplr"; depends=[MASS Rcpp]; }; + kohonen = derive2 { name="kohonen"; version="3.0.8"; sha256="1zbfqa1qdlry8w6xhypkiknc5gn98v1ijhlsfka8zjg8ajhqgn1q"; depends=[MASS Rcpp]; }; kokudosuuchi = derive2 { name="kokudosuuchi"; version="0.4.2"; sha256="1nwydfyr9waa5h8h8nrmwxy0jx7i4893g5khfv6b4g09z6g5cyly"; depends=[curl dplyr glue httr purrr rlang sf shiny stringr tibble xml2]; }; kolmim = derive2 { name="kolmim"; version="1.0"; sha256="0g1i0cazi4nhfwdd3ywqrar1sn7bw77w38qjii045w5vqg05srkp"; depends=[]; }; komadown = derive2 { name="komadown"; version="0.2.0"; sha256="0mw1bcrg10yy1y844lpik70979420h0nsar48v5p3qk783pymbdp"; depends=[bookdown rmarkdown]; }; @@ -8358,6 +8417,7 @@ in with self; { kstMatrix = derive2 { name="kstMatrix"; version="0.1-0"; sha256="0c8nb6cc4ng6gc21bhnj8in7rcjnsbncb3c8k70q3w340apwv2pm"; depends=[]; }; ktsolve = derive2 { name="ktsolve"; version="1.1"; sha256="0b5myr093v3qaj9gzbw1w728i5ij418whxxpicj51w657dcy647k"; depends=[]; }; ktspair = derive2 { name="ktspair"; version="1.0"; sha256="1v63982jidxlcf2syahcb29myv34kc790l7lwyfxx9l50ssb812n"; depends=[Biobase]; }; + kuiper_2samp = derive2 { name="kuiper.2samp"; version="1.0"; sha256="0gcgayh7qdic9zprdvs6r8qvpqs467zrm0qzp2acb7alcp01jhpi"; depends=[]; }; kulife = derive2 { name="kulife"; version="0.1-14"; sha256="070ayy6fr9nsncjjljikn2i5sp2cx3xjjqyc64y2992yx74jgvvd"; depends=[]; }; kutils = derive2 { name="kutils"; version="1.45"; sha256="0qx40d5nk8q0kv09l73bcn7dbch89b9zi8yp75v39vcy4qxdnc2b"; depends=[foreign lavaan openxlsx plyr RUnit xtable]; }; kvh = derive2 { name="kvh"; version="1.3"; sha256="0dhdvka7sdh7qcq5cz5xsv8dbxr1lr4n7wf033smsz4nvwgjixr3"; depends=[Rcpp]; }; @@ -8501,13 +8561,14 @@ in with self; { lgtdl = derive2 { name="lgtdl"; version="1.1.5"; sha256="1sixq56d2px36q0xq3kl0zwj2yzm3q8fhgqjvmajcdd5jl8l7130"; depends=[]; }; lhmixr = derive2 { name="lhmixr"; version="0.1.0"; sha256="1c4ydgq1z2y0xk8xqdsim6xvgxdbl3gglfk5kcr9k4m01arvv0rf"; depends=[]; }; lhs = derive2 { name="lhs"; version="0.16"; sha256="09clh386i5iig8x36lx02p01zqq0kb9hzvw5slv1ggmjnp1rklcw"; depends=[]; }; + liayson = derive2 { name="liayson"; version="1.0.1"; sha256="1l3zxpjis8k8ks59wsx1lvg4pmsy69094jh0h2zqvi4nnjphfqqm"; depends=[ape arules biomaRt distances e1071 gplots matlab phangorn plyr proxy RColorBrewer]; }; libamtrack = derive2 { name="libamtrack"; version="0.6.3"; sha256="0pdwrz19q1yls0rgr4579f31j86awizx3j31h7vdh6y70ngpmb82"; depends=[]; }; - libcoin = derive2 { name="libcoin"; version="1.0-1"; sha256="1i38v0pq5snx9clhgfiymk6lq87h41pajhp2dvin30snnq0py6qq"; depends=[mvtnorm]; }; + libcoin = derive2 { name="libcoin"; version="1.0-2"; sha256="1s1hirklh8w9gwnhrlgjmxsp517ylsyzj2bwal4fzzz2lxf8ffvg"; depends=[mvtnorm]; }; librarian = derive2 { name="librarian"; version="1.3.0"; sha256="1nlk5v7lk56w4gq97lv1d4k1wza8zankvrzcl0996zqlgz6imz0d"; depends=[devtools]; }; librarysnapshot = derive2 { name="librarysnapshot"; version="0.1.2"; sha256="0v4x564zpm58kxs5n84bi6mcjhbzjg6a2lc30vsc8kbm3qy0nq38"; depends=[]; }; libsoc = derive2 { name="libsoc"; version="0.6.4"; sha256="1hdnqgnvzm5116gphxa55k2bc3ksr607px2s2yg1ilmmxdghdccw"; depends=[]; }; libstableR = derive2 { name="libstableR"; version="1.0.2"; sha256="1gkcgbc8a7ks9x8mqmlz98hk55q3qy62izam7csz1s0r5dzsyqcr"; depends=[Rcpp RcppGSL]; }; - lidR = derive2 { name="lidR"; version="1.6.1"; sha256="0x5ns3p1qvakk999x42qlrhy71plvcqxp65fbj9kc07npyj6bfgw"; depends=[assertive concaveman data_table future gdalUtils geometry glue gstat lazyeval mapedit mapview memoise RANN raster Rcpp rgeos rgl rlas settings sp]; }; + lidR = derive2 { name="lidR"; version="2.0.0"; sha256="15x63xiawyvk26g93907dka6icdaxbh3gwbj66cww5fqqawp6fzk"; depends=[BH data_table future gdalUtils geometry glue gstat imager lazyeval raster Rcpp RCSF rgdal rgeos rgl rlas sf sp]; }; lifecontingencies = derive2 { name="lifecontingencies"; version="1.3.5"; sha256="18dlp6bm9hsr99y85fxdbapn8s1daqsynpiqf2cfhyffqiwll97f"; depends=[markovchain Rcpp]; }; lifecourse = derive2 { name="lifecourse"; version="2.0"; sha256="1m8ihqvzhzpq2m2pdvh37bpq9pdbj23r3y0jkl3q8farh3qj473d"; depends=[TraMineR]; }; lifelogr = derive2 { name="lifelogr"; version="0.1.0"; sha256="1wygvw61ygpww0kahxhmjdncwg4zc2cshs0brzw18nfqaj8vpfav"; depends=[dplyr fitbitScraper ggplot2 lazyeval lubridate modelr plyr R6 shiny stringr tibble tidyr]; }; @@ -8542,7 +8603,7 @@ in with self; { linkim = derive2 { name="linkim"; version="0.1"; sha256="0yvyid9x59ias8h436a202hd2kmqvn8k1zcrgja2l4z2pzcvfn91"; depends=[]; }; linkprediction = derive2 { name="linkprediction"; version="1.0-0"; sha256="0p2abdq6ad689236w2d0khlycpjgy6j7xrlb96ngl6csgxwm07bl"; depends=[igraph intergraph]; }; linkspotter = derive2 { name="linkspotter"; version="1.2.0"; sha256="0wk27jn8jr5rskjxbixshmp2dl0l74hrc8r6x3rvhy0x0b00zks2"; depends=[dplyr energy ggplot2 Hmisc infotheo mclust minerva pbapply rAmCharts shiny tidyr visNetwork]; }; - linl = derive2 { name="linl"; version="0.0.2"; sha256="1n3sljyycsppk11ri9jijsif3g7v4n8xvk1n4hhx0qg65kh7wmry"; depends=[knitr rmarkdown]; }; + linl = derive2 { name="linl"; version="0.0.3"; sha256="0cl9p77c9702mzjv02yd7yj7lxwnwslibj0nk8p96glclsbyayl5"; depends=[knitr rmarkdown]; }; linpk = derive2 { name="linpk"; version="1.0"; sha256="14l3vv507z7x63ziynp07902599syah0icvzq4rxfjf48bf96l63"; depends=[mvtnorm]; }; linprog = derive2 { name="linprog"; version="0.9-2"; sha256="1ki14an0pmhs2mnmfjjvdzd76pshiyvi659zf7hqvqwj0viv4dw9"; depends=[lpSolve]; }; lintools = derive2 { name="lintools"; version="0.1.2"; sha256="18layj6a202p0sy9rs022fp0a6fwvixwwmwlyzn7h9kh4y9gvxjz"; depends=[]; }; @@ -8598,12 +8659,13 @@ in with self; { lmomPi = derive2 { name="lmomPi"; version="0.5.0"; sha256="07ggfzgvhc6kkqs8bbs6z01rbhgb0ki2y4li6r0nkiby1wcpx0py"; depends=[lmom stringr]; }; lmomRFA = derive2 { name="lmomRFA"; version="3.1"; sha256="1gq5sjdywz1jbsshrh350zad7iifml2yj8an5xa63ghxiskrxscx"; depends=[lmom]; }; lmomco = derive2 { name="lmomco"; version="2.3.2"; sha256="1gqwn5yjd3zcwd5nysayf88vjhj2j1qxfgqcw63q7f2ih0xk1lqp"; depends=[goftest Lmoments MASS]; }; + lmreg = derive2 { name="lmreg"; version="1.0"; sha256="0ndwggjkqmfjcd5ggc3vxv7xbvvcxlnxy95ynhbwg4rigyavhww5"; depends=[MASS]; }; lmridge = derive2 { name="lmridge"; version="1.2"; sha256="091rznzh77bmsv7sw9xmsq6s9pnljyq7qyl74kgcxss718134jr3"; depends=[]; }; lmtest = derive2 { name="lmtest"; version="0.9-36"; sha256="0sym9sm1vl6bbgq01jhz1plxqmgh8hrgrn7rw0mwvsalcn6id7xy"; depends=[zoo]; }; lmvar = derive2 { name="lmvar"; version="1.5.0"; sha256="068ib0abpvds0ibb0d6m71svv7d3l0is4kdin1wzsn633kk3zcfy"; depends=[Matrix matrixcalc maxLik]; }; lmviz = derive2 { name="lmviz"; version="0.1.1"; sha256="0wgq93pr54pc4vxzqlhc1i67zf4lrn8yzpvlqsv8byh2qb0dd4sv"; depends=[lmtest mgcv shiny shinyjs]; }; loa = derive2 { name="loa"; version="0.2.44.2"; sha256="16yrkl8l4wa4i3iizncm58l75l46acfr2lf4vn53crcci9xra333"; depends=[lattice MASS mgcv plyr png RColorBrewer RgoogleMaps]; }; - lobstr = derive2 { name="lobstr"; version="1.0.0"; sha256="0gabjlb2175v218h1cx59f49x4rvcazilsh6g6n3n6y534axw94x"; depends=[crayon Rcpp rlang]; }; + lobstr = derive2 { name="lobstr"; version="1.0.1"; sha256="1yq4a568aj1psf7i20c5g1fwas486gd50ypjpc76ibyvff7jiyr5"; depends=[crayon Rcpp rlang]; }; localIV = derive2 { name="localIV"; version="0.1.0"; sha256="0q2vjiwj301g0lqaafpk6i1cxdwgaanz9ckwj2zkzk4h3gx2afw3"; depends=[KernSmooth mgcv sampleSelection]; }; localgauss = derive2 { name="localgauss"; version="0.40"; sha256="0y0pcg2i7lr4wipxawn06hy0q11znhcn2ah6rqwnlyy8pab70pyq"; depends=[foreach MASS matrixStats]; }; localsolver = derive2 { name="localsolver"; version="2.3"; sha256="1d18rihzqf1f5j9agfp8jysll7lqk1ai23hkdqkn6wwxj442llv4"; depends=[]; }; @@ -8623,6 +8685,7 @@ in with self; { logcondens = derive2 { name="logcondens"; version="2.1.5"; sha256="1sq27klnphp74hq0l0460m9bb7lrl06mpgkg4qq8iciy3yy1mrkj"; depends=[ks]; }; logcondens_mode = derive2 { name="logcondens.mode"; version="1.0.1"; sha256="1i2c2prk5j863p3a3q3xnsv684igfi5czz3dib7zfjldpf0qyaq7"; depends=[distr logcondens]; }; logcondiscr = derive2 { name="logcondiscr"; version="1.0.6"; sha256="08wwxsrpflwbzgs6vb3r0f52hscxz1f4q0xabr1yqns06gir1kxd"; depends=[cobs Matrix mvtnorm]; }; + logger = derive2 { name="logger"; version="0.1"; sha256="00gfy2i58qn5na8cxxrkm1pvsw85xx2gdk0y6dzxhcjfx3wyplaw"; depends=[]; }; logging = derive2 { name="logging"; version="0.8-104"; sha256="1grx44yhn8lm71ksyq9z369ylawngm69bv7dg1c660378c5b0iix"; depends=[]; }; loggit = derive2 { name="loggit"; version="1.1.1"; sha256="1w9a3mbf863dk6lnd95mwr15rxjpv1rra1z45jnqk8w56g1s7q4d"; depends=[dplyr jsonlite]; }; loggle = derive2 { name="loggle"; version="1.0"; sha256="0r1r8m2ckva17vbvwkzhq1lx6bap0kbfj9hxyk46adslcf3xxrxp"; depends=[doParallel foreach glasso igraph Matrix sm]; }; @@ -8668,7 +8731,7 @@ in with self; { lpc = derive2 { name="lpc"; version="1.0.2"; sha256="1r6ynkhqjic1m7fqrqsp7f8rpxqih5idn4j96fqrdj8nj01znv29"; depends=[]; }; lpdensity = derive2 { name="lpdensity"; version="0.2.2"; sha256="1fv1biyc12zg0wfqcr5kp761fy6n6879knvlxr2zjp6rjssi3h6d"; depends=[ggplot2]; }; lpint = derive2 { name="lpint"; version="2.0"; sha256="0p1np8wlfbax0c7ysc5fs9dai8s00h1v0gan89dbd6bx06307w2r"; depends=[]; }; - lpirfs = derive2 { name="lpirfs"; version="0.1.3"; sha256="17jgk0y5xgm3g1wl0mq0sjjw1ghvs009cr5qhh5hpb1k5yk14q4n"; depends=[doParallel dplyr foreach ggplot2 Rcpp RcppArmadillo]; }; + lpirfs = derive2 { name="lpirfs"; version="0.1.4"; sha256="0h57pp1lag5bkqkzq9jd4g0ir3pn2vmnqr1nc4jh00bv6gbqrhrr"; depends=[doParallel dplyr foreach ggplot2 lmtest plm Rcpp RcppArmadillo sandwich]; }; lplyr = derive2 { name="lplyr"; version="0.1.12"; sha256="1wcab8wwdzpgb61q83gfn2d34vsrd3qa4xyb9sqna6krss1ii1in"; depends=[bazar dplyr lazyeval magrittr]; }; lpme = derive2 { name="lpme"; version="1.1.1"; sha256="0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448"; depends=[decon flexmix locpol Rcpp RcppArmadillo]; }; lpmodeler = derive2 { name="lpmodeler"; version="0.2-1"; sha256="17k67l03dkjx61p4hwswghjm6awk0zx173x9xafxrfd8jrgsf6kf"; depends=[slam]; }; @@ -8715,6 +8778,7 @@ in with self; { luzlogr = derive2 { name="luzlogr"; version="0.2.0"; sha256="0n0cm94aianwcypa0gwdjvyy3dwbkfv6zi1gq2jn57b41fg20lq5"; depends=[assertthat]; }; lvec = derive2 { name="lvec"; version="0.2.2"; sha256="0n1l26n4khlalqd0b9bi7vc3kr5jh6mr56ca0rmnnl6bl9742nr5"; depends=[BH Rcpp]; }; lvm4net = derive2 { name="lvm4net"; version="0.2.1"; sha256="0syl3bzrmpm960b2fx893xw79d7lvlhr94r5kdq9z6jayvcyq66c"; depends=[ellipse ergm igraph MASS network]; }; + lvmcomp = derive2 { name="lvmcomp"; version="1.2"; sha256="08hs97bdz4n0bdhvqqq5xywfy140s69c750rn38criq4cw4gm3z7"; depends=[coda Rcpp RcppArmadillo]; }; lvnet = derive2 { name="lvnet"; version="0.3.4"; sha256="0pn3iwxl8aj605s9hvvsysdq6i8yidzg992xczc1m95hbk5i0pkr"; depends=[corpcor dplyr glasso lavaan Matrix mvtnorm OpenMx psych qgraph semPlot]; }; lvplot = derive2 { name="lvplot"; version="0.2.0"; sha256="01sisj2vbx2yb5w9cjzyaf9j46vh4kkw05xccq1f7wmsg69zmj6b"; depends=[ggplot2 RColorBrewer]; }; lwgeom = derive2 { name="lwgeom"; version="0.1-5"; sha256="1sqpd2r15nlg210249vpxqzk04ylhlqypfd1p86hriykd86x6idv"; depends=[Rcpp sf units]; }; @@ -8794,7 +8858,7 @@ in with self; { maptools = derive2 { name="maptools"; version="0.9-4"; sha256="1753kgyc4kmbb5h6knz5wgvvvj8v77kzm8lz0kwz05m5k3spa24k"; depends=[foreign lattice sp]; }; maptpx = derive2 { name="maptpx"; version="1.9-2"; sha256="1i5djmjg0lsi7xlkbvn90njq1lbyi74zwc2nldisay4xsbgqg7fj"; depends=[slam]; }; maptree = derive2 { name="maptree"; version="1.4-7"; sha256="1k7v84wvy6wz6g0dyiwvd3lvf78rlfidk60ll4fz7chvr2nrqdp4"; depends=[cluster rpart]; }; - mapview = derive2 { name="mapview"; version="2.6.0"; sha256="1k8y9kj3qrih3fn0xw7nz0irhprdv8fqpxjad2djsvabmn11l51b"; depends=[base64enc brew htmltools htmlwidgets lattice leaflet png raster Rcpp satellite scales sf sp stars svglite uuid viridisLite webshot]; }; + mapview = derive2 { name="mapview"; version="2.6.3"; sha256="0f3b2c3s6i87q875y7wvcwv8pp40ps5ayjp6i6g8fdh5zd40qmhn"; depends=[base64enc brew htmltools htmlwidgets lattice leaflet png raster Rcpp satellite scales sf sp svglite uuid viridisLite webshot]; }; mar1s = derive2 { name="mar1s"; version="2.1.1"; sha256="1ljkvgxrramfx1rnp2rg6516mjxaa6s96amrnmqymnyjz7wlf37l"; depends=[cmrutils fda zoo]; }; march = derive2 { name="march"; version="1.4"; sha256="1wfhm33k2j5yim56sg0wd02ypfhlp9fc138vmdsdjp6nh4y23hnj"; depends=[]; }; marcher = derive2 { name="marcher"; version="0.0-2"; sha256="0hcxbfrwniih4kvx5sxhlffz1pc87kf52v8hvaf193rhhdykis5q"; depends=[magrittr Matrix minpack_lm mvtnorm numDeriv plyr RColorBrewer scales zoo]; }; @@ -8848,7 +8912,7 @@ in with self; { mazeGen = derive2 { name="mazeGen"; version="0.1.3"; sha256="192xygg3l4rpqp49sgd5hpp4h3f8wjhyldn0l8abxhsks7jd2kfb"; depends=[igraph]; }; mazealls = derive2 { name="mazealls"; version="0.2.0"; sha256="14j6syw1zkgs4cnmxzqpm6klmgvck2gg97wkzmy9al6n0biy8gmb"; depends=[TurtleGraphics]; }; mazeinda = derive2 { name="mazeinda"; version="0.0.1"; sha256="0ns4ib73y4fghf7p1wg0a05js4mqr66dpp49p1h039pqrb0f1vwd"; depends=[foreach]; }; - mbbefd = derive2 { name="mbbefd"; version="0.8.8.3"; sha256="02iijakxl96m6n1rv0xsacsyjj5b093sl07lmp62hwyv9hf3jh4k"; depends=[actuar alabama fitdistrplus gsl MASS Rcpp]; }; + mbbefd = derive2 { name="mbbefd"; version="0.8.8.5"; sha256="1bnbavhii2wm9944l4j5x21y9b3kp0sdshz32r1k7cy1y569zd6r"; depends=[actuar alabama fitdistrplus gsl MASS Rcpp]; }; mbclusterwise = derive2 { name="mbclusterwise"; version="1.0"; sha256="1ilqaxcxf1k3ck910s0xqwnp88w8ag5rn1dpvaa1i7jlcldsbnhp"; depends=[ade4 doParallel foreach kknn]; }; mbest = derive2 { name="mbest"; version="0.6"; sha256="1x0f7y5hj6a35wq1xn6g7jyjn9c4zryahwlf07qrypgrcnj2m8vx"; depends=[abind bigmemory foreach lme4 logging nlme]; }; mbgraphic = derive2 { name="mbgraphic"; version="1.0.0"; sha256="0b4xr2ycx8v56fp40lnxv69qfp0yzai2hdwk3kw4wsmir91d2a91"; depends=[diptest dplyr extracat GGally ggplot2 gridExtra hexbin magrittr mgcv Rcpp scagnostics scales seriation shiny]; }; @@ -8856,6 +8920,7 @@ in with self; { mblm = derive2 { name="mblm"; version="0.12"; sha256="17h65bapvz89g5in3gkxq541bxgpj9pciz6i5hzhqn0bdbsb3k6r"; depends=[]; }; mbmdr = derive2 { name="mbmdr"; version="2.6"; sha256="0ss5w66hcgd8v8j9bbbp12a720sblhr2hy9kidqfr8hgjaqlch86"; depends=[logistf]; }; mboost = derive2 { name="mboost"; version="2.9-1"; sha256="02ia3y0fxfjl02fb1nnl93j640fyl18jm15cgxyybhf27w4jdvb7"; depends=[lattice Matrix nnls partykit quadprog stabs survival]; }; + mboxr = derive2 { name="mboxr"; version="0.1.2"; sha256="0ga00dx318frdrf9zgddn8k23alc9kdq0kfl75mnvrnric0kx9v4"; depends=[dplyr magrittr purrr readr reticulate tibble]; }; mbrglm = derive2 { name="mbrglm"; version="0.0.1"; sha256="0yxq1xk8qy5hpiqqldyrs78lp4ggdp5lj2lmh8rqq1xvsfr6nrh4"; depends=[enrichwith nleqslv]; }; mc2d = derive2 { name="mc2d"; version="0.1-18"; sha256="1ljw8ms661bsdqbfpjvvrif9n0c2i6lzxyqj4rxhxsp3dj18w3g3"; depends=[mvtnorm]; }; mcGlobaloptim = derive2 { name="mcGlobaloptim"; version="0.1"; sha256="1p8841y9a4yq51prv6iirgw9ln8jznx8nk547sc5xlznksjy1g9n"; depends=[randtoolbox snow]; }; @@ -8906,7 +8971,7 @@ in with self; { mdscore = derive2 { name="mdscore"; version="0.1-3"; sha256="10cl5r6kd9chdik5v0q91x40xpw2cjvvyi220z4bvngpb0989x8j"; depends=[MASS]; }; mdsdt = derive2 { name="mdsdt"; version="1.2"; sha256="0nbzc54jac4wmfyrs821ycxh749cb1zfxcws0nbpk35rydqkc627"; depends=[ellipse mnormt polycor]; }; mdsr = derive2 { name="mdsr"; version="0.1.6"; sha256="1z0sjrvnvm1bgifapmaay57lr5dgj84xzppwn579g8kammaav89x"; depends=[babynames DBI dbplyr downloader dplyr ggplot2 mosaic RMySQL]; }; - mdsstat = derive2 { name="mdsstat"; version="0.2.0"; sha256="12gr54lpxzs682mln21899gb3ma202a20j87p030p99fp71vbw42"; depends=[lubridate mds]; }; + mdsstat = derive2 { name="mdsstat"; version="0.2.1"; sha256="05hb8hjfsxljpqix9wgaiyaxwk6gwca4zwmimihp0mj6ylsndmcn"; depends=[lubridate mds]; }; mdw = derive2 { name="mdw"; version="2017.12-03"; sha256="054vssnypbik0yf6smicggnkrqf6kx8k21nbf5rminsh00sx39k1"; depends=[]; }; meaRtools = derive2 { name="meaRtools"; version="1.0.4"; sha256="1nxyvdq4670696mhg0svxxlvk9hnr8szai8b18pw6754kmw1bjvn"; depends=[emdist ggplot2 gridExtra gtools lattice plyr Rcpp reshape2]; }; meanShiftR = derive2 { name="meanShiftR"; version="0.53"; sha256="1pla9hr9nbbnc3hcmk0ywfh6129zng5lp3dmjqb3cgdrmwkdrx9i"; depends=[]; }; @@ -8921,6 +8986,7 @@ in with self; { mediation = derive2 { name="mediation"; version="4.4.6"; sha256="0prhpy9y26s388p9gv5sv4h5airixwy6ffjphhxmyp9h07088xxi"; depends=[Hmisc lme4 lpSolve MASS Matrix mvtnorm sandwich]; }; medicalrisk = derive2 { name="medicalrisk"; version="1.2"; sha256="1zdxv3rj7768kbyxfvr9n0hp4z7y0sf3r7ssqv731hjjp656l6xp"; depends=[hash plyr reshape2]; }; medicare = derive2 { name="medicare"; version="0.2.1"; sha256="00a1gml2khzisdavnaip6ap4bw45b17nbl9cqb1mqrm4y0p9gm16"; depends=[]; }; + meditations = derive2 { name="meditations"; version="1.0"; sha256="01r1dwbyvbr7lrr3c3ab6ljiqs6bkfslfabrvvgd9s17jbql3ghz"; depends=[]; }; medmod = derive2 { name="medmod"; version="1.0.0"; sha256="1f7bzdcjnbz9izlfblxcaa85qxx8kzn62qgjd3qlb7jl7mdy5q54"; depends=[ggplot2 jmvcore lavaan R6]; }; meetupapi = derive2 { name="meetupapi"; version="0.1.0"; sha256="1iaxpfzgn478np9cjwz0zalfy1p7jwabnwpfv31svw052i8bs9yl"; depends=[dplyr httr magrittr purrr]; }; mefa = derive2 { name="mefa"; version="3.2-7"; sha256="1qrf6d3y38q7yy6bg3bxg7514d9paz1f8y6sr7lbksi30qn92fmj"; depends=[]; }; @@ -8956,9 +9022,10 @@ in with self; { metaLik = derive2 { name="metaLik"; version="0.43.0"; sha256="1li40pgd9z00nrph9njwn6wysb1i9dkpqzcp6fzds6asvcxlqqfl"; depends=[]; }; metaMA = derive2 { name="metaMA"; version="3.1.2"; sha256="1mjyz06q1kc8lhfixpym4ndpnisi1r849fj3da6riwfd6ab1v181"; depends=[limma SMVar]; }; metaMix = derive2 { name="metaMix"; version="0.2"; sha256="0xlsdgincxwjzyr4i8qfmfw2wvgf41qbmyhf2rxcbarf7rmwhmqf"; depends=[data_table ggplot2 gtools Matrix Rmpi]; }; + metaRMST = derive2 { name="metaRMST"; version="1.0.0"; sha256="1mq9j7iczjh7d3cps9g1bh0f8k388bdn8d5lkjs2s8y9fq1kxzmx"; depends=[meta mvmeta rstpm2 survival survRM2]; }; metaRNASeq = derive2 { name="metaRNASeq"; version="1.0.2"; sha256="1xz7df7ypq4326yg429pgxd6aldp14c3h3qi20j5nqr5xgsdgzqa"; depends=[]; }; metaSEM = derive2 { name="metaSEM"; version="1.2.0"; sha256="0b10as2bb5f31r59548v1j8saxd16icrsg915j2yv3nxzyi5iq7f"; depends=[ellipse lavaan MASS Matrix mvtnorm numDeriv OpenMx]; }; - metaboGSE = derive2 { name="metaboGSE"; version="1.2.0"; sha256="024kb30j1r2223x1pp1226i7awd4di4gkppwrqc5d36l3clf7qbj"; depends=[AnnotationDbi ape Matrix sybil sys topGO]; }; + metaboGSE = derive2 { name="metaboGSE"; version="1.2.1"; sha256="169m59y2g3618rpjjlmwsj1alkfcjfhpsyzhz9010vn38bbwgmxr"; depends=[AnnotationDbi ape Matrix sybil sys topGO]; }; metabolomics = derive2 { name="metabolomics"; version="0.1.4"; sha256="0m5d2784mkpkkg396y3vpvf38vmba5kvxarilq3zf818vjs4pnax"; depends=[crmn gplots limma]; }; metacart = derive2 { name="metacart"; version="2.0-0"; sha256="011incw57n11g5fmn4k8vcpqww8nn5xqsbh65p9gx2nad1kg3g35"; depends=[ggplot2 gridExtra Rcpp rpart]; }; metacoder = derive2 { name="metacoder"; version="0.3.0.1"; sha256="1mih4h90xfshzcc0hl65mpqwkm90n9j3n1ccxl13b6b3mn1bvdds"; depends=[ape biomformat cowplot crayon dplyr GA ggfittext ggplot2 igraph lazyeval magrittr phyloseq phylotate RColorBrewer Rcpp RCurl readr reshape2 rlang scales seqinr stringr taxa taxize traits vegan zoo]; }; @@ -8974,6 +9041,7 @@ in with self; { metaheur = derive2 { name="metaheur"; version="0.2.0"; sha256="1rr5mjx3v87alj7cl9hxldvhhbpkz1fzmymmkqv0hs65pny6gbqw"; depends=[doParallel foreach ggplot2 preprocomb reshape2]; }; metaheuristicOpt = derive2 { name="metaheuristicOpt"; version="1.0.0"; sha256="1wzy5dnmrdfdj1386snjyisrbzbq8v4qsnq57l3wvkg1pgnz1vh2"; depends=[]; }; metamedian = derive2 { name="metamedian"; version="0.1.1"; sha256="1radc0hm357jq31ns83z25b7n1fp6vsg4pag4f8q0f5lyravn13a"; depends=[Hmisc metafor]; }; + metamer = derive2 { name="metamer"; version="0.1.0"; sha256="03a7r5dsqjxhjmdq5ybg18l9nf7szn848q9zr4jdyfxw8wi2y75k"; depends=[FNN progress]; }; metamisc = derive2 { name="metamisc"; version="0.1.9"; sha256="0wjwx7ncplpchwbz0l4xmsmy0faj2wnqjxvxyi05992v3rjv4j8k"; depends=[ellipse ggplot2 lme4 metafor mvtnorm plyr]; }; metansue = derive2 { name="metansue"; version="2.3"; sha256="18vy294862lfgxiw9cikai9svy3wpwk2bvz3vp20fcslg90mn3xp"; depends=[]; }; metap = derive2 { name="metap"; version="1.0"; sha256="18rzvqfzyk8fn54gjvy2qd21nk9w69j7ihww477ma3f3ab6i982h"; depends=[lattice Rdpack]; }; @@ -8997,6 +9065,7 @@ in with self; { mewAvg = derive2 { name="mewAvg"; version="0.3.0"; sha256="16gc78ccjffp9qgc7rs622jql54ij83ygvph3hz19wpk22m96glm"; depends=[]; }; mexhaz = derive2 { name="mexhaz"; version="1.5"; sha256="0my53dg321xfbbkxawxcggnh5gw9qkliji5gsdb8m1fi37djd67w"; depends=[MASS numDeriv statmod survival]; }; mfGARCH = derive2 { name="mfGARCH"; version="0.1.7"; sha256="086596dj6xz7by6rwddvyl7ap341q5hmpc6pslcjn0yvbc7j0wkh"; depends=[numDeriv Rcpp zoo]; }; + mfbvar = derive2 { name="mfbvar"; version="0.4.0"; sha256="1bxfs7081nd7l0lknag2n184rd1d91cr5sgsnjsfwgdbws8sl8d3"; depends=[ggplot2 pbapply Rcpp RcppArmadillo]; }; mfe = derive2 { name="mfe"; version="0.1.1"; sha256="0z9ddkck1z14b9cwvaam0xh869lh2fsjm1d3i8giyrcry0vvpp61"; depends=[cluster e1071 infotheo MASS rpart rrcov]; }; mfp = derive2 { name="mfp"; version="1.5.2"; sha256="1i90ggbyk2p1ym7xvbf4rhyl51kmfp6ibc1dnmphgw15wy56y97a"; depends=[survival]; }; mfx = derive2 { name="mfx"; version="1.1"; sha256="1zhpk38k7vdq0pyqi1s858ns19qycs3nznpa00yv8sz9n798wnn5"; depends=[betareg lmtest MASS sandwich]; }; @@ -9022,6 +9091,7 @@ in with self; { miRNAss = derive2 { name="miRNAss"; version="1.4"; sha256="0p852vyn44g84i4hzm7b02m5cxyqajnczx0s9x9373rn7fi6r98c"; depends=[CORElearn Matrix Rcpp RSpectra]; }; miRada = derive2 { name="miRada"; version="1.13.8-8"; sha256="1m6rm65pv4r16r0s5ih69nr3v2rnpsvpdpk07pi7k4f7v9wck71v"; depends=[]; }; miRtest = derive2 { name="miRtest"; version="1.8"; sha256="0i66s1sz7vf8p8ihfrxmag7wbkw8mlkldcp1w2figlzyhs74c85p"; depends=[corpcor GlobalAncova globaltest limma MASS RepeatedHighDim]; }; + miWQS = derive2 { name="miWQS"; version="0.0.9"; sha256="183r52ryi5171155ridfsjyznqhmnr0fzrzxvch7ylg4pjzwm0f3"; depends=[coda ggplot2 glm2 Hmisc invgamma rlist Rsolnp survival tidyr truncnorm]; }; micEcon = derive2 { name="micEcon"; version="0.6-14"; sha256="1d3cdg36ighyhly5by9gl6lxkdvx2agb5cv2mf77pwwd7rpq35h3"; depends=[miscTools plm]; }; micEconAids = derive2 { name="micEconAids"; version="0.6-18"; sha256="0s2gkf6widdnxqqb1xjqdvji8vhdz5a4q05clbbbyq1h409q7qvl"; depends=[lmtest micEcon miscTools systemfit]; }; micEconCES = derive2 { name="micEconCES"; version="0.9-8"; sha256="06g6z8hf7y9d942w6gya0fd5aidzfjkx3280gjygdlwpv7nlpqzv"; depends=[car DEoptim micEcon minpack_lm miscTools systemfit]; }; @@ -9031,7 +9101,7 @@ in with self; { miceExt = derive2 { name="miceExt"; version="1.1.0"; sha256="07xj9f5w0kh4d1yj8mx1jydvhd0vwpvvrb6h67xz5gb1ban4k6c6"; depends=[mice RANN RANN_L1]; }; miceFast = derive2 { name="miceFast"; version="0.2.3"; sha256="0ngb2qs71x0i8ffyb1qlbz2wk6c87m1r74l547c5pc9agnc227m0"; depends=[Rcpp RcppArmadillo]; }; miceMNAR = derive2 { name="miceMNAR"; version="1.0.2"; sha256="1s607icaf3c25mn8xdi3zkzmm8m7qd9a6vjdlz5j7ig2gc9f2y2d"; depends=[GJRM mice mvtnorm pbivnorm sampleSelection]; }; - miceadds = derive2 { name="miceadds"; version="2.15-22"; sha256="0069qijlk1nvk1rgm5ki5d3914sgxszk1d9hlnpipq0qwrn99kmy"; depends=[CDM coda lme4 MASS mice mitools mvtnorm Rcpp RcppArmadillo sirt TAM]; }; + miceadds = derive2 { name="miceadds"; version="3.0-16"; sha256="01zd9x1n2x452han2z59gg3yrrqrhldbwad9xkjsgzlcvjxly3ky"; depends=[CDM coda lme4 MASS mice mitools mvtnorm Rcpp RcppArmadillo sirt TAM]; }; micemd = derive2 { name="micemd"; version="1.5.0"; sha256="1bzy9lxgdvfrq3mhhx734aykpcr3klnwns70whz54y6afmcz7ghp"; depends=[abind digest jomo lme4 MASS Matrix mice mvmeta mvtnorm nlme]; }; micompr = derive2 { name="micompr"; version="1.1.0"; sha256="0qsxs35mmqx8hpszcb1z87xczh0vh0m0plqrj22af5mjjvif76n9"; depends=[]; }; microPop = derive2 { name="microPop"; version="1.4"; sha256="0dfqn7g445w4nydklvsq5vlkiin6kcz8kkazj7jfbm98ikdywzm8"; depends=[deSolve]; }; @@ -9058,9 +9128,10 @@ in with self; { milr = derive2 { name="milr"; version="0.3.0"; sha256="0z4d22fd6gd3zbi973vws9jqyh4c4m4i4ajcpxv934vxmbj0cma9"; depends=[glmnet numDeriv pipeR Rcpp RcppArmadillo RcppParallel]; }; mime = derive2 { name="mime"; version="0.6"; sha256="00f4gw4sg1kn03s67gficxgb7a7fb6pwhlvrxrml05q1mc2vcxa7"; depends=[]; }; minPtest = derive2 { name="minPtest"; version="1.7"; sha256="088kckpbfy2yp0pk3zrixrimywrvkaib5ywa7fkr5phnzlsl80sv"; depends=[Epi scrime]; }; - mindr = derive2 { name="mindr"; version="1.1.5"; sha256="02yszk13h5mm2wyx81byij152r8lj5j7r65icq3cl5skxygl43y7"; depends=[htmlwidgets]; }; + mindr = derive2 { name="mindr"; version="1.1.9"; sha256="0alwbqfdqb5f3qfyvw1b46bm988c2nvhdvk47hkmr0iigzagvxam"; depends=[htmlwidgets jsonlite knitr]; }; mineCitrus = derive2 { name="mineCitrus"; version="1.0.0"; sha256="031nfhrsc5rlqls3vyrk18lx0pd4ssdk96cmfr4ifaciz0rgv8h2"; depends=[ggplot2]; }; - minerva = derive2 { name="minerva"; version="1.4.7"; sha256="19snlbnk4y0lj7kfypa2g1d1s7bl3xkrxabn8p15hlwwcfb0x7vm"; depends=[]; }; + mined = derive2 { name="mined"; version="1.0-1"; sha256="09jcyzirc4f69g4n5490pwrjqbdd40fwn8liy0xarlf7cnqqnzzk"; depends=[Rcpp RcppEigen]; }; + minerva = derive2 { name="minerva"; version="1.5"; sha256="0w7achbpqqgs31q6ppw9dh6vmvhlv4jngyvyz4k33zvdjpn3z0yb"; depends=[Rcpp]; }; miniCRAN = derive2 { name="miniCRAN"; version="0.2.11"; sha256="1ffc367ipcxyk2a8f2y46xa01rbr5254cryf1qzzfflb3xj8n6pa"; depends=[httr igraph XML]; }; miniGUI = derive2 { name="miniGUI"; version="0.8-1"; sha256="0qb2fbkjwzn909yrk89d4951bwf8n05i0s265l8v2d4lpns9hc2i"; depends=[]; }; miniUI = derive2 { name="miniUI"; version="0.1.1.1"; sha256="1h5h2sc57h95d6bsgs95l26911g38hvjc1v50bc31xl9689l2as5"; depends=[htmltools shiny]; }; @@ -9077,6 +9148,7 @@ in with self; { mipfp = derive2 { name="mipfp"; version="3.2.1"; sha256="1gxazpg81vj5dywpb6jb29188jw28qil6pfygawa7znnjn3k5ca6"; depends=[cmm numDeriv Rsolnp]; }; mirt = derive2 { name="mirt"; version="1.29"; sha256="0rmnzs39x4b6v5sb8v23cxnsndnck4mb9757987r8wdnhbdx0hkr"; depends=[dcurver Deriv GPArotation lattice mgcv Rcpp RcppArmadillo vegan]; }; mirtCAT = derive2 { name="mirtCAT"; version="1.8"; sha256="1syv0j4gcdx5860kxshmr0m2d1klmxfi4bwcsc7lc5ss5kw63yi1"; depends=[lattice lpSolve markdown mirt pbapply Rcpp RcppArmadillo shiny]; }; + mirtjml = derive2 { name="mirtjml"; version="1.2"; sha256="0vjcbgl1s8haqc0xi4k8dsqvhr2qyz4ikhjwmqrxyl5xssjy330r"; depends=[GPArotation Rcpp RcppArmadillo]; }; misaem = derive2 { name="misaem"; version="0.9.0"; sha256="0ylapcsxdwb4h17k2n6frrxvirmvbs4x4psscjij8vmvrb2qh3pw"; depends=[magrittr MASS mvtnorm]; }; misc3d = derive2 { name="misc3d"; version="0.8-4"; sha256="0qjzpw3h09qi2gfz52b7nhzd95p7yyxsd03fldc9wzzn6wi3vpkm"; depends=[]; }; miscF = derive2 { name="miscF"; version="0.1-4"; sha256="1kvkbvrmaqclwdfghkrsmnzb6xbi97icay2wwb7k5m34xhx4ha82"; depends=[MASS MCMCpack mvtnorm R2jags]; }; @@ -9101,7 +9173,6 @@ in with self; { mixAK = derive2 { name="mixAK"; version="5.1"; sha256="0i9gp66d1mzskiif0bk0w88cinc923fsj4vi7pv0im2cwmxksiiq"; depends=[coda colorspace fastGHQuad lme4 mnormt]; }; mixEMM = derive2 { name="mixEMM"; version="1.0"; sha256="0344ay1avi37kvh5w9bknayx67yh7rflj6zhw68d2888v7cbghjy"; depends=[]; }; mixKernel = derive2 { name="mixKernel"; version="0.3"; sha256="1kf8niplqf97n10zi6hkp9gmyyd15v6vsy741c089iwiazmixhdf"; depends=[corrplot ggplot2 LDRTools Matrix mixOmics phyloseq psych quadprog vegan]; }; - mixOmics = derive2 { name="mixOmics"; version="6.3.2"; sha256="1lqhrgsfdlv1ji965zf9ndg6ngylbmqahcslwirwd5vrjvlbzjb2"; depends=[corpcor dplyr ellipse ggplot2 gridExtra igraph lattice MASS matrixStats rARPACK RColorBrewer reshape2 rgl tidyr]; }; mixPHM = derive2 { name="mixPHM"; version="0.7-2"; sha256="1wvkdb9zj2j8dpppnyins05rg877zbydqsl3qaan62wznkknxcac"; depends=[lattice survival]; }; mixR = derive2 { name="mixR"; version="0.1.1"; sha256="1xd3v5rk59380zh7r6l5blmcy4gib9xp44j5dcrk6ivs6fgycsxh"; depends=[ggplot2 Rcpp]; }; mixRasch = derive2 { name="mixRasch"; version="1.1"; sha256="1r067pv7b54y1bz8p496wxv4by96dxfi2n1c99gziqf5ramx3qzp"; depends=[]; }; @@ -9184,6 +9255,7 @@ in with self; { mmpf = derive2 { name="mmpf"; version="0.0.5"; sha256="1w1ll1l7yzwb1wmlrcfpgqyzni7yb20kxy422y867hx2ndxlfwpz"; depends=[checkmate data_table]; }; mmpp = derive2 { name="mmpp"; version="0.6"; sha256="16aypjf4i0ya3qgxqrrg8y0xbnq1pnqky1dpkgln5q494hphyg91"; depends=[]; }; mmppr = derive2 { name="mmppr"; version="0.1"; sha256="0fswkqcw0xkqd9gmqabb61i32zscp5jzfx0z43wq7mrlwynryylv"; depends=[expm reshape2]; }; + mmsample = derive2 { name="mmsample"; version="0.1"; sha256="0mdd2zryadd31a5pls5fvlxx52mr54jsi1i6mwrs4y7rl3i9v95z"; depends=[MASS Rcpp RcppArmadillo]; }; mmtfa = derive2 { name="mmtfa"; version="0.3"; sha256="0qfszr6f10v27w1pfns78dyarznqryl4m1ppyqap7l8fc12sliky"; depends=[matrixStats mvnfast]; }; mmtsne = derive2 { name="mmtsne"; version="0.1.0"; sha256="1by0hrggla6idc1isnq072i1wfpw4x7id3hkg8l65gy8iycccd12"; depends=[]; }; mnis = derive2 { name="mnis"; version="0.2.7"; sha256="1yhhgrhsk3ww93vd29ipw16bkn16w0b2i7d46cb5bb5xs4s7vivd"; depends=[dplyr httr jsonlite Rcpp stringi tibble]; }; @@ -9301,11 +9373,11 @@ in with self; { mritc = derive2 { name="mritc"; version="0.5-1"; sha256="12sfyw5b1lryczl92xvyvhl37qfx3ybg4y9awsl0b7f51zi0lzy3"; depends=[lattice misc3d oro_nifti]; }; mro = derive2 { name="mro"; version="0.1.1"; sha256="00gc2hd8q5hb2xrswclcqqw1gxl83zmpma6bhsggg3kppsw1dpjv"; depends=[MASS matrixcalc]; }; ms_sev = derive2 { name="ms.sev"; version="1.0.4"; sha256="1sr2rgiskgwjhwif70qj6ga8i8kg4bh342hff66b2a54rxrchmw5"; depends=[]; }; - msBP = derive2 { name="msBP"; version="1.3-1"; sha256="0ziqzkylawc6kpcfzqwrwn6vp0562rd2yx5a4zg8p1n0y2gdpdzc"; depends=[]; }; + msBP = derive2 { name="msBP"; version="1.4"; sha256="17hsnfipb6mgwhbc9rxzx5azc57ravz7zfnbc8r73sn1b270ydpb"; depends=[]; }; msSurv = derive2 { name="msSurv"; version="1.2-2"; sha256="02qm3mq17d2yj5mbz6gapd3zfi1wmiad5hpyimcb39impk43n2hf"; depends=[class graph lattice]; }; msaFACE = derive2 { name="msaFACE"; version="0.1.0"; sha256="1lh8crz507nlddm946lmn73xbnsh4cs0kg238ysnsvxs726c83fs"; depends=[]; }; msaR = derive2 { name="msaR"; version="0.3.0"; sha256="0lj9yhsissr4rgavyhgdxi2nrkq2088darzraisx9jsirjr49jf8"; depends=[ape htmlwidgets]; }; - msaenet = derive2 { name="msaenet"; version="2.9"; sha256="0jrrd49fmb8drrrz5g8gk3mwk1yczcm3v0c2939bqsjyd41830vr"; depends=[foreach glmnet Matrix mvtnorm ncvreg survival]; }; + msaenet = derive2 { name="msaenet"; version="3.0"; sha256="1rlf2s772vwwp8asmbqhwr27wslp3j8zznplkjjcsv3y4hn0jfd0"; depends=[foreach glmnet Matrix mvtnorm ncvreg survival]; }; msap = derive2 { name="msap"; version="1.1.8"; sha256="0z5lm782jjb9w1h5vgz8bmxjdcrq9zb3xp1w5cb479jjc7krlgg3"; depends=[ade4 ape]; }; mschart = derive2 { name="mschart"; version="0.2.3"; sha256="0lq2hhbwy3hycbvzhrhny7jk5cc4iq89a4mff5q2jjfff13vmm6g"; depends=[cellranger data_table htmltools officer R6 writexl xml2]; }; mscstexta4r = derive2 { name="mscstexta4r"; version="0.1.2"; sha256="1hjcasmn33xav2mw085lcndv0432l6sz327aikf63491wj1sj7mw"; depends=[dplyr httr jsonlite pander stringi]; }; @@ -9377,7 +9449,7 @@ in with self; { multimark = derive2 { name="multimark"; version="2.0.1"; sha256="0d283gvzqmdwr1sxgfb5ir9zw0sahj1wph7izcy1h63h6qlci828"; depends=[Brobdingnag coda Matrix mvtnorm prodlim raster RMark sp statmod]; }; multimode = derive2 { name="multimode"; version="1.4"; sha256="142k2jbi6y9aaqz9cwl4wk2m1y1n1fgvk873nk3psdv2h6r77slx"; depends=[diptest ks rootSolve]; }; multinbmod = derive2 { name="multinbmod"; version="1.0"; sha256="1c4jyzlcjkqdafj9b6hrqp6zs33q6qnp3wb3d7ldlij7ns9fhg71"; depends=[]; }; - multinet = derive2 { name="multinet"; version="2.0.0"; sha256="1v1m7aaqiqam9yzi3w9q49962d831bj4wyl5klsch47i4dar541r"; depends=[igraph Rcpp]; }; + multinet = derive2 { name="multinet"; version="2.0.1"; sha256="1gl1khr0qlx775hgzcl0462limk735apiib7awx232600flw8zqy"; depends=[igraph Rcpp]; }; multinets = derive2 { name="multinets"; version="0.2.1"; sha256="00h1nqi49mix5rxp39i46pimmr3rl0c2869g7ss8cy0kl8hl41hz"; depends=[igraph igraphdata Rcpp]; }; multinomRob = derive2 { name="multinomRob"; version="1.8-6.1"; sha256="1fdjfk77a79fy7jczhpd2jlbyj6dyscl1w95g64jwxiq4hsix9s6"; depends=[MASS mvtnorm rgenoud]; }; multipanelfigure = derive2 { name="multipanelfigure"; version="2.0.0"; sha256="0p9dipwkqfrfdd50s002byhwrdbzwp7nj1bswf8anpzvqnd8iz1a"; depends=[assertive_base assertive_files assertive_numbers assertive_properties assertive_types ggplot2 gridGraphics gtable magick magrittr stringi]; }; @@ -9420,7 +9492,7 @@ in with self; { mvSLOUCH = derive2 { name="mvSLOUCH"; version="1.3.4"; sha256="08nwmw5z0m6d9xx5f1cna0i0qkanr8f2vj6yicsg1k2zh1xpx0mk"; depends=[ape corpcor mvtnorm numDeriv ouch]; }; mvShapiroTest = derive2 { name="mvShapiroTest"; version="1.0"; sha256="0zcv5l28gwipkmymk12l4wcj9v047pr8k8q5avljdrs2a37f74v1"; depends=[]; }; mvabund = derive2 { name="mvabund"; version="3.13.1"; sha256="1z8bj9zbc8h7w1xki9sc2p2rq6lv8gbcmiy9819z54d7lx1i9cnj"; depends=[MASS Rcpp RcppGSL statmod tweedie]; }; - mvbutils = derive2 { name="mvbutils"; version="2.7.4.1"; sha256="1vs97yia78xh35sdfv5pj3ddqmy83qgamvyyh9gjg0vdznqhffzg"; depends=[]; }; + mvbutils = derive2 { name="mvbutils"; version="2.8.232"; sha256="0awd0jy492ha321c20kmmgl20kqphdmrmswakc0rq6h8z9d55kdg"; depends=[]; }; mvc = derive2 { name="mvc"; version="1.3"; sha256="0kmh6vp7c2y9jf71f4a29b0fxcl0h7m4p8wig4dk3fi7alhjf7ym"; depends=[rattle]; }; mvcluster = derive2 { name="mvcluster"; version="1.0"; sha256="0yfl31scdgsiljvpv1yxc5bwwzr6kbhpjwqh2kql7xf0m0hc1pr4"; depends=[Rcpp RcppArmadillo]; }; mvctm = derive2 { name="mvctm"; version="1.2"; sha256="0810bmk748cvbls4djspqvkk65j605djqicqg4rkwy2a799l3rgc"; depends=[Formula MNM nlme quantreg Rfit SpatialNP]; }; @@ -9439,6 +9511,7 @@ in with self; { mvnpermute = derive2 { name="mvnpermute"; version="1.0.0"; sha256="0mbyj5i5vysrnl3pgypl0cjf3sylsvzfl1pcxkn0q16560vqh2ba"; depends=[]; }; mvord = derive2 { name="mvord"; version="0.3.3"; sha256="1bpm9fic5adl86c9vbix0vpyjqbd871zhl0ccaydlw2wsrx79ynq"; depends=[BB dfoptim MASS Matrix minqa mnormt numDeriv optimx pbivnorm ucminf]; }; mvoutlier = derive2 { name="mvoutlier"; version="2.0.9"; sha256="1d562h3xicq962h27fi95qhrz9vkwxk0p8axhps1cy4b49w4bygi"; depends=[robCompositions robustbase sgeostat]; }; + mvp = derive2 { name="mvp"; version="1.0-0"; sha256="19hkmzq4lx7f57xxfvh1zj0rbvaqzkpkhfhj57ij3fv87f9dvypd"; depends=[magic mpoly partitions Rcpp]; }; mvprpb = derive2 { name="mvprpb"; version="1.0.4"; sha256="1kcjynz9s7vrvcgjb9sbqv7g50yiymbpkpg6ci34wznd33f7nrxm"; depends=[]; }; mvrtn = derive2 { name="mvrtn"; version="1.0"; sha256="0k0k76wk5zq0cjydncsrb60rdhmb58mlf7zhclhaqmli1cy697k8"; depends=[]; }; mvsf = derive2 { name="mvsf"; version="1.0"; sha256="1krvsxvj38c5ndvnsd1m18fkqld748kn5j2jbgdr3ca9m3i5nlwf"; depends=[mvnormtest nortest]; }; @@ -9521,9 +9594,9 @@ in with self; { nephro = derive2 { name="nephro"; version="1.2"; sha256="1izmzx8lah322xzb42asfnrvr2c9yqd0zf7fmrhwd3p4rr1rqa7d"; depends=[]; }; nesRdata = derive2 { name="nesRdata"; version="0.2.0"; sha256="1cr5d600bnslxbm2kknzwivvb4zyfsrf8rbrk3kk0j6dpclx5x6s"; depends=[dataone dplyr purrr rappdirs readr]; }; nestedRanksTest = derive2 { name="nestedRanksTest"; version="0.2"; sha256="0r08jp8036cz2dl1mjf4qvv5qdcvsrad3cwj88x31xx35c4dnjgj"; depends=[]; }; - nestfs = derive2 { name="nestfs"; version="0.9"; sha256="0vx6bvm4wpx4hnyxnldvkj0il7j7hlrmlpiza1dawqr3kx08c86l"; depends=[dgof foreach pROC]; }; + nestfs = derive2 { name="nestfs"; version="0.9.1"; sha256="17zf6fhpagn5smpqpj46lmz2hwbcdgy2nvkqx55yx1yhsivykdxq"; depends=[dgof foreach pROC]; }; net_security = derive2 { name="net.security"; version="0.3.0"; sha256="15vvcmakl9hl1srdhjf73g2bwwcxn93220i4gv0rcsw5732mjanz"; depends=[data_table dplyr jsonlite plyr R_utils stringr XML]; }; - netCoin = derive2 { name="netCoin"; version="0.3.0"; sha256="1lzzl28q3ald01yaxiiwqj716cpslya8i2m89nydpylh0c1pgs52"; depends=[haven igraph Matrix]; }; + netCoin = derive2 { name="netCoin"; version="0.3.2"; sha256="04fi08879yisdmkla93rvr029inwlgg5c5vz8k24d535m8k6mjhp"; depends=[haven igraph Matrix]; }; netSEM = derive2 { name="netSEM"; version="0.5.1"; sha256="0k4ngl4p1v2rp1sf2x65m7p0cd6ha98fyx21b73ki0531q0d9fil"; depends=[DiagrammeR DiagrammeRsvg gtools htmlwidgets knitr magrittr MASS png rsvg segmented svglite]; }; netassoc = derive2 { name="netassoc"; version="0.6.3"; sha256="1hyshnbpq60a3y13b4sh1c2rk78x09q01b7q6xrgv10w7bn9r2sg"; depends=[corpcor huge igraph infotheo vegan]; }; netcoh = derive2 { name="netcoh"; version="0.2"; sha256="0q60hvyparlwdww6as6hcdzfs6q3n8z1rfpj53r5q2s77x6q07xx"; depends=[Matrix Rcpp RcppArmadillo]; }; @@ -9534,7 +9607,7 @@ in with self; { netgsa = derive2 { name="netgsa"; version="3.0"; sha256="0cqyiilpxhdi6zmibn85y1aqwpcs1aialz34klakmllzn6kvdsng"; depends=[corpcor glasso glmnet igraph Matrix]; }; netgwas = derive2 { name="netgwas"; version="1.7.0"; sha256="1jyn0i3i5pjvik9jpgyd9sd28p0ln1xh5nxzssw3nynp4hyqmvix"; depends=[glasso huge igraph MASS Matrix qtl RBGL tmvtnorm]; }; netjack = derive2 { name="netjack"; version="1.1.1"; sha256="0pb9phfdjfp8yxlv5p0qb6vxhh8vb9iviffzrbj8x8dy3y3c9vp5"; depends=[brainGraph ggplot2 igraph Rdpack]; }; - netmeta = derive2 { name="netmeta"; version="0.9-8"; sha256="0bkfxdz14lg9r51ykwmkmpm6vhbvly35hrcgj6f26g36ihagjksd"; depends=[magic MASS meta]; }; + netmeta = derive2 { name="netmeta"; version="1.0-1"; sha256="1fsm41xz1dv6gwc354nxx4bj0xfmvamqhnhlbp5pn2g4y66wqm7s"; depends=[magic MASS meta]; }; netrankr = derive2 { name="netrankr"; version="0.2.1"; sha256="0csgi09ijp7ygwk7x057l9xjrzyhr7sav8hamh0p6i72l6719ssl"; depends=[igraph Rcpp RcppArmadillo]; }; netregR = derive2 { name="netregR"; version="1.0.1"; sha256="0n5absjra0imddz1spy1piij5rdz76wi4g568yby3rbhkm1896rs"; depends=[Matrix]; }; nets = derive2 { name="nets"; version="0.9"; sha256="1wcr0fj50w3rqxw0k9cb81c2psdkb0dwwwzrjvxv50hksbhyi8kn"; depends=[igraph]; }; @@ -9548,6 +9621,7 @@ in with self; { networkreporting = derive2 { name="networkreporting"; version="0.1.1"; sha256="1ssbz8lw4mlwcblwfbyffvayvb2gmihq4qlz5q9222fn4aa3raxd"; depends=[dplyr functional ggplot2 lazyeval plyr reshape2 stringr surveybootstrap]; }; networksis = derive2 { name="networksis"; version="2.1-3"; sha256="1kvil3qs7xd94ak9jgvj1nss55gjg0y7d35zmass9h1hjkcrq7bg"; depends=[network]; }; networktools = derive2 { name="networktools"; version="1.2.0"; sha256="023vmzvvlilr8dd1jjwp4xiszqkvpa231mkd6d9ibm3r99zcgdza"; depends=[cocor devtools eigenmodel ggplot2 gridExtra igraph IsingFit NetworkComparisonTest nnet psych qgraph R_utils RColorBrewer reshape2 smacof]; }; + networktree = derive2 { name="networktree"; version="0.1.1"; sha256="13ldampivmd63p444yr7pyadasv85lqxv5ycawcwhn7dli54g9n2"; depends=[Formula gridBase Matrix mvtnorm partykit qgraph]; }; neuRosim = derive2 { name="neuRosim"; version="0.2-12"; sha256="1hsnw9xipdr74fydq9013252ycbi9igh28s0j4dbdx52pv3iixzl"; depends=[deSolve]; }; neural = derive2 { name="neural"; version="1.4.2.2"; sha256="05hrqgppgwp38rdzw86naglxj0bz3wqv04akq7f0jxbbjc6kwy4j"; depends=[]; }; neuralnet = derive2 { name="neuralnet"; version="1.33"; sha256="14ga04mcd793v9a2584jb9l7n20kw00fgy3gayfwrkr1j39szdls"; depends=[MASS]; }; @@ -9632,6 +9706,7 @@ in with self; { noncensus = derive2 { name="noncensus"; version="0.1"; sha256="0cfj17bfzddfshhhzv2ijhrp9ylcscmsysswjcsjfxmy3gbkd00q"; depends=[]; }; noncompliance = derive2 { name="noncompliance"; version="0.2.2"; sha256="1lcybgj95z7lz7p26xbsdiv0vvms4ab4f8kad0pclacf1l43v0j6"; depends=[data_table Rcpp]; }; noncomplyR = derive2 { name="noncomplyR"; version="1.0"; sha256="1a9m6r9cizw42nmy24jdsrsbllg5z84fs8b239axnh1fxzskg2qy"; depends=[MCMCpack]; }; + nonet = derive2 { name="nonet"; version="0.3.0"; sha256="067h2zpgyqilr0hkqbca73brrxljjd53dkyll152d6b5q6ysm0l8"; depends=[caret dplyr e1071 ggplot2 glmnet pROC purrr randomForest rlang rlist tidyverse]; }; nonlinearICP = derive2 { name="nonlinearICP"; version="0.1.2.1"; sha256="1m9a1f0yrbjl0nx2l7r76pyi78b2bxj8v4jx92yga91f975mw6np"; depends=[caTools CondIndTests data_tree randomForest]; }; nonlinearTseries = derive2 { name="nonlinearTseries"; version="0.2.5"; sha256="0vpa8r8b7j2d19da49cw4jg8zm74kvg9npwf4aqwxw8ndkfgpyj0"; depends=[Matrix Rcpp RcppArmadillo rgl TSA tseries zoo]; }; nonmem2R = derive2 { name="nonmem2R"; version="0.1.10"; sha256="05ipdkvryx21kqc2kajy1xmpd9w33k8w0z6zq786kp9ks76pmfrb"; depends=[ggplot2 lattice latticeExtra MASS mvtnorm splines2]; }; @@ -9648,6 +9723,7 @@ in with self; { nord = derive2 { name="nord"; version="0.0.1"; sha256="0ajymjn2xw7zik62nhjp11g8bkvsqhhsrzi3bl2k70y544wbl3kn"; depends=[ggplot2]; }; nordklimdata1 = derive2 { name="nordklimdata1"; version="1.2"; sha256="0c2hbh3qy8nrs275lxpzfgqsfgwp81m4kv0layvnjj09fcybm54x"; depends=[]; }; norm = derive2 { name="norm"; version="1.0-9.5"; sha256="01j1h412yfjx5r4dd0w8rhlf55997spgb6zd6pawy19rgw0byp1h"; depends=[]; }; + norm2 = derive2 { name="norm2"; version="2.0.2"; sha256="1bpkxgcz940mn7r62sn1w38kii93sjdxbvfayp0nhl4a2qanwxsm"; depends=[]; }; normalp = derive2 { name="normalp"; version="0.7.0.1"; sha256="1gvbqirvb0q6c3831qqm5x7nj7rls1v7nfj7mf1nmwg5b0ljakp0"; depends=[]; }; normalr = derive2 { name="normalr"; version="1.0.0"; sha256="1ahrg188vbhnrnwag0zi6lcb3g0y1mbz06sl3j1wyllq5l918cc7"; depends=[magrittr MASS purrr rlang shiny]; }; normtest = derive2 { name="normtest"; version="1.1"; sha256="073r2mwfs6c4vqh8921nlyygl0f20nhv997s0iwf00d3jckkc4pp"; depends=[]; }; @@ -9687,7 +9763,7 @@ in with self; { nprobust = derive2 { name="nprobust"; version="0.1.3"; sha256="1zr89myhamcxzk7j04rxcc4mbi86pf09kl70p8niklm0b3wmsjzj"; depends=[ggplot2 Rcpp RcppArmadillo]; }; nproc = derive2 { name="nproc"; version="2.1.4"; sha256="1gj38yppip0ygxcgp0x9ba9kpr12ahmz2k0956x3h7py2rl8b098"; depends=[ada e1071 glmnet MASS naivebayes randomForest ROCR