Merge branch 'master' into haskell-updates

.github/CODEOWNERS

@@ -45,6 +45,7 @@
 /pkgs/build-support/setup-hooks                  @Ericson2314
 /pkgs/build-support/setup-hooks/auto-patchelf.sh @layus
 /pkgs/build-support/setup-hooks/auto-patchelf.py @layus
+/pkgs/pkgs-lib                                   @infinisil
 
 # Nixpkgs build-support
 /pkgs/build-support/writers @lassulus @Profpatsch

doc/builders/special/darwin-builder.section.md

@@ -61,3 +61,89 @@ builders-use-substitutes = true
 ```ShellSession
 $ sudo launchctl kickstart -k system/org.nixos.nix-daemon
 ```
+
+## Example flake usage
+
+```
+{
+  inputs = {
+    nixpkgs.url = "github:nixos/nixpkgs/nixpkgs-22.11-darwin";
+    darwin.url = "github:lnl7/nix-darwin/master";
+    darwin.inputs.nixpkgs.follows = "nixpkgs";
+  };
+
+  outputs = { self, darwin, nixpkgs, ... }@inputs:
+  let
+
+    inherit (darwin.lib) darwinSystem;
+    system = "aarch64-darwin";
+    pkgs = nixpkgs.legacyPackages."${system}";
+    linuxSystem = builtins.replaceStrings [ "darwin" ] [ "linux" ] system;
+
+    darwin-builder = nixpkgs.lib.nixosSystem {
+      system = linuxSystem;
+      modules = [
+        "${nixpkgs}/nixos/modules/profiles/macos-builder.nix"
+        { virtualisation.host.pkgs = pkgs; }
+      ];
+    };
+  in {
+
+    darwinConfigurations = {
+      machine1 = darwinSystem {
+        inherit system;
+        modules = [
+          {
+            nix.distributedBuilds = true;
+            nix.buildMachines = [{
+              hostName = "ssh://builder@localhost";
+              system = linuxSystem;
+              maxJobs = 4;
+              supportedFeatures = [ "kvm" "benchmark" "big-parallel" ];
+            }];
+
+            launchd.daemons.darwin-builder = {
+              command = "${darwin-builder.config.system.build.macos-builder-installer}/bin/create-builder";
+              serviceConfig = {
+                KeepAlive = true;
+                RunAtLoad = true;
+                StandardOutPath = "/var/log/darwin-builder.log";
+                StandardErrorPath = "/var/log/darwin-builder.log";
+              };
+            };
+          }
+        ];
+      };
+    };
+
+  };
+}
+```
+
+## Reconfiguring the builder
+
+Initially you should not change the builder configuration else you will not be
+able to use the binary cache. However, after you have the builder running locally
+you may use it to build a modified builder with additional storage or memory.
+
+To do this, you just need to set the `virtualisation.darwin-builder.*` parameters as
+in the example below and rebuild.
+
+```
+    darwin-builder = nixpkgs.lib.nixosSystem {
+      system = linuxSystem;
+      modules = [
+        "${nixpkgs}/nixos/modules/profiles/macos-builder.nix"
+        {
+          virtualisation.host.pkgs = pkgs;
+          virtualisation.darwin-builder.diskSize = 5120;
+          virtualisation.darwin-builder.memorySize = 1024;
+          virtualisation.darwin-builder.hostPort = 33022;
+          virtualisation.darwin-builder.workingDirectory = "/var/lib/darwin-builder";
+        }
+      ];
+```
+
+You may make any other changes to your VM in this attribute set. For example,
+you could enable Docker or X11 forwarding to your Darwin host.
+

maintainers/maintainer-list.nix

@@ -9449,6 +9449,12 @@
     githubId = 43853194;
     name = "Matheus Vieira";
   };
+  mathiassven = {
+    email = "github@mathiassven.com";
+    github = "MathiasSven";
+    githubId = 24759037;
+    name = "Mathias Sven";
+  };
   mathnerd314 = {
     email = "mathnerd314.gph+hs@gmail.com";
     github = "Mathnerd314";
@@ -17119,6 +17125,12 @@
     githubId = 20029431;
     name = "Zyansheep";
   };
+  zygot = {
+    email = "stefan.bordei13@gmail.com";
+    github = "stefan-bordei";
+    githubId = 71881325;
+    name = "Stefan Bordei";
+  };
   zzamboni = {
     email = "diego@zzamboni.org";
     github = "zzamboni";

nixos/doc/manual/release-notes/rl-2305.section.md

@@ -45,6 +45,8 @@ In addition to numerous new and upgraded packages, this release has the followin
 
 - [gmediarender](https://github.com/hzeller/gmrender-resurrect), a simple, headless UPnP/DLNA renderer.  Available as [services.gmediarender](options.html#opt-services.gmediarender.enable).
 
+- [hyprland](https://github.com/hyprwm/hyprland), a dynamic tiling Wayland compositor that doesn't sacrifice on its looks. Available as [programs.hyprland](#opt-programs.hyprland.enable).
+
 - [stevenblack-blocklist](https://github.com/StevenBlack/hosts), A unified hosts file with base extensions for blocking unwanted websites. Available as [networking.stevenblack](options.html#opt-networking.stevenblack.enable).
 
 - [Budgie Desktop](https://github.com/BuddiesOfBudgie/budgie-desktop), a familiar, modern desktop environment. Availabe as [services.xserver.desktopManager.budgie](options.html#opt-services.xserver.desktopManager.budgie).
@@ -215,6 +217,9 @@ In addition to numerous new and upgraded packages, this release has the followin
 
 - `go-ethereum` package has been updated to v1.11.5 and the `puppeth` command is no longer available as of v1.11.0.
 
+- The `pnpm` package has be updated to from version 7.29.1 to version 8.1.1 and Node.js 14 support has been discontinued (though, there are workarounds if Node.js 14 is still required)
+  - Migration instructions: ["Before updating pnpm to v8 in your CI, regenerate your pnpm-lock.yaml. To upgrade your lockfile, run pnpm install and commit the changes. Existing dependencies will not be updated; however, due to configuration changes in pnpm v8, some missing peer dependencies may be added to the lockfile and some packages may get deduplicated. You can commit the new lockfile even before upgrading Node.js in the CI, as pnpm v7 already supports the new lockfile format."](https://github.com/pnpm/pnpm/releases/tag/v8.0.0)
+
 ## Other Notable Changes {#sec-release-23.05-notable-changes}
 
 <!-- To avoid merge conflicts, consider adding your item at an arbitrary place in the list instead. -->
@@ -385,6 +390,8 @@ In addition to numerous new and upgraded packages, this release has the followin
 
 - Lisp gained a [manual section](https://nixos.org/manual/nixpkgs/stable/#lisp), documenting a new and backwards incompatible interface. The previous interface will be removed in a future release.
 
+- The `bind` module now allows the per-zone `allow-query` setting to be configured (previously it was hard-coded to `any`; it still defaults to `any` to retain compatibility).
+
 ## Detailed migration information {#sec-release-23.05-migration}
 
 ### Pipewire configuration overrides {#sec-release-23.05-migration-pipewire}

nixos/modules/module-list.nix

@@ -179,6 +179,7 @@
   ./programs/haguichi.nix
   ./programs/hamster.nix
   ./programs/htop.nix
+  ./programs/hyprland.nix
   ./programs/iay.nix
   ./programs/iftop.nix
   ./programs/i3lock.nix

nixos/modules/profiles/macos-builder.nix

@@ -7,6 +7,8 @@ let
 
   keyType = "ed25519";
 
+  cfg = config.virtualisation.darwin-builder;
+
 in
 
 {
@@ -24,156 +26,214 @@ in
     }
   ];
 
-  # The builder is not intended to be used interactively
-  documentation.enable = false;
-
-  environment.etc = {
-    "ssh/ssh_host_ed25519_key" = {
-      mode = "0600";
-
-      source = ./keys/ssh_host_ed25519_key;
+  options.virtualisation.darwin-builder = with lib; {
+    diskSize = mkOption {
+      default = 20 * 1024;
+      type = types.int;
+      example = 30720;
+      description = "The maximum disk space allocated to the runner in MB";
     };
-
-    "ssh/ssh_host_ed25519_key.pub" = {
-      mode = "0644";
-
-      source = ./keys/ssh_host_ed25519_key.pub;
+    memorySize = mkOption {
+      default = 3 * 1024;
+      type = types.int;
+      example = 8192;
+      description = "The runner's memory in MB";
     };
-  };
-
-  # DNS fails for QEMU user networking (SLiRP) on macOS.  See:
-  #
-  # https://github.com/utmapp/UTM/issues/2353
-  #
-  # This works around that by using a public DNS server other than the DNS
-  # server that QEMU provides (normally 10.0.2.3)
-  networking.nameservers = [ "8.8.8.8" ];
-
-  nix.settings = {
-    auto-optimise-store = true;
-
-    min-free = 1024 * 1024 * 1024;
-
-    max-free = 3 * 1024 * 1024 * 1024;
-
-    trusted-users = [ "root" user ];
-  };
-
-  services = {
-    getty.autologinUser = user;
-
-    openssh = {
-      enable = true;
-
-      authorizedKeysFiles = [ "${keysDirectory}/%u_${keyType}.pub" ];
-    };
-  };
-
-  system.build.macos-builder-installer =
-    let
-      privateKey = "/etc/nix/${user}_${keyType}";
-
-      publicKey = "${privateKey}.pub";
-
-      # This installCredentials script is written so that it's as easy as
-      # possible for a user to audit before confirming the `sudo`
-      installCredentials = hostPkgs.writeShellScript "install-credentials" ''
-        KEYS="''${1}"
-        INSTALL=${hostPkgs.coreutils}/bin/install
-        "''${INSTALL}" -g nixbld -m 600 "''${KEYS}/${user}_${keyType}" ${privateKey}
-        "''${INSTALL}" -g nixbld -m 644 "''${KEYS}/${user}_${keyType}.pub" ${publicKey}
+    min-free = mkOption {
+      default = 1024 * 1024 * 1024;
+      type = types.int;
+      example = 1073741824;
+      description = ''
+        The threshold (in bytes) of free disk space left at which to
+        start garbage collection on the runner
       '';
-
-      hostPkgs = config.virtualisation.host.pkgs;
-
-      script = hostPkgs.writeShellScriptBin "create-builder" ''
-        KEYS="''${KEYS:-./keys}"
-        ${hostPkgs.coreutils}/bin/mkdir --parent "''${KEYS}"
-        PRIVATE_KEY="''${KEYS}/${user}_${keyType}"
-        PUBLIC_KEY="''${PRIVATE_KEY}.pub"
-        if [ ! -e "''${PRIVATE_KEY}" ] || [ ! -e "''${PUBLIC_KEY}" ]; then
-            ${hostPkgs.coreutils}/bin/rm --force -- "''${PRIVATE_KEY}" "''${PUBLIC_KEY}"
-            ${hostPkgs.openssh}/bin/ssh-keygen -q -f "''${PRIVATE_KEY}" -t ${keyType} -N "" -C 'builder@localhost'
-        fi
-        if ! ${hostPkgs.diffutils}/bin/cmp "''${PUBLIC_KEY}" ${publicKey}; then
-          (set -x; sudo --reset-timestamp ${installCredentials} "''${KEYS}")
-        fi
-        KEYS="$(nix-store --add "$KEYS")" ${config.system.build.vm}/bin/run-nixos-vm
+    };
+    max-free = mkOption {
+      default = 3 * 1024 * 1024 * 1024;
+      type = types.int;
+      example = 3221225472;
+      description = ''
+        The threshold (in bytes) of free disk space left at which to
+        stop garbage collection on the runner
       '';
+    };
+    workingDirectory = mkOption {
+       default = ".";
+       type = types.str;
+       example = "/var/lib/darwin-builder";
+       description = ''
+         The working directory to use to run the script. When running
+         as part of a flake will need to be set to a non read-only filesystem.
+       '';
+    };
+    hostPort = mkOption {
+      default = 22;
+      type = types.int;
+      example = 31022;
+      description = ''
+        The localhost host port to forward TCP to the guest port.
+      '';
+    };
+  };
 
-    in
-    script.overrideAttrs (old: {
-      meta = (old.meta or { }) // {
-        platforms = lib.platforms.darwin;
+  config = {
+    # The builder is not intended to be used interactively
+    documentation.enable = false;
+
+    environment.etc = {
+      "ssh/ssh_host_ed25519_key" = {
+        mode = "0600";
+
+        source = ./keys/ssh_host_ed25519_key;
       };
-    });
 
-  system = {
-    # To prevent gratuitous rebuilds on each change to Nixpkgs
-    nixos.revision = null;
+      "ssh/ssh_host_ed25519_key.pub" = {
+        mode = "0644";
 
-    stateVersion = lib.mkDefault (throw ''
-      The macOS linux builder should not need a stateVersion to be set, but a module
-      has accessed stateVersion nonetheless.
-      Please inspect the trace of the following command to figure out which module
-      has a dependency on stateVersion.
-
-        nix-instantiate --attr darwin.builder --show-trace
-    '');
-  };
-
-  users.users."${user}" = {
-    isNormalUser = true;
-  };
-
-  security.polkit.enable = true;
-
-  security.polkit.extraConfig = ''
-    polkit.addRule(function(action, subject) {
-      if (action.id === "org.freedesktop.login1.power-off" && subject.user === "${user}") {
-        return "yes";
-      } else {
-        return "no";
-      }
-    })
-  '';
-
-  virtualisation = {
-    diskSize = 20 * 1024;
-
-    memorySize = 3 * 1024;
-
-    forwardPorts = [
-      { from = "host"; guest.port = 22; host.port = 22; }
-    ];
-
-    # Disable graphics for the builder since users will likely want to run it
-    # non-interactively in the background.
-    graphics = false;
-
-    sharedDirectories.keys = {
-      source = "\"$KEYS\"";
-      target = keysDirectory;
+        source = ./keys/ssh_host_ed25519_key.pub;
+      };
     };
 
-    # If we don't enable this option then the host will fail to delegate builds
-    # to the guest, because:
+    # DNS fails for QEMU user networking (SLiRP) on macOS.  See:
     #
-    # - The host will lock the path to build
-    # - The host will delegate the build to the guest
-    # - The guest will attempt to lock the same path and fail because
-    #   the lockfile on the host is visible on the guest
+    # https://github.com/utmapp/UTM/issues/2353
     #
-    # Snapshotting the host's /nix/store as an image isolates the guest VM's
-    # /nix/store from the host's /nix/store, preventing this problem.
-    useNixStoreImage = true;
+    # This works around that by using a public DNS server other than the DNS
+    # server that QEMU provides (normally 10.0.2.3)
+    networking.nameservers = [ "8.8.8.8" ];
 
-    # Obviously the /nix/store needs to be writable on the guest in order for it
-    # to perform builds.
-    writableStore = true;
+    nix.settings = {
+      auto-optimise-store = true;
 
-    # This ensures that anything built on the guest isn't lost when the guest is
-    # restarted.
-    writableStoreUseTmpfs = false;
+      min-free = cfg.min-free;
+
+      max-free = cfg.max-free;
+
+      trusted-users = [ "root" user ];
+    };
+
+    services = {
+      getty.autologinUser = user;
+
+      openssh = {
+        enable = true;
+
+        authorizedKeysFiles = [ "${keysDirectory}/%u_${keyType}.pub" ];
+      };
+    };
+
+    system.build.macos-builder-installer =
+      let
+        privateKey = "/etc/nix/${user}_${keyType}";
+
+        publicKey = "${privateKey}.pub";
+
+        # This installCredentials script is written so that it's as easy as
+        # possible for a user to audit before confirming the `sudo`
+        installCredentials = hostPkgs.writeShellScript "install-credentials" ''
+          KEYS="''${1}"
+          INSTALL=${hostPkgs.coreutils}/bin/install
+          "''${INSTALL}" -g nixbld -m 600 "''${KEYS}/${user}_${keyType}" ${privateKey}
+          "''${INSTALL}" -g nixbld -m 644 "''${KEYS}/${user}_${keyType}.pub" ${publicKey}
+        '';
+
+        hostPkgs = config.virtualisation.host.pkgs;
+
+  script = hostPkgs.writeShellScriptBin "create-builder" (
+          # When running as non-interactively as part of a DarwinConfiguration the working directory
+          # must be set to a writeable directory.
+        (if cfg.workingDirectory != "." then ''
+          ${hostPkgs.coreutils}/bin/mkdir --parent "${cfg.workingDirectory}"
+          cd "${cfg.workingDirectory}"
+  '' else "") + ''
+          KEYS="''${KEYS:-./keys}"
+          ${hostPkgs.coreutils}/bin/mkdir --parent "''${KEYS}"
+          PRIVATE_KEY="''${KEYS}/${user}_${keyType}"
+          PUBLIC_KEY="''${PRIVATE_KEY}.pub"
+          if [ ! -e "''${PRIVATE_KEY}" ] || [ ! -e "''${PUBLIC_KEY}" ]; then
+              ${hostPkgs.coreutils}/bin/rm --force -- "''${PRIVATE_KEY}" "''${PUBLIC_KEY}"
+              ${hostPkgs.openssh}/bin/ssh-keygen -q -f "''${PRIVATE_KEY}" -t ${keyType} -N "" -C 'builder@localhost'
+          fi
+          if ! ${hostPkgs.diffutils}/bin/cmp "''${PUBLIC_KEY}" ${publicKey}; then
+            (set -x; sudo --reset-timestamp ${installCredentials} "''${KEYS}")
+          fi
+          KEYS="$(${hostPkgs.nix}/bin/nix-store --add "$KEYS")" ${config.system.build.vm}/bin/run-nixos-vm
+        '');
+
+      in
+      script.overrideAttrs (old: {
+        meta = (old.meta or { }) // {
+          platforms = lib.platforms.darwin;
+        };
+      });
+
+    system = {
+      # To prevent gratuitous rebuilds on each change to Nixpkgs
+      nixos.revision = null;
+
+      stateVersion = lib.mkDefault (throw ''
+        The macOS linux builder should not need a stateVersion to be set, but a module
+        has accessed stateVersion nonetheless.
+        Please inspect the trace of the following command to figure out which module
+        has a dependency on stateVersion.
+
+          nix-instantiate --attr darwin.builder --show-trace
+      '');
+    };
+
+    users.users."${user}" = {
+      isNormalUser = true;
+    };
+
+    security.polkit.enable = true;
+
+    security.polkit.extraConfig = ''
+      polkit.addRule(function(action, subject) {
+        if (action.id === "org.freedesktop.login1.power-off" && subject.user === "${user}") {
+          return "yes";
+        } else {
+          return "no";
+        }
+      })
+    '';
+
+    virtualisation = {
+      diskSize = cfg.diskSize;
+
+      memorySize = cfg.memorySize;
+
+      forwardPorts = [
+        { from = "host"; guest.port = 22; host.port = cfg.hostPort; }
+      ];
+
+      # Disable graphics for the builder since users will likely want to run it
+      # non-interactively in the background.
+      graphics = false;
+
+      sharedDirectories.keys = {
+        source = "\"$KEYS\"";
+        target = keysDirectory;
+      };
+
+      # If we don't enable this option then the host will fail to delegate builds
+      # to the guest, because:
+      #
+      # - The host will lock the path to build
+      # - The host will delegate the build to the guest
+      # - The guest will attempt to lock the same path and fail because
+      #   the lockfile on the host is visible on the guest
+      #
+      # Snapshotting the host's /nix/store as an image isolates the guest VM's
+      # /nix/store from the host's /nix/store, preventing this problem.
+      useNixStoreImage = true;
+
+      # Obviously the /nix/store needs to be writable on the guest in order for it
+      # to perform builds.
+      writableStore = true;
+
+      # This ensures that anything built on the guest isn't lost when the guest is
+      # restarted.
+      writableStoreUseTmpfs = false;
+    };
   };
 }