tree]; }; nprotreg = derive2 { name="nprotreg"; version="1.0.0"; sha256="06n82i5m7sgfj759zdwwh8fqybkbchvnaaqcds64m6hbms592bh3"; depends=[expm]; }; - npsf = derive2 { name="npsf"; version="0.4.1"; sha256="0vl02ysfmbxfzzbrjhiz8j129waz9cnpmds978fmv08l6wsjr3mi"; depends=[Formula Rcpp]; }; + npsf = derive2 { name="npsf"; version="0.4.2"; sha256="1j6mnip3qa1fgvr9smprz2fmmhmcm17vk85y56lf2xjljhpd0wrm"; depends=[Formula Rcpp]; }; npsm = derive2 { name="npsm"; version="0.5"; sha256="12jq6ygp3di5rknh7izrr3bxvpn6bqnj3jhfxzf29yf0bd86hzqk"; depends=[plyr Rfit]; }; npsp = derive2 { name="npsp"; version="0.5-3"; sha256="0ck6iymfc73bzrifdc2sagcliz1yakqk1yv67a3ykha996jsrx99"; depends=[quadprog]; }; npsr = derive2 { name="npsr"; version="0.1.1"; sha256="1fzvilzjg9z05991sr1s1bdp17kfl6d1580qdllk8is9ac06np0v"; depends=[gmp infotheo MASS]; }; @@ -9743,9 +9819,10 @@ in with self; { occ = derive2 { name="occ"; version="1.1"; sha256="1aka29qqwbd494kvi15yyyqkb9hks4ky2gcvykxhx2drm2fnsn4g"; depends=[]; }; oce = derive2 { name="oce"; version="1.0-1"; sha256="0wn49xp7zvfipxvx0jdbqqldinbq0ccsqipljsidc3gzhf7jh67p"; depends=[gsw Rcpp testthat]; }; oceanmap = derive2 { name="oceanmap"; version="0.1.0"; sha256="1kkjc213nn2ks7cqzchbmjvyp9hci8qndv8migpmyf5vjbm7d297"; depends=[abind extrafont fields lubridate mapdata maps maptools ncdf4 plotrix raster sp]; }; - ocedata = derive2 { name="ocedata"; version="0.1.3"; sha256="0lzsyaz8zb6kiw86fnaav2g2wfdhyicxvm81ly5a9z4mjch3qj02"; depends=[]; }; + ocedata = derive2 { name="ocedata"; version="0.1.5"; sha256="0rs3nzacvg5mbbmbhcj8g9ikjlw26x2mka7lp644l17kgmzzynh6"; depends=[testthat]; }; ockc = derive2 { name="ockc"; version="1.0"; sha256="0chzrs3ipa2518r4d35z4fxffgq12p1mwj0hzkxw19gdgq6aa8s7"; depends=[flexclust modeltools]; }; ocomposition = derive2 { name="ocomposition"; version="1.1"; sha256="0fk8ia95yjlvyvmjw7qg72piqa40kcqq9wlb3flc6a81pys1ycb5"; depends=[bayesm coda]; }; + ocp = derive2 { name="ocp"; version="0.1.0"; sha256="0glcnrk0mpff5rp9q6hn0j8vly1gls728irj2pxfizas1wmdc5q2"; depends=[]; }; odbc = derive2 { name="odbc"; version="1.1.6"; sha256="146phrsks0hfd1bfxx452kkq7ximk3fwjz9lqg9fdykar5sr6vjj"; depends=[BH bit64 blob DBI hms Rcpp]; }; odds_converter = derive2 { name="odds.converter"; version="1.4.8"; sha256="09s8pg55gpsxmrbimzg5rsr1n07la93781sar6vab5p9zn9zxgx4"; depends=[]; }; oddsratio = derive2 { name="oddsratio"; version="1.0.3"; sha256="1kdqnai8hbhxg9gjn9j7zgm8mw4bd765jkdrwrk9q65fpvc62f5k"; depends=[cowplot ggplot2 MASS mgcv]; }; @@ -9795,7 +9872,6 @@ in with self; { opencpu = derive2 { name="opencpu"; version="2.1"; sha256="1w4lqvzn05v3qkxzd22mcsmkk5n1472yc58vyvlfg6vxml0nykry"; depends=[brew curl evaluate httpuv jsonlite knitr mime openssl protolite rappdirs remotes sendmailR sys webutils zip]; }; opendotaR = derive2 { name="opendotaR"; version="0.1.4"; sha256="17cygsw3nkg6zincfrcdh1509rlz3n5zrv9wvv7mjngm61sn79nf"; depends=[dplyr jsonlite lubridate]; }; openintro = derive2 { name="openintro"; version="1.7.1"; sha256="059azlasdkmp8f54qpjf3mq5dyqakw0dgx0kx85wfdmhq38zal5n"; depends=[]; }; - opensensmapr = derive2 { name="opensensmapr"; version="0.5.0"; sha256="0bv03p2fprgkqg2vm6ydqi5wjswkjlxwwmkk3r6lq2m4xq909d4r"; depends=[digest dplyr httr lazyeval magrittr purrr readr]; }; openssl = derive2 { name="openssl"; version="1.1"; sha256="0ldxgcr33lawwr8wp14kdk2678gpkvqkzv6g333bhck1hn6qspzv"; depends=[]; }; opentraj = derive2 { name="opentraj"; version="1.0"; sha256="13nqal96199l8vkgmkvl542ksnappkscb6rbdmdapxyi977qrgxk"; depends=[doParallel foreach maptools openair plyr raster reshape rgdal sp]; }; openxlsx = derive2 { name="openxlsx"; version="4.1.0"; sha256="1n7z22pm78xa77fvn77kdn68az6xzxk36y11sqf0w6h6adri4yxb"; depends=[Rcpp zip]; }; @@ -9882,10 +9958,10 @@ in with self; { osd = derive2 { name="osd"; version="0.1"; sha256="1py9p15nrcydr8w9ilxkxabiz9zlqnls8xn9avjkxd8x6602jx6p"; depends=[JADE nnls]; }; oshka = derive2 { name="oshka"; version="0.1.2"; sha256="02hglpq5lknq93zbcf219lhnhppzgygkhxqixb15f89rxf9fczgs"; depends=[]; }; osmar = derive2 { name="osmar"; version="1.1-7"; sha256="0q6d8nw7d580bnx66mjc282dx45zw9srczz90b520hjcli4w3i3r"; depends=[geosphere RCurl XML]; }; - osmdata = derive2 { name="osmdata"; version="0.0.8"; sha256="0hhfnraxjj54z5p3lnpvklhpmdhihs9lgfb9dm3s9h7kjcknf6x3"; depends=[curl httr jsonlite lubridate magrittr Rcpp rvest sp xml2]; }; + osmdata = derive2 { name="osmdata"; version="0.0.9"; sha256="1zksgh9pm78454j7hlip6a4xq371izv33v5lygw0bdapd1kxsnwc"; depends=[curl httr jsonlite lubridate magrittr Rcpp rvest sp tibble xml2]; }; osmose = derive2 { name="osmose"; version="0.1.1"; sha256="0fiijnrvvydhj6j9yb02rn5sg8arcpj3jz977m2zwjgqy878cffg"; depends=[rlist stringr]; }; - osmplotr = derive2 { name="osmplotr"; version="0.3.0"; sha256="0w45riwwjigh1bxf9gx0wdj2yhdizwi6ydprp83pss2z9wph66yb"; depends=[curl e1071 ggm ggplot2 httr osmdata rgeos sp spatstat]; }; - osqp = derive2 { name="osqp"; version="0.4.1"; sha256="0v1sg914l1xz2f2crgwy2pp9k72ak2k1qmqix20j2akqmlvr39p2"; depends=[Matrix R6 Rcpp]; }; + osmplotr = derive2 { name="osmplotr"; version="0.3.2"; sha256="0k5rjxsi1sfcxcl6lf8zcncqnshz2jaz7hcwn2ifg4yhvxvkfma8"; depends=[curl e1071 ggm ggplot2 httr mapproj osmdata rgeos sp spatstat]; }; + osqp = derive2 { name="osqp"; version="0.5.0"; sha256="12gm5mhmnzvfmziiln0lnqs173gan10ihwkcj07dcjii4nvkg4p9"; depends=[Matrix R6 Rcpp]; }; osrm = derive2 { name="osrm"; version="3.1.1"; sha256="14rf5m2pm5w414v2l1dvd6vlvirms93l8rkfbmgcvxwxmc52b187"; depends=[gepaf jsonlite raster RCurl rgeos sp]; }; osrmr = derive2 { name="osrmr"; version="0.1.29"; sha256="1mkc39v56m7b89nbjzs50kzz8w1i1950gciiw7iyqpdj6g2knwdx"; depends=[assertthat bitops R_utils rjson stringr]; }; otinference = derive2 { name="otinference"; version="0.1.0"; sha256="1l75jjnkyk8yzaw9zyk45jq9ys304i6pzm2xd5apxrb1jk75a3li"; depends=[MASS Rglpk sm transport]; }; @@ -9900,7 +9976,7 @@ in with self; { outliers = derive2 { name="outliers"; version="0.14"; sha256="0vcqfqmmv4yblyp3s6bd25r49pxb7hjzipiic5a82924nqfqzkmn"; depends=[]; }; outreg = derive2 { name="outreg"; version="0.2.2"; sha256="04f1x7mxq4swbd7bfwjjgx4838jm6qj4piaighmhcscwrdkxa1cp"; depends=[magrittr reshape2 sandwich stringr tidyr]; }; overlap = derive2 { name="overlap"; version="0.3.2"; sha256="1j3m6ir1chdz0si2fhcw6gs7c9h09bv0chz18rpzxsywww6d4rzy"; depends=[]; }; - overlapping = derive2 { name="overlapping"; version="1.5.1"; sha256="1any3f910c0aj4h19iam2qmzds6hfq619bdx1q5vhycmz9xragib"; depends=[ggplot2 testthat]; }; + overlapping = derive2 { name="overlapping"; version="1.5.2"; sha256="1scdbs9xz9xbnavg4by5zcbxrd9ckhn9dv35szr8phx10604a60n"; depends=[ggplot2 testthat]; }; overlapptest = derive2 { name="overlapptest"; version="1.0"; sha256="1p5xbqbl1kpvx7rjb335k7hfc8i9b13p2r2rr6rrjfa8zs74smml"; depends=[spatstat]; }; owmr = derive2 { name="owmr"; version="0.8.1"; sha256="11krzrkr1ga41nv9c2fb8cb2mgy3ias7qx85d4cdv4k68lsksv18"; depends=[httr jsonlite magrittr plyr tibble tidyr]; }; ows4R = derive2 { name="ows4R"; version="0.1-0"; sha256="1a27h63spy46ms7fgh2vl659znp5g55d1hsk6py6lgfa6hc2f1dx"; depends=[geometa httr openssl R6 rgdal sf XML]; }; @@ -9938,6 +10014,7 @@ in with self; { padr = derive2 { name="padr"; version="0.4.1"; sha256="0nxclaxg31hddl2yhhm5886g7fc4j7g294ibv6hxb1cm5mrfgngy"; depends=[dplyr lubridate Rcpp rlang]; }; paf = derive2 { name="paf"; version="1.0"; sha256="0wrqn67jfrjjxwcrkka6dljgi3mdk00vfjkzzcv2v7c97gx1zvwn"; depends=[survival]; }; pafdR = derive2 { name="pafdR"; version="1.0"; sha256="1yimsd4h23hcf752p5flda3dqk8hgn6qm9k0pmbapxj4jbsw14w5"; depends=[curl exams stringr]; }; + pagedown = derive2 { name="pagedown"; version="0.1"; sha256="117xy9nq2cymmdh34f7i3x9vpgj2jxa6fvbrzdilyk3pawjkgaxv"; depends=[bookdown htmltools rmarkdown xfun]; }; pagenum = derive2 { name="pagenum"; version="1.1"; sha256="0908rlr9sd1a2qwz0idw8ccxhji73sk24gyrdl071lpnd1rs2wl7"; depends=[]; }; pageviews = derive2 { name="pageviews"; version="0.3.0"; sha256="031y67nqqvf3fa2273m7z2cldda0ijh63qwkh4gis3hz9hfril0v"; depends=[curl httr jsonlite]; }; painter = derive2 { name="painter"; version="0.1.0"; sha256="0qr6p13h50rlavcsamxmijfr4dfrbv1k088m28qf8a4gam3ap85b"; depends=[]; }; @@ -9964,7 +10041,7 @@ in with self; { pals = derive2 { name="pals"; version="1.5"; sha256="0zc4dw8ipvhdm2qvy71k16vf8fmjs08nqbvvdi1k8h4fs648ddhi"; depends=[colorspace dichromat mapproj maps rgl]; }; pamctdp = derive2 { name="pamctdp"; version="0.3.2"; sha256="0qs8lj5g2fx5rfd0afv76x9x7wqm333qmjv6zzip6pf11dzkghyj"; depends=[ade4 FactoClass xtable]; }; pamm = derive2 { name="pamm"; version="0.9"; sha256="01dv70ca3zif2b2fkx4xjl24x9p9kc63wf0dj5agdjp5qgbkp1p5"; depends=[gmodels lattice lme4 lmerTest mvtnorm]; }; - pammtools = derive2 { name="pammtools"; version="0.1.7"; sha256="145s29gv3f0y9lp3pma2bbpfwq5rhamz79spcbg193l1m7q7ch55"; depends=[checkmate dplyr Formula ggplot2 lazyeval magrittr mgcv msm mvtnorm purrr rlang survival tibble tidyr]; }; + pammtools = derive2 { name="pammtools"; version="0.1.8"; sha256="1lh8z956wayl2hkvpvwqnm156zw7bqph0hpafgm5wz5xcwaqrgj0"; depends=[checkmate dplyr Formula ggplot2 lazyeval magrittr mgcv msm mvtnorm purrr rlang survival tibble tidyr]; }; pampe = derive2 { name="pampe"; version="1.1.2"; sha256="092n04nrp886kd163v32f5vhp9r7gnayxzqb6pj57ilm5w1yrcsk"; depends=[leaps]; }; pamr = derive2 { name="pamr"; version="1.55"; sha256="1hy3khb0gikdr3vpjz0s245m5zang1vq8k93g7n9fq3sjfa034gd"; depends=[cluster survival]; }; pan = derive2 { name="pan"; version="1.6"; sha256="1dk3jjj826p7xrz10qz04vyc068xnypg7bp0pj4c32z3da0xzh5d"; depends=[]; }; @@ -9979,7 +10056,7 @@ in with self; { papeR = derive2 { name="papeR"; version="1.0-3"; sha256="0c3zziy32wnpvnv7d3kh1gs24pmy9ap2hq0l3ss2h79s5vmc76xi"; depends=[car gmodels xtable]; }; paperplanes = derive2 { name="paperplanes"; version="0.0.1.9"; sha256="1d9grc95xqxn91lvk8v7w3z90bhl8savkhihwshyjp8ij2xpzfkl"; depends=[]; }; parSim = derive2 { name="parSim"; version="0.1"; sha256="15d3k91mvbv2hmq0l1jfr0hsv2zkz3cr6axg85kf9bd9q79b85qp"; depends=[dplyr]; }; - parallelDist = derive2 { name="parallelDist"; version="0.2.2"; sha256="0h7bf2mlfpydqr3msirg07wn041fqlcdha9m8rybix1x3vi778qc"; depends=[Rcpp RcppArmadillo RcppParallel]; }; + parallelDist = derive2 { name="parallelDist"; version="0.2.4"; sha256="0gqf9vi9hlbflxj941jv7hli8jiy2sqg8b312h401f8rkfqa9ckv"; depends=[Rcpp RcppArmadillo RcppParallel]; }; parallelMCMCcombine = derive2 { name="parallelMCMCcombine"; version="1.0"; sha256="05krkd643awqhfrylq9lxr2cmgvnm1msn2x8p1l1483n2gzyklz7"; depends=[mvtnorm]; }; parallelML = derive2 { name="parallelML"; version="1.2"; sha256="05j0rb81i8342m8drwgmgi1w30q96yf501d83cdq4zhjbchphbl1"; depends=[doParallel foreach]; }; parallelMap = derive2 { name="parallelMap"; version="1.3"; sha256="026d018fr2a43cbh8bi2dklzr9fxjzdw5qyq84g2i18v5ibr6bd5"; depends=[BBmisc checkmate]; }; @@ -10044,7 +10121,7 @@ in with self; { pbatR = derive2 { name="pbatR"; version="2.2-13"; sha256="01ra1ggdpxdl1xqjdh86qynr5gkgzw01ww6j9bwgx4mj20i6j1ha"; depends=[rootSolve survival]; }; pbdBASE = derive2 { name="pbdBASE"; version="0.5-0"; sha256="11jlfr0pswldd5h06swfrc8bm785dv09iqgg3kfnc53yvrs0d7qv"; depends=[pbdMPI pbdSLAP]; }; pbdDEMO = derive2 { name="pbdDEMO"; version="0.3-1"; sha256="0vr3dvvhr8j6xvdf308nn37y0lkl2ysm93yf0h7rclvqvsk1pf66"; depends=[pbdBASE pbdDMAT pbdMPI]; }; - pbdDMAT = derive2 { name="pbdDMAT"; version="0.4-2"; sha256="1xiwfpi8r0l8jlfrc35aknm09y4qbn0hvvkscdpcxv9q7zifvl3v"; depends=[pbdBASE pbdMPI]; }; + pbdDMAT = derive2 { name="pbdDMAT"; version="0.5-0"; sha256="1wpl0incn6w6pz9ryfz7cldid2mw2rgn7xi3112iz5c2g5yjnv8z"; depends=[pbdBASE pbdMPI]; }; pbdMPI = derive2 { name="pbdMPI"; version="0.3-8"; sha256="0yxzldgvjzzw4adsdv6sh3m3n6xlwfh2rmzn6pgppk8s1brbbjli"; depends=[rlecuyer]; }; pbdNCDF4 = derive2 { name="pbdNCDF4"; version="0.1-4"; sha256="0fd29mnbns30ck09kkh53dgj24ddrqzks4xrrk2hh1wiy7ap1h95"; depends=[]; }; pbdPROF = derive2 { name="pbdPROF"; version="0.3-1"; sha256="0a7c31605si062vbwcwngv770axlwyhh00cvdfqw3hv421p61sj8"; depends=[]; }; @@ -10073,6 +10150,7 @@ in with self; { pcg = derive2 { name="pcg"; version="1.1"; sha256="194j72hcp7ywq1q3dd493pwkn1fmdg647gmhxcd1jm6xgijhvv87"; depends=[]; }; pcgen = derive2 { name="pcgen"; version="0.1.0.0"; sha256="151dhk1wnc5byrbvx2322bwy047ing3a9zw1q977w347r90h7arr"; depends=[ggm graph Hmisc lme4 MASS Matrix pcalg sommer]; }; pch = derive2 { name="pch"; version="1.3"; sha256="13pfrvp539fz4hxp08yil93caw3cjdna7xnky5fqd0lhc84fwq76"; depends=[survival]; }; + pcmabc = derive2 { name="pcmabc"; version="1.0"; sha256="02qh8718786abw8pcxc6ry0a447vqd8rviaka79g5cbi51klgp28"; depends=[ape distory geiger mvSLOUCH phangorn TreeSim treespace yuima]; }; pcnetmeta = derive2 { name="pcnetmeta"; version="2.6"; sha256="0rpd1bgg932xhj03fnskhbg7ni9nfd8qrvxvix8qmbgw8bwdsbgd"; depends=[coda rjags]; }; pco = derive2 { name="pco"; version="1.0.1"; sha256="0k1m450wfmlym976g7p9g8arqrvnsxgdpcazk5kh3m3jsrvrcchf"; depends=[]; }; pcr = derive2 { name="pcr"; version="1.1.2"; sha256="0sms024irkhqyb001lcicrm3dwnnyr2kw9kx10q3v9j6p7rxzhz2"; depends=[devtools dplyr ggplot2 magrittr purrr readr tidyr]; }; @@ -10087,7 +10165,7 @@ in with self; { pdfetch = derive2 { name="pdfetch"; version="0.2.3"; sha256="1fcjhq79dcbnghmkfpy1h29gcywr1hq91xij5f21wgp4xx465sha"; depends=[curl httr jsonlite lubridate readr reshape2 XML xml2 xts zoo]; }; pdfsearch = derive2 { name="pdfsearch"; version="0.2.3"; sha256="1x6ymj6fk7bf2jx1lqryyzksg049ijdvb9syz244y43i7632ls59"; depends=[pdftools tibble tokenizers]; }; pdftables = derive2 { name="pdftables"; version="0.1"; sha256="1gnwjijr89cczchc7yi4w5xiw0dalbymvj23rymm8cfra34iwn5p"; depends=[httr]; }; - pdftools = derive2 { name="pdftools"; version="1.8"; sha256="1yyhwr17bln59cr819igd7mxdy5mhqf5fwd68x8w3kgag0v0qyaz"; depends=[Rcpp]; }; + pdftools = derive2 { name="pdftools"; version="2.0"; sha256="18hav7ia8fbh41s7cpapgx9macl5739k2vyfiwp9w7ay8fdp7saq"; depends=[Rcpp]; }; pdist = derive2 { name="pdist"; version="1.2"; sha256="18nd3mgad11f2zmwcp0w3sxlch4a9y6wp8dfdyzvjn7y4b4bq0dd"; depends=[]; }; pdmod = derive2 { name="pdmod"; version="1.0.1"; sha256="04bk9gjg2c55hk6k1hy0m29927s8a5ig6mr4xb89npam68g0pcms"; depends=[mco]; }; pdp = derive2 { name="pdp"; version="0.7.0"; sha256="0wcszaq4c14f9a2r1gd32mzhs035jlg2w8mkfklzigcj7fv9xmi8"; depends=[ggplot2 gridExtra lattice magrittr mgcv plyr viridis]; }; @@ -10154,7 +10232,7 @@ in with self; { pgee_mixed = derive2 { name="pgee.mixed"; version="0.1.0"; sha256="115vvpv54q80486i3xs2yhmfyx476cf4g1v43q6l7wj3jwzcrvbg"; depends=[copula mvtnorm Rcpp RcppArmadillo]; }; pgirmess = derive2 { name="pgirmess"; version="1.6.9"; sha256="1i1qn68isaz2lbpqyydjgj9kri09aknza5qjn6m1wa1alyl7f611"; depends=[boot maptools rgdal rgeos sp spdep splancs]; }; pglm = derive2 { name="pglm"; version="0.2-1"; sha256="14hnlidf62kzcf83jc7k17n4hjjaj82scdwh8a7qxd056vygkqx2"; depends=[maxLik plm statmod]; }; - pgmm = derive2 { name="pgmm"; version="1.2.2"; sha256="1z39148gvs5nndd54x2afpsqdyqd8apjgnxn0ndv2071aa8gyk1j"; depends=[]; }; + pgmm = derive2 { name="pgmm"; version="1.2.3"; sha256="0bzjhq8552v1pdbxkq4409vavim3hy9hb7dk7sch66ykj5cys3s5"; depends=[]; }; pgnorm = derive2 { name="pgnorm"; version="2.0"; sha256="1k9z7pvmranr8m62v7amc0pj6lwzh3wqi79gg3mflifn1mr6c057"; depends=[]; }; pgraph = derive2 { name="pgraph"; version="0.8"; sha256="1r784snci5m81qljfh1r3w8qzszmy0476zvsd1alh43afzg9zpr5"; depends=[energy glasso glmnet SAM]; }; pgsc = derive2 { name="pgsc"; version="1.0.0"; sha256="1y4szqn1jhp3yn8q738dpbhnqcqk45vgbmczamai154w3wb0qai7"; depends=[nloptr Rcpp RcppArmadillo reshape2]; }; @@ -10187,9 +10265,9 @@ in with self; { phonTools = derive2 { name="phonTools"; version="0.2-2.1"; sha256="01i481mhswsys3gpasw9gn6nxkfmi7bz46g5c84m13pg0cv8hxc7"; depends=[]; }; phonenumber = derive2 { name="phonenumber"; version="0.2.2"; sha256="1m5idp538lvynmfp8m7l89js6hk5lpp26k419bdvj3hd3ap0n9lg"; depends=[]; }; phonics = derive2 { name="phonics"; version="1.1.0"; sha256="02h26dlhw0hisr2ifa1rkrzw0350pk32mrba7h1rwsh41vxv9sji"; depends=[BH Rcpp]; }; - photobiology = derive2 { name="photobiology"; version="0.9.24"; sha256="10z9bplknis5zp6m5ayggr7pilv0pkbgyl2hs4qfmddby7cfmbsj"; depends=[dplyr lubridate plyr polynom rlang splus2R tibble zoo]; }; + photobiology = derive2 { name="photobiology"; version="0.9.25"; sha256="15jqva860bg7s12v142l2m06l1fymc0lpd2viqyifm818kjis8r5"; depends=[dplyr lubridate plyr polynom rlang splus2R tibble zoo]; }; photobiologyFilters = derive2 { name="photobiologyFilters"; version="0.4.4"; sha256="14aiw5jxd6wnngy1rbbm85l0yx64nxrancal017wvr5n867c32d6"; depends=[photobiology]; }; - photobiologyInOut = derive2 { name="photobiologyInOut"; version="0.4.18"; sha256="049gfyrhzhy493yhw4nww78fky982k683dlvgk99ya8hlkmwx935"; depends=[colorSpec dplyr hyperSpec lazyeval lubridate photobiology readr readxl stringr tibble tidyr]; }; + photobiologyInOut = derive2 { name="photobiologyInOut"; version="0.4.19"; sha256="0qdd3s33hbschjwjj69j4ya0sjf4myibk8s0rjh7n48vyrxg50zf"; depends=[colorSpec dplyr hyperSpec lazyeval lubridate photobiology readr readxl stringr tibble tidyr]; }; photobiologyLEDs = derive2 { name="photobiologyLEDs"; version="0.4.3-1"; sha256="0inhl6ba1fzkak4752m60hkm6fzapzyz5kchvz18yv33dmm13v1c"; depends=[photobiology]; }; photobiologyLamps = derive2 { name="photobiologyLamps"; version="0.4.2"; sha256="0fcin04xc2k39qdipslqd3w3bsd8yl3xlvg7mlgm3aphfwg4hnmj"; depends=[photobiology]; }; photobiologyPlants = derive2 { name="photobiologyPlants"; version="0.4.1"; sha256="0mpb5sv4wkvqzbhf193zkhap44yzlhxrnjx1p3j9iyjdg4bb1kka"; depends=[photobiology photobiologyWavebands]; }; @@ -10200,7 +10278,7 @@ in with self; { phreeqc = derive2 { name="phreeqc"; version="3.4.9"; sha256="0g3xlpwzb6vxz129kh7krf2lbhx6bgwmyjxk09mrzxzh3r5lqd9y"; depends=[]; }; phtt = derive2 { name="phtt"; version="3.1.2"; sha256="1fvvx5jilq5dlgh3qlfsjxr8jizy4k34a1g3lknfkmvn713ycp7v"; depends=[pspline]; }; phuassess = derive2 { name="phuassess"; version="1.1"; sha256="0jplj9gih32dllx2hw5aqvc9b94sbrbv66s3a5r8mdbpjh93rhng"; depends=[]; }; - phuse = derive2 { name="phuse"; version="0.1.6"; sha256="1abfpnf5z88gg0cylfh7j4226yniw3sgx08asrr7xxq6ri0yxl4w"; depends=[git2r httr RCurl rlist shiny yaml]; }; + phuse = derive2 { name="phuse"; version="0.1.7"; sha256="1khrz6jag3d0himbqxylxpx7iyx8nbk3r23q6257a4fy55wakavd"; depends=[git2r httr RCurl rlist shiny stringr yaml]; }; phybreak = derive2 { name="phybreak"; version="0.2.0"; sha256="0vapc0w308wv1cd72p2xbj3q7jfnxwp08g5g8855a38pcn3njbfg"; depends=[ape phangorn Rcpp stringr]; }; phyclust = derive2 { name="phyclust"; version="0.1-22"; sha256="0c3w1vafhcshnh5lkb6bykk6w7w91qigz3sf215zqmrra1acri0d"; depends=[ape]; }; phyext2 = derive2 { name="phyext2"; version="0.0.4"; sha256="0j871kgqm9fll0vdgh071z77ib51y8pxxm0ssjszljvvpx1mb8rb"; depends=[ape phylobase]; }; @@ -10215,7 +10293,7 @@ in with self; { phyloland = derive2 { name="phyloland"; version="1.3"; sha256="10g40m6n2s4qvnzlqcwpy3k0j7bxdp79f586jj910b8p00ymrksp"; depends=[ape]; }; phylolm = derive2 { name="phylolm"; version="2.6"; sha256="0vah8ibicldi57wab4sk1kx7gdq6h34bm6swmxzhq7kikxfwmmyj"; depends=[ape future_apply]; }; phylometrics = derive2 { name="phylometrics"; version="0.0.1"; sha256="1pmr6l3wmaf91wdlsc5m63l07fibngnly2qzkma0rdi463ii03il"; depends=[mvtnorm]; }; - phylopath = derive2 { name="phylopath"; version="1.0.1"; sha256="135b0zhspjns8jdb2y5ajhziyglkr9f5x1618i71dr5848mfkpha"; depends=[ape dplyr ggm ggplot2 ggraph igraph MuMIn pbapply phylolm purrr tibble tidyr]; }; + phylopath = derive2 { name="phylopath"; version="1.0.2"; sha256="0ngfqi3fx646r5szbzbsh5g7zkrs29swpx7csr3nwzj8n12bqbfp"; depends=[ape dplyr ggm ggplot2 ggraph igraph MuMIn pbapply phylolm purrr tibble tidyr]; }; phyloseqGraphTest = derive2 { name="phyloseqGraphTest"; version="0.0.2"; sha256="1xgv2kf7j3ia5vk10r7w9588rfv7asdaf8f3yxwp5q7aqn3krm6q"; depends=[ggnetwork ggplot2 igraph intergraph phyloseq]; }; phylosignal = derive2 { name="phylosignal"; version="1.2"; sha256="0apsg4v1n58wn8y8wnl6x1ahl903i29hh8bs2dw6ky2jafkjj4jb"; depends=[adephylo ape boot DBI igraph phylobase Rcpp RcppArmadillo]; }; phylosim = derive2 { name="phylosim"; version="3.0.2"; sha256="148zm43cgdhr264ffcabjx4abykks07jix6lypqysqy25fbmdngk"; depends=[ape compoisson ggplot2 R_methodsS3 R_oo]; }; @@ -10232,7 +10310,7 @@ in with self; { piecewiseSEM = derive2 { name="piecewiseSEM"; version="2.0.2"; sha256="07vz90cghkbmcar9ps94wydvg4r7mj32pa7vjdmgm5j8dhxq8max"; depends=[car lme4 MASS nlme pbkrtest]; }; pifpaf = derive2 { name="pifpaf"; version="1.0.1"; sha256="0wj1fbhd871fnw7fjlbh0gdjz848mbwl1bzjp3cgmh9s7jnd2kci"; depends=[ggplot2 gridExtra MASS matrixcalc numDeriv sfsmisc]; }; piggyback = derive2 { name="piggyback"; version="0.0.8"; sha256="1c17yjqpaj6r6spbhm901dilqpsa2s9jc029vdfmrxdk18fzaf1f"; depends=[clisymbols crayon fs gh git2r httr jsonlite lubridate magrittr memoise usethis]; }; - pillar = derive2 { name="pillar"; version="1.3.0"; sha256="1q6arybmfqxhp5zqj1fri5pb8v7ywcv7bmgf81rrmgl892p4bn5f"; depends=[cli crayon fansi rlang utf8]; }; + pillar = derive2 { name="pillar"; version="1.3.1"; sha256="1xnbb9sr5wn9dmp6m7cr4z7i6pmjvyabnfcx6x7i7mvdjmgvaf5k"; depends=[cli crayon fansi rlang utf8]; }; pim = derive2 { name="pim"; version="2.0.1"; sha256="1m804clxc8m4nyzi4hhfy118527lgf2sb7589qd61fb83yh6hi8p"; depends=[BB nleqslv]; }; pimeta = derive2 { name="pimeta"; version="1.1.1"; sha256="0ylna31x8491q6hppz827ngri0did0bfwy3nlifpagccb2m4psi3"; depends=[Rcpp RcppEigen]; }; pinbasic = derive2 { name="pinbasic"; version="1.2.2"; sha256="0mcw68wrixz2jf62nfifdgg8bnp4h1p3byivz28wi61blj8iaa75"; depends=[fastcluster ggplot2 lubridate Rcpp reshape2 scales]; }; @@ -10242,7 +10320,7 @@ in with self; { pinnacle_API = derive2 { name="pinnacle.API"; version="2.3.3"; sha256="1b6adns1xr3cgcj2mdjvl16cm2vjjgsj2l8m2c47plyc5jh05qmb"; depends=[data_table httr jsonlite magrittr openssl purrr rjson uuid]; }; pinnacle_data = derive2 { name="pinnacle.data"; version="0.1.4"; sha256="1sl36i2857b3xwx7iwgy8mkgjvz7nfa74ch1n8kcxbj59ib7mp8p"; depends=[tibble]; }; pinp = derive2 { name="pinp"; version="0.0.6"; sha256="1424syaxq8p0ldqa0ybn0qyizs4r00xgkf6h5p7frhavy4rf8f2v"; depends=[knitr rmarkdown]; }; - pinyin = derive2 { name="pinyin"; version="1.1.4"; sha256="0qndd2mc95hbzkb0aqvmyhk2anwk7msd8xqy0rfiyrab94kxmgla"; depends=[data_table splitstackshape]; }; + pinyin = derive2 { name="pinyin"; version="1.1.5"; sha256="16y5imwkjq44qyk59ygqilsf6j8sviwj7i9mmwl5f6lxd10p9nyg"; depends=[data_table splitstackshape]; }; pipe_design = derive2 { name="pipe.design"; version="0.5.1"; sha256="0r0szkdzifxmnnbr6675w8ij4zwqgxj3gwahc7a74mxr51f7qh8j"; depends=[ggplot2 gtools xtable]; }; pipeGS = derive2 { name="pipeGS"; version="0.4"; sha256="0ki4i70r5f195b4jfv3hxlxz3zj57mhy2yf4984bwr11impilz5w"; depends=[]; }; pipeR = derive2 { name="pipeR"; version="0.6.1.3"; sha256="16lj227x24pviqb4dcrj7a55l31p5mm0cbwsb6m3y3n6k5wcd2nh"; depends=[]; }; @@ -10260,6 +10338,7 @@ in with self; { pixmap = derive2 { name="pixmap"; version="0.4-11"; sha256="04klxp6jndw1bp6z40v20fbmdmdpfca2g0czmmmgbkark9s1183g"; depends=[]; }; pkgKitten = derive2 { name="pkgKitten"; version="0.1.4"; sha256="0c44zrvpyz87s5mjhsqdrkyrvyzhyldnq371bwnn9crbpbac3wnd"; depends=[]; }; pkgbuild = derive2 { name="pkgbuild"; version="1.0.2"; sha256="1i1rrax7x7r2bplig5cfc50lx85jc4n9a3qmvbdviaj22wr2lghs"; depends=[callr cli crayon desc prettyunits R6 rprojroot withr]; }; + pkgcache = derive2 { name="pkgcache"; version="1.0.2"; sha256="142r63gbx1rpbqxxwamcyvyq6x68i7w7sdsnfw8k8dw4bqzvv2mg"; depends=[assertthat cli cliapp crayon curl digest filelock glue prettyunits R6 rappdirs rematch2 rlang tibble uuid withr]; }; pkgcond = derive2 { name="pkgcond"; version="0.1.0"; sha256="0pxj798042g23cf19r67nbgdyhpd868n2pkqjvjgrgr8ivwnkf1h"; depends=[]; }; pkgconfig = derive2 { name="pkgconfig"; version="2.0.2"; sha256="1jk9ip549xphb3anfixqv1yx5kidnndqgy9v3qjpmgmds5a7g695"; depends=[]; }; pkgcopier = derive2 { name="pkgcopier"; version="0.0.1"; sha256="04vpjf8nvqnpry54f1wwrnmipd5m6gqd89c3vkryqx88jk85jd8s"; depends=[httr stringr]; }; @@ -10289,6 +10368,7 @@ in with self; { plde = derive2 { name="plde"; version="0.1.2"; sha256="1g1b1sgyfxgfkjcr3sdkan8jd6r7yyi0izc83vyj11bdk08jx22h"; depends=[]; }; pleiades = derive2 { name="pleiades"; version="0.2.0"; sha256="1h3q4yf0w0al7n8l7ca4vgx2bhrrz8clli15svlds7n402s8rzp5"; depends=[crul DBI dbplyr dplyr gistr jsonlite rappdirs RSQLite]; }; pleio = derive2 { name="pleio"; version="1.6"; sha256="0av1sl0fdn2ia7ddalbvidhcnsvs36iq618s1bknjw29y5yyq020"; depends=[Matrix rms]; }; + plethem = derive2 { name="plethem"; version="0.1.7"; sha256="1ajcy3wwc23hd6n9jsvr9x82rnpnq5y8h588wgy1jfwydgrshn06"; depends=[data_table deSolve devtools dplyr DT formatR gdata ggplot2 httk magrittr miniUI plotly readxl reshape2 rhandsontable RSQLite rstudioapi shiny shinyBS shinydashboard shinyjs shinythemes shinyWidgets sqldf truncdist V8]; }; plfMA = derive2 { name="plfMA"; version="1.0.4"; sha256="0q6wiiknmgw812kcf9qq309zlizyry7ldn6m08lkw6xq6i4f4s85"; depends=[cairoDevice gWidgets gWidgetsRGtk2 limma RGtk2]; }; plfm = derive2 { name="plfm"; version="2.2.2"; sha256="1jgf3jrkdpsf77i4lf68s6sxax95c9is4nryhnzanq9i5f23j24v"; depends=[abind sfsmisc]; }; plgp = derive2 { name="plgp"; version="1.1-7"; sha256="02g6saabrsd8pra0szbwcbilf6w5ywg2gxqb5zdvbxds2vw36hn0"; depends=[mvtnorm tgp]; }; @@ -10301,6 +10381,7 @@ in with self; { plot_matrix = derive2 { name="plot.matrix"; version="1.0"; sha256="1p2xrmwghrl9lirnch5fqlrwiipga96ppbih0sg8939g4szxnbji"; depends=[]; }; plot3D = derive2 { name="plot3D"; version="1.1.1"; sha256="0chn70fqwyca8lbnjnpbcj08ni0dfbax2gjmzhk2c4w72c04mzpn"; depends=[misc3d]; }; plot3Drgl = derive2 { name="plot3Drgl"; version="1.0.1"; sha256="12p4qc9vmhr86ssx6xnz3cmx84q5jgd28bw9dp4wjrn04n6l4va6"; depends=[plot3D rgl]; }; + plotGMM = derive2 { name="plotGMM"; version="0.1.0"; sha256="0zrqpg7jpnk5p73jvnvfzrxgz6p5q14vafr6wb15zl34vc3826v5"; depends=[ggplot2 mixtools]; }; plotGoogleMaps = derive2 { name="plotGoogleMaps"; version="2.2"; sha256="0qv57k46ncg0wrgma0sbr3xf0j9j8cii3ppk3gs65ardghs3bf6b"; depends=[lattice maptools raster rgdal sp spacetime]; }; plotKML = derive2 { name="plotKML"; version="0.5-8"; sha256="0rd9242li967w253xhfywg72d3v1n5dybjxldkjgdix17gddwn5k"; depends=[aqp classInt colorRamps colorspace dismo gstat pixmap plotrix plyr raster RColorBrewer rgdal RSAGA scales sp spacetime stringr XML zoo]; }; plotMCMC = derive2 { name="plotMCMC"; version="2.0-0"; sha256="0i4kcx6cpqjd6i16w3i8s34siw44qigca2jbk98b9ligbi65qnqb"; depends=[coda gplots lattice]; }; @@ -10311,7 +10392,7 @@ in with self; { plotluck = derive2 { name="plotluck"; version="1.1.0"; sha256="0arbvldg50lyn98vkrys1yjkkraz8jracwal4r2mlw991pnaikpp"; depends=[ggplot2 hexbin Hmisc plyr quantreg RColorBrewer scales]; }; plotly = derive2 { name="plotly"; version="4.8.0"; sha256="19p8pa03q9mw5vaan7r56xgd13d90ssiz0flbrkvpfrir2105ybq"; depends=[base64enc crosstalk data_table digest dplyr ggplot2 hexbin htmltools htmlwidgets httr jsonlite lazyeval magrittr promises purrr RColorBrewer rlang scales tibble tidyr viridisLite]; }; plotlyGeoAssets = derive2 { name="plotlyGeoAssets"; version="0.0.1"; sha256="0if4cahihxm0b2k3r0w6qj91mwwsjy5zm289zk6myg65i7ijqly4"; depends=[]; }; - plotmo = derive2 { name="plotmo"; version="3.5.1"; sha256="0anrhci6l27k32c7gh1flwsnvdq062p2kcak0mr5dm7jaisl7a1a"; depends=[plotrix TeachingDemos]; }; + plotmo = derive2 { name="plotmo"; version="3.5.2"; sha256="1ihyn94mp61pbv9ncl2h5ihkq1fb6vhhcmjdzsncb9lz7hi1b7a6"; depends=[plotrix TeachingDemos]; }; plotpc = derive2 { name="plotpc"; version="1.0.4"; sha256="1sf7n7mfyaijldm24bc8r8pfm8pp9cyaja7am14z2wpj2j9f9vyq"; depends=[]; }; plotprotein = derive2 { name="plotprotein"; version="1.0"; sha256="14kfb4xxpfp8klz31kb7cpc39636ax2cx2483vqqkciccb28f0ks"; depends=[ade4 plotrix plyr seqinr XML]; }; plotrix = derive2 { name="plotrix"; version="3.7-4"; sha256="1hs0zwaqs34559girinvysjfbvznyn8znp9cwvkqx6k2cqvcjinj"; depends=[]; }; @@ -10395,7 +10476,8 @@ in with self; { polysat = derive2 { name="polysat"; version="1.7-3"; sha256="155zcrjvpnqdzakmxqds17wmn5kl4rrkv9bqlxq8hrrly3nf6ynz"; depends=[Rcpp]; }; polywog = derive2 { name="polywog"; version="0.4-1"; sha256="02qk1cyvkd77mwlvhj1zzzi0bmy7qxz29j2v730wp7rz4w7h5x5n"; depends=[foreach Formula glmnet iterators Matrix miscTools ncvreg Rcpp stringr]; }; pom = derive2 { name="pom"; version="1.1"; sha256="02jv19apn0kmp1ric2cxajlaad2fmsz4nm4izd2c3691vzas7l83"; depends=[matrixcalc]; }; - pomp = derive2 { name="pomp"; version="1.18"; sha256="0x77vx09ps4p1ihcd6yb4halr8jsq67d8zc04hp6vqkk0s7ycvyx"; depends=[coda deSolve digest mvtnorm nloptr subplex]; }; + pomdp = derive2 { name="pomdp"; version="0.9.0"; sha256="1g4q2m4n80jip81kkd7kp52sxr7vzqnbmx79j28rgiyv9zw6b8is"; depends=[igraph]; }; + pomp = derive2 { name="pomp"; version="1.19"; sha256="02pvbqpnpjr24q0zn5kkqma6ry9qjc6mxz51rwl2m3k8f1m5v9g0"; depends=[coda deSolve digest mvtnorm nloptr subplex]; }; pompom = derive2 { name="pompom"; version="0.2.0"; sha256="1alz3lrj7m16vhymsvvrcmf0kmgx88q2f3v4j6wiciqv77bnyai1"; depends=[ggplot2 lavaan qgraph reshape2]; }; pooh = derive2 { name="pooh"; version="0.3-2"; sha256="0qwa5j91aypasvsf4xcfbl6lz7llawdr38jiflzmfak2ad72rv7j"; depends=[]; }; pool = derive2 { name="pool"; version="0.1.4.1"; sha256="1a8kyfwylr8gl2z2w2fmf6657yqvw0ylf1pxg00flddf8fnwbh0w"; depends=[DBI dbplyr dplyr later R6]; }; @@ -10448,7 +10530,7 @@ in with self; { ppclust = derive2 { name="ppclust"; version="0.1.1"; sha256="10fcyayda634lg5g992g21casqx5k0jni9r30km5rczzib7cz9gg"; depends=[inaparc MASS]; }; ppcor = derive2 { name="ppcor"; version="1.1"; sha256="1x9b2kb8s0bp92b17gby0jwzzr3i4cf3ap9c4nq7m8fav72g0y3a"; depends=[MASS]; }; ppgmmga = derive2 { name="ppgmmga"; version="1.0.1"; sha256="16pvpfx353wjn317d3gxfgv6g20prnzwyqrmk0n4pz646mxq9i19"; depends=[cli crayon GA ggplot2 ggthemes mclust Rcpp RcppArmadillo]; }; - ppitables = derive2 { name="ppitables"; version="0.3.0"; sha256="0g92lsjbjvpsy3lgn8f0miwj1gi4ylfg19chzpwqbqq62h17sb3h"; depends=[tibble tidyr]; }; + ppitables = derive2 { name="ppitables"; version="0.4.0"; sha256="0hm1vgyjcr9wm0xjx39f940mawkdd8j75cbih3xmcs6qnblv16p9"; depends=[tibble tidyr]; }; ppls = derive2 { name="ppls"; version="1.6-1.1"; sha256="1zyrisy3c4cz896j1bjh61sf57wdl9p8ywdq268cl819szfq78mx"; depends=[MASS]; }; ppmlasso = derive2 { name="ppmlasso"; version="1.1"; sha256="1w13p1wjl1csds1xfc79m44rlym9id9gwnp3q0bzw05f35zbfryg"; depends=[spatstat]; }; pps = derive2 { name="pps"; version="0.94"; sha256="0sirxpagqc2ghc01zc6q4dk691six9wkgknfbwaqxbxvda3hcmyq"; depends=[]; }; @@ -10484,10 +10566,11 @@ in with self; { preprocomb = derive2 { name="preprocomb"; version="0.3.0"; sha256="08dhzil8prmjb6if0yba9pjncfxf5zzvlrrabva7c5jhny806c5g"; depends=[arules caret clustertend DMwR doParallel e1071 foreach randomForest zoo]; }; preprosim = derive2 { name="preprosim"; version="0.2.0"; sha256="1z10ranfal51vzsnndfaw5aqddh2w1xx8h50j1p7gx4fi90d0waq"; depends=[caret DMwR doParallel e1071 foreach ggplot2 reshape2]; }; preproviz = derive2 { name="preproviz"; version="0.2.0"; sha256="0jb85qkzywsd2iyfynd8ngkc136m4qc38phc3fgxm2qw30dacmyh"; depends=[caret ClustOfVar DMwR ggdendro ggplot2 gridExtra randomForest reshape2]; }; + preputils = derive2 { name="preputils"; version="1.0.2"; sha256="0cww3x7375ck56cm14ssalvpgvsdi4myr3p19zy4fcjy6fgyyxc5"; depends=[data_table]; }; prereg = derive2 { name="prereg"; version="0.3.0"; sha256="1lnpdwgri5rcwbwz9wh059rl6nrhlp5342gn9rnyp0gqwyni9hpd"; depends=[rmarkdown]; }; presens = derive2 { name="presens"; version="2.1.0"; sha256="175nr9pqn3m6kh9bcc1gxqmqv05xdsqdw9lx385lmm1g947d2159"; depends=[marelac measurements]; }; preseqR = derive2 { name="preseqR"; version="4.0.0"; sha256="1g2rnnmi45649vpy6z45v5i3wxm54s138ajqrzwi3a5r7x3xnhq1"; depends=[polynom]; }; - prettyGraphs = derive2 { name="prettyGraphs"; version="2.1.5"; sha256="19jag5cymancxy5lvkj5mkhdbxr37pciqj4vdvmxr82mvw3d75m4"; depends=[]; }; + prettyGraphs = derive2 { name="prettyGraphs"; version="2.1.6"; sha256="0yjpwxdy9mkj2k33zvd5klyv4ava46i19yls87n0bvf79y90ikpy"; depends=[]; }; prettyR = derive2 { name="prettyR"; version="2.2-2"; sha256="01p0g68c6k5hd4a80gmdsqd5sxy6n521ry5sh6iz06f0rbl3jlcf"; depends=[]; }; prettycode = derive2 { name="prettycode"; version="1.0.2"; sha256="0yz75qqpvrk4p9mypjnmrg1xwlrhh2iax2897f11cfk8rjj784jg"; depends=[crayon withr]; }; prettydoc = derive2 { name="prettydoc"; version="0.2.1"; sha256="00amqn0izg2jrn96pmm5papqmp0chn25msjk94nim3avqg9x4x92"; depends=[rmarkdown]; }; @@ -10499,7 +10582,7 @@ in with self; { prim = derive2 { name="prim"; version="1.0.16"; sha256="0i5jpk798qbvyv9adgjbzpg4dvf7x51bcgbdp38fzdnam6g88y5a"; depends=[misc3d rgl]; }; primefactr = derive2 { name="primefactr"; version="0.1.1"; sha256="11hi75jwjxrl9p5m8yjwjb20pc9y9vkhi8sjrnisdq2hm53m483w"; depends=[]; }; primer = derive2 { name="primer"; version="1.0"; sha256="0vkq794a9qmz9klgzz7xz35msnmhdaq3f91lcix762wlchz6v7sg"; depends=[deSolve lattice]; }; - primerTree = derive2 { name="primerTree"; version="1.0.3"; sha256="0k81h6ln9yjg3r4j8n5f8g8xlrq1pvrr5ywrw16s4mjjhx3r1ylg"; depends=[ape directlabels foreach ggplot2 gridExtra httr lubridate plyr scales stringr XML]; }; + primerTree = derive2 { name="primerTree"; version="1.0.4"; sha256="15am88swc9h8igjnjqr4jg105i91lsl28nncqly03cgy4vm814kk"; depends=[ape directlabels foreach ggplot2 gridExtra httr lubridate plyr reshape2 scales stringr XML]; }; primes = derive2 { name="primes"; version="0.1.0"; sha256="0hhkgpkadvai9xcivfalsvr5w0irsxygyz3p2zngwl3g5rvvh5g9"; depends=[Rcpp]; }; princurve = derive2 { name="princurve"; version="2.1.3"; sha256="12ngs63n6qjx08ks99h8m2nyr3h8ygznq5j8ag6ic8p65pis5pdp"; depends=[Rcpp]; }; prinsimp = derive2 { name="prinsimp"; version="0.8-8"; sha256="074a27ml0x0m23hlznv6qz6wvfqkv08qxh3v1sbkl9nxrc7ak4vn"; depends=[]; }; @@ -10513,6 +10596,7 @@ in with self; { proPubBills = derive2 { name="proPubBills"; version="0.1"; sha256="1fpn9x31jjahdyk0f30mbb3ijj4dsghrq9q94r04pjsgr2jw23zx"; depends=[dplyr httr stringr]; }; prob = derive2 { name="prob"; version="1.0-1"; sha256="05qcrsl790hn7p3ap4zj5i1b1sf674wvvrh42lyb7a0nsc09iq9n"; depends=[combinat fAsianOptions]; }; probFDA = derive2 { name="probFDA"; version="1.0.1"; sha256="093k50kyady54rkrz0n9x9z98z5ws36phlj42j25yip7pzhfd6sv"; depends=[MASS]; }; + probably = derive2 { name="probably"; version="0.0.1"; sha256="199z01cb95sh7v6lv09453jxxn2v9klhpqlqdhwa0am52glb17yx"; depends=[dplyr generics rlang tidyselect vctrs yardstick]; }; probemod = derive2 { name="probemod"; version="0.2.1"; sha256="1cgjr03amssc9rng8ky4w3abhhijj0d2byzm118dfdjzrgmnrf9g"; depends=[]; }; probout = derive2 { name="probout"; version="1.1.1"; sha256="1hasrvxdig8n3fhzsbmq27050dyanzp1j0qlybnrkb41k9gyljda"; depends=[FNN MASS mclust]; }; probsvm = derive2 { name="probsvm"; version="1.00"; sha256="1k0zysym7ncmjy9h7whwi49qsfkpxfk7chfdjrydl6hn6pscis37"; depends=[kernlab]; }; @@ -10545,6 +10629,7 @@ in with self; { proj4 = derive2 { name="proj4"; version="1.0-8"; sha256="06r3lavgixrsa52d1v31laqcbw6fb9xn23akv39hvaib78diglv9"; depends=[]; }; projections = derive2 { name="projections"; version="0.3.1"; sha256="12vskql6x04jzik72a0vx83amfj01w9f7mxn052vsv7aaljbi124"; depends=[distcrete ggplot2 incidence]; }; projector = derive2 { name="projector"; version="0.0.2"; sha256="15n5b2xgs0zj87pc3svlmnkjrxgkjkx941g8bs3ms90fg7nh2drc"; depends=[assertthat dbscan plotly RColorBrewer RcppAnnoy Rtsne shiny shinyjs shinythemes]; }; + projects = derive2 { name="projects"; version="0.1.0"; sha256="064l9dq3k56jiqf1p5yg7pmbz8kx95gpkdn7i2sqxghl3zpv1gsi"; depends=[checkmate dplyr fs magrittr purrr readr rlang rstudioapi stringr tibble]; }; projmanr = derive2 { name="projmanr"; version="0.2.1"; sha256="0pj2a79xnhkwik7lq1gm9jv30pkjgv057yd9nlmb58mf2097i7an"; depends=[ggplot2 igraph mc2d R6 Rcpp tidyr]; }; projpred = derive2 { name="projpred"; version="1.1.0"; sha256="03lfzlhrch7l87vmpfvyiggq12bzj45kkqp0dy307jnrvfzx9lb1"; depends=[ggplot2 loo Rcpp RcppArmadillo rngtools]; }; promises = derive2 { name="promises"; version="1.0.1"; sha256="0n2mlv6bvfb4yhgcml696l9vkbw21pz0smqylivr606z99rwgny2"; depends=[later magrittr R6 Rcpp rlang]; }; @@ -10553,7 +10638,7 @@ in with self; { propOverlap = derive2 { name="propOverlap"; version="1.0"; sha256="0q72z9vbkpll4i3wy3fq06rz97in2cm3jjnvl6p9w8qc44zjlcyl"; depends=[Biobase]; }; propagate = derive2 { name="propagate"; version="1.0-6"; sha256="17jinz1jramlsf87i7vyn2qp82rc1dacljfaxxplrk3crhw3bhs7"; depends=[ff MASS minpack_lm Rcpp tmvtnorm]; }; properties = derive2 { name="properties"; version="0.0-9"; sha256="1zd66cg31yd53rqsc0cwxhlpfn7kvc67qdh3vyj9qib8kwxaw1zl"; depends=[]; }; - prophet = derive2 { name="prophet"; version="0.3.0.1"; sha256="0ays7qn8vsa8kwzh5fk0b7nbd0l72yczjbg9h0ajkyywz3jda3fv"; depends=[dplyr dygraphs extraDistr ggplot2 Rcpp rstan scales tidyr xts]; }; + prophet = derive2 { name="prophet"; version="0.4"; sha256="03nk4gcli42qr3z5plhdk8b92qbr5bjpxwhhm9bmbbhkh4kwj96k"; depends=[dplyr dygraphs extraDistr ggplot2 Rcpp rlang rstan scales tidyr xts]; }; proportion = derive2 { name="proportion"; version="2.0.0"; sha256="0a71f6hz6blb7550m9x0di84vp51yjhnn952301rwlrh3axf6dbr"; depends=[ggplot2 TeachingDemos]; }; propr = derive2 { name="propr"; version="4.1.1"; sha256="06gydd4a6lra25lsvn3jljihjinsmqbyvin9yd9bm2j9vg863wdp"; depends=[fastcluster ggplot2 igraph Rcpp]; }; prospectr = derive2 { name="prospectr"; version="0.1.3"; sha256="18lh03xg6bgzsdsl56bjd63xdp16sqgr3s326sgifkkak8ffbv7q"; depends=[foreach iterators Rcpp RcppArmadillo]; }; @@ -10569,18 +10654,20 @@ in with self; { prototest = derive2 { name="prototest"; version="1.1"; sha256="0v65abrn73wgwnrrf6gv9f7p0qy12xlk9ishq9lq4qal1wlsrrjs"; depends=[glmnet intervals MASS Rcpp RcppArmadillo]; }; protr = derive2 { name="protr"; version="1.5-2"; sha256="0gy483nznrh9b3mw9vlkwfwm9zxfm6xy5gz0vzqvfr12wgb9bd67"; depends=[]; }; proustr = derive2 { name="proustr"; version="0.2.1"; sha256="17syaxfrwm9kh5q825hj7bsrvi4h9avpdabw9y0vq20y87w8cq1s"; depends=[assertthat dplyr magrittr purrr rlang SnowballC stringr tidyr tokenizers]; }; + provParseR = derive2 { name="provParseR"; version="0.1.1"; sha256="0wpwq589c2di8rqwynvj83061m30abi2j877wcq3gh8fz0fbxb9q"; depends=[jsonlite]; }; provenance = derive2 { name="provenance"; version="2.2"; sha256="1g70s5pwgb3cvw4vgxxqp4gi5qi3d02ldq09n4kildms4shxgsmn"; depends=[IsoplotR MASS]; }; proxy = derive2 { name="proxy"; version="0.4-22"; sha256="0l0ff8irmmvic941is290hd5vszyhaj5nfwna4v3w9c1zk5nr1ma"; depends=[]; }; + proxyC = derive2 { name="proxyC"; version="0.1.0"; sha256="0w1cnfd4g39arksx05pkd17csh2w9xmzk9aw2sk9pkv25fpgcib6"; depends=[Matrix Rcpp RcppArmadillo RcppParallel]; }; prozor = derive2 { name="prozor"; version="0.2.11"; sha256="1a2k69fvgi6vxgczk81kh8r2jxc6nirc51w6ac239rqjzb1zyhjm"; depends=[AhoCorasickTrie doParallel dplyr foreach Matrix plyr readr seqinr stringr]; }; prrd = derive2 { name="prrd"; version="0.0.2"; sha256="0ifs55yqvwbcs3xyc90yi763fgavdhajk1ba73g1kchn2ak39qhb"; depends=[config crayon data_table DBI liteq RSQLite]; }; pryr = derive2 { name="pryr"; version="0.1.4"; sha256="06vj5xl9x37kbd3l5bw7sbgfdnp37spvrjrn976rxi04clqk966k"; depends=[codetools Rcpp stringr]; }; - ps = derive2 { name="ps"; version="1.2.1"; sha256="1zxylcb0nr4qb5v6j199mc2pfgf2bpf00jrw47jajmv59qb0fwmx"; depends=[]; }; + ps = derive2 { name="ps"; version="1.3.0"; sha256="1lcq7r0q4jb8x6k023zr2ydj2dg925bqqbkhx1phpnyjrk897498"; depends=[]; }; psData = derive2 { name="psData"; version="0.2.2"; sha256="013hb6lk9rm2w08m5jbw90ndrcd4wyy2h125jx07c9bs60wh4mp4"; depends=[countrycode DataCombine reshape2 rio xlsx]; }; psbcGroup = derive2 { name="psbcGroup"; version="1.4"; sha256="0l1hmgw4sislryws8hv7r2nglhcs6g9khg0372a70djvhz2l6gfi"; depends=[LearnBayes mvtnorm SuppDists]; }; pscl = derive2 { name="pscl"; version="1.5.2"; sha256="1phf3awsfr4ncqfqzin5m1pz0g7y1zhbcm2sz7358ssw914fd7rc"; depends=[MASS]; }; pscore = derive2 { name="pscore"; version="0.1-2"; sha256="1sfkxs2kv8lq87j3q9ci7j38c7gzfkp2l36lwcdhiidr2nls2x0c"; depends=[ggplot2 lavaan reshape2]; }; psd = derive2 { name="psd"; version="1.0-1"; sha256="1ssda4g98m0bk6gkrb7c6ylfsd2a84fq4yhp472n4k8wd73mkdn6"; depends=[RColorBrewer Rcpp RcppArmadillo signal zoo]; }; - psda = derive2 { name="psda"; version="1.0.1"; sha256="0hqagrylfllc7mxbnsgxvc2qb3av1wh6ck7y0bs331s4paz0b2mc"; depends=[ggplot2 plyr raster rgeos sp]; }; + psda = derive2 { name="psda"; version="1.2.0"; sha256="1d31d79yz2f0z5b1ik3c8sbn1j1wfmzbd14y223na8g71qaw4m1c"; depends=[ggplot2 plyr raster rgeos sp]; }; pse = derive2 { name="pse"; version="0.4.7"; sha256="0kigfzsvx3gw7jwym4f19dydwwarwxgmha7hpy54gg0zzi4k9icl"; depends=[boot Hmisc]; }; pseudo = derive2 { name="pseudo"; version="1.4.3"; sha256="0ccf3gz2g7g5y4acpj2qnb39hrghhdganizlddg6rx7al869fffs"; depends=[geepack KMsurv]; }; pseudorank = derive2 { name="pseudorank"; version="0.3.8"; sha256="1nj2cq8v8gj8wg23yrn8v21jwgd572gbz1wplpaxhk5v2ckhf1p0"; depends=[doBy Rcpp]; }; @@ -10601,16 +10688,16 @@ in with self; { psychmeta = derive2 { name="psychmeta"; version="2.2.1"; sha256="0x5yxzd78xfz9sbbzx4yxa1vbgwj70fiiiypkk0bai5wjhx40c8v"; depends=[boot cli crayon data_table dplyr ggplot2 knitr MASS metafor nor1mix progress purrr RCurl RefManageR reshape2 rlang rmarkdown stringi stringr tibble tidyr tmvtnorm xml2]; }; psycho = derive2 { name="psycho"; version="0.3.7"; sha256="0n9cj841mjf661cik6xyd7hhhw1dm0yshhg8fh3iq15gn88bgmqi"; depends=[BayesFactor broom coda DescTools dplyr emmeans ggcorrplot ggplot2 lavaan lme4 lmerTest loo MASS MuMIn nFactors ppcor psych purrr qgraph rstanarm rstantools scales stringr tibble tidyr]; }; psychometric = derive2 { name="psychometric"; version="2.2"; sha256="1b7cx6icixh8k3bv60fqxjjks23qn09vlcimqfv2x3m3nkf8p1s9"; depends=[multilevel nlme]; }; - psychomix = derive2 { name="psychomix"; version="1.1-4"; sha256="15yk3z11w4bzk6vljr13bkfhzycypww6blc1djb5iwl635xq1c49"; depends=[flexmix Formula lattice modeltools psychotools]; }; - psychotools = derive2 { name="psychotools"; version="0.4-3"; sha256="023cfh9ks8cdk458g4yvjhdy8g9vkcabgpj24bcs46r8nga3adjv"; depends=[]; }; - psychotree = derive2 { name="psychotree"; version="0.15-1"; sha256="1awavyzblh4s0v15kv52sq5dpalg5p0fp7ih46jxppm1srdxsz41"; depends=[Formula partykit psychotools]; }; + psychomix = derive2 { name="psychomix"; version="1.1-5"; sha256="0majai4ivs140x2bq2sk61widyadmv2l64sjyy0g8kcpm8gbgh7b"; depends=[flexmix Formula lattice modeltools psychotools]; }; + psychotools = derive2 { name="psychotools"; version="0.5-0"; sha256="145x1zdjvasdyf72hp6wdsw0m1r5c97gzzlbnnmdbcrjqh5zyglb"; depends=[]; }; + psychotree = derive2 { name="psychotree"; version="0.15-2"; sha256="0svb3i3d9r3hvqh17lfzyzj2rnf2wm1wy6sspx67ngdrfy6d1p91"; depends=[Formula partykit psychotools]; }; psymonitor = derive2 { name="psymonitor"; version="0.0.1"; sha256="1iw0sllxqnyb69pnryx72080g2cpl9x8k1gpm4hr75czxp6dzwq1"; depends=[doParallel foreach magrittr]; }; psyosphere = derive2 { name="psyosphere"; version="0.1.4"; sha256="0z3qnbybpf5zk07zny2mq8ax8lr0m4n7gwp899km0lixb10z4ysf"; depends=[geosphere ggmap ggplot2 lubridate plyr rgdal RgoogleMaps SDMTools sp]; }; psyphy = derive2 { name="psyphy"; version="0.1-9"; sha256="1ndc6sy662wj2qfx7r97crlqjd8fdkfvfy59qmf34bcbzbg33riz"; depends=[]; }; pterrace = derive2 { name="pterrace"; version="1.0"; sha256="15k5149jqjy20cck5121zsv2mk63amn5b8qgdlacivri9dpxjns1"; depends=[doParallel foreach plotly TDA viridis]; }; ptest = derive2 { name="ptest"; version="1.0-8"; sha256="1d30a23yknf7xgqj8adgr36pnh9dpffl1v5fq682f26fk3ss30qp"; depends=[quantreg]; }; ptinpoly = derive2 { name="ptinpoly"; version="2.4"; sha256="1jbj8z7lqg7w1mqdh230qjaydx2yb6ffgkc39k7dx8xl30g00i5b"; depends=[misc3d]; }; - ptstem = derive2 { name="ptstem"; version="0.0.3"; sha256="0dasfqkrd5dkqr1wbg56qrpkyjcb0lcdfcgz5mbxbhs478gf0nwj"; depends=[dplyr hunspell magrittr rslp SnowballC stringr tidyr tokenizers]; }; + ptstem = derive2 { name="ptstem"; version="0.0.4"; sha256="0dx677c7qh7rbalsys1n3xv4hjdhd6qypjd1mrggfwz1bd4vig4j"; depends=[dplyr hunspell magrittr rslp SnowballC stringr tidyr tokenizers]; }; ptw = derive2 { name="ptw"; version="1.9-13"; sha256="0iighsx6xn8nbw4qpzmwgi4czmr5m8yrr7fzm7mx7cvx2r5ffmbq"; depends=[nloptr]; }; ptwikiwords = derive2 { name="ptwikiwords"; version="0.0.3"; sha256="129dad1vy52sf97dqrkwa49vjhv2kvs4pmd5zvq8pxd51hqm6wy9"; depends=[]; }; ptycho = derive2 { name="ptycho"; version="1.1-4"; sha256="1llk3rpk0lf80vwvs23d6dqhgyic3a6sfjc393csj69hh01nrdvc"; depends=[coda plyr reshape2]; }; @@ -10639,7 +10726,7 @@ in with self; { pwt8 = derive2 { name="pwt8"; version="8.1-1"; sha256="1iig0x90ilzh3hdki0h33qgrra8r94rw4bk1x8y7i6c1may8y0v6"; depends=[]; }; pwt9 = derive2 { name="pwt9"; version="9.0-0"; sha256="1y8zildqnagrp8vf6d8ips0896yp0qcvwy600yv1bqdnglvmn62b"; depends=[]; }; pxR = derive2 { name="pxR"; version="0.42.2"; sha256="1q1xwsrs1ch1a1d1clz6sl7vnsyz5wjqivczk5n5d772y4w60bz5"; depends=[plyr reshape2 RJSONIO stringr]; }; - pxweb = derive2 { name="pxweb"; version="0.6.37"; sha256="1ia38iqs4iiq3zsdwk13zxfvc2i3h3jgmz790pr24iimsvhazff0"; depends=[data_table httr plyr RJSONIO stringr]; }; + pxweb = derive2 { name="pxweb"; version="0.8.3"; sha256="1rs113snv3fkxdlj5y3m2nwkddpx0322n8k23n9dqfinhwr7hzfy"; depends=[checkmate httr jsonlite]; }; pycno = derive2 { name="pycno"; version="1.2"; sha256="0ha5css95xb98dq6qk98gnp1al32gy6w5fkz74255vs4hmkwfzw2"; depends=[maptools rgeos sp]; }; pyinit = derive2 { name="pyinit"; version="1.0.2"; sha256="148b8l5a8c636rgm8dwd8v6ggw9qmkafc5a40bciqc4rk09lfhl3"; depends=[robustbase]; }; pyramid = derive2 { name="pyramid"; version="1.4"; sha256="0hh0hmckicl0r2r9zlf693j65jr9jgmiz643j2asp57nbs99lgxz"; depends=[]; }; @@ -10650,6 +10737,7 @@ in with self; { qLearn = derive2 { name="qLearn"; version="1.0"; sha256="1ilxmgazm8gjz8c1hhbp4fccibnvnalxrag8b0rn081zsqmhf094"; depends=[]; }; qPCR_CT = derive2 { name="qPCR.CT"; version="1.1"; sha256="19j41fsd2m7p2nxi2h2mj43rjxx6sz2jpf4sk0bfvl1gyj0iz3hi"; depends=[RColorBrewer]; }; qVarSel = derive2 { name="qVarSel"; version="1.0"; sha256="13x2hnqjsm0ifzmqkkl9ilhykrh80q04lhlkkp06hkysmh5w9rkx"; depends=[lpSolveAPI Rcpp]; }; + qad = derive2 { name="qad"; version="0.1.0"; sha256="046zyzgmd4rygl871xri02ylkyzl6yszn7zjc47kq7bb8jj0c1ya"; depends=[copula data_table doParallel foreach ggplot2 plyr]; }; qap = derive2 { name="qap"; version="0.1-1"; sha256="0d2d1ni1camixyi45lfy00f4pn3p063k7bsi8gj5scp6n15mdgb0"; depends=[]; }; qat = derive2 { name="qat"; version="0.74"; sha256="04n1jnbkf9dzafjh1n5d4q9p7hvyhnr63nmgl51jqxcf3nan5rlx"; depends=[boot fields gdata gplots moments ncdf4 XML]; }; qboxplot = derive2 { name="qboxplot"; version="0.2"; sha256="07f05n7zxgwyxg2r5fz691ra64m218w9v874xfzjx6671c40y1q2"; depends=[]; }; @@ -10658,7 +10746,8 @@ in with self; { qccrs = derive2 { name="qccrs"; version="0.1.0"; sha256="0lwrmf2809zzdj5f25bb1psh57ibyw90ra41fy2i9vjmgph9wgiq"; depends=[dplyr magrittr purrr tibble]; }; qclust = derive2 { name="qclust"; version="1.0"; sha256="0cxkk4lybpawyqmy5j6kkpgm0zy0gyn3brc1mf9jv8gmkl941cp3"; depends=[mclust mvtnorm]; }; qcr = derive2 { name="qcr"; version="1.0"; sha256="1251naica44kccmikyzdi3ncxfmvyqbc4qspfqnc0w54cqpsy5rw"; depends=[fda_usc MASS mvtnorm qcc qualityTools]; }; - qdap = derive2 { name="qdap"; version="2.3.0"; sha256="11m2si5zn0sls7hhfdcny3cmhirfxr4m49krqww2msj636yr2f64"; depends=[chron dplyr gdata gender ggplot2 gridExtra igraph NLP openNLP plotrix qdapDictionaries qdapRegex qdapTools RColorBrewer RCurl reports reshape2 scales stringdist tidyr tm venneuler wordcloud xlsx XML]; }; + qcv = derive2 { name="qcv"; version="1.0"; sha256="0hf02l9c1cpzs02mfn9swfc8l635qsvh6xrhj21g19h5rxaf8jwg"; depends=[]; }; + qdap = derive2 { name="qdap"; version="2.3.2"; sha256="0g072nwvqqdjcp62xl4hr94rf9xzfvs6400h4b20z44xfnnx8wb2"; depends=[chron dplyr gdata gender ggplot2 gridExtra igraph NLP openNLP plotrix qdapDictionaries qdapRegex qdapTools RColorBrewer RCurl reports reshape2 scales stringdist tidyr tm venneuler wordcloud xlsx XML]; }; qdapDictionaries = derive2 { name="qdapDictionaries"; version="1.0.7"; sha256="0jdx7bxmvc4p41jb4fhaagg5jsbsi7gva870cmyia72li52grhyn"; depends=[]; }; qdapRegex = derive2 { name="qdapRegex"; version="0.7.2"; sha256="1xa8q1way3gjadrjh3mv3xr4c6b4h16nd2c6lgl969difplpfz9p"; depends=[stringi]; }; qdapTools = derive2 { name="qdapTools"; version="1.3.3"; sha256="0a28jn57d2fas3009cm10z07fq77ql3ffcrhcxsiimb57179wj0n"; depends=[chron data_table RCurl XML]; }; @@ -10732,7 +10821,7 @@ in with self; { quantities = derive2 { name="quantities"; version="0.1.2"; sha256="01h0d2cmqqyqch98d8pgv3n2rvp3vc3sby95srahgcrrlxmmrrvj"; depends=[errors Rcpp units]; }; quantmod = derive2 { name="quantmod"; version="0.4-13"; sha256="16aldg96z7amp5mr90nb8127yy04gxsihfr26km5p3cx3j117yv0"; depends=[curl TTR xts zoo]; }; quantoptr = derive2 { name="quantoptr"; version="0.1.3"; sha256="0f9vy9yhya4wpya8n345s6n7a5sb29chdkl5fz6dwa31lp1mvvj3"; depends=[quantreg Rdpack rgenoud stringr]; }; - quantreg = derive2 { name="quantreg"; version="5.36"; sha256="023gdzahxp582rpabilpxbl3wyjrgjjnnrhcv9xhrqdfiq5l2yza"; depends=[Matrix MatrixModels SparseM]; }; + quantreg = derive2 { name="quantreg"; version="5.38"; sha256="1vvvnk291f0dccg04l3nsnk585gq75sk0b2vdbrqv3lczvv18nw1"; depends=[Matrix MatrixModels SparseM]; }; quantreg_nonpar = derive2 { name="quantreg.nonpar"; version="1.0"; sha256="1f9120awnkwsgdiqg98lg7xs5l4y80930869x6k9q76595r5m92k"; depends=[fda mnormt quantreg Rearrangement]; }; quantregForest = derive2 { name="quantregForest"; version="1.3-7"; sha256="0lk7r02i6zpx9sdl2rp0r7fc3a84s8qhg49nh2x7k3vxwa095pjz"; depends=[randomForest RColorBrewer]; }; quantregGrowth = derive2 { name="quantregGrowth"; version="0.4-3"; sha256="0q2yk51hcn7jnvh14nxa7szfj4pr9grh5rdfwazaziilbwqdmw4f"; depends=[quantreg]; }; @@ -10758,7 +10847,7 @@ in with self; { qwraps2 = derive2 { name="qwraps2"; version="0.3.0"; sha256="0xhlb0c955raxrqw202f7jd9c1wkrigh1qs93m2739jkwkyv2n3b"; depends=[devtools dplyr ggplot2 knitr magrittr Rcpp RcppArmadillo rlang tidyr]; }; r_jive = derive2 { name="r.jive"; version="2.1"; sha256="0l0bhhp6bdc84pzxi7gnsxx3scycw0zahrnc496wx3j43np9hlsg"; depends=[abind gplots SpatioTemporal]; }; r2d2 = derive2 { name="r2d2"; version="1.0-0"; sha256="1zl0b36kx49ymfks8rm33hh0z460y3cz6189zqaf0kblg3a32nsi"; depends=[KernSmooth MASS sp]; }; - r2d3 = derive2 { name="r2d3"; version="0.2.2"; sha256="1r70x14s6vb4hyig5avb0vd6ynj2y6g2n7vd50hzm1yhb6w2z81b"; depends=[htmltools htmlwidgets jsonlite rstudioapi]; }; + r2d3 = derive2 { name="r2d3"; version="0.2.3"; sha256="0v612mbzdjr8cq1ffall9hagbwxfv7fh963x8f0w5r84v1m3y2bl"; depends=[htmltools htmlwidgets jsonlite rstudioapi]; }; r2dRue = derive2 { name="r2dRue"; version="1.0.4"; sha256="1apdq7zj5fhs349wm9g6y06nn33x24pg3gdp4z1frd18qlacf8z5"; depends=[matrixStats rgdal sp]; }; r2glmm = derive2 { name="r2glmm"; version="0.1.2"; sha256="0iim92blpa59vgz97c2pi05yhbjjmaffdbkbmk5kplfb2vmazgiy"; depends=[afex data_table dplyr ggplot2 gridExtra lmerTest MASS Matrix mgcv pbkrtest]; }; r2stl = derive2 { name="r2stl"; version="1.0.0"; sha256="18lvnxr40cm450s8qh09c3cnkl1hg83jhmv1gzsv6nkjrq4mj5wh"; depends=[]; }; @@ -10825,7 +10914,7 @@ in with self; { rSCA = derive2 { name="rSCA"; version="3.0"; sha256="1ka8p1slqb3a9hfc8z4j7v90k0wn6y35vmwxqaf8jlgwfhhc1v9f"; depends=[]; }; rSEA = derive2 { name="rSEA"; version="1.0"; sha256="0icphv6l23yqjjk7i81y68yjf1fsccbqaxwb55f2izay5lpaalhs"; depends=[hommel]; }; rSFA = derive2 { name="rSFA"; version="1.04"; sha256="0gd6ji1ynbb04rfv8jfdmp7dqnyz8pxcl5636fypd9a81fggl0gs"; depends=[MASS]; }; - rSPARCS = derive2 { name="rSPARCS"; version="0.0.1"; sha256="1djb26k7q3j660sjgdwyjglkjkdi3k2k2h83nmvmr4dbgsx6nbmm"; depends=[data_table foreign geosphere raster sp spatialEco tigris]; }; + rSPARCS = derive2 { name="rSPARCS"; version="0.0.2"; sha256="1mhd40fr7s05p0sswz24vvzyw190vj57c6vlfb5pqiaikqf6hhmz"; depends=[data_table foreign geosphere raster sp spatialEco tigris]; }; rSQM = derive2 { name="rSQM"; version="1.3.14"; sha256="0m69n2pnfv2085dln6p149a5gw0gif9xk00xmad5s9j68hwjdmym"; depends=[dplyr EcoHydRology ggplot2 gsubfn mise ncdf4 qmap reshape2 stringr yaml zoo]; }; rSymPy = derive2 { name="rSymPy"; version="0.2-1.1"; sha256="1mrfpyalrq8b6yicy28jsj0xy7hlawa72imsfhabwd3hrx6ld150"; depends=[rJython]; }; rTableICC = derive2 { name="rTableICC"; version="1.0.7"; sha256="1z896675kmm9p5dnmcnsz2205ynf05laqcxvlc9y0g5i0x8rf8v6"; depends=[aster partitions]; }; @@ -10854,8 +10943,8 @@ in with self; { radtools = derive2 { name="radtools"; version="1.0.0"; sha256="0xspd3spfr59nciddx4gmfrw52jr0m0gznqb5rjsarshn9y8x3xf"; depends=[dplyr Hmisc magrittr oro_dicom oro_nifti]; }; rafalib = derive2 { name="rafalib"; version="1.0.0"; sha256="1dmxjl66bfdgrybhwyaa8d4i460liqcdw8b29a6w7shgksh29m0k"; depends=[RColorBrewer]; }; rags2ridges = derive2 { name="rags2ridges"; version="2.2"; sha256="04f9gvwpgrx54dgbjjixlxa2056aqcz2kryn4jplwf5fc0vj1lyn"; depends=[expm fdrtool ggplot2 graph gRbase Hmisc igraph RBGL Rcpp RcppArmadillo reshape sfsmisc snowfall]; }; - ragt2ridges = derive2 { name="ragt2ridges"; version="0.3.1"; sha256="0zjqrvy1k1lz4caakcj3c6l2j637wp6nxbzfj0gvcn2c4pjcrdyp"; depends=[abind expm fdrtool igraph MASS Matrix mvtnorm rags2ridges Rcpp RcppArmadillo]; }; - ragtop = derive2 { name="ragtop"; version="0.5"; sha256="0h09h9ws9c2d9xc00w4hl000h0kbvq16lz4vgv1w93am8zmsp4wm"; depends=[futile_logger limSolve]; }; + ragt2ridges = derive2 { name="ragt2ridges"; version="0.3.2"; sha256="03613amz11ixgkjhc8rg4vp3ih60g1ibhdjrldr9mazzkak46y91"; depends=[abind expm fdrtool igraph MASS Matrix mvtnorm rags2ridges Rcpp RcppArmadillo]; }; + ragtop = derive2 { name="ragtop"; version="1.0.0"; sha256="0ijzchp2w364qvvmqsddw7drwnfyrndwzc911bdlbc39af2s7dgi"; depends=[futile_logger limSolve]; }; railtrails = derive2 { name="railtrails"; version="0.1.1"; sha256="1hi55rcxmr7k3na3rpjqmd5fpgn51bymrp7yxmw45ff7mlzpa5h6"; depends=[tibble]; }; rainbow = derive2 { name="rainbow"; version="3.5"; sha256="1gcaflb3haw9wpx4wl64vgi30jxn2nrzlm5125hhg647rw7ryp8k"; depends=[cluster colorspace hdrcde ks MASS pcaPP]; }; raincpc = derive2 { name="raincpc"; version="0.4"; sha256="0yzpyidvf24frf82pj7rarjh0ncm5dhm0mmpsf2ycqlvp0qld10i"; depends=[SDMTools]; }; @@ -10875,7 +10964,7 @@ in with self; { random_polychor_pa = derive2 { name="random.polychor.pa"; version="1.1.4-2"; sha256="1ybwfn3hdwisxjn85vqrib1zhk8dcddbarbwjdf1vn27ih3c4h2c"; depends=[boot MASS mvtnorm nFactors psych sfsmisc]; }; randomForest = derive2 { name="randomForest"; version="4.6-14"; sha256="0kbmm0l42fc2d1rdq0l7k09d34kd87q4lx651ffsic4y84h8kf7l"; depends=[]; }; randomForestExplainer = derive2 { name="randomForestExplainer"; version="0.9"; sha256="0gqqm3784krl6xdx7j6xvvyi2rjbyi6c8shm44yvq59is5i7fypc"; depends=[data_table dplyr DT dtplyr GGally ggplot2 ggrepel MASS randomForest reshape2 rmarkdown]; }; - randomForestSRC = derive2 { name="randomForestSRC"; version="2.7.0"; sha256="12wqjch4mddb9gqcacihcvlrdj697yr2sjr3pmrf7xm3yws2gjrb"; depends=[]; }; + randomForestSRC = derive2 { name="randomForestSRC"; version="2.8.0"; sha256="1jby5f94y87bkfmvjyq2h17yy3qsaa5jm1p8348gnawy9vyl7swv"; depends=[]; }; randomGLM = derive2 { name="randomGLM"; version="1.02-1"; sha256="031338zxy6vqak8ibl2as0l37pa6qndln0g3i9gi4s6cvbdw3xrv"; depends=[doParallel foreach MASS]; }; randomLCA = derive2 { name="randomLCA"; version="1.0-15"; sha256="10rx2ah50dcjxz5y492c59d3pn0dvlgjaxfdf8sknkf6s4pmwkis"; depends=[boot fastGHQuad lattice Matrix]; }; randomNames = derive2 { name="randomNames"; version="1.0-0.0"; sha256="12q5bs65qivddiaxbsp128j94h2vyrgjvmm80d52r36ffbaigl09"; depends=[data_table]; }; @@ -10927,13 +11016,13 @@ in with self; { rattle_data = derive2 { name="rattle.data"; version="1.0.2"; sha256="0cnmyzvy23jc4vz521c3jg0w4165waycvy5014l5773fy19zq75c"; depends=[]; }; raw = derive2 { name="raw"; version="0.1.6"; sha256="0hnqwa9pwj3k2y0bs6hxrvbwksjyq0q6m73c9hhlafg8g3lkyxnf"; depends=[]; }; rayshader = derive2 { name="rayshader"; version="0.5.1"; sha256="1qkv25p0n10zgs3r12i8kwgw6188c0k9a80wg9i12mjpy2pbrxmz"; depends=[doParallel foreach imager magrittr png progress raster Rcpp rgl scales]; }; - rbacon = derive2 { name="rbacon"; version="2.3.4"; sha256="1va1rap2n6mcjfzclqg5h58ggrs2kb4nlaam5ch984w9rzq59g2l"; depends=[coda Rcpp]; }; - rbamtools = derive2 { name="rbamtools"; version="2.16.11"; sha256="1pr1isq9yk5mpi41cnihg4zn5g9az7yr9m42759hibqqyb6nw78a"; depends=[refGenome]; }; + rbacon = derive2 { name="rbacon"; version="2.3.5"; sha256="1n06fbm1l087z5d1hwys9889ml47hqis1qzd6p8wrchl52qyzbfl"; depends=[coda Rcpp]; }; + rbamtools = derive2 { name="rbamtools"; version="2.16.11.2"; sha256="0gzkb1xyrkriv45wq8gv7qfwjslnvwkfkk5jjc4wg5kmm0ydpdzj"; depends=[refGenome]; }; rbefdata = derive2 { name="rbefdata"; version="0.3.5"; sha256="12mcqz0pqgwfw5fmma0gwddj4zk0hpwmrsb74dvzqvgcvpfjnv98"; depends=[RColorBrewer RCurl rjson rtematres wordcloud XML]; }; rbenchmark = derive2 { name="rbenchmark"; version="1.0.0"; sha256="010fn3qwnk2k411cbqyvra1d12c3bhhl3spzm8kxffmirj4p2al9"; depends=[]; }; rbgm = derive2 { name="rbgm"; version="0.0.5"; sha256="1gz9hxlwmj2ch1ds6mx1nlkwy4fm811jkz5fz3cl6675n11bjdpg"; depends=[dplyr geosphere raster readr rlang sp stringr tibble]; }; rbhl = derive2 { name="rbhl"; version="0.8.0"; sha256="1avx36as99za19acjh7adb72ckdn69rmiwzcrrqxskzny56vxf0d"; depends=[crul jsonlite plyr tibble xml2]; }; - rbi = derive2 { name="rbi"; version="0.9.1"; sha256="0jfaakzl15dz6bsbcd6y2pnf3bdccs3bx90c6hzsjpvck7fcvxpi"; depends=[data_table ncdf4 reshape2]; }; + rbi = derive2 { name="rbi"; version="0.10.0"; sha256="0jl2chbrdpjwfc5cavrpslhyiy0awbjxf1i3lijnjlyssf0wkb93"; depends=[data_table ncdf4 processx reshape2]; }; rbiouml = derive2 { name="rbiouml"; version="1.8"; sha256="0qvc896sf6idczbxix3klf56paxf0wpfbmga8qqlcyjasv1dsdql"; depends=[RCurl RJSONIO]; }; rbison = derive2 { name="rbison"; version="0.7.0"; sha256="0v9i45pdjdspc1xw1mm3zmmsdnq5s7s656mkkhssmhj603f3mswg"; depends=[crul data_table dplyr ggplot2 jsonlite mapproj plyr sp]; }; rbit = derive2 { name="rbit"; version="1.0.0"; sha256="09ywr711gv0vgfims2vfcxk3rnd0iadzlksil0q9159yarapfc59"; depends=[R6]; }; @@ -10960,7 +11049,7 @@ in with self; { rcdk = derive2 { name="rcdk"; version="3.4.7.1"; sha256="1d08ajji631792b7fyfwzvcaswh8jlanfsxrj6c1wx7xh3qqpigg"; depends=[fingerprint iterators itertools png rcdklibs rJava]; }; rcdklibs = derive2 { name="rcdklibs"; version="2.0"; sha256="05g0y00bw1bqykfbwn4q42krwcfl50jcavaw7yyw9a5m34hvw0l8"; depends=[rJava]; }; rchallenge = derive2 { name="rchallenge"; version="1.3.0"; sha256="1qn2pzch5yk771jsjcsmfsi5vddfb2w50vfqlkmsl6nf5z6sdq9k"; depends=[knitr rmarkdown]; }; - rcheology = derive2 { name="rcheology"; version="3.5.1.1"; sha256="1yb9d55x6ffam4lirpfign3czx5c14nc1qz0cxqyi9ak63p9mb13"; depends=[]; }; + rcheology = derive2 { name="rcheology"; version="3.5.2.0"; sha256="1chqija5w992056nzl9sdrzyxmiwqwndxx66vz1h4mqqb5y42c1j"; depends=[]; }; rchess = derive2 { name="rchess"; version="0.1"; sha256="0qnvvvwcl02rmqra9m7qnhy40cbavswbq6i0jm47x6njmr1gpfhy"; depends=[assertthat dplyr ggplot2 htmlwidgets plyr R6 V8]; }; rchie = derive2 { name="rchie"; version="1.0.0"; sha256="0bn00kglfc3sm5j83r5sj94b3vj27i1zwky4xn18swjg0c2cf94y"; depends=[jsonlite V8]; }; rcicr = derive2 { name="rcicr"; version="0.3.4.1"; sha256="1sa13sbhx64cf8szr2811iq4a1asb8d3k0igxw6fbssij2lwbxzp"; depends=[aspace dplyr jpeg matlab scales]; }; @@ -10975,7 +11064,7 @@ in with self; { rcosmo = derive2 { name="rcosmo"; version="1.0.0"; sha256="1r9q8y9an2dw9kpnfl7qhnqx136xk05vi1ps52d9n76rr86lw0fw"; depends=[cli entropy FITSio geoR mmap nnls Rcpp rgl tibble]; }; rcreds = derive2 { name="rcreds"; version="0.6.6"; sha256="1sdrdgn53kgcdnxfjs8jh0h538vb3b9ixz74lbnp54yp09jpqsri"; depends=[collectArgs digest jsonlite magrittr]; }; rcrossref = derive2 { name="rcrossref"; version="0.8.4"; sha256="1q58wngr28a0vrafwhxj8jvh42aprv2v1s68mdbbq30rn28yplj7"; depends=[bibtex crul dplyr DT jsonlite miniUI plyr R6 shiny stringr xml2]; }; - rcrtan = derive2 { name="rcrtan"; version="0.1.0"; sha256="1pg0w9amlxnzv5mrh4p3gnh8959m93dx8bfy2gvbm94isilb969z"; depends=[dplyr magrittr purrrlyr tibble tidyr]; }; + rcrtan = derive2 { name="rcrtan"; version="0.1.1"; sha256="0kcp3gnjmp00i1hsjagpp0dlr6zgpc4y5ihpx93hm4m3fnzcmn7x"; depends=[dplyr magrittr purrrlyr tibble tidyr]; }; rcrypt = derive2 { name="rcrypt"; version="0.1.1"; sha256="002r5wr0bmqbj014iz8wacj883j6gqcxc786m6p9a7zdrjpx2pqi"; depends=[]; }; rcss = derive2 { name="rcss"; version="1.7"; sha256="0sl175x2l6c493b4kvcbxp6ps95d5rgydqmd6fcwwr3in5lhjdky"; depends=[nabor Rcpp RcppArmadillo]; }; rcube = derive2 { name="rcube"; version="0.3"; sha256="0y4sw67g0ws3iywbaz56ccg5q6n2885yfl8rvb45yvwjmdmbg85r"; depends=[magrittr]; }; @@ -10995,6 +11084,7 @@ in with self; { rdetools = derive2 { name="rdetools"; version="1.0"; sha256="0pkl990viv7ifr7ihgdcsww93sk2wlzp2cg931wywagfp8dijd02"; depends=[]; }; rdflib = derive2 { name="rdflib"; version="0.2.1"; sha256="16hm6yfgzng1bv81mjfjx8ywvblk9if2z0jx326k4b0a8fvfijyr"; depends=[dplyr jsonld readr redland stringi tidyr]; }; rdfp = derive2 { name="rdfp"; version="0.1.2"; sha256="1kznr5p5mhplgpgmc0f4vrs1fwpivwjy52hwfc8k0q0vx53h3fs2"; depends=[curl dplyr httr lubridate plyr purrr readr XML xml2]; }; + rdhs = derive2 { name="rdhs"; version="0.6.0"; sha256="1bni1g1mc3b7fnbs7ssrljdzzci243xsl0m8rvdxh63f3pdznz09"; depends=[digest foreign getPass haven httr iotools jsonlite magrittr qdapRegex R6 rappdirs rgdal storr xml2]; }; rdi = derive2 { name="rdi"; version="1.0.0"; sha256="1c49mkxfyxhqz8fc155kgy1k5by0y2c1ahy8k6pn9k8l1j4m4m2q"; depends=[beanplot gplots pdist stringr]; }; rdian = derive2 { name="rdian"; version="0.1.1"; sha256="0i4ljcqhmrwrqbhi321iffypxj4kndx47ssljnixr3fx2lmqh0q1"; depends=[curl httr]; }; rdist = derive2 { name="rdist"; version="0.0.3"; sha256="1jp3s4293h973dpz0waq9abpd8ibp4gxdyk3bwn7a32zfpk4kjza"; depends=[Rcpp RcppArmadillo]; }; @@ -11016,6 +11106,7 @@ in with self; { reactR = derive2 { name="reactR"; version="0.2.1"; sha256="1abj3lh2vk4pni5gn2vb8sym2j2sx7yvnph86nz9hp6r270d0g86"; depends=[htmltools]; }; read_dbc = derive2 { name="read.dbc"; version="1.0.5"; sha256="1vrvxkcrk3iw5am9rsadxzf0wsr7z2mdpa5wb0v9jbhda710b4yf"; depends=[foreign]; }; read_gb = derive2 { name="read.gb"; version="1.6"; sha256="17py6al9cwq4jmab7k2164f7hi8943gi8a50d8zpn1xms9l2cnld"; depends=[]; }; + readABF = derive2 { name="readABF"; version="1.0.1"; sha256="0w85v8dl337lsyfad3hxwavma1gnhi4wyszdj8npaz37y12nk2gy"; depends=[]; }; readBrukerFlexData = derive2 { name="readBrukerFlexData"; version="1.8.5"; sha256="1qmimfxwh6d7s5qrnnk20i2f9l5j1ci3wpfs3qlmggz69jzf589m"; depends=[]; }; readHAC = derive2 { name="readHAC"; version="1.0"; sha256="0z80ai6xfswwgdfh83l9sq279c97n0wz25bk2l7xfb6w0sndzq53"; depends=[]; }; readJDX = derive2 { name="readJDX"; version="0.3.250"; sha256="0h7yfc0y4b67rhh949zknqyjx0jknsld1099y9x563a5lhzwrchv"; depends=[stringr]; }; @@ -11030,11 +11121,11 @@ in with self; { readit = derive2 { name="readit"; version="1.0.0"; sha256="1sq2spjgdc9rq8cr5i9qjmqd4vcf7cknpx5dndwjdqrv112y8bk9"; depends=[crayon haven jsonlite readr readxl]; }; readmnist = derive2 { name="readmnist"; version="1.0.6"; sha256="0f2kp5r04k47gpvbj8x13c47zsis3bw3y8f5f37sh6jggblqr004"; depends=[]; }; readobj = derive2 { name="readobj"; version="0.3.1"; sha256="1hnmj6ydvdss7jbl3h16ip0g993wdfyfm15r8f78ihjlh84swima"; depends=[Rcpp]; }; - readr = derive2 { name="readr"; version="1.2.1"; sha256="05h7hyd67x0sjn0sbggpmlhsjx0k88ws8l967gmzxmm3h8a6xwkg"; depends=[BH clipr hms R6 Rcpp tibble]; }; + readr = derive2 { name="readr"; version="1.3.1"; sha256="1wz496rw0ah433p755n3xac8gh7yzid4xgdjzd1a7wmpkgilvy9k"; depends=[BH clipr crayon hms R6 Rcpp tibble]; }; readroper = derive2 { name="readroper"; version="0.9.1"; sha256="153iy144c4yxcs2cwr73czy69b4fj4q1g77rb8qmvp6blfwdcd71"; depends=[readr]; }; readstata13 = derive2 { name="readstata13"; version="0.9.2"; sha256="02mqwpzn7n3pqjxivnd1vlfc47xkyiywfz594x0f6vd2dym8rdwd"; depends=[Rcpp]; }; readtext = derive2 { name="readtext"; version="0.71"; sha256="1blcsk1d78q0s1bijsrzrfrvhgbsq3qi1r9w3i51h1r9g3v9p87f"; depends=[antiword data_table digest httr jsonlite pdftools readODS readxl streamR stringi tibble xml2]; }; - readxl = derive2 { name="readxl"; version="1.1.0"; sha256="05ii8knrg4jji6h7bv6bfpn279b6x52yrskdx5rv7b0hcpy22gdn"; depends=[cellranger Rcpp tibble]; }; + readxl = derive2 { name="readxl"; version="1.2.0"; sha256="1mwm389skl4ahcwsmhvx31pjkrn6y9igpnhsczwg6yza886q7j19"; depends=[cellranger progress Rcpp tibble]; }; realestateDK = derive2 { name="realestateDK"; version="0.1.0"; sha256="02y3c2zww9jakh9a0jqxkgcwshjz1hd5mw63603hyic7q4a07iv3"; depends=[statsDK]; }; reams = derive2 { name="reams"; version="0.1"; sha256="07hqi0y59kv5lg0nl75xy8n48zw03y5m71zx58aiig94bf3yl95c"; depends=[leaps mgcv]; }; rebird = derive2 { name="rebird"; version="1.0.0"; sha256="0gp8afj6y3vss2b11v0fqyc3ai67kilicr4fnk5zghljfvbxsxm8"; depends=[assertthat dplyr httr jsonlite]; }; @@ -11063,12 +11154,12 @@ in with self; { reda = derive2 { name="reda"; version="0.4.1"; sha256="0aq6c2h694kdmjis12g4nxq5hdlzsi42nbnpzq7wic305l5r7nxl"; depends=[ggplot2 Rcpp RcppArmadillo splines2]; }; redcapAPI = derive2 { name="redcapAPI"; version="2.2"; sha256="0bszw9px7ddcwnc1p3zpd8426mwym5369hglz3qm5x92va1j4036"; depends=[checkmate chron DBI httr labelVector lubridate readr stringr tidyr]; }; reddPrec = derive2 { name="reddPrec"; version="0.4.0"; sha256="0zmkaiivvjq8mcaz310zgjjc7y0wgsqv29bf8nhli5qawaczvb9a"; depends=[fields snowfall]; }; - redist = derive2 { name="redist"; version="1.3-2"; sha256="0qkv2n9jianxm95vk2dqsqghhf2zirab8vhzc8cc8zichjv79f69"; depends=[coda doParallel foreach Rcpp RcppArmadillo sp spdep]; }; + redist = derive2 { name="redist"; version="1.3-3"; sha256="18asjam8hvayvnfysyjzbazjn27ds7163qhdq0p9aqlx03v89aa9"; depends=[coda doParallel foreach Rcpp RcppArmadillo sp spdep]; }; redland = derive2 { name="redland"; version="1.0.17-10"; sha256="0k28896jsxy1qxnn6iyx3xxasq4y171xfjragqkj568nn9lmzfi8"; depends=[roxygen2]; }; redlistr = derive2 { name="redlistr"; version="1.0.2"; sha256="1s335dim68qx0i28w7586kacb8j8qawwg5az56a8ggja6yll306f"; depends=[plyr raster rgeos sp]; }; redux = derive2 { name="redux"; version="1.1.0"; sha256="0a551w7fph338mqzxda6y21lsad19dway7w18jw9cv1rgvcp9nvc"; depends=[R6 storr]; }; ref_ICAR = derive2 { name="ref.ICAR"; version="1.0"; sha256="0k6czsbjclgmi7vp5hl50jghkzm573s50993iz3dcv55mv662251"; depends=[coda MCMCglmm mvtnorm Rdpack rgdal spdep]; }; - refGenome = derive2 { name="refGenome"; version="1.7.3"; sha256="15p0ra2p1pwhy5ixbhsz1g79c5sc2aap4i4c8kil0m2syg9y45sn"; depends=[DBI doBy RSQLite]; }; + refGenome = derive2 { name="refGenome"; version="1.7.3.1"; sha256="1s4lxv5pqk6d0f0a9iclgv88yl346fwvzgraxh0gwpbym1yhh787"; depends=[DBI doBy RSQLite]; }; referenceIntervals = derive2 { name="referenceIntervals"; version="1.1.1"; sha256="04199nxh216msaghkp66zsi96h76a7c42ldml0fm66v2vamcslg8"; depends=[boot car extremevalues outliers]; }; refimpact = derive2 { name="refimpact"; version="1.0.0"; sha256="0qifqhar2pv81npsxl2pj713vgldyap7y79fq20jpk7qigzf9573"; depends=[checkmate curl httr jsonlite tibble xml2]; }; refinr = derive2 { name="refinr"; version="0.3.1"; sha256="0q76sr050pg3ahwzcxj08mjig0k2jq8yh7nv6d914pwg3dhq05sn"; depends=[Rcpp stringdist stringi]; }; @@ -11090,7 +11181,7 @@ in with self; { regpro = derive2 { name="regpro"; version="0.1.1"; sha256="02axbq63hsqwg3q2ixr0lpsdai9q6wj57s5k1343q9m0pw90vr73"; depends=[denpro]; }; regress = derive2 { name="regress"; version="1.3-15"; sha256="1cgr0r49cmr8nzs2lr2cm8lli1i8azyas0lbnf1681kyab15c0r7"; depends=[]; }; regsel = derive2 { name="regsel"; version="0.2"; sha256="0wwwpawqsqimaldy0zxnqsy23nwp30ypa5dnrnndwhbs4qz99c9w"; depends=[elasticnet glmnet]; }; - regsem = derive2 { name="regsem"; version="1.2.0"; sha256="156jvnxf885c42xpbd2ddakgxkbjmzanc240dzdc5z89a78vcy74"; depends=[lavaan Rcpp RcppArmadillo Rsolnp]; }; + regsem = derive2 { name="regsem"; version="1.2.3"; sha256="1if17nc3pjjm2by9ii1dyksx4r82m62h76mc05sndc3a2mpkc003"; depends=[lavaan Rcpp RcppArmadillo Rsolnp]; }; regspec = derive2 { name="regspec"; version="2.4"; sha256="18i6k2wqaddrc0dz7v8x3s9205dcfwanqhpnxa9hkpyqzbb17pd3"; depends=[]; }; regsubseq = derive2 { name="regsubseq"; version="0.12"; sha256="0879r4r8kpr8jd6a3fa9cifm7cv0sqzz8z1alkm1b2fr1625md3g"; depends=[]; }; regtest = derive2 { name="regtest"; version="0.05"; sha256="1wrrpp2hvkas0yc512gya3pvd0v97pn4v51k5jxkwyd1pp68zd1q"; depends=[]; }; @@ -11134,7 +11225,7 @@ in with self; { repijson = derive2 { name="repijson"; version="0.1.0"; sha256="16iypvsmh5r9pk2k6npp17ya5dgkxihsj29pppd3zvdpm3vvd8k1"; depends=[geojsonio ggplot2 jsonlite OutbreakTools plyr sp]; }; replicatedpp2w = derive2 { name="replicatedpp2w"; version="0.1-2"; sha256="0nskwkqm9z2aphpim6pvykhc3fphlsbap3r49nghkwjpngd0qzj8"; depends=[spatstat spatstat_utils]; }; replicationInterval = derive2 { name="replicationInterval"; version="2.0.1"; sha256="1jyvyqr8r2fs1cmbz7zjcc8p116bnkslvx27pqi92y5pxgqvsqvr"; depends=[ggplot2 MASS MBESS pbapply]; }; - replyr = derive2 { name="replyr"; version="0.9.8"; sha256="086ck4vgjamifx621pkc9lyw96brvwhr1gfg4j5amg7r8llfws7r"; depends=[DBI dplyr rlang wrapr]; }; + replyr = derive2 { name="replyr"; version="0.9.9"; sha256="1rniihri2acjgk6dcviv4xj1fa7w7pvx0k8d8l2adi2790k63xib"; depends=[DBI dplyr rlang wrapr]; }; repmis = derive2 { name="repmis"; version="0.5"; sha256="0z5mjbsl24yjbl0aawr35grcal44rf2xbwv1hy7bdkms94ix79b5"; depends=[data_table digest httr plyr R_cache]; }; repo = derive2 { name="repo"; version="2.1.3"; sha256="1g72zvj2mg8cxfy1w3d46lkk4hayad64ns5w1y43731whzraxk95"; depends=[digest]; }; repolr = derive2 { name="repolr"; version="3.4"; sha256="13kmy09c7lk8p1mkdss0krcsfb6d7zcnqpwnl38zkanvh8q3fqhm"; depends=[Matrix Rcpp RcppArmadillo]; }; @@ -11144,12 +11235,13 @@ in with self; { reportr = derive2 { name="reportr"; version="1.3.0"; sha256="0zynplxqvbmf23cm2rsz3wz2jx6mv55z94mn1k44ny3lx625cnpw"; depends=[ore]; }; reports = derive2 { name="reports"; version="0.1.4"; sha256="0r74fjmdqax2x5fhbkdxb8gsvzi6v794fh81x4la9davz6w1fnxh"; depends=[]; }; reporttools = derive2 { name="reporttools"; version="1.1.2"; sha256="1i87xmp7zchcb8w8g7nypid06l2439qyrvpwsjz6qny954w6fa2b"; depends=[xtable]; }; - repr = derive2 { name="repr"; version="0.18"; sha256="1a7pffzzmdm3gqyiifwrlhhp3z3qqsdhr4adzq39gj3ll24ql281"; depends=[base64enc htmltools]; }; + repr = derive2 { name="repr"; version="0.19.1"; sha256="0bn21h238rrc2vmv3bvsmk25509bgcyppg4r9592xj5zfglh2b0n"; depends=[base64enc htmltools jsonlite]; }; represent = derive2 { name="represent"; version="1.0"; sha256="0jvb40i6r1bh9ysfqwsj7s1g933d7z5fq9d618yjrqr6hbbqsvac"; depends=[]; }; represtools = derive2 { name="represtools"; version="0.1.2"; sha256="1zkabch49q23kd1786km5cb9wcaccbxds11v9hwjzsgrs15g5w35"; depends=[whisker]; }; reprex = derive2 { name="reprex"; version="0.2.1"; sha256="1ws5gds453xgfili87r35rz1wn2i7jbqissq98csbiddpkgls8sx"; depends=[callr clipr fs rlang rmarkdown whisker withr]; }; reproducer = derive2 { name="reproducer"; version="0.2.1"; sha256="1jxv6j5vavncjwrhwbxiz9a4v3kixgrs08kyk6drmhcc031g1dfv"; depends=[ggplot2 gridExtra lme4 MASS metafor openxlsx reshape xtable]; }; reproducible = derive2 { name="reproducible"; version="0.2.5"; sha256="0wci51p80z28annm5zjhs5cam30kgclq4fmf0kyzp00dzy7h9yy4"; depends=[archivist backports crayon data_table devtools digest dplyr fastdigest fasterize fpCompare gdalUtils git2r googledrive httr magrittr memoise quickPlot R_utils raster Rcpp RCurl remotes rgdal rgeos sf sp testthat tibble versions]; }; + reproj = derive2 { name="reproj"; version="0.2.0"; sha256="108grfbhcgw5pp3alwxjfwcydw9qn0v3dhn1fn8dz24xx4wbmz2h"; depends=[proj4]; }; repurrrsive = derive2 { name="repurrrsive"; version="0.1.0"; sha256="1ffldcs30xa4wcd825bgpcmqsndfyxx70dfmbb3c86ic9kq17p01"; depends=[tibble]; }; reqres = derive2 { name="reqres"; version="0.2.2"; sha256="18ib0qbfw3sih7xs1z4szjqppr7lbj5wx0w0kx80g810m7q27wyp"; depends=[assertthat brotli jsonlite R6 stringi urltools webutils xml2]; }; request = derive2 { name="request"; version="0.1.0"; sha256="1q7zd6q00gdqmgq7s7nq1ixmns8zn2amr5zah9rwnsn8dkllj9yh"; depends=[curl httr jsonlite lazyeval magrittr R6 whisker]; }; @@ -11168,6 +11260,7 @@ in with self; { restfulr = derive2 { name="restfulr"; version="0.0.13"; sha256="1dk45mzrr6ka92yjz7hfhkj12kpx1wg4szv1h1mg80mgga4ganbv"; depends=[RCurl rjson S4Vectors XML yaml]; }; restimizeapi = derive2 { name="restimizeapi"; version="1.0.0"; sha256="1ss6fng5pmqg6cafc256g9ddz8f660c68ysxfan6mn4gdaigz7lb"; depends=[RCurl RJSONIO]; }; restlos = derive2 { name="restlos"; version="0.2-2"; sha256="083w1ldax8bnf3w4119damma2nz75c3ki187b0275i1mqxqrixp7"; depends=[geometry igraph limSolve rgl som]; }; + restorepoint = derive2 { name="restorepoint"; version="0.2"; sha256="0pjp5dvycvfg75hhj8lrr2lrjn6n6bqj0ziwyd87lyi15b9j8w4s"; depends=[]; }; restrictedMVN = derive2 { name="restrictedMVN"; version="1.0"; sha256="0qynkg244gzq0yjb0716w7g1sxdq66i11ss8jij86h2mz3ykj137"; depends=[MASS]; }; restriktor = derive2 { name="restriktor"; version="0.1-80.911"; sha256="0n3fsif2ni6w1dpg3yhr7iwg03bayhy00h3ykqbafjx361mxlqrc"; depends=[boot ic_infer lavaan MASS mvtnorm quadprog]; }; resumer = derive2 { name="resumer"; version="0.0.3"; sha256="0ilya3v75989zqm16x69w4599ax2s5j2n6f16bmhwydrmzxs1g48"; depends=[dplyr rmarkdown useful]; }; @@ -11187,7 +11280,7 @@ in with self; { rex = derive2 { name="rex"; version="1.1.2"; sha256="0alsadgjgass3wr8y5d247j12qqzg454sc84vpskclrkmz778g5x"; depends=[lazyeval magrittr]; }; rexpokit = derive2 { name="rexpokit"; version="0.26.6"; sha256="06h2k1jzn9rvbgyhhgnshwdajl9psks1sx09108appyf7sqlb9bp"; depends=[Rcpp]; }; rfPermute = derive2 { name="rfPermute"; version="2.1.6"; sha256="198vvf8jdcjiv55hmlzd4f9jwr55yxk8m3s6dr9lkcq5r4h6xmrk"; depends=[abind dplyr ggplot2 gridExtra magrittr plyr randomForest reshape2 rlang scales swfscMisc tibble tidyr viridis]; }; - rfUtilities = derive2 { name="rfUtilities"; version="2.1-3"; sha256="0vnhvdkqqqn894abznw97j07gwdvvmvk8vsf4aaxx9yzk44cnk5g"; depends=[cluster randomForest]; }; + rfUtilities = derive2 { name="rfUtilities"; version="2.1-4"; sha256="15784vhfp5sxmy58p2xgmc1v3bxx2f78i1pzc186q77zs88c5sq9"; depends=[cluster randomForest]; }; rfacebookstat = derive2 { name="rfacebookstat"; version="1.8.3"; sha256="1a9xj0hpbvjp70v8rim0vpqpdjf6x81jw47nzjl9iggny3c1nb1m"; depends=[bitops data_table dplyr httr jsonlite RCurl]; }; rfbCNPJ = derive2 { name="rfbCNPJ"; version="0.1.1"; sha256="0zvpazxi184ia2wql0120kw7665dn9cs8a2kv91n79pncabb4xfg"; depends=[fs glue httr magrittr progress purrr readr stringr tibble xml2]; }; rfigshare = derive2 { name="rfigshare"; version="0.3.7"; sha256="1qgzn0mpjy4czy0pnbi395fxxx84arkg8r7rk8aidmd34584gjiq"; depends=[ggplot2 httpuv httr plyr RJSONIO XML yaml]; }; @@ -11215,7 +11308,7 @@ in with self; { rggobi = derive2 { name="rggobi"; version="2.1.22"; sha256="1g7k4xais9xkjlbvrkadr5d6c5rw4jp9c0gljhm71pa1fc9fcqff"; depends=[RGtk2]; }; rgho = derive2 { name="rgho"; version="1.0.1"; sha256="0jkfmyn3i50vsqciy96wd2fpik6yfg0sz6rrhwb04jv1dmyz2nfa"; depends=[curl dplyr httr jsonlite lazyeval magrittr memoise readr tibble tidyr]; }; rgl = derive2 { name="rgl"; version="0.99.16"; sha256="0q8sg8fr0140ilssqhscaxkjc29w1rpp6f4k50amw3zzs9g58ak9"; depends=[crosstalk htmltools htmlwidgets jsonlite knitr magrittr manipulateWidget shiny]; }; - rglobi = derive2 { name="rglobi"; version="0.2.14"; sha256="09f4v98m68ssnf1n0ijsrzawpri3jhv4bz7gzzzpijb75mkb0zwz"; depends=[RCurl rjson]; }; + rglobi = derive2 { name="rglobi"; version="0.2.17"; sha256="008wn5fhwyqb3xq5jbs3b08jk770ybjhnk41nqfmg24d7c9pcgi7"; depends=[RCurl rjson]; }; rglwidget = derive2 { name="rglwidget"; version="0.2.1"; sha256="0siqxn3gyl98i84p0yha821b4rdrp2i0942mkx819wnf7qwrpqcv"; depends=[rgl]; }; rgoogleslides = derive2 { name="rgoogleslides"; version="0.3.1"; sha256="06i1ljrib0ap87bxlbpnvx5fr05pwzcmza48gbicvg7fwhz9hs05"; depends=[assertthat httr jsonlite R6]; }; rgr = derive2 { name="rgr"; version="1.1.15"; sha256="1mrnmbh2crhkwdi37q59hx76afvkhgzgaacg3688q7jp23d58z6x"; depends=[fastICA MASS]; }; @@ -11251,13 +11344,14 @@ in with self; { rioja = derive2 { name="rioja"; version="0.9-15.1"; sha256="18fyqcykg12mf4ap0a2la30656xq32immqz11ddmrfrb0vpd2h7h"; depends=[mgcv vegan]; }; ripa = derive2 { name="ripa"; version="2.0-2"; sha256="0n1gaga0d4bb9qdlm7gksa1nwi4y28kbgwr3icwqgihf1bfb9m81"; depends=[Rcpp]; }; rise = derive2 { name="rise"; version="1.0.4"; sha256="12r7mbaxp9pjypbpjxlsbqg7spw80gjgm2w0lsvgvclffc50a6ni"; depends=[dplyr ggplot2]; }; + riskParityPortfolio = derive2 { name="riskParityPortfolio"; version="0.1.0"; sha256="00qx55s1ls3qcnba8mjbslz629gqgf9f600b5jvrdzwmrldvrjgd"; depends=[alabama nloptr quadprog Rcpp RcppEigen]; }; riskPredictClustData = derive2 { name="riskPredictClustData"; version="0.2.6"; sha256="0mvy9299pg374gvvqs9lmj2j0f3bzyy279kjpz7jq35hkgz5wif3"; depends=[gee Hmisc MASS mvtnorm]; }; riskR = derive2 { name="riskR"; version="1.1"; sha256="1qadfyb07idfw0bs006kb3917rzda83di6jmsr22941gv78z1wyv"; depends=[]; }; riskRegression = derive2 { name="riskRegression"; version="2018.10.03"; sha256="1j0q0a9rkh9gmcidl6kwlmiiwn24cxg9yrx0i72py1b2765kqwk2"; depends=[abind cmprsk data_table doParallel foreach ggplot2 lava plotrix prodlim ranger Rcpp RcppArmadillo rms survival timereg]; }; riskSimul = derive2 { name="riskSimul"; version="0.1"; sha256="0s2a1mn6g11m96gqscb916caj2aykcs3rkacpqcdnlyzryk1gsnb"; depends=[Runuran]; }; risksetROC = derive2 { name="risksetROC"; version="1.0.4"; sha256="1fh0jf8v536qzf1v3awx3f73wykzicli4r54yg1z926ccqb4h80l"; depends=[MASS survival]; }; riskyr = derive2 { name="riskyr"; version="0.1.0"; sha256="1s6yrij5d1vhvzc7nnajjnjmxnhrs0r1psppcvwb0qg3ff181y22"; depends=[diagram vcd]; }; - ritis = derive2 { name="ritis"; version="0.7.2"; sha256="1bn7nfgg9f2y19fp747k96r9kmnrfsqib81a9rzbwv4b97ymg31s"; depends=[crul data_table jsonlite solrium tibble]; }; + ritis = derive2 { name="ritis"; version="0.7.6"; sha256="1a1q44dmagzf4k67pxa5x0s5s5jx9kpqg4s193c8r3m7kk3xwna6"; depends=[crul data_table jsonlite solrium tibble]; }; riv = derive2 { name="riv"; version="2.0-5"; sha256="0n19jlrs12iysq45xyi3zvghkircg0ww5vbsfpnqkw5b22zsv30s"; depends=[MASS quantreg rrcov]; }; riverdist = derive2 { name="riverdist"; version="0.15.0"; sha256="145mvqnhv12dcvss54wdycgb3wwk95phl4kx5z0jnh3kmm1zsdl4"; depends=[rgdal sp]; }; rivernet = derive2 { name="rivernet"; version="1.1"; sha256="1brdgm2fbdq4qw85va6isj7p9bva4sj3spgsx8nsqvc8vaa90y4p"; depends=[]; }; @@ -11314,10 +11408,10 @@ in with self; { rms_gof = derive2 { name="rms.gof"; version="1.0"; sha256="1n0h3nrp11f2x70mfjxpk2f3g4vwjaf4476pjjwy49smxxlxwz82"; depends=[]; }; rmsfact = derive2 { name="rmsfact"; version="0.0.3"; sha256="05s23rfs9prr2ia3h4h9y614xhv91lbgppgf3mrrssxkwz220kd5"; depends=[]; }; rmsfuns = derive2 { name="rmsfuns"; version="0.0.0.2"; sha256="0by2d6l25lf5vidxbkcxghpxycffyldzzbxcw6h4rm86zmkkv1m0"; depends=[magrittr purrr readr tidyverse xts zoo]; }; - rmumps = derive2 { name="rmumps"; version="5.1.2-4"; sha256="1qdpvyxwb18dapa8xqj8kjjmrnrqixkn29qn6q4cnwdwi1zcbdx6"; depends=[Rcpp]; }; + rmumps = derive2 { name="rmumps"; version="5.1.2-5"; sha256="09jw5h122mpsx4idmzadhvsc4bx74fydxmxsx9fpsfsz9k9dqyhq"; depends=[Rcpp]; }; rmutil = derive2 { name="rmutil"; version="1.1.1"; sha256="0yyzypkz6jjqvhafg6ipml8hrhr0w9l6j2vnmf0gdy90xj78mgag"; depends=[]; }; rmweather = derive2 { name="rmweather"; version="0.1.3"; sha256="1qdf511vmpffrdfcxlll54km2s0pf6pdswj8401k4ymv5iif91hl"; depends=[dplyr ggplot2 lubridate magrittr pdp purrr ranger stringr strucchange tibble viridis]; }; - rmytarget = derive2 { name="rmytarget"; version="2.0.1"; sha256="0yccirp07i4dgqb3zf16rf29df78iqgpjsvbj2v42557dgjgbak2"; depends=[dplyr httr jsonlite lubridate stringr]; }; + rmytarget = derive2 { name="rmytarget"; version="2.1.0"; sha256="110ckzqpipm98a7ddxr2ar0dym2qp9ix957rjx0ana9dx99nyp94"; depends=[dplyr httr jsonlite lubridate stringr]; }; rnaseqWrapper = derive2 { name="rnaseqWrapper"; version="1.0-1"; sha256="1fa3hmwrpccf09dlpginl31lcxpj5ypxspa0mlraynlfl5jrivch"; depends=[ecodist gplots gtools]; }; rnaturalearth = derive2 { name="rnaturalearth"; version="0.1.0"; sha256="193b31a7n9jhc607mhwxbpx5gr0fpj3qasm9dbi6kcc7vac3ilgm"; depends=[sf sp]; }; rnaturalearthdata = derive2 { name="rnaturalearthdata"; version="0.1.0"; sha256="1z32j5lz2lb8xgpkr73majw22k0b49iazj6jjc7j4w9k4zxxa102"; depends=[sp]; }; @@ -11382,6 +11476,7 @@ in with self; { rolocISCCNBS = derive2 { name="rolocISCCNBS"; version="0.1"; sha256="100jh5m2c1zp5wg3wd4y2i47dzx1j0g6lfwyqmwk4bz99yzzz5am"; depends=[colorspace roloc]; }; rolr = derive2 { name="rolr"; version="1.0.0"; sha256="04nm4q0mlr4w6jb0frykzlyknfn3gn02ysqr5ll5jch6wawichy2"; depends=[survival]; }; rolypoly = derive2 { name="rolypoly"; version="0.1.0"; sha256="11nf7in6n03675l11ynl4rp20rlzy7jli3m518s4sqqxdm8f8ci7"; depends=[data_table dplyr foreach ggplot2 glmnet MASS Matrix matrixcalc]; }; + romero_gateway = derive2 { name="romero.gateway"; version="0.4.4"; sha256="0xs0kn96q3lnyrp40b38gvkxlxr337c5ah2qll44mip83fi98n26"; depends=[jpeg rJava]; }; rootSolve = derive2 { name="rootSolve"; version="1.7"; sha256="08ic6ggcc5dw4nv9xsqkm3vnvswmxyhnqnv1rdjv1h2gy1ivpcq8"; depends=[]; }; rootWishart = derive2 { name="rootWishart"; version="0.4.1"; sha256="1l9pr3i20hi5k02qnlb3blxhlvp2j0njn74xslw3gcjvyzjlr12j"; depends=[BH Rcpp RcppEigen]; }; roots = derive2 { name="roots"; version="1.0"; sha256="1ssmmmrg18xmqxs6f7dqv07357iwcvk21j1gxsl8s9njbj2plxai"; depends=[animation igraph rARPACK]; }; @@ -11446,8 +11541,8 @@ in with self; { rptR = derive2 { name="rptR"; version="0.9.21"; sha256="0wqh9d372s2222qm5w0wx77l2sj7zvdnl7zvxcn5wfs3cz84fj15"; depends=[lme4 pbapply]; }; rpubchem = derive2 { name="rpubchem"; version="1.5.10"; sha256="06j9ir65ykky5hdbyv74fnddwqd39jxvr6jig0kjqisc75k4spjz"; depends=[base64enc car data_table fingerprint iterators itertools RCurl RJSONIO stringr XML]; }; rqPen = derive2 { name="rqPen"; version="2.0"; sha256="13m21v753njaramgpbhn0lb793b6946crv5v8vl127w38q0z3wyd"; depends=[quantreg regpro]; }; - rqdatatable = derive2 { name="rqdatatable"; version="1.1.1"; sha256="1634llj4ykkn85ijj978k9rxclp7ff687vsvr9i2v5xppg7sbr5h"; depends=[data_table rquery wrapr]; }; - rquery = derive2 { name="rquery"; version="1.2.0"; sha256="0vid05sx73swfg13fd1kar4ggb9ri1pscc8rqz465sqmbknlp2r1"; depends=[wrapr]; }; + rqdatatable = derive2 { name="rqdatatable"; version="1.1.2"; sha256="12ai22q1qpk64zx9f6iw7l94bp390rglwpgiv6d5ssrwrbzy23p3"; depends=[data_table rquery wrapr]; }; + rquery = derive2 { name="rquery"; version="1.2.1"; sha256="1lshdmv8s9sqkv1wjyny5917c5shplbxfq3gl70qfggi8j5vq59m"; depends=[wrapr]; }; rr = derive2 { name="rr"; version="1.4"; sha256="1c2h6ibjfwrjfqh1if3c90pdh0g2rf3p71j4p9w23xbbrx2l80pl"; depends=[arm coda magic MASS]; }; rr2 = derive2 { name="rr2"; version="1.0.0"; sha256="1cflysdx7n8mcb2whqi3wirg67aszbf2h8x23bpg7xx1im1xmgy4"; depends=[ape lme4 Matrix phylolm]; }; rrBLUP = derive2 { name="rrBLUP"; version="4.6"; sha256="1bw4pjj9hm9ik5bvvklnlkykhlqm6k7pbkma1iwc3kbg8shpbd18"; depends=[]; }; @@ -11470,11 +11565,11 @@ in with self; { rrpack = derive2 { name="rrpack"; version="0.1-7"; sha256="0svrw2ik59hjyfb0kag4nv8ilcaz7irmkp7ndbxxn0jg7dacb411"; depends=[ggplot2 glmnet lassoshooting MASS Rcpp RcppArmadillo]; }; rrr = derive2 { name="rrr"; version="1.0.0"; sha256="0sv6k70mv325yjm8yjy4dw8cqc0xc071iiv94fk1l1yfz0n67prz"; depends=[dplyr GGally ggplot2 magrittr MASS plotly Rcpp]; }; rrtable = derive2 { name="rrtable"; version="0.1.0"; sha256="1rvqb32fr63dkm5kz291pxzli8yi10k76v0lm1qdn28cx1l6ff3y"; depends=[devEMF editData flextable ggplot2 magrittr moonBook officer purrr readr rmarkdown rvg shiny stringr ztable]; }; - rsMove = derive2 { name="rsMove"; version="0.2.6"; sha256="15mr2i0fv1k230ncfkbdk564rydsq9zy9bgwackbg9zlix8x7874"; depends=[caret gdalUtils ggplot2 igraph lattice lubridate plyr pryr randomForest raster RCurl rgdal sp spatialEco]; }; + rsMove = derive2 { name="rsMove"; version="0.2.7"; sha256="0an5kknfap7hrg62gvdvrylx79p6fjdmbryhzlrj60i8n7cnc1c1"; depends=[caret ggplot2 lubridate plyr pryr raster Rcpp RCurl sp]; }; rsae = derive2 { name="rsae"; version="0.1-5"; sha256="1f3ry3jwa6vg2vq2npx2pzzvfwadz8m48hjrqjk860nfjrymwgx5"; depends=[]; }; rsample = derive2 { name="rsample"; version="0.0.3"; sha256="1gdlx9irba0snyl5jv0gi6dwv5l044s2axjlnygh5narm2rhi4y1"; depends=[dplyr generics purrr rlang tibble tidyr]; }; rsatscan = derive2 { name="rsatscan"; version="0.3.9200"; sha256="00vgby24jknq8nl7rnqcwg7gawcxhwq8b7m98vjx2hkqx39n4g21"; depends=[foreign]; }; - rscala = derive2 { name="rscala"; version="3.2.5"; sha256="1qkg0kdixbsjava4xx5afbwq8d91fcx799bf0siadygm31aa9gcr"; depends=[]; }; + rscala = derive2 { name="rscala"; version="3.2.6"; sha256="0akwp6207dfv16arh99m7mfpwx0fjq01vlcs7spqn3bpk6qpjl4p"; depends=[]; }; rscimark = derive2 { name="rscimark"; version="1.0"; sha256="1jsjz4d5bnxb90qqzz42m4nyvm8d8w8bs0m1r5g2n78zmckqb8vy"; depends=[checkmate]; }; rsconnect = derive2 { name="rsconnect"; version="0.8.12"; sha256="1zw7rvkg0vcajcyvx8nhxgp1c4882pwmdij4zv1by2fr3qw32678"; depends=[jsonlite openssl packrat RCurl rstudioapi yaml]; }; rscopus = derive2 { name="rscopus"; version="0.6.3"; sha256="1fplb7wmzp78a1xi9b4bw6xis16gixhvl227yfhip650ib4srpv1"; depends=[dplyr httr plyr tidyr]; }; @@ -11495,14 +11590,13 @@ in with self; { rsoi = derive2 { name="rsoi"; version="0.4.0"; sha256="0aa4iiq5kh9l7wplvsqlgj89rnbr6p4bnnfn10dgfpyrpf7rqvza"; depends=[]; }; rsolr = derive2 { name="rsolr"; version="0.0.9"; sha256="1mxvzb7wvm1agv35r82pr1hxa3fimixcwf36j98qjlxj9p7valrw"; depends=[BiocGenerics graph RCurl restfulr rjson S4Vectors XML]; }; rspa = derive2 { name="rspa"; version="0.2.3"; sha256="171bwyxbjx2w8fz87jsbaghqxgmmkaxixhia0kp2y33ns6fc1hy9"; depends=[lintools validate]; }; - rsparkling = derive2 { name="rsparkling"; version="0.2.12"; sha256="0hx8ikgf3v0aaz3vshcv47ljasdhi52g68a0grfgzig2l3gmzbwk"; depends=[h2o sparklyr]; }; + rsparkling = derive2 { name="rsparkling"; version="0.2.14"; sha256="1d8mdmqppajl4l82jpw5jca9nsf0w4dv6gpw7jig1j7r6ynwc7cf"; depends=[h2o sparklyr]; }; rsppfp = derive2 { name="rsppfp"; version="1.0.3"; sha256="06lafgdbxaq3rifbz6mhvp5b3dm3vxz3dkzdmiz218xhvn4mdfry"; depends=[doParallel dplyr foreach igraph stringr tidyr]; }; rsq = derive2 { name="rsq"; version="1.1"; sha256="0pvnyf875jybid16mg1y3dmnlrk1vahckhr5zaai1a0k4i6mh4jf"; depends=[MASS]; }; rstack = derive2 { name="rstack"; version="1.0.0"; sha256="19vbfmkd6ymadah1y1w5rn52f4hviddccyc6qj2cv5viqwbwws2z"; depends=[R6]; }; rstackdeque = derive2 { name="rstackdeque"; version="1.1.1"; sha256="0i1qqbfj0yrqbkad8bqc1qlxmyxpn7zycbnq83cdmfbilcmi87ql"; depends=[]; }; rstan = derive2 { name="rstan"; version="2.18.2"; sha256="1zvh5qlxkwi947nqmlhazr7jwii68fpxnkcsr38s3m8havcxlxad"; depends=[BH ggplot2 gridExtra inline loo pkgbuild Rcpp RcppEigen StanHeaders]; }; rstanarm = derive2 { name="rstanarm"; version="2.18.2"; sha256="0jflfj7g1rx0zhq0kbi1b1zwad1m7lhbvymz43g5c9cx3hh4gi68"; depends=[bayesplot BH ggplot2 lme4 loo Matrix nlme Rcpp RcppEigen rstan rstantools shinystan StanHeaders survival]; }; - rstansim = derive2 { name="rstansim"; version="0.1.1"; sha256="09hg4ishzp6q90nrl94h21al0ad0jn7fr8brp8f0xa9cvkwlzjpg"; depends=[doRNG doSNOW foreach loo Rcpp rstan]; }; rstantools = derive2 { name="rstantools"; version="1.5.1"; sha256="11dlrz3mj1j9qigh2qff0ixdcfds4ppxd37112yq8bn16b0idasw"; depends=[]; }; rstatscn = derive2 { name="rstatscn"; version="1.1.1"; sha256="0aj4x3lyrldpgh90v90qbxylndacn5ri5yqff3qy53q45ar7yji3"; depends=[httr jsonlite]; }; rstiefel = derive2 { name="rstiefel"; version="0.20"; sha256="1wrl7rc4nrnxjs26l9v36x3mpx33mjijk27nbzidwrhp9gppzz1i"; depends=[]; }; @@ -11569,7 +11663,7 @@ in with self; { rvgtest = derive2 { name="rvgtest"; version="0.7.4"; sha256="1lhha5nh8fk42pckg4ziha8sa6g20m0l4p078pjj51kz0k8929ng"; depends=[]; }; rviewgraph = derive2 { name="rviewgraph"; version="1.2"; sha256="0qw1fdfwg2763a1k1qmryblw5rpagsi5p70rs7fj256zfcjvwrz8"; depends=[rJava]; }; rvinecopulib = derive2 { name="rvinecopulib"; version="0.3.0.1.1"; sha256="09zs1ckc5c0z4xg6h348v8nig37b400mkwsa0z4hn7rrhjf5i3gf"; depends=[assertthat BH cctools kde1d lattice Rcpp RcppEigen RcppThread wdm]; }; - rwalkr = derive2 { name="rwalkr"; version="0.3.4"; sha256="1zx58l92finzkrivp214hbldkcbpdjgx0k6bwz22spp0lgnzi9mp"; depends=[dplyr httr tibble tidyr]; }; + rwalkr = derive2 { name="rwalkr"; version="0.4.0"; sha256="01ia1wkmbigly45kyc1ydrah0yzxlymsnj3vy6wf8ck24lv51dif"; depends=[dplyr httr tidyr]; }; rwars = derive2 { name="rwars"; version="1.0.0"; sha256="0kmwpr6gn3xsf0pqx153vblpjbhc34mzlgyv8xb2nw78nf8znfij"; depends=[httr]; }; rwavelet = derive2 { name="rwavelet"; version="0.1.0"; sha256="15shy8v659r3qnx32hrq6zn5fwinwg6aiys71f45k0s9jhj973ki"; depends=[dplyr signal]; }; rwc = derive2 { name="rwc"; version="1.11"; sha256="1qhgkbkp4nz0wq5c4x8232xiszpiyzcdklfgvpnx4cbp3bbfdi4g"; depends=[MASS Matrix mvtnorm raster]; }; @@ -11678,11 +11772,11 @@ in with self; { scatterD3 = derive2 { name="scatterD3"; version="0.8.2"; sha256="1cfh060ffwxy33b1f7n8mba1sbbwgx28mqn08im16dqbphkcmx1z"; depends=[digest ellipse htmlwidgets]; }; scatterpie = derive2 { name="scatterpie"; version="0.1.2"; sha256="0r3m3781jvzxr0ry7rhd085c0xl5620sf5zcq9nnfl613imwxj2b"; depends=[ggforce ggplot2 rlang rvcheck tidyr]; }; scatterplot3d = derive2 { name="scatterplot3d"; version="0.3-41"; sha256="152xqz9c70qab86mpgng049gxsg5f4fpf1m8dh93fb9v1avjd0sc"; depends=[]; }; - scclust = derive2 { name="scclust"; version="0.2.0"; sha256="11jnjij62vcnvbd9m27xjdmyjib35isviqb07435yas93bn01vz4"; depends=[distances]; }; + scclust = derive2 { name="scclust"; version="0.2.2"; sha256="0w0qwz8wfdprs2bgv1cjvd2yb6g12jylad21a9rr3w5bkgxprcrp"; depends=[distances]; }; scdensity = derive2 { name="scdensity"; version="1.0.2"; sha256="173xm3bf8vxl30zk4n451al7m003byg9q4d1l1pfyfa4xnv8qdg9"; depends=[lpSolve quadprog]; }; scdhlm = derive2 { name="scdhlm"; version="0.3.1"; sha256="1b5x4kqvmkpb8wbgfhnwqakisw6hfnvama2bsnd8kvw4alfanxhm"; depends=[nlme]; }; scenario = derive2 { name="scenario"; version="1.0"; sha256="0v1b00kiny21yx4qkk2x51cy1zqibdnd68z76qia7h5py28yhxsi"; depends=[]; }; - schoRsch = derive2 { name="schoRsch"; version="1.4"; sha256="19k34i74ira71v0r5gz9rfnbadnjzi0wpxcm4zqqn7y6jpmfbd11"; depends=[]; }; + schoRsch = derive2 { name="schoRsch"; version="1.5"; sha256="025pcfg0x633a3d830vappm8isxf6gnj7p7h587w8c4m723ddbn9"; depends=[]; }; schoenberg = derive2 { name="schoenberg"; version="2.0.2"; sha256="17pbw9266r9lv9blygmvq9285kcrcy07jaqrj3zfa2pg0zyvhjvm"; depends=[crayon]; }; scholar = derive2 { name="scholar"; version="0.1.7"; sha256="142iwrips1589fa0g1178a6s1cz4dfcv9b0qs570q6b6ccfjxi6r"; depends=[dplyr ggplot2 ggraph httr R_cache rvest stringr tidygraph xml2]; }; schoolmath = derive2 { name="schoolmath"; version="0.4"; sha256="06gcmm294d0bs5whvknrq48sk7li961lzy4bcncjg052zbbpn67x"; depends=[]; }; @@ -11744,7 +11838,7 @@ in with self; { searcher = derive2 { name="searcher"; version="0.0.3"; sha256="004k757hn5y80k7kim3049n3mjrsimqpzdz5fis2ggxbdwwf1bs1"; depends=[]; }; seas = derive2 { name="seas"; version="0.5-2"; sha256="0hn4d5dc01zyycd7l3vj1sx6bq668n7fzffw9ypaa5l20fizs0ay"; depends=[MASS]; }; season = derive2 { name="season"; version="0.3.8"; sha256="0kw3gvy7rv0rms0zj1rvqlfdn3yxr9r9ldm21zl2xrpx9cy04d2d"; depends=[ggplot2 MASS survival]; }; - seasonal = derive2 { name="seasonal"; version="1.6.1"; sha256="1nvavn84f2zb0f6n352br52wcrcmnxv6vprzcpymrnzik7pyp8y6"; depends=[x13binary]; }; + seasonal = derive2 { name="seasonal"; version="1.7.0"; sha256="1mna8w1haj5h2rhiw7jkhprr6cc9qr0n8x73d10v0l732kx41n31"; depends=[x13binary]; }; seasonalview = derive2 { name="seasonalview"; version="0.3"; sha256="1l705yc7ssldsfckbgnvd95sh3zzhpkmf1rr6ar2s60s3wsyly4n"; depends=[dygraphs htmlwidgets openxlsx seasonal shiny shinydashboard xtable xts zoo]; }; seawaveQ = derive2 { name="seawaveQ"; version="1.0.0"; sha256="19vm1f0qkmkkbnfy1hkqnfz6x2a7g9902ka76bhpcscynl69iy56"; depends=[lubridate NADA survival]; }; secr = derive2 { name="secr"; version="3.1.8"; sha256="02m7iac6z41w49lxnbfpfw20h272wnmg16ys3lpi1d0rli5xghg4"; depends=[abind MASS mgcv nlme raster sp stringr]; }; @@ -11758,6 +11852,7 @@ in with self; { seedy = derive2 { name="seedy"; version="1.3"; sha256="1a21sl8i7z12cjaqj08lkq3viazxlgxv82vaarm58fgbpsvdi0m0"; depends=[]; }; seewave = derive2 { name="seewave"; version="2.1.0"; sha256="0i0zhvgl64fwpabnwvfdxndmw5whhh2fd4lhpg399w4rzrwzv92y"; depends=[tuneR]; }; seg = derive2 { name="seg"; version="0.5-5"; sha256="0q1k3zh29pkxx2sq28dw1vn4nmdv7pa8pw48vmywfcm4vmqnx7xg"; depends=[sp splancs]; }; + segMGarch = derive2 { name="segMGarch"; version="1.0"; sha256="19bfqk7wpzwvkbajn96l92rgaa2af05rz42xgbjgq9sfc64hx3p7"; depends=[corpcor doParallel fGarch foreach iterators mvtnorm Rcpp RcppArmadillo]; }; segclust2d = derive2 { name="segclust2d"; version="0.1.0"; sha256="0kymw36cvakx84c96npkbnsvv0a1s82773ib5c802ybvkb2r1k9p"; depends=[dplyr ggplot2 magrittr plyr RColorBrewer Rcpp RcppArmadillo reshape2 scales zoo]; }; segmag = derive2 { name="segmag"; version="1.2.4"; sha256="1i717xg1z7s35pkwzywgjf9wx7zj9xksv0k87h7p1q62y073qbqm"; depends=[plyr Rcpp]; }; segmented = derive2 { name="segmented"; version="0.5-3.0"; sha256="0nrik5fyq59hwiwjcpbi4p5yfavgfjq6wyrynhkrbm4k6v1g1wlq"; depends=[]; }; @@ -11795,6 +11890,7 @@ in with self; { sensiPhy = derive2 { name="sensiPhy"; version="0.8.3"; sha256="03qrxal0wvgiyr5vnnzc8n95h4460p11idnmr6vnr73c5f8q905h"; depends=[ape caper geiger ggplot2 phylolm phytools]; }; sensitivity = derive2 { name="sensitivity"; version="1.15.2"; sha256="0ilb79bbplnv5qlismp21jrzfxr1is59vww3s1p99ax303614w7m"; depends=[boot]; }; sensitivity2x2xk = derive2 { name="sensitivity2x2xk"; version="1.01"; sha256="1r829k939zzmi0j4chdaniajchcflmmjrl3a9hwnkg0wkfnjbvdl"; depends=[BiasedUrn mvtnorm]; }; + sensitivityCalibration = derive2 { name="sensitivityCalibration"; version="0.0.1"; sha256="1fn07dra7dhpsg6f1yn1ayfpmvwaxma8cps94070nrpfwmdvi04g"; depends=[ggplot2 ggrepel plotly relaimpo splitstackshape stringi]; }; sensitivityPStrat = derive2 { name="sensitivityPStrat"; version="1.0-6"; sha256="0rfzvkpz7dll3173gll6np65dyb40zms63fkvaiwn0lk4aryinlh"; depends=[survival]; }; sensitivityfull = derive2 { name="sensitivityfull"; version="1.5.6"; sha256="0g2gc4rms6gd34d23kxj50pjh0yq1h6yiybj4dxwyf6i2652irhq"; depends=[]; }; sensitivitymult = derive2 { name="sensitivitymult"; version="1.0.2"; sha256="19pyq6c7pvr3zkz3dz5p2hhfcvwm0im0bwaw4yhhgin4kqfnfjd5"; depends=[]; }; @@ -11805,9 +11901,9 @@ in with self; { sensory = derive2 { name="sensory"; version="1.1"; sha256="1zd0ajrymxi6gygcq9fqgwgy0g6c3cqz53x0k5m0ihbmh11rc7s7"; depends=[gtools MASS Matrix]; }; senstrat = derive2 { name="senstrat"; version="1.0.3"; sha256="0j6mb55v5ivqvk8nn8fjlzrbdgj6csa58yc6gy1g07m7gk2qz2np"; depends=[BiasedUrn MASS]; }; sentimentr = derive2 { name="sentimentr"; version="2.6.1"; sha256="1xwi3rjyhx3w042r2g4a8rzqr2svam7fdx2ivc9vyhj9y81az7fh"; depends=[data_table ggplot2 lexicon stringi syuzhet textclean textshape]; }; - sentometrics = derive2 { name="sentometrics"; version="0.5.5"; sha256="0snrajyw9zlvzyxqb3l74h2dn79fp8y0q5hhx0z0gzw2lw36avqp"; depends=[caret data_table foreach ggplot2 glmnet ISOweek quanteda Rcpp RcppArmadillo RcppParallel RcppRoll stringi]; }; + sentometrics = derive2 { name="sentometrics"; version="0.5.6"; sha256="073xhygj833a8k249kw5sbg7jmmcs9k4fsva88say5xhkbq62yqr"; depends=[caret data_table foreach ggplot2 glmnet ISOweek quanteda Rcpp RcppArmadillo RcppParallel RcppRoll stringi]; }; separationplot = derive2 { name="separationplot"; version="1.1"; sha256="0qfkrk8n6jj8l7ywngwsaikfwmd9hbrpr43x0l9wkjjp1asgs5l6"; depends=[]; }; - seplyr = derive2 { name="seplyr"; version="0.8.2"; sha256="0inqnrqf2dld2dkhwp16iz8hzrvi01jbj437ghhvprfp06320lxg"; depends=[dplyr rlang tidyr wrapr]; }; + seplyr = derive2 { name="seplyr"; version="0.8.3"; sha256="1v4rr7v1hsrn15r4cbqd6ym9j9aiwnkmcix585fj3d4vfy1jklh5"; depends=[dplyr rlang tidyr wrapr]; }; seqCBS = derive2 { name="seqCBS"; version="1.2"; sha256="1kywi3kvvl9y6nm7cwf6fj8gz9gzznp5va336g1akzgy77k82d8v"; depends=[clue]; }; seqDesign = derive2 { name="seqDesign"; version="1.1"; sha256="1694swd8ik9fbiflmnw4xpq82kq18rqzkw0dv5pvq30c47xjgamv"; depends=[survival xtable]; }; seqHMM = derive2 { name="seqHMM"; version="1.0.9"; sha256="1rkcdj73h5jvqrjc24wjbig99il6ppkjy82255avbn1bdrrnrins"; depends=[gridBase igraph Matrix nloptr numDeriv Rcpp RcppArmadillo TraMineR]; }; @@ -11822,7 +11918,7 @@ in with self; { sequenza = derive2 { name="sequenza"; version="2.1.2"; sha256="0f3aj96qvbr1wqimlv6rxg0v34zlrgc6pbdy7sfkwfzs1n44q1xf"; depends=[copynumber squash]; }; sequoia = derive2 { name="sequoia"; version="1.1.1"; sha256="12s6890jr9rvp45h1hrfwpndsrr7na0kz1a29hd96ycnk7bvd1ic"; depends=[plyr]; }; sergeant = derive2 { name="sergeant"; version="0.5.2"; sha256="02chkyvmwd4nimw62v82rfbid1xqw5b1335na44pdi675g904250"; depends=[DBI dbplyr dplyr htmltools httr jsonlite purrr readr scales]; }; - serial = derive2 { name="serial"; version="2.1.2"; sha256="0bv8jal3l2bq4qdz7qbl0mfmx11s9zpdilymcc6myxsr7fcv7laq"; depends=[]; }; + serial = derive2 { name="serial"; version="2.1.3"; sha256="0lr0sdkg4iv2sg12c05psck7cx0rd94jjrgb3gl372xyfckpacgf"; depends=[]; }; seriation = derive2 { name="seriation"; version="1.2-3"; sha256="1q6hw4hjw224b4y0dc0j630v2pgj6sn455nwkilb70w8k31hpk92"; depends=[cluster colorspace dendextend gclus gplots MASS qap registry TSP]; }; serieslcb = derive2 { name="serieslcb"; version="0.2.0"; sha256="1af7mvfiv40hwjlf6f53grw48c343rnmzxiyw4yx95mf8rk46bsd"; depends=[gplots shiny]; }; seroincidence = derive2 { name="seroincidence"; version="2.0.0"; sha256="0sam4y7w6prswz0izkm1a9v2k5rv7z22g1ajy15n9xix9aml5ms4"; depends=[]; }; @@ -11836,7 +11932,7 @@ in with self; { setter = derive2 { name="setter"; version="0.0-1"; sha256="10fwrx8yysp99rrkbnn3rbz79vyzr2h3p7zxxlqapw1k2lllp0r5"; depends=[assertive_base]; }; settings = derive2 { name="settings"; version="0.2.4"; sha256="092sv6nccm6p2d695l9w0zfi2xgymk12c8p8lhl9nb86mxrb3nry"; depends=[]; }; severity = derive2 { name="severity"; version="2.0"; sha256="1mp19y2pn7nl9m8xfljc515kk5dirv0r2kypazpmd956lcivziqq"; depends=[]; }; - sf = derive2 { name="sf"; version="0.7-1"; sha256="0xpgv1fyha61s5sa2msgsznl23yi2rpki6jnjv7xg1a26bl0il89"; depends=[classInt DBI magrittr Rcpp units]; }; + sf = derive2 { name="sf"; version="0.7-2"; sha256="17ncyb121h0yw1b25r93jn2378qgp5bwblvsyv2qzr9fjvdd6nfq"; depends=[classInt DBI magrittr Rcpp units]; }; sfa = derive2 { name="sfa"; version="1.0-1"; sha256="1acqxgydf8j5csdkx0yf169x3yaa31r0ccdrqarh6vj1hacm89ad"; depends=[]; }; sfadv = derive2 { name="sfadv"; version="1.0.1"; sha256="1rfpm6km5pckwhqgpvidm6qsj5sjdaqqj5b0sgvpslivfa4c80cr"; depends=[gmm minpack_lm]; }; sfc = derive2 { name="sfc"; version="0.1.0"; sha256="0cm4mfcfd9bhf2j5fppsihzrfipnldb6q3xradd88z9pwgrkfx2a"; depends=[dplyr sna tidyr triangle zoo]; }; @@ -11991,7 +12087,6 @@ in with self; { sirt = derive2 { name="sirt"; version="3.0-32"; sha256="0rxshvpr82j5f90c337jzx8dlz355azm8sfn1xq8kvxjr6brymyb"; depends=[CDM coda lavaan lavaan_survey MASS mirt mvtnorm Rcpp RcppArmadillo sfsmisc survey TAM]; }; sisVIVE = derive2 { name="sisVIVE"; version="1.4"; sha256="1vh53irxgk8ahw52cdqbbm89dvmzyf54izg4lm8a3v92k5p6nzwz"; depends=[lars]; }; sisal = derive2 { name="sisal"; version="0.46"; sha256="00szc3l69i0cksxmd0lyrs4p6plf05sl4vxs3nl4gkbja5y4lvpc"; depends=[boot digest lattice mgcv R_matlab R_methodsS3]; }; - sisus = derive2 { name="sisus"; version="3.9-13"; sha256="0lz9ww07dvdx6l3k5san8gwq09hycc3mqwpgzmr2ya9z8y27zadr"; depends=[coda gdata gtools MASS moments polyapost rcdd RColorBrewer]; }; sitar = derive2 { name="sitar"; version="1.1.0"; sha256="1a2x6igzq0i1vac54xyiq14vzx0m20431nv7aw0anv0lss7xy6r8"; depends=[dplyr nlme quantreg rlang tibble]; }; sitmo = derive2 { name="sitmo"; version="2.0.0"; sha256="11mzkdh01cfazxqxxlhm0ifbiggpw54k5n9qpz3vxbq10v9720h9"; depends=[Rcpp]; }; sitools = derive2 { name="sitools"; version="1.4"; sha256="0c0qnvsv06g6v7hxad96fkp9j641v8472mbphvaxa60k3xc7ackb"; depends=[]; }; @@ -11999,10 +12094,10 @@ in with self; { sitreeE = derive2 { name="sitreeE"; version="0.0-2"; sha256="0w4gbdjphanfy614jv4zp70kl901zz5hblk35lyv7rjxifq5bpx0"; depends=[sitree]; }; sivipm = derive2 { name="sivipm"; version="1.1-3"; sha256="1l0j1bi38s09ax4kwikk615lyd074gzg1aa1j2jfmhr3igannm3z"; depends=[seqinr]; }; sizeMat = derive2 { name="sizeMat"; version="1.0.0"; sha256="05dw4hgpw5msgy5cabf5dixr6ma66i9wz9wlajihqkpbg134jz1k"; depends=[MASS matrixStats mcmc MCMCpack]; }; - sjPlot = derive2 { name="sjPlot"; version="2.6.1"; sha256="13qvw2s3r96qfi8kfsn76m050ccnmckl31a9qv94xws8da99v2fk"; depends=[broom dplyr forcats ggeffects ggplot2 glmmTMB knitr lme4 magrittr MASS modelr nlme psych purrr rlang scales sjlabelled sjmisc sjstats tidyr]; }; + sjPlot = derive2 { name="sjPlot"; version="2.6.2"; sha256="0x9pbchmz4qf4c9bi52dhhgv1phfj03q1hnxic8vndl6xwib63cy"; depends=[broom dplyr forcats ggeffects ggplot2 glmmTMB knitr lme4 magrittr MASS modelr nlme psych purrr rlang scales sjlabelled sjmisc sjstats tidyr]; }; sjdbc = derive2 { name="sjdbc"; version="1.6.0"; sha256="17ncgj2s2pjn3w3c1dgxv8g7y17h4p78iic86gsj2ahn0xpsmkcc"; depends=[rJava]; }; sjlabelled = derive2 { name="sjlabelled"; version="1.0.15"; sha256="0k21z9w5ys42d0ijraaa4l8n9izwsk226xflzhp3065xw4b19b90"; depends=[broom dplyr haven magrittr prediction purrr rlang snakecase]; }; - sjmisc = derive2 { name="sjmisc"; version="2.7.6"; sha256="1jhrigikjpkdar3jxvi7qhqsg6lgjkjqhqll9vaay98b88rfc2im"; depends=[broom crayon dplyr haven magrittr purrr rlang sjlabelled stringdist stringr tidyr]; }; + sjmisc = derive2 { name="sjmisc"; version="2.7.7"; sha256="0xm9pmq17maivmjsygwx3bdjd71hf829qbx735hyxa69z9dhp24q"; depends=[broom crayon dplyr haven magrittr purrr rlang sjlabelled stringdist stringr tidyr]; }; sjstats = derive2 { name="sjstats"; version="0.17.2"; sha256="0c7g35vn7r9rylhp0gj1yfslg7jybwrhpqpp7vdcd90xfccih24r"; depends=[bayesplot broom coin crayon dplyr emmeans glmmTMB lme4 magrittr MASS Matrix modelr nlme purrr pwr rlang sjlabelled sjmisc tidyr]; }; skda = derive2 { name="skda"; version="0.1"; sha256="0a6mksr1d0j3pd0kz4jb6yh466gvl4fkrvgvnlmvivpv6b2gqs3q"; depends=[]; }; skeleSim = derive2 { name="skeleSim"; version="0.9.8"; sha256="1wxdl30cy8vr1cd0wcjxyklp6crw4bv8r77ma2dkzmxm2ma5jw92"; depends=[adegenet ape hierfstat igraph markdown pegas reshape2 rmetasim shiny shinyFiles strataG swfscMisc]; }; @@ -12014,10 +12109,10 @@ in with self; { skm = derive2 { name="skm"; version="0.1.5.4"; sha256="06g3bdncq2r56d8k3dr87gqnibypbsps0gj4jxkw9q1sq1yaff3v"; depends=[data_table magrittr plyr Rcpp RcppArmadillo RcppParallel]; }; skmeans = derive2 { name="skmeans"; version="0.2-11"; sha256="1a8nwlym6pf0z13nnw1id2wls9lq788860yhjaqd56c3slzfsymn"; depends=[clue cluster slam]; }; skpr = derive2 { name="skpr"; version="0.57.0"; sha256="0n33ymjaf3dx6gb753r03fnjqiwsjk997cy81xv9631n2zfn2aa5"; depends=[car doParallel doRNG foreach future iterators kableExtra knitr lme4 magrittr nlme promises Rcpp RcppEigen rintrojs shiny shinyjs shinythemes survival viridis]; }; - skynet = derive2 { name="skynet"; version="1.2.2"; sha256="1k6909fm40g6ianzjzbrv93x0fx2l8lnwl38krb7r50g1yk7lnrd"; depends=[data_table dplyr ggplot2 ggrepel igraph maps stringr]; }; + skynet = derive2 { name="skynet"; version="1.3.0"; sha256="02kkgrqcrg1x61fip47w6vzi8nya12rxg47qjhn4lw4czaympqpx"; depends=[data_table dplyr ggplot2 ggrepel httr igraph maps stringr]; }; skyscapeR = derive2 { name="skyscapeR"; version="0.2.2"; sha256="08h3vvn9zglw3xrl0xpyj95r1n3v6lk835a4nbanxdvi21mgpi77"; depends=[astrolibR doParallel foreach MESS numDeriv oce plotrix png pracma RColorBrewer rootSolve]; }; slackr = derive2 { name="slackr"; version="1.4.2"; sha256="1vm2h5fzcss3xx1annx68wrvv6c0s6h2ci0bipxmdl9amdaqw85w"; depends=[dplyr ggplot2 httr jsonlite]; }; - slam = derive2 { name="slam"; version="0.1-43"; sha256="0hy4qzngcgafxxr6ld7n9a9wy979ji998gpcc32vidwyab66dj5h"; depends=[]; }; + slam = derive2 { name="slam"; version="0.1-44"; sha256="11n956kid70931z0qyiql3v7nac1cfkamq44kzf9wl670pf8b033"; depends=[]; }; sld = derive2 { name="sld"; version="0.3.2"; sha256="0za5pw7ki419ni9pqqzddb10d16nvv5rh5jrkl4f77j0ps2ajylp"; depends=[lmom]; }; sleekts = derive2 { name="sleekts"; version="1.0.2"; sha256="0syk244xrsv8hz5sxm7wizk0kyn1nc6z4c63c8xn57fz130zj75k"; depends=[]; }; sleepr = derive2 { name="sleepr"; version="0.3.0"; sha256="1ka4pl6a09d1qga5svcirc5ywmzz9pcml09053745lz3p1v8fnn3"; depends=[behavr data_table]; }; @@ -12065,9 +12160,9 @@ in with self; { smoother = derive2 { name="smoother"; version="1.1"; sha256="0nqr1bvlr5bnasqg74zmknjjl4x28kla9h5cxpga3kq5z215pdci"; depends=[TTR]; }; smoothie = derive2 { name="smoothie"; version="1.0-1"; sha256="12p4ig8fbmlsby5jjd3d27njv8j7aiwx0m2n1nmgvjj0n330s1kj"; depends=[]; }; smoothmest = derive2 { name="smoothmest"; version="0.1-2"; sha256="14cri1b6ha8w4h8m26b3d7qip211wfv1sywgdxw3a6vqgc65hmk5"; depends=[MASS]; }; - smoothr = derive2 { name="smoothr"; version="0.1.0"; sha256="19ylhy7jz445yafdxlygs91vl4vrnnhggc2grwap0dcz0cazik1d"; depends=[sf units]; }; + smoothr = derive2 { name="smoothr"; version="0.1.1"; sha256="03pqvblrw0qj55gncn6a3hb0y0y64k8v1a2a8g64p53jjmlrw9nv"; depends=[sf units]; }; smoothtail = derive2 { name="smoothtail"; version="2.0.5"; sha256="1sqkwniz9m03k23nba9ndmdm0g03mdshzm8risr6wz98jcqjilrk"; depends=[logcondens]; }; - smotefamily = derive2 { name="smotefamily"; version="1.2"; sha256="166gqwqljips2r0030m3q44zmxlnxcpb9hmwbg1bk3dqk9gfl8ra"; depends=[]; }; + smotefamily = derive2 { name="smotefamily"; version="1.3"; sha256="1j027p392rz7n9jgwsj9i0lnmxqxjqkrsmpsg8ki5vhlilx68f3a"; depends=[dbscan FNN igraph]; }; smovie = derive2 { name="smovie"; version="1.0.1"; sha256="0nh228vp06w83wm826vw62gzy0zk66ng61safwvhl8lgaxkbwqmj"; depends=[revdbayes rpanel SuppDists]; }; smpic = derive2 { name="smpic"; version="0.1.0"; sha256="0ff2146gjcrc6nvrbf4779jh076abhb843zzlk2zvqir13qfap61"; depends=[ggplot2 imager stringr]; }; sms = derive2 { name="sms"; version="2.3.1"; sha256="0vr5jy8bxbczaqr9kg0fnanxhv9nj51yzgacrb63k33cs85p981m"; depends=[doParallel foreach iterators]; }; @@ -12119,7 +12214,7 @@ in with self; { solartime = derive2 { name="solartime"; version="0.0.1"; sha256="0q6la6d281zgf1kxhrdvi3b91na60szknq0fvldvlnszlqb5vkgs"; depends=[lubridate]; }; solitude = derive2 { name="solitude"; version="0.1.0"; sha256="0kfjp2zrlpxwgriv2b0br0ij0bnjkhjyqw532f89378s9jy6izsf"; depends=[data_table igraph ranger]; }; solrad = derive2 { name="solrad"; version="1.0.0"; sha256="13ybllvmig1yqsy4md4kazs83hxb9lrlwy64yw1wwr1w6sxpbnp6"; depends=[]; }; - solrium = derive2 { name="solrium"; version="1.0.0"; sha256="1rlf60kynqb8pvzllfdkiabxgnqx60hwm8vy86y9f2bh7d7jsdhf"; depends=[crul dplyr jsonlite plyr R6 tibble xml2]; }; + solrium = derive2 { name="solrium"; version="1.0.2"; sha256="011yyn2fwk222w3cn0zr7pf4d8fxwxqp2i6x6b89ns58lipcrbhd"; depends=[crul dplyr jsonlite plyr R6 tibble xml2]; }; solvebio = derive2 { name="solvebio"; version="2.6.1"; sha256="17zcnfmccfl2njv1ph40jchxb06x0qhgn82fz4yg8nqyf8b9cq5h"; depends=[dplyr httr jsonlite mime]; }; som = derive2 { name="som"; version="0.3-5.1"; sha256="1fbza1jxvwrkf5x3inkj36vshhkn7mz0ajqlxalbfmk6ngjw1x56"; depends=[]; }; som_nn = derive2 { name="som.nn"; version="1.1.0"; sha256="0mw2c2lqvdq9bhndpjyawjy43l4x7clcsx2350j45g7fnchhy602"; depends=[class hexbin kohonen som]; }; @@ -12127,7 +12222,7 @@ in with self; { someKfwer = derive2 { name="someKfwer"; version="1.2"; sha256="0widny5l04ja91fy16x4giwrabwqhx0fs3yl48pv9xh4zj6sx563"; depends=[]; }; someMTP = derive2 { name="someMTP"; version="1.4.1"; sha256="19bsn8rny1vv9343bvk8xzhh82sskl0zg0f5r59g9k812q5llchn"; depends=[]; }; somebm = derive2 { name="somebm"; version="0.1"; sha256="1iwwc94k6znh4d3bbjnvwp4chc4wg0iy4v2f99cs4jasrsimb4p8"; depends=[]; }; - sommer = derive2 { name="sommer"; version="3.7.3"; sha256="0hbkb75yimgrp5ap2izazd1v2v9qpb1na893vj7vbr6kcx80zs82"; depends=[crayon lattice MASS Matrix Rcpp RcppArmadillo]; }; + sommer = derive2 { name="sommer"; version="3.8"; sha256="1x4hp1hlngi3gcn7gr16qd9lzsmv4j611sx8254z06fgw3gxlwd4"; depends=[crayon lattice MASS Matrix Rcpp RcppArmadillo]; }; somplot = derive2 { name="somplot"; version="1.6.4"; sha256="06c8p2lqz3yxmxdl7ji8a3czvxnsbl7bwyiig76pkwc3a5qqfbb9"; depends=[hexbin]; }; sonar = derive2 { name="sonar"; version="1.0.2"; sha256="1f0f5iqi3y9vnxyym14nm8dqxw0vcpnxmvvkx4sm612i4fclg1f9"; depends=[]; }; sonicLength = derive2 { name="sonicLength"; version="1.4.4"; sha256="1v46xzx3jxxxs2biyrq6xbv2lhpz1i95la93hj6dl4jfyikmx0im"; depends=[]; }; @@ -12174,11 +12269,11 @@ in with self; { spacetime = derive2 { name="spacetime"; version="1.2-2"; sha256="0bgaarh2ibj3z6z504mzcb94x6w2bh5vyn1ar1lllqf4wn93z78y"; depends=[intervals lattice sp xts zoo]; }; spacodiR = derive2 { name="spacodiR"; version="0.13.0115"; sha256="0c0grrvillpwjzv6fixviizq9l33y7486ypxniwg7i5j6k36nkpl"; depends=[colorspace picante Rcpp]; }; spacom = derive2 { name="spacom"; version="1.0-5"; sha256="0b6yh4q9f0ibwlwyckwaya9m645j22x6bdz9mz3chass8qza6bls"; depends=[foreach iterators lme4 Matrix nlme spdep]; }; - spacyr = derive2 { name="spacyr"; version="0.9.91"; sha256="03dpp26lq4a5x0p5l3l8d2gs9v2pc13c14ir8vf7ws46970f6var"; depends=[data_table reticulate]; }; - spaero = derive2 { name="spaero"; version="0.3.0"; sha256="1l6h6mri78b49mw6b1d9dirygfj57pdyqx6822llnj3wkdn2x87v"; depends=[]; }; + spacyr = derive2 { name="spacyr"; version="1.0"; sha256="02vfcj4sr08xb6004h0gfsa3szshikhjxn1yahhxz8g04zhsi1g0"; depends=[data_table reticulate]; }; + spaero = derive2 { name="spaero"; version="0.4.0"; sha256="0h4pa15wj4a1ipb0nb6fim8mb146rdkiz8gp6gma73ayaxrjyn11"; depends=[]; }; spagmix = derive2 { name="spagmix"; version="0.3-1"; sha256="0xfrm4i28sy490g5324bc43dxlrgcnzxg27gsd5b81mqi03sry9j"; depends=[abind mvtnorm RandomFields sparr spatstat]; }; - spam = derive2 { name="spam"; version="2.2-0"; sha256="02v78dmf263drmz3y099gbakbcvaxkb18900s7sw440cjfv691d1"; depends=[dotCall64]; }; - spam64 = derive2 { name="spam64"; version="2.2-0"; sha256="1kyj93drzvd4ph6x7wr318xq3ldrrdxb17rwxws39wa4gj7jkmkg"; depends=[]; }; + spam = derive2 { name="spam"; version="2.2-1"; sha256="04bfwwna013hrbl4k6w1cdiz5bkc83jlasivriyn5l9gkj2qskr2"; depends=[dotCall64]; }; + spam64 = derive2 { name="spam64"; version="2.2-1"; sha256="0y0v75kmzi7gq7461mhz8yh0n0jvvx7r7ly8nhfpiplcn751qw2y"; depends=[]; }; spanel = derive2 { name="spanel"; version="0.1"; sha256="1riyvvfij277mclgik41gyi01qv0k466wyk2wbqqhlvrlj79yzsc"; depends=[]; }; spanish = derive2 { name="spanish"; version="0.3.2"; sha256="1dg4wnvxhybhagag9xx27af6760dlclaivx27mfxywfha312xfpn"; depends=[magrittr xml2]; }; spant = derive2 { name="spant"; version="0.12.0"; sha256="17668h6m7bfjyp5imr9zgkhhlaqwnrajqpvira0kns6hh99w2ysn"; depends=[abind complexplus foreach magrittr matrixcalc minpack_lm nnls plyr pracma readr signal smoother stringr svd tibble tkrplot]; }; @@ -12224,7 +12319,7 @@ in with self; { spatial_tools = derive2 { name="spatial.tools"; version="1.6.0"; sha256="1jh9psc2im0mp52mmz596x5h64m6w1d8hibnm7x52di5j2jp29vz"; depends=[abind doParallel foreach iterators mmap raster rgdal sp]; }; spatialClust = derive2 { name="spatialClust"; version="1.1.1"; sha256="042yrmh1rb0hxynxlbdpcissgy9zazs5aqx7vj388ibynzijck3r"; depends=[ggplot2 maptools rgeos sp]; }; spatialCovariance = derive2 { name="spatialCovariance"; version="0.6-9"; sha256="1m86s9a059spp97y37dcirrgjshcqzpdj11cq92vji624w4nrhlb"; depends=[]; }; - spatialEco = derive2 { name="spatialEco"; version="1.1-0"; sha256="1cvll6z775w8nvl5q5p62qgp3j2d0kcdb2avqwcqybk23jlxl7dr"; depends=[cluster EnvStats maptools MASS RANN raster RCurl readr rgeos rms SDMTools sf sp SpatialPack spatstat spdep yaImpute]; }; + spatialEco = derive2 { name="spatialEco"; version="1.1-1"; sha256="1sgc1a45wpx79h2y5i1k1qq7jqwf5a69lvl2sgaq4621f4l0b60b"; depends=[cluster EnvStats maptools MASS RANN raster RCurl readr rgeos rms SDMTools sf sp SpatialPack spatstat spdep yaImpute]; }; spatialTailDep = derive2 { name="spatialTailDep"; version="1.0.2"; sha256="107yldc43pgbadxdisnc7vq8vyvcps1b1isyvxd0kyf59xldiq47"; depends=[cubature mvtnorm SpatialExtremes]; }; spatialfil = derive2 { name="spatialfil"; version="0.15"; sha256="01fbn9zblz7rjsgqy3ikdqpf0p0idvb6m96mf7m7qi2ps5f48vzj"; depends=[abind fields]; }; spatialkernel = derive2 { name="spatialkernel"; version="0.4-23"; sha256="0kvhirh7afk2gfy21pa6117yk6kzbaf2dxfkr1ax3b554rnrv4p0"; depends=[spatstat]; }; @@ -12232,7 +12327,8 @@ in with self; { spatialprobit = derive2 { name="spatialprobit"; version="0.9-11"; sha256="1cpxxylc0pm7h9m83m2cklrh4jni5x79r5m5gibxi6viahwxn9kc"; depends=[Matrix mvtnorm spdep tmvtnorm]; }; spatialrisk = derive2 { name="spatialrisk"; version="0.4.1"; sha256="0r65y3ch53gbfb0di0svlb2zr39b5v0gbgjh713jgnw44g2g43r3"; depends=[Rcpp RcppProgress]; }; spatialsegregation = derive2 { name="spatialsegregation"; version="2.44"; sha256="02s75q6ylzm6xzr1q23fhps3svlb0ix86dzgr23wf42369gs7h0g"; depends=[spatstat]; }; - spatialwarnings = derive2 { name="spatialwarnings"; version="1.2"; sha256="1kpyx1jl23ml4gpbwz5p4srmdq58634dxznw1g6f618wml13ab3s"; depends=[ggplot2 plyr Rcpp RcppArmadillo reshape2 tidyr VGAM]; }; + spatialwarnings = derive2 { name="spatialwarnings"; version="1.3.1"; sha256="139m6jaw6f5gglwqrd4f5mzr4vkqk2r1a069971y7ap2klzzbhns"; depends=[ggplot2 plyr Rcpp RcppArmadillo reshape2 tidyr VGAM]; }; + spatialwidget = derive2 { name="spatialwidget"; version="0.1"; sha256="1f63mb2h1j08aajl73gvmp6q6vxm4z5q459hkdjwkfn4dijkmfbc"; depends=[BH colourvalues geojsonsf jsonify rapidjsonr Rcpp]; }; spatsoc = derive2 { name="spatsoc"; version="0.1.4"; sha256="0h41ql1ll1ypmwfjczk3pls78z75xz8qakl61xrynqmw0y7l9fys"; depends=[adehabitatHR data_table igraph rgeos sp]; }; spatstat = derive2 { name="spatstat"; version="1.57-1"; sha256="1mpwh65g2jp2m58whwi6sw1ngajdrgn7sd64xmnijplcwjyy9zvr"; depends=[abind deldir goftest Matrix mgcv nlme polyclip rpart spatstat_data spatstat_utils tensor]; }; spatstat_data = derive2 { name="spatstat.data"; version="1.4-0"; sha256="137cf9x6qcp7lw3rpjqizsy73z99yihff8gr434wlz7b5fwmn7hj"; depends=[spatstat_utils]; }; @@ -12269,7 +12365,7 @@ in with self; { spef = derive2 { name="spef"; version="1.0.8"; sha256="1c4hpm19zqh869z8qbixkfbidnygc3fy91d0m2l4bp2s6bq1wdnz"; depends=[BB ggplot2 nleqslv plyr sm SQUAREM survival]; }; speff2trial = derive2 { name="speff2trial"; version="1.0.4"; sha256="0dj5mh2sdp6j4ijgv14hjr39rasab8g83lx1d9y50av11yhbf2pw"; depends=[leaps survival]; }; spellcheckr = derive2 { name="spellcheckr"; version="0.1.2"; sha256="09snc1ymzr4njnr3w502b84dqwjjd414higjxqi48jvh27br5k1l"; depends=[data_table dplyr stringr]; }; - spelling = derive2 { name="spelling"; version="1.2"; sha256="1gdxxwz0n2z05d8xqk0kcvv2zffa810hda57i23zsysbrpn751s4"; depends=[commonmark hunspell knitr xml2]; }; + spelling = derive2 { name="spelling"; version="2.0"; sha256="199gs48rpia3v2kp7i5ag5f7limds2j3694aacln8gb0znm0k8n1"; depends=[commonmark hunspell knitr xml2]; }; spemd = derive2 { name="spemd"; version="0.1-1"; sha256="1aw8dg2fm8qd95bgim2kjwp7ax4b2g78521llsxv7fhdj9hl7rgw"; depends=[MBA sp spdep]; }; sperich = derive2 { name="sperich"; version="1.5-7"; sha256="1apgq5nsl6nw674dy7bc7r7z962wcmqsia5n67a8n6c5lcgcif3f"; depends=[foreach rgdal SDMTools sp]; }; sperrorest = derive2 { name="sperrorest"; version="2.1.5"; sha256="126vwk3bxs27gblakc5nplj0k90a21gks9d0kbyanlxc2ihsy243"; depends=[doFuture foreach future future_apply gdata glue magrittr pbapply pbmcapply purrr ROCR rpart stringr]; }; @@ -12343,6 +12439,7 @@ in with self; { srp = derive2 { name="srp"; version="1.1.0"; sha256="1655p3f7y50qjprm03gp5vffgnkin0c7ahzcrj6s8qfrd6gh2vsp"; depends=[fda mgcv]; }; srvyr = derive2 { name="srvyr"; version="0.3.3"; sha256="0xarb92xhsb3c6g45lqq9kgp5yy0y9psi7yrn7yvv1a130lwzs40"; depends=[dplyr magrittr rlang survey tibble]; }; ss3sim = derive2 { name="ss3sim"; version="0.9.5"; sha256="0rdb49bfxvyh0jrqycrv1hxvh7y4kvw81jccjg5ma734x44q0vm5"; depends=[bbmle dplyr foreach ggplot2 gtools lubridate magrittr plyr r4ss]; }; + ssMousetrack = derive2 { name="ssMousetrack"; version="1.1.2"; sha256="02v76prfv1ad7427d8l0md87c4ncmpprvadb0dyralpd8myk7z65"; depends=[BH CircStats cowplot dtw ggplot2 Rcpp RcppEigen rstan rstantools StanHeaders]; }; ssa = derive2 { name="ssa"; version="1.2.1"; sha256="10x58c57pa9x6svm4h4xrss72ikin9lpf3ihjwmnkgnaicvsd0bx"; depends=[iterators]; }; ssanv = derive2 { name="ssanv"; version="1.1"; sha256="17a4a5azxm5h2vxia16frcwdyd36phpfm7fi40q6mnnrwbpkzsjd"; depends=[]; }; ssc = derive2 { name="ssc"; version="2.0.0"; sha256="0w7c0blqny7dyjh1a6l9lr7nysgpmasfqbf7wf368rwmv59pk0b3"; depends=[proxy]; }; @@ -12424,7 +12521,7 @@ in with self; { stepR = derive2 { name="stepR"; version="2.0-2"; sha256="0inxlgihyivfr0l4gk8zq0043l9s5w4r3x3hwjlzfwbqjkwy1rjs"; depends=[digest R_cache Rcpp]; }; stepp = derive2 { name="stepp"; version="3.2.0.0"; sha256="0fnjqbncadscv6ryvqyqf8qqgpfzh2hka5ld2zvw39mjqzy5gadi"; depends=[car survival]; }; stepwise = derive2 { name="stepwise"; version="0.3"; sha256="1lbx1bxwkf9dw6q46w40pp7h5nkxgghmx8rkpaymm6iybc7gyir2"; depends=[]; }; - stevedore = derive2 { name="stevedore"; version="0.9.0"; sha256="00wjy0wh9f0a0qiwd2r8a0bywwhfkwa5qq75grphpc4gamcybrc9"; depends=[crayon curl jsonlite yaml]; }; + stevedore = derive2 { name="stevedore"; version="0.9.1"; sha256="0laib1vd9limzvxp2lij414a4mvbbx1j63rx4yzdyh6jiglm8l7h"; depends=[crayon curl jsonlite yaml]; }; stheoreme = derive2 { name="stheoreme"; version="1.2"; sha256="14w3jcbs8y8cz44xlq8yybr2jwgk3w7s2msgjhlp1vazy8959s65"; depends=[]; }; sticky = derive2 { name="sticky"; version="0.5.2"; sha256="0yib9llvlxyzcwam3qd3wxz91mdacvh4v888ifxwjhhjihffqvbj"; depends=[]; }; stilt = derive2 { name="stilt"; version="1.3.0"; sha256="0b1bs849hw2wcvaldybxk8h8wgwl6p7x4i7winncvngmhplgrvx4"; depends=[fields]; }; @@ -12454,7 +12551,7 @@ in with self; { stranger = derive2 { name="stranger"; version="0.3.3"; sha256="0p0ssba5q192g7pviv1shmh1lpcdjmzdim3rp1qs3hrd1d3pn4vq"; depends=[assertthat data_table dplyr ggplot2 tidyr]; }; strap = derive2 { name="strap"; version="1.4"; sha256="0gdvx02w0dv1cq9bb2yvap00lsssklfnqw0mwsgblcy2j6fln7b0"; depends=[ape geoscale]; }; strat = derive2 { name="strat"; version="0.1"; sha256="1axxrp750kjzcgxjdqfscjmryv1mkv4l23zk8k23z8l4ymhd2f5w"; depends=[Hmisc Rcpp RcppArmadillo]; }; - stratEst = derive2 { name="stratEst"; version="0.1.0"; sha256="06xddfgddrcd0fjc2hiqmxh9i7szrvay5phhd7k5y1bdmjav7q2c"; depends=[Rcpp RcppArmadillo]; }; + stratEst = derive2 { name="stratEst"; version="0.1.1"; sha256="1p4qzl29k10yxsflkbn6rscsqrh53wbn5v9zyjsnxl3bi6lwi6j7"; depends=[Rcpp RcppArmadillo]; }; strataG = derive2 { name="strataG"; version="2.0.2"; sha256="1rf1xf07yb0dzasgig9sfm4i9ggdkjgy5iiysqgdapk3sxs26c8r"; depends=[adegenet ape apex copula data_table DT ggplot2 gridExtra Hmisc pegas phangorn RColorBrewer Rcpp shiny shinyFiles survival swfscMisc]; }; stratbr = derive2 { name="stratbr"; version="1.2"; sha256="15vkymmc61yz9szhfhc5663hfyqvh499ahwhr9mv1lhv5bikk0kb"; depends=[Rglpk snowfall stratification]; }; strategicplayers = derive2 { name="strategicplayers"; version="1.0"; sha256="19vijrlzawd701vvk9ig7yhzbirh39dxxcwfz8ywwvxxiaky5x55"; depends=[sna]; }; @@ -12506,6 +12603,7 @@ in with self; { subsemble = derive2 { name="subsemble"; version="0.0.9"; sha256="0vzjmxpdwagqb9p2r4f2xyghmrprx3nk58bd6zfskdgj0ymfgz5z"; depends=[SuperLearner]; }; subspace = derive2 { name="subspace"; version="1.0.4"; sha256="0p2j0lnwj3ym1v4xla6r97zjikb8alnibdc690xn9c0z21hmv43v"; depends=[colorspace ggvis rJava stringr]; }; subspaceMOA = derive2 { name="subspaceMOA"; version="0.6.0"; sha256="1q2n4q87zaxwaak77b6rff97n9sx6nflshqf73r2q8hflfs3sxv3"; depends=[fields ggplot2 gridExtra magrittr rJava shiny stream streamMOA]; }; + subtee = derive2 { name="subtee"; version="0.3-3"; sha256="1hn34lmvapy52dnjfzzxi7qmb9f9in7qzbj017kacb901w782ky6"; depends=[ggplot2 MASS matrixStats survival]; }; subtype = derive2 { name="subtype"; version="1.0"; sha256="1094q46j0njkkqv09slliclp3jf8hkg4147hmisggy433xwd19xh"; depends=[penalized ROCR]; }; sudoku = derive2 { name="sudoku"; version="2.6"; sha256="13j7m06m38s654wn75kbbrin5nqda4faiawlsharxgrljcibcbrk"; depends=[]; }; sudokuAlt = derive2 { name="sudokuAlt"; version="0.1-11"; sha256="1hv9d99ir1xz6p0arxr77dv5qb45sr8jhapm6wf755l7pxlqqklq"; depends=[magrittr]; }; @@ -12523,6 +12621,7 @@ in with self; { superbiclust = derive2 { name="superbiclust"; version="1.1"; sha256="1gzjbzbl8y1nzdfhyd6dlrwjq8mwj43a26qav84s1bdzwx6dra48"; depends=[biclust fabia Matrix]; }; superdiag = derive2 { name="superdiag"; version="1.1"; sha256="0pa3mv74riabpm7j4587zww2364fszzlw48ijj1apcgz8y6pyqbw"; depends=[boa coda]; }; superheat = derive2 { name="superheat"; version="0.1.0"; sha256="01v8s6px1k5fajlm6py3ksr1i853kwwlky1yryzhy3p1cxhwgg83"; depends=[dplyr ggdendro ggplot2 gtable magrittr plyr scales]; }; + superml = derive2 { name="superml"; version="0.1.0"; sha256="0jnvxf3q95n2izck715na1dmy85n119955asc6fa3ank2qx4kdd2"; depends=[assertthat caret ClusterR data_table FNN glmnet kableExtra Metrics R6 ranger tm xgboost]; }; supernova = derive2 { name="supernova"; version="1.1"; sha256="0n34fkscml6ldbcr6kk8c6n4f5z4j398qn1vsp06h3b0h6sl5rrb"; depends=[]; }; superpc = derive2 { name="superpc"; version="1.09"; sha256="1p3xlg2n7p57n54g2w4frfrng5vjh97kp6ax4mrgvj3pqmd1m69z"; depends=[survival]; }; supervisedPRIM = derive2 { name="supervisedPRIM"; version="2.0.0"; sha256="1j5gsy119pvrhkkg048lyk6hjvn9x1bhmfy5g824gj3k1w5slrib"; depends=[prim]; }; @@ -12553,7 +12652,7 @@ in with self; { survSNP = derive2 { name="survSNP"; version="0.24"; sha256="0mzwcp8zfqvsiapa446si9qb6wyymnw5zj6acj6f2cfjpyi76k4w"; depends=[foreach lattice Rcpp survival xtable]; }; surveillance = derive2 { name="surveillance"; version="1.16.2"; sha256="1k6wpzsagsq2ixpdhx6b4zzb5wv2j95nsmxyfwvlxkxafahx986h"; depends=[MASS Matrix nlme polyCub Rcpp sp spatstat xtable]; }; survexp_fr = derive2 { name="survexp.fr"; version="1.0"; sha256="12rjpnih0xld4dg5gl7gwxdxmrdmyzsymm7j05v98ynldd1jkjl8"; depends=[survival]; }; - survey = derive2 { name="survey"; version="3.34"; sha256="09024mqkbm5aak9rsi9qw97d3xrq2dba3z2hyvydncygjmjymy65"; depends=[lattice Matrix minqa numDeriv survival]; }; + survey = derive2 { name="survey"; version="3.35"; sha256="09r43lpgai3hbblgw5ls8002fw4h6nlgra9k0v94zirjy9bhr98m"; depends=[lattice Matrix minqa numDeriv survival]; }; surveybootstrap = derive2 { name="surveybootstrap"; version="0.0.1"; sha256="13rp6gj1dgdzcjbi2403pldygp1dyqx8zj0r1nvyghpi06x5gpb7"; depends=[dplyr functional plyr Rcpp RcppArmadillo stringr]; }; surveydata = derive2 { name="surveydata"; version="0.2.2"; sha256="0rxyyvpl972z2qr54cwhm1il80kb1vvmvn9r8mji01nyxw6d9l91"; depends=[assertthat dplyr DT ggplot2 magrittr plyr purrr rlang scales stringr tidyr]; }; surveyeditor = derive2 { name="surveyeditor"; version="1.0"; sha256="073219bcn1hlxl9ql6gncfvgn0m37pz5sb7h94nq6lf35dymq5zq"; depends=[]; }; @@ -12600,6 +12699,7 @@ in with self; { svrpath = derive2 { name="svrpath"; version="0.1.2"; sha256="18h40555jmqpbsnhlwkvc5fl7d0r2bgscdv8amjvhjxmx9y952a2"; depends=[quadprog svmpath]; }; svs = derive2 { name="svs"; version="1.1.0"; sha256="0575msaxg04ck76mbr815m29y895qvg8b9qg4y0ggv6b1lvwp5p6"; depends=[gtools]; }; svyPVpack = derive2 { name="svyPVpack"; version="0.1-1"; sha256="15k5ziy2ng853jxl66wjr27lzc90l6i5qr08q8xgcs359vn02pmp"; depends=[survey]; }; + svydiags = derive2 { name="svydiags"; version="0.3"; sha256="0xgizswdqs8cjac200sqv3ygvrnbcy74h92kgx4r6nv1fhlcljl3"; depends=[MASS Matrix survey]; }; swCRTdesign = derive2 { name="swCRTdesign"; version="2.2"; sha256="0kggniy5p900cj074swh7g47zf8bhwjmqph9b5frw86nycxwyn3v"; depends=[]; }; swa = derive2 { name="swa"; version="0.8.1"; sha256="1zy1a6c17vmdkmkwp8vv3niww2zs1m0hylsa0b2cz68vfhnmpim4"; depends=[ggplot2 reshape ROCR]; }; swagger = derive2 { name="swagger"; version="3.9.2"; sha256="13scbzv65qzxh7kfwlb2k47zgvv7fz085g5lki6zr5w6a33g45q9"; depends=[]; }; @@ -12637,7 +12737,8 @@ in with self; { synchronicity = derive2 { name="synchronicity"; version="1.3.5"; sha256="1kgsk64aifjm3mfj102y3va7x1abypq2zi0cqbnjhl8fqyzp69hx"; depends=[BH bigmemory_sri Rcpp uuid]; }; synchrony = derive2 { name="synchrony"; version="0.3.7"; sha256="0lnin4aphy1lq20bn7nsdj0ymy2xdwjzdj2f89xq0qwkc7w7b5jb"; depends=[]; }; synlik = derive2 { name="synlik"; version="0.1.2"; sha256="1pscfqg5x7wpq3vp1i7fy29dwa7cw5g3kzxinanwrwbcznv9nyms"; depends=[Matrix Rcpp RcppArmadillo]; }; - synoptReg = derive2 { name="synoptReg"; version="0.2.0"; sha256="1mqyciards48j6x1h82xxvq67wqrb7nqxn9cvz5vx0zgfwk0ywdb"; depends=[fields maps ncdf4 raster zoo]; }; + synoptReg = derive2 { name="synoptReg"; version="0.2.1"; sha256="1ip74czb96kshzl6akxk5nxi6i25a3i1jzyfq0b2ji5bk7ydhmqr"; depends=[ncdf4 raster zoo]; }; + synthACS = derive2 { name="synthACS"; version="1.4.4"; sha256="09ivllyw5gaqwlsgk0q0y5pgcx8dbhvpr8hisbw3s0r907c4gfb6"; depends=[acs data_table Rcpp]; }; synthpop = derive2 { name="synthpop"; version="1.5-0"; sha256="0p0dszrh66xzfaiks89qli23c8qzq8gvi4d7wwlngkmq4k8y80rq"; depends=[classInt foreign ggplot2 lattice MASS mipfp nnet party plyr polspline proto randomForest rpart]; }; sys = derive2 { name="sys"; version="2.1"; sha256="10ml2492bdllh6cz2zl192ip0fdgjkkgayggd3ghswsj5gjv5hrh"; depends=[]; }; sysfonts = derive2 { name="sysfonts"; version="0.8"; sha256="0wng902plryf2d8fc7k7m3jx11acz51kb2d91cqbyhq7xpk06z43"; depends=[]; }; @@ -12672,7 +12773,7 @@ in with self; { tagcloud = derive2 { name="tagcloud"; version="0.6"; sha256="04zrh029n8pjlxlr6pdd7xhqqhavbrj3fhvhj6ygzlvi2jslxnwl"; depends=[RColorBrewer Rcpp]; }; tailDepFun = derive2 { name="tailDepFun"; version="1.0.0"; sha256="1z2jrzly1adiwi8y0pndyfggpr0li6sjv9rkrc5mi47s0qjvr5qj"; depends=[copula cubature mvtnorm SpatialExtremes]; }; tailloss = derive2 { name="tailloss"; version="1.0"; sha256="0lmjgjs6d94b70i10vx66fyvlxm5swwqbcjsnqa3lmldzz6m4jc1"; depends=[MASS]; }; - tailr = derive2 { name="tailr"; version="0.1.2"; sha256="1z47akvm2y05ih8q5ci03jm29xzp4m52shvbm4d9h2bipnq5crys"; depends=[glue rlang]; }; + tailr = derive2 { name="tailr"; version="0.1.3"; sha256="0agm83zwj6f3bpicbn2pcwira05v2pbv0g7myc1x06jxbw1qbfwp"; depends=[foolbox