nixos/modules/programs/hyprland.nix

@@ -0,0 +1,84 @@
+{ config
+, lib
+, pkgs
+, ...
+}:
+with lib; let
+  cfg = config.programs.hyprland;
+
+  defaultHyprlandPackage = pkgs.hyprland.override {
+    enableXWayland = cfg.xwayland.enable;
+    hidpiXWayland = cfg.xwayland.hidpi;
+    nvidiaPatches = cfg.nvidiaPatches;
+  };
+in
+{
+  options.programs.hyprland = {
+    enable = mkEnableOption null // {
+      description = mdDoc ''
+        Hyprland, the dynamic tiling Wayland compositor that doesn't sacrifice on its looks.
+
+        You can manually launch Hyprland by executing {command}`Hyprland` on a TTY.
+
+        A configuration file will be generated in {file}`~/.config/hypr/hyprland.conf`.
+        See <https://wiki.hyprland.org> for more information.
+      '';
+    };
+
+    package = mkOption {
+      type = types.path;
+      default = defaultHyprlandPackage;
+      defaultText = literalExpression ''
+        pkgs.hyprland.override {
+          enableXWayland = config.programs.hyprland.xwayland.enable;
+          hidpiXWayland = config.programs.hyprland.xwayland.hidpi;
+          nvidiaPatches = config.programs.hyprland.nvidiaPatches;
+        }
+      '';
+      example = literalExpression "<Hyprland flake>.packages.<system>.default";
+      description = mdDoc ''
+        The Hyprland package to use.
+        Setting this option will make {option}`programs.hyprland.xwayland` and
+        {option}`programs.hyprland.nvidiaPatches` not work.
+      '';
+    };
+
+    xwayland = {
+      enable = mkEnableOption (mdDoc "XWayland") // { default = true; };
+      hidpi = mkEnableOption null // {
+        description = mdDoc ''
+          Enable HiDPI XWayland, based on [XWayland MR 733](https://gitlab.freedesktop.org/xorg/xserver/-/merge_requests/733).
+          See <https://wiki.hyprland.org/Nix/Options-Overrides/#xwayland-hidpi> for more info.
+        '';
+      };
+    };
+
+    nvidiaPatches = mkEnableOption (mdDoc "patching wlroots for better Nvidia support");
+  };
+
+  config = mkIf cfg.enable {
+    environment = {
+      systemPackages = [ cfg.package ];
+
+    };
+
+    fonts.enableDefaultFonts = mkDefault true;
+    hardware.opengl.enable = mkDefault true;
+
+    programs = {
+      dconf.enable = mkDefault true;
+      xwayland.enable = mkDefault true;
+    };
+
+    security.polkit.enable = true;
+
+    services.xserver.displayManager.sessionPackages = [ cfg.package ];
+
+    xdg.portal = {
+      enable = mkDefault true;
+      extraPortals = [
+        pkgs.xdg-desktop-portal-hyprland
+      ];
+    };
+  };
+}

nixos/modules/services/networking/bind.nix

@@ -36,6 +36,17 @@ let
         description = lib.mdDoc "Addresses who may request zone transfers.";
         default = [ ];
       };
+      allowQuery = mkOption {
+        type = types.listOf types.str;
+        description = lib.mdDoc ''
+          List of address ranges allowed to query this zone. Instead of the address(es), this may instead
+          contain the single string "any".
+
+          NOTE: This overrides the global-level `allow-query` setting, which is set to the contents
+          of `cachenetworks`.
+        '';
+        default = [ "any" ];
+      };
       extraConfig = mkOption {
         type = types.str;
         description = lib.mdDoc "Extra zone config to be appended at the end of the zone section.";
@@ -69,7 +80,7 @@ let
       ${cfg.extraConfig}
 
       ${ concatMapStrings
-          ({ name, file, master ? true, slaves ? [], masters ? [], extraConfig ? "" }:
+          ({ name, file, master ? true, slaves ? [], masters ? [], allowQuery ? [], extraConfig ? "" }:
             ''
               zone "${name}" {
                 type ${if master then "master" else "slave"};
@@ -87,7 +98,7 @@ let
                      };
                    ''
                 }
-                allow-query { any; };
+                allow-query { ${concatMapStrings (ip: "${ip}; ") allowQuery}};
                 ${extraConfig}
               };
             '')
@@ -120,7 +131,9 @@ in
         description = lib.mdDoc ''
           What networks are allowed to use us as a resolver.  Note
           that this is for recursive queries -- all networks are
-          allowed to query zones configured with the `zones` option.
+          allowed to query zones configured with the `zones` option
+          by default (although this may be overridden within each
+          zone's configuration, via the `allowQuery` option).
           It is recommended that you limit cacheNetworks to avoid your
           server being used for DNS amplification attacks.
         '';

nixos/tests/libreswan.nix

@@ -107,6 +107,8 @@ in
 
       with subtest("Network is up"):
           alice.wait_until_succeeds("ping -c1 bob")
+          alice.succeed("systemctl restart ipsec")
+          bob.succeed("systemctl restart ipsec")
 
       with subtest("Eve can eavesdrop cleartext traffic"):
           eavesdrop()

pkgs/applications/audio/mympd/default.nix

@@ -16,13 +16,13 @@
 
 stdenv.mkDerivation rec {
   pname = "mympd";
-  version = "10.2.5";
+  version = "10.2.6";
 
   src = fetchFromGitHub {
     owner = "jcorporation";
     repo = "myMPD";
     rev = "v${version}";
-    sha256 = "sha256-ZxGMvbm9GKhhfCNZdeIYUh2FF4c3vXtvRdu24u3Zrtg=";
+    sha256 = "sha256-a/HjuBeq7ySDUcEcR6KKnwlvzUInjWmio/zI59sNsak=";
   };
 
   nativeBuildInputs = [

pkgs/applications/audio/squeezelite/default.nix

@@ -34,13 +34,13 @@ stdenv.mkDerivation {
   pname = binName;
   # versions are specified in `squeezelite.h`
   # see https://github.com/ralph-irving/squeezelite/issues/29
-  version = "1.9.9.1419";
+  version = "1.9.9.1428";
 
   src = fetchFromGitHub {
     owner = "ralph-irving";
     repo = "squeezelite";
-    rev = "226efa300c4cf037e8486bad635e9deb3104636f";
-    hash = "sha256-ZZWliw1prFbBZMFp0QmXg6MKuHPNuFh2lFxQ8bbuWAM=";
+    rev = "74fe7934ec60cc31565f088796f56e911f51679c";
+    hash = "sha256-85Pz6psyK3VXOIrINcoIeHZT5j9UfJqWIxTavwqHx04=";
   };
 
   buildInputs = [ flac libmad libvorbis mpg123 ]
@@ -78,6 +78,8 @@ stdenv.mkDerivation {
     runHook postInstall
   '';
 
+  passthru.updateScript = ./update.sh;
+
   meta = with lib; {
     description = "Lightweight headless squeezebox client emulator";
     homepage = "https://github.com/ralph-irving/squeezelite";

pkgs/applications/audio/squeezelite/update.sh

@@ -0,0 +1,19 @@
+#!/usr/bin/env nix-shell
+#!nix-shell -i bash -p common-updater-scripts coreutils curl gnused jq nix nix-prefetch-github ripgrep
+
+set -euo pipefail
+
+latestRev="$(curl -s "https://api.github.com/repos/ralph-irving/squeezelite/commits?per_page=1" | jq -r ".[0].sha")"
+latestVersion="$( curl -s https://raw.githubusercontent.com/ralph-irving/squeezelite/${latestRev}/squeezelite.h | rg 'define (MAJOR|MINOR|MICRO)_VERSION' | sed 's/#.*VERSION //' | tr '\n' '.' | sed  -e 's/"//g' -e 's/\.$//')"
+currentVersion=$(nix-instantiate --eval -E "with import ./. {}; squeezelite.version or (lib.getVersion squeezelite)" | tr -d '"')
+
+if [[ "$currentVersion" == "$latestVersion" ]]; then
+  echo "squeezelite is up-to-date: $currentVersion"
+  exit 0
+fi
+
+srcHash=$(nix-prefetch-github ralph-irving squeezelite --rev "$latestRev" | jq -r .sha256)
+srcHash=$(nix hash to-sri --type sha256 "$srcHash")
+
+
+update-source-version squeezelite "$latestVersion" "$srcHash" --rev="${latestRev}"

pkgs/applications/audio/streamripper/default.nix

@@ -12,6 +12,10 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ pkg-config ];
   buildInputs = [ glib libogg libvorbis libmad ];
 
+  makeFlags = [
+    "AR:=$(AR)"
+  ];
+
   meta = with lib; {
     homepage = "https://streamripper.sourceforge.net/";
     description = "Application that lets you record streaming mp3 to your hard drive";

pkgs/applications/blockchains/electrs/default.nix

@@ -12,16 +12,16 @@ let
 in
 rustPlatform.buildRustPackage rec {
   pname = "electrs";
-  version = "0.9.11";
+  version = "0.9.13";
 
   src = fetchFromGitHub {
     owner = "romanz";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-iudHdsSjoPal+ORMB3lU7ejGYv69q/8HcxScZS8D/u8=";
+    hash = "sha256-GV/cwFdYpXJXRTgdVfuzJpmwNhe0kVJnYAJe+DPmRV8=";
   };
 
-  cargoHash = "sha256-Ft1AluPfV6BIRGEddrrIGNRmaZIzUsA2DN2TcghCnSQ=";
+  cargoHash = "sha256-eQAizO26oQRosbMGJLwMmepBN3pocmnbc0qsHsAJysg=";
 
   # needed for librocksdb-sys
   nativeBuildInputs = [ rustPlatform.bindgenHook ];

pkgs/applications/editors/android-studio/common.nix

@@ -227,6 +227,7 @@ in runCommand
         canary = [ alapshin ];
         dev = canary;
       }."${channel}";
+      mainProgram = pname;
     };
   }
   ''

pkgs/applications/editors/neovim/utils.nix

@@ -77,18 +77,6 @@ let
 
       luaEnv = neovim-unwrapped.lua.withPackages(extraLuaPackages);
 
-      # Mapping a boolean argument to a key that tells us whether to add or not to
-      # add to nvim's 'embedded rc' this:
-      #    let g:<key>_host_prog=$out/bin/nvim-<key>
-      # Or this:
-      #    let g:loaded_${prog}_provider=0
-      # While the latter tells nvim that this provider is not available
-      hostprog_check_table = {
-        node = withNodeJs;
-        python = false;
-        python3 = withPython3;
-        ruby = withRuby;
-      };
       # as expected by packdir
       packpathDirs.myNeovimPackages = myVimPackage;
       ## Here we calculate all of the arguments to the 1st call of `makeWrapper`
@@ -98,22 +86,9 @@ let
       makeWrapperArgs =
         let
           binPath = lib.makeBinPath (lib.optionals withRuby [ rubyEnv ] ++ lib.optionals withNodeJs [ nodejs ]);
-
-          hostProviderViml = lib.mapAttrsToList genProviderSettings hostprog_check_table;
-
-          # as expected by packdir
-          packDirArgs.myNeovimPackages = myVimPackage;
-
-          # vim accepts a limited number of commands so we join them all
-          flags = [
-            "--cmd" (lib.intersperse "|" hostProviderViml)
-          ] ++ lib.optionals (myVimPackage.start != [] || myVimPackage.opt != []) [
-            "--cmd" "set packpath^=${vimUtils.packDir packDirArgs}"
-            "--cmd" "set rtp^=${vimUtils.packDir packDirArgs}"
-          ];
         in
         [
-          "--inherit-argv0" "--add-flags" (lib.escapeShellArgs flags)
+          "--inherit-argv0"
         ] ++ lib.optionals withRuby [
           "--set" "GEM_HOME" "${rubyEnv}/${rubyEnv.ruby.gemPath}"
         ] ++ lib.optionals (binPath != "") [
@@ -144,12 +119,6 @@ let
       inherit rubyEnv;
     };
 
-    genProviderSettings = prog: withProg:
-      if withProg then
-        "let g:${prog}_host_prog='${placeholder "out"}/bin/nvim-${prog}'"
-      else
-        "let g:loaded_${prog}_provider=0"
-    ;
 
   # to keep backwards compatibility for people using neovim.override
   legacyWrapper = neovim: {
@@ -191,9 +160,43 @@ let
       wrapperArgs = lib.escapeShellArgs res.wrapperArgs + " " + extraMakeWrapperArgs;
       wrapRc = (configure != {});
   });
+
+  /* Generate vim.g.<LANG>_host_prog lua rc to setup host providers
+
+  Mapping a boolean argument to a key that tells us whether to add
+      vim.g.<LANG>_host_prog=$out/bin/nvim-<LANG>
+  Or this:
+      let g:loaded_${prog}_provider=0
+  While the latter tells nvim that this provider is not available */
+  generateProviderRc = {
+      withPython3 ? true
+    , withNodeJs ? false
+    , withRuby ? true
+
+    # so that we can pass the full neovim config while ignoring it
+    , ...
+    }: let
+      hostprog_check_table = {
+        node = withNodeJs;
+        python = false;
+        python3 = withPython3;
+        ruby = withRuby;
+      };
+
+      genProviderCommand = prog: withProg:
+        if withProg then
+          "vim.g.${prog}_host_prog='${placeholder "out"}/bin/nvim-${prog}'"
+        else
+          "vim.g.loaded_${prog}_provider=0";
+
+      hostProviderLua = lib.mapAttrsToList genProviderCommand hostprog_check_table;
+    in
+        lib.concatStringsSep ";" hostProviderLua;
+
 in
 {
   inherit makeNeovimConfig;
+  inherit generateProviderRc;
   inherit legacyWrapper;
 
   buildNeovimPluginFrom2Nix = callPackage ./build-neovim-plugin.nix {

pkgs/applications/editors/neovim/wrapper.nix

@@ -4,6 +4,8 @@
 , python3
 , python3Packages
 , callPackage
+, neovimUtils
+, vimUtils
 }:
 neovim:
 
@@ -12,6 +14,7 @@ let
       extraName ? ""
     # should contain all args but the binary. Can be either a string or list
     , wrapperArgs ? []
+    # a limited RC script used only to generate the manifest for remote plugins
     , manifestRc ? null
     , withPython2 ? false
     , withPython3 ? true,  python3Env ? python3
@@ -26,12 +29,30 @@ let
     # (e.g., in ~/.config/init.vim or project/.nvimrc)
     , wrapRc ? true
     , neovimRcContent ? ""
+    # entry to load in packpath
+    , packpathDirs
     , ...
   }@args:
   let
 
     wrapperArgsStr = if lib.isString wrapperArgs then wrapperArgs else lib.escapeShellArgs wrapperArgs;
 
+    # "--add-flags" (lib.escapeShellArgs flags)
+    # wrapper args used both when generating the manifest and in the final neovim executable
+    commonWrapperArgs = (lib.optionals (lib.isList wrapperArgs) wrapperArgs)
+      # vim accepts a limited number of commands so we join them all
+          ++ [
+            "--add-flags" ''--cmd "lua ${providerLuaRc}"''
+            # (lib.intersperse "|" hostProviderViml)
+          ] ++ lib.optionals (packpathDirs.myNeovimPackages.start != [] || packpathDirs.myNeovimPackages.opt != []) [
+            "--add-flags" ''--cmd "set packpath^=${vimUtils.packDir packpathDirs}"''
+            "--add-flags" ''--cmd "set rtp^=${vimUtils.packDir packpathDirs}"''
+          ]
+          ;
+
+    providerLuaRc = neovimUtils.generateProviderRc args;
+    # providerLuaRc = "toto";
+
     # If configure != {}, we can't generate the rplugin.vim file with e.g
     # NVIM_SYSTEM_RPLUGIN_MANIFEST *and* NVIM_RPLUGIN_MANIFEST env vars set in
     # the wrapper. That's why only when configure != {} (tested both here and
@@ -42,6 +63,7 @@ let
       [ "${neovim}/bin/nvim" "${placeholder "out"}/bin/nvim" ]
       ++ [ "--set" "NVIM_SYSTEM_RPLUGIN_MANIFEST" "${placeholder "out"}/rplugin.vim" ]
       ++ lib.optionals wrapRc [ "--add-flags" "-u ${writeText "init.vim" neovimRcContent}" ]
+      ++ commonWrapperArgs
       ;
   in
   assert withPython2 -> throw "Python2 support has been removed from the neovim wrapper, please remove withPython2 and python2Env.";
@@ -72,7 +94,7 @@ let
       ''
       + lib.optionalString (manifestRc != null) (let
         manifestWrapperArgs =
-          [ "${neovim}/bin/nvim" "${placeholder "out"}/bin/nvim-wrapper" ];
+          [ "${neovim}/bin/nvim" "${placeholder "out"}/bin/nvim-wrapper" ] ++ commonWrapperArgs;
       in ''
         echo "Generating remote plugin manifest"
         export NVIM_RPLUGIN_MANIFEST=$out/rplugin.vim
@@ -116,6 +138,7 @@ let
 
     nativeBuildInputs = [ makeWrapper ];
     passthru = {
+      inherit providerLuaRc packpathDirs;
       unwrapped = neovim;
       initRc = neovimRcContent;
 

pkgs/applications/misc/blender/default.nix

@@ -73,6 +73,8 @@ stdenv.mkDerivation rec {
   pythonPath = with python310Packages; [ numpy requests ];
 
   postPatch = ''
+    # allow usage of dynamically linked embree
+    rm build_files/cmake/Modules/FindEmbree.cmake
   '' +
     (if stdenv.isDarwin then ''
       : > build_files/cmake/platform/platform_apple_xcode.cmake

pkgs/applications/misc/copyq/default.nix

@@ -17,13 +17,13 @@
 
 stdenv.mkDerivation rec {
   pname = "CopyQ";
-  version = "6.4.0";
+  version = "7.0.0";
 
   src = fetchFromGitHub {
     owner = "hluk";
     repo = "CopyQ";
     rev = "v${version}";
-    hash = "sha256-HpWzIABzg0oJqzIehIGpeATLs3ZlmLgtRKaiMIUNAFI=";
+    hash = "sha256-Wk1kTbL6LYgs1edazU39LlNZMAAm6wDbEPjuXvb5EkE=";
   };
 
   nativeBuildInputs = [

pkgs/applications/misc/slmenu/default.nix

@@ -1,19 +0,0 @@
-{lib, stdenv, fetchhg}:
-
-stdenv.mkDerivation {
-  pname = "slmenu";
-  version = "hg-2012-02-01";
-
-  src = fetchhg {
-    url = "https://bitbucket.org/rafaelgg/slmenu/";
-    rev = "7e74fa5db73e8b018da48d50dbbaf11cb5c62d13";
-    sha256 = "0zb7mm8344d3xmvrl62psazcabfk75pp083jqkmywdsrikgjagv6";
-  };
-  makeFlags = [ "PREFIX=$(out)" ];
-  meta = with lib; {
-    description = "A console dmenu-like tool";
-    license = licenses.mit;
-    maintainers = with maintainers; [ raskin ];
-    platforms = platforms.linux;
-  };
-}

pkgs/applications/misc/syncthingtray/default.nix

@@ -28,14 +28,14 @@ https://github.com/NixOS/nixpkgs/issues/199596#issuecomment-1310136382 */
 }:
 
 mkDerivation rec {
-  version = "1.3.3";
+  version = "1.4.1";
   pname = "syncthingtray";
 
   src = fetchFromGitHub {
     owner = "Martchus";
     repo = "syncthingtray";
     rev = "v${version}";
-    sha256 = "sha256-6H5pV7/E4MP9UqVpm59DqfcK8Z8GwknO3+oWxAcnIsk=";
+    sha256 = "sha256-6s78vytYxU7FWGQRO56qgmtZBlHbXMz3iVAbBXycDmI=";
   };
 
   buildInputs = [

pkgs/applications/misc/tandoor-recipes/default.nix

@@ -1,12 +1,25 @@
 { callPackage
 , nixosTests
 , python3
+, fetchFromGitHub
 }:
 let
   python = python3.override {
     packageOverrides = self: super: {
       django = super.django_4;
 
+      django-crispy-forms = super.django-crispy-forms.overridePythonAttrs (_: rec {
+        version = "1.14.0";
+        format = "setuptools";
+
+        src = fetchFromGitHub {
+          owner = "django-crispy-forms";
+          repo = "django-crispy-forms";
+          rev = "refs/tags/${version}";
+          hash = "sha256-NZ2lWxsQHc7Qc4HDoWgjJTZ/bJHmjpBf3q1LVLtzA+8=";
+        };
+      });
+
       # Tests are incompatible with Django 4
       django-js-reverse = super.django-js-reverse.overridePythonAttrs (_: {
         doCheck = false;

pkgs/applications/misc/ttyper/default.nix

@@ -2,16 +2,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "ttyper";
-  version = "1.0.0";
+  version = "1.1.0";
 
   src = fetchFromGitHub {
     owner = "max-niederman";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-yReDHe5UJfBnEIhOp/3nHQkhp6YQQGDWqihLYi9IxdM=";
+    sha256 = "sha256-6oqUBLda6/qcRza5898WXjdopF8jKBDd93FdM0QwNUo=";
   };
 