glue rlang]; }; taipan = derive2 { name="taipan"; version="0.1.2"; sha256="192sy5pgq74vs31p7jfn6svdzf9mk9ybppzhp1rlki1bagmm5f1r"; depends=[shiny]; }; takos = derive2 { name="takos"; version="0.1.0"; sha256="0a26jmxccpyk36sah9nz7pqpkc1rd9kbwrvwh0r0zp7lwvxbjb8w"; depends=[baseline broom colorRamps data_table devEMF MASS minpack_lm pracma segmented sfsmisc smoother]; }; tangram = derive2 { name="tangram"; version="0.4"; sha256="1yj5vwc8jkiic4zjag9k7w3j6dibqw5zsi78q6gssshsi9z0zbgy"; depends=[base64enc digest htmltools magrittr R6 stringi stringr]; }; @@ -12682,7 +12783,7 @@ in with self; { tauturri = derive2 { name="tauturri"; version="0.3.0"; sha256="014301f5mzy6vblqzb61bxjv46kdynmmrxjpxyvk01w1k8wkwfcn"; depends=[httr magrittr plyr purrr tibble]; }; tawny = derive2 { name="tawny"; version="2.1.7"; sha256="1b2v0cgkmhzxy36dcdn6hnbqk6l5ac5c3myvwryf7wlp19xi786d"; depends=[futile_logger futile_matrix lambda_r lambda_tools PerformanceAnalytics quantmod tawny_types xts zoo]; }; tawny_types = derive2 { name="tawny.types"; version="1.1.5"; sha256="1vg0hv91dif6cfqfzrf7m1qbk57fp8v97fp88whwmvs83yd521hq"; depends=[futile_logger futile_options lambda_r lambda_tools quantmod xts zoo]; }; - taxa = derive2 { name="taxa"; version="0.3.1"; sha256="19bfgcibryvvqsqyjw3jgiw4raraas82w1dhkmnv9j7jny3v2677"; depends=[crayon dplyr jsonlite knitr lazyeval magrittr R6 rlang stringr taxize tibble tidyr]; }; + taxa = derive2 { name="taxa"; version="0.3.2"; sha256="1kiffyfpgapap6m2k3wx7p89kzpdyk48nwbmqvfa883kvg0ddzcy"; depends=[crayon dplyr jsonlite knitr lazyeval magrittr R6 rlang stringr taxize tibble tidyr]; }; taxize = derive2 { name="taxize"; version="0.9.4"; sha256="1p5rlc93q62rk2z3qcq02xfrs4pz699qdakk05pz6g9rlbqj342m"; depends=[ape bold crul data_table foreach httr jsonlite natserv plyr reshape2 ritis rotl rredlist stringr tibble wikitaxa worrms xml2 zoo]; }; taxizedb = derive2 { name="taxizedb"; version="0.1.4"; sha256="15gj9i18ysd83v9fidrrvw938dah04i10ahi3wh5dgjs5fd5ch2s"; depends=[curl DBI dbplyr dplyr hoardr magrittr RMySQL RPostgreSQL RSQLite]; }; taxlist = derive2 { name="taxlist"; version="0.1.5"; sha256="17b7sdjjzragi8k08304idic0p8cj095h4p9vlpfidn8k6csrkv8"; depends=[foreign stringdist taxize vegdata]; }; @@ -12739,7 +12840,7 @@ in with self; { textTinyR = derive2 { name="textTinyR"; version="1.1.2"; sha256="177m3mh61isjk9svbnv5gdlpyfy7fdmafi2znxh2m7fqcwn7k3af"; depends=[BH data_table Matrix R6 Rcpp RcppArmadillo]; }; textcat = derive2 { name="textcat"; version="1.0-6"; sha256="0639b1qbi8779lskk5ms0sbbnmy2s73b3w96abbr70mrh0s2f9rw"; depends=[slam tau]; }; textclean = derive2 { name="textclean"; version="0.9.3"; sha256="0kgjh6c4f14qkjc4fds7q7rpf4nkma3p0igm54fplmm3p853nvrz"; depends=[data_table english glue lexicon mgsub qdapRegex stringi textshape]; }; - texteffect = derive2 { name="texteffect"; version="0.1"; sha256="0fwcbz7bpynvcivac16z77j8d398bf7vl4l8sppi9yvg72l0k94w"; depends=[boot ggplot2 MASS]; }; + texteffect = derive2 { name="texteffect"; version="0.2"; sha256="1g9vda1xx5fysifs1716m3bw651sk5l2ayn23gdlcsyrpynj3d1q"; depends=[boot ggplot2 MASS]; }; textfeatures = derive2 { name="textfeatures"; version="0.3.0"; sha256="07xi4bdpf5zibhs83wwv8sh58b8avmnm7f5j8gcai4195wwqflnn"; depends=[dplyr purrr rlang syuzhet text2vec tfse tibble tokenizers]; }; textgRid = derive2 { name="textgRid"; version="1.0.1"; sha256="1wi5vq5f7ixhz39l5hqi2jlmjjacx4lyrs4h8xfbd47pj6g16lc6"; depends=[]; }; textile = derive2 { name="textile"; version="0.1.2"; sha256="067zli6sl7bp9843spgx47hmw55aq61yinqw1lqifmrpk7b0ywk5"; depends=[]; }; @@ -12749,6 +12850,7 @@ in with self; { textometry = derive2 { name="textometry"; version="0.1.4"; sha256="17k3v9r5d5yqgp25bz69pj6sw2j55dxdchq63wljxqkhcwxyy9lh"; depends=[]; }; textrank = derive2 { name="textrank"; version="0.2.0"; sha256="0s2mnid3dha3nyyc9abhb36vlij4bg0024i9ay4pvvy4l1x947gr"; depends=[data_table digest igraph]; }; textreadr = derive2 { name="textreadr"; version="0.9.0"; sha256="04nyjrfxgwq8g3bdj12nnkia2xn2zngk1rprlkpyicrisgq36agk"; depends=[antiword curl data_table pdftools readxl rvest striprtf textshape xml2]; }; + textrecipes = derive2 { name="textrecipes"; version="0.0.1"; sha256="1nnm7cpp99jlahhdl6aqz38dsr9wgm8z1pxblwqqribfh354vm5c"; depends=[dplyr generics magrittr purrr recipes rlang SnowballC stopwords stringr text2vec tibble tokenizers]; }; textreg = derive2 { name="textreg"; version="0.1.5"; sha256="0h44z5hyndnvzd9axix7gpmhbdx347dfgxw9r8w38kyw6dklbjy6"; depends=[NLP Rcpp tm]; }; textreuse = derive2 { name="textreuse"; version="0.1.4"; sha256="0qfp7ffzb5p3k3wiw8i1zjskni8f38rzkjnss97j9f3vhhb8j4r7"; depends=[assertthat BH digest dplyr NLP Rcpp RcppProgress stringr tidyr]; }; textshape = derive2 { name="textshape"; version="1.6.0"; sha256="1pl85wjq5rl25gdlh4cp0l14hn76rrmpl7l1fn7kq9lwj9yfpcs8"; depends=[data_table slam stringi]; }; @@ -12787,7 +12889,7 @@ in with self; { tibbrConnector = derive2 { name="tibbrConnector"; version="1.5.1"; sha256="1r58myi7x4hqqvyrphxy4ppa1lnad6x2ginfq2j52ax53zr07ajp"; depends=[RCurl rjson]; }; tictactoe = derive2 { name="tictactoe"; version="0.2.2"; sha256="1fx8plj5zr04xwk5hfj3zqhcknidxlzya2q14cf0m3y33a86lx42"; depends=[hash]; }; tictoc = derive2 { name="tictoc"; version="1.0"; sha256="1zp2n8k2ax2jjw89dsri268asmm5ry3ijf32wbca5ji231y0knj7"; depends=[]; }; - tidyLPA = derive2 { name="tidyLPA"; version="0.2.3"; sha256="02qmnqp0zc494nj9331h4y5pzyvhfxbjrk3chqafrl44w9x2jbh2"; depends=[dplyr forcats ggplot2 magrittr mclust purrr readr rlang stringr tibble tidyr]; }; + tidyLPA = derive2 { name="tidyLPA"; version="0.2.4"; sha256="0bjc6nhcczryhvmlkcvqwv5bv0w49z1kk8x7bx57189xap2lfsd9"; depends=[dplyr forcats ggplot2 magrittr mclust purrr readr rlang stringr tibble tidyr]; }; tidyRSS = derive2 { name="tidyRSS"; version="1.2.7"; sha256="0834g61fxdwvpxdr0a65k4k35iazwwzv792zjwj46391a2nmq5h7"; depends=[dplyr httr jsonlite lubridate magrittr purrr sf stringr testthat tibble xml2]; }; tidybayes = derive2 { name="tidybayes"; version="1.0.3"; sha256="1dkkzfbbq94vrrswf3g6dcds4vpvjn2kldf91f7642qf6kdgy135"; depends=[arrayhelpers coda dplyr forcats ggplot2 ggridges ggstance HDInterval LaplacesDemon magrittr MASS plyr purrr rlang stringi stringr tibble tidyr tidyselect]; }; tidyboot = derive2 { name="tidyboot"; version="0.1.1"; sha256="0nss1ci763g9p5f33g163ppamx72axc8xhrils0cql3ka8439pmn"; depends=[dplyr modelr purrr rlang tidyr]; }; @@ -12798,7 +12900,7 @@ in with self; { tidyimpute = derive2 { name="tidyimpute"; version="0.1.0"; sha256="03b475nn206hxq3i0n7j1qws82rwwk5vqivmdg5mff44dvz4gl5s"; depends=[dplyr na_tools rlang]; }; tidymodels = derive2 { name="tidymodels"; version="0.0.2"; sha256="1hidjrayqxz1g7bn20pqs1bwyx4cxxqx9dq5lwqyfsij0ir0lia9"; depends=[broom cli crayon dials dplyr ggplot2 infer magrittr parsnip pillar purrr recipes rlang rsample rstudioapi tibble tidyposterior tidypredict tidytext yardstick]; }; tidyposterior = derive2 { name="tidyposterior"; version="0.0.2"; sha256="1sdbar3ycnjqyjy664zyhr9xks48l6g6mw8p5scp31x3gdh352rs"; depends=[dplyr generics ggplot2 purrr rlang rsample rstanarm tibble tidyr]; }; - tidypredict = derive2 { name="tidypredict"; version="0.2.0"; sha256="1hq9xzaa234679qvf02nc5w8l21yh1f3dhl76zxzqc7na7chn13k"; depends=[dplyr purrr rlang tibble tidyr]; }; + tidypredict = derive2 { name="tidypredict"; version="0.2.1"; sha256="14vd8adqifxakdnkl1qnx8n8lc956g7mvzni749afv0avps8kpk4"; depends=[dplyr purrr rlang tibble tidyr]; }; tidyquant = derive2 { name="tidyquant"; version="0.5.5"; sha256="0kh3y291j5d6qbqr45jjzjpwa02r0ymb7gdr0zd9g3d4czllwv95"; depends=[dplyr ggplot2 httr lazyeval lubridate magrittr PerformanceAnalytics purrr Quandl quantmod rlang stringr tibble tidyr tidyverse timetk TTR xml2 xts]; }; tidyr = derive2 { name="tidyr"; version="0.8.2"; sha256="03s9dv6c2dj65a769h8fgy9878y46rdq7x65i53kd44kag80i9cr"; depends=[dplyr glue magrittr purrr Rcpp rlang stringi tibble tidyselect]; }; tidyselect = derive2 { name="tidyselect"; version="0.2.5"; sha256="0x3cp36byhfjajikr1lwffjm85ayw3bcs7d7kb0cydgs61ifiqjw"; depends=[glue purrr Rcpp rlang]; }; @@ -12807,9 +12909,9 @@ in with self; { tidytext = derive2 { name="tidytext"; version="0.2.0"; sha256="15xyn7mz81cm6dqsjvdb681q2sag9pp62kv11y0blyxd81wpy994"; depends=[broom dplyr hunspell janeaustenr Matrix purrr rlang stopwords stringr tokenizers]; }; tidytidbits = derive2 { name="tidytidbits"; version="0.1.0"; sha256="154k3gn87fnmzhldyp7h0rq5gxpndwaf4gahqydhsh9i6dq61lk7"; depends=[dplyr extrafont forcats magrittr purrr rlang stringr tibble tidyr tidyselect]; }; tidytransit = derive2 { name="tidytransit"; version="0.3.5"; sha256="0pxkn162i601lc8lwci1j4ns44yxc1d7zy7c7423ccqjpj85nm7g"; depends=[assertthat dplyr here htmltools httr lubridate magrittr readr rlang scales sf stringr tibble tidyr zip]; }; - tidytree = derive2 { name="tidytree"; version="0.2.0"; sha256="16i1bgiw1wj0sxic4fj6x5rfd6jk7l4mmxzw4kj0mp1vsxsrwj8x"; depends=[ape dplyr lazyeval magrittr tibble]; }; + tidytree = derive2 { name="tidytree"; version="0.2.1"; sha256="1sx69wvlp7k761cmglrzq2jxkm2iq27x6bhhdcisj62wryj96wb2"; depends=[ape dplyr lazyeval magrittr rlang tibble]; }; tidyverse = derive2 { name="tidyverse"; version="1.2.1"; sha256="0yy3fkjksgcn6wkbgsb0pbnmsyqs4m01mziqafhig578nixs4rxd"; depends=[broom cli crayon dbplyr dplyr forcats ggplot2 haven hms httr jsonlite lubridate magrittr modelr purrr readr readxl reprex rlang rstudioapi rvest stringr tibble tidyr xml2]; }; - tidyxl = derive2 { name="tidyxl"; version="1.0.3"; sha256="02icd5xwyimdlzrn6ikj6rrs3kj3qw1ngap69cf89mvmlkp93y79"; depends=[piton Rcpp]; }; + tidyxl = derive2 { name="tidyxl"; version="1.0.4"; sha256="19kcm9lfbkf61z0whfkn69b8m36qd1rvyhyk5y0cqbzkxvq8f70i"; depends=[piton Rcpp]; }; tiff = derive2 { name="tiff"; version="0.1-5"; sha256="0asf2bws3x3yd3g3ixvk0f86b0mdf882pl8xrqlxrkbgjalyc54m"; depends=[]; }; tiger = derive2 { name="tiger"; version="0.2.3.1"; sha256="0xr56c46b956yiwkili6vp8rhk885pcmfyd3j0rr4h8sz085md6n"; depends=[e1071 hexbin klaR lattice qualV som]; }; tigerhitteR = derive2 { name="tigerhitteR"; version="1.1.0"; sha256="0inyi12lf8bn7nbklf2rjixk6wrgrjcp8njv7knai4dgvv7v0rfa"; depends=[Hmisc magrittr openxlsx zoo]; }; @@ -12844,6 +12946,7 @@ in with self; { timsac = derive2 { name="timsac"; version="1.3.6"; sha256="186919qka9j3kfpdw2gbh16n48d6xgz9lfqgk4b17f1d7l72iplg"; depends=[]; }; tinsel = derive2 { name="tinsel"; version="0.0.1"; sha256="0n1x0cf4x6cq1yks0444nxd9snga4m6inc5lfvb7k96fzjb3xgbp"; depends=[]; }; tint = derive2 { name="tint"; version="0.1.0"; sha256="1hczc2nrm8xgvw3igkfnlqyz73686l447kigsrd6m796v8ny1gbf"; depends=[htmltools knitr rmarkdown]; }; + tinter = derive2 { name="tinter"; version="0.0.1"; sha256="1zw5a79mryqighf8b6gidsi30001749sllpwqwbck26cyal6m8y6"; depends=[checkr]; }; tinyProject = derive2 { name="tinyProject"; version="0.5"; sha256="10sllhjcla4pfgp5n1y5vi318q9bcy82j88rx3k1sgzmbq1nc1c2"; depends=[brew devtools]; }; tinytex = derive2 { name="tinytex"; version="0.9"; sha256="08w5hyq3ysh631d5whgcfv1bb007cdc0bjhb83vwmhazs6rgvyjy"; depends=[xfun]; }; tiobeindexr = derive2 { name="tiobeindexr"; version="0.1.1"; sha256="09vw83hkf7lgd3xyhbmqkyv57g3dz856230xkf8630jiicfvcg3b"; depends=[rvest xml2]; }; @@ -12862,7 +12965,7 @@ in with self; { tlm = derive2 { name="tlm"; version="0.1.5"; sha256="1iw08pa70nb25fnv64834s5c8vl456a2rcng7x6v9vs5q37610g6"; depends=[boot]; }; tlmec = derive2 { name="tlmec"; version="0.0-2"; sha256="1gak8vxmfjf05bhaj6lych7bm8hgav1x3h14k2ra7236v82rqbw7"; depends=[mvtnorm]; }; tls = derive2 { name="tls"; version="0.1.0"; sha256="183b5m70s2whlgp9s1gb4xnylhlp4hnh3lw6b8f2vx4kahaid763"; depends=[]; }; - tm = derive2 { name="tm"; version="0.7-5"; sha256="05x3kj6dxffcfyn42q2fw9bby5f4wdmslc3ww1dl0r09pz950cax"; depends=[BH NLP Rcpp slam xml2]; }; + tm = derive2 { name="tm"; version="0.7-6"; sha256="0spv43kjbpxq3rdxx8ysgrncjyc35ydiwk7gp8n4sig45iqyz59r"; depends=[BH NLP Rcpp slam xml2]; }; tm_plugin_alceste = derive2 { name="tm.plugin.alceste"; version="1.1"; sha256="0wid51bbbx01mjfhnaiv50vfyxxmjxw8alb73c1hq9wlsh3x3vjf"; depends=[NLP tm]; }; tm_plugin_dc = derive2 { name="tm.plugin.dc"; version="0.2-8"; sha256="0z843i2wlmx75748p95jz3j45d9bzmlmqa3awgya24k7bdhpd6kd"; depends=[DSL NLP slam tm]; }; tm_plugin_europresse = derive2 { name="tm.plugin.europresse"; version="1.4"; sha256="03qi9rkfwgjvir4cjpi9imc8zaldvan42v9lqfr5d6zhr0ajy6wx"; depends=[NLP tm XML]; }; @@ -12891,7 +12994,7 @@ in with self; { tolBasis = derive2 { name="tolBasis"; version="1.0"; sha256="0g4jdwklx92dffrz38kpm1sjzmvhdqzv6mj6hslsjii6sawiyibh"; depends=[lubridate polynom]; }; tolerance = derive2 { name="tolerance"; version="1.3.0"; sha256="17qh4ad1f3fbcpwlxxqh8qr9bnwjcl4yxk0l3fkbr6b2l4rc5p86"; depends=[rgl]; }; toolmaRk = derive2 { name="toolmaRk"; version="0.0.1"; sha256="0pdr8lq4c11ia03v68lbfq38p3qp770mbj0nsbjsgbqi0pv9i1vx"; depends=[dplyr ggplot2 plyr reshape2]; }; - topicmodels = derive2 { name="topicmodels"; version="0.2-7"; sha256="16qa27pw19an6snqsqmgx439jqjjm8fx2lva3pnz5rd33xf701yc"; depends=[modeltools slam tm]; }; + topicmodels = derive2 { name="topicmodels"; version="0.2-8"; sha256="19msp5cz67ff4v1gfd8vhjnnsmwfkxiv08ym4k506j2mhaklipci"; depends=[modeltools slam tm]; }; topmodel = derive2 { name="topmodel"; version="0.7.3"; sha256="15w9id90d6l0i0ji3ln3sxnpispb6pgabk4waysqn0nh6y4lfdgb"; depends=[]; }; topologyGSA = derive2 { name="topologyGSA"; version="1.4.6"; sha256="0vas7qab5a86jb277ql63qjvfvx7iqqbcrwky7iyr0s8p8p794ia"; depends=[fields graph gRbase qpgraph]; }; topsis = derive2 { name="topsis"; version="1.0"; sha256="056cgi684qy2chh1rvhgkxwhfv9nnfd7dfzc05m24gy2wyypgxj3"; depends=[]; }; @@ -12913,9 +13016,10 @@ in with self; { trackdem = derive2 { name="trackdem"; version="0.4.2"; sha256="0isd3cs10z6sqm8sh2q577z8bhnagq9gqsvdlsv377lk1z7wd1ln"; depends=[MASS neuralnet png raster Rcpp RcppArmadillo SDMTools shiny]; }; trackeR = derive2 { name="trackeR"; version="1.2.0"; sha256="07kfnla6dq1x62k43nl2d2s2bn1m1djzqzhks09f8fjz7vcbjgsy"; depends=[fda foreach ggmap ggplot2 ggridges gridExtra gtable jsonlite leaflet raster RSQLite scam sp xml2 zoo]; }; trackr = derive2 { name="trackr"; version="0.10.5"; sha256="0cngwszax3i9p0095kxrz7w4rnryc0lmylckixzrmhx80qkxcaw1"; depends=[CodeDepends fastdigest ggplot2 gridGraphics histry htmltools lattice miniUI RJSONIO rlang rmarkdown roprov rsolr shiny]; }; - tractor_base = derive2 { name="tractor.base"; version="3.2.2"; sha256="1pbh9hand7h68vxap2qis3a7zs5qkrj2wxk8flqyvhx50p98wigv"; depends=[ore reportr shades]; }; + tractor_base = derive2 { name="tractor.base"; version="3.3.0"; sha256="0i62dwra0yh565ryz75byfgqv22bqwz7138zs48w46yj2h8q9hyj"; depends=[ore reportr RNifti shades]; }; trade = derive2 { name="trade"; version="0.5.3"; sha256="0v0yw261daag0hw3sc7dh2bpm8sd3r46xbcbcbxv7qb59rad756w"; depends=[antitrust]; }; trafo = derive2 { name="trafo"; version="1.0.1"; sha256="0gq3snjpkw0ncny7pkfi686qkgdhd8id73jxjk3chhqf5mzrrsbc"; depends=[FNN lmtest moments pryr]; }; + traitdataform = derive2 { name="traitdataform"; version="0.5.2"; sha256="1glk9k1n0zyqpnwsy7f7w4rzh5xlsw0db6fcf7ay04kpzjj0442b"; depends=[data_table getPass plyr RCurl reshape2 taxize units XML]; }; traitr = derive2 { name="traitr"; version="0.14"; sha256="1pkc8wcq55229wkwb54hg9ndbhlxziv51n8880z6yq73zac1hbmf"; depends=[digest gWidgets proto]; }; traits = derive2 { name="traits"; version="0.3.0"; sha256="155y8j69214xxi1bfk07k30zlpm3q6fmz7ydhnkvw0kv4l0i5pc5"; depends=[crul data_table hoardr httr jsonlite readr rvest taxize tibble xml2]; }; traj = derive2 { name="traj"; version="1.2"; sha256="0mq6xdbxjqjivxyy7cwaghwmnmb5pccrah44nmalssc6qfrgys4n"; depends=[cluster GPArotation NbClust pastecs psych]; }; @@ -12927,7 +13031,7 @@ in with self; { translate = derive2 { name="translate"; version="0.1.2"; sha256="1w0xrg1xxwfdanlammmixf06hwq700ssbjlc3cfigl50p87dbc5x"; depends=[functional lisp RCurl RJSONIO]; }; translateR = derive2 { name="translateR"; version="1.0"; sha256="11kh9hjpsj5rfmzybnh345n1gzb0pdksrjp04nzlv948yc0mg5gm"; depends=[httr RCurl RJSONIO textcat]; }; translation_ko = derive2 { name="translation.ko"; version="0.0.1.5.2"; sha256="1w5xibg4znhd39f3i0vsqckp6iia43nblqxnzgj0ny6s7zmdq1wd"; depends=[]; }; - transport = derive2 { name="transport"; version="0.9-4"; sha256="0ham0cla4qwfd6fqyckpdl2n2gm3qnl7ry1xi9kjvbajlcc0xwi2"; depends=[Rcpp]; }; + transport = derive2 { name="transport"; version="0.10-0"; sha256="15x366mlmb0iickgsa7lmgkdn25pfs9mn71vn96rks1a9xyl7qam"; depends=[Rcpp]; }; trapezoid = derive2 { name="trapezoid"; version="2.0-0"; sha256="0f6rwmnn61bj97xxdgbydi94jizv1dbq0qycl60jb4dsxvif8l3n"; depends=[]; }; trawl = derive2 { name="trawl"; version="0.2.1"; sha256="1ns4nk8zdnl2z9clc2q38sbb1ijkj86lcifxq7d111mcwsmpb6fi"; depends=[DEoptim MASS rootSolve Runuran squash TSA]; }; treatSens = derive2 { name="treatSens"; version="2.1.3"; sha256="159dpd4wg0i4cidg40lad665sm3j4qch8d1y3k9chwggbhcad5jn"; depends=[BH dbarts lme4 mvtnorm nlme Rcpp RcppEigen]; }; @@ -13003,8 +13107,8 @@ in with self; { tsfa = derive2 { name="tsfa"; version="2014.10-1"; sha256="0gkgl55v08dr288nf8r769f96qri7qbi5src7y6azrykb37nz6iz"; depends=[dse EvalEst GPArotation setRNG tfplot tframe]; }; tsfknn = derive2 { name="tsfknn"; version="0.1.0"; sha256="0gzij2fbgwavpsqmr7cp012lhii23fav4nsrbc2w9qingglcnqd1"; depends=[ggplot2]; }; tsgui = derive2 { name="tsgui"; version="0.0.3"; sha256="16cx68gq2f63wx7mhbv0aq6pr71wfbc035kjbjjsfrbagaq4ib13"; depends=[RandomFieldsUtils tcltk2 tkrplot]; }; - tsiR = derive2 { name="tsiR"; version="0.3.0"; sha256="1brlwsbs4rac8z6cf1q3xm1apdi4ban5hj7p3qvz2yx810gbxp1d"; depends=[ggplot2 kernlab reshape2]; }; - tsibble = derive2 { name="tsibble"; version="0.6.1"; sha256="1qmz260jlypqbqj5ngas06k35flikk6z0qfq87m2q7mxls2cshqg"; depends=[anytime dplyr lubridate purrr Rcpp rlang tibble tidyr tidyselect]; }; + tsiR = derive2 { name="tsiR"; version="0.4.0"; sha256="1mgiyj25kp8iyll5hfg99iyr8c0wai3hcgglgmfqc96wfgpijfbf"; depends=[ggplot2 kernlab reshape2]; }; + tsibble = derive2 { name="tsibble"; version="0.6.2"; sha256="11ibcx9xfvh6v0lvsx70mb1sq1fk1ydsgy1b3kw6gpydh7yz4rjk"; depends=[anytime dplyr lubridate purrr Rcpp rlang tibble tidyr tidyselect]; }; tsintermittent = derive2 { name="tsintermittent"; version="1.9"; sha256="1mrb6yrsjwj6j40n97sgg42ddvwhjnaiq9k7ka249bbq01gf2975"; depends=[MAPA]; }; tsmp = derive2 { name="tsmp"; version="0.3.2"; sha256="1q1rdlx90dwk2p9s7i3246yi192pwysflphfvd20ldc0qm815sml"; depends=[audio doSNOW foreach magrittr progress]; }; tsna = derive2 { name="tsna"; version="0.2.0"; sha256="09q01jzj1rnv2f2jf7djnq5xrkp7lvykdbf4bfswsy0f95j0asx2"; depends=[network networkDynamic statnet_common]; }; @@ -13014,7 +13118,7 @@ in with self; { tsqn = derive2 { name="tsqn"; version="1.0.0"; sha256="1iv1wwa6a9824dbgfk5a609szppc3a8j250z74hb8csjvwwx9qq9"; depends=[fracdiff MASS robustbase]; }; tstools = derive2 { name="tstools"; version="0.3.8"; sha256="0daxrp91hxc367hlzla0s7x5dddnx462239jcq0ickx6awkk753g"; depends=[data_table jsonlite xts zoo]; }; tswge = derive2 { name="tswge"; version="1.0.0"; sha256="0wj0kyb1dcwfn8wjp7skgcflc48cr4va0i0jg8x970658if7z6fz"; depends=[astsa MASS PolynomF signal waveslim]; }; - tsxtreme = derive2 { name="tsxtreme"; version="0.3.1"; sha256="0cfska93ws5x11pslcdhf5rrshxzh6ddlgmfkl9zlci2rqdbwz35"; depends=[evd MASS mvtnorm]; }; + tsxtreme = derive2 { name="tsxtreme"; version="0.3.2"; sha256="1lmvwk83186qb59k3i4ppv85dvz7fww8wr97mvkl8457mf4n6kg0"; depends=[evd MASS mvtnorm]; }; ttScreening = derive2 { name="ttScreening"; version="1.6"; sha256="1i8c9l3sdkzl99zxxyfqm84vkh6wjdh3a32l5q8ikf74g9dhxkf4"; depends=[corpcor limma MASS matrixStats simsalapar sva]; }; ttbbeer = derive2 { name="ttbbeer"; version="1.1.0"; sha256="1azffcizm3460kxvrxxkilc6qxspyi247x8drrw5ywfichwhmdhc"; depends=[]; }; ttestshiny = derive2 { name="ttestshiny"; version="0.1.0"; sha256="186569p9h3597z9lxyzm7fj8k6bzgm2kw757dcv2qhhf2k7nfch9"; depends=[dplyr shiny shinyAce shinyjs]; }; @@ -13044,7 +13148,7 @@ in with self; { tvm = derive2 { name="tvm"; version="0.3.0"; sha256="1iv0qrks1zdiq8jaqr1h46snq8wc3g3q017hxc8zc6fqnsz1whf6"; depends=[ggplot2 reshape2]; }; twang = derive2 { name="twang"; version="1.5"; sha256="1sp1vb6l0mwpy9b9my5d3spc0q0zs7xg4dkmi4cl7hy7m9xy1dbk"; depends=[gbm lattice latticeExtra survey xtable]; }; tweedie = derive2 { name="tweedie"; version="2.3.2"; sha256="10fv998qjxsyx0h94fi0xbh6xbf24nwgh254n9zfnmix9vk2cqls"; depends=[]; }; - tweenr = derive2 { name="tweenr"; version="1.0.0"; sha256="0r98ln17fdzdda66rsj6lqwi843anl6m7c287kbzc4gkj931cifh"; depends=[farver magrittr Rcpp rlang]; }; + tweenr = derive2 { name="tweenr"; version="1.0.1"; sha256="0sq90pbln6lkc2q3zflhkxxwpqdw5dd7igrxhdnlynkdrmi83mpg"; depends=[farver magrittr Rcpp rlang]; }; tweet2r = derive2 { name="tweet2r"; version="1.1"; sha256="1ivzc05af3fbdxn99lcphm74qs64lz8577zzi6r52r9xjpsqpqzi"; depends=[ggmap ggplot2 maptools plyr rgdal ROAuth RPostgreSQL RSQLite sp spacetime spatstat splancs streamR]; }; twfy = derive2 { name="twfy"; version="0.1.0"; sha256="14xxl9y8iagnn5jd06k6jyy4wk7crm64svz8h0zmzcvg47k8bwc7"; depends=[httr jsonlite]; }; twiddler = derive2 { name="twiddler"; version="0.5-0"; sha256="0r16nfk2afcw7w0j0n3g0sjs07dnafrp88abwcqg3jyvldp3kxnx"; depends=[]; }; @@ -13078,7 +13182,7 @@ in with self; { ukgasapi = derive2 { name="ukgasapi"; version="0.15"; sha256="051bavhsqybg0m1nkv52k9vy5a80aanas146ndx0k9dn2mqmpsw7"; depends=[RCurl XML]; }; umap = derive2 { name="umap"; version="0.2.0.0"; sha256="1qdq3isrv6dqz462sfwk1albbs6h8lcnqidhwr1jxa09bwinhk7q"; depends=[Rcpp reticulate RSpectra]; }; ump = derive2 { name="ump"; version="0.5-8"; sha256="1sg226caq9y41cwl7wr5s9z3bpq2j5p6rj6fy2pasbzimgzw0byx"; depends=[]; }; - umx = derive2 { name="umx"; version="2.8.5"; sha256="1fi4k6asw3rmh88rvdwrf63xi5yqdd9h0bq1bs10j7h9mw9a119j"; depends=[cowplot DiagrammeR ggplot2 knitr MASS Matrix MuMIn mvtnorm nlme numDeriv OpenMx polycor R2HTML RCurl sfsmisc xtable]; }; + umx = derive2 { name="umx"; version="2.9.0"; sha256="17flp57xknmskmf1hpllm6v9pxs6kmkrz02ch1qhcr6g5cs1f7l6"; depends=[cowplot DiagrammeR ggplot2 knitr MASS Matrix MuMIn mvtnorm nlme numDeriv OpenMx polycor R2HTML RCurl sfsmisc xtable]; }; unbalanced = derive2 { name="unbalanced"; version="2.0"; sha256="18hy9nnq42s1viij0a5i9wzrrfmmbf7y3yzjzymz2wnrx4f2pqwv"; depends=[doParallel FNN foreach mlr RANN]; }; unbalhaar = derive2 { name="unbalhaar"; version="2.0"; sha256="0v6bkin1cakwl9lmv49s0jnccl9d6vdslbi1a7kfvmr5dgy760hs"; depends=[]; }; uncertainty = derive2 { name="uncertainty"; version="0.2.0"; sha256="1mq14ny7l3gy3wjsqijnm37azavyapxszjnckd861h4hgcpdcdjz"; depends=[mvtnorm triangle]; }; @@ -13102,7 +13206,7 @@ in with self; { unix = derive2 { name="unix"; version="1.3"; sha256="1l5w22j0h3qzya13wx7y8lx2baw496vcmn39l2y8r1v38as9dybc"; depends=[]; }; unjoin = derive2 { name="unjoin"; version="0.0.3"; sha256="08vjgl4dnh9kycrvdq5ngf57fy61n0nc582bi4znv06pq696rkwp"; depends=[dplyr rlang tibble]; }; unmarked = derive2 { name="unmarked"; version="0.12-2"; sha256="1ql8l7kc8py7zand164w3yszqbmwyxvrkjvr10l4hx2mkcnvxzx0"; depends=[lattice plyr raster Rcpp RcppArmadillo reshape]; }; - unpivotr = derive2 { name="unpivotr"; version="0.4.0"; sha256="0zixkrxizfa309bfscivdjkz0c62xxrrfnbp829pgj2pvyicki50"; depends=[cellranger dplyr forcats magrittr pillar purrr rlang tibble tidyr xml2]; }; + unpivotr = derive2 { name="unpivotr"; version="0.5.0"; sha256="1w0gc15wy9901nb9l2srqbanpcs5zy7bhrmzlqbqhrpa1rdsbf2f"; depends=[cellranger dplyr forcats magrittr pillar purrr rlang tibble tidyr xml2]; }; unrepx = derive2 { name="unrepx"; version="1.0"; sha256="1dzvwpza60y9p7kz1f0bm20wid5jyxx9pma4w41az9shq5kkr0aj"; depends=[]; }; unrtf = derive2 { name="unrtf"; version="1.3"; sha256="06v6hjpbybv07vqfq23i2s6j0ic035vnm0i4wfqgiw0pw6c85242"; depends=[sys]; }; unsystation = derive2 { name="unsystation"; version="0.2.0"; sha256="02da7wzzk5bwd475i67v5x04ay2bn5yd5xffl1asqcqxcc5sy0m8"; depends=[doParallel foreach iterators Rcpp RcppArmadillo]; }; @@ -13167,9 +13271,9 @@ in with self; { varhandle = derive2 { name="varhandle"; version="2.0.3"; sha256="11yisjgqc8fq0sj1kzgp51i926cs4yqkpfmbis5ak786wqalc6na"; depends=[]; }; variables = derive2 { name="variables"; version="1.0-1"; sha256="05bqhkzava24z7dqg79vf9144d226rr5mby6ry32lqyx7w0gql9x"; depends=[]; }; varian = derive2 { name="varian"; version="0.2.2"; sha256="0jyw46qx2w19h02mrwv3w3n8qc1n4b3ckm38qly1y4a4w9ib6c2i"; depends=[Formula ggplot2 gridExtra MASS rstan]; }; - variosig = derive2 { name="variosig"; version="0.2"; sha256="10cw7i7sdachv7hmzw8sbhldgwddk3k165klrhiagarmfgplxi1b"; depends=[geoR gstat sp testthat]; }; + variosig = derive2 { name="variosig"; version="0.3"; sha256="0pffkhxkxp1bmyqdvwixfw8kqdvf0p4c9ff44cbhnc8lcyv5qpj2"; depends=[geoR gstat sp testthat]; }; varjmcm = derive2 { name="varjmcm"; version="0.1.0"; sha256="02l0d896faakh9pdq2rzl2psmrj7l2pvacz7nk3r6552glsk7h18"; depends=[expm jmcm MASS Matrix]; }; - varrank = derive2 { name="varrank"; version="0.1"; sha256="1ynpnzfvwbwfpcv7rqlkvxmmafnjgdssr5l42rr3bklm9j1z71vm"; depends=[FNN]; }; + varrank = derive2 { name="varrank"; version="0.2"; sha256="19c40wwiadyqwn4z7nd22ynpa4wxr2anr2487mllmpg1d7wz3y38"; depends=[FNN]; }; vars = derive2 { name="vars"; version="1.5-3"; sha256="0zc6v827ll19n088n31afgjf65zqwvyzmmj4q3ab1xhqzxfsgbw6"; depends=[lmtest MASS sandwich strucchange urca]; }; vbdm = derive2 { name="vbdm"; version="0.0.4"; sha256="1rbff0whhbfcf6q5wpr3ws1n4n2kcr79yifcni12vxg69a3v6dd3"; depends=[]; }; vbsr = derive2 { name="vbsr"; version="0.0.5"; sha256="1avskbxxyinjjdga4rnghcfvd4sypv4m39ysfaij5avvmi89bx3b"; depends=[]; }; @@ -13181,7 +13285,7 @@ in with self; { vcrpart = derive2 { name="vcrpart"; version="1.0-2"; sha256="1xfvsxgyf39d2qxnm40nzkqp7q12y8nbpn9h154n876zxxfs7gh1"; depends=[formula_tools nlme numDeriv partykit rpart sandwich strucchange ucminf zoo]; }; vctrs = derive2 { name="vctrs"; version="0.1.0"; sha256="13w1r8zpalirpfaz5sykpn0mj4jmhxi2qkdcfq081ixlfjyzwa6c"; depends=[backports digest glue rlang zeallot]; }; vdg = derive2 { name="vdg"; version="1.2.0"; sha256="1hi5d14nh9q784sbdk018awrawh9f1aix0wl26x7n0xb4707rcmy"; depends=[ggplot2 gridExtra proxy quantreg]; }; - vdiffr = derive2 { name="vdiffr"; version="0.2.3"; sha256="0rsznvbymlwdjl9qdll98x8cqkf8rdi20c5sw4w547sfxr664yl0"; depends=[devtools fontquiver gdtools glue htmlwidgets purrr R6 Rcpp rlang shiny svglite testthat xml2]; }; + vdiffr = derive2 { name="vdiffr"; version="0.3.0"; sha256="1hl3fj5ml7pkq567nxsn1b1xh92a0isc8c86sa35zxf7jbd38pjd"; depends=[BH devtools diffobj fontquiver freetypeharfbuzz gdtools glue htmltools htmlwidgets purrr R6 Rcpp rlang shiny testthat usethis xml2]; }; vdmR = derive2 { name="vdmR"; version="0.2.6"; sha256="15d3yrwiqs7cfyzl6v5vqgi33arx9lxjbqpif9zzfb56j0x1xsk5"; depends=[broom dplyr GGally ggplot2 gridSVG maptools plyr Rdpack rgdal rgeos rjson Rook sp]; }; vec2dtransf = derive2 { name="vec2dtransf"; version="1.1"; sha256="029xynay9f9rn0syphh2rhd3szv50ib4r0h0xfhhvbbb37h5dc9s"; depends=[sp]; }; veccompare = derive2 { name="veccompare"; version="0.1.0"; sha256="03nyyxvhhwfxxg5w6qflk7q234ipbhj9fd4abcp50sxz3diabch1"; depends=[corrplot gtools pander purrr qgraph reshape2 VennDiagram]; }; @@ -13230,7 +13334,7 @@ in with self; { visreg = derive2 { name="visreg"; version="2.5-0"; sha256="0n19k6rsmpqga6r8lyhjviqs3nw881dhr211621m2cl7knqhhi4y"; depends=[lattice]; }; vistime = derive2 { name="vistime"; version="0.6.0"; sha256="1ah3zwz2ikzd8y2rbff65mdd9lp4yd328mb2971afr2xdd9gvvqd"; depends=[plotly RColorBrewer]; }; vistributions = derive2 { name="vistributions"; version="0.1.0"; sha256="1kpl11l0yp4rhcx9zcfsdk5n62ir92lwjlyqzirrkkfvqpwkmcay"; depends=[ggplot2 magrittr shiny tibble]; }; - visualFields = derive2 { name="visualFields"; version="0.5.5"; sha256="0hn59gjpdmq5m5bnjc2k31xf9l9k678djdv02mxcvjdkghpgmfpv"; depends=[deldir flip gtools Hmisc matrixStats spatstat]; }; + visualFields = derive2 { name="visualFields"; version="0.6"; sha256="1w6wkyzjakj6ss9nv4gzkgva4m21jbsz10c2jy660bjb25rf59ih"; depends=[deldir flip gtools Hmisc matrixStats spatstat]; }; visualize = derive2 { name="visualize"; version="4.3.0"; sha256="1s49sx828f25d4n93mn28xdbc81zflk2sr3h8ffs2mkjr888qd8y"; depends=[]; }; visvow = derive2 { name="visvow"; version="0.3.0"; sha256="1q1i1vnr3zzls3p6rk1c2r89xmxlc11xzkl1r5pbd3ydgppllhna"; depends=[Cairo DT ggdendro ggplot2 ggrepel MASS plot3D plyr pracma psych Rdpack readxl Rtsne shiny shinyBS svglite WriteXLS]; }; vita = derive2 { name="vita"; version="1.0.0"; sha256="114p2lzcr8rn68f0z4kmjdnragqlmi18axda9ma4sbqh8mrmjs9v"; depends=[randomForest Rcpp]; }; @@ -13258,7 +13362,7 @@ in with self; { vscc = derive2 { name="vscc"; version="0.2"; sha256="1p14v8vd8kckd44g4dvzh51gdkd8jvsc4bkd2i4csx8vjiwrni5w"; depends=[mclust teigen]; }; vsgoftest = derive2 { name="vsgoftest"; version="0.3-2"; sha256="020kghcfv8h0i7fzq3p2grhhbwvqmc9ya9r7lc1kiqg1bfgljg91"; depends=[fitdistrplus Rcpp]; }; vstsr = derive2 { name="vstsr"; version="1.0.0"; sha256="0flsw5yw1vmj5x866klxmjqz5aimkvjiwl1zdciz63p9zffmb4gz"; depends=[httr jsonlite magrittr R6 RCurl xml2]; }; - vtreat = derive2 { name="vtreat"; version="1.3.2"; sha256="1p7afvy6y0y4667d4rjhjaa540cc7xwhr27j0mz35zn30vralbyw"; depends=[wrapr]; }; + vtreat = derive2 { name="vtreat"; version="1.3.4"; sha256="14vhmam8j431xb06c2yafa8nkc7ia1in43dsx62s4797nxx2sg3y"; depends=[wrapr]; }; vtree = derive2 { name="vtree"; version="0.1.4"; sha256="1wmvvg7mlbifg3cbjv9qm9rsnl3bs624wm0xnaf489grix92csjb"; depends=[DiagrammeR DiagrammeRsvg rsvg]; }; vudc = derive2 { name="vudc"; version="1.1"; sha256="0zxz6n3ixa3xjzcinky8ymqjx9w8y8z65mz8d84dl00mxzkmkz4h"; depends=[]; }; vwr = derive2 { name="vwr"; version="0.3.0"; sha256="1h790vjcdfngs1siwldvqz8jrxpkajl3266lzadfnmchfan1x7xv"; depends=[lattice latticeExtra stringdist]; }; @@ -13291,6 +13395,7 @@ in with self; { waterData = derive2 { name="waterData"; version="1.0.8"; sha256="0884agh876wf3qlbc75fbaa47x2iwvncz7r2l25qw34n8lxq1yr6"; depends=[dataRetrieval lattice latticeExtra lubridate xml2]; }; waterfall = derive2 { name="waterfall"; version="1.0.2"; sha256="0jy6l9mx0dixwnkychdl18sf4xh73pm0qd1jyxp9rlnv1vcragjp"; depends=[lattice]; }; waterfalls = derive2 { name="waterfalls"; version="0.1.2"; sha256="01gby1mlhrwcalizpywxcakkx2zifswb0188nrl6z9dkkd1866lm"; depends=[ggplot2]; }; + waterquality = derive2 { name="waterquality"; version="0.2.2"; sha256="1hl0mndwbin026w9250llxmss5w9yykvrf1fgkslnyw1ln9pbqyn"; depends=[raster rgdal]; }; waveband = derive2 { name="waveband"; version="4.7"; sha256="0b57g7jwvqgqjzd7x1pd4nqpx22rmiskvf8wjwrgplqzx4daxny2"; depends=[wavethresh]; }; waved = derive2 { name="waved"; version="1.2"; sha256="0zv4rgazk9s295pggzfa7sc062zv68dgds1ngxcz7vg1fx0qkgxg"; depends=[]; }; wavefunction = derive2 { name="wavefunction"; version="1.0.0"; sha256="1g0g9i0s93lcpcx7icqn15bvkmd79slkgimspvvwp2bxdsc5nnf2"; depends=[]; }; @@ -13309,6 +13414,7 @@ in with self; { weatherr = derive2 { name="weatherr"; version="0.1.2"; sha256="11sb5bmqccqkvlabsw4siy9n6ivsrvxavywvaffgrs3blmnygql9"; depends=[ggmap lubridate RJSONIO XML]; }; webTRISr = derive2 { name="webTRISr"; version="0.1.1"; sha256="044a079fj4ryykj2n8zlfipmjyrfyfvhrqcd1wbb6r440yjkvali"; depends=[dplyr httr jsonlite lubridate magrittr purrr readr stringr]; }; webchem = derive2 { name="webchem"; version="0.4.0"; sha256="032bsfnkn7s33y42fyf8yradsh8jhms4ryjkh0r76hqnx3j00ph0"; depends=[httr jsonlite RCurl rvest stringr xml2]; }; + webddx = derive2 { name="webddx"; version="0.1.0"; sha256="0w72pp0f77glq460mjagm30y3nd9dmhjkbb0w06ycsjdqvr8qji7"; depends=[jsonlite]; }; webdriver = derive2 { name="webdriver"; version="1.0.5"; sha256="0l3nz7gf62jlkvkn5sfxfvn0prxz3ds7nlpfb1yhnmdljhbzrgzf"; depends=[base64enc callr curl debugme httr jsonlite R6 showimage withr]; }; webglobe = derive2 { name="webglobe"; version="1.0.2"; sha256="1277d6fkgrgixlhikfwf0r6z8g5b7mah905xi219qsfycxmifgn9"; depends=[geojsonio httpuv jsonlite]; }; webmockr = derive2 { name="webmockr"; version="0.2.9"; sha256="01fk50n3fakjz4fdgix14iavcnnsipdyl2w436irkkgmrqv7kd5l"; depends=[crul curl fauxpas jsonlite lazyeval magrittr R6 urltools]; }; @@ -13323,6 +13429,7 @@ in with self; { weco = derive2 { name="weco"; version="1.2"; sha256="1prk8hn782pd8g2rbbaj7y10vjimqs9n8i4rab6aw6fc3k759d6b"; depends=[]; }; weibullness = derive2 { name="weibullness"; version="1.18.6"; sha256="046fs6b5yb6ckddcb9vplc5478c7xprnafsj4rvzb1gmcpcrqqck"; depends=[]; }; weibulltools = derive2 { name="weibulltools"; version="0.5.4"; sha256="0xxqcvxd489qhdais7f2xnscz8bfcsl4k1qggl35v65bn7bm7hjw"; depends=[dplyr magrittr plotly Rcpp sandwich segmented SPREDA survival]; }; + weightQuant = derive2 { name="weightQuant"; version="1.0"; sha256="1ngz51wr5qpnb98lfbddwvipcra86dq5whm6z8c4xd921anb15bx"; depends=[doParallel foreach quantreg]; }; weightTAPSPACK = derive2 { name="weightTAPSPACK"; version="0.1"; sha256="0kpfw477qka5qrc6sh73had38xbrwrqp1yv0dj2qiihkiyrp67ks"; depends=[HotDeckImputation mice plyr survey]; }; weightedScores = derive2 { name="weightedScores"; version="0.9.5.1"; sha256="118hzwaarcb8pk2zz83m6zzzndlpbbzb7gz87vc7zggpa998k1gr"; depends=[mvtnorm rootSolve]; }; weightr = derive2 { name="weightr"; version="1.1.2"; sha256="13wy7ygx7khbmymg2r0rr6mrl4lbapf5bnnq1rq8izl38sjk7csx"; depends=[]; }; @@ -13331,7 +13438,7 @@ in with self; { welchADF = derive2 { name="welchADF"; version="0.3"; sha256="0k2di5fwh5jv87mw4bjnhbk2rmhf2v2f5ksjr5dgnyhnawwxqq97"; depends=[lme4]; }; wellknown = derive2 { name="wellknown"; version="0.5.0"; sha256="1y3hi5ajqaxx3s40cx24ayfcd3c6d1ydlhsm0gg2fxgmidm6bhwy"; depends=[jsonlite V8]; }; wesanderson = derive2 { name="wesanderson"; version="0.3.6"; sha256="09mr6p2jmqdjq27cz974w5hyxgn929zp9z3inhxqmmh1582fmdi2"; depends=[]; }; - wevid = derive2 { name="wevid"; version="0.5.1"; sha256="1dw4ypdmhnvwv89ydjbl2jbaf6913gx966qvcbm82apvjbb624vy"; depends=[ggplot2 pROC reshape2 zoo]; }; + wevid = derive2 { name="wevid"; version="0.5.2"; sha256="0275vf49ryw6ljpibz138xci236bhqvwz59nc33qplqvankfsgcs"; depends=[ggplot2 pROC reshape2 zoo]; }; wfe = derive2 { name="wfe"; version="1.7"; sha256="058rbg6b8l3sndqlm493z6s4b2ylk0194gqdbbsfamnpygl21x0d"; depends=[arm MASS Matrix]; }; wfg = derive2 { name="wfg"; version="0.1"; sha256="1r6wb8v42mpapjfhmkmghm9fq21c3s4zmdxy8nlh31nsja71c37d"; depends=[igraph]; }; wfindr = derive2 { name="wfindr"; version="0.1.0"; sha256="0m5xj50hqdjj4lpbgx1kp3my4njr0nz09hd63rf4qf1ls8r7zil9"; depends=[dplyr magrittr]; }; @@ -13364,7 +13471,7 @@ in with self; { windfarmGA = derive2 { name="windfarmGA"; version="1.2.1"; sha256="1v4brwi92a2kchak43z0vxjq11373amh190fnmpmnpz58zbls448"; depends=[calibrate data_table doParallel dplyr foreach geoR ggplot2 googleVis gstat gtools leaflet magrittr maptools RandomFields raster RColorBrewer rgdal rgeos rgl RgoogleMaps sp spatstat]; }; wingui = derive2 { name="wingui"; version="0.2"; sha256="0yf6k33qpcjzyb7ckwsxpdw3pcsja2wsf08vaca7qw27yxrbmaa3"; depends=[Rcpp]; }; wiod = derive2 { name="wiod"; version="0.3.0"; sha256="1f151xmc6bm5d28w5123nm0hv7j1v8hay4jk5fk8pwn6yljl1pah"; depends=[decompr gvc]; }; - wiqid = derive2 { name="wiqid"; version="0.1.5"; sha256="02ssj0f12if3bic614bp9klzcag121rbqw4g0awvcpk9jql8k5dr"; depends=[coda HDInterval MASS truncnorm]; }; + wiqid = derive2 { name="wiqid"; version="0.2.1"; sha256="15jh60vb6waxmg0w0vc753p3z4wkszjhk90j2j15wky13dbs77sr"; depends=[coda HDInterval MASS truncnorm]; }; wiseR = derive2 { name="wiseR"; version="1.0.1"; sha256="187ylwhk06957x9zm5r0m6w9wg08im83myz3s4gr927ig8yv3b5f"; depends=[arules bnlearn DescTools dplyr DT graph HydeNet igraph linkcomm missRanger psych RBGL Rgraphviz rhandsontable rintrojs shiny shinyalert shinyBS shinycssloaders shinydashboard shinyWidgets visNetwork]; }; withr = derive2 { name="withr"; version="2.1.2"; sha256="11j6zykklxnvp4xqsr6a2xib665i38m3khdspp887nwagmvnydj1"; depends=[]; }; wkb = derive2 { name="wkb"; version="0.3-0"; sha256="0s7libkg27jdmcw5qmk5j0cmz3nqq7ny4q8gy4vhbgsgj4gbbdn9"; depends=[sp]; }; @@ -13400,7 +13507,7 @@ in with self; { wql = derive2 { name="wql"; version="0.4.9"; sha256="0m16l807mhcjkbqhlzhc24pw4hl78fjyykiszlg337x3qs803fg2"; depends=[ggplot2 reshape2 zoo]; }; wqs = derive2 { name="wqs"; version="0.0.1"; sha256="14qaa9g9v4nqrv897laflib3wwhflyfaf9wpllmbi5xfv9223rcg"; depends=[glm2 Rsolnp]; }; wrangle = derive2 { name="wrangle"; version="0.4"; sha256="0d1xdcvgcv8bn20s90sn1dmzhcdz39yr1m2bkcjbvavm132p96bl"; depends=[dplyr lazyeval magrittr tidyr]; }; - wrapr = derive2 { name="wrapr"; version="1.7.0"; sha256="0vl8ajk32zhnaj7mz0qd9d1lcxvg7fldkv6bxjfjprpkjda67bxj"; depends=[]; }; + wrapr = derive2 { name="wrapr"; version="1.8.0"; sha256="1z9nb95z4565ibz36j7kadi481kwq3sqk8b36qb7rfq5p783sm57"; depends=[]; }; wrassp = derive2 { name="wrassp"; version="0.1.8"; sha256="052x0lxpchr6f97yfj3vmhh8gc8qg5pp1m91h5akrav4yfawbs7k"; depends=[]; }; write_snns = derive2 { name="write.snns"; version="0.0-4.2"; sha256="0sxg7z8rnh4lssbivkrfxldv4ivy37wkndzzndpbvq2gbvbjnp4l"; depends=[]; }; writexl = derive2 { name="writexl"; version="1.1"; sha256="0w4wnpl3yhaqp63p32bk60xrbmd7xd11kxifjbzrghi7d4483a46"; depends=[]; }; @@ -13459,9 +13566,10 @@ in with self; { xseq = derive2 { name="xseq"; version="0.2.1"; sha256="0bsakbfvkfv39q2ch2g21b17g84470sq4v73355cljlshsi6404i"; depends=[e1071 gptk impute preprocessCore RColorBrewer sfsmisc]; }; xslt = derive2 { name="xslt"; version="1.3"; sha256="0giqzmdby9ax8gwx9b7xqka28k3hgymv4289k8p8dvg26d683p3l"; depends=[Rcpp xml2]; }; xsp = derive2 { name="xsp"; version="0.1.2"; sha256="1jbmxa234v52qji8sz4bkg24c2n65b0zh9py1wyyfzw9n1wx5w0r"; depends=[ggplot2 reshape2]; }; + xspliner = derive2 { name="xspliner"; version="0.0.2"; sha256="07niy8dl4fcp1pv8dl4h9vyw8slxvhjj7qc5x7ywabyfh140pvyh"; depends=[dplyr ggplot2 magrittr mgcv pdp purrr tidyr]; }; xtable = derive2 { name="xtable"; version="1.8-3"; sha256="09f311gq9g7dzf8jdvcx72j11xb7p00jlg066jjbpa6pz3zv1cjk"; depends=[]; }; xtal = derive2 { name="xtal"; version="1.15"; sha256="1zq3vd5x3vw6acn47yd2x7kflr9sm3znmdkm68cs64ha54jbl3vs"; depends=[]; }; - xtensor = derive2 { name="xtensor"; version="0.8.1-0"; sha256="0qyqadg2yvvf51ch2w1aqsi1j0yfgw1167fps4s0k7gjvv692zfx"; depends=[Rcpp]; }; + xtensor = derive2 { name="xtensor"; version="0.9.0-0"; sha256="18v653pjqr1hnv6mmrfxvlssx83245dzhg8772s6m80awkzzljpj"; depends=[Rcpp]; }; xtermStyle = derive2 { name="xtermStyle"; version="3.0.5"; sha256="1q4qq8w4sgxbbb1x0i4k5xndvwisvjszg830wspwb37wigxz8xvz"; depends=[]; }; xtractomatic = derive2 { name="xtractomatic"; version="3.4.2"; sha256="1w70kk608avnf7zdjx79gxqmj12cw86ma4x0b9j92md1vmpw5389"; depends=[dplyr httr ncdf4 readr sp]; }; xts = derive2 { name="xts"; version="0.11-2"; sha256="1f0kxrvn13py3hk2gh2m56cqm39x3bqp1i350r5viddacrm2yxqj"; depends=[zoo]; }; From bc1b9dd1fe86df5ccd07c6e7520969354b2609d8 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Tue, 8 Jan 2019 01:24:10 -0800 Subject: [PATCH 173/247] calibre: 3.36.0 -> 3.37.0 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/calibre/versions --- pkgs/applications/misc/calibre/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/misc/calibre/default.nix b/pkgs/applications/misc/calibre/default.nix index 7b01f5c53d77..a9e047170e2a 100644 --- a/pkgs/applications/misc/calibre/default.nix +++ b/pkgs/applications/misc/calibre/default.nix @@ -5,12 +5,12 @@ }: stdenv.mkDerivation rec { - version = "3.36.0"; + version = "3.37.0"; name = "calibre-${version}"; src = fetchurl { url = "https://download.calibre-ebook.com/${version}/${name}.tar.xz"; - sha256 = "0fbf4b29vkka3gg8c5n9dc7qhv43jpw6naz6w83jkz7andypikb8"; + sha256 = "12si7jag5ildy08h0nfs4rfpn417i82valxbk2wjkypp226gqi05"; }; patches = [ From 68982ea9383c2ea601fcb77b90d31d64b3c1b2ee Mon Sep 17 00:00:00 2001 From: Sean Haugh Date: Tue, 8 Jan 2019 04:11:37 -0600 Subject: [PATCH 174/247] zsh: move --enable-zprofile into configureFlags (#52718) --- pkgs/shells/zsh/default.nix | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/pkgs/shells/zsh/default.nix b/pkgs/shells/zsh/default.nix index 472b78c4a6d0..bebf219d9b25 100644 --- a/pkgs/shells/zsh/default.nix +++ b/pkgs/shells/zsh/default.nix @@ -34,10 +34,8 @@ stdenv.mkDerivation { "--enable-multibyte" "--with-tcsetpgrp" "--enable-pcre" + "--enable-zprofile=${placeholder "out"}/etc/zprofile" ]; - preConfigure = '' - configureFlagsArray+=(--enable-zprofile=$out/etc/zprofile) - ''; # the zsh/zpty module is not available on hydra # so skip groups Y Z From 6c6a899f324aa2325f9f4e3a28a5786843939034 Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Tue, 8 Jan 2019 10:49:05 +0100 Subject: [PATCH 175/247] minio: 2018-12-06T01-27-43Z -> 2018-12-27T18-33-08Z --- pkgs/servers/minio/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/servers/minio/default.nix b/pkgs/servers/minio/default.nix index 5b19d6dd37eb..2afcea8a73ea 100644 --- a/pkgs/servers/minio/default.nix +++ b/pkgs/servers/minio/default.nix @@ -3,13 +3,13 @@ buildGoPackage rec { name = "minio-${version}"; - version = "2018-12-06T01-27-43Z"; + version = "2018-12-27T18-33-08Z"; src = fetchFromGitHub { owner = "minio"; repo = "minio"; rev = "RELEASE.${version}"; - sha256 = "0j10rhrg98zsv62sdc9wgrh2kdpv2179szvzyg8rm9rb89rzdhd2"; + sha256 = "076m4w6z2adl8pi9x7in8s2pa51vj4qlk3m32ibh6yhqfzpbfgd2"; }; goPackagePath = "github.com/minio/minio"; From fd9029796016bea43be555f9ae756a7a28a5e180 Mon Sep 17 00:00:00 2001 From: Florian Klink Date: Tue, 8 Jan 2019 11:25:00 +0100 Subject: [PATCH 176/247] minio-client: 2018-12-05T22-59-07Z -> 2018-12-27T00-37-49Z --- pkgs/tools/networking/minio-client/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/networking/minio-client/default.nix b/pkgs/tools/networking/minio-client/default.nix index 8b8991db86c2..7234d73e1144 100644 --- a/pkgs/tools/networking/minio-client/default.nix +++ b/pkgs/tools/networking/minio-client/default.nix @@ -3,13 +3,13 @@ buildGoPackage rec { name = "minio-client-${version}"; - version = "2018-12-05T22-59-07Z"; + version = "2018-12-27T00-37-49Z"; src = fetchFromGitHub { owner = "minio"; repo = "mc"; rev = "RELEASE.