-  cargoSha256 = "sha256-5vhtF8GKg4Cw3F1GlhpWz2VMZfcMpCijlHTGmbKHjP8=";
+  cargoSha256 = "sha256-SfcO8nMle1ku3lK2UPW/Z+J4JzmhcoFr+UCGIidXOa0=";
 
   meta = with lib; {
     description = "Terminal-based typing test";

pkgs/applications/networking/browsers/vieb/default.nix

@@ -2,20 +2,20 @@
 
 buildNpmPackage rec {
   pname = "vieb";
-  version = "9.6.0";
+  version = "9.7.0";
 
   src = fetchFromGitHub {
     owner = "Jelmerro";
     repo = pname;
     rev = version;
-    hash = "sha256-846yfD8B0/fX5cJOK62f/Uc+iS5WY0odKN7CXAUL6qY=";
+    hash = "sha256-uo5V5RRDSR+f9+AqojikrlybmtcWTmB7TPXEvLG9n4E=";
   };
 
   postPatch = ''
     sed -i '/"electron"/d' package.json
   '';
 
-  npmDepsHash = "sha256-IOlYip1AXsqsjRD/5Cd/E+hsT3ZbXP7qSHfCDzESisc=";
+  npmDepsHash = "sha256-RUpeqbb8bnSQ6sCYH8O9mL3Rpb+ZlcPi7fq6LlbkSic=";
   dontNpmBuild = true;
 
   nativeBuildInputs = [ makeWrapper ] ++ lib.optional stdenv.isAarch64 python3;

pkgs/applications/networking/cluster/rke2/default.nix

@@ -0,0 +1,27 @@
+{ lib, buildGoModule, fetchFromGitHub }:
+
+buildGoModule rec {
+  pname = "rke2";
+  version = "1.26.3+rke2r1";
+
+  src = fetchFromGitHub {
+    owner = "rancher";
+    repo = pname;
+    rev = "v${version}";
+    hash = "sha256-MC3INsuXV2JmazdXOAAslFlApvql6uOnOkWV8u0diOw=";
+  };
+
+  vendorHash = "sha256-W9Phc1JYa3APAKvI34RWqMy4xfmwgX3BaOh4bQYFEnU=";
+
+  subPackages = [ "." ];
+
+  ldflags = [ "-s" "-w" "-X github.com/k3s-io/k3s/pkg/version.Version=v${version}" ];
+
+  meta = with lib; {
+    homepage = "https://github.com/rancher/rke2";
+    description = "RKE2, also known as RKE Government, is Rancher's next-generation Kubernetes distribution.";
+    changelog = "https://github.com/rancher/rke2/releases/tag/v${version}";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ zygot ];
+  };
+}

pkgs/applications/networking/cluster/terraform-providers/default.nix

@@ -95,6 +95,7 @@ let
       b2 = removed "b2" "2022/06";
       checkpoint = removed "checkpoint" "2022/11";
       dome9 = removed "dome9" "2022/08";
+      ksyun = removed "ksyun" "2023/04";
       logicmonitor = license "logicmonitor" "2022/11";
       ncloud = removed "ncloud" "2022/08";
       nsxt = license "nsxt" "2022/11";

pkgs/applications/networking/cluster/terraform-providers/providers.json

@@ -28,13 +28,13 @@
     "vendorHash": "sha256-jK7JuARpoxq7hvq5+vTtUwcYot0YqlOZdtDwq4IqKvk="
   },
   "aiven": {
-    "hash": "sha256-dOdq/At0aUTaivvm557sgPwxC9EfRBexYrtpri8tzg4=",
+    "hash": "sha256-I8w8hnts3bELUm2e0fRfRcfK9uoS0ZbymZZPEVcizEI=",
     "homepage": "https://registry.terraform.io/providers/aiven/aiven",
     "owner": "aiven",
     "repo": "terraform-provider-aiven",
-    "rev": "v4.2.0",
+    "rev": "v4.2.1",
     "spdx": "MIT",
-    "vendorHash": "sha256-QDO/xE9ZK7+UscjVBV06BMGavExD248PhLIrDB5oROU="
+    "vendorHash": "sha256-nF/efMhmrXfBlF9w9tC4npHxjX2/299OfqTpvPapfMo="
   },
   "akamai": {
     "hash": "sha256-ofwJs9rOi8l9O2g9adFr3LI4M4pjIc1GzZ5TD70Lgto=",
@@ -110,13 +110,13 @@
     "vendorHash": null
   },
   "aws": {
-    "hash": "sha256-cOK4/hmLZuL9ER/nv9h7jA4/uJumc+iCrOCrfrY9Pic=",
+    "hash": "sha256-vV1I9hQOil1ume9+GV14fBVo6NaBZlElemhFhnQ7rl4=",
     "homepage": "https://registry.terraform.io/providers/hashicorp/aws",
     "owner": "hashicorp",
     "repo": "terraform-provider-aws",
-    "rev": "v4.61.0",
+    "rev": "v4.62.0",
     "spdx": "MPL-2.0",
-    "vendorHash": "sha256-YlHIvO6qa2XfgVTIMehfVujJN4ChmVVagrg9R+5xn5U="
+    "vendorHash": "sha256-2OmadSxpr3buMukM25mb/xXnI5rVkIuX0sbbI0zqRYE="
   },
   "azuread": {
     "hash": "sha256-MGCGfocs16qmJnvMRRD7TRHnPkS17h+oNUkMARAQhLs=",
@@ -128,11 +128,11 @@
     "vendorHash": null
   },
   "azurerm": {
-    "hash": "sha256-ClkqHRHuYXf/uTMaWFnCNeY8jCTAS48IDGnBnOz0RbA=",
+    "hash": "sha256-NffjRiJz92MwTo6K0H2nuqcfdvmhj9i8Xre0T7gaPeA=",
     "homepage": "https://registry.terraform.io/providers/hashicorp/azurerm",
     "owner": "hashicorp",
     "repo": "terraform-provider-azurerm",
-    "rev": "v3.50.0",
+    "rev": "v3.51.0",
     "spdx": "MPL-2.0",
     "vendorHash": null
   },
@@ -182,14 +182,13 @@
     "vendorHash": "sha256-dm+2SseBeS49/QoepRwJ1VFwPCtU+6VymvyEH/sLkvI="
   },
   "buildkite": {
-    "hash": "sha256-Sy0MbPbTunc2WmSLTuek72hg+PP+2YE3RO/J4dEm65k=",
+    "hash": "sha256-4Bbod7IuinZE28AZ2r1BBrexgbS29jEpwtG8aTKj7M8=",
     "homepage": "https://registry.terraform.io/providers/buildkite/buildkite",
     "owner": "buildkite",
-    "proxyVendor": true,
     "repo": "terraform-provider-buildkite",
-    "rev": "v0.12.2",
+    "rev": "v0.14.0",
     "spdx": "MIT",
-    "vendorHash": "sha256-C7bm9wDNEO7fJuqssUxQ4t9poVkPkKd8MU7S9MJTOW4="
+    "vendorHash": "sha256-dN5oNNO5lf8dUfk9SDUH3f3nA0CNoJyfTqk+Z5lwTz8="
   },
   "checkly": {
     "hash": "sha256-tdimESlkfRO/kdA6JOX72vQNXFLJZ9VKwPRxsJo5WFI=",
@@ -274,13 +273,13 @@
     "vendorHash": "sha256-v1RHxXYTvpyWzyph6qg3GW75OPYc5qYQ/yyDI8WkbNc="
   },
   "ct": {
-    "hash": "sha256-NuspY7hvnEo7IAUa1ixv8CzdWo39vEDh3HOvy+A0XjY=",
+    "hash": "sha256-c1cqTfMlZ5fXDNMYLsk4447X0p/qIQYvRTqVY8cSs+E=",
     "homepage": "https://registry.terraform.io/providers/poseidon/ct",
     "owner": "poseidon",
     "repo": "terraform-provider-ct",
-    "rev": "v0.12.0",
+    "rev": "v0.13.0",
     "spdx": "Apache-2.0",
-    "vendorHash": "sha256-cDt7eC1GjGnvFLelAi3sF6XjP0QQi9eWW6iHroYZ4pA="
+    "vendorHash": "sha256-ZCMSmOCPEMxCSpl3DjIUGPj1W/KNJgyjtHpmQ19JquA="
   },
   "datadog": {
     "hash": "sha256-rbBLyCxGB1W7VCPs1f/7PQnyvdWo+uhze6p4cucdEG0=",
@@ -424,7 +423,7 @@
     "homepage": "https://registry.terraform.io/providers/integrations/github",
     "owner": "integrations",
     "repo": "terraform-provider-github",
-    "rev": "v5.20.0",
+    "rev": "v5.21.1",
     "spdx": "MIT",
     "vendorHash": null
   },
@@ -438,22 +437,22 @@
     "vendorHash": "sha256-s4FynUO6bT+8uZYkecbQCtFw1jFTAAYUkSzONI6Ba9g="
   },
   "google": {
-    "hash": "sha256-/35j6kmJ+R0ZSt0CpQe29cTcKSOEZJ+BV0x3BYQV8aA=",
+    "hash": "sha256-fkbuqlx8uP3Z6v0eQHamLlmWCU8Gciw6tdH20NunStM=",
     "homepage": "https://registry.terraform.io/providers/hashicorp/google",
     "owner": "hashicorp",
     "proxyVendor": true,
     "repo": "terraform-provider-google",
-    "rev": "v4.60.1",
+    "rev": "v4.60.2",
     "spdx": "MPL-2.0",
     "vendorHash": "sha256-ztoWOiqyOrusSo0peigEV9wy2f387gVGfcolkYoJvhw="
   },
   "google-beta": {
-    "hash": "sha256-rCCzPvaZGoQLES0QzYaRLWlaiZI8QIPb8bxGBJ8ERmk=",
+    "hash": "sha256-yUUwqGUs1FSZufZiFamIxz9bu1BIMTGXhGJbpgD+J0A=",
     "homepage": "https://registry.terraform.io/providers/hashicorp/google-beta",
     "owner": "hashicorp",
     "proxyVendor": true,
     "repo": "terraform-provider-google-beta",
-    "rev": "v4.60.1",
+    "rev": "v4.60.2",
     "spdx": "MPL-2.0",
     "vendorHash": "sha256-ztoWOiqyOrusSo0peigEV9wy2f387gVGfcolkYoJvhw="
   },
@@ -629,15 +628,6 @@
     "spdx": "MIT",
     "vendorHash": "sha256-UnWHUD9T4nTT6Y2UrvBIdIk9eA8l0vWJ/IpEY3PIzDU="
   },
-  "ksyun": {
-    "hash": "sha256-NcXYCdWNpH5sX9+LMASCRWsgNRtbYOTK0sOailPw+44=",
-    "homepage": "https://registry.terraform.io/providers/kingsoftcloud/ksyun",
-    "owner": "kingsoftcloud",
-    "repo": "terraform-provider-ksyun",
-    "rev": "v1.3.68",
-    "spdx": "MPL-2.0",
-    "vendorHash": "sha256-miHKAz+ONXtuC1DNukcyZbbaYReY69dz9Zk6cJdORdQ="
-  },
   "kubectl": {
     "hash": "sha256-UkUwWi7Z9cSMyZakD6JxMl+qdczAYfZQgwroCUjFIUM=",
     "homepage": "https://registry.terraform.io/providers/gavinbunney/kubectl",
@@ -865,13 +855,13 @@
     "vendorHash": "sha256-62q67aaOZA3fQmyL8bEHB+W497bcx9Xy7kKrbkjkbaI="
   },
   "opentelekomcloud": {
-    "hash": "sha256-ZDhihbYH6O6UCU2WOkPE+tcOODkAsbx7v9Vg1wrbklg=",
+    "hash": "sha256-QcpA7FreTgITmnt0fQHUmUK6FZMP0QCeQK2MN2Y9tFQ=",
     "homepage": "https://registry.terraform.io/providers/opentelekomcloud/opentelekomcloud",
     "owner": "opentelekomcloud",
     "repo": "terraform-provider-opentelekomcloud",
-    "rev": "v1.34.0",
+    "rev": "v1.34.1",
     "spdx": "MPL-2.0",
-    "vendorHash": "sha256-tLtgg6QQiXivDxDVEYeOnLqXobwN7ZFqQrI0d3pUHeE="
+    "vendorHash": "sha256-4tJe8v31txzLBbruicOI6WUdDk38CqfLniFyc3hWVxg="
   },
   "opsgenie": {
     "hash": "sha256-Wbe+DyK5wKuZZX8yd3DJN+2wT8KZt+YsBwJYKnZnfcI=",
@@ -892,11 +882,11 @@
     "vendorHash": null
   },
   "pagerduty": {
-    "hash": "sha256-yQjpU5lO0BbYBLOJOp3FzAbKyaUYqzWAmtsaA7TLnxg=",
+    "hash": "sha256-SyDX3L8L4MLoo9IfjB8LfG34BGNV+gRVXnPB0dFvATg=",
     "homepage": "https://registry.terraform.io/providers/PagerDuty/pagerduty",
     "owner": "PagerDuty",
     "repo": "terraform-provider-pagerduty",
-    "rev": "v2.11.3",
+    "rev": "v2.12.1",
     "spdx": "MPL-2.0",
     "vendorHash": null
   },
@@ -1054,13 +1044,13 @@
     "vendorHash": "sha256-NO1r/EWLgH1Gogru+qPeZ4sW7FuDENxzNnpLSKstnE8="
   },
   "spotinst": {
-    "hash": "sha256-sBfNolPMCPM8xI1K3lgV0X8kmwET8RYij4AcYv1UMqA=",
+    "hash": "sha256-g/kELVG+hsR+RynLfyB0MQkjC7eUeUUVn/h7S/MABXU=",
     "homepage": "https://registry.terraform.io/providers/spotinst/spotinst",
     "owner": "spotinst",
     "repo": "terraform-provider-spotinst",
-    "rev": "v1.109.0",
+    "rev": "v1.110.0",
     "spdx": "MPL-2.0",
-    "vendorHash": "sha256-cuhijHsEsMGuK2+Gvm2zL3diN523wRroKmnDsQZ5wKA="
+    "vendorHash": "sha256-2HApI9Cw63zxzgSP9Xe6xAcqHDx8KSlRiIh+IVSEUfo="
   },
   "stackpath": {
     "hash": "sha256-7KQUddq+M35WYyAIAL8sxBjAaXFcsczBRO1R5HURUZg=",
@@ -1108,11 +1098,11 @@
     "vendorHash": "sha256-GkmUKSnqkabwGCl22/90529BWb0oJaIJHYHlS/h3KNY="
   },
   "tencentcloud": {
-    "hash": "sha256-N8+voF13P+uWtFYCYVItcqtPBxFiDDz1yp5gSpTTXPM=",
+    "hash": "sha256-glMhevT9UlhaNITeLexTpCtSROv1UTyFZZTOuJdz2Ys=",
     "homepage": "https://registry.terraform.io/providers/tencentcloudstack/tencentcloud",
     "owner": "tencentcloudstack",
     "repo": "terraform-provider-tencentcloud",
-    "rev": "v1.80.0",
+    "rev": "v1.80.1",
     "spdx": "MPL-2.0",
     "vendorHash": null
   },
@@ -1263,13 +1253,13 @@
     "vendorHash": "sha256-itSr5HHjus6G0t5/KFs0sNiredH9m3JnQ3siLtm+NHs="
   },
   "yandex": {
-    "hash": "sha256-bkKGZAGxeJC5JeVwRB+moChFvTF2zUHxB75H82RSACI=",
+    "hash": "sha256-UFAWifGu/3QKH8JLBYObLhO/PdCQ1f5e9hmehF8grak=",
     "homepage": "https://registry.terraform.io/providers/yandex-cloud/yandex",
     "owner": "yandex-cloud",
     "proxyVendor": true,
     "repo": "terraform-provider-yandex",
-    "rev": "v0.88.0",
+    "rev": "v0.89.0",
     "spdx": "MPL-2.0",
-    "vendorHash": "sha256-X8jQnuTtuN1M2qDYaE0dgOdB2DdgyQashsGb8mZOycQ="
+    "vendorHash": "sha256-RfSPCBDb4crv6GZPhsVSQOWnZ3xHa/VWln5pSg68Exg="
   }
 }

pkgs/applications/networking/flexget/default.nix

@@ -31,7 +31,7 @@ let
 in
 python.pkgs.buildPythonApplication rec {
   pname = "flexget";
-  version = "3.5.33";
+  version = "3.5.36";
   format = "pyproject";
 
   # Fetch from GitHub in order to use `requirements.in`
@@ -39,7 +39,7 @@ python.pkgs.buildPythonApplication rec {
     owner = "Flexget";
     repo = "Flexget";
     rev = "refs/tags/v${version}";
-    hash = "sha256-LzDXNl2IQ3+j9uP+nE6JS8E+pO0n9zwmA7wrMeKR6Ms=";
+    hash = "sha256-Aj3dOdZTpqBocBFySPZjvjeOZs7eAJeKqm7ykh0Y1CE=";
   };
 
   postPatch = ''

pkgs/applications/networking/syncplay/default.nix

@@ -13,6 +13,7 @@ buildPythonApplication rec {
     sha256 = "0qm3qn4a1nahhs7q81liz514n9blsi107g9s9xfw2i8pzi7v9v0v";
   };
 
+  buildInputs = lib.optionals enableGUI [ qt5.qtbase ];
   propagatedBuildInputs = [ twisted certifi ]
     ++ twisted.optional-dependencies.tls
     ++ lib.optional enableGUI pyside2;

pkgs/applications/office/antiword/default.nix

@@ -11,11 +11,15 @@ stdenv.mkDerivation rec{
 
   prePatch = ''
     sed -i -e "s|/usr/local/bin|$out/bin|g" -e "s|/usr/share|$out/share|g" Makefile antiword.h
-    substituteInPlace Makefile --replace "gcc" "cc"
+    substituteInPlace Makefile --replace "gcc" '$(CC)'
   '';
 
   patches = [ ./10_fix_buffer_overflow_wordole_c_CVE-2014-8123.patch ];
 
+  makeFlags = [
+    "CC=${stdenv.cc.targetPrefix}cc"
+  ];
+
   installTargets = [ "global_install" ];
 
   meta = {

pkgs/applications/office/ledger/default.nix

@@ -3,13 +3,13 @@
 
 stdenv.mkDerivation rec {
   pname = "ledger";
-  version = "3.3.1";
+  version = "3.3.2";
 
   src = fetchFromGitHub {
     owner  = "ledger";
     repo   = "ledger";
     rev    = "v${version}";
-    hash   = "sha256-CnMzsFKBNiXmatgY7aiK8UCqIL6qifA4KbV6BJaza40=";
+    hash   = "sha256-Uym4s8EyzXHlISZqThcb6P1H5bdgD9vmdIOLkk5ikG0=";
   };
 
   outputs = [ "out" "dev" ] ++ lib.optionals usePython [ "py" ];

pkgs/applications/office/libreoffice/default.nix

@@ -349,6 +349,7 @@ in
       sed -e /CppunitTest_sw_layoutwriter/d -i sw/Module_sw.mk
       sed -e /CppunitTest_sw_htmlimport/d -i sw/Module_sw.mk
       sed -e /CppunitTest_sw_core_layout/d -i sw/Module_sw.mk
+      sed -e /CppunitTest_sw_uiwriter6/d -i sw/Module_sw.mk
       sed -e /CppunitTest_sdext_pdfimport/d -i sdext/Module_sdext.mk
       sed -e /CppunitTest_vcl_pdfexport/d -i vcl/Module_vcl.mk
       sed -e "s/DECLARE_SW_ROUNDTRIP_TEST(\([_a-zA-Z0-9.]\+\)[, ].*, *\([_a-zA-Z0-9.]\+\))/class \\1: public \\2 { public: void verify() override; }; void \\1::verify() /" -i "sw/qa/extras/ooxmlexport/ooxmlexport9.cxx"

pkgs/applications/radio/tqsl/default.nix

@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "tqsl";
-  version = "2.5.9";
+  version = "2.6.5";
 
   src = fetchurl {
     url = "https://www.arrl.org/files/file/LoTW%20Instructions/${pname}-${version}.tar.gz";
-    sha256 = "sha256-flv7tI/SYAxxJsHFa3QUgnO0glAAQF87EgP4wyTWnNU=";
+    sha256 = "sha256-UGPMp1mAarHWuLbZu2wWpjgCdf8ZKj0Mwkqp32U5/8w=";
   };
 
   nativeBuildInputs = [ cmake makeWrapper ];

pkgs/applications/radio/wsjtx/default.nix

@@ -4,12 +4,12 @@
 
 stdenv.mkDerivation rec {
   pname = "wsjtx";
-  version = "2.5.4";
+  version = "2.6.1";
 