${version}"; - sha256 = "01vjgs96sb792rggc7da9fzbpam5pyr7x9zd4r8wv6jc6xnv7n3x"; + sha256 = "1hbw3yam5lc9414f3f8yh32ycj0wz2xc934ksvjnrhkk4xzyal6h"; }; goPackagePath = "github.com/minio/mc"; From 5da2848c1df3c56fc3b331711f7bfec4175f604c Mon Sep 17 00:00:00 2001 From: Jethro Kuan Date: Tue, 8 Jan 2019 21:25:00 +0800 Subject: [PATCH 177/247] emacsPackages.pdf-tools: 0.80 -> 0.90 --- pkgs/top-level/emacs-packages.nix | 18 ++---------------- 1 file changed, 2 insertions(+), 16 deletions(-) diff --git a/pkgs/top-level/emacs-packages.nix b/pkgs/top-level/emacs-packages.nix index 9cd38e066d38..d7c196376cb0 100644 --- a/pkgs/top-level/emacs-packages.nix +++ b/pkgs/top-level/emacs-packages.nix @@ -73,27 +73,13 @@ let pdf-tools = melpaBuild rec { pname = "pdf-tools"; - version = "0.80"; + version = "0.90"; src = fetchFromGitHub { owner = "politza"; repo = "pdf-tools"; rev = "v${version}"; - sha256 = "1i4647vax5na73basc5dz4lh9kprir00fh8ps4i0l1y3ippnjs2s"; + sha256 = "0iv2g5kd14zk3r5dzdw7b7hk4b5w7qpbilcqkja46jgxbb6xnpl9"; }; - patches = [ - (fetchpatch { - url = https://github.com/politza/pdf-tools/commit/6505a0e817495b85897c9380161034ae611ddd90.patch; - sha256 = "122ycbja8ckaysp58xqfcv11sgpbcp78pll5mywf9hgr0qap9jsy"; - }) - (fetchpatch { - url = https://github.com/politza/pdf-tools/commit/ded6341b0e3ad97e8b14f68c1796ba66dc155fd1.patch; - sha256 = "0hd2v4c6xq2jzg2m6s5kzs0fldgygf1pnfqd11v6x4w05zvxn6a2"; - }) - (fetchpatch { - url = https://github.com/politza/pdf-tools/commit/50a5297b82e26cfd52f6c00645ddc1057099d6a7.patch; - sha256 = "107rqzldg06h8k3pmdinkl78dr4xycm570sp2an4ihjmpmph0z39"; - }) - ]; nativeBuildInputs = [ external.pkgconfig ]; buildInputs = with external; [ autoconf automake libpng zlib poppler ]; preBuild = "make server/epdfinfo"; From 2c9de98dbaddc25520296ad22c55eae961cb21a3 Mon Sep 17 00:00:00 2001 From: Corbin Date: Mon, 7 Jan 2019 17:12:07 -0800 Subject: [PATCH 178/247] pythonPackages.zfec: patch out argparse dependency Since `argparse` stopped doing anything a while ago, we'll just patch it out of setup.py and nobody will notice. --- pkgs/development/python-modules/zfec/default.nix | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/zfec/default.nix b/pkgs/development/python-modules/zfec/default.nix index caca5be7b9fe..0e18de7d5026 100644 --- a/pkgs/development/python-modules/zfec/default.nix +++ b/pkgs/development/python-modules/zfec/default.nix @@ -3,7 +3,6 @@ , fetchPypi , setuptoolsDarcs , pyutil -, argparse , isPyPy }: @@ -18,7 +17,12 @@ buildPythonPackage rec { }; buildInputs = [ setuptoolsDarcs ]; - propagatedBuildInputs = [ pyutil argparse ]; + propagatedBuildInputs = [ pyutil ]; + + # argparse is in the stdlib but zfec doesn't know that. + postPatch = '' + sed -i -e '/argparse/d' setup.py + ''; meta = with stdenv.lib; { homepage = http://allmydata.org/trac/zfec; From c38ff237f2543ba6eaacd4050ee84174270d0c27 Mon Sep 17 00:00:00 2001 From: Will Dietz Date: Mon, 7 Jan 2019 04:09:13 -0600 Subject: [PATCH 179/247] xterm: 341 -> 342 --- pkgs/applications/misc/xterm/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/misc/xterm/default.nix b/pkgs/applications/misc/xterm/default.nix index e29bdd46e26a..905bff4a6727 100644 --- a/pkgs/applications/misc/xterm/default.nix +++ b/pkgs/applications/misc/xterm/default.nix @@ -3,14 +3,14 @@ }: stdenv.mkDerivation rec { - name = "xterm-341"; + name = "xterm-342"; src = fetchurl { urls = [ "ftp://ftp.invisible-island.net/xterm/${name}.tgz" "https://invisible-mirror.net/archives/xterm/${name}.tgz" ]; - sha256 = "0i6b6gpr5qzbgv3jfl86q8d47bgppxr5gq503ng1ll2x5gx7v833"; + sha256 = "1y8ldzl4h1872fxvpvi2zwa9y3d34872vfdvfasap79lpn8208l0"; }; buildInputs = From 4d29e16bf2dcf642dc1ad4ceb066a6fcc5b4ac73 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= Date: Wed, 19 Dec 2018 14:53:12 +0100 Subject: [PATCH 180/247] python.pkgs.graphviz: hardcode path to graphviz's bin/ --- .../python-modules/graphviz/default.nix | 44 +++++++-- .../graphviz/hardcode-graphviz-path.patch | 95 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 4 +- 3 files changed, 133 insertions(+), 10 deletions(-) create mode 100644 pkgs/development/python-modules/graphviz/hardcode-graphviz-path.patch diff --git a/pkgs/development/python-modules/graphviz/default.nix b/pkgs/development/python-modules/graphviz/default.nix index 3e9ee8b17f7c..572fdcaee51a 100644 --- a/pkgs/development/python-modules/graphviz/default.nix +++ b/pkgs/development/python-modules/graphviz/default.nix @@ -1,25 +1,51 @@ -{ stdenv +{ lib , buildPythonPackage -, fetchPypi -, pkgs +, fetchFromGitHub +, substituteAll +, graphviz +, makeFontsConf +, freefont_ttf +, mock +, pytest +, pytest-mock +, pytestcov }: buildPythonPackage rec { pname = "graphviz"; version = "0.10.1"; - src = fetchPypi { - inherit pname version; - extension = "zip"; - sha256 = "d311be4fddfe832a56986ac5e1d6e8715d7fcb0208560da79d1bb0f72abef41f"; + # patch does not apply to PyPI tarball due to different line endings + src = fetchFromGitHub { + owner = "xflr6"; + repo = "graphviz"; + rev = version; + sha256 = "1vqk4xy45c72la56j24z9jmjp5a0aa2k32fybnlbkzqjvvbl72d8"; }; - propagatedBuildInputs = [ pkgs.graphviz ]; + patches = [ + (substituteAll { + src = ./hardcode-graphviz-path.patch; + inherit graphviz; + }) + ]; - meta = with stdenv.lib; { + # Fontconfig error: Cannot load default config file + FONTCONFIG_FILE = makeFontsConf { + fontDirectories = [ freefont_ttf ]; + }; + + checkInputs = [ mock pytest pytest-mock pytestcov ]; + + checkPhase = '' + pytest + ''; + + meta = with lib; { description = "Simple Python interface for Graphviz"; homepage = https://github.com/xflr6/graphviz; license = licenses.mit; + maintainers = with maintainers; [ dotlambda ]; }; } diff --git a/pkgs/development/python-modules/graphviz/hardcode-graphviz-path.patch b/pkgs/development/python-modules/graphviz/hardcode-graphviz-path.patch new file mode 100644 index 000000000000..ad632974c28c --- /dev/null +++ b/pkgs/development/python-modules/graphviz/hardcode-graphviz-path.patch @@ -0,0 +1,95 @@ +diff --git a/graphviz/backend.py b/graphviz/backend.py +index 704017b..fe4aefe 100644 +--- a/graphviz/backend.py ++++ b/graphviz/backend.py +@@ -114,7 +114,7 @@ def command(engine, format, filepath=None, renderer=None, formatter=None): + suffix = '.'.join(reversed(format_arg)) + format_arg = ':'.join(format_arg) + +- cmd = [engine, '-T%s' % format_arg] ++ cmd = [os.path.join('@graphviz@/bin', engine), '-T%s' % format_arg] + rendered = None + if filepath is not None: + cmd.extend(['-O', filepath]) +@@ -217,7 +217,7 @@ def version(): + subprocess.CalledProcessError: If the exit status is non-zero. + RuntimmeError: If the output cannot be parsed into a version number. + """ +- cmd = ['dot', '-V'] ++ cmd = ['@graphviz@/bin/dot', '-V'] + out, _ = run(cmd, check=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) + + info = out.decode('ascii') +diff --git a/tests/test_backend.py b/tests/test_backend.py +index 7ec12f7..2e8550d 100644 +--- a/tests/test_backend.py ++++ b/tests/test_backend.py +@@ -47,6 +47,7 @@ def test_render_formatter_unknown(): + render('dot', 'ps', 'nonfilepath', 'ps', '') + + ++@pytest.mark.skip(reason='empty $PATH has no effect') + @pytest.mark.usefixtures('empty_path') + def test_render_missing_executable(): + with pytest.raises(ExecutableNotFound, match=r'execute'): +@@ -85,7 +86,7 @@ def test_render_mocked(capsys, mocker, Popen, quiet): + + assert render('dot', 'pdf', 'nonfilepath', quiet=quiet) == 'nonfilepath.pdf' + +- Popen.assert_called_once_with(['dot', '-Tpdf', '-O', 'nonfilepath'], ++ Popen.assert_called_once_with(['@graphviz@/bin/dot', '-Tpdf', '-O', 'nonfilepath'], + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + startupinfo=mocker.ANY) +@@ -94,6 +95,7 @@ def test_render_mocked(capsys, mocker, Popen, quiet): + assert capsys.readouterr() == ('', '' if quiet else 'stderr') + + ++@pytest.mark.skip(reason='empty $PATH has no effect') + @pytest.mark.usefixtures('empty_path') + def test_pipe_missing_executable(): + with pytest.raises(ExecutableNotFound, match=r'execute'): +@@ -143,7 +145,7 @@ def test_pipe_pipe_invalid_data_mocked(mocker, py2, Popen, quiet): # noqa: N803 + assert e.value.returncode is mocker.sentinel.returncode + assert e.value.stdout is mocker.sentinel.out + assert e.value.stderr is err +- Popen.assert_called_once_with(['dot', '-Tpng'], ++ Popen.assert_called_once_with(['@graphviz@/bin/dot', '-Tpng'], + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, +@@ -166,7 +168,7 @@ def test_pipe_mocked(capsys, mocker, Popen, quiet): # noqa: N803 + + assert pipe('dot', 'png', b'nongraph', quiet=quiet) is mocker.sentinel.out + +- Popen.assert_called_once_with(['dot', '-Tpng'], ++ Popen.assert_called_once_with(['@graphviz@/bin/dot', '-Tpng'], + stdin=subprocess.PIPE, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, +@@ -176,6 +178,7 @@ def test_pipe_mocked(capsys, mocker, Popen, quiet): # noqa: N803 + assert capsys.readouterr() == ('', '' if quiet else 'stderr') + + ++@pytest.mark.skip(reason='empty $PATH has no effect') + @pytest.mark.usefixtures('empty_path') + def test_version_missing_executable(): + with pytest.raises(ExecutableNotFound, match=r'execute'): +@@ -196,7 +199,7 @@ def test_version_parsefail_mocked(mocker, Popen): + with pytest.raises(RuntimeError): + version() + +- Popen.assert_called_once_with(['dot', '-V'], ++ Popen.assert_called_once_with(['@graphviz@/bin/dot', '-V'], + stdout=subprocess.PIPE, + stderr=subprocess.STDOUT, + startupinfo=mocker.ANY) +@@ -211,7 +214,7 @@ def test_version_mocked(mocker, Popen): + + assert version() == (1, 2, 3) + +- Popen.assert_called_once_with(['dot', '-V'], ++ Popen.assert_called_once_with(['@graphviz@/bin/dot', '-V'], + stdout=subprocess.PIPE, + stderr=subprocess.STDOUT, + startupinfo=mocker.ANY) diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 66ca01dc7b48..143bbe3b97c8 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -3067,7 +3067,9 @@ in { pyte = callPackage ../development/python-modules/pyte { }; - graphviz = callPackage ../development/python-modules/graphviz { }; + graphviz = callPackage ../development/python-modules/graphviz { + inherit (pkgs) graphviz; + }; pygraphviz = callPackage ../development/python-modules/pygraphviz { graphviz = pkgs.graphviz; # not the python package From 2357d57e94aa44fb1f7a5ffb03142196c14f76b8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= Date: Wed, 19 Dec 2018 15:14:29 +0100 Subject: [PATCH 181/247] python.pkgs.objgraph: hardcode path to graphviz's bin/ --- .../python-modules/objgraph/default.nix | 9 +++ .../objgraph/hardcode-graphviz-path.patch | 61 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 4 +- 3 files changed, 73 insertions(+), 1 deletion(-) create mode 100644 pkgs/development/python-modules/objgraph/hardcode-graphviz-path.patch diff --git a/pkgs/development/python-modules/objgraph/default.nix b/pkgs/development/python-modules/objgraph/default.nix index 16dc60fc28a3..0eb1deee0d39 100644 --- a/pkgs/development/python-modules/objgraph/default.nix +++ b/pkgs/development/python-modules/objgraph/default.nix @@ -2,6 +2,8 @@ , buildPythonPackage , fetchPypi , isPyPy +, substituteAll +, graphvizPkg , graphviz , mock }: @@ -18,6 +20,13 @@ buildPythonPackage rec { # Tests fail with PyPy. disabled = isPyPy; + patches = [ + (substituteAll { + src = ./hardcode-graphviz-path.patch; + graphviz = graphvizPkg; + }) + ]; + propagatedBuildInputs = [ graphviz ]; checkInputs = [ mock ]; diff --git a/pkgs/development/python-modules/objgraph/hardcode-graphviz-path.patch b/pkgs/development/python-modules/objgraph/hardcode-graphviz-path.patch new file mode 100644 index 000000000000..c5be5de64eed --- /dev/null +++ b/pkgs/development/python-modules/objgraph/hardcode-graphviz-path.patch @@ -0,0 +1,61 @@ +diff --git a/objgraph.py b/objgraph.py +index 88e307b..0369f49 100755 +--- a/objgraph.py ++++ b/objgraph.py +@@ -1045,12 +1045,12 @@ def _present_graph(dot_filename, filename=None): + if not filename and _program_in_path('xdot'): + print("Spawning graph viewer (xdot)") + subprocess.Popen(['xdot', dot_filename], close_fds=True) +- elif _program_in_path('dot'): ++ elif True: # path to dot is hardcoded and hence always in $PATH + if not filename: + print("Graph viewer (xdot) not found, generating a png instead") + filename = dot_filename[:-4] + '.png' + stem, ext = os.path.splitext(filename) +- cmd = ['dot', '-T' + ext[1:], '-o' + filename, dot_filename] ++ cmd = ['@graphviz@/bin/dot', '-T' + ext[1:], '-o' + filename, dot_filename] + dot = subprocess.Popen(cmd, close_fds=False) + dot.wait() + if dot.returncode != 0: +diff --git a/tests.py b/tests.py +index 7db2888..bdb666e 100755 +--- a/tests.py ++++ b/tests.py +@@ -557,7 +557,7 @@ class PresentGraphTest(CaptureMixin, TemporaryDirectoryMixin, + self.programsInPath(['dot']) + objgraph._present_graph('foo.dot', 'bar.png') + self.assertOutput(""" +- subprocess.Popen(['dot', '-Tpng', '-obar.png', 'foo.dot']) ++ subprocess.Popen(['@graphviz@/bin/dot', '-Tpng', '-obar.png', 'foo.dot']) + Image generated as bar.png + """) + +@@ -566,11 +566,12 @@ class PresentGraphTest(CaptureMixin, TemporaryDirectoryMixin, + objgraph.subprocess.should_fail = True + objgraph._present_graph('f.dot', 'b.png') + self.assertOutput(""" +- subprocess.Popen(['dot', '-Tpng', '-ob.png', 'f.dot']) +- dot failed (exit code 1) while executing "dot -Tpng -ob.png f.dot" ++ subprocess.Popen(['@graphviz@/bin/dot', '-Tpng', '-ob.png', 'f.dot']) ++ dot failed (exit code 1) while executing "@graphviz@/bin/dot -Tpng -ob.png f.dot" + """) + +- def test_present_png_no_dot(self): ++ @unittest.skip("empty $PATH has no effect") ++ def no_test_present_png_no_dot(self): + self.programsInPath([]) + objgraph._present_graph('foo.dot', 'bar.png') + self.assertOutput(""" +@@ -591,10 +592,11 @@ class PresentGraphTest(CaptureMixin, TemporaryDirectoryMixin, + objgraph._present_graph('foo.dot') + self.assertOutput(""" + Graph viewer (xdot) not found, generating a png instead +- subprocess.Popen(['dot', '-Tpng', '-ofoo.png', 'foo.dot']) ++ subprocess.Popen(['@graphviz@/bin/dot', '-Tpng', '-ofoo.png', 'foo.dot']) + Image generated as foo.png + """) + ++ @unittest.skip("empty $PATH has no effect") + def test_present_no_xdot_and_no_not(self): + self.programsInPath([]) + objgraph._present_graph('foo.dot') diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 143bbe3b97c8..396970cd8359 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -3205,7 +3205,9 @@ in { obfsproxy = callPackage ../development/python-modules/obfsproxy { }; - objgraph = callPackage ../development/python-modules/objgraph { }; + objgraph = callPackage ../development/python-modules/objgraph { + graphvizPkg = pkgs.graphviz; + }; odo = callPackage ../development/python-modules/odo { }; From d034fb84786789412c436d932f320880963d95be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= Date: Wed, 19 Dec 2018 15:41:10 +0100 Subject: [PATCH 182/247] python.pkgs.pydot: hardcode path to graphviz's bin/ --- .../python-modules/pydot/default.nix | 29 ++++++++++++++++--- .../pydot/hardcode-graphviz-path.patch | 13 +++++++++ pkgs/top-level/python-packages.nix | 4 ++- 3 files changed, 41 insertions(+), 5 deletions(-) create mode 100644 pkgs/development/python-modules/pydot/hardcode-graphviz-path.patch diff --git a/pkgs/development/python-modules/pydot/default.nix b/pkgs/development/python-modules/pydot/default.nix index ddbc0a5bfdd7..694315f2013e 100644 --- a/pkgs/development/python-modules/pydot/default.nix +++ b/pkgs/development/python-modules/pydot/default.nix @@ -1,9 +1,11 @@ { lib , buildPythonPackage , fetchPypi +, substituteAll +, graphviz +, python , chardet , pyparsing -, graphviz }: buildPythonPackage rec { @@ -14,10 +16,29 @@ buildPythonPackage rec { inherit pname version; sha256 = "02yp2k7p1kh0azwd932jhvfc3nxxdv9dimh7hdgwdnmp05yms6cq"; }; + + patches = [ + (substituteAll { + src = ./hardcode-graphviz-path.patch; + inherit graphviz; + }) + ]; + + postPatch = '' + # test_graphviz_regression_tests also fails upstream: https://github.com/pydot/pydot/pull/198 + substituteInPlace test/pydot_unittest.py \ + --replace "test_graphviz_regression_tests" "no_test_graphviz_regression_tests" + ''; + + propagatedBuildInputs = [ pyparsing ]; + checkInputs = [ chardet ]; - # No tests in archive - doCheck = false; - propagatedBuildInputs = [pyparsing graphviz]; + + checkPhase = '' + cd test + ${python.interpreter} pydot_unittest.py + ''; + meta = { homepage = https://github.com/erocarrera/pydot; description = "Allows to easily create both directed and non directed graphs from Python"; diff --git a/pkgs/development/python-modules/pydot/hardcode-graphviz-path.patch b/pkgs/development/python-modules/pydot/hardcode-graphviz-path.patch new file mode 100644 index 000000000000..e862f1e7c2c3 --- /dev/null +++ b/pkgs/development/python-modules/pydot/hardcode-graphviz-path.patch @@ -0,0 +1,13 @@ +diff --git a/pydot.py b/pydot.py +index 3c7da4d..582c5bc 100644 +--- a/pydot.py ++++ b/pydot.py +@@ -124,7 +124,7 @@ def call_graphviz(program, arguments, working_dir, **kwargs): + 'LD_LIBRARY_PATH': os.environ.get('LD_LIBRARY_PATH', ''), + } + +- program_with_args = [program, ] + arguments ++ program_with_args = ['@graphviz@/bin/' + program, ] + arguments + + process = subprocess.Popen( + program_with_args, diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 396970cd8359..d0fab989dbc3 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -3514,7 +3514,9 @@ in { pydispatcher = callPackage ../development/python-modules/pydispatcher { }; - pydot = callPackage ../development/python-modules/pydot { }; + pydot = callPackage ../development/python-modules/pydot { + inherit (pkgs) graphviz; + }; pydot_ng = callPackage ../development/python-modules/pydot_ng { }; From 354b0d48d8aeeac62ee1acb849134ace3f7c9b54 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= Date: Wed, 19 Dec 2018 15:42:05 +0100 Subject: [PATCH 183/247] python.pkgs.pydot: 1.4.0 -> 1.4.1 --- pkgs/development/python-modules/pydot/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/pydot/default.nix b/pkgs/development/python-modules/pydot/default.nix index 694315f2013e..021043d9e9db 100644 --- a/pkgs/development/python-modules/pydot/default.nix +++ b/pkgs/development/python-modules/pydot/default.nix @@ -10,11 +10,11 @@ buildPythonPackage rec { pname = "pydot"; - version = "1.4.0"; + version = "1.4.1"; src = fetchPypi { inherit pname version; - sha256 = "02yp2k7p1kh0azwd932jhvfc3nxxdv9dimh7hdgwdnmp05yms6cq"; + sha256 = "d49c9d4dd1913beec2a997f831543c8cbd53e535b1a739e921642fe416235f01"; }; patches = [ From 3ace9a76167a12aafd8caa96ce493691c02f7f01 Mon Sep 17 00:00:00 2001 From: Will Dietz Date: Tue, 8 Jan 2019 10:08:12 -0600 Subject: [PATCH 184/247] pubs: 0.7.0 -> 0.8.2 (#53658) --- pkgs/tools/misc/pubs/default.nix | 37 ++++++-------------------------- 1 file changed, 6 insertions(+), 31 deletions(-) diff --git a/pkgs/tools/misc/pubs/default.nix b/pkgs/tools/misc/pubs/default.nix index c9ab32035de4..393300ddd9e9 100644 --- a/pkgs/tools/misc/pubs/default.nix +++ b/pkgs/tools/misc/pubs/default.nix @@ -1,46 +1,21 @@ -{ stdenv, fetchFromGitHub, python3 }: +{ stdenv, fetchFromGitHub, python3Packages }: -let - python3Packages = (python3.override { - packageOverrides = self: super: { - # https://github.com/pubs/pubs/issues/131 - pyfakefs = super.pyfakefs.overridePythonAttrs (oldAttrs: rec { - version = "3.3"; - src = self.fetchPypi { - pname = "pyfakefs"; - inherit version; - sha256 = "e3e198dea5e0d5627b73ba113fd0b139bb417da6bc15d920b2c873143d2f12a6"; - }; - postPatch = ""; - doCheck = false; - }); - }; - }).pkgs; - -in python3Packages.buildPythonApplication rec { +python3Packages.buildPythonApplication rec { pname = "pubs"; - version = "0.7.0"; + version = "0.8.2"; src = fetchFromGitHub { owner = "pubs"; repo = "pubs"; rev = "v${version}"; - sha256 = "0n5wbjx9wqy6smfg625mhma739jyg7c92766biaiffp0a2bzr475"; + sha256 = "16zwdqfbmlla6906g3a57a4nj8wnl11fq78r20qms717bzv211j0"; }; propagatedBuildInputs = with python3Packages; [ - dateutil configobj bibtexparser pyyaml requests beautifulsoup4 + argcomplete dateutil configobj feedparser bibtexparser pyyaml requests six beautifulsoup4 ]; - checkInputs = with python3Packages; [ pyfakefs ddt ]; - - preCheck = '' - # API tests require networking - rm tests/test_apis.py - - # pyfakefs works weirdly in the sandbox - export HOME=/ - ''; + checkInputs = with python3Packages; [ pyfakefs mock ddt ]; meta = with stdenv.lib; { description = "Command-line bibliography manager"; From 114a9e6bd49e9634ccc66c72f9b106b39ad354b4 Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Tue, 8 Jan 2019 17:55:56 +0100 Subject: [PATCH 185/247] vimPlugins: update --- pkgs/misc/vim-plugins/generated.nix | 195 ++++++++++++++-------------- 1 file changed, 98 insertions(+), 97 deletions(-) diff --git a/pkgs/misc/vim-plugins/generated.nix b/pkgs/misc/vim-plugins/generated.nix index c4772d65dbd7..cdb747daca3c 100644 --- a/pkgs/misc/vim-plugins/generated.nix +++ b/pkgs/misc/vim-plugins/generated.nix @@ -61,12 +61,12 @@ let ale = buildVimPluginFrom2Nix { pname = "ale"; - version = "2018-12-20"; + version = "2019-01-08"; src = fetchFromGitHub { owner = "w0rp"; repo = "ale"; - rev = "73ca1e71918a0b50b7bbcbed91857c3618ad93cc"; - sha256 = "0q2wmpprr6mva6k7d8280cpf8ia6g7fbzw309fb0291y7241v5j1"; + rev = "f23811770a8104346b7e9ccc6e586da828c8f41d"; + sha256 = "07njkd4nm8rc64mzhn1qvm8m8fm1771m46yp86xx0l49cxvrn336"; }; }; @@ -83,12 +83,12 @@ let ansible-vim = buildVimPluginFrom2Nix { pname = "ansible-vim"; - version = "2.0"; + version = "2018-07-01"; src = fetchFromGitHub { owner = "pearofducks"; repo = "ansible-vim"; - rev = "01d0e7d4b87936d9cfe5a6038a6c9cec409a3c15"; - sha256 = "14x7lxwvfrvi27qmffh66fpc3fk21xkzfzps0vx6n3n7h56a7r2g"; + rev = "f1c9be3cdca55c90cc190f8fc38c6c8ac7e8d371"; + sha256 = "0hjqrm4n4nyj39afq8xa0kfzdfqvc3vz2p72pz7mvlsqbcic3zs8"; }; }; @@ -127,12 +127,12 @@ let awesome-vim-colorschemes = buildVimPluginFrom2Nix { pname = "awesome-vim-colorschemes"; - version = "2018-12-16"; + version = "2018-12-31"; src = fetchFromGitHub { owner = "rafi"; repo = "awesome-vim-colorschemes"; - rev = "680930f34bf5d4007dbaee66aba2dd688cbb3098"; - sha256 = "0jk4fm2ivf6r91yra7ddyxfbh2swf315zvmrm5ym605xcsiwv0nw"; + rev = "b4acabd696ee5d52e07c46c0f378b3f9c3072b7a"; + sha256 = "0g1mlqlvd354lha6v6f5yssm3nk6r5c778vqijlj76lkrdxi38wq"; }; }; @@ -392,12 +392,12 @@ let denite-nvim = buildVimPluginFrom2Nix { pname = "denite-nvim"; - version = "2018-12-24"; + version = "2018-12-31"; src = fetchFromGitHub { owner = "Shougo"; repo = "denite.nvim"; - rev = "f20cd55d249712dd4d5ab7c2b9d8b7f0005c6290"; - sha256 = "0g31p4n1hvl0vxn7gczbkfs6bvfhabmyfggcc5sfsd27chf49q43"; + rev = "65bce80f269016d99e305cf710bd563fd07eb551"; + sha256 = "1bz5ww3bbfyxwpfwi8rfw99qhdmqij1cdk6mfs0xsfl9k8xipmnz"; }; }; @@ -472,23 +472,23 @@ let deoplete-ternjs = buildVimPluginFrom2Nix { pname = "deoplete-ternjs"; - version = "2018-11-29"; + version = "2019-01-03"; src = fetchFromGitHub { owner = "carlitux"; repo = "deoplete-ternjs"; - rev = "ebdc48ecd29f8cae0659e5cdd2c30bd869839ca8"; - sha256 = "19zlgnavlqqq4rqwa1j1wglg921xdjhy8c71wfgh5492gmm1vr5x"; + rev = "185b01109fac17ad7e56ce542df6d689e94f65a6"; + sha256 = "1a78yk2d9navbmlk2y45qygv3las5xlhfvnw9l3mkijsira1v8ib"; }; }; deoplete-nvim = buildVimPluginFrom2Nix { pname = "deoplete-nvim"; - version = "2018-12-27"; + version = "2019-01-07"; src = fetchFromGitHub { owner = "Shougo"; repo = "deoplete.nvim"; - rev = "dc745e2a97025310c5439d304b5a8486550384bc"; - sha256 = "1y6ygh3qvcgzxj1kg2lw9mxpa7y3q4cbkhryg771863nxg66wdzs"; + rev = "bf6db3bede2097a0f5572aea19fffc3b98e6a884"; + sha256 = "08v8c49mwp2zxdkm7w0gc8l4f48vqgc17h8c2v77nd5bddb2agxk"; }; }; @@ -584,23 +584,23 @@ let fastfold = buildVimPluginFrom2Nix { pname = "fastfold"; - version = "2018-09-24"; + version = "2019-01-08"; src = fetchFromGitHub { owner = "konfekt"; repo = "fastfold"; - rev = "cdd44dcf54dd6900e9699e957ba4b203d3021d1d"; - sha256 = "1a7x026cjd6nc9l0gx3cvfvhwalxj8d4361yvy6krpjaha4yk43j"; + rev = "50b11c5617d06e2fd8c3165f8aa258bf1c8467c6"; + sha256 = "07sfjfi45xzgkkiiaydb01kgmgym42r826njc3xh0b0xrq2a4fid"; }; }; ferret = buildVimPluginFrom2Nix { pname = "ferret"; - version = "2018-12-25"; + version = "2019-01-08"; src = fetchFromGitHub { owner = "wincent"; repo = "ferret"; - rev = "890a01f85a5ac50ad16f151aacd828b31cbe6889"; - sha256 = "0882mxa5n1cbvq4vzxnv2d5id3lxbv23anjrilbnkklgk1i5fq47"; + rev = "6a0b0848c4b85e1edaa5712d943589b973c0480a"; + sha256 = "0cf4lcn4rnay0g1x4nlfpfpd54han2psy84mmyax3jnpw0m2z8ff"; }; }; @@ -640,12 +640,12 @@ let fugitive-gitlab-vim = buildVimPluginFrom2Nix { pname = "fugitive-gitlab-vim"; - version = "2018-07-04"; + version = "2019-01-05"; src = fetchFromGitHub { owner = "shumphrey"; repo = "fugitive-gitlab.vim"; - rev = "b8e7b6986c5d13f3e2de2163816af06f74a6f838"; - sha256 = "1lvll9hjqsm79f0ls84d8b8s12043b9p5qa4i6iwf3v1qbq7kb8d"; + rev = "43a13dbbc9aae85338877329ed28c9e4d8488db1"; + sha256 = "1in6r6p5mbcdpgpvmsl6k5nm1nhp4wfxs3wfy2vhswhw1c7ja1dd"; }; }; @@ -684,12 +684,12 @@ let gitv = buildVimPluginFrom2Nix { pname = "gitv"; - version = "2018-11-24"; + version = "2019-01-04"; src = fetchFromGitHub { owner = "gregsexton"; repo = "gitv"; - rev = "38daefcbb4375f79396c81860f077264fe9a3ae4"; - sha256 = "19v1v1wb1shh50if1jgiqy4bvja1lv6zy1fald3c48zl9303x8gq"; + rev = "e9486c2da297634dde7bc591b87fb8c0779b7789"; + sha256 = "1gs98c3s744fn4kxnkk1knh6lxykvryjk7gmyi149kvc0sklfwqh"; }; }; @@ -761,12 +761,12 @@ let iceberg-vim = buildVimPluginFrom2Nix { pname = "iceberg-vim"; - version = "2018-10-17"; + version = "2019-01-04"; src = fetchFromGitHub { owner = "cocopon"; repo = "iceberg.vim"; - rev = "0a18b0fbfdcdace35ee7ff4397ab6932d6dae1da"; - sha256 = "1p5x8kzxs491c2naxqhmqwdk85p3b6qr1aini746qm9ks5afhcgn"; + rev = "8b5ca0059c0f5f0bf0f78d7c5fbd3e83b7a5d5b6"; + sha256 = "1522psnakmcsm781lpnq09i3ylrg0lj8kx3nb7xm4wi6m100zzlk"; }; }; @@ -960,12 +960,12 @@ let ncm2 = buildVimPluginFrom2Nix { pname = "ncm2"; - version = "2018-12-27"; + version = "2019-01-08"; src = fetchFromGitHub { owner = "ncm2"; repo = "ncm2"; - rev = "ec1b0c917d1b2086bff1b67b86ff54cfaf4aadd0"; - sha256 = "18nbr7d7y60l87q8rc4r85ngknbf1x5q5zmnxicxh6xrkl1hmf58"; + rev = "b022eafc43a4811cc218a15d62e4fb6ffcb9e3e7"; + sha256 = "1cih481kg7wkhq6kl2srsgcrqyy1ids4766v6hn2x5g6k0ipg03m"; }; }; @@ -1114,12 +1114,12 @@ let neomake = buildVimPluginFrom2Nix { pname = "neomake"; - version = "2018-12-27"; + version = "2019-01-08"; src = fetchFromGitHub { owner = "benekastah"; repo = "neomake"; - rev = "dc894f78ea9466aae2281fec081fd76f6f19d0c8"; - sha256 = "1j6k80p5s02xznkk8hd3d74mgwz9n3kyvrnaf4f43v392a23k70r"; + rev = "7113111a2ec6e1b6e5b9acda0f0dcfaf025a5f5d"; + sha256 = "0nnqkbjj0h6i48ga64ymyqdl39q0gk06jwh6g9n9s6392x0j8shr"; }; }; @@ -1499,12 +1499,12 @@ let rust-vim = buildVimPluginFrom2Nix { pname = "rust-vim"; - version = "2018-12-23"; + version = "2019-01-01"; src = fetchFromGitHub { owner = "rust-lang"; repo = "rust.vim"; - rev = "c6312525ce948e603aec827fba8842a5dea92a9c"; - sha256 = "11ki4zfnnizvdpymddxb7l1qmx1090xn5hiwhxifsrlg1c0dn3dp"; + rev = "0c9409fb01a5f6142195517028092986bf2e66d5"; + sha256 = "1dk2lfa1gay29y9mcrg50asfbbf6n4bqhjhls66yzfjn9bqvn0gx"; }; }; @@ -1675,12 +1675,12 @@ let targets-vim = buildVimPluginFrom2Nix { pname = "targets-vim"; - version = "2018-12-21"; + version = "2019-01-07"; src = fetchFromGitHub { owner = "wellle"; repo = "targets.vim"; - rev = "55c9c40e47af660677725b68fcfe7e88d9985889"; - sha256 = "0jywlb5yxkyxn6vrdd3vd7q522llr2jplcl9yf97v89x3kmwpbqy"; + rev = "c2a8a2546aa5dc21445f033d28a04868f1465f48"; + sha256 = "1xq0h7865mw5n76qrslxdsihfsdzdspbhgavjnxhzqzq368g2yqz"; }; }; @@ -1730,12 +1730,12 @@ let traces-vim = buildVimPluginFrom2Nix { pname = "traces-vim"; - version = "2018-12-25"; + version = "2019-01-04"; src = fetchFromGitHub { owner = "markonm"; repo = "traces.vim"; - rev = "7fd6019cd817842ec45836c2cec575e3c21fedca"; - sha256 = "19pdpipng98s7kypkflfaxkhcskrppyb6714xf7y86adi1d2vly1"; + rev = "22c2a15651c2b77883947e5cdbfddc434da23288"; + sha256 = "09gspl5vkcpwn10vdm07hs2p47m9zm7gfbyzs538xf6zk31hf08g"; }; }; @@ -2313,12 +2313,12 @@ let vim-dispatch = buildVimPluginFrom2Nix { pname = "vim-dispatch"; - version = "2018-10-31"; + version = "2019-01-03"; src = fetchFromGitHub { owner = "tpope"; repo = "vim-dispatch"; - rev = "d4b8940fd1cd77fc6d300f003b18745a584295b2"; - sha256 = "06g0xc55z9jpa5rl8c5af5apb8b2agahsxxzayl2vn763v9p1n6b"; + rev = "9abd7cf09a5b00b3194a71f84e2911b280f30b1e"; + sha256 = "0mmh3vl8z12i3klk8rnkrivm3d1g7x0jl4x2njscmqyzdpdrlp96"; }; }; @@ -2390,12 +2390,12 @@ let vim-elixir = buildVimPluginFrom2Nix { pname = "vim-elixir"; - version = "2018-12-28"; + version = "2018-12-31"; src = fetchFromGitHub { owner = "elixir-lang"; repo = "vim-elixir"; - rev = "c1c3dca09f68970ee0fcb48d5022bc2de1a294a5"; - sha256 = "0f77gljvfzfzgp9kdscv2f04wdysaflk3vknd1pdc5gkz0m77qiy"; + rev = "e2be90dd910db0890edcfb08c0837e9da8e37439"; + sha256 = "0r5fj6jl53adkllx9alpmah6f1qqkhy589n0l9sphsadr6rx8hr1"; }; }; @@ -2478,23 +2478,23 @@ let vim-fugitive = buildVimPluginFrom2Nix { pname = "vim-fugitive"; - version = "2018-12-29"; + version = "2019-01-07"; src = fetchFromGitHub { owner = "tpope"; repo = "vim-fugitive"; - rev = "682b2acdac89dccbb3f4a449ac2d20283eb7c26a"; - sha256 = "02hrlidpfqhrz60ddhfwdj2kh5w33b2sq8cw9icbdhqbr6z1w3bl"; + rev = "bb466308282c3d3ef9007ecceb45db931f606ae7"; + sha256 = "1ccc8jrxmj9nskgzby544hdb1ja2zk30s3mlwl37mx873nn615zh"; }; }; vim-ghost = buildVimPluginFrom2Nix { pname = "vim-ghost"; - version = "2018-12-30"; + version = "2019-01-05"; src = fetchFromGitHub { owner = "raghur"; repo = "vim-ghost"; - rev = "cc54b45b9bd9610d2fc2bdbc4c6c0ed215a50dbb"; - sha256 = "1ri35acv3wysklz7ghazsn1lp440m4szzxqmzwyz03ybwshbyfaf"; + rev = "156f393d9c45a5c9dd16f9316a9ad125da67c449"; + sha256 = "0b21yamsfrljk3mfjql0gzsv5mv24qwbs551hxqsapgmrv7j2acg"; }; }; @@ -2522,12 +2522,12 @@ let vim-gitgutter = buildVimPluginFrom2Nix { pname = "vim-gitgutter"; - version = "2018-12-15"; + version = "2019-01-08"; src = fetchFromGitHub { owner = "airblade"; repo = "vim-gitgutter"; - rev = "1d422b9f98194e38bc56e54192c9bc66d95c21f1"; - sha256 = "1xv4brbhpxx23q2wklxxclzj9n1fi34m2rj0syf7ggp9fy7y50dk"; + rev = "8d7a71ddd64ca2aca0e06fe6182e88197232defd"; + sha256 = "0g1d8n80i3i2qc7bdfp3id7sil6np6cpyp2xnmyiv3kzyb5qf1zc"; }; }; @@ -2544,12 +2544,12 @@ let vim-go = buildVimPluginFrom2Nix { pname = "vim-go"; - version = "2018-12-29"; + version = "2019-01-05"; src = fetchFromGitHub { owner = "fatih"; repo = "vim-go"; - rev = "cbdd072534c0b59dfa8c1d69c73b053364cc9cbd"; - sha256 = "12sh9q52rp095la0ligvmij4s2bnzz8wk2hgwfwkhbfnla44ch7d"; + rev = "8342cd4ffdadccfc30284088560939f4c1ab2789"; + sha256 = "0cj9wxjxdj7rvvkcf65flmp8nl0s4a0iwhs5v0kvqj6v1nkdn6xs"; }; }; @@ -2764,12 +2764,12 @@ let vim-javacomplete2 = buildVimPluginFrom2Nix { pname = "vim-javacomplete2"; - version = "2018-12-28"; + version = "2019-01-07"; src = fetchFromGitHub { owner = "artur-shaik"; repo = "vim-javacomplete2"; - rev = "5a4d405c9e23e0a295aa965d18bd0b36b06de600"; - sha256 = "04clpab5zb0xk061i4i2yw91582ra12bnk1kkk2mmrldk1dr43xa"; + rev = "8abca8da03c1459ca82d52f487c5ec6792e563e0"; + sha256 = "1af824snhn537xgmkc9hbfp2ggzgfn9gadh9dm2x3s7d36qf9qqd"; }; }; @@ -3127,7 +3127,8 @@ let }; vim-parinfer = buildVimPluginFrom2Nix { - name = "vim-parinfer-2018-08-31"; + pname = "vim-parinfer"; + version = "2018-08-31"; src = fetchFromGitHub { owner = "bhurlow"; repo = "vim-parinfer"; @@ -3303,12 +3304,12 @@ let vim-ruby = buildVimPluginFrom2Nix { pname = "vim-ruby"; - version = "2018-12-11"; + version = "2019-01-06"; src = fetchFromGitHub { owner = "vim-ruby"; repo = "vim-ruby"; - rev = "0e57d862250bb4ce56e30e2c4e10781b8b1776ac"; - sha256 = "18z6170nm1vz4hh52qgiqhj9p7ak3d363rxh0q9si4hc6w56agzx"; + rev = "b3a4af9295184689896db1d168c9f02b96a0d883"; + sha256 = "1zq4n9m7i7fcx9xv71b34lhs460frfkd9vsr54lnpaid1r6h9h63"; }; }; @@ -3424,12 +3425,12 @@ let vim-snippets = buildVimPluginFrom2Nix { pname = "vim-snippets"; - version = "2018-12-14"; + version = "2019-01-08"; src = fetchFromGitHub { owner = "honza"; repo = "vim-snippets"; - rev = "a6090b9bffeec418ee7deaa31f90c4a8fd3b1170"; - sha256 = "1f0jnsdn0zavpz5727683442c22mjgcnj1j5dkhaysrkdzn4qc64"; + rev = "9ccd25a150663bfe6e5132ebeceb997a1b420c2a"; + sha256 = "1plka5dlvjyjyybdzhc65b08i6p2iwpxw7jwy1cv27c8jpc9fgcn"; }; }; @@ -3523,12 +3524,12 @@ let vim-table-mode = buildVimPluginFrom2Nix { pname = "vim-table-mode"; - version = "2018-10-21"; + version = "2019-01-02"; src = fetchFromGitHub { owner = "dhruvasagar"; repo = "vim-table-mode"; - rev = "130e835ff73ae16c5827fe37f1d1b09456c5f7dc"; - sha256 = "1dlyszky76z8kj6vy4sfn5zkjdi12hwfn29g8adds04zbaxi61gg"; + rev = "cdf33f680f3802de7a816922b6134c3d278ae93c"; + sha256 = "1vc391h42qwaywpmg9ncqakliv9kmahmgihk7b5dqrj0ym7a8x36"; }; }; @@ -3556,12 +3557,12 @@ let vim-terraform = buildVimPluginFrom2Nix { pname = "vim-terraform"; - version = "2018-12-25"; + version = "2019-01-07"; src = fetchFromGitHub { owner = "hashivim"; repo = "vim-terraform"; - rev = "259481e063e79392c25f293f8459462f942dd6f9"; - sha256 = "0w3kwjd5ywnjkkc3cn765ra8mqqmxvk328b0d14b9hndyhs6v8gi"; + rev = "d8c5580b41875972ce849c097cb73c8161f79cbc"; + sha256 = "14aw8n885ygw07ibfb6wdqap76s5xrwwxm1lcahx40m45gyp43la"; }; }; @@ -3644,12 +3645,12 @@ let vim-unimpaired = buildVimPluginFrom2Nix { pname = "vim-unimpaired"; - version = "2018-12-20"; + version = "2018-12-30"; src = fetchFromGitHub { owner = "tpope"; repo = "vim-unimpaired"; - rev = "9da253e92ca8444be9f67a5b0086c9213b8772e9"; - sha256 = "0s5jvc618nncsc4dzgr30nf2xfm71jpdsxq90gnxm1730fyln8f3"; + rev = "b3f0f752d7563d24753b23698d073632267af3d1"; + sha256 = "01s4fb4yj960qjdrakyw3v08jrsajqidx8335c1z9c9j1736svj8"; }; }; @@ -3809,12 +3810,12 @@ let vimtex = buildVimPluginFrom2Nix { pname = "vimtex"; - version = "2018-12-28"; + version = "2019-01-01"; src = fetchFromGitHub { owner = "lervag"; repo = "vimtex"; - rev = "2433268711e72735700687f2d4aa785305c9d025"; - sha256 = "1zppdlaj9sbq4qhxmydw38pzajyddl2g319zyzbi4a0g1p4b2hqf"; + rev = "cf6ac500f45d7cce4a52d6bdb4ecbec811922fbc"; + sha256 = "0x2gksvcix1wxfkr8nb5263f6vdsrrvxcli89xw4dn5wm0cjqbji"; }; }; @@ -3864,12 +3865,12 @@ let wal-vim = buildVimPluginFrom2Nix { pname = "wal-vim"; - version = "2018-06-04"; + version = "2019-01-04"; src = fetchFromGitHub { owner = "dylanaraps"; repo = "wal.vim"; - rev = "fb6ce53632f93c31cad66398636bfb383ad64d52"; - sha256 = "1f0rpaff7q9xswc1p5pmwzmhb70s4q148dj2apg98d4qywa9j8ah"; + rev = "64ac52e606a17f7ccf0e185d8e39f78043b34be0"; + sha256 = "1ji7c61lbz9sv62kq9digb6v6nvmw53bl23gcwc5131nz7sf2gpv"; }; }; @@ -3953,12 +3954,12 @@ let youcompleteme = buildVimPluginFrom2Nix { pname = "youcompleteme"; - version = "2018-12-28"; + version = "2019-01-05"; src = fetchFromGitHub { owner = "valloric"; repo = "youcompleteme"; - rev = "c209cdbbfcc90c9ab8fa078beb2fe668743b4d0e"; - sha256 = "0gq66mcrz4xrn3x6mccgm08gz3cjgb99649548wz8rs5nafvid6r"; + rev = "ccc06c2c423e7ee7008f7439ff99c604d474cec1"; + sha256 = "0b7n2fv49vr1jw9x6nf30f77gg6pm5a3wj8zq98wsknkjq40bqrm"; fetchSubmodules = true; }; }; @@ -3998,12 +3999,12 @@ let zig-vim = buildVimPluginFrom2Nix { pname = "zig-vim"; - version = "2018-12-12"; + version = "2019-01-02"; src = fetchFromGitHub { owner = "zig-lang"; repo = "zig.vim"; - rev = "c24d058fef53601b1381d80243bffcb356815e31"; - sha256 = "1nsji87vbz5rpl25rysy4np7zdwyqzv6qh8g15pvll0jqmsd5z0v"; + rev = "6e8b24f97152952e89979eb2638dd0963b3a1567"; + sha256 = "0y5f6lbkizspab35dym3f634b24vjfda8zi09ayvy9bi8g0zmmx3"; }; }; From f7367cbf1c0179fed1301c75a789230e431fdc4d Mon Sep 17 00:00:00 2001 From: Simon Lackerbauer Date: Mon, 7 Jan 2019 10:41:11 -0500 Subject: [PATCH 186/247] abella: 2.0.5 -> 2.0.6 --- pkgs/applications/science/logic/abella/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/science/logic/abella/default.nix b/pkgs/applications/science/logic/abella/default.nix index 7d71a56fa23e..bc23454edfc7 100644 --- a/pkgs/applications/science/logic/abella/default.nix +++ b/pkgs/applications/science/logic/abella/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "abella-${version}"; - version = "2.0.5"; + version = "2.0.6"; src = fetchurl { url = "http://abella-prover.org/distributions/${name}.tar.gz"; - sha256 = "0bry4pj6p9y7sg79ygdksynml4rdsjhqi959vnnwwsbaysa3bci0"; + sha256 = "164q9gngckg6q69k13lwx2pq3cnc9ckw1qi8dnpxqfjgwfqr7xyi"; }; buildInputs = [ rsync ] ++ (with ocamlPackages; [ ocaml ocamlbuild findlib ]); From c86e00ecc4380dc4024e7fe0d9143c8ae6147a1d Mon Sep 17 00:00:00 2001 From: Ivan Kozik Date: Tue, 8 Jan 2019 15:42:31 +0000 Subject: [PATCH 187/247] ibus-engines.mozc: 2.20.2673.102 -> 2.23.2815.102 --- pkgs/tools/inputmethods/ibus-engines/ibus-mozc/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/tools/inputmethods/ibus-engines/ibus-mozc/default.nix b/pkgs/tools/inputmethods/ibus-engines/ibus-mozc/default.nix index 01b092ef2a61..5699a7931dbc 100644 --- a/pkgs/tools/inputmethods/ibus-engines/ibus-mozc/default.nix +++ b/pkgs/tools/inputmethods/ibus-engines/ibus-mozc/default.nix @@ -10,7 +10,7 @@ let }; in clangStdenv.mkDerivation rec { name = "ibus-mozc-${version}"; - version = "2.20.2673.102"; + version = "2.23.2815.102"; meta = with clangStdenv.lib; { isIbusEngine = true; @@ -27,8 +27,8 @@ in clangStdenv.mkDerivation rec { src = fetchFromGitHub { owner = "google"; repo = "mozc"; - rev = "280e38fe3d9db4df52f0713acf2ca65898cd697a"; - sha256 = "0s599f817gjgqynm4n1yll1ipd25ai2c55y8k6wvhg9s7qaxnyhs"; + rev = "afb03ddfe72dde4cf2409863a3bfea160f7a66d8"; + sha256 = "0w2dy2j9x5nc7x3g95j17r3m60vbfyn5j617h7js9xryv33yzpgx"; }; postUnpack = '' From e6133502a281e7a0be4981aa2997ad6dabf2dd0a Mon Sep 17 00:00:00 2001 From: Orivej Desh Date: Tue, 8 Jan 2019 07:54:40 +0000 Subject: [PATCH 188/247] bento4: 1.5.1-624 -> 1.5.1-627 --- pkgs/tools/video/bento4/default.nix | 9 +++++++-- pkgs/tools/video/bento4/libap4.patch | 5 +++++ 2 files changed, 12 insertions(+), 2 deletions(-) create mode 100644 pkgs/tools/video/bento4/libap4.patch diff --git a/pkgs/tools/video/bento4/default.nix b/pkgs/tools/video/bento4/default.nix index 75964a3c2e5e..d1c6f310df92 100644 --- a/pkgs/tools/video/bento4/default.nix +++ b/pkgs/tools/video/bento4/default.nix @@ -3,16 +3,21 @@ }: stdenv.mkDerivation rec { name = "bento4-${version}"; - version = "1.5.1-624"; + version = "1.5.1-627"; src = fetchFromGitHub { owner = "axiomatic-systems"; repo = "Bento4"; rev = "v${version}"; - sha256 = "1cq6vhrq3n3lc1n454slbc66qdyqam2srxgdhfpyfxbq5c4y06nf"; + sha256 = "1nczv7vqgjryzdn9vkxz93awd7zyj5kwiz8llbb25nnqnqgfq170"; }; + patches = [ ./libap4.patch ]; + nativeBuildInputs = [ cmake ]; + + cmakeFlags = [ "-DBUILD_SHARED_LIBS=ON" ]; + installPhase = '' mkdir -p $out/{lib,bin} find -iname '*.so' -exec mv --target-directory="$out/lib" {} \; diff --git a/pkgs/tools/video/bento4/libap4.patch b/pkgs/tools/video/bento4/libap4.patch new file mode 100644 index 000000000000..ca2936003b84 --- /dev/null +++ b/pkgs/tools/video/bento4/libap4.patch @@ -0,0 +1,5 @@ +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -36 +36 @@ endif() +-add_library(ap4 STATIC ${AP4_SOURCES}) ++add_library(ap4 ${AP4_SOURCES}) From c869fc2ac1319abf730cd2065fc9d0e774fbe65b Mon Sep 17 00:00:00 2001 From: klntsky Date: Tue, 8 Jan 2019 21:16:59 +0300 Subject: [PATCH 189/247] pax-rs: init at 0.4.0 (#53660) --- maintainers/maintainer-list.nix | 6 +++- pkgs/development/tools/pax-rs/default.nix | 40 +++++++++++++++++++++++ pkgs/top-level/all-packages.nix | 6 ++-- 3 files changed, 49 insertions(+), 3 deletions(-) create mode 100644 pkgs/development/tools/pax-rs/default.nix diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix index c76210d86a46..2d892408712d 100644 --- a/maintainers/maintainer-list.nix +++ b/maintainers/maintainer-list.nix @@ -2312,7 +2312,11 @@ email = "tierpluspluslists@gmail.com"; name = "Karn Kallio"; }; - + klntsky = { + email = "klntsky@gmail.com"; + name = "Vladimir Kalnitsky"; + github = "8084"; + }; kmeakin = { email = "karlwfmeakin@gmail.com"; name = "Karl Meakin"; diff --git a/pkgs/development/tools/pax-rs/default.nix b/pkgs/development/tools/pax-rs/default.nix new file mode 100644 index 000000000000..3a4f35c0412b --- /dev/null +++ b/pkgs/development/tools/pax-rs/default.nix @@ -0,0 +1,40 @@ +{ stdenv, fetchFromGitHub, fetchurl, rustPlatform, runCommand } : +with rustPlatform; + +buildRustPackage rec { + name = "pax-rs-${version}"; + version = "0.4.0"; + + meta = with stdenv.lib; { + description = "The fastest JavaScript bundler in the galaxy."; + longDescription = '' + The fastest JavaScript bundler in the galaxy. Fully supports ECMAScript module syntax (import/export) in addition to CommonJS require(). + ''; + homepage = https://github.com/nathan/pax; + license = licenses.mit; + maintainers = [ maintainers.klntsky ]; + platforms = platforms.all; + }; + + src = + let + source = fetchFromGitHub { + owner = "nathan"; + repo = "pax"; + rev = "pax-v${version}"; + sha256 = "1l2xpgsms0bfc0i3l0hyw4dbp6d4qdxa9vxyp704p27vvn4ndhv2"; + }; + + cargo-lock = fetchurl { + url = "https://gist.github.com/8084/c7863424d7df0c379782015f6bb3b399/raw/1cf7481e33984fd1510dc77ed677606d08fa8eb6/Cargo.lock"; + sha256 = "0ff1b64b99cbca1cc2ceabcd2e4f7bc3411e3a2a9fbb9db2204d9240fe38ddeb"; + }; + in + runCommand "pax-rs-src" {} '' + cp -R ${source} $out + chmod +w $out + cp ${cargo-lock} $out/Cargo.lock + ''; + + cargoSha256 = "0sdk090sp89vgwz5a71f481a5sk13kcqb29cx1dslfq59sp4j6y7"; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 2d5f77585eb3..6e7ca1c7b8da 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -6529,9 +6529,9 @@ in fish-foreign-env = callPackage ../shells/fish/fish-foreign-env { }; ion = callPackage ../shells/ion { }; - + ksh = callPackage ../shells/ksh { }; - + mksh = callPackage ../shells/mksh { }; oh = callPackage ../shells/oh { }; @@ -8929,6 +8929,8 @@ in patchelfUnstable = lowPrio (callPackage ../development/tools/misc/patchelf/unstable.nix { }); + pax-rs = callPackage ../development/tools/pax-rs { }; + peg = callPackage ../development/tools/parsing/peg { }; pgcli = callPackage ../development/tools/database/pgcli {}; From 5a42b5d076a5c1ecbcccb300ec84bd92399806e4 Mon Sep 17 00:00:00 2001 From: Joachim Fasting Date: Thu, 27 Dec 2018 21:21:51 +0100 Subject: [PATCH 190/247] pacman: set localstatedir to standard FHS path Fixes https://github.com/NixOS/nixpkgs/issues/52981 --- pkgs/tools/package-management/pacman/default.nix | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/package-management/pacman/default.nix b/pkgs/tools/package-management/pacman/default.nix index 461e8ff1ec5d..b4383fde3409 100644 --- a/pkgs/tools/package-management/pacman/default.nix +++ b/pkgs/tools/package-management/pacman/default.nix @@ -10,8 +10,12 @@ stdenv.mkDerivation rec { sha256 = "17g497q6ylq73rql9k2ji2l2b2bj3dd4am30z8i6khnhc0x8s2il"; }; - # trying to build docs fails with a2x errors, unable to fix through asciidoc - configureFlags = [ "--disable-doc" ]; + configureFlags = [ + # trying to build docs fails with a2x errors, unable to fix through asciidoc + "--disable-doc" + + "--localstatedir=/var" + ]; nativeBuildInputs = [ autoreconfHook pkgconfig ]; buildInputs = [ perl libarchive openssl zlib bzip2 lzma ]; From 485f5443df89ec2181371ba894c9fe37bab8756c Mon Sep 17 00:00:00 2001 From: Ingo Blechschmidt Date: Tue, 8 Jan 2019 19:49:56 +0100 Subject: [PATCH 191/247] tikzit: 2.0 -> 2.1 --- pkgs/tools/typesetting/tikzit/default.nix | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/pkgs/tools/typesetting/tikzit/default.nix b/pkgs/tools/typesetting/tikzit/default.nix index 23d8093606be..69e3995bf624 100644 --- a/pkgs/tools/typesetting/tikzit/default.nix +++ b/pkgs/tools/typesetting/tikzit/default.nix @@ -1,18 +1,23 @@ -{ stdenv, fetchFromGitHub, qmake, qttools, qtbase, flex, bison }: +{ stdenv, fetchFromGitHub, qmake, qttools, qtbase, libsForQt5, flex, bison }: stdenv.mkDerivation rec { name = "tikzit-${version}"; - version = "2.0"; + version = "2.1"; src = fetchFromGitHub { owner = "tikzit"; repo = "tikzit"; - rev = "v${version}"; - sha256 = "0fwxr9rc9vmw2jzpj084rygzyhp4xm3vm737668az600ln2scyad"; + # We don't reference the revision by the appropriate tag (v2.1) here, + # as the version of that tag still has the old version number in the + # relevant header file. This would cause a bad user experience, as + # "Help > About" would still display the old version number even though + # we indeed ship the new version 2.1. + rev = "97c2a2a7ecae12bf376558997805c24c3b6e3e07"; + sha256 = "0sbgijbln18gac9989x484r62jlxyagkq0ap0fvzislrkac4z3y9"; }; nativeBuildInputs = [ qmake qttools flex bison ]; - buildInputs = [ qtbase ]; + buildInputs = [ qtbase libsForQt5.poppler ]; enableParallelBuilding = true; @@ -22,6 +27,7 @@ stdenv.mkDerivation rec { TikZiT is a simple GUI editor for graphs and string diagrams. Its native file format is a subset of PGF/TikZ, which means TikZiT files can be included directly in papers typeset using LaTeX. + For preview support the texlive package 'preview' has to be installed. ''; homepage = https://tikzit.github.io/; license = licenses.gpl3Plus; From a3a07429191533f578a4340e166b0fe6da2dc53a Mon Sep 17 00:00:00 2001 From: Roman Volosatovs Date: Mon, 7 Jan 2019 19:40:17 +0100 Subject: [PATCH 192/247] kbfs: 2.10.1 -> 2.11.0 --- pkgs/tools/security/kbfs/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/tools/security/kbfs/default.nix b/pkgs/tools/security/kbfs/default.nix index e8824bd73fcd..7c96085d37f6 100644 --- a/pkgs/tools/security/kbfs/default.nix +++ b/pkgs/tools/security/kbfs/default.nix @@ -2,7 +2,7 @@ buildGoPackage rec { name = "kbfs-${version}"; - version = "2.10.1"; + version = "2.11.0"; goPackagePath = "github.com/keybase/kbfs"; subPackages = [ "kbfsfuse" "kbfsgit/git-remote-keybase" ]; @@ -13,7 +13,7 @@ buildGoPackage rec { owner = "keybase"; repo = "kbfs"; rev = "v${version}"; - sha256 = "0c03jm4pxqh4cfg1d7c833hdl8l57f1sbfqxwdq16y5s2cac1yss"; + sha256 = "1qlns7vpyj3ivm7d3vvlmx3iksl7hpcg87yh30f3n64c8jk0xc83"; }; buildFlags = [ "-tags production" ]; @@ -22,7 +22,7 @@ buildGoPackage rec { homepage = https://www.keybase.io; description = "The Keybase FS FUSE driver"; platforms = platforms.linux; - maintainers = with maintainers; [ bennofs np ]; + maintainers = with maintainers; [ rvolosatovs bennofs np ]; license = licenses.bsd3; }; } From 563d4e2a770e824d57992d26957d78d1e5edc2e3 Mon Sep 17 00:00:00 2001 From: Roman Volosatovs Date: Mon, 7 Jan 2019 19:41:18 +0100 Subject: [PATCH 193/247] keybase: 2.10.1 -> 2.11.0 --- pkgs/tools/security/keybase/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/security/keybase/default.nix b/pkgs/tools/security/keybase/default.nix index a13adad037d1..b27b4ac24c0a 100644 --- a/pkgs/tools/security/keybase/default.nix +++ b/pkgs/tools/security/keybase/default.nix @@ -5,7 +5,7 @@ buildGoPackage rec { name = "keybase-${version}"; - version = "2.10.1"; + version = "2.11.0"; goPackagePath = "github.com/keybase/client"; subPackages = [ "go/keybase" ]; @@ -16,7 +16,7 @@ buildGoPackage rec { owner = "keybase"; repo = "client"; rev = "v${version}"; - sha256 = "1gfxnqzs8msxmykg1zrhrrl2slmb29gl7b8s4m2g44zxaj91gfi9"; + sha256 = "1mj78cs6j0f1f86c71j4gdphas75j3rfaqygpy87dc40kc2yj0gd"; }; buildInputs = lib.optionals stdenv.isDarwin [ From 3bc377267794b23de1107c28b1b19cd7fbf535fe Mon Sep 17 00:00:00 2001 From: Roman Volosatovs Date: Mon, 7 Jan 2019 19:41:48 +0100 Subject: [PATCH 194/247] keybase-gui: 2.11.0 -> 2.13.0 --- pkgs/tools/security/keybase/gui.nix | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pkgs/tools/security/keybase/gui.nix b/pkgs/tools/security/keybase/gui.nix index 422ca4ac9cfa..a8c2d5ea4837 100644 --- a/pkgs/tools/security/keybase/gui.nix +++ b/pkgs/tools/security/keybase/gui.nix @@ -3,16 +3,16 @@ , libnotify, nspr, nss, pango, systemd, xorg, autoPatchelfHook, wrapGAppsHook }: let - versionSuffix = "20181121195344.99751ac04f"; + versionSuffix = "20190104191034.69b3ee25b7"; in stdenv.mkDerivation rec { name = "keybase-gui-${version}"; - version = "2.11.0"; # Find latest version from https://prerelease.keybase.io/deb/dists/stable/main/binary-amd64/Packages + version = "2.13.0"; # Find latest version from https://prerelease.keybase.io/deb/dists/stable/main/binary-amd64/Packages src = fetchurl { url = "https://s3.amazonaws.com/prerelease.keybase.io/linux_binaries/deb/keybase_${version + "-" + versionSuffix}_amd64.deb"; - sha256 = "1gh7brdw2p4xfdgc43vrmv0lvki2f3691mfh6lvksy1dv43yb8zl"; + sha256 = "5b188185dc6d594cd18876a2c955bb6481598c206f048cfd80ac2e7e8022241e"; }; nativeBuildInputs = [ @@ -106,7 +106,7 @@ stdenv.mkDerivation rec { homepage = https://www.keybase.io/; description = "The Keybase official GUI"; platforms = platforms.linux; - maintainers = with maintainers; [ puffnfresh np ]; + maintainers = with maintainers; [ rvolosatovs puffnfresh np ]; license = licenses.bsd3; }; } From ca4104cc07916f3ccad1e7b6381413f124e8182c Mon Sep 17 00:00:00 2001 From: James Kay Date: Thu, 29 Nov 2018 11:01:43 +0000 Subject: [PATCH 195/247] pythonPackages.boltons: init at 2019-01-07 --- .../python-modules/boltons/default.nix | 39 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 41 insertions(+) create mode 100644 pkgs/development/python-modules/boltons/default.nix diff --git a/pkgs/development/python-modules/boltons/default.nix b/pkgs/development/python-modules/boltons/default.nix new file mode 100644 index 000000000000..655af7c66f2c --- /dev/null +++ b/pkgs/development/python-modules/boltons/default.nix @@ -0,0 +1,39 @@ +{ stdenv, buildPythonPackage, fetchFromGitHub, pytest }: + +buildPythonPackage rec { + pname = "boltons"; + version = "2019-01-07"; + + # No tests in PyPi Tarball + src = fetchFromGitHub { + owner = "mahmoud"; + repo = "boltons"; + rev = "3584ac9399f227a2a11b74153140ee171fd49783"; + sha256 = "13xngjw249sk4vmr5kqqnia0npw0kpa0gm020a4dqid0cjyvj0rv"; + }; + + checkInputs = [ pytest ]; + checkPhase = "pytest tests"; + + meta = with stdenv.lib; { + homepage = https://github.com/mahmoud/boltons; + description = "220+ constructs, recipes, and snippets extending (and relying on nothing but) the Python standard library"; + longDescription = '' + Boltons is a set of over 220 BSD-licensed, pure-Python utilities + in the same spirit as — and yet conspicuously missing from — the + standard library, including: + + - Atomic file saving, bolted on with fileutils + - A highly-optimized OrderedMultiDict, in dictutils + - Two types of PriorityQueue, in queueutils + - Chunked and windowed iteration, in iterutils + - Recursive data structure iteration and merging, with iterutils.remap + - Exponential backoff functionality, including jitter, through + iterutils.backoff + - A full-featured TracebackInfo type, for representing stack + traces, in tbutils + ''; + license = licenses.bsd3; + maintainers = with maintainers; [ twey ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index d0d12d2ca729..af0f255b05cf 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -270,6 +270,8 @@ in { blivet = callPackage ../development/python-modules/blivet { }; + boltons = callPackage ../development/python-modules/boltons { }; + breathe = callPackage ../development/python-modules/breathe { }; brotli = callPackage ../development/python-modules/brotli { }; From a5a6b8eaa2e78df3955dc1c2e0f6d655b056a3c8 Mon Sep 17 00:00:00 2001 From: James Kay Date: Thu, 29 Nov 2018 11:05:59 +0000 Subject: [PATCH 196/247] pythonPackages.face: init at 0.1.0 --- .../python-modules/face/default.nix | 31 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 ++ 2 files changed, 33 insertions(+) create mode 100644 pkgs/development/python-modules/face/default.nix diff --git a/pkgs/development/python-modules/face/default.nix b/pkgs/development/python-modules/face/default.nix new file mode 100644 index 000000000000..107259854976 --- /dev/null +++ b/pkgs/development/python-modules/face/default.nix @@ -0,0 +1,31 @@ +{ stdenv, buildPythonPackage, fetchPypi, boltons, pytest }: + +buildPythonPackage rec { + pname = "face"; + version = "0.1.0"; + + src = fetchPypi { + inherit pname version; + sha256 = "0zdp5qlrhxf4dypvvd0zr7zxj2svkz9wblp37vgw01wvcy9b1ds7"; + }; + + propagatedBuildInputs = [ boltons ]; + + checkInputs = [ pytest ]; + checkPhase = "pytest face/test"; + + # ironically, test_parse doesn't parse, but fixed in git so no point + # reporting + doCheck = false; + + meta = with stdenv.lib; { + homepage = https://github.com/mahmoud/face; + description = "A command-line interface parser and framework"; + longDescription = '' + A command-line interface parser and framework, friendly for + users, full-featured for developers. + ''; + license = licenses.bsd3; + maintainers = with maintainers; [ twey ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index af0f255b05cf..12b43833681e 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -354,6 +354,8 @@ in { eradicate = callPackage ../development/python-modules/eradicate { }; + face = callPackage ../development/python-modules/face { }; + fastpbkdf2 = callPackage ../development/python-modules/fastpbkdf2 { }; fido2 = callPackage ../development/python-modules/fido2 { }; From 7cd403e33128b7fc029454b7345f5768b2d04cc1 Mon Sep 17 00:00:00 2001 From: James Kay Date: Mon, 31 Dec 2018 17:05:32 +0000 Subject: [PATCH 197/247] pythonPackages.glom: init at 18.4.0 --- .../python-modules/glom/default.nix | 38 +++++++++++++++++++ pkgs/top-level/python-packages.nix | 2 + 2 files changed, 40 insertions(+) create mode 100644 pkgs/development/python-modules/glom/default.nix diff --git a/pkgs/development/python-modules/glom/default.nix b/pkgs/development/python-modules/glom/default.nix new file mode 100644 index 000000000000..f24dd2b7249e --- /dev/null +++ b/pkgs/development/python-modules/glom/default.nix @@ -0,0 +1,38 @@ +{ stdenv +, buildPythonPackage +, fetchPypi +, boltons +, attrs +, face +, pytest +, pyyaml +, isPy37 +}: + +buildPythonPackage rec { + pname = "glom"; + version = "18.4.0"; + + src = fetchPypi { + inherit pname version; + sha256 = "0rfikq27a9wwfkd4k3bk7x4fssw6r7z138g9i3wpzvjc7anlzk24"; + }; + + propagatedBuildInputs = [ boltons attrs face ]; + + checkInputs = [ pytest pyyaml ]; + checkPhase = "pytest glom/test"; + + doCheck = !isPy37; # https://github.com/mahmoud/glom/issues/72 + + meta = with stdenv.lib; { + homepage = https://github.com/mahmoud/glom; + description = "Restructuring data, the Python way"; + longDescription = '' + glom helps pull together objects from other objects in a + declarative, dynamic, and downright simple way. + ''; + license = licenses.bsd3; + maintainers = with maintainers; [ twey ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 12b43833681e..167888b325df 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -378,6 +378,8 @@ in { globus-sdk = callPackage ../development/python-modules/globus-sdk { }; + glom = callPackage ../development/python-modules/glom { }; + goocalendar = callPackage ../development/python-modules/goocalendar { }; gsd = callPackage ../development/python-modules/gsd { }; From 0eed2c701324d2d125671bde5d0c6686719a4f1a Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 20:14:08 -0800 Subject: [PATCH 198/247] gnome-menus: 3.10.1 -> 3.31.3 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/gnome-menus/versions --- pkgs/development/libraries/gnome-menus/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/gnome-menus/default.nix b/pkgs/development/libraries/gnome-menus/default.nix index 0538b8ec06be..8249ac5ce3a9 100644 --- a/pkgs/development/libraries/gnome-menus/default.nix +++ b/pkgs/development/libraries/gnome-menus/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "gnome-menus"; - version = "3.10.1"; + version = "3.31.3"; src = fetchurl { url = "mirror://gnome/sources/${pname}/${stdenv.lib.versions.majorMinor version}/${pname}-${version}.tar.xz"; - sha256 = "0wcacs1vk3pld8wvrwq7fdrm11i56nrajkrp6j1da6jc4yx0m5a6"; + sha256 = "11i5m0w15by1k8d94xla54nr4r8nnb63wk6iq0dzki4cv5d55qgw"; }; makeFlags = "INTROSPECTION_GIRDIR=$(out)/share/gir-1.0/ INTROSPECTION_TYPELIBDIR=$(out)/lib/girepository-1.0"; From cb0b629894f860b32f59eb4ee451c975202692e2 Mon Sep 17 00:00:00 2001 From: Claudio Bley Date: Tue, 8 Jan 2019 21:39:18 +0100 Subject: [PATCH 199/247] nixos/luksroot: Fix typo `Verifiying` -> `Verifying` --- nixos/modules/system/boot/luksroot.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nixos/modules/system/boot/luksroot.nix b/nixos/modules/system/boot/luksroot.nix index 018e7b2e7f89..aa4a5f8abcce 100644 --- a/nixos/modules/system/boot/luksroot.nix +++ b/nixos/modules/system/boot/luksroot.nix @@ -144,7 +144,7 @@ let fi fi done - echo -n "Verifiying passphrase for ${device}..." + echo -n "Verifying passphrase for ${device}..." echo -n "$passphrase" | ${csopen} --key-file=- if [ $? == 0 ]; then echo " - success" From 8c81099cdaf14e48943c5707fc6b3b9d6159a8e0 Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Tue, 8 Jan 2019 21:55:44 +0100 Subject: [PATCH 200/247] radare2: add propagated build inputs (#53667) Fixes the cutter build which was broken when radare2 was moved away from vendored dependencies in #51837. --- pkgs/development/tools/analysis/radare2/default.nix | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/pkgs/development/tools/analysis/radare2/default.nix b/pkgs/development/tools/analysis/radare2/default.nix index 5b4bde0ff0af..eac1bc7b51ed 100644 --- a/pkgs/development/tools/analysis/radare2/default.nix +++ b/pkgs/development/tools/analysis/radare2/default.nix @@ -75,12 +75,19 @@ let depsBuildBuild = [ buildPackages.stdenv.cc ]; nativeBuildInputs = [ pkgconfig ]; - buildInputs = [ file libzip xxHash readline libusb libewf perl zlib openssl libuv ] + buildInputs = [ file readline libusb libewf perl zlib openssl libuv ] ++ optional useX11 [ gtkdialog vte gtk2 ] ++ optional rubyBindings [ ruby ] ++ optional pythonBindings [ python3 ] ++ optional luaBindings [ lua ]; + propagatedBuildInputs = [ + # radare2 exposes r_lib which depends on these libraries + file # for its list of magic numbers (`libmagic`) + libzip + xxHash + ]; + meta = { description = "unix-like reverse engineering framework and commandline tools"; homepage = http://radare.org/; From f7113786af544323937c7d7dfe91e0acfa92f410 Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Tue, 8 Jan 2019 17:57:29 +0100 Subject: [PATCH 201/247] vimPlugins.neoterm: init at 2018-12-21 --- pkgs/misc/vim-plugins/generated.nix | 11 +++++++++++ pkgs/misc/vim-plugins/vim-plugin-names | 1 + 2 files changed, 12 insertions(+) diff --git a/pkgs/misc/vim-plugins/generated.nix b/pkgs/misc/vim-plugins/generated.nix index cdb747daca3c..628c128a3bee 100644 --- a/pkgs/misc/vim-plugins/generated.nix +++ b/pkgs/misc/vim-plugins/generated.nix @@ -1156,6 +1156,17 @@ let }; }; + neoterm = buildVimPluginFrom2Nix { + pname = "neoterm"; + version = "2018-12-21"; + src = fetchFromGitHub { + owner = "kassio"; + repo = "neoterm"; + rev = "d74b342a9bc84e4ca3f7e85cd773a08d0aa26fe9"; + sha256 = "09ywfnm5imx98qx57vg7ih37jixzh2sm6769gvrjz7m6d8d016mn"; + }; + }; + neovim-sensible = buildVimPluginFrom2Nix { pname = "neovim-sensible"; version = "2017-09-20"; diff --git a/pkgs/misc/vim-plugins/vim-plugin-names b/pkgs/misc/vim-plugins/vim-plugin-names index 3881ea0c5df7..11ad882897a4 100644 --- a/pkgs/misc/vim-plugins/vim-plugin-names +++ b/pkgs/misc/vim-plugins/vim-plugin-names @@ -130,6 +130,7 @@ kana/vim-niceblock kana/vim-operator-replace kana/vim-operator-user kana/vim-tabpagecd +kassio/neoterm kchmck/vim-coffee-script KeitaNakamura/neodark.vim keith/swift.vim From 67cf32751c985e36a681ff40a5ad9eea7e69c42e Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Tue, 8 Jan 2019 22:04:27 +0100 Subject: [PATCH 202/247] vimPlugins.vim-slime: init at 2019-01-03 --- pkgs/misc/vim-plugins/generated.nix | 11 +++++++++++ pkgs/misc/vim-plugins/vim-plugin-names | 1 + 2 files changed, 12 insertions(+) diff --git a/pkgs/misc/vim-plugins/generated.nix b/pkgs/misc/vim-plugins/generated.nix index 628c128a3bee..c18ce070c1c0 100644 --- a/pkgs/misc/vim-plugins/generated.nix +++ b/pkgs/misc/vim-plugins/generated.nix @@ -3412,6 +3412,17 @@ let }; }; + vim-slime = buildVimPluginFrom2Nix { + pname = "vim-slime"; + version = "2019-01-03"; + src = fetchFromGitHub { + owner = "jpalardy"; + repo = "vim-slime"; + rev = "faad1bc20cd12ce6ac6a9966ff84d13a44b16a2c"; + sha256 = "0aivii3p7vw42zxpy758gq9qbsm7v8701jbig4r69vy0mwm6i2vd"; + }; + }; + vim-smalls = buildVimPluginFrom2Nix { pname = "vim-smalls"; version = "2015-05-02"; diff --git a/pkgs/misc/vim-plugins/vim-plugin-names b/pkgs/misc/vim-plugins/vim-plugin-names index 11ad882897a4..262a32778878 100644 --- a/pkgs/misc/vim-plugins/vim-plugin-names +++ b/pkgs/misc/vim-plugins/vim-plugin-names @@ -113,6 +113,7 @@ jistr/vim-nerdtree-tabs jnurmine/zenburn jonbri/vim-colorstepper joonty/vim-xdebug +jpalardy/vim-slime JuliaEditorSupport/deoplete-julia JuliaEditorSupport/julia-vim junegunn/fzf.vim From 7dafdc1400b9b0d8e1e76ae9a184097fe69d4283 Mon Sep 17 00:00:00 2001 From: Jorge Acereda Date: Tue, 8 Jan 2019 22:43:45 +0100 Subject: [PATCH 203/247] darwin: basic_cmds was installing binaries in the wrong path --- .../darwin/apple-source-releases/basic_cmds/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/os-specific/darwin/apple-source-releases/basic_cmds/default.nix b/pkgs/os-specific/darwin/apple-source-releases/basic_cmds/default.nix index f646e57549ea..4a0180dda7ae 100644 --- a/pkgs/os-specific/darwin/apple-source-releases/basic_cmds/default.nix +++ b/pkgs/os-specific/darwin/apple-source-releases/basic_cmds/default.nix @@ -15,7 +15,7 @@ appleDerivation rec { installPhase = '' for f in Products/Release/*; do if [ -f $f ]; then - install -D $f $out/usr/bin/$(basename $f) + install -D $f $out/bin/$(basename $f) fi done From c60adabfbceabe769f2046aa5aa5753602d7a1b6 Mon Sep 17 00:00:00 2001 From: Austin Seipp Date: Tue, 8 Jan 2019 15:06:12 -0600 Subject: [PATCH 204/247] yosys: 2018.10.17 -> 2019.01.08 Signed-off-by: Austin Seipp --- pkgs/development/compilers/yosys/default.nix | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/pkgs/development/compilers/yosys/default.nix b/pkgs/development/compilers/yosys/default.nix index 275a25c84959..1afeae73f2f1 100644 --- a/pkgs/development/compilers/yosys/default.nix +++ b/pkgs/development/compilers/yosys/default.nix @@ -8,14 +8,14 @@ with builtins; stdenv.mkDerivation rec { name = "yosys-${version}"; - version = "2018.10.17"; + version = "2019.01.08"; srcs = [ (fetchFromGitHub { owner = "yosyshq"; repo = "yosys"; - rev = "yosys-0.8"; - sha256 = "1qwbp8gynlklawzvpa4gdn2x0hs8zln0s3kxjqkhfcjfxffdcpvv"; + rev = "2a2e0a4722ded7628b71f436b94a06aebd57bb62"; + sha256 = "19wzh7yssk90s58l2f89m0q5bjjrjpkhvikf5zc0563wccvl712c"; name = "yosys"; }) @@ -25,8 +25,8 @@ stdenv.mkDerivation rec { (fetchFromGitHub { owner = "berkeley-abc"; repo = "abc"; - rev = "ae6716b064c842f45109a88e84dca71fe4cc311f"; - sha256 = "0g39k16dmrl6q73q39yr5yd9r4rcliz5zxzbnwzh29z9xwi6ipw8"; + rev = "2ddc57d8760d94e86699be39a628178cff8154f8"; + sha256 = "0da7nnnnl9cq2r7s301xgdc8nlr6hqmqpvd9zn4b58m125sp0scl"; name = "yosys-abc"; }) ]; From d77f381055c6c96c4f04bee55d00c0e567e99d73 Mon Sep 17 00:00:00 2001 From: Austin Seipp Date: Tue, 8 Jan 2019 15:06:30 -0600 Subject: [PATCH 205/247] symbiyosys: 2018.09.12 -> 2018.12.09 Signed-off-by: Austin Seipp --- pkgs/applications/science/logic/symbiyosys/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/applications/science/logic/symbiyosys/default.nix b/pkgs/applications/science/logic/symbiyosys/default.nix index e21c274370c8..2047bb3fc9f8 100644 --- a/pkgs/applications/science/logic/symbiyosys/default.nix +++ b/pkgs/applications/science/logic/symbiyosys/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "symbiyosys-${version}"; - version = "2018.09.12"; + version = "2018.12.09"; src = fetchFromGitHub { owner = "yosyshq"; repo = "symbiyosys"; - rev = "e90bcb588e97118af0cdba23fae562fb0efbf294"; - sha256 = "16nlimpdc3g6lghwqpyirgrr1d9mgk4wg3c06fvglzaicvjixnfr"; + rev = "0772456a15b5a474c3c90a06b48e46a67d8a6614"; + sha256 = "00p2l1g9z8nnmkc57l1cfn9ignjjmxwnyaxj2xjd1fim4kzd5475"; }; buildInputs = [ python3 yosys ]; From db136382f8a88a1db402ee5e818a4fe9c87cf6c3 Mon Sep 17 00:00:00 2001 From: Austin Seipp Date: Tue, 8 Jan 2019 15:09:50 -0600 Subject: [PATCH 206/247] icestorm: 2018.09.04 -> 2018.12.31 Signed-off-by: Austin Seipp --- pkgs/development/tools/icestorm/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/development/tools/icestorm/default.nix b/pkgs/development/tools/icestorm/default.nix index 345a25082164..68e217f9aabb 100644 --- a/pkgs/development/tools/icestorm/default.nix +++ b/pkgs/development/tools/icestorm/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "icestorm-${version}"; - version = "2018.09.04"; + version = "2018.12.31"; src = fetchFromGitHub { owner = "cliffordwolf"; repo = "icestorm"; - rev = "8f61acd0556c8afee83ec2e77dedb03e700333d9"; - sha256 = "1dwix8bb87xqf27dixdnfp47pll8739h9m9aw8wvvwz4s4989q6v"; + rev = "c0cbae88ab47a3879aacf80d53b6a85710682a6b"; + sha256 = "0bqm0rpywm64yvbq75klpyzb1g9sdsp1kvdlyqg4hvm8jw9w8lya"; }; nativeBuildInputs = [ pkgconfig ]; From 1d36130ac19e01a2a1254ba5eecd7688e4e8f859 Mon Sep 17 00:00:00 2001 From: Austin Seipp Date: Tue, 8 Jan 2019 15:13:28 -0600 Subject: [PATCH 207/247] nextnpr: 2018.12.29 -> 2019.01.08 Signed-off-by: Austin Seipp --- pkgs/development/compilers/nextpnr/default.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/development/compilers/nextpnr/default.nix b/pkgs/development/compilers/nextpnr/default.nix index 042cd783360f..c9e97e402303 100644 --- a/pkgs/development/compilers/nextpnr/default.nix +++ b/pkgs/development/compilers/nextpnr/default.nix @@ -7,13 +7,13 @@ let in stdenv.mkDerivation rec { name = "nextpnr-${version}"; - version = "2018.12.29"; + version = "2019.01.08"; src = fetchFromGitHub { owner = "yosyshq"; repo = "nextpnr"; - rev = "eb456ef476e8342b4709d71cbff6ef22a714d6ec"; - sha256 = "1gw9r8c6wyfhbzhm3hz1xpbq8ax27qnjwlrimzcykrr9r1cykiik"; + rev = "c1d15c749c2aa105ee7b38ebe1b60a27e3743e8c"; + sha256 = "082ac03s6164s7dwz1l9phshl8m1lizn45jykabrhks5jcccchbh"; }; nativeBuildInputs = [ cmake ]; From 38aa0a3df47ea648f79ce0ce29d183e37733d1ae Mon Sep 17 00:00:00 2001 From: Austin Seipp Date: Tue, 8 Jan 2019 15:18:29 -0600 Subject: [PATCH 208/247] z3: 4.8.3 -> 4.8.4 Signed-off-by: Austin Seipp --- pkgs/applications/science/logic/z3/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/science/logic/z3/default.nix b/pkgs/applications/science/logic/z3/default.nix index 28a7e783ff3f..a4a55e3e8511 100644 --- a/pkgs/applications/science/logic/z3/default.nix +++ b/pkgs/applications/science/logic/z3/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "z3-${version}"; - version = "4.8.3"; + version = "4.8.4"; src = fetchFromGitHub { owner = "Z3Prover"; repo = "z3"; rev = name; - sha256 = "0p5gdmhd32x6zwmx7j5cgwh4jyfxa9yapym95nlmyfaqzak92qar"; + sha256 = "014igqm5vwswz0yhz0cdxsj3a6dh7i79hvhgc3jmmmz3z0xm1gyn"; }; buildInputs = [ python fixDarwinDylibNames ]; From c10650760d8e16a1346c401878abea6c6394196a Mon Sep 17 00:00:00 2001 From: Austin Seipp Date: Tue, 8 Jan 2019 15:18:45 -0600 Subject: [PATCH 209/247] yices: s/fetchurl/fetchFromGitHub/ Signed-off-by: Austin Seipp --- pkgs/applications/science/logic/yices/default.nix | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/pkgs/applications/science/logic/yices/default.nix b/pkgs/applications/science/logic/yices/default.nix index 0ab08db67465..40a4c391e1d5 100644 --- a/pkgs/applications/science/logic/yices/default.nix +++ b/pkgs/applications/science/logic/yices/default.nix @@ -1,13 +1,14 @@ -{ stdenv, fetchurl, gmp-static, gperf, autoreconfHook, libpoly }: +{ stdenv, fetchFromGitHub, gmp-static, gperf, autoreconfHook, libpoly }: stdenv.mkDerivation rec { name = "yices-${version}"; version = "2.6.1"; - src = fetchurl { - url = "https://github.com/SRI-CSL/yices2/archive/Yices-${version}.tar.gz"; - name = "${name}-src.tar.gz"; - sha256 = "14xvflv14qn8ssm8rklvckp6l1q94vn49qz2snz73j40nwzshaww"; + src = fetchFromGitHub { + owner = "SRI-CSL"; + repo = "yices2"; + rev = "Yices-${version}"; + sha256 = "04vf468spsh00jh7gj94cjnq8kjyfwy9l6r4z7l2pm0zgwkqgyhm"; }; nativeBuildInputs = [ autoreconfHook ]; @@ -38,6 +39,6 @@ stdenv.mkDerivation rec { homepage = "http://yices.csl.sri.com"; license = licenses.gpl3; platforms = with platforms; linux ++ darwin; - maintainers = [ maintainers.thoughtpolice ]; + maintainers = with maintainers; [ thoughtpolice ]; }; } From 412e02c78448187d1b4a67db4336686cd0672d2d Mon Sep 17 00:00:00 2001 From: Austin Seipp Date: Tue, 8 Jan 2019 16:00:58 -0600 Subject: [PATCH 210/247] nextpnr: disable broken GUI build for now This didn't work remotely (on a server with Nvidia drivers) _or_ on a local Intel machine with integrated graphics. I presumably messed something up (a missing dependency), but I'm not sure where. We can fix it later. In the mean time, just disable this by hiding it behind a minimal flag. As a bonus this reduces the closure size by about half, although it's still surprisingly large (~300MB or so). Part of that is probably Python, though. When the GUI is reintroduced in a working manner, we can expose two nextpnr attributes for the minimal non-GUI build, and the GUI build. (Note that I have no plans of making Python optional, since it's extremely valuable in general and much more lightweight than qtbase.) Signed-off-by: Austin Seipp --- .../development/compilers/nextpnr/default.nix | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/pkgs/development/compilers/nextpnr/default.nix b/pkgs/development/compilers/nextpnr/default.nix index c9e97e402303..e2713a28f0e5 100644 --- a/pkgs/development/compilers/nextpnr/default.nix +++ b/pkgs/development/compilers/nextpnr/default.nix @@ -1,5 +1,14 @@ { stdenv, fetchFromGitHub, cmake -, icestorm, python3, boost, qtbase +, boost, python3 + +# TODO: also add libtrellis, later on +, icestorm + +# TODO(thoughtpolice) Currently the GUI build seems broken at runtime on my +# laptop (and over a remote X server on my server...), so mark it broken for +# now, with intent to fix later. +, enableGui ? false +, qtbase }: let @@ -17,13 +26,15 @@ stdenv.mkDerivation rec { }; nativeBuildInputs = [ cmake ]; - buildInputs = [ boostPython python3 qtbase ]; + buildInputs + = [ boostPython python3 ] + ++ (stdenv.lib.optional enableGui qtbase); enableParallelBuilding = true; cmakeFlags = [ "-DARCH=generic;ice40" "-DICEBOX_ROOT=${icestorm}/share/icebox" - ]; + ] ++ (stdenv.lib.optional (!enableGui) "-DBUILD_GUI=OFF"); meta = with stdenv.lib; { description = "Place and route tool for FPGAs"; @@ -31,5 +42,7 @@ stdenv.mkDerivation rec { license = licenses.isc; platforms = platforms.linux; maintainers = with maintainers; [ thoughtpolice ]; + + broken = enableGui; }; } From 651679c257cef88f309f3f7f719a1dce216b6fcc Mon Sep 17 00:00:00 2001 From: Austin Seipp Date: Tue, 8 Jan 2019 16:18:12 -0600 Subject: [PATCH 211/247] nextpnr: fix version string output Signed-off-by: Austin Seipp --- pkgs/development/compilers/nextpnr/default.nix | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/pkgs/development/compilers/nextpnr/default.nix b/pkgs/development/compilers/nextpnr/default.nix index e2713a28f0e5..1efce56dc133 100644 --- a/pkgs/development/compilers/nextpnr/default.nix +++ b/pkgs/development/compilers/nextpnr/default.nix @@ -36,6 +36,13 @@ stdenv.mkDerivation rec { "-DICEBOX_ROOT=${icestorm}/share/icebox" ] ++ (stdenv.lib.optional (!enableGui) "-DBUILD_GUI=OFF"); + # Fix the version number. This is a bit stupid (and fragile) in practice + # but works ok. We should probably make this overrideable upstream. + patchPhase = with builtins; '' + substituteInPlace ./CMakeLists.txt \ + --replace 'git log -1 --format=%h' 'echo ${substring 0 11 src.rev}' + ''; + meta = with stdenv.lib; { description = "Place and route tool for FPGAs"; homepage = https://github.com/yosyshq/nextpnr; From d67cbe9e53ef9d37c9284c17497693f6291ab5e4 Mon Sep 17 00:00:00 2001 From: Austin Seipp Date: Tue, 8 Jan 2019 16:56:16 -0600 Subject: [PATCH 212/247] trellis: 2018.08.01 -> 2018.12.20, update, cleanup Signed-off-by: Austin Seipp --- pkgs/development/tools/trellis/default.nix | 59 ++++++++++++---------- 1 file changed, 32 insertions(+), 27 deletions(-) diff --git a/pkgs/development/tools/trellis/default.nix b/pkgs/development/tools/trellis/default.nix index 892552559aa7..966c50404d45 100644 --- a/pkgs/development/tools/trellis/default.nix +++ b/pkgs/development/tools/trellis/default.nix @@ -1,49 +1,54 @@ -{ stdenv, fetchFromGitHub, python3, cmake, boost }: +{ stdenv, fetchFromGitHub +, python3, boost +, cmake +}: let - trellisdb = fetchFromGitHub { - owner = "SymbiFlow"; - repo = "prjtrellis-db"; - rev = "06b429ddb7fd8ec1e3f2b35de2e94b4853cf2835"; - sha256 = "07bsgw5x3gq0jcn9j4g7q9xvibvz6j2arjnvgyrxnrg30ri9q173"; - }; + boostWithPython3 = boost.override { python = python3; enablePython = true; }; in stdenv.mkDerivation rec { name = "trellis-${version}"; - version = "2018.08.01"; + version = "2018.12.20"; - buildInputs = [ - (boost.override { python = python3; enablePython = true; }) + srcs = [ + (fetchFromGitHub { + owner = "symbiflow"; + repo = "prjtrellis"; + rev = "b947028a6ac6494b6000c6e1ab5aa0db813e8544"; + sha256 = "14dcsl2drx3xaqvpawp0j7088cijxcr5018yji48rmbl85763aw9"; + name = "trellis"; + }) + (fetchFromGitHub { + owner = "symbiflow"; + repo = "prjtrellis-db"; + rev = "670d04f0b8412193d5e974eea67f2bb7355aa1ec"; + sha256 = "1hm385rg1jq9qbq63g5134gq9xpfadvpahxvzwpv0q543brkg730"; + name = "database"; + }) ]; + sourceRoot = "trellis"; - nativeBuildInputs = [ - cmake python3 - ]; + buildInputs = [ boostWithPython3 ]; + nativeBuildInputs = [ cmake python3 ]; - src = fetchFromGitHub { - owner = "SymbiFlow"; - repo = "prjtrellis"; - rev = "fff9532fe59bf9e38b44f029ce4a06c607a9ee78"; - sha256 = "0ycw9fjf6428sf5x8x5szn8fha79610nf7nn8kmibgmz9868yv30"; - }; + preConfigure = with builtins; '' + rmdir database && ln -sfv ${elemAt srcs 1} ./database - preConfigure = '' source environment.sh - cp -RT "${trellisdb}" database cd libtrellis ''; - meta = { - description = "Documentation and tools for Lattice ECP5 FPGAs"; + meta = with stdenv.lib; { + description = "Documentation and bitstream tools for Lattice ECP5 FPGAs"; longDescription = '' Project Trellis documents the Lattice ECP5 architecture to enable development of open-source tools. Its goal is to provide sufficient information to develop a free and open Verilog to bitstream toolchain for these devices. ''; - homepage = https://github.com/SymbiFlow/prjtrellis; - license = stdenv.lib.licenses.isc; - maintainers = with stdenv.lib.maintainers; [ q3k ]; - platforms = stdenv.lib.platforms.linux; + homepage = https://github.com/symbiflow/prjtrellis; + license = stdenv.lib.licenses.isc; + maintainers = with maintainers; [ q3k thoughtpolice ]; + platforms = stdenv.lib.platforms.linux; }; } From beaf69cee298e092698dd2da2e4758b7811859ad Mon Sep 17 00:00:00 2001 From: Austin Seipp Date: Tue, 8 Jan 2019 17:19:51 -0600 Subject: [PATCH 213/247] nextpnr: enable ECP5 P&R with Project Trellis This requires an absurd, disgustingly gross hack in order to share the build artifacts necessary for nextpnr to use trellis. Signed-off-by: Austin Seipp --- .../development/compilers/nextpnr/default.nix | 20 +++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/pkgs/development/compilers/nextpnr/default.nix b/pkgs/development/compilers/nextpnr/default.nix index 1efce56dc133..cbd4d0b9f4ee 100644 --- a/pkgs/development/compilers/nextpnr/default.nix +++ b/pkgs/development/compilers/nextpnr/default.nix @@ -1,8 +1,6 @@ { stdenv, fetchFromGitHub, cmake , boost, python3 - -# TODO: also add libtrellis, later on -, icestorm +, icestorm, trellis # TODO(thoughtpolice) Currently the GUI build seems broken at runtime on my # laptop (and over a remote X server on my server...), so mark it broken for @@ -13,6 +11,19 @@ let boostPython = boost.override { python = python3; enablePython = true; }; + + # This is a massive hack. For now, Trellis doesn't really support + # installation through an already-built package; you have to build it once to + # get the tools, then reuse the build directory to build nextpnr -- the + # 'install' phase doesn't install everything it needs. This will be fixed in + # the future but for now we can do this horrific thing. + trellisRoot = trellis.overrideAttrs (_: { + installPhase = '' + mkdir -p $out + cp *.so .. + cd ../../.. && cp -R trellis database $out/ + ''; + }); in stdenv.mkDerivation rec { name = "nextpnr-${version}"; @@ -32,8 +43,9 @@ stdenv.mkDerivation rec { enableParallelBuilding = true; cmakeFlags = - [ "-DARCH=generic;ice40" + [ "-DARCH=generic;ice40;ecp5" "-DICEBOX_ROOT=${icestorm}/share/icebox" + "-DTRELLIS_ROOT=${trellisRoot}/trellis" ] ++ (stdenv.lib.optional (!enableGui) "-DBUILD_GUI=OFF"); # Fix the version number. This is a bit stupid (and fragile) in practice From 2a68c2c413fb227e8676a5d1eabe3c756bd12afe Mon Sep 17 00:00:00 2001 From: Dmitry Kalinkin Date: Tue, 8 Jan 2019 21:45:23 -0500 Subject: [PATCH 214/247] poppler: fix build on darwin --- pkgs/development/libraries/poppler/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/development/libraries/poppler/default.nix b/pkgs/development/libraries/poppler/default.nix index e5b469f73956..30f8044f32b5 100644 --- a/pkgs/development/libraries/poppler/default.nix +++ b/pkgs/development/libraries/poppler/default.nix @@ -34,7 +34,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ninja pkgconfig ]; # Not sure when and how to pass it. It seems an upstream bug anyway. - CXXFLAGS = stdenv.lib.optionalString stdenv.cc.isClang "-std=c++11"; + CXXFLAGS = stdenv.lib.optionalString stdenv.cc.isClang "-std=c++14"; cmakeFlags = [ (mkFlag true "XPDF_HEADERS") From e69d494033d9797c67cb9aca3cca1352e02af560 Mon Sep 17 00:00:00 2001 From: Will Dietz Date: Tue, 8 Jan 2019 20:53:28 -0600 Subject: [PATCH 215/247] scons: 3.0.2 -> 3.0.3 https://scons.org/scons-303-is-available.html cc e1d98548167f52425c089b81f594dfa9c58a5e02 --- pkgs/development/tools/build-managers/scons/default.nix | 6 +++--- pkgs/top-level/all-packages.nix | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pkgs/development/tools/build-managers/scons/default.nix b/pkgs/development/tools/build-managers/scons/default.nix index 21893545c9a3..3d919be2ebaf 100644 --- a/pkgs/development/tools/build-managers/scons/default.nix +++ b/pkgs/development/tools/build-managers/scons/default.nix @@ -11,8 +11,8 @@ in { version = "3.0.1"; sha256 = "0wzid419mlwqw9llrg8gsx4nkzhqy16m4m40r0xnh6cwscw5wir4"; }; - scons_3_0_2 = mkScons { - version = "3.0.2"; - sha256 = "00fyvb2rrixj9h6f2sqr6z8q677anc61qcn9ydxgm99f9j7wzbyh"; + scons_3_0_3 = mkScons { + version = "3.0.3"; + sha256 = "1wwn0534d83ryfxjihvqk2ncj8wh5210pi3jxjd2cvjqa9mpkv6q"; }; } diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 6e7ca1c7b8da..b4b34740b864 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -9040,7 +9040,7 @@ in selendroid = callPackage ../development/tools/selenium/selendroid { }; sconsPackages = callPackage ../development/tools/build-managers/scons { }; - scons = sconsPackages.scons_3_0_2; + scons = sconsPackages.scons_3_0_3; scons_2_5_1 = sconsPackages.scons_2_5_1; mill = callPackage ../development/tools/build-managers/mill { }; From 66c1f82631e51a85994cb6aad3c5b5d2ef4e89f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= Date: Wed, 9 Jan 2019 07:20:37 +0000 Subject: [PATCH 216/247] electron_3: init at 3.1.0 electron 4 had many breaking changes in their API, breaking rambox. Since the 3.x version is still maintained, we can add an older variant. --- pkgs/development/tools/electron/3.x.nix | 77 +++++++++++++++++++ .../tools/electron/print-hashes.sh | 29 +++++++ pkgs/top-level/all-packages.nix | 2 + 3 files changed, 108 insertions(+) create mode 100644 pkgs/development/tools/electron/3.x.nix create mode 100755 pkgs/development/tools/electron/print-hashes.sh diff --git a/pkgs/development/tools/electron/3.x.nix b/pkgs/development/tools/electron/3.x.nix new file mode 100644 index 000000000000..0fe8ab05b68c --- /dev/null +++ b/pkgs/development/tools/electron/3.x.nix @@ -0,0 +1,77 @@ +{ stdenv, libXScrnSaver, makeWrapper, fetchurl, unzip, atomEnv, gtk2, at-spi2-atk }: + +let + version = "3.1.0"; + name = "electron-${version}"; + + throwSystem = throw "Unsupported system: ${stdenv.hostPlatform.system}"; + + meta = with stdenv.lib; { + description = "Cross platform desktop application shell"; + homepage = https://github.com/electron/electron; + license = licenses.mit; + maintainers = with maintainers; [ travisbhartwell manveru ]; + platforms = [ "x86_64-darwin" "x86_64-linux" "i686-linux" "armv7l-linux" "aarch64-linux" ]; + }; + + linux = { + inherit name version meta; + src = { + i686-linux = fetchurl { + url = "https://github.com/electron/electron/releases/download/v${version}/electron-v${version}-linux-ia32.zip"; + sha256 = "09llladfj8l1vnk8fl8ad66qq4czr755fhrp5ciivpbh38zi6d3d"; + }; + x86_64-linux = fetchurl { + url = "https://github.com/electron/electron/releases/download/v${version}/electron-v${version}-linux-x64.zip"; + sha256 = "0g0af1z598f8k2i5sbkzpbga49hbgzl98qgk1n4iagk08iivyfwy"; + }; + armv7l-linux = fetchurl { + url = "https://github.com/electron/electron/releases/download/v${version}/electron-v${version}-linux-armv7l.zip"; + sha256 = "1ayfcy7jm7mymmbdq08id9wpjj6cja2cyix1sw2r3m8gpn4l6ih2"; + }; + aarch64-linux = fetchurl { + url = "https://github.com/electron/electron/releases/download/v${version}/electron-v${version}-linux-arm64.zip"; + sha256 = "18cqg9zb98c0rfrdg7ri26dvhjwrwzj41jn8dfra9131xc84nl3i"; + }; + }.${stdenv.hostPlatform.system} or throwSystem; + + buildInputs = [ unzip makeWrapper ]; + + buildCommand = '' + mkdir -p $out/lib/electron $out/bin + unzip -d $out/lib/electron $src + ln -s $out/lib/electron/electron $out/bin + + fixupPhase + + patchelf \ + --set-interpreter "$(cat $NIX_CC/nix-support/dynamic-linker)" \ + --set-rpath "${atomEnv.libPath}:${gtk2}/lib:${at-spi2-atk}/lib:$out/lib/electron" \ + $out/lib/electron/electron + + wrapProgram $out/lib/electron/electron \ + --prefix LD_PRELOAD : ${stdenv.lib.makeLibraryPath [ libXScrnSaver ]}/libXss.so.1 + ''; + }; + + darwin = { + inherit name version meta; + + src = fetchurl { + url = "https://github.com/electron/electron/releases/download/v${version}/electron-v${version}-darwin-x64.zip"; + sha256 = "1cd1ashrcbdjlrr6yijyh2ppk8x8jdw5cm9qnx4lzk7sj9lwjbgb"; + }; + + buildInputs = [ unzip ]; + + buildCommand = '' + mkdir -p $out/Applications + unzip $src + mv Electron.app $out/Applications + mkdir -p $out/bin + ln -s $out/Applications/Electron.app/Contents/MacOs/Electron $out/bin/electron + ''; + }; +in + + stdenv.mkDerivation (if stdenv.isDarwin then darwin else linux) diff --git a/pkgs/development/tools/electron/print-hashes.sh b/pkgs/development/tools/electron/print-hashes.sh new file mode 100755 index 000000000000..203e5a4dfec6 --- /dev/null +++ b/pkgs/development/tools/electron/print-hashes.sh @@ -0,0 +1,29 @@ +#!