   # This is a "superbuild" tarball containing both wsjtx and a hamlib fork
   src = fetchurl {
-    url = "http://physics.princeton.edu/pulsar/k1jt/wsjtx-${version}.tgz";
-    sha256 = "sha256-Gz84Rq0sCl9BAXi2YSdl1Z7mPbJJ62z8MyrOF/CjCJg=";
+    url = "https://sourceforge.net/projects/wsjt/files/wsjtx-${version}/wsjtx-${version}.tgz";
+    sha256 = "sha256-YNDiy0WkmmrVhbCQiCGp/yw6wlZNYQQmIP82wt3Mdl8=";
   };
 
   # Hamlib builds with autotools, wsjtx builds with cmake

pkgs/applications/version-management/mercurial/default.nix

@@ -1,4 +1,4 @@
-{ lib, stdenv, fetchurl, python3Packages, makeWrapper, gettext, installShellFiles
+{ lib, stdenv, fetchurl, fetchpatch, python3Packages, makeWrapper, gettext, installShellFiles
 , re2Support ? true
 , rustSupport ? stdenv.hostPlatform.isLinux, rustPlatform
 , fullBuild ? false
@@ -21,11 +21,11 @@ let
 
   self = python3Packages.buildPythonApplication rec {
     pname = "mercurial${lib.optionalString fullBuild "-full"}";
-    version = "6.3.3";
+    version = "6.4";
 
     src = fetchurl {
       url = "https://mercurial-scm.org/release/mercurial-${version}.tar.gz";
-      sha256 = "sha256-E8l/9YnHYF6ApIjzNoUs4dU4xdQUPPszvmm9rd2RV70=";
+      sha256 = "sha256-6Iv7y5kR52kEoxuXLlf4bajmzliSuYw53VHTuVmcE0c=";
     };
 
     format = "other";
@@ -35,7 +35,7 @@ let
     cargoDeps = if rustSupport then rustPlatform.fetchCargoTarball {
       inherit src;
       name = "mercurial-${version}";
-      sha256 = "sha256-ZQYNFEbvSwiJ/BSQ0ZxpjFrmyXkKjVJciwz45Br7Rl8=";
+      sha256 = "sha256-jgB9UMuZ9v+euGN2LPzg0vNK0KeEa8GpQxLJYgQzzbw=";
       sourceRoot = "mercurial-${version}/rust";
     } else null;
     cargoRoot = if rustSupport then "rust" else null;
@@ -110,6 +110,22 @@ let
       gnupg
     ];
 
+    patches = [
+      # remove dependency over packaging for test runner
+      # https://bz.mercurial-scm.org/show_bug.cgi?id=6805
+      (fetchpatch {
+        url = "https://foss.heptapod.net/mercurial/mercurial-devel/-/commit/5e5e3733082a25856038f0fde66d4e08d8881539.patch";
+        hash = "sha256-JNxESWpWZW3AENz57tNJTV/ALnJjkmG1ZnTWSvTr4qY=";
+      })
+
+      # sligthly different test output matching
+      # https://bz.mercurial-scm.org/show_bug.cgi?id=6807
+      (fetchpatch {
+        url = "https://foss.heptapod.net/mercurial/mercurial-devel/-/commit/2231f7d8a60266bb6907b1708400c970ed799017.patch";
+        hash = "sha256-Lm5qXvM9nbmTpuMuvDoWhY4cQQQN7PFZtmu5e7mQVw4=";
+      })
+    ];
+
     postPatch = ''
       patchShebangs .
 
@@ -149,10 +165,6 @@ let
     # doesn't like the extra setlocale warnings emitted by our bash wrappers
     test-locale.t
 
-    # Python 3.10-3.12 deprecation warning: distutils
-    # https://bz.mercurial-scm.org/show_bug.cgi?id=6729
-    test-hghave.t
-
     # Python 3.10-3.12 deprecation warning: asyncore
     # https://bz.mercurial-scm.org/show_bug.cgi?id=6727
     test-patchbomb-tls.t

pkgs/applications/video/mkvtoolnix/default.nix

@@ -47,13 +47,13 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "mkvtoolnix";
-  version = "74.0.0";
+  version = "75.0.0";
 
   src = fetchFromGitLab {
     owner = "mbunkus";
     repo = "mkvtoolnix";
     rev = "release-${version}";
-    sha256 = "sha256-p8rIAHSqYCOlNbuxisQlIkMh2OArc+MOYn1kgC5kJsc=";
+    sha256 = "c3I2ULSvKBTYIm1chVHPkaV0TxblLglBjzeUJ5TRmGw=";
   };
 
   nativeBuildInputs = [

pkgs/applications/video/vlc/default.nix

@@ -197,9 +197,10 @@ stdenv.mkDerivation rec {
       sha256 = "0kyi8q2zn2ww148ngbia9c7qjgdrijf4jlvxyxgrj29cb5iy1kda";
     })
     # patch to build with recent libplacebo
+    # https://code.videolan.org/videolan/vlc/-/merge_requests/3027
     (fetchpatch {
-      url = "https://code.videolan.org/videolan/vlc/-/merge_requests/3027.patch";
-      hash = "sha256-aV+YT1l0ND/USoIIpxcPhdIlP/06J2FxVW4uArS8j88=";
+      url = "https://code.videolan.org/videolan/vlc/-/commit/65ea8d19d91ac1599a29e8411485a72fe89c45e2.patch";
+      hash = "sha256-Zz+g75V6X9OZI3sn614K9Uenxl3WtRHKSdLkWP3b17w=";
     })
   ];
 

pkgs/applications/window-managers/sway/swayest-workstyle/default.nix

@@ -5,16 +5,16 @@
 
 rustPlatform.buildRustPackage rec {
   pname = "swayest-workstyle";
-  version = "1.3.2";
+  version = "1.3.3";
 
   src = fetchFromGitHub {
     owner = "Lyr-7D1h";
     repo = "swayest_workstyle";
     rev = version;
-    sha256 = "sha256-C2Nz6fBwaj+cOxIfoBu+9T+CoJ5Spc1TAJcQWdIF/+I=";
+    sha256 = "sha256-N6z8xNT4vVULt8brOLlVAkJaqYnACMhoHJLGmyE7pZ0=";
   };
 
-  cargoHash = "sha256-6pAlJmpyv2a1XCZQLOYilxJAGPbPmkEz1ynTLa0RjE0=";
+  cargoHash = "sha256-DiNhHuHUgJc9ea+EanaCybXzbrX2PEBdlR0h0zQQLn8=";
 
   doCheck = false; # No tests
 

pkgs/applications/window-managers/weston/default.nix

@@ -6,16 +6,17 @@
 , pipewire ? null, pango ? null, libunwind ? null, freerdp ? null, vaapi ? null
 , libva ? null, libwebp ? null, xwayland ? null
 # beware of null defaults, as the parameters *are* supplied by callPackage by default
-, buildDemo ? false
+, buildDemo ? true
+, buildRemoting ? true, gst_all_1
 }:
 
 stdenv.mkDerivation rec {
   pname = "weston";
-  version = "11.0.0";
+  version = "11.0.1";
 
   src = fetchurl {
-    url = "https://gitlab.freedesktop.org/wayland/weston/-/releases/${version}/downloads/weston-${version}.tar.xz";
-    sha256 = "078y14ff9wmmbzq314f7bq1bxx0rc12xy4j362n60iamr56qs4x6";
+    url = "https://gitlab.freedesktop.org/wayland/weston/uploads/f5648c818fba5432edc3ea63c4db4813/weston-${version}.tar.xz";
+    sha256 = "sha256-pBP2jCUpV/wxkcNlCCPsNWrowSTMwMtEDaXNxOLLnlc=";
   };
 
   depsBuildBuild = [ pkg-config ];
@@ -24,20 +25,21 @@ stdenv.mkDerivation rec {
     cairo colord dbus freerdp lcms2 libGL libXcursor libdrm libevdev libinput
     libjpeg seatd libunwind libva libwebp libxcb libxkbcommon mesa mtdev pam
     pango pipewire udev vaapi wayland wayland-protocols
+  ] ++ lib.optionals buildRemoting [
+    gst_all_1.gstreamer
+    gst_all_1.gst-plugins-base
   ];
 
   mesonFlags= [
     "-Dbackend-drm-screencast-vaapi=${lib.boolToString (vaapi != null)}"
     "-Dbackend-rdp=${lib.boolToString (freerdp != null)}"
     "-Dxwayland=${lib.boolToString (xwayland != null)}" # Default is true!
-    "-Dremoting=false" # TODO
+    (lib.mesonBool "remoting" buildRemoting)
     "-Dpipewire=${lib.boolToString (pipewire != null)}"
     "-Dimage-webp=${lib.boolToString (libwebp != null)}"
     (lib.mesonBool "demo-clients" buildDemo)
     "-Dsimple-clients="
     "-Dtest-junit-xml=false"
-    # TODO:
-    #"--enable-clients"
   ] ++ lib.optionals (xwayland != null) [
     "-Dxwayland-path=${xwayland.out}/bin/Xwayland"
   ];

pkgs/build-support/fetchurl/mirrors.nix

@@ -43,6 +43,11 @@
     "http://bioconductor.jp/packages/"
   ];
 
+  # CRAN mirrors
+  cran = [
+    "https://cran.r-project.org/src/contrib/"
+  ];
+
   # BitlBee mirrors, see https://www.bitlbee.org/main.php/mirrors.html
   bitlbee = [
     "https://get.bitlbee.org/"

pkgs/desktops/deepin/apps/deepin-album/default.nix

@@ -8,6 +8,8 @@
 , dtkwidget
 , qt5integration
 , qt5platform-plugins
+, qtbase
+, qtsvg
 , udisks2-qt5
 , gio-qt
 , image-editor
@@ -16,7 +18,6 @@
 , opencv
 , ffmpeg
 , ffmpegthumbnailer
-, qtbase
 }:
 
 stdenv.mkDerivation rec {
@@ -35,9 +36,7 @@ stdenv.mkDerivation rec {
     substituteInPlace libUnionImage/CMakeLists.txt \
       --replace "/usr" "$out"
     substituteInPlace src/CMakeLists.txt \
-      --replace "set(PREFIX /usr)" "set(PREFIX $out)" \
-      --replace "/usr/bin" "$out/bin" \
-      --replace "/usr/share/deepin-manual/manual-assets/application/)" "share/deepin-manual/manual-assets/application/)"
+      --replace "/usr" "$out"
   '';
 
   nativeBuildInputs = [
@@ -49,7 +48,10 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     dtkwidget
+    qt5integration
     qt5platform-plugins
+    qtbase
+    qtsvg
     udisks2-qt5
     gio-qt
     image-editor
@@ -60,10 +62,7 @@ stdenv.mkDerivation rec {
     ffmpegthumbnailer
   ];
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
+  strictDeps = true;
 
   cmakeFlags = [ "-DVERSION=${version}" ];
 

pkgs/desktops/deepin/apps/deepin-calculator/default.nix

@@ -4,9 +4,10 @@
 , dtkwidget
 , qt5integration
 , qt5platform-plugins
+, qtbase
+, qtsvg
 , dde-qt-dbus-factory
 , cmake
-, qtbase
 , qttools
 , pkg-config
 , wrapQtAppsHook
@@ -33,14 +34,15 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     dtkwidget
+    qt5integration
+    qt5platform-plugins
+    qtbase
+    qtsvg
     dde-qt-dbus-factory
     gtest
   ];
 
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-    "--prefix QT_QPA_PLATFORM_PLUGIN_PATH : ${qt5platform-plugins}/${qtbase.qtPluginPrefix}"
-  ];
+  strictDeps = true;
 
   cmakeFlags = [ "-DVERSION=${version}" ];
 

pkgs/desktops/deepin/apps/deepin-camera/default.nix

@@ -36,11 +36,11 @@ stdenv.mkDerivation rec {
 
   postPatch = ''
     substituteInPlace src/CMakeLists.txt \
-      --replace "/usr/share/libimagevisualresult/filter_cube" "${image-editor}/share/libimagevisualresult/filter_cube" \
+      --replace "/usr/share/libimagevisualresult" "${image-editor}/share/libimagevisualresult" \
       --replace "/usr/include/libusb-1.0" "${lib.getDev libusb1}/include/libusb-1.0"
     substituteInPlace src/com.deepin.Camera.service \
       --replace "/usr/bin/qdbus" "${lib.getBin qttools}/bin/qdbus" \
-      --replace "/usr/share/applications/deepin-camera.desktop" "$out/share/applications/deepin-camera.desktop"
+      --replace "/usr/share" "$out/share"
   '';
 
   nativeBuildInputs = [
@@ -52,6 +52,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     dtkwidget
+    qt5integration
     qt5platform-plugins
     image-editor
     qtbase
@@ -70,14 +71,14 @@ stdenv.mkDerivation rec {
 
   cmakeFlags = [ "-DVERSION=${version}" ];
 
+  strictDeps = true;
+
   env.NIX_CFLAGS_COMPILE = toString [
     "-I${gst_all_1.gstreamer.dev}/include/gstreamer-1.0"
     "-I${gst_all_1.gst-plugins-base.dev}/include/gstreamer-1.0"
   ];
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
   qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
     "--prefix LD_LIBRARY_PATH : ${lib.makeLibraryPath [ ffmpeg ffmpegthumbnailer gst_all_1.gstreamer gst_all_1.gst-plugins-base libusb1 libv4l portaudio systemd ]}"
   ];
 

pkgs/desktops/deepin/apps/deepin-clone/default.nix

@@ -49,6 +49,7 @@ stdenv.mkDerivation rec {
   buildInputs = [
     qtbase
     dtkwidget
+    qt5integration
     qt5platform-plugins
     libuuid
     parted
@@ -61,11 +62,6 @@ stdenv.mkDerivation rec {
 
   strictDeps = true;
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
-
   meta = with lib; {
     description = "Disk and partition backup/restore tool";
     homepage = "https://github.com/linuxdeepin/deepin-clone";

pkgs/desktops/deepin/apps/deepin-compressor/default.nix

@@ -44,6 +44,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     dtkwidget
+    qt5integration
     qt5platform-plugins
     udisks2-qt5
     kcodecs
@@ -60,11 +61,6 @@ stdenv.mkDerivation rec {
 
   strictDeps = true;
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
-
   meta = with lib; {
     description = "A fast and lightweight application for creating and extracting archives";
     homepage = "https://github.com/linuxdeepin/deepin-compressor";

pkgs/desktops/deepin/apps/deepin-draw/default.nix

@@ -46,6 +46,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     qtbase
+    qt5integration
     qtsvg
     dtkwidget
     qt5platform-plugins
@@ -55,11 +56,6 @@ stdenv.mkDerivation rec {
 
   strictDeps = true;
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
-
   meta = with lib; {
     description = "Lightweight drawing tool for users to freely draw and simply edit images";
     homepage = "https://github.com/linuxdeepin/deepin-draw";

pkgs/desktops/deepin/apps/deepin-editor/default.nix

@@ -54,6 +54,7 @@ stdenv.mkDerivation rec {
     qtbase
     qtsvg
     dtkwidget
+    qt5integration
     qt5platform-plugins
     dde-qt-dbus-factory
     kcodecs
@@ -68,11 +69,6 @@ stdenv.mkDerivation rec {
 
   cmakeFlags = [ "-DVERSION=${version}" ];
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
-
   meta = with lib; {
     description = "A desktop text editor that supports common text editing features";
     homepage = "https://github.com/linuxdeepin/deepin-editor";

pkgs/desktops/deepin/apps/deepin-image-viewer/default.nix

@@ -59,6 +59,7 @@ stdenv.mkDerivation rec {
     qtbase
     qtsvg
     dtkwidget
+    qt5integration
     qt5platform-plugins
     gio-qt
     udisks2-qt5
@@ -71,11 +72,6 @@ stdenv.mkDerivation rec {
 
   cmakeFlags = [ "-DVERSION=${version}" ];
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
-
   meta = with lib; {
     description = "An image viewing tool with fashion interface and smooth performance";
     homepage = "https://github.com/linuxdeepin/deepin-image-viewer";

pkgs/desktops/deepin/apps/deepin-movie-reborn/default.nix

@@ -73,6 +73,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     dtkwidget
+    qt5integration
     qt5platform-plugins
     qtx11extras
     qtmultimedia
@@ -99,12 +100,6 @@ stdenv.mkDerivation rec {
     gst-plugins-base
   ]);
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-    "--prefix LD_LIBRARY_PATH : ${lib.makeLibraryPath [ mpv ffmpeg ffmpegthumbnailer gst_all_1.gstreamer gst_all_1.gst-plugins-base ]}"
-  ];
-
   env.NIX_CFLAGS_COMPILE = toString [
     "-I${gst_all_1.gstreamer.dev}/include/gstreamer-1.0"
     "-I${gst_all_1.gst-plugins-base.dev}/include/gstreamer-1.0"
@@ -114,6 +109,12 @@ stdenv.mkDerivation rec {
     "-DVERSION=${version}"
   ];
 
+  strictDeps = true;
+
+  qtWrapperArgs = [
+    "--prefix LD_LIBRARY_PATH : ${lib.makeLibraryPath [ mpv ffmpeg ffmpegthumbnailer gst_all_1.gstreamer gst_all_1.gst-plugins-base ]}"
+  ];
+
   preFixup = ''
     glib-compile-schemas ${glib.makeSchemaPath "$out" "${pname}-${version}"}
     qtWrapperArgs+=(--prefix GST_PLUGIN_SYSTEM_PATH_1_0 : "$GST_PLUGIN_SYSTEM_PATH_1_0")

pkgs/desktops/deepin/apps/deepin-music/default.nix

@@ -38,8 +38,7 @@ stdenv.mkDerivation rec {
 
   postPatch = ''
     substituteInPlace src/music-player/CMakeLists.txt \
-      --replace "include_directories(/usr/include/vlc)" "include_directories(${libvlc}/include/vlc)" \
-      --replace "include_directories(/usr/include/vlc/plugins)" "include_directories(${libvlc}/include/vlc/plugins)" \
+      --replace "/usr/include/vlc" "${libvlc}/include/vlc" \
       --replace "/usr/share" "$out/share"
     substituteInPlace src/libmusic-plugin/CMakeLists.txt \
       --replace "/usr/lib/deepin-aiassistant" "$out/lib/deepin-aiassistant"
@@ -56,6 +55,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     dtkwidget
+    qt5integration
     qt5platform-plugins
     dde-qt-dbus-factory
     udisks2-qt5
@@ -76,15 +76,12 @@ stdenv.mkDerivation rec {
     gst-plugins-good
   ]);
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
-
   cmakeFlags = [
     "-DVERSION=${version}"
   ];
 
+  strictDeps = true;
+
   preFixup = ''
     qtWrapperArgs+=(--prefix GST_PLUGIN_SYSTEM_PATH_1_0 : "$GST_PLUGIN_SYSTEM_PATH_1_0")
   '';

pkgs/desktops/deepin/apps/deepin-reader/default.nix

@@ -46,6 +46,7 @@ stdenv.mkDerivation rec {
 
   buildInputs = [
     dtkwidget
+    qt5integration
     qt5platform-plugins
     dde-qt-dbus-factory
     qtwebengine
@@ -61,11 +62,6 @@ stdenv.mkDerivation rec {
     "DEFINES+=VERSION=${version}"
   ];
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
-
   meta = with lib; {
     description = "A simple memo software with texts and voice recordings";
     homepage = "https://github.com/linuxdeepin/deepin-reader";

pkgs/desktops/deepin/apps/deepin-shortcut-viewer/default.nix

@@ -32,6 +32,7 @@ stdenv.mkDerivation rec {
   buildInputs = [
     qtbase
     dtkwidget
+    qt5integration
     qt5platform-plugins
   ];
 