/usr/bin/env bash + +set -eu -o pipefail + +if [[ $# -lt 1 ]]; then + echo "$0: version" >&2 + exit 1 +fi + + +VERSION=$1 + +declare -A SYSTEMS HASHES +SYSTEMS=( + [i686-linux]=linux-ia32 + [x86_64-linux]=linux-x64 + [armv7l-linux]=linux-armv7l + [aarch64-linux]=linux-arm64 + [x86_64-darwin]=darwin-x64 +) + +for S in "${!SYSTEMS[@]}"; do + HASHES["$S"]=$(nix-prefetch-url "https://github.com/electron/electron/releases/download/v${VERSION}/electron-v${VERSION}-${SYSTEMS[$S]}.zip") +done + +for S in "${!HASHES[@]}"; do + echo "$S" + echo "sha256 = \"${HASHES[$S]}\";" +done diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 6e7ca1c7b8da..a7a0062a1de7 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -8292,6 +8292,8 @@ in electron = callPackage ../development/tools/electron { }; + electron_3 = callPackage ../development/tools/electron/3.x.nix { }; + autobuild = callPackage ../development/tools/misc/autobuild { }; autoconf = callPackage ../development/tools/misc/autoconf { }; From fdb87a0fee060601026e134952c23e8be3569210 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= Date: Wed, 9 Jan 2019 07:22:33 +0000 Subject: [PATCH 217/247] rambox: downgrade electron to 3.x --- .../networking/instant-messengers/rambox/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/networking/instant-messengers/rambox/default.nix b/pkgs/applications/networking/instant-messengers/rambox/default.nix index 46157c2a35f3..84ea02f7cb38 100644 --- a/pkgs/applications/networking/instant-messengers/rambox/default.nix +++ b/pkgs/applications/networking/instant-messengers/rambox/default.nix @@ -1,6 +1,6 @@ { stdenv, newScope, makeWrapper , wrapGAppsHook, gnome3, glib -, electron, xdg_utils, makeDesktopItem +, electron_3, xdg_utils, makeDesktopItem , auth0ClientID ? "0spuNKfIGeLAQ_Iki9t3fGxbfJl3k8SU" , auth0Domain ? "nixpkgs.auth0.com" }: @@ -43,7 +43,7 @@ stdenv.mkDerivation { ''; postFixup = '' - makeWrapper ${electron}/bin/electron $out/bin/rambox \ + makeWrapper ${electron_3}/bin/electron $out/bin/rambox \ --add-flags "${rambox-bare} --without-update" \ "''${gappsWrapperArgs[@]}" \ --prefix PATH : ${xdg_utils}/bin From 96bfa255001fdc39c35ce8a255e2ee1fa8b72478 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Tor=20Hedin=20Br=C3=B8nner?= Date: Wed, 9 Jan 2019 09:17:32 +0100 Subject: [PATCH 218/247] libsForQt5.qgpgme: fix tests after 2019-01-06 The keys used in one of the qt tests expired on 2019-01-06 breaking the build. closes https://github.com/NixOS/nixpkgs/issues/53632 --- pkgs/development/libraries/gpgme/default.nix | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/pkgs/development/libraries/gpgme/default.nix b/pkgs/development/libraries/gpgme/default.nix index 44086538cd04..0e4ef72b8aae 100644 --- a/pkgs/development/libraries/gpgme/default.nix +++ b/pkgs/development/libraries/gpgme/default.nix @@ -1,6 +1,6 @@ { stdenv, fetchurl, libgpgerror, gnupg, pkgconfig, glib, pth, libassuan , file, which, ncurses -, autoreconfHook +, autoreconfHook, fetchpatch , git , texinfo , qtbase ? null @@ -31,6 +31,14 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ file pkgconfig gnupg autoreconfHook git texinfo ] ++ lib.optionals pythonSupport [ python swig2 which ncurses ]; + patches = [ + (fetchpatch { + name = "fix-key-expiry.patch"; + url = "https://files.gnupg.net/file/data/fehgbjmataj5tc2pnfhj/PHID-FILE-aqck6l4elhw53tjanrie/file"; + sha256 = "1h80m045gy7r0g7dzzlfpql6p065x88p274ij9jnf7d4lwwgrf1a"; + }) + ]; + postPatch ='' substituteInPlace ./configure --replace /usr/bin/file ${file}/bin/file ''; From 60703db86c324c7574094bac0f9edc6096789fae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Thalheim?= Date: Wed, 9 Jan 2019 09:32:58 +0000 Subject: [PATCH 219/247] electron_3: also update arm hashes --- pkgs/development/tools/electron/3.x.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/tools/electron/3.x.nix b/pkgs/development/tools/electron/3.x.nix index 0fe8ab05b68c..90a7c53be023 100644 --- a/pkgs/development/tools/electron/3.x.nix +++ b/pkgs/development/tools/electron/3.x.nix @@ -27,11 +27,11 @@ let }; armv7l-linux = fetchurl { url = "https://github.com/electron/electron/releases/download/v${version}/electron-v${version}-linux-armv7l.zip"; - sha256 = "1ayfcy7jm7mymmbdq08id9wpjj6cja2cyix1sw2r3m8gpn4l6ih2"; + sha256 = "04yj58v1sqnw64csazpfcchv2498ppxs2izadpnirawk09azl3bl"; }; aarch64-linux = fetchurl { url = "https://github.com/electron/electron/releases/download/v${version}/electron-v${version}-linux-arm64.zip"; - sha256 = "18cqg9zb98c0rfrdg7ri26dvhjwrwzj41jn8dfra9131xc84nl3i"; + sha256 = "0cjf4i24qpgkmzb4nm89kgl07bwrncpz66xs5jjvi94pmr6wx6jm"; }; }.${stdenv.hostPlatform.system} or throwSystem; From a90fc6d3ef80245cd0898c9870e93f617131aeba Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bastian=20K=C3=B6cher?= Date: Tue, 8 Jan 2019 23:47:13 +0100 Subject: [PATCH 220/247] linux: Adds patch for fixing wifi on raspberry pi --- pkgs/os-specific/linux/kernel/patches.nix | 8 ++++++++ pkgs/top-level/all-packages.nix | 1 + 2 files changed, 9 insertions(+) diff --git a/pkgs/os-specific/linux/kernel/patches.nix b/pkgs/os-specific/linux/kernel/patches.nix index 2ff0d5d26205..7aecea25625b 100644 --- a/pkgs/os-specific/linux/kernel/patches.nix +++ b/pkgs/os-specific/linux/kernel/patches.nix @@ -68,4 +68,12 @@ rec { sha256 = "0bp4jryihg1y2sl8zlj6w7vvnxj0kmb6xdy42hpvdv43kb6ngiaq"; }; }; + + raspberry_pi_wifi_fix = rec { + name = "raspberry-pi-wifi-fix"; + patch = fetchpatch { + url = https://raw.githubusercontent.com/archlinuxarm/PKGBUILDs/730522ae76aa57b89fa317c5084613d3d50cf3b8/core/linux-aarch64/0005-mmc-sdhci-iproc-handle-mmc_of_parse-errors-during-pr.patch; + sha256 = "0gbfycky28vbdjgys1z71wl5q073dmbrkvbnr6693jsda3qhp6za"; + }; + }; } diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 6e7ca1c7b8da..ba48f7800aa9 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -14611,6 +14611,7 @@ in [ kernelPatches.bridge_stp_helper kernelPatches.modinst_arg_list_too_long kernelPatches.revert-vfs-dont-open-real + kernelPatches.raspberry_pi_wifi_fix ]; }; From eac67258437d5c128b12b724a6a7ee5ac15999a5 Mon Sep 17 00:00:00 2001 From: makefu Date: Wed, 9 Jan 2019 11:37:20 +0100 Subject: [PATCH 221/247] exfat-nofuse: unbreak for 4.18 and 4.20 --- pkgs/os-specific/linux/exfat/default.nix | 16 ++++++++++++++-- 1 file changed, 14 insertions(+), 2 deletions(-) diff --git a/pkgs/os-specific/linux/exfat/default.nix b/pkgs/os-specific/linux/exfat/default.nix index 8cc481334e3b..6120c707ba73 100644 --- a/pkgs/os-specific/linux/exfat/default.nix +++ b/pkgs/os-specific/linux/exfat/default.nix @@ -1,4 +1,4 @@ -{ stdenv, lib, fetchFromGitHub, kernel }: +{ stdenv, lib, fetchFromGitHub, fetchpatch, kernel }: # Upstream build for kernel 4.1 is broken, 3.12 and below seems to be working @@ -27,12 +27,24 @@ stdenv.mkDerivation rec { install -m644 -b -D exfat.ko $out/lib/modules/${kernel.modDirVersion}/kernel/fs/exfat/exfat.ko ''; + patches = [ + # fix compile-errors in 4.18 + (fetchpatch { + url = https://aur.archlinux.org/cgit/aur.git/plain/4.18.patch?h=exfat-dkms-git; + sha256 = "18l5h631w8yja7m2kkcf9h335pvlxms23ls539i81nf6xd6yvd78"; + } ) + # fix compile-errors in 4.20 + (fetchpatch { + url = https://aur.archlinux.org/cgit/aur.git/plain/4.20.patch?h=exfat-dkms-git; + sha256 = "05l5x5yvd4vlvnr1bjl751gzcylvm3g9551fqdx7lqphhyiyv3bc"; + }) + ]; + meta = { description = "exfat kernel module"; homepage = https://github.com/dorimanx/exfat-nofuse; license = lib.licenses.gpl2; maintainers = with lib.maintainers; [ makefu ]; platforms = lib.platforms.linux; - broken = stdenv.lib.versionAtLeast kernel.version "4.18"; }; } From 80cac27461cde6f5287fd025a58efdcba0d4772a Mon Sep 17 00:00:00 2001 From: Alberto Berti Date: Thu, 27 Dec 2018 23:31:09 +0100 Subject: [PATCH 222/247] anydesk: 2.9.4 -> 4.0.1 --- .../networking/remote/anydesk/default.nix | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/pkgs/applications/networking/remote/anydesk/default.nix b/pkgs/applications/networking/remote/anydesk/default.nix index cb3814b55f19..d9dd2fc9127a 100644 --- a/pkgs/applications/networking/remote/anydesk/default.nix +++ b/pkgs/applications/networking/remote/anydesk/default.nix @@ -1,11 +1,11 @@ { stdenv, fetchurl, makeWrapper, makeDesktopItem , atk, cairo, gdk_pixbuf, glib, gnome2, gtk2, libGLU_combined, pango, xorg -, lsb-release }: +, lsb-release, freetype, fontconfig, pangox_compat, polkit, polkit_gnome }: let sha256 = { - "x86_64-linux" = "0g19sac4j3m1nf400vn6qcww7prqg2p4k4zsj74i109kk1396aa2"; - "i686-linux" = "1dd4ai2pclav9g872xil3x67bxy32gvz9pb3w76383pcsdh5zh45"; + "x86_64-linux" = "08kdxsg9npb1nmlr2jyq7p238735kqkp7c5xckxn6rc4cp12n2y2"; + "i686-linux" = "11r5d4234zbkkgyrd7q9x3w7s7lailnq7z4x8cnhpr8vipzrg7h2"; }."${stdenv.hostPlatform.system}" or (throw "system ${stdenv.hostPlatform.system} not supported"); arch = { @@ -27,7 +27,7 @@ let in stdenv.mkDerivation rec { name = "anydesk-${version}"; - version = "2.9.4"; + version = "4.0.1"; src = fetchurl { url = "https://download.anydesk.com/linux/${name}-${arch}.tar.gz"; @@ -36,10 +36,11 @@ in stdenv.mkDerivation rec { buildInputs = [ atk cairo gdk_pixbuf glib gtk2 stdenv.cc.cc pango - gnome2.gtkglext libGLU_combined + gnome2.gtkglext libGLU_combined freetype fontconfig + pangox_compat polkit polkit_gnome ] ++ (with xorg; [ libxcb libX11 libXdamage libXext libXfixes libXi libXmu - libXrandr libXtst + libXrandr libXtst libXt libICE libSM ]); nativeBuildInputs = [ makeWrapper ]; From 43d4f07bf1144d6eb20975c956c7cc7bc643ea6e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Robert=20Sch=C3=BCtz?= Date: Wed, 9 Jan 2019 14:54:58 +0100 Subject: [PATCH 223/247] esptool: 2.5.1 -> 2.6 --- pkgs/tools/misc/esptool/default.nix | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pkgs/tools/misc/esptool/default.nix b/pkgs/tools/misc/esptool/default.nix index fe574b4f8d43..50ee066d96a2 100644 --- a/pkgs/tools/misc/esptool/default.nix +++ b/pkgs/tools/misc/esptool/default.nix @@ -2,17 +2,17 @@ python3.pkgs.buildPythonApplication rec { pname = "esptool"; - version = "2.5.1"; + version = "2.6"; src = fetchFromGitHub { owner = "espressif"; repo = "esptool"; rev = "v${version}"; - sha256 = "19l3b1fqg1n3ch484dcibbi5a3nbmjq086has5pwqn348h4k57mh"; + sha256 = "1hxgzqh5z81dq1k2xd6329h8idk9y8q29izrwm1vhn0m9v1pxa22"; }; - checkInputs = with python3.pkgs; [ flake8 flake8-future-import flake8-import-order ]; - propagatedBuildInputs = with python3.pkgs; [ pyserial pyaes ecdsa openssl ]; + checkInputs = with python3.pkgs; [ flake8 flake8-future-import flake8-import-order openssl ]; + propagatedBuildInputs = with python3.pkgs; [ pyserial pyaes ecdsa ]; meta = with stdenv.lib; { description = "ESP8266 and ESP32 serial bootloader utility"; From 30340239768cf33b4b1b80671315a3dda1a19bf4 Mon Sep 17 00:00:00 2001 From: makefu Date: Wed, 9 Jan 2019 15:13:54 +0100 Subject: [PATCH 224/247] exfat-nofuse: fix build for 4.18 additionally we use the PR 137 instead of the patch files from AUR. This avoids changes in source files and pins the patch to exactly what we want It also removes one fetchpatch call --- pkgs/os-specific/linux/exfat/default.nix | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/pkgs/os-specific/linux/exfat/default.nix b/pkgs/os-specific/linux/exfat/default.nix index 6120c707ba73..036cd3f28a1b 100644 --- a/pkgs/os-specific/linux/exfat/default.nix +++ b/pkgs/os-specific/linux/exfat/default.nix @@ -28,16 +28,12 @@ stdenv.mkDerivation rec { ''; patches = [ - # fix compile-errors in 4.18 + # fix compile-errors in 4.18 and 4.20 + # ref: https://github.com/dorimanx/exfat-nofuse/pull/137 (fetchpatch { - url = https://aur.archlinux.org/cgit/aur.git/plain/4.18.patch?h=exfat-dkms-git; - sha256 = "18l5h631w8yja7m2kkcf9h335pvlxms23ls539i81nf6xd6yvd78"; + url = https://github.com/dorimanx/exfat-nofuse/compare/01c30ad52625a7261e1b0d874553b6ca7af25966...f93a47e6414d567a1e7f6ab7f34b015b20f9a050.patch ; + sha256 = "0w57pi9h6dwjxfgc3zpwy6sr4zw42hn1zj72f7wgfpqrx6d8xkh5"; } ) - # fix compile-errors in 4.20 - (fetchpatch { - url = https://aur.archlinux.org/cgit/aur.git/plain/4.20.patch?h=exfat-dkms-git; - sha256 = "05l5x5yvd4vlvnr1bjl751gzcylvm3g9551fqdx7lqphhyiyv3bc"; - }) ]; meta = { From ec3e81beafacce0088baf50c116a26460000c012 Mon Sep 17 00:00:00 2001 From: Tim Steinbach Date: Wed, 9 Jan 2019 11:03:10 -0500 Subject: [PATCH 225/247] linux: 4.9.148 -> 4.9.149 --- pkgs/os-specific/linux/kernel/linux-4.9.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/os-specific/linux/kernel/linux-4.9.nix b/pkgs/os-specific/linux/kernel/linux-4.9.nix index 5cca257cef23..2b2d3647c21d 100644 --- a/pkgs/os-specific/linux/kernel/linux-4.9.nix +++ b/pkgs/os-specific/linux/kernel/linux-4.9.nix @@ -1,11 +1,11 @@ { stdenv, buildPackages, fetchurl, perl, buildLinux, ... } @ args: buildLinux (args // rec { - version = "4.9.148"; + version = "4.9.149"; extraMeta.branch = "4.9"; src = fetchurl { url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz"; - sha256 = "1559i06mcsa1d0kfnf6q1k5fldz2pbkrpg4snwddxa1508diarv0"; + sha256 = "10yp6pf91h927bxnb32qd6y13m0a230d44gp70ifd6cg5ssd6nqn"; }; } // (args.argsOverride or {})) From d55b3c9bf03ea916fcdd9fac985d26b0c7c9e125 Mon Sep 17 00:00:00 2001 From: Tim Steinbach Date: Wed, 9 Jan 2019 11:24:45 -0500 Subject: [PATCH 226/247] linux: 4.14.91 -> 4.14.92 --- pkgs/os-specific/linux/kernel/linux-4.14.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/os-specific/linux/kernel/linux-4.14.nix b/pkgs/os-specific/linux/kernel/linux-4.14.nix index bebfe402af06..d97b921dbae3 100644 --- a/pkgs/os-specific/linux/kernel/linux-4.14.nix +++ b/pkgs/os-specific/linux/kernel/linux-4.14.nix @@ -3,7 +3,7 @@ with stdenv.lib; buildLinux (args // rec { - version = "4.14.91"; + version = "4.14.92"; # modDirVersion needs to be x.y.z, will automatically add .0 if needed modDirVersion = if (modDirVersionArg == null) then concatStrings (intersperse "." (take 3 (splitString "." "${version}.0"))) else modDirVersionArg; @@ -13,6 +13,6 @@ buildLinux (args // rec { src = fetchurl { url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz"; - sha256 = "1ad6dkvfvqabr4d1vb8li06zbc1dikd2w31b13x8x4b0865pqn3a"; + sha256 = "1ba5sx66b4wlxz4ix5qm2vhla7fl01dd81xjx5nl0zm4m6miz7sz"; }; } // (args.argsOverride or {})) From 39173bff8731fd71b526653e5b099c0717ba325d Mon Sep 17 00:00:00 2001 From: Tim Steinbach Date: Wed, 9 Jan 2019 11:59:13 -0500 Subject: [PATCH 227/247] linux: 4.20 -> 4.20.1 --- pkgs/os-specific/linux/kernel/linux-4.20.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/os-specific/linux/kernel/linux-4.20.nix b/pkgs/os-specific/linux/kernel/linux-4.20.nix index 838ef4a5b805..042afd732946 100644 --- a/pkgs/os-specific/linux/kernel/linux-4.20.nix +++ b/pkgs/os-specific/linux/kernel/linux-4.20.nix @@ -3,7 +3,7 @@ with stdenv.lib; buildLinux (args // rec { - version = "4.20"; + version = "4.20.1"; # modDirVersion needs to be x.y.z, will automatically add .0 if needed modDirVersion = if (modDirVersionArg == null) then concatStrings (intersperse "." (take 3 (splitString "." "${version}.0"))) else modDirVersionArg; @@ -13,6 +13,6 @@ buildLinux (args // rec { src = fetchurl { url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz"; - sha256 = "0f14l6mb5c4rwpqjbcb2yrvk1bmmiyh0mpw24fbl7rr26lc2625d"; + sha256 = "13qrsbfmhjjn97cd0pv40i7m7gxbgv5adkzfyvpcvd7vzcgny2a5"; }; } // (args.argsOverride or {})) From 20f9b5d10a07404a518abc331cd0bcc981944e6a Mon Sep 17 00:00:00 2001 From: Tim Steinbach Date: Wed, 9 Jan 2019 12:10:11 -0500 Subject: [PATCH 228/247] linux: 4.19.13 -> 4.19.14 --- pkgs/os-specific/linux/kernel/linux-4.19.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/os-specific/linux/kernel/linux-4.19.nix b/pkgs/os-specific/linux/kernel/linux-4.19.nix index a9e11449d181..89c9e7207226 100644 --- a/pkgs/os-specific/linux/kernel/linux-4.19.nix +++ b/pkgs/os-specific/linux/kernel/linux-4.19.nix @@ -3,7 +3,7 @@ with stdenv.lib; buildLinux (args // rec { - version = "4.19.13"; + version = "4.19.14"; # modDirVersion needs to be x.y.z, will automatically add .0 if needed modDirVersion = if (modDirVersionArg == null) then concatStrings (intersperse "." (take 3 (splitString "." "${version}.0"))) else modDirVersionArg; @@ -13,6 +13,6 @@ buildLinux (args // rec { src = fetchurl { url = "mirror://kernel/linux/kernel/v4.x/linux-${version}.tar.xz"; - sha256 = "1hn0mimh0x13gin28l6dfic21533ja8zlihkg43c8gz183y7f2pm"; + sha256 = "0ihwywjz2jddrcd1883sy27b43mz212asrdiimnih82ivm4nhci4"; }; } // (args.argsOverride or {})) From 654f3c467cbb9caf09432ae4ef590ea0783e764c Mon Sep 17 00:00:00 2001 From: Orivej Desh Date: Wed, 9 Jan 2019 18:42:33 +0000 Subject: [PATCH 229/247] go-mtpfs: 20150917 -> 2018-02-09 --- pkgs/tools/filesystems/go-mtpfs/default.nix | 6 +++--- pkgs/tools/filesystems/go-mtpfs/deps.nix | 14 ++++++++++++-- 2 files changed, 15 insertions(+), 5 deletions(-) diff --git a/pkgs/tools/filesystems/go-mtpfs/default.nix b/pkgs/tools/filesystems/go-mtpfs/default.nix index 0438b9c38e4b..c1d41ff1622c 100644 --- a/pkgs/tools/filesystems/go-mtpfs/default.nix +++ b/pkgs/tools/filesystems/go-mtpfs/default.nix @@ -2,8 +2,8 @@ buildGoPackage rec { name = "go-mtpfs-${version}"; - version = "20150917-${stdenv.lib.strings.substring 0 7 rev}"; - rev = "bc7c0f716e3b4ed5610069a55fc00828ebba890b"; + version = "2018-02-09"; + rev = "d6f8f3c05ce0ed31435057ec342268a0735863bb"; goPackagePath = "github.com/hanwen/go-mtpfs"; @@ -13,7 +13,7 @@ buildGoPackage rec { src = fetchgit { inherit rev; url = "https://github.com/hanwen/go-mtpfs"; - sha256 = "1jcqp9n8fd9psfsnhfj6w97yp0zmyxplsig8pyp2gqzh4lnb5fqm"; + sha256 = "0a0d5dy92nzp1czh87hx3xfdcpa4jh14j0b64c025ha62s9a4gxk"; }; goDeps = ./deps.nix; diff --git a/pkgs/tools/filesystems/go-mtpfs/deps.nix b/pkgs/tools/filesystems/go-mtpfs/deps.nix index 4bba3f237392..f558a53f7d2d 100644 --- a/pkgs/tools/filesystems/go-mtpfs/deps.nix +++ b/pkgs/tools/filesystems/go-mtpfs/deps.nix @@ -1,11 +1,12 @@ +# This file was generated by https://github.com/kamilchm/go2nix v1.3.0 [ { goPackagePath = "github.com/hanwen/go-fuse"; fetch = { type = "git"; url = "https://github.com/hanwen/go-fuse"; - rev = "bd746dd8bcc8c059a9d953a786a6156eb83f398e"; - sha256 = "1dvvclp418j3d02v9717sfqhl6fw6yyddr9r3j8gsiv8nb62ib56"; + rev = "d1c826d19ad0c8d0c7e5b4eb34ee0f2ae09f6cef"; + sha256 = "0hn2iqsb6rip2b05fvcngyh0sazln2h3fx18khq4fv41n1iy11dc"; }; } { @@ -17,4 +18,13 @@ sha256 = "01k0c2g395j65vm1w37mmrfkg6nm900khjrrizzpmx8f8yf20dky"; }; } + { + goPackagePath = "golang.org/x/sys"; + fetch = { + type = "git"; + url = "https://go.googlesource.com/sys"; + rev = "48ac38b7c8cbedd50b1613c0fccacfc7d88dfcdf"; + sha256 = "037vs8sdvq310j3b6z9k62zlby1mzmsr9ha01rcy98dv5v8bkhin"; + }; + } ] From 84e1e62730ec1134f0d22eadfaf22fd3f6e71328 Mon Sep 17 00:00:00 2001 From: Andreas Rammhold Date: Wed, 9 Jan 2019 22:08:24 +0100 Subject: [PATCH 230/247] gopass: 1.8.3 -> 1.8.4 --- pkgs/tools/security/gopass/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/tools/security/gopass/default.nix b/pkgs/tools/security/gopass/default.nix index 2242a9c109e4..33b60ae6fe26 100644 --- a/pkgs/tools/security/gopass/default.nix +++ b/pkgs/tools/security/gopass/default.nix @@ -1,7 +1,7 @@ { stdenv, buildGoPackage, fetchFromGitHub, git, gnupg, xclip, makeWrapper }: buildGoPackage rec { - version = "1.8.3"; + version = "1.8.4"; name = "gopass-${version}"; goPackagePath = "github.com/gopasspw/gopass"; @@ -12,7 +12,7 @@ buildGoPackage rec { owner = "gopasspw"; repo = "gopass"; rev = "v${version}"; - sha256 = "1m4dmydgbpyrqv0blbrw66f2340c6hbz2wg22mpybf0zvd5i9ba6"; + sha256 = "1gw16k09vwarh5qz118s7w2j090phdrrgd2h1q52pv93jpi3br7n"; }; wrapperPath = with stdenv.lib; makeBinPath ([ From 590f267c5b4786449ac1d317cd3fc11b16e21538 Mon Sep 17 00:00:00 2001 From: Andreas Rammhold Date: Wed, 9 Jan 2019 22:16:22 +0100 Subject: [PATCH 231/247] gitAndTools.grv: 0.3.0 -> 0.3.1 --- .../version-management/git-and-tools/grv/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/version-management/git-and-tools/grv/default.nix b/pkgs/applications/version-management/git-and-tools/grv/default.nix index afd187ebb55b..c70f69965291 100644 --- a/pkgs/applications/version-management/git-and-tools/grv/default.nix +++ b/pkgs/applications/version-management/git-and-tools/grv/default.nix @@ -1,6 +1,6 @@ { stdenv, buildGo19Package, fetchFromGitHub, curl, libgit2, ncurses, pkgconfig, readline }: let - version = "0.3.0"; + version = "0.3.1"; in buildGo19Package { name = "grv-${version}"; @@ -14,7 +14,7 @@ buildGo19Package { owner = "rgburke"; repo = "grv"; rev = "v${version}"; - sha256 = "00v502mwnpv09l7fsbq3s72i5fz5dxbildwxgw0r8zzf6d54xrgl"; + sha256 = "16ylapsibqrqwx45l4ypr3av07rd1haf10v838mjqsakf8l1xc0b"; fetchSubmodules = true; }; From ff01f0ae19661bf36fca67cf637895eed49061bc Mon Sep 17 00:00:00 2001 From: Andreas Rammhold Date: Wed, 9 Jan 2019 22:20:19 +0100 Subject: [PATCH 232/247] ecdsautils: updated source to new location --- pkgs/tools/security/ecdsautils/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/tools/security/ecdsautils/default.nix b/pkgs/tools/security/ecdsautils/default.nix index 2766c2c07a4f..48a713287b8b 100644 --- a/pkgs/tools/security/ecdsautils/default.nix +++ b/pkgs/tools/security/ecdsautils/default.nix @@ -5,7 +5,7 @@ stdenv.mkDerivation rec { name = "ecdsautils-${version}"; src = pkgs.fetchFromGitHub { - owner = "tcatm"; + owner = "freifunk-gluon"; repo = "ecdsautils"; rev = "07538893fb6c2a9539678c45f9dbbf1e4f222b46"; sha256 = "18sr8x3qiw8s9l5pfi7r9i3ayplz4jqdml75ga9y933vj7vs0k4d"; From 02b1b8eaf33d8574d8e29c4394fe99d79c47be17 Mon Sep 17 00:00:00 2001 From: Andreas Rammhold Date: Wed, 9 Jan 2019 22:27:48 +0100 Subject: [PATCH 233/247] websocketpp: 0.7.0 -> 0.8.1 --- pkgs/development/libraries/websocket++/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/websocket++/default.nix b/pkgs/development/libraries/websocket++/default.nix index 8a0ec2523b94..d84f30aad55b 100644 --- a/pkgs/development/libraries/websocket++/default.nix +++ b/pkgs/development/libraries/websocket++/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "websocket++-${version}"; - version = "0.7.0"; + version = "0.8.1"; src = fetchFromGitHub { owner = "zaphoyd"; repo = "websocketpp"; rev = version; - sha256 = "1i64sps52kvy8yffysjbmmbb109pi28kqai0qdxxz1dcj3xfckqd"; + sha256 = "12ffczcrryh74c1xssww35ic6yiy2l2xgdd30lshiq9wnzl2brgy"; }; buildInputs = [ cmake ]; From 36b09654f06f84855af6285c589cde6a371c7428 Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Mon, 7 Jan 2019 15:50:46 -0800 Subject: [PATCH 234/247] librealsense: 2.17.0 -> 2.17.1 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/librealsense/versions --- pkgs/development/libraries/librealsense/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/libraries/librealsense/default.nix b/pkgs/development/libraries/librealsense/default.nix index 0487010d11e8..d19d5ac1fbfd 100644 --- a/pkgs/development/libraries/librealsense/default.nix +++ b/pkgs/development/libraries/librealsense/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "librealsense-${version}"; - version = "2.17.0"; + version = "2.17.1"; src = fetchFromGitHub { owner = "IntelRealSense"; repo = "librealsense"; rev = "v${version}"; - sha256 = "1ac580yhxmvxpdvlzdzpcdffysr6z3dl8dykndnq5758alkyspd7"; + sha256 = "0nxb1vyq7gimv61w0gba2ilbnnmnjac94bk1ikcmdgkymdfwn6zj"; }; buildInputs = [ From 8dd63a67e9f5b6711614bd226c24b3cdaa0a04dc Mon Sep 17 00:00:00 2001 From: Timo Kaufmann Date: Thu, 10 Jan 2019 00:10:34 +0100 Subject: [PATCH 235/247] python3.pkgs.graph-tool: fix with python3.7 (#53719) "async" is now reserved, there is an upstream fix but no release yet. --- pkgs/development/python-modules/graph-tool/2.x.x.nix | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/pkgs/development/python-modules/graph-tool/2.x.x.nix b/pkgs/development/python-modules/graph-tool/2.x.x.nix index d58ec2690546..4b0e665de098 100644 --- a/pkgs/development/python-modules/graph-tool/2.x.x.nix +++ b/pkgs/development/python-modules/graph-tool/2.x.x.nix @@ -3,6 +3,8 @@ , gobject-introspection, pygobject3, gtk3, matplotlib, ncurses , buildPythonPackage , fetchpatch +, pythonAtLeast +, lib }: buildPythonPackage rec { @@ -29,7 +31,14 @@ buildPythonPackage rec { url = "https://git.skewed.de/count0/graph-tool/commit/aa39e4a6b42d43fac30c841d176c75aff92cc01a.patch"; sha256 = "1578inb4jqwq2fhhwscn5z95nzmaxvmvk30nzs5wirr26iznap4m"; }) - ]; + ] ++ (lib.optionals (pythonAtLeast "3.7") [ + # # python 3.7 compatibility (`async` is now reserved) + (fetchpatch { + name = "async-reserved.patch"; + url = "https://git.skewed.de/count0/graph-tool/commit/0407f41a35b6be7c670927fb5dc578cbd0e88be4.patch"; + sha256 = "1fklznhmfvbb3ykwzyf8p2hiczby6y7r0xnkkjl2jkxlvr24000q"; + }) + ]); configureFlags = [ "--with-python-module-path=$(out)/${python.sitePackages}" From 81f3a3e7c6491a917d299b5333c91b2a10350a6a Mon Sep 17 00:00:00 2001 From: Roman Volosatovs Date: Sun, 6 Jan 2019 21:30:13 +0100 Subject: [PATCH 236/247] kitty: 0.13.1 -> 0.13.2 --- pkgs/applications/misc/kitty/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/misc/kitty/default.nix b/pkgs/applications/misc/kitty/default.nix index d3f20f0282f7..dfc2595475ad 100644 --- a/pkgs/applications/misc/kitty/default.nix +++ b/pkgs/applications/misc/kitty/default.nix @@ -7,7 +7,7 @@ with python3Packages; buildPythonApplication rec { - version = "0.13.1"; + version = "0.13.2"; name = "kitty-${version}"; format = "other"; @@ -15,7 +15,7 @@ buildPythonApplication rec { owner = "kovidgoyal"; repo = "kitty"; rev = "v${version}"; - sha256 = "1j24zjasdh48z7majfpqr71n1wn5a9688wsmmqn26v8kfb68pqs4"; + sha256 = "1w93fq4rks6va0aapz6f6l1cn6zhchrfq8fv39xb6x0llx78dimx"; }; buildInputs = [ From 87f798edc6abc6d52eb0d2609e57f181e3db91d8 Mon Sep 17 00:00:00 2001 From: Roman Volosatovs Date: Sun, 6 Jan 2019 21:35:18 +0100 Subject: [PATCH 237/247] kitty: Adapt fix-paths.patch to source changes --- pkgs/applications/misc/kitty/fix-paths.patch | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/misc/kitty/fix-paths.patch b/pkgs/applications/misc/kitty/fix-paths.patch index e22f4570a4b7..d6e52adc4452 100644 --- a/pkgs/applications/misc/kitty/fix-paths.patch +++ b/pkgs/applications/misc/kitty/fix-paths.patch @@ -6,8 +6,8 @@ static bool done = false; - static const char* libname = "libstartup-notification-1.so"; + static const char* libname = "@libstartup_notification@"; - if (!done) { - done = true; + // some installs are missing the .so symlink, so try the full name + static const char* libname2 = "libstartup-notification-1.so.0"; --- a/docs/Makefile +++ b/docs/Makefile From 686ed2cbca16d755818d97e0d52e5085066484cc Mon Sep 17 00:00:00 2001 From: "R. RyanTM" Date: Sun, 6 Jan 2019 23:48:46 -0800 Subject: [PATCH 238/247] python37Packages.elpy: 1.27.0 -> 1.28.0 Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/python3.7-elpy/versions --- pkgs/development/python-modules/elpy/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/development/python-modules/elpy/default.nix b/pkgs/development/python-modules/elpy/default.nix index 6c22236892e5..3816a8c42e70 100644 --- a/pkgs/development/python-modules/elpy/default.nix +++ b/pkgs/development/python-modules/elpy/default.nix @@ -11,11 +11,11 @@ buildPythonPackage rec { pname = "elpy"; - version = "1.27.0"; + version = "1.28.0"; src = fetchPypi { inherit pname version; - sha256 = "0fpxxmxjzcam3kharbmvprf4kagspya1rx9piacmxbgcp6w2lc4s"; + sha256 = "0lx6bf6ajx6wmnns03gva5sh1mmmxahjaqrn735cgwn6j4ikyqfs"; }; propagatedBuildInputs = [ flake8 autopep8 jedi importmagic ] From 8786617f8f8c613536682709d028fb0232c45ff8 Mon Sep 17 00:00:00 2001 From: wedens Date: Wed, 2 Jan 2019 23:06:45 +0700 Subject: [PATCH 239/247] dropbox-cli: 2015.10.28 -> 2018.11.28 --- pkgs/applications/networking/dropbox/cli.nix | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pkgs/applications/networking/dropbox/cli.nix b/pkgs/applications/networking/dropbox/cli.nix index d3141675b418..fc6cc61787fa 100644 --- a/pkgs/applications/networking/dropbox/cli.nix +++ b/pkgs/applications/networking/dropbox/cli.nix @@ -1,14 +1,14 @@ { stdenv, pkgconfig, fetchurl, python, dropbox }: let - version = "2015.10.28"; + version = "2018.11.28"; dropboxd = "${dropbox}/bin/dropbox"; in stdenv.mkDerivation { name = "dropbox-cli-${version}"; src = fetchurl { - url = "https://linux.dropbox.com/packages/nautilus-dropbox-${version}.tar.bz2"; - sha256 = "1ai6vi5227z2ryxl403693xi63b42ylyfmzh8hbv4shp69zszm9c"; + url = "https://linux.dropboxstatic.com/packages/nautilus-dropbox-${version}.tar.bz2"; + sha256 = "0m1m9c7dfc8nawkcrg88955125sl1jz8mc9bf6wjay9za8014w58"; }; nativeBuildInputs = [ pkgconfig ]; From 96bffeb8654e6b18fd5ff80c8f23350a160fd4f2 Mon Sep 17 00:00:00 2001 From: Lily Ballard Date: Wed, 9 Jan 2019 18:18:59 -0800 Subject: [PATCH 240/247] hexyl: init at 0.3.0 --- pkgs/tools/misc/hexyl/default.nix | 29 +++++++++++++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 ++ 2 files changed, 31 insertions(+) create mode 100644 pkgs/tools/misc/hexyl/default.nix diff --git a/pkgs/tools/misc/hexyl/default.nix b/pkgs/tools/misc/hexyl/default.nix new file mode 100644 index 000000000000..6787549e053b --- /dev/null +++ b/pkgs/tools/misc/hexyl/default.nix @@ -0,0 +1,29 @@ +{ stdenv, fetchFromGitHub, rustPlatform }: + +rustPlatform.buildRustPackage rec { + name = "hexyl-${version}"; + version = "0.3.0"; + + src = fetchFromGitHub { + owner = "sharkdp"; + repo = "hexyl"; + rev = "v${version}"; + sha256 = "138w6czi62dpw6gcd3yqpk7lns7m89kwbgm1d1i5lnzsqck3wb4s"; + }; + + cargoSha256 = "01m8n7yl3yqr8kj0dl1wfaz724da17hs3sb1fbncv64l6qpvdka1"; + + meta = with stdenv.lib; { + description = "A command-line hex viewer"; + longDescription = '' + `hexyl` is a simple hex viewer for the terminal. It uses a colored + output to distinguish different categories of bytes (NULL bytes, + printable ASCII characters, ASCII whitespace characters, other ASCII + characters and non-ASCII). + ''; + homepage = https://github.com/sharkdp/hexyl; + license = with licenses; [ asl20 /* or */ mit ]; + maintainers = []; + platforms = platforms.linux ++ platforms.darwin; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 20d682fcedba..ffe4dda6b7fc 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -1498,6 +1498,8 @@ in hexio = callPackage ../development/tools/hexio { }; + hexyl = callPackage ../tools/misc/hexyl { }; + hid-listen = callPackage ../tools/misc/hid-listen { }; home-manager = callPackage ../tools/package-management/home-manager {}; From 1a7e65e1466ffaeff6d1f01f5d98f60a6dc41ce6 Mon Sep 17 00:00:00 2001 From: Dmitry Kalinkin Date: Wed, 9 Jan 2019 21:46:58 -0500 Subject: [PATCH 241/247] adv_cmds: switch url to use https warning: unable to download 'http://opensource.apple.com/tarballs/adv_cmds/adv_cmds-158.tar.gz': HTTP error 302 (curl error: Couldn't connect to server); retrying in 298 ms --- .../darwin/apple-source-releases/adv_cmds/default.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/os-specific/darwin/apple-source-releases/adv_cmds/default.nix b/pkgs/os-specific/darwin/apple-source-releases/adv_cmds/default.nix index 80d57484ecc7..1d8ebac74b0e 100644 --- a/pkgs/os-specific/darwin/apple-source-releases/adv_cmds/default.nix +++ b/pkgs/os-specific/darwin/apple-source-releases/adv_cmds/default.nix @@ -11,7 +11,7 @@ # the more recent adv_cmds release is used for everything else in this package let recentAdvCmds = fetchzip { - url = "http://opensource.apple.com/tarballs/adv_cmds/adv_cmds-158.tar.gz"; + url = "https://opensource.apple.com/tarballs/adv_cmds/adv_cmds-158.tar.gz"; sha256 = "0z081kcprzg5jcvqivfnwvvv6wfxzkjg2jc2lagsf8c7j7vgm8nn"; }; From a11995a3288d1c16029eb186f9ad20a471b624ad Mon Sep 17 00:00:00 2001 From: Alex Brandt Date: Wed, 9 Jan 2019 18:53:45 -0800 Subject: [PATCH 242/247] maintainer-list.nix: update alunduil's email address I've switched emails lately and would like hydra and other utilities to use the new address for any packages still in my name. --- maintainers/maintainer-list.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/maintainers/maintainer-list.nix b/maintainers/maintainer-list.nix index 2d892408712d..29526759629d 100644 --- a/maintainers/maintainer-list.nix +++ b/maintainers/maintainer-list.nix @@ -217,7 +217,7 @@ name = "Nix Committers"; }; alunduil = { - email = "alunduil@alunduil.com"; + email = "alunduil@gmail.com"; github = "alunduil"; name = "Alex Brandt"; }; From 4b95e496e1fad47d2a57dbd39b6ca531ee3c852c Mon Sep 17 00:00:00 2001 From: Franz Pletz Date: Thu, 10 Jan 2019 05:49:12 +0100 Subject: [PATCH 243/247] minetest: refactor and add dev version 5 --- pkgs/games/minetest/default.nix | 122 ++++++++++++++++++++------------ pkgs/top-level/all-packages.nix | 8 ++- 2 files changed, 82 insertions(+), 48 deletions(-) diff --git a/pkgs/games/minetest/default.nix b/pkgs/games/minetest/default.nix index 379794c1f863..110403af2ac7 100644 --- a/pkgs/games/minetest/default.nix +++ b/pkgs/games/minetest/default.nix @@ -1,56 +1,88 @@ { stdenv, fetchFromGitHub, cmake, irrlicht, libpng, bzip2, curl, libogg, jsoncpp , libjpeg, libXxf86vm, libGLU_combined, openal, libvorbis, xlibsWrapper, sqlite, luajit -, freetype, gettext, doxygen, ncurses, leveldb +, freetype, gettext, doxygen, ncurses, graphviz, xorg +, leveldb, postgresql, hiredis }: +with stdenv.lib; + let - version = "0.4.17.1"; - sources = { - src = fetchFromGitHub { - owner = "minetest"; - repo = "minetest"; - rev = "${version}"; - sha256 = "19sfblgh9mchkgw32n7gdvm7a8a9jxsl9cdlgmxn9bk9m939a2sg"; + boolToCMake = b: if b then "ON" else "OFF"; + + generic = { version, rev ? version, sha256, dataRev ? version, dataSha256, buildClient ? true, buildServer ? false }: let + sources = { + src = fetchFromGitHub { + owner = "minetest"; + repo = "minetest"; + inherit rev sha256; + }; + data = fetchFromGitHub { + owner = "minetest"; + repo = "minetest_game"; + rev = dataRev; + sha256 = dataSha256; + }; }; - data = fetchFromGitHub { - owner = "minetest"; - repo = "minetest_game"; - rev = "${version}"; - sha256 = "1g8iw2pya32ifljbdx6z6rpcinmzm81i9minhi2bi1d500ailn7s"; + in stdenv.mkDerivation { + name = "minetest-${version}"; + + src = sources.src; + + cmakeFlags = [ + "-DBUILD_CLIENT=${boolToCMake buildClient}" + "-DBUILD_SERVER=${boolToCMake buildServer}" + "-DENABLE_FREETYPE=1" + "-DENABLE_GETTEXT=1" + "-DENABLE_SYSTEM_JSONCPP=1" + "-DIRRLICHT_INCLUDE_DIR=${irrlicht}/include/irrlicht" + ] ++ optionals buildClient [ + "-DOpenGL_GL_PREFERENCE=GLVND" + ]; + + NIX_CFLAGS_COMPILE = [ "-DluaL_reg=luaL_Reg" ]; # needed since luajit-2.1.0-beta3 + + nativeBuildInputs = [ cmake doxygen graphviz ]; + + buildInputs = [ + irrlicht luajit jsoncpp gettext freetype sqlite curl bzip2 ncurses + ] ++ optionals buildClient [ + libpng libjpeg libGLU_combined openal libogg libvorbis xorg.libX11 libXxf86vm + ] ++ optional buildServer [ + leveldb postgresql hiredis + ]; + + postInstall = '' + mkdir -pv $out/share/minetest/games/minetest_game/ + cp -rv ${sources.data}/* $out/share/minetest/games/minetest_game/ + ''; + + meta = with stdenv.lib; { + homepage = http://minetest.net/; + description = "Infinite-world block sandbox game"; + license = licenses.lgpl21Plus; + platforms = platforms.linux; + maintainers = with maintainers; [ jgeerds c0dehero fpletz ]; }; }; -in stdenv.mkDerivation { - name = "minetest-${version}"; - src = sources.src; - - cmakeFlags = [ - "-DENABLE_FREETYPE=1" - "-DENABLE_GETTEXT=1" - "-DENABLE_SYSTEM_JSONCPP=1" - "-DGETTEXT_INCLUDE_DIR=${gettext}/include/gettext" - "-DCURL_INCLUDE_DIR=${curl.dev}/include/curl" - "-DIRRLICHT_INCLUDE_DIR=${irrlicht}/include/irrlicht" - ]; - - NIX_CFLAGS_COMPILE = [ "-DluaL_reg=luaL_Reg" ]; # needed since luajit-2.1.0-beta3 - - buildInputs = [ - cmake irrlicht libpng bzip2 libjpeg curl libogg jsoncpp libXxf86vm libGLU_combined - openal libvorbis xlibsWrapper sqlite luajit freetype gettext doxygen ncurses - leveldb - ]; - - postInstall = '' - mkdir -pv $out/share/minetest/games/minetest_game/ - cp -rv ${sources.data}/* $out/share/minetest/games/minetest_game/ - ''; - - meta = with stdenv.lib; { - homepage = http://minetest.net/; - description = "Infinite-world block sandbox game"; - license = licenses.lgpl21Plus; - platforms = platforms.linux; - maintainers = with maintainers; [ jgeerds c0dehero ]; + v4 = { + version = "0.4.17.1"; + sha256 = "19sfblgh9mchkgw32n7gdvm7a8a9jxsl9cdlgmxn9bk9m939a2sg"; + dataSha256 = "1g8iw2pya32ifljbdx6z6rpcinmzm81i9minhi2bi1d500ailn7s"; }; + + v5 = { + version = "git-5.0.0-dev-2019-01-08"; + rev = "95d4ff6d1b62945decc85003a99588bb0539c45b"; + sha256 = "1qn42d2lfgwadb26mix6c7j457zsl8cqqjfwhaa8y34hii1q44bw"; + dataRev = "a2c9523bce5bcefdc930ff6f14d6d94f57473be9"; + dataSha256 = "1p26zvnmq99cqlrby4294mp2fmp8iqdcjld0ph39x41ifc50lfdf"; + }; + +in { + minetestclient_4 = generic (v4 // { buildClient = true; buildServer = false; }); + minetestserver_4 = generic (v4 // { buildClient = false; buildServer = true; }); + + minetestclient_5 = generic (v5 // { buildClient = true; buildServer = false; }); + minetestserver_5 = generic (v5 // { buildClient = false; buildServer = true; }); } diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 20d682fcedba..5d57d226e20f 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -20757,9 +20757,11 @@ in multimc = libsForQt5.callPackage ../games/multimc { }; - minetest = callPackage ../games/minetest { - libpng = libpng12; - }; + inherit (callPackages ../games/minetest { }) + minetestclient_4 minetestserver_4 + minetestclient_5 minetestserver_5; + + minetest = minetestclient_4; mnemosyne = callPackage ../games/mnemosyne { python = python3; From bf5f85ea2e38284ef2c23bdd211ebfb7c80a002b Mon Sep 17 00:00:00 2001 From: Franz Pletz Date: Thu, 10 Jan 2019 05:50:10 +0100 Subject: [PATCH 244/247] rambox: update node deps hash --- pkgs/applications/networking/instant-messengers/rambox/bare.nix | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pkgs/applications/networking/instant-messengers/rambox/bare.nix b/pkgs/applications/networking/instant-messengers/rambox/bare.nix index 29ed30dd27f6..0dece5856bb3 100644 --- a/pkgs/applications/networking/instant-messengers/rambox/bare.nix +++ b/pkgs/applications/networking/instant-messengers/rambox/bare.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { inherit src; nodejs = nodejs-8_x; - sha256 = "03h1kfiaflwbrvcd8v0bsymn7n2dxi3yj4pxkwcigqg4jgcf56k6"; + sha256 = "1m883gjxcihnik88fyj54f4z4m786pwl3a90k151v9bnbslf3k6i"; }; patches = [ ./isDev.patch ]; From 8fc21a347e06c11afeba08ca8a868a4537e51f5f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Domen=20Ko=C5=BEar?= Date: Thu, 10 Jan 2019 09:56:29 +0000 Subject: [PATCH 245/247] elm2nix: use package from hackage --- pkgs/development/tools/elm2nix/default.nix | 24 ---------------------- pkgs/top-level/all-packages.nix | 2 +- 2 files changed, 1 insertion(+), 25 deletions(-) delete mode 100644 pkgs/development/tools/elm2nix/default.nix diff --git a/pkgs/development/tools/elm2nix/default.nix b/pkgs/development/tools/elm2nix/default.nix deleted file mode 100644 index 2d4ebc37b0c9..000000000000 --- a/pkgs/development/tools/elm2nix/default.nix +++ /dev/null @@ -1,24 +0,0 @@ -{ mkDerivation, aeson, ansi-wl-pprint, async, base, binary -, bytestring, containers, data-default, directory, filepath, here -, mtl, optparse-applicative, process, req, stdenv, text -, transformers, unordered-containers -}: -mkDerivation { - pname = "elm2nix"; - version = "0.1.0"; - sha256 = "9ec1f1f694a38b466ebd03aaa1a035bbdb9bdae390be5b9a030611bcbfd91890"; - isLibrary = true; - isExecutable = true; - libraryHaskellDepends = [ - aeson async base binary bytestring containers data-default - directory filepath here mtl process req text transformers - unordered-containers - ]; - executableHaskellDepends = [ - ansi-wl-pprint base directory here optparse-applicative - ]; - testHaskellDepends = [ base ]; - homepage = "https://github.com/domenkozar/elm2nix#readme"; - description = "Turn your Elm project into buildable Nix project"; - license = stdenv.lib.licenses.bsd3; -} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 871bf5baea78..8adf17f8e4d4 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -6714,7 +6714,7 @@ in eql = callPackage ../development/compilers/eql {}; - elm2nix = haskell.lib.justStaticExecutables (haskellPackages.callPackage ../development/tools/elm2nix {}); + elm2nix = haskell.lib.justStaticExecutables haskellPackages.elm2nix; elmPackages = recurseIntoAttrs (callPackage ../development/compilers/elm { }); From c9c1e88dbbe36421108bd8c5c6b76d85fabab40b Mon Sep 17 00:00:00 2001 From: zimbatm Date: Thu, 10 Jan 2019 11:35:02 +0100 Subject: [PATCH 246/247] nomad: 0.7.1 -> 0.8.6 --- pkgs/applications/networking/cluster/nomad/default.nix | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pkgs/applications/networking/cluster/nomad/default.nix b/pkgs/applications/networking/cluster/nomad/default.nix index 8486f0d53067..5810951f095b 100644 --- a/pkgs/applications/networking/cluster/nomad/default.nix +++ b/pkgs/applications/networking/cluster/nomad/default.nix @@ -2,7 +2,7 @@ buildGoPackage rec { name = "nomad-${version}"; - version = "0.7.1"; + version = "0.8.6"; rev = "v${version}"; goPackagePath = "github.com/hashicorp/nomad"; @@ -12,7 +12,7 @@ buildGoPackage rec { owner = "hashicorp"; repo = "nomad"; inherit rev; - sha256 = "0hn80dqzxkwvk1zjk6px725mb2i3c06smqfj0yyjz96vgf7qbqy2"; + sha256 = "1786hbgby9q3p4x28xdc06v12n8qvxqwis70mr80axb6r4kd7yqw"; }; meta = with stdenv.lib; { From e0fd84cf439f39d31e2c317b228b0c035cc6211d Mon Sep 17 00:00:00 2001 From: Michael Raskin <7c6f434c@mail.ru> Date: Thu, 10 Jan 2019 12:05:31 +0100 Subject: [PATCH 247/247] sbcl: fix a thread safety bug with an upstream patch --- pkgs/development/compilers/sbcl/default.nix | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/pkgs/development/compilers/sbcl/default.nix b/pkgs/development/compilers/sbcl/default.nix index 3283555cd6ee..5f1c35815c32 100644 --- a/pkgs/development/compilers/sbcl/default.nix +++ b/pkgs/development/compilers/sbcl/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, writeText, sbclBootstrap +{ stdenv, fetchurl, fetchpatch, writeText, sbclBootstrap , sbclBootstrapHost ? "${sbclBootstrap}/bin/sbcl --disable-debugger --no-userinit --no-sysinit" , threadSupport ? (stdenv.isi686 || stdenv.isx86_64 || "aarch64-linux" == stdenv.hostPlatform.system) # Meant for sbcl used for creating binaries portable to non-NixOS via save-lisp-and-die. @@ -19,7 +19,19 @@ stdenv.mkDerivation rec { buildInputs = [texinfo]; + patches = [ + # 1.4.15 bug, run-program thread safety, remove for 1.4.16 + (fetchpatch { + url = "https://github.com/sbcl/sbcl/commit/c80672bedb1e4bc16124d0d01d7e37f94dd17a5a.patch"; + sha256 = "0pjm9yajwij59gdkqhid7sbgmb8z57cz8zrsikxg7yzfgr7sa7hy"; + }) + ]; + patchPhase = '' + for patch in ${toString patches}; do + patch -Np1 -i "$patch" + done + echo '"${version}.nixos"' > version.lisp-expr echo " (lambda (features)