@@ -40,11 +41,6 @@ stdenv.mkDerivation rec {
     "PREFIX=${placeholder "out"}"
   ];
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
-
   meta = with lib; {
     description = "Deepin Shortcut Viewer";
     homepage = "https://github.com/linuxdeepin/deepin-shortcut-viewer";

pkgs/desktops/deepin/apps/deepin-terminal/default.nix

@@ -53,6 +53,7 @@ stdenv.mkDerivation rec {
     qtbase
     qtsvg
     dtkwidget
+    qt5integration
     qt5platform-plugins
     dde-qt-dbus-factory
     qtx11extras
@@ -64,11 +65,6 @@ stdenv.mkDerivation rec {
 
   strictDeps = true;
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
-
   meta = with lib; {
     description = "Terminal emulator with workspace, multiple windows, remote management, quake mode and other features";
     homepage = "https://github.com/linuxdeepin/deepin-terminal";

pkgs/desktops/deepin/apps/deepin-voice-note/default.nix

@@ -44,6 +44,7 @@ stdenv.mkDerivation rec {
   buildInputs = [
     qtbase
     dtkwidget
+    qt5integration
     qt5platform-plugins
     dde-qt-dbus-factory
     qtmultimedia
@@ -62,11 +63,6 @@ stdenv.mkDerivation rec {
 
   env.NIX_CFLAGS_COMPILE = "-I${dde-qt-dbus-factory}/include/libdframeworkdbus-2.0";
 
-  # qt5integration must be placed before qtsvg in QT_PLUGIN_PATH
-  qtWrapperArgs = [
-    "--prefix QT_PLUGIN_PATH : ${qt5integration}/${qtbase.qtPluginPrefix}"
-  ];
-
   preFixup = ''
     qtWrapperArgs+=(--prefix GST_PLUGIN_SYSTEM_PATH_1_0 : "$GST_PLUGIN_SYSTEM_PATH_1_0")
   '';

pkgs/desktops/pantheon/apps/elementary-files/default.nix

@@ -1,7 +1,6 @@
 { lib
 , stdenv
 , fetchFromGitHub
-, fetchpatch
 , nix-update-script
 , pkg-config
 , meson
@@ -29,7 +28,7 @@
 
 stdenv.mkDerivation rec {
   pname = "elementary-files";
-  version = "6.3.0";
+  version = "6.3.1";
 
   outputs = [ "out" "dev" ];
 
@@ -37,18 +36,9 @@ stdenv.mkDerivation rec {
     owner = "elementary";
     repo = "files";
     rev = version;
-    sha256 = "sha256-DS39jCeN+FFiEqJqxa5F2XRKF7SJsm2qi5KKb79guKo=";
+    sha256 = "sha256-JFkyO4r/Fb8bjWn+wVS2rIpFz19/uBVCsLt8091xzVI=";
   };
 
-  patches = [
-    # Avoid crash due to ref counting issues in Directory cache
-    # https://github.com/elementary/files/pull/2149
-    (fetchpatch {
-      url = "https://github.com/elementary/files/commit/6a0d16e819dea2d0cd2d622414257da9433afe2f.patch";
-      sha256 = "sha256-ijuSMZzVbSwWMWsK24A/24NfxjxgK/BU2qZlq6xLBEU=";
-    })
-  ];
-
   nativeBuildInputs = [
     desktop-file-utils
     meson

pkgs/development/compilers/abcl/default.nix

@@ -1,38 +1,67 @@
-{lib, stdenv, fetchurl, ant, jre, jdk}:
+{ stdenv
+, lib
+, fetchurl
+, ant
+, jre
+, jdk
+, makeWrapper
+}:
+
 stdenv.mkDerivation rec {
   pname = "abcl";
   version = "1.9.1";
-  # or fetchFromGitHub(owner,repo,rev) or fetchgit(rev)
+
   src = fetchurl {
     url = "https://common-lisp.net/project/armedbear/releases/${version}/${pname}-src-${version}.tar.gz";
     sha256 = "sha256-pbxnfJRB9KgzwgpUG93Rb/+SZIRmkd6aHa9mmfj/EeI=";
   };
+
   configurePhase = ''
+    runHook preConfigure
+
     mkdir nix-tools
     export PATH="$PWD/nix-tools:$PATH"
     echo "echo nix-builder.localdomain" > nix-tools/hostname
     chmod a+x nix-tools/*
 
     hostname
+
+    runHook postConfigure
   '';
+
+  buildInputs = [ jre ant jdk jre ];
+
+  nativeBuildInputs = [ makeWrapper ];
+
   buildPhase = ''
+    runHook preBuild
+
     ant
+
+    runHook postBuild
   '';
-  # Fix for https://github.com/armedbear/abcl/issues/484
-  javaOpts =
-    lib.optionalString
-      (lib.versionAtLeast jre.version "17")
-      "--add-opens=java.base/java.util.jar=ALL-UNNAMED";
+
   installPhase = ''
+    runHook preInstall
+
     mkdir -p "$out"/{bin,share/doc/abcl,lib/abcl}
     cp -r README COPYING CHANGES examples/  "$out/share/doc/abcl/"
     cp -r dist/*.jar contrib/ "$out/lib/abcl/"
 
-    echo "#! ${stdenv.shell}" >> "$out/bin/abcl"
-    echo "${jre}/bin/java $javaOpts -cp \"$out/lib/abcl/abcl.jar:$out/lib/abcl/abcl-contrib.jar:\$CLASSPATH\" org.armedbear.lisp.Main \"\$@\"" >> "$out/bin/abcl"
-    chmod a+x "$out"/bin/*
+    makeWrapper ${jre}/bin/java $out/bin/abcl \
+      --prefix CLASSPATH : $out/lib/abcl/abcl.jar \
+      --prefix CLASSPATH : $out/lib/abcl/abcl-contrib.jar \
+      ${lib.optionalString (lib.versionAtLeast jre.version "17")
+        # Fix for https://github.com/armedbear/abcl/issues/484
+        "--add-flags --add-opens=java.base/java.util.jar=ALL-UNNAMED \\"
+      }
+      --add-flags org.armedbear.lisp.Main
+
+    runHook postInstall
   '';
-  buildInputs = [jre ant jdk jre];
+
+  passthru.updateScript = ./update.sh;
+
   meta = {
     description = "A JVM-based Common Lisp implementation";
     license = lib.licenses.gpl3 ;

pkgs/development/compilers/abcl/update.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env nix-shell
+#!nix-shell -i bash -p nix-update curl
+
+new_version=$(curl https://armedbear.common-lisp.dev/ | grep abcl-src | sed 's;[^>]*>abcl-src-\(.*\).tar[^$]*;\1;' | head -n 1)
+nix-update abcl --version "$new_version"

pkgs/development/compilers/cudatoolkit/common.nix

@@ -29,6 +29,7 @@ args@
 , python3 # FIXME: CUDAToolkit 10 may still need python27
 , pulseaudio
 , requireFile
+, stdenv
 , backendStdenv # E.g. gcc11Stdenv, set in extension.nix
 , unixODBC
 , wayland
@@ -136,8 +137,8 @@ backendStdenv.mkDerivation rec {
     (placeholder "lib")
     (placeholder "out")
     "${placeholder "out"}/nvvm"
-    # Is it not handled by autoPatchelf automatically?
-    "${lib.getLib backendStdenv.cc.cc}/lib64"
+    # NOTE: use the same libstdc++ as the rest of nixpkgs, not from backendStdenv
+    "${lib.getLib stdenv.cc.cc}/lib64"
     "${placeholder "out"}/jre/lib/amd64/jli"
     "${placeholder "out"}/lib64"
     "${placeholder "out"}/nvvm/lib64"
@@ -219,6 +220,7 @@ backendStdenv.mkDerivation rec {
 
       mv pkg/builds/nsight_systems/target-linux-x64 $out/target-linux-x64
       mv pkg/builds/nsight_systems/host-linux-x64 $out/host-linux-x64
+      rm $out/host-linux-x64/libstdc++.so*
     ''}
       ${lib.optionalString (lib.versionAtLeast version "11.8")
       # error: auto-patchelf could not satisfy dependency libtiff.so.5 wanted by /nix/store/.......-cudatoolkit-12.0.1/host-linux-x64/Plugins/imageformats/libqtiff.so

pkgs/development/compilers/cudatoolkit/extension.nix

@@ -10,11 +10,17 @@ final: prev: let
   finalVersion = cudatoolkitVersions.${final.cudaVersion};
 
   # Exposed as cudaPackages.backendStdenv.
-  # We don't call it just "stdenv" to avoid confusion: e.g. this toolchain doesn't contain nvcc.
-  # Instead, it's the back-end toolchain for nvcc to use.
-  # We also use this to link a compatible libstdc++ (backendStdenv.cc.cc.lib)
+  # This is what nvcc uses as a backend,
+  # and it has to be an officially supported one (e.g. gcc11 for cuda11).
+  #
+  # It, however, propagates current stdenv's libstdc++ to avoid "GLIBCXX_* not found errors"
+  # when linked with other C++ libraries.
+  # E.g. for cudaPackages_11_8 we use gcc11 with gcc12's libstdc++
   # Cf. https://github.com/NixOS/nixpkgs/pull/218265 for context
-  backendStdenv = prev.pkgs."${finalVersion.gcc}Stdenv";
+  backendStdenv = final.callPackage ./stdenv.nix {
+    nixpkgsStdenv = prev.pkgs.stdenv;
+    nvccCompatibleStdenv = prev.pkgs.buildPackages."${finalVersion.gcc}Stdenv";
+  };
 
   ### Add classic cudatoolkit package
   cudatoolkit =

pkgs/development/compilers/cudatoolkit/redist/build-cuda-redist-package.nix

@@ -1,4 +1,5 @@
 { lib
+, stdenv
 , backendStdenv
 , fetchurl
 , autoPatchelfHook
@@ -30,11 +31,11 @@ backendStdenv.mkDerivation {
   ];
 
   buildInputs = [
-    # autoPatchelfHook will search for a libstdc++ and we're giving it a
-    # "compatible" libstdc++ from the same toolchain that NVCC uses.
-    #
+    # autoPatchelfHook will search for a libstdc++ and we're giving it
+    # one that is compatible with the rest of nixpkgs, even when
+    # nvcc forces us to use an older gcc
     # NB: We don't actually know if this is the right thing to do
-    backendStdenv.cc.cc.lib
+    stdenv.cc.cc.lib
   ];
 
   dontBuild = true;

pkgs/development/compilers/cudatoolkit/stdenv.nix

@@ -0,0 +1,17 @@
+{ nixpkgsStdenv
+, nvccCompatibleStdenv
+, overrideCC
+, wrapCCWith
+}:
+
+overrideCC nixpkgsStdenv (wrapCCWith {
+  cc = nvccCompatibleStdenv.cc.cc;
+
+  # This option is for clang's libcxx, but we (ab)use it for gcc's libstdc++.
+  # Note that libstdc++ maintains forward-compatibility: if we load a newer
+  # libstdc++ into the process, we can still use libraries built against an
+  # older libstdc++. This, in practice, means that we should use libstdc++ from
+  # the same stdenv that the rest of nixpkgs uses.
+  # We currently do not try to support anything other than gcc and linux.
+  libcxx = nixpkgsStdenv.cc.cc.lib;
+})

pkgs/development/compilers/hare/hare/default.nix

@@ -14,13 +14,13 @@ let
 in
 stdenv.mkDerivation (self: {
   pname = "hare";
-  version = "unstable-2023-02-10";
+  version = "unstable-2023-03-15";
 
   src = fetchFromSourcehut {
     owner = "~sircmpwn";
     repo = "hare";
-    rev = "52b3f2d0c7a85e04a79666a954101e527b7f1272";
-    hash = "sha256-/zP8LbZ113Ar06MZF1zP20LKMGko+4HcOXSntLVAQAU=";
+    rev = "488771bc8cef15557a44815eb6f7808df40a09f7";
+    hash = "sha256-1cSXWD8jpW1VJZDTDOkIabczqbaDCOWsyaUSGtsKsUM=";
   };
 
   patches = [

pkgs/development/compilers/hare/harec/default.nix

@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation (self: {
   pname = "harec";
-  version = "unstable-2023-02-08";
+  version = "unstable-2023-02-18";
 
   src = fetchFromSourcehut {
     owner = "~sircmpwn";
     repo = "harec";
-    rev = "4730fa6b835f08c44bd7991cc8b264fbc27d752b";
-    hash = "sha256-XOhZWdmkMAuXbj7svILJI3wI7RF9OAb/OE1uGel4/vE=";
+    rev = "dd50ca7740408e3c6e41c0ca48b59b9f7f5911f2";
+    hash = "sha256-616mPMdy4yHHuwGcq+aDdEOteEiWgufRzreXHGhmHr0=";
   };
 
   nativeBuildInputs = [

pkgs/development/interpreters/clojure/default.nix

@@ -2,12 +2,12 @@
 
 stdenv.mkDerivation rec {
   pname = "clojure";
-  version = "1.11.1.1262";
+  version = "1.11.1.1273";
 
   src = fetchurl {
     # https://clojure.org/releases/tools
     url = "https://download.clojure.org/install/clojure-tools-${version}.tar.gz";
-    sha256 = "sha256-k++uGj1CdOjPXYAVERs6UqLnrUXE1Bv/hm1JXRxAHuI=";
+    sha256 = "sha256-X4uvzyS9FIrJvL5gqOe4CTye2OuODzhxmXcOOPDkDOY=";
   };
 
   nativeBuildInputs = [

pkgs/development/interpreters/quickjs/default.nix

@@ -15,6 +15,10 @@ stdenv.mkDerivation rec {
     hash = "sha256-VMaxVVQuJ3DAwYrC14uJqlRBg0//ugYvtyhOXsTUbCA=";
   };
 
+  postPatch = lib.optionalString stdenv.isDarwin ''
+    substituteInPlace Makefile --replace "CONFIG_LTO=y" ""
+  '';
+
   makeFlags = [ "prefix=${placeholder "out"}" ];
   enableParallelBuilding = true;
 
@@ -45,15 +49,15 @@ stdenv.mkDerivation rec {
     temp=$(mktemp).js
     echo "console.log('Output from compiled program');" > "$temp"
     set -o verbose
-    out=$(mktemp) && qjsc         "$temp" -o "$out" && "$out" | grep -q "Output from compiled program"
-    out=$(mktemp) && qjsc   -flto "$temp" -o "$out" && "$out" | grep -q "Output from compiled program"
+    out=$(mktemp) && qjsc         -o "$out" "$temp" && "$out" | grep -q "Output from compiled program"
+    out=$(mktemp) && qjsc   -flto -o "$out" "$temp" && "$out" | grep -q "Output from compiled program"
   '';
 
   meta = with lib; {
     description = "A small and embeddable Javascript engine";
     homepage = "https://bellard.org/quickjs/";
     maintainers = with maintainers; [ stesie AndersonTorres ];
-    platforms = platforms.linux;
+    platforms = platforms.unix;
     license = licenses.mit;
     mainProgram = "qjs";
   };

pkgs/development/libraries/cpp-utilities/default.nix

@@ -7,13 +7,13 @@
 
 stdenv.mkDerivation rec {
   pname = "cpp-utilities";
-  version = "5.21.0";
+  version = "5.22.0";
 
   src = fetchFromGitHub {
     owner = "Martchus";
     repo = pname;
     rev = "v${version}";
-    sha256 = "sha256-jva/mVk20xqEcHlUMnOBy2I09oGoLkKaqwRSg0kIKS0=";
+    sha256 = "sha256-c36FzKDAaalKVIrqVSCoslrKVopW77cGdGwfiMbaXe4=";
   };
 
   nativeBuildInputs = [ cmake ];

pkgs/development/libraries/gstreamer/default.nix

@@ -1,4 +1,19 @@
-{ callPackage, AudioToolbox, AVFoundation, Cocoa, CoreFoundation, CoreMedia, CoreServices, CoreVideo, DiskArbitration, Foundation, IOKit, MediaToolbox, OpenGL, VideoToolbox }:
+{ callPackage
+, AVFoundation
+, AudioToolbox
+, Cocoa
+, CoreFoundation
+, CoreMedia
+, CoreServices
+, CoreVideo
+, DiskArbitration
+, Foundation
+, IOKit
+, MediaToolbox
+, OpenGL
+, VideoToolbox
+, ipu6ep-camera-hal
+}:
 
 {
   gstreamer = callPackage ./core { inherit CoreServices; };
@@ -25,7 +40,10 @@
 
   gst-vaapi = callPackage ./vaapi { };
 
-  icamerasrc = callPackage ./icamerasrc { };
+  icamerasrc-ipu6 = callPackage ./icamerasrc { };
+  icamerasrc-ipu6ep = callPackage ./icamerasrc {
+    ipu6-camera-hal = ipu6ep-camera-hal;
+  };
 
   # note: gst-python is in ./python/default.nix - called under pythonPackages
 }

pkgs/development/libraries/gstreamer/icamerasrc/default.nix

@@ -9,14 +9,14 @@
 }:
 
 stdenv.mkDerivation rec {
-  pname = "icamerasrc";
-  version = "20221209";
+  pname = "icamerasrc-${ipu6-camera-hal.ipuVersion}";
+  version = "unstable-2023-03-09";
 
   src = fetchFromGitHub {
     owner = "intel";
     repo = "icamerasrc";
-    rev = "refs/tags/rpl_plat_${version}_pv";
-    hash = "sha256-qlV363l4tUjUAa1LiZQq55byKpz1tLESKAXEmgiYHVo=";
+    rev = "17841ab6249aaa69bd9b3959262bf182dee74111";
+    hash = "sha256-j8ZYe4nyy5yfo10CGeXDwbAaAPvdr0ptMWB8hQDyESQ=";
   };
 
   nativeBuildInputs = [
@@ -45,6 +45,10 @@ stdenv.mkDerivation rec {
 
   enableParallelBuilding = true;
 
+  passthru = {
+    inherit (ipu6-camera-hal) ipuVersion;
+  };
+
   meta = with lib; {
     description = "GStreamer Plugin for MIPI camera support through the IPU6/IPU6EP/IPU6SE on Intel Tigerlake/Alderlake/Jasperlake platforms";
     homepage = "https://github.com/intel/icamerasrc/tree/icamerasrc_slim_api";

pkgs/development/libraries/ipu6-camera-hal/default.nix

@@ -14,14 +14,14 @@
 }:
 
 stdenv.mkDerivation {
-  pname = "ipu6-camera-hal";
-  version = "unstable-2023-01-09";
+  pname = "${ipu6-camera-bin.ipuVersion}-camera-hal";
+  version = "unstable-2023-02-08";
 
   src = fetchFromGitHub {
     owner = "intel";
     repo = "ipu6-camera-hal";
-    rev = "37292891c73367d22ba1fc96ea9b6e4546903037";
-    hash = "sha256-dJvTZt85rt5/v2JXOsfbSY933qffyXW74L0nWdIlqug=";
+    rev = "884b81aae0ea19a974eb8ccdaeef93038136bdd4";
+    hash = "sha256-AePL7IqoOhlxhfPRLpCman5DNh3wYS4MUcLgmgBUcCM=";
   };
 
   nativeBuildInputs = [
@@ -52,16 +52,20 @@ stdenv.mkDerivation {
     gst_all_1.gst-plugins-base
   ];
 
-  preFixup = ''
-    ls -lah $out/lib/pkgconfig/
-    sed -Ei \
-      -e "s,^prefix=.*,prefix=$out," \
-      -e "s,^exec_prefix=.*,exec_prefix=''${prefix}," \
-      -e "s,^libdir=.*,libdir=''${prefix}/lib," \
-      -e "s,^includedir=.*,includedir=''${prefix}/include/libcamhal," \
-      $out/lib/pkgconfig/libcamhal.pc
+  postPatch = ''
+    substituteInPlace src/platformdata/PlatformData.h \
+      --replace '/usr/share/' "${placeholder "out"}/share/"
   '';
 
+  postFixup = ''
+    substituteInPlace $out/lib/pkgconfig/libcamhal.pc \
+      --replace 'prefix=/usr' "prefix=$out"
+  '';
+
+  passthru = {
+    inherit (ipu6-camera-bin) ipuVersion;
+  };
+
   meta = with lib; {
     description = "HAL for processing of images in userspace";
     homepage = "https://github.com/intel/ipu6-camera-hal";

pkgs/development/libraries/libpg_query/default.nix

@@ -13,13 +13,17 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ which ];
 
-  makeFlags = [ "build" ];
+  makeFlags = [ "build" "build_shared" ];
 
   installPhase = ''
     install -Dm644 -t $out/lib libpg_query.a
     install -Dm644 -t $out/include pg_query.h
+    install -Dm644 -t $out/lib libpg_query${stdenv.hostPlatform.extensions.sharedLibrary}
   '';
 
+  doCheck = true;
+  checkTarget = "test";
+
   meta = with lib; {
     homepage = "https://github.com/pganalyze/libpg_query";
     description = "C library for accessing the PostgreSQL parser outside of the server environment";

pkgs/development/libraries/librem/default.nix

@@ -18,6 +18,7 @@ stdenv.mkDerivation rec {
   makeFlags = [
     "LIBRE_MK=${libre}/share/re/re.mk"
     "PREFIX=$(out)"
+    "AR=${stdenv.cc.targetPrefix}ar"
   ]
   ++ lib.optional (stdenv.cc.cc != null) "SYSROOT_ALT=${lib.getDev stdenv.cc.cc}"
   ++ lib.optional (stdenv.cc.libc != null) "SYSROOT=${lib.getDev stdenv.cc.libc}"

pkgs/development/libraries/qtutilities/default.nix

@@ -9,13 +9,13 @@
 
 stdenv.mkDerivation rec {
   pname = "qtutilities";
-  version = "6.11.0";
+  version = "6.12.0";
 
   src = fetchFromGitHub {
     owner = "Martchus";
     repo = pname;
     rev = "v${version}";
-    hash = "sha256-eMQyXxBupqcLmNtAcVBgTWtAtuyRlWB9GKNpomM10B0=";
+    hash = "sha256-zkuVD6TH3eHFMu31PmKF2qlQ3itwWHMzVp0ZjdspWTk=";
   };
 
   buildInputs = [ qtbase cpp-utilities ];

pkgs/development/libraries/science/math/cudnn/generic.nix

@@ -1,4 +1,4 @@
-{
+{ stdenv,
   backendStdenv,
   lib,
   zlib,
@@ -26,7 +26,6 @@
   maxCudaVersion,
 }:
 assert useCudatoolkitRunfile || (libcublas != null); let
-  inherit (backendStdenv) cc;
   inherit (lib) lists strings trivial versions;
 
   # majorMinorPatch :: String -> String
@@ -63,7 +62,10 @@ in
 
     # Used by autoPatchelfHook
     buildInputs = [
-      cc.cc.lib # libstdc++
+      # Note this libstdc++ isn't from the (possibly older) nvcc-compatible
+      # stdenv, but from the (newer) stdenv that the rest of nixpkgs uses
+      stdenv.cc.cc.lib
+
       zlib
       cudatoolkit_root
     ];

pkgs/development/libraries/science/math/faiss/default.nix

@@ -25,7 +25,7 @@
   builtins.head optLevels
 , faiss # To run demos in the tests
 , runCommand
-}:
+}@inputs:
 
 assert cudaSupport -> nvidia-thrust.cudaSupport;
 
@@ -33,9 +33,11 @@ let
   pname = "faiss";
   version = "1.7.2";
 
-  inherit (cudaPackages) cudaFlags;
+  inherit (cudaPackages) cudaFlags backendStdenv;
   inherit (cudaFlags) cudaCapabilities dropDot;
 
+  stdenv = if cudaSupport then backendStdenv else inputs.stdenv;
+
   cudaJoined = symlinkJoin {
     name = "cuda-packages-unsplit";
     paths = with cudaPackages; [

pkgs/development/node-packages/node-packages.nix

@@ -131006,10 +131006,10 @@ in
   pnpm = nodeEnv.buildNodePackage {
     name = "pnpm";
     packageName = "pnpm";
-    version = "7.29.1";
+    version = "8.1.1";
     src = fetchurl {
-      url = "https://registry.npmjs.org/pnpm/-/pnpm-7.29.1.tgz";
-      sha512 = "dn+65B2XpMIin7sQZvBIJ2Zyx8Z7LK95qyAvgEPE8qXkWYL/LuwpfMfK9Muc7+zNnpPwiQgtGEsxgOtuabFibQ==";
+      url = "https://registry.npmjs.org/pnpm/-/pnpm-8.1.1.tgz";
+      sha512 = "XLzcc4O8YrqfQ1+qjPtHGDFcdUeno2Zk+kuuSc9CagIiY8y4uhnqQ2B7jW8tgwQDNmehewGZuqrAoskgCkbTnw==";
     };
     buildInputs = globalBuildInputs;
     meta = {

pkgs/development/ocaml-modules/lwt_ssl/default.nix

@@ -1,14 +1,14 @@
-{ lib, fetchFromGitHub, buildDunePackage, ssl, lwt }:
+{ lib, fetchurl, buildDunePackage, ssl, lwt }:
 
 buildDunePackage rec {
   pname = "lwt_ssl";
-  version = "1.1.3";
+  version = "1.2.0";
 
-  src = fetchFromGitHub {
-    owner = "aantron";
-    repo = "lwt_ssl";
-    rev = version;
-    sha256 = "sha256-d/jkTI/D2LVi9nrndRGgqg6ca1FcmRKknR7YXyA7gWw=";
+  duneVersion = "3";
+
+  src = fetchurl {
+    url = "https://github.com/ocsigen/lwt_ssl/releases/download/${version}/lwt_ssl-${version}.tbz";
+    hash = "sha256-swIK0nrs83fhw/J0Cgizbcu6mR+EMGZRE1dBBUiImnc=";
   };
 
   propagatedBuildInputs = [ ssl lwt ];

pkgs/development/ocaml-modules/ssl/default.nix

@@ -12,6 +12,8 @@ buildDunePackage rec {
   pname = "ssl";
   version = "0.5.13";
 
+  duneVersion = "3";
+
   src = fetchFromGitHub {
     owner = "savonet";
     repo = "ocaml-ssl";

pkgs/development/python-modules/adafruit-platformdetect/default.nix

@@ -7,7 +7,7 @@
 
 buildPythonPackage rec {
   pname = "adafruit-platformdetect";
-  version = "3.43.0";
+  version = "3.44.0";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
@@ -15,7 +15,7 @@ buildPythonPackage rec {
   src = fetchPypi {
     pname = "Adafruit-PlatformDetect";
     inherit version;
-    hash = "sha256-7JsdHeYjPSXGdnvs67haOYqX+le+RmivfXPtxDT6BJ8=";
+    hash = "sha256-mEs1HnMn+3p4+YAyOmqFGrcMpeUwMbpkGQAx/pdDqhk=";
   };
 
   SETUPTOOLS_SCM_PRETEND_VERSION = version;

pkgs/development/python-modules/ancp-bids/default.nix

@@ -0,0 +1,41 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, pythonOlder
+, pytestCheckHook
+, setuptools
+, numpy
+, pandas
+}:
+
+buildPythonPackage rec {
+  pname = "ancp-bids";
+  version = "0.2.1";
+  disabled = pythonOlder "3.7";
+  format = "pyproject";
+
+  # `tests/data` dir missing from PyPI dist
+  src = fetchFromGitHub {
+     owner = "ANCPLabOldenburg";
+     repo = pname;
+     rev = "refs/tags/${version}";
+     hash = "sha256-Nu9pulVSZysgm/F7jl+VpoqMCiHeysZjQDQ1dT7AnpE=";
+  };
+
+  nativeBuildInputs = [ setuptools ] ;
+
+  checkInputs = [ numpy pandas pytestCheckHook ];
+  pythonImportsCheck = [
+    "ancpbids"
+  ];
+
+  pytestFlagsArray = [ "tests/auto" ];
+  disabledTests = [ "test_fetch_dataset" ];
+
+  meta = with lib; {
+    homepage = "https://ancpbids.readthedocs.io";
+    description = "Read/write/validate/query BIDS datasets";
+    license = licenses.mit;
+    maintainers = with maintainers; [ bcdarwin ];
+  };
+}

pkgs/development/python-modules/calysto-scheme/default.nix

@@ -0,0 +1,32 @@
+{ lib
+, python3
+, fetchFromGitHub
+}:
+
+python3.pkgs.buildPythonPackage rec {
+  pname = "calysto-scheme";
+  version = "1.4.7";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "Calysto";
+    repo = "calysto_scheme";
+    rev = "v${version}";
+    hash = "sha256-5InImTbucggjf/tl8K31ZtLrwu5hqvggl7sYb0eqIEg=";
+  };
+
+  propagatedBuildInputs = with python3.pkgs; [
+    yasi
+    metakernel
+  ];
+
+  pythonImportsCheck = [ "calysto_scheme" ];
+
+  meta = with lib; {
+    description = "A Scheme kernel for Jupyter that can use Python libraries";
+    homepage = "https://github.com/Calysto/calysto_scheme";
+    changelog = "https://github.com/Calysto/calysto_scheme/blob/${src.rev}/ChangeLog.md";
+    license = licenses.bsd3;
+    maintainers = with maintainers; [ kranzes ];
+  };
+}

pkgs/development/python-modules/calysto/default.nix

@@ -0,0 +1,37 @@
+{ lib
+, python3
+, fetchFromGitHub
+}:
+
+python3.pkgs.buildPythonPackage rec {
+  pname = "calysto";
+  version = "1.0.6";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "Calysto";
+    repo = "calysto";
+    rev = "v${version}";
+    hash = "sha256-lr/cHFshpFs/PGMCsa3FKMRPTP+eE9ziH5XCpV+KzO8=";
+  };
+
+  propagatedBuildInputs = with python3.pkgs; [
+    metakernel
+    svgwrite
+    ipywidgets
+    cairosvg
+    numpy
+  ];
+
+  # Tests are failing not because of Nix.
+  doCheck = false;
+
+  pythonImportsCheck = [ "calysto" ];
+
+  meta = with lib; {
+    description = "Tools for Jupyter and Python";
+    homepage = "https://github.com/Calysto/calysto";
+    license = licenses.bsd2;
+    maintainers = with maintainers; [ kranzes ];
+  };
+}

pkgs/development/python-modules/django-crispy-forms/default.nix

@@ -2,6 +2,7 @@
 , buildPythonPackage
 , fetchFromGitHub
 , django
+, setuptools
 , pytestCheckHook
 , pytest-django
 }:
@@ -9,6 +10,7 @@
 buildPythonPackage rec {
   pname = "django-crispy-forms";
   version = "2.0";
+  format = "pyproject";
 
   src = fetchFromGitHub {
     owner = "django-crispy-forms";
@@ -19,6 +21,7 @@ buildPythonPackage rec {
 
   propagatedBuildInputs = [
     django
+    setuptools
   ];
 
   # FIXME: RuntimeError: Model class source.crispy_forms.tests.forms.CrispyTestModel doesn't declare an explicit app_label and isn't in an application in INSTALLED_APPS.

pkgs/development/python-modules/functiontrace/default.nix

@@ -0,0 +1,31 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, setuptools
+, toml
+}:
+
+buildPythonPackage rec {
+  pname = "functiontrace";
+  version = "0.3.7";
+  format = "pyproject";
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-3bnxZFq1/D9ntwfv7O2YU6MnKEDWWIG4zX0e3cgCleg=";
+  };
+
+  nativeBuildInputs = [
+    setuptools
+    toml
+  ];
+
+  pythonImportsCheck = [ "functiontrace" ];
+
+  meta = with lib; {
+    homepage = "https://functiontrace.com";
+    description = "The Python module for Functiontrace";
+    license = licenses.prosperity30;
+    maintainers = with maintainers; [ mathiassven ];
+  };
+}

pkgs/development/python-modules/pydevtool/default.nix

@@ -0,0 +1,37 @@
+{ lib
+, fetchPypi
+, setuptools
+, buildPythonPackage
+, doit
+}:
+
+buildPythonPackage rec {
+  pname = "pydevtool";
+  version = "0.3.0";
+  format = "pyproject";
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-JeO6Tz0zzKwz7iuXdZlYSNSemzGLehRkd/tdUveG/Io=";
+  };
+
+  nativeBuildInputs = [
+    setuptools
+  ];
+
+  propagatedBuildInputs = [
+    doit
+  ];
+
+  pythonImportsCheck = [
+    "pydevtool"
+  ];
+
+  meta = with lib; {
+    homepage = "https://github.com/pydoit/pydevtool";
+    description = "CLI dev tools powered by pydoit";
+    license = licenses.mit;
+    maintainers = with maintainers; [ doronbehar ];
+  };
+
+}

pkgs/development/python-modules/pyephember/default.nix

@@ -1,23 +1,25 @@
 { lib
 , buildPythonPackage
 , fetchPypi
+, paho-mqtt
 , pythonOlder
 , requests
 }:
 
 buildPythonPackage rec {
   pname = "pyephember";
-  version = "0.3.1";
+  version = "0.4.0";
   format = "setuptools";
 
   disabled = pythonOlder "3.8";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "3eMdkP7u3TTg1AUK4OR7AGZkD0FxUUPp/etvZ2Rw74E=";
+    sha256 = "sha256-j3SftxXKs9EZwdio26W5U0y5owH4yTteS4RUmzkZkoE=";
   };
 
   propagatedBuildInputs = [
+    paho-mqtt
     requests
   ];
 

pkgs/development/python-modules/pykulersky/default.nix

@@ -11,7 +11,7 @@
 
 buildPythonPackage rec {
   pname = "pykulersky";
-  version = "0.5.4";
+  version = "0.5.5";
   format = "setuptools";
 
   disabled = pythonOlder "3.6";
@@ -20,7 +20,7 @@ buildPythonPackage rec {
     owner = "emlove";
     repo = pname;
     rev = version;
-    hash = "sha256-voD4tR+k5TKGjLXFK94GJy4+wUoP2cSFc5BWkCiinOg=";
+    hash = "sha256-coO+WBnv5HT14ym719qr3Plm1JuiaNdAvD1QVPj65oU=";
   };
 
   propagatedBuildInputs = [

pkgs/development/python-modules/pyrainbird/default.nix

@@ -21,7 +21,7 @@
 
 buildPythonPackage rec {
   pname = "pyrainbird";
-  version = "2.0.0";
+  version = "2.0.1";
   format = "setuptools";
 
   disabled = pythonOlder "3.9";
@@ -30,7 +30,7 @@ buildPythonPackage rec {
     owner = "allenporter";
     repo = pname;
     rev = "refs/tags/${version}";
-    hash = "sha256-fQHWamtGA1Cz/9Hbxbns5lDd08Q01nIvaMXp9PWrelM=";
+    hash = "sha256-ssm/nFciUeWexgsKUpF4qZHz/grG8OYJV7roBAjMsac=";
   };
 
   postPatch = ''

pkgs/development/python-modules/pytapo/default.nix

@@ -5,6 +5,7 @@
 # propagates
 , pycryptodome
 , requests
+, rtp
 , urllib3
 }:
 
@@ -21,6 +22,7 @@ buildPythonPackage rec {
   propagatedBuildInputs = [
     pycryptodome
     requests
+    rtp
     urllib3
   ];
 

pkgs/development/python-modules/pyzerproc/default.nix

@@ -11,7 +11,7 @@
 
 buildPythonPackage rec {
   pname = "pyzerproc";
-  version = "0.4.11";
+  version = "0.4.12";
   format = "setuptools";
 
   disabled = pythonOlder "3.9";
@@ -20,7 +20,7 @@ buildPythonPackage rec {
     owner = "emlove";
     repo = pname;
     rev = "refs/tags/${version}";
-    hash = "sha256-FNiq/dbh5PMTxnKCKDSHEvllehAEUYvWZS+OyP3lSW8=";
+    hash = "sha256-vS0sk/KjDhWispZvCuGlmVLLfeFymHqxwNzNqNRhg6k=";
   };
 
   postPatch = ''

pkgs/development/python-modules/rtp/default.nix

@@ -0,0 +1,40 @@
+{ lib
+, buildPythonPackage
+, fetchPypi
+, python3
+
+  # nativeCheckInputs
+, hypothesis
+, unittestCheckHook
+
+}:
+
+buildPythonPackage rec {
+  pname = "rtp";
+  version = "0.0.3";
+  format = "setuptools";
+
+  src = fetchPypi {
+    inherit pname version;
+    hash = "sha256-I5k3uF5lSLDdCWjBEQC4kl2dWyAKcHEJIYwqnEvJDBI=";
+  };
+
+  nativeCheckInputs = [
+    hypothesis
+    unittestCheckHook
+  ];
+
+  unittestFlagsArray = [ "-s" "tests" "-v" ];
+
+  pythonImportsCheck = [
+    "rtp"
+  ];
+
+
+  meta = with lib; {
+    description = "A library for decoding/encoding rtp packets";
+    homepage = "https://github.com/bbc/rd-apmm-python-lib-rtp";
+    license = licenses.asl20;
+    maintainers = with maintainers; [ fleaz ];
+  };
+}

pkgs/development/python-modules/slowapi/default.nix

@@ -16,7 +16,7 @@
 
 buildPythonPackage rec {
   pname = "slowapi";
-  version = "0.1.7";
+  version = "0.1.8";
   format = "pyproject";
 
   disabled = pythonOlder "3.7";
@@ -25,7 +25,7 @@ buildPythonPackage rec {
     owner = "laurentS";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-IAB7JW8iVb5M610GVK0POXlSiya22KzNgr26BNvPC4Q=";
+    hash = "sha256-xgHz8b95SXf/GwzKPfQ/RHbUNJfCx6+7a2HB8+6hjsw=";
   };
 
   pythonRelaxDeps = [

pkgs/development/python-modules/torchaudio/default.nix

@@ -0,0 +1,63 @@
+{ lib
+, buildPythonPackage
+, fetchFromGitHub
+, cmake
+, pkg-config
+, ninja
+, pybind11
+, torch
+, cudaSupport ? false
+, cudaPackages
+}:
+
+buildPythonPackage rec {
+  pname = "torchaudio";
+  version = "2.0.1";
+
+  src = fetchFromGitHub {
+    owner = "pytorch";
+    repo = "audio";
+    rev = "v${version}";
+    hash = "sha256-qrDWFY+6eVV9prUzUzb5yzyFYtEvaSyEW0zeKqAg2Vk=";
+  };
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace 'print(" --- Initializing submodules")' "return" \
+      --replace "_fetch_archives(_parse_sources())" "pass"
+  '';
+
+  nativeBuildInputs = [
+    cmake
+    pkg-config
+    ninja
+  ] ++ lib.optionals cudaSupport [
+    cudaPackages.cudatoolkit
+  ];
+  buildInputs = [
+    pybind11
+  ] ++ lib.optionals cudaSupport [
+    cudaPackages.cudnn
+  ];
+  propagatedBuildInputs = [
+    torch
+  ];
+
+  BUILD_SOX=0;
+  BUILD_KALDI=0;
+  BUILD_RNNT=0;
+  BUILD_CTC_DECODER=0;
+
+  dontUseCmakeConfigure = true;
+
+  doCheck = false; # requires sox backend
+
+  meta = with lib; {
+    description = "PyTorch audio library";
+    homepage = "https://pytorch.org/";
+    changelog = "https://github.com/pytorch/audio/releases/tag/v${version}";
+    license = licenses.bsd2;
+    platforms = platforms.unix;
+    maintainers = with maintainers; [ junjihashimoto ];
+  };
+}

pkgs/development/python-modules/yasi/default.nix

@@ -0,0 +1,36 @@
+{ lib
+, python3
+, fetchFromGitHub
+}:
+
+python3.pkgs.buildPythonApplication rec {
+  pname = "yasi";
+  version = "2.1.2";
+  format = "setuptools";
+
+  src = fetchFromGitHub {
+    owner = "nkmathew";
+    repo = "yasi-sexp-indenter";
+    rev = "v${version}";
+    hash = "sha256-xKhVTmh/vrtBkatxtk8R4yqbGroH0I+xTKNYUpuikt4=";
+  };
+
+  propagatedBuildInputs = with python3.pkgs; [
+    colorama
+  ];
+
+  postPatch = ''
+    substituteInPlace setup.py \
+      --replace "test.test_yasi" "tests.test_yasi"
+  '';
+
+  pythonImportsCheck = [ "yasi" ];
+
+  meta = with lib; {
+    description = "A dialect-aware s-expression indenter written in Python and newLISP";
+    homepage = "https://github.com/nkmathew/yasi-sexp-indenter";
+    changelog = "https://github.com/nkmathew/yasi-sexp-indenter/blob/${src.rev}/CHANGELOG.md";
+    license = licenses.mit;
+    maintainers = with maintainers; [ kranzes ];
+  };
+}

pkgs/development/r-modules/bioc-packages.nix

@@ -17,7 +17,7 @@ in with self; {
   AGDEX = derive2 { name="AGDEX"; version="1.46.0"; sha256="0yvdx32yr4mv7dl5ycpbxhrkm6csrr7k3398ggjavdcfhz54dgr8"; depends=[Biobase GSEABase]; };
   AIMS = derive2 { name="AIMS"; version="1.30.0"; sha256="1civ4a14ynccv6xs27fm95fw6254l1z0q37546ivyv2mhbz0d2i1"; depends=[Biobase e1071]; };
   ALDEx2 = derive2 { name="ALDEx2"; version="1.30.0"; sha256="0585s5pb8zr9il1vhxw9vjzzajmdcjmf9zz3zlc5vpczd3fnzfkf"; depends=[BiocParallel GenomicRanges IRanges multtest Rfast S4Vectors SummarizedExperiment zCompositions]; };
-  AMARETTO = derive2 { name="AMARETTO"; version="1.13.0"; sha256="18w65sf3h4yzw9v5xgkalxnkmgzgsx100v7qc7z4ifx10lgpji5n"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; };
+  AMARETTO = derive2 { name="AMARETTO"; version="1.14.0"; sha256="06j75c4j71fkkw5s52nbzb3k084y2f4v4h3js9dgsxxrd6jkzfz9"; depends=[BiocFileCache callr circlize ComplexHeatmap curatedTCGAData doParallel dplyr DT foreach ggplot2 glmnet gridExtra httr impute knitr limma Matrix matrixStats MultiAssayExperiment Rcpp readr reshape2 rmarkdown tibble]; };
   AMOUNTAIN = derive2 { name="AMOUNTAIN"; version="1.24.0"; sha256="0zzl5dv64yhdivsm2pgsfjikygib9pkfiv34h1lnmqrj6yivvvw8"; depends=[]; };
   ANCOMBC = derive2 { name="ANCOMBC"; version="2.0.2"; sha256="0dlinv4vhxgni8ygzvfw8pbc6d1v9x5chhrpxblhs2c65bkgyxz5"; depends=[CVXR DescTools doParallel doRNG dplyr emmeans energy foreach Hmisc lme4 lmerTest magrittr MASS mia nloptr Rdpack rlang rngtools S4Vectors SingleCellExperiment SummarizedExperiment tibble tidyr TreeSummarizedExperiment]; };
   ANF = derive2 { name="ANF"; version="1.20.0"; sha256="0yfwvgx7144r894fr13sx4gyyq6ljh7y734wx74sb7q80cl2gs1j"; depends=[Biobase igraph MASS RColorBrewer survival]; };
@@ -45,14 +45,14 @@ in with self; {
   AllelicImbalance = derive2 { name="AllelicImbalance"; version="1.36.0"; sha256="0zn8pp4pl5wr957mf6agjpn61f9qpnjx0nbxb5wnbr40672x0263"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridExtra Gviz IRanges lattice latticeExtra nlme Rsamtools S4Vectors seqinr SummarizedExperiment VariantAnnotation]; };
   AlphaBeta = derive2 { name="AlphaBeta"; version="1.12.0"; sha256="000apg879li9wkbyrl8cm73z6h0xasqp41h9ir9hywy2v38rmc5b"; depends=[BiocParallel data_table dplyr expm ggplot2 gtools igraph optimx plotly stringr]; };
   AlpsNMR = derive2 { name="AlpsNMR"; version="4.0.4"; sha256="19j97qsa1vnxw05dlllbwzdap0xgnmgxyqbi5dy8w2ppwdzxgsfv"; depends=[baseline BiocParallel cli dplyr fs future generics ggplot2 glue htmltools magrittr matrixStats mixOmics pcaPP purrr readxl reshape2 rlang rmarkdown scales signal speaq stringr tibble tidyr tidyselect vctrs]; };
-  AnVIL = derive2 { name="AnVIL"; version="1.10.1"; sha256="0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv"; depends=[BiocManager dplyr DT futile_logger htmltools httr jsonlite miniUI rapiclient rlang shiny tibble tidyr tidyselect]; };
+  AnVIL = derive2 { name="AnVIL"; version="1.10.2"; sha256="1j7n8c47j3njd5rnlrj8bkn4q5z7jpm0c9rdq1mlwd2i1yy9fz9b"; depends=[BiocManager dplyr DT futile_logger htmltools httr jsonlite miniUI rapiclient rlang shiny tibble tidyr tidyselect]; };
   AnVILBilling = derive2 { name="AnVILBilling"; version="1.8.0"; sha256="13qcp2s012ai44dkddk71ga44y87jnl0vljyd93lj1dlh8nw7c00"; depends=[bigrquery DBI dplyr DT ggplot2 lubridate magrittr plotly shiny shinytoastr]; };
   AnVILPublish = derive2 { name="AnVILPublish"; version="1.8.0"; sha256="1i5zf7pyrzi6v13gpscmdb5qdb5gknicc8fk9s9nmsl1wpj6wlsw"; depends=[AnVIL httr jsonlite readr rmarkdown whisker yaml]; };
   Anaquin = derive2 { name="Anaquin"; version="2.22.0"; sha256="08y2syaacy15rxcf3x2r3906kfm58fkx7ainaqvy5inlc9f670j5"; depends=[DESeq2 ggplot2 knitr locfit plyr qvalue ROCR]; };
   AneuFinder = derive2 { name="AneuFinder"; version="1.26.0"; sha256="154cg63n7h9h5jkj00aqf0hzbmmjg16bzvvk50fyixwq0a4q1j00"; depends=[AneuFinderData bamsignals BiocGenerics Biostrings cowplot DNAcopy doParallel ecp foreach GenomeInfoDb GenomicAlignments GenomicRanges ggdendro ggplot2 ggrepel IRanges mclust reshape2 Rsamtools S4Vectors]; };
   AnnotationDbi = derive2 { name="AnnotationDbi"; version="1.60.2"; sha256="1c7f2vgdnh99zp83pvmghb7l0rihdijlhdj6ff992h7wrrha8lhg"; depends=[Biobase BiocGenerics DBI IRanges KEGGREST RSQLite S4Vectors]; };
   AnnotationFilter = derive2 { name="AnnotationFilter"; version="1.22.0"; sha256="0m16kfssxbblf03ykawkmqa038cl90prhb23k6y88g2hwm00wynk"; depends=[GenomicRanges lazyeval]; };
-  AnnotationForge = derive2 { name="AnnotationForge"; version="1.40.1"; sha256="16wdcl56d5i8wrmin610kzs9ldy7h9w5fbnysjb1crkcgbikq1yy"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
+  AnnotationForge = derive2 { name="AnnotationForge"; version="1.40.2"; sha256="1ab7nl9zrlhlkwjrjr69zqq5hy9a8rp457hcr075n8qm5r5lf6wd"; depends=[AnnotationDbi Biobase BiocGenerics DBI RCurl RSQLite S4Vectors XML]; };
   AnnotationHub = derive2 { name="AnnotationHub"; version="3.6.0"; sha256="1hk02q6mwx49khbhydndfa1qry8ylhmwz2dff8845a510hm0di7n"; depends=[AnnotationDbi BiocFileCache BiocGenerics BiocManager BiocVersion curl dplyr httr interactiveDisplayBase rappdirs RSQLite S4Vectors yaml]; };
   AnnotationHubData = derive2 { name="AnnotationHubData"; version="1.28.0"; sha256="0mcx09kcxccw2gkf4c3w7sxgb7v3gwbvahvx9wgq8f93q85yzg95"; depends=[AnnotationDbi AnnotationForge AnnotationHub Biobase BiocCheck BiocGenerics BiocManager biocViews Biostrings DBI futile_logger GenomeInfoDb GenomicFeatures GenomicRanges graph IRanges jsonlite OrganismDbi RCurl Rsamtools RSQLite rtracklayer S4Vectors XML]; };
   ArrayExpress = derive2 { name="ArrayExpress"; version="1.57.0"; sha256="1fzi951mjc4kbkkvlfvwlfrpfnjckkmw4xz4m5dapy1z2jkgp8w6"; depends=[Biobase limma oligo XML]; };
@@ -104,7 +104,7 @@ in with self; {
   BioMM = derive2 { name="BioMM"; version="1.14.0"; sha256="06c36lpbmcz0s8v6dsjbmlmisab3h02jx67ycwlnymfwzw1hq1cb"; depends=[BiocParallel CMplot e1071 ggplot2 glmnet imager lattice nsprcomp precrec ranger rms topGO vioplot xlsx]; };
   BioMVCClass = derive2 { name="BioMVCClass"; version="1.66.0"; sha256="1xclmwxps7yvqnaw8kn6z4mlpx6v8xfzyly4cadsjaj2qm535xxk"; depends=[Biobase graph MVCClass Rgraphviz]; };
   BioNAR = derive2 { name="BioNAR"; version="1.0.0"; sha256="1z0ln7j4ack0pv8bzxjfrq6ncsnd0jif5s42njm94c7j408fj9kz"; depends=[AnnotationDbi clusterCons dplyr fgsea ggplot2 ggrepel GO_db igraph latex2exp org_Hs_eg_db poweRlaw Rdpack RSpectra rSpectral scales stringr synaptome_db WGCNA]; };
-  BioNERO = derive2 { name="BioNERO"; version="1.6.0"; sha256="10nwgp8a9chn33p5k7cdp920rraiw187xfrylyd9bq010c7vp7xh"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggnetwork ggnewscale ggplot2 ggrepel igraph intergraph matrixStats minet NetRep networkD3 patchwork RColorBrewer reshape2 SummarizedExperiment sva WGCNA]; };
+  BioNERO = derive2 { name="BioNERO"; version="1.6.1"; sha256="0ijdnl43cgzywgsz80jd6q0irixh6367qm1ll5ww1rcr4xas2nsl"; depends=[BiocParallel ComplexHeatmap dynamicTreeCut GENIE3 ggnetwork ggnewscale ggplot2 ggrepel igraph intergraph matrixStats minet NetRep networkD3 patchwork RColorBrewer reshape2 SummarizedExperiment sva WGCNA]; };
   BioNet = derive2 { name="BioNet"; version="1.58.0"; sha256="12c6m7dzwkdh4bk1c5xmzm5ajrsba7v62mag1f3rrpmrapdh6s0j"; depends=[AnnotationDbi Biobase graph igraph RBGL]; };
   BioNetStat = derive2 { name="BioNetStat"; version="1.18.0"; sha256="1h99d6gnqw5v9ha2169zfhw9cvxhyjgkf4zm8qj1i03h2cywapgv"; depends=[BiocParallel DT ggplot2 Hmisc igraph knitr markdown pathview pheatmap plyr psych RColorBrewer RJSONIO rmarkdown shiny shinyBS whisker yaml]; };
   BioQC = derive2 { name="BioQC"; version="1.26.0"; sha256="1ssxsxdm8vmlrmvvdz5p98apd3xsal1h3ss8556g83kgw830zsxf"; depends=[Biobase edgeR Rcpp]; };
@@ -119,7 +119,7 @@ in with self; {
   BiocIO = derive2 { name="BiocIO"; version="1.8.0"; sha256="15d4xsn3k32q7lzcyxvs70f0jbh9fgwl3vi7xd6sqpggar12hh9f"; depends=[BiocGenerics S4Vectors]; };
   BiocNeighbors = derive2 { name="BiocNeighbors"; version="1.16.0"; sha256="09f00rf5gwwlxxaycsciq4l53gjg5kjayx8xzhns2yf1fv297j9p"; depends=[BiocParallel Matrix Rcpp RcppHNSW S4Vectors]; };
   BiocOncoTK = derive2 { name="BiocOncoTK"; version="1.18.0"; sha256="1x4mzzjvjgcxg5xyxjib8r2n55hpf2vzcci0xkb7d8frakfncn9s"; depends=[bigrquery car ComplexHeatmap curatedTCGAData DBI dplyr DT GenomicFeatures GenomicRanges ggplot2 ggpubr graph httr IRanges magrittr plyr Rgraphviz rjson S4Vectors scales shiny SummarizedExperiment]; };
-  BiocParallel = derive2 { name="BiocParallel"; version="1.32.5"; sha256="1yd6ln9cl3dcvfziar52fkvqi2lzm31l7j21r1rwl1mpkz0xapir"; depends=[BH codetools cpp11 futile_logger snow]; };
+  BiocParallel = derive2 { name="BiocParallel"; version="1.32.6"; sha256="1aq3b5fjs8j0d6nf3992a6gnzvmmaxbbkrj1im0k6ppsqac6dlj0"; depends=[BH codetools cpp11 futile_logger snow]; };
   BiocPkgTools = derive2 { name="BiocPkgTools"; version="1.16.1"; sha256="0cl88adkbxv7sz07b8h5qpwwkwg85jx6xjinkd0yjac4xm7s4lyf"; depends=[BiocFileCache BiocManager biocViews dplyr DT gh graph htmltools htmlwidgets httr igraph jsonlite magrittr RBGL readr rlang rorcid rvest stringr tibble xml2]; };
   BiocSet = derive2 { name="BiocSet"; version="1.12.1"; sha256="1cqp5m6yic5vsp8k05r50sx2cmi9cwzxfmlswcjw28nascq3gpv0"; depends=[AnnotationDbi BiocIO dplyr KEGGREST ontologyIndex plyr rlang S4Vectors tibble tidyr]; };
   BiocSingular = derive2 { name="BiocSingular"; version="1.14.0"; sha256="041izymcifvi0pa97fh5000bwlyl0mdk9003i5bbvlld6mbbv2kk"; depends=[beachmat BiocGenerics BiocParallel DelayedArray irlba Matrix Rcpp rsvd S4Vectors ScaledMatrix]; };
@@ -168,7 +168,7 @@ in with self; {
   CNVMetrics = derive2 { name="CNVMetrics"; version="1.2.0"; sha256="11i47ml2y5s8adh3qysasjl8b3w4xhg5h7v9rcdmd1hysjl4d4hi"; depends=[BiocParallel GenomicRanges gridExtra IRanges magrittr pheatmap S4Vectors]; };
   CNVPanelizer = derive2 { name="CNVPanelizer"; version="1.30.0"; sha256="02k6bbzaj7q87nsg9zqda8dz44q3wshsps5pzm2764gxcwn4sz0z"; depends=[BiocGenerics exomeCopy foreach GenomeInfoDb GenomicRanges ggplot2 gplots IRanges NOISeq openxlsx plyr reshape2 Rsamtools S4Vectors shiny shinyFiles shinyjs stringr testthat]; };
   CNVRanger = derive2 { name="CNVRanger"; version="1.14.0"; sha256="1if6k9iakrvq0fw6j2xpd26l13ikkpni8px3w76c9z0wsvbjf0cc"; depends=[BiocGenerics BiocParallel data_table edgeR GDSArray gdsfmt GenomeInfoDb GenomicRanges IRanges lattice limma plyr qqman RaggedExperiment rappdirs reshape2 S4Vectors SNPRelate SummarizedExperiment]; };
-  CNVfilteR = derive2 { name="CNVfilteR"; version="1.12.1"; sha256="0jkd65ncsbgwrrg0xs8ycj2lm9ailrayqqd6a453sbhx74gjsnyy"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; };
+  CNVfilteR = derive2 { name="CNVfilteR"; version="1.12.2"; sha256="07jjrzkf8bk20wb8wiw155bq0dhgnz24bhwzsdh2dakirmjhfpzb"; depends=[assertthat Biostrings CopyNumberPlots GenomeInfoDb GenomicRanges IRanges karyoploteR pracma regioneR Rsamtools SummarizedExperiment VariantAnnotation]; };
   CNVgears = derive2 { name="CNVgears"; version="1.6.0"; sha256="0gqw8l7pswamjm4j1jr8ri1rpf31szlx9ba6b99j3iypisxq1r1r"; depends=[data_table ggplot2]; };
   CNViz = derive2 { name="CNViz"; version="1.6.0"; sha256="1nm8k4ry8p6k8cb6bqi6dyffi48fyhv1gq1277cz1nys31y0pdnv"; depends=[CopyNumberPlots dplyr DT GenomicRanges karyoploteR magrittr plotly scales shiny]; };
   CNVrd2 = derive2 { name="CNVrd2"; version="1.36.0"; sha256="0jr9m08ip17l9w9i62nqdv13p5f3s7n0zyj4y3vy671s6c1syfiv"; depends=[DNAcopy ggplot2 gridExtra IRanges rjags Rsamtools VariantAnnotation]; };
@@ -245,7 +245,7 @@ in with self; {
   CrispRVariants = derive2 { name="CrispRVariants"; version="1.26.0"; sha256="184bn5gyjj0s7wpnyrqxrsh47f7f9w020p5fbhbi48nnks38j7ca"; depends=[AnnotationDbi BiocParallel Biostrings GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 gridExtra IRanges reshape2 Rsamtools S4Vectors]; };
   CyTOFpower = derive2 { name="CyTOFpower"; version="1.4.0"; sha256="0g3629xi5hvkds2ixibr9p2ipjyr341nksafh38ap2w870whc31j"; depends=[CytoGLMM diffcyt dplyr DT ggplot2 magrittr rlang shiny shinyFeedback shinyjs shinyMatrix SummarizedExperiment tibble tidyr]; };
   CytoDx = derive2 { name="CytoDx"; version="1.18.0"; sha256="1w5xy40wpyw6fj42zj2zf79r0kkdhn6h7wxzilh1dhnqkd0k8ay1"; depends=[doParallel dplyr flowCore glmnet rpart rpart_plot]; };
-  CytoGLMM = derive2 { name="CytoGLMM"; version="1.6.0"; sha256="1vvzw440blicfmdidr1sh8wiyfwmgrhmvazikm4f7g8jcw0cn9dm"; depends=[BiocParallel caret cowplot doParallel dplyr factoextra flexmix ggplot2 ggrepel logging magrittr MASS Matrix mbest pheatmap RColorBrewer rlang speedglm stringr strucchange tibble tidyr]; };
+  CytoGLMM = derive2 { name="CytoGLMM"; version="1.6.0"; sha256="1vvzw440blicfmdidr1sh8wiyfwmgrhmvazikm4f7g8jcw0cn9dm"; depends=[BiocParallel caret cowplot doParallel dplyr factoextra flexmix ggplot2 ggrepel logging magrittr MASS Matrix mbest pheatmap RColorBrewer rlang stringr strucchange tibble tidyr]; };
   CytoML = derive2 { name="CytoML"; version="2.10.0"; sha256="105vdmwwglknwk7x7cb6b2jf6bngbxsly0ymjf8175p2lfv98jsa"; depends=[BH Biobase cpp11 cytolib data_table dplyr flowCore flowWorkspace ggcyto graph jsonlite openCyto RBGL Rgraphviz Rhdf5lib RProtoBufLib tibble XML yaml]; };
   DAMEfinder = derive2 { name="DAMEfinder"; version="1.10.1"; sha256="1cgykb70mxnhilwwp1jr4dr523zvjxpix173s4ldfh49064gzwc1"; depends=[BiocGenerics Biostrings bumphunter cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 IRanges limma plyr readr reshape2 Rsamtools S4Vectors stringr SummarizedExperiment VariantAnnotation]; };
   DAPAR = derive2 { name="DAPAR"; version="1.30.6"; sha256="1z0p3aiypi5lpa4nam45klcf9dq8k18aig917w0v73ix3l88bmad"; depends=[Biobase DAPARdata foreach highcharter MSnbase]; };
@@ -267,7 +267,7 @@ in with self; {
   DExMA = derive2 { name="DExMA"; version="1.6.0"; sha256="04j5h3ijmhzkgs02r0vsq3p00i4ydcnnis4kn1a69bp3x1bnv0n9"; depends=[Biobase bnstruct DExMAdata GEOquery impute limma pheatmap plyr RColorBrewer scales snpStats sva swamp]; };
   DFP = derive2 { name="DFP"; version="1.56.0"; sha256="1pkg4461ib1iplcrlwkwrqzdzqixj2rhwwfkhjw87z4rx04hz3gf"; depends=[Biobase]; };
   DIAlignR = derive2 { name="DIAlignR"; version="2.6.0"; sha256="04kpdab8h0krxqzsxl3sb1gsxqwrrdpsn7irgdpns8qqjlzcbzv5"; depends=[ape bit64 data_table DBI dplyr ggplot2 magrittr mzR phangorn pracma Rcpp RcppEigen reticulate rlang RMSNumpress RSQLite signal tidyr zoo]; };
-  DMCFB = derive2 { name="DMCFB"; version="1.12.0"; sha256="00j362frx70vj326xjppkzfd36mvfq3ym58dnckz3c0jb2dxv3wr"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors speedglm SummarizedExperiment tibble]; };
+  DMCFB = derive2 { name="DMCFB"; version="1.12.0"; sha256="00j362frx70vj326xjppkzfd36mvfq3ym58dnckz3c0jb2dxv3wr"; depends=[arm benchmarkme BiocParallel data_table fastDummies GenomicRanges IRanges MASS matrixStats rtracklayer S4Vectors SummarizedExperiment tibble]; };
   DMCHMM = derive2 { name="DMCHMM"; version="1.20.0"; sha256="1cf5i3ikn81qw0s3kbx2yl15fmgwal22yqpys8wya8pd2agbi4lj"; depends=[BiocParallel calibrate fdrtool GenomicRanges IRanges multcomp rtracklayer S4Vectors SummarizedExperiment]; };
   DMRScan = derive2 { name="DMRScan"; version="1.20.0"; sha256="1mx0kk1rbn0mkk94mm1a7mk64ia315fvwwb34adyslmyq5gq93i5"; depends=[GenomeInfoDb GenomicRanges IRanges MASS Matrix mvtnorm RcppRoll]; };
   DMRcaller = derive2 { name="DMRcaller"; version="1.30.0"; sha256="03d7rl5z1pxdwxya53mkf8a8n9jzp8rb8awhfhfd22dgdf2l327h"; depends=[betareg GenomicRanges IRanges Rcpp RcppRoll S4Vectors]; };
@@ -327,13 +327,13 @@ in with self; {
   EasyCellType = derive2 { name="EasyCellType"; version="1.0.0"; sha256="1xry2kgb7ha2hg82jap88px9xxcq609il85xi0k0gilla1swvjc1"; depends=[AnnotationDbi clusterProfiler dplyr forcats ggplot2 magrittr org_Hs_eg_db org_Mm_eg_db rlang]; };
   EmpiricalBrownsMethod = derive2 { name="EmpiricalBrownsMethod"; version="1.26.0"; sha256="1vws49a204xkwixdvp5l62in7vxbpf4qsfcnm34zkc4kx5hval9j"; depends=[]; };
   EnhancedVolcano = derive2 { name="EnhancedVolcano"; version="1.16.0"; sha256="1nbg2r097rz24ybzh9ww6myd6kc2rz02vbg6g0rb3dlng0002xsm"; depends=[ggplot2 ggrepel]; };
-  EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.27.2"; sha256="1il5cj5zmjwp3drw9psj1nsp94yxd421kd7jqrv34p4r1v0zw5z5"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; };
-  EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.28.1"; sha256="1phcd2j19a7n2crqdigkh4bf8xn10drvsm1y6ny6hrk7scrnxz4j"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; };
+  EnrichedHeatmap = derive2 { name="EnrichedHeatmap"; version="1.28.1"; sha256="0ikvs91qfswnyc2p6pn5b0n7rz0szx65pv0ywgzr94arm85gwirc"; depends=[circlize ComplexHeatmap GenomicRanges GetoptLong IRanges locfit matrixStats Rcpp]; };
+  EnrichmentBrowser = derive2 { name="EnrichmentBrowser"; version="2.28.2"; sha256="03z0ya3qsg4drsjiqb5akbjivbsmqjv8r52y8nhrc5kqa04zffxk"; depends=[AnnotationDbi BiocFileCache BiocManager edgeR GO_db graph graphite GSEABase hwriter KEGGgraph KEGGREST limma pathview Rgraphviz S4Vectors safe SPIA SummarizedExperiment]; };
   EpiCompare = derive2 { name="EpiCompare"; version="1.2.0"; sha256="0h0ap1xa0g57zh4djr263d97firklsvb6nwq0dk1h39j8wyp5j54"; depends=[AnnotationHub BiocGenerics BRGenomics ChIPseeker data_table genomation GenomeInfoDb GenomicRanges ggplot2 htmltools IRanges plotly reshape2 rmarkdown rtracklayer stringr]; };
   EpiDISH = derive2 { name="EpiDISH"; version="2.14.1"; sha256="02pf0y8sj1j48qfmfjckr4vx9rz3aypb6iydlpfvhcm829jr51cl"; depends=[e1071 locfdr MASS Matrix matrixStats quadprog stringr]; };
   EpiMix = derive2 { name="EpiMix"; version="1.0.1"; sha256="1rn6hpxxiw8n7im2dnb2x19ahvahljxac6853qkwxb7a8gwvwlad"; depends=[AnnotationDbi AnnotationHub Biobase biomaRt data_table doParallel doSNOW downloader dplyr ELMER_data EpiMix_data ExperimentHub foreach GenomeInfoDb GenomicFeatures GenomicRanges GEOquery ggplot2 impute IRanges limma plyr progress R_matlab RColorBrewer RCurl rlang RPMM S4Vectors SummarizedExperiment tibble tidyr]; };
   EpiTxDb = derive2 { name="EpiTxDb"; version="1.10.0"; sha256="152snn75nixdas9n3g80f32hmdrqdyv71cl8fkax5jl4mqrp6px5"; depends=[AnnotationDbi BiocFileCache BiocGenerics Biostrings curl DBI GenomeInfoDb GenomicFeatures GenomicRanges httr IRanges Modstrings RSQLite S4Vectors tRNAdbImport xml2]; };
-  EventPointer = derive2 { name="EventPointer"; version="3.6.0"; sha256="0z9bcqfwi8mym1pwywmvdmiszw0whpz4svh7jgwjvza94z5w5ly5"; depends=[abind affxparser Biostrings BSgenome cobs doParallel fgsea foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq speedglm stringr SummarizedExperiment tximport]; };
+  EventPointer = derive2 { name="EventPointer"; version="3.6.0"; sha256="0z9bcqfwi8mym1pwywmvdmiszw0whpz4svh7jgwjvza94z5w5ly5"; depends=[abind affxparser Biostrings BSgenome cobs doParallel fgsea foreach GenomeInfoDb GenomicFeatures GenomicRanges glmnet graph igraph IRanges iterators limma lpSolve MASS Matrix matrixStats nnls poibin prodlim qvalue RBGL rhdf5 S4Vectors SGSeq stringr SummarizedExperiment tximport]; };
   ExCluster = derive2 { name="ExCluster"; version="1.16.0"; sha256="0m635as5xigkjqlmwh32afbbxffjf6ahrr83gr8z886z365h4m81"; depends=[GenomicRanges IRanges matrixStats Rsubread rtracklayer]; };
   ExiMiR = derive2 { name="ExiMiR"; version="2.40.0"; sha256="02aw2kjpg2xfmx0xjphsalw81gixwd2yrw73rcbcxyz7fpq98c5h"; depends=[affy affyio Biobase limma preprocessCore]; };
   ExperimentHub = derive2 { name="ExperimentHub"; version="2.6.0"; sha256="1j71zmxwiz82gg6kii2bmynzwll1r6fmsq972kmvxvm6crpvi15s"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocManager curl rappdirs S4Vectors]; };
@@ -592,8 +592,8 @@ in with self; {
   MSPrep = derive2 { name="MSPrep"; version="1.8.0"; sha256="05bq27v2iwmrf92y6fyzczvnrwmpqy5b7faa3z4si68fhpa81p2s"; depends=[crmn dplyr magrittr missForest pcaMethods preprocessCore rlang S4Vectors stringr SummarizedExperiment sva tibble tidyr VIM]; };
   MSnID = derive2 { name="MSnID"; version="1.32.0"; sha256="1ljhxbyq5pa32sh44f06cwcdq79xh5nm51bpx1i8xig3bvwyg7p9"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics BiocStyle Biostrings data_table doParallel dplyr foreach ggplot2 iterators msmsTests MSnbase mzID mzR ProtGenerics purrr R_cache Rcpp reshape2 rlang RUnit stringr tibble xtable]; };
   MSnbase = derive2 { name="MSnbase"; version="2.24.2"; sha256="0jdq41rhn9qyhxfihvrgim76fzdrycc02wjsjdrff42gmray49w7"; depends=[affy Biobase BiocGenerics BiocParallel digest ggplot2 impute IRanges lattice MALDIquant MASS MsCoreUtils mzID mzR pcaMethods plyr ProtGenerics Rcpp S4Vectors scales vsn XML]; };
-  MSstats = derive2 { name="MSstats"; version="4.6.3"; sha256="0zivmbkf5k21r0wg2p2gzhhb53qynf5yr2p4rd0dscb60ngsv0y3"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo survival]; };
-  MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.8.2"; sha256="0nvmpjp4bf8gbx3701phfwlc8jjdnxdh9hi6vzsmn8sf0k43l6dk"; depends=[checkmate data_table log4r stringi]; };
+  MSstats = derive2 { name="MSstats"; version="4.6.5"; sha256="12gxr7615fp4yks0mqs6ikzhalihf0bq7kkc7sflpjqgzdv3jmws"; depends=[checkmate data_table ggplot2 ggrepel gplots limma lme4 marray MASS MSstatsConvert preprocessCore Rcpp RcppArmadillo statmod survival]; };
+  MSstatsConvert = derive2 { name="MSstatsConvert"; version="1.8.3"; sha256="1488vl6ijnb415510pa381206xjwzn64bjvvz4vm0s80h6bzpsix"; depends=[checkmate data_table log4r stringi]; };
   MSstatsLOBD = derive2 { name="MSstatsLOBD"; version="1.6.0"; sha256="1hg9bjx9rwsdpj65mzd931lbyj4gb26x32mly4n1gkk1rf6iplry"; depends=[ggplot2 minpack_lm Rcpp]; };
   MSstatsLiP = derive2 { name="MSstatsLiP"; version="1.4.1"; sha256="0hj10r3x1pql0497x3clk9wlv8xvbcvbv35q45x1ki8hfc5b3ifc"; depends=[Biostrings checkmate data_table dplyr factoextra ggplot2 ggpubr gridExtra MSstats MSstatsConvert MSstatsPTM purrr Rcpp scales stringr tibble tidyr tidyverse]; };
   MSstatsPTM = derive2 { name="MSstatsPTM"; version="2.0.3"; sha256="1n0hf9xxqpq5yp23hdlv0ki919m69adr6a0m7577zx0icg30c0gy"; depends=[Biostrings checkmate data_table dplyr ggplot2 ggrepel gridExtra MSstats MSstatsConvert MSstatsTMT Rcpp stringr]; };
@@ -670,7 +670,7 @@ in with self; {
   NBSplice = derive2 { name="NBSplice"; version="1.15.0"; sha256="0yn7s7igshall34cflmdwvmknv8h1zdi6vg8svvcyn9fvzlgjdm8"; depends=[BiocParallel car edgeR ggplot2 MASS reshape2]; };
   NCIgraph = derive2 { name="NCIgraph"; version="1.46.0"; sha256="06y04lbp1wn1w9xy3lsqcdsycp4cdlrcyhga5kn1a4skb48bc6rc"; depends=[graph KEGGgraph R_methodsS3 RBGL RCy3]; };
   NOISeq = derive2 { name="NOISeq"; version="2.42.0"; sha256="1j0yafl5r1vsn99zkhvaz2mrwv37l4p8ldgiq09d9hxpjq9ls7i2"; depends=[Biobase Matrix]; };
-  NPARC = derive2 { name="NPARC"; version="1.10.0"; sha256="0zph5lxw7ysra897jkbrmxjvb4zd5q2knl07xw8q5dyphjw8bbr3"; depends=[BiocParallel broom dplyr magrittr MASS rlang tidyr]; };
+  NPARC = derive2 { name="NPARC"; version="1.10.1"; sha256="09xh883v929zabr6g1prr80885b4q0mhlvlw9mlycprrd8l2qch9"; depends=[BiocParallel broom dplyr magrittr MASS rlang tidyr]; };
   NTW = derive2 { name="NTW"; version="1.48.0"; sha256="0vx5swxmw76vba5wwl1qjyyb2dm7vg9wa7jsky93knhdl0s2fli9"; depends=[mvtnorm]; };
   NanoMethViz = derive2 { name="NanoMethViz"; version="2.4.2"; sha256="0qfw2smqqv6pj0a34plbxgdk49zh6nbf2r077hldbmp23ml6l6qj"; depends=[AnnotationDbi assertthat BiocSingular bsseq cpp11 data_table dplyr e1071 forcats fs GenomicRanges ggplot2 ggrastr glue limma patchwork purrr R_utils Rcpp readr rlang Rsamtools RSQLite S4Vectors scales scico stringr SummarizedExperiment tibble tidyr withr zlibbioc]; };
   NanoStringDiff = derive2 { name="NanoStringDiff"; version="1.28.0"; sha256="1fjmp78q3hsnslarb7w39r3kcvf8m9jrzcw4na6k55dqp5917lys"; depends=[Biobase matrixStats Rcpp]; };
@@ -757,7 +757,7 @@ in with self; {
   PloGO2 = derive2 { name="PloGO2"; version="1.10.0"; sha256="0sq2x68bcslzldrh367hh9r1vrnk56mkc6iqiq3zy7rzgxhjigpl"; depends=[GO_db GOstats httr lattice openxlsx xtable]; };
   PoDCall = derive2 { name="PoDCall"; version="1.6.0"; sha256="1x368wc96nn4k17kbbwavriqfp6qywxivdas6sp069c053xkjxrq"; depends=[diptest DT ggplot2 gridExtra LaplacesDemon mclust purrr readr rlist shiny shinyjs]; };
   PoTRA = derive2 { name="PoTRA"; version="1.13.0"; sha256="1a32d1wndb24pxza3h53yddj9z2clff5srny2k00pbbfq1h99mjf"; depends=[BiocGenerics graph graphite igraph org_Hs_eg_db]; };
-  PrInCE = derive2 { name="PrInCE"; version="1.14.0"; sha256="07q3x6rx3raz187akwfdd01x57hxbf6njbrydnl9r6a8q0b0gb0b"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase speedglm tester tidyr]; };
+  PrInCE = derive2 { name="PrInCE"; version="1.14.0"; sha256="07q3x6rx3raz187akwfdd01x57hxbf6njbrydnl9r6a8q0b0gb0b"; depends=[Biobase dplyr forecast Hmisc LiblineaR magrittr MSnbase naivebayes progress purrr ranger Rdpack robustbase tester tidyr]; };
   Prostar = derive2 { name="Prostar"; version="1.30.7"; sha256="10lzh7gib43f8l2a9p2bnvyf23llzm1931kpna1vpf6p1hswsxzv"; depends=[DAPAR DAPARdata data_table future ggplot2 gplots highcharter htmlwidgets later promises rhandsontable shiny shinyAce shinyBS shinycssloaders shinyjqui shinyjs shinythemes tibble vioplot webshot]; };
   ProtGenerics = derive2 { name="ProtGenerics"; version="1.30.0"; sha256="1k5pg0zbhz9mjsl5i3j33p7qv2adax2lf7yqv6qz229fxxaxs5li"; depends=[]; };
   ProteoDisco = derive2 { name="ProteoDisco"; version="1.4.0"; sha256="0df39hwg5kmc900b57dxw76mz11a7h4nb9kq1z1wl6ampx27w0ks"; depends=[BiocGenerics BiocParallel Biostrings checkmate cleaver dplyr GenomeInfoDb GenomicFeatures GenomicRanges IRanges ParallelLogger plyr rlang S4Vectors tibble tidyr VariantAnnotation XVector]; };
@@ -805,7 +805,7 @@ in with self; {
   RMassBank = derive2 { name="RMassBank"; version="3.8.0"; sha256="1zlv2vyarj0przwdn39iybk9fkghqbiic5y24i603jzajv9hqxz0"; depends=[assertthat Biobase ChemmineOB ChemmineR data_table digest enviPat httr logger MSnbase mzR R_utils rcdk Rcpp RCurl readJDX rjson S4Vectors webchem XML yaml]; };
   RNAAgeCalc = derive2 { name="RNAAgeCalc"; version="1.10.0"; sha256="0zj6ham16bjycdh1qids0pfq6xdbp8y1hdjm966ba6cwl9xxwl5d"; depends=[AnnotationDbi ggplot2 impute org_Hs_eg_db recount SummarizedExperiment]; };
   RNASeqPower = derive2 { name="RNASeqPower"; version="1.38.0"; sha256="1f8jiljxacqjj0vf2v01fclhl3i0w7xddxcs6ajxzlmmpqs19b8a"; depends=[]; };
-  RNASeqR = derive2 { name="RNASeqR"; version="1.15.1"; sha256="0rkn98mp6d9lzm82r37mixfq7vka71c9nwkzkixajpsba2915sh6"; 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]; };
+  RNASeqR = derive2 { name="RNASeqR"; version="1.16.0"; sha256="0m7d3mm644n81630v2m6vv7798x3rjshb9jcp63xq631j1wmk63i"; 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="1.18.0"; sha256="1zf5gg25lyn4z8yq8mmysxzpm7jkpspawyv7siwzb0m80h59rpiy"; depends=[ggplot2 gplots nloptr scales TMB]; };
   RNAinteract = derive2 { name="RNAinteract"; version="1.46.0"; sha256="18yhkkwq4gvwvph8pz53cl7id644vv1n2d3jngwrfk918jay5d0s"; depends=[abind Biobase cellHTS2 geneplotter gplots hwriter ICS ICSNP lattice latticeExtra limma locfit RColorBrewer splots]; };
   RNAmodR = derive2 { name="RNAmodR"; version="1.12.0"; sha256="0xhz2fz0lw2yw14cw8fcnghk9y9q0v75b4bkf7bg5v0jrcgg6bc4"; depends=[BiocGenerics BiocParallel Biostrings BSgenome colorRamps GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 Gviz IRanges matrixStats Modstrings RColorBrewer reshape2 ROCR Rsamtools rtracklayer S4Vectors]; };
@@ -825,7 +825,7 @@ in with self; {
   RSeqAn = derive2 { name="RSeqAn"; version="1.18.0"; sha256="0fjcwm3fw13yv3vdawwdbmbqws3n47f5s10rcvllm3wrbb1zrwb6"; depends=[Rcpp]; };
   RTCA = derive2 { name="RTCA"; version="1.50.0"; sha256="1jd5rknlbhdi650xg1isqxmgvi797c4jimn53x4nzaq88b8rabsc"; depends=[Biobase gtools RColorBrewer]; };
   RTCGA = derive2 { name="RTCGA"; version="1.28.0"; sha256="1h7x1hb7lnjaq842k72l76j7l4d9130vfh8flvsjvzyc3l98cywq"; depends=[assertthat data_table dplyr ggplot2 ggthemes htmltools knitr purrr RCurl rmarkdown rvest scales stringi survival survminer viridis XML xml2]; };
-  RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.28.0"; sha256="0w02191nj94wapywy43r33f04ck92mww49lg1gik38pbafaahv68"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges httr limma RaggedExperiment RCircos RCurl RJSONIO rvest S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; };
+  RTCGAToolbox = derive2 { name="RTCGAToolbox"; version="2.28.4"; sha256="14pw75cy4y5s6y2szdy8hwf8q1cysxiln6z45yn5lgdha96c6zdp"; depends=[BiocGenerics data_table DelayedArray GenomeInfoDb GenomicRanges httr limma RaggedExperiment RCircos RCurl RJSONIO rvest S4Vectors stringr SummarizedExperiment survival TCGAutils XML]; };
   RTN = derive2 { name="RTN"; version="2.22.1"; sha256="0ga96f1qmbq5a8nxb94b60ml2fwynnz590xjbzcx1g5vhrblkj42"; depends=[car data_table igraph IRanges limma minet mixtools pheatmap pwr RedeR S4Vectors snow SummarizedExperiment viper]; };
   RTNduals = derive2 { name="RTNduals"; version="1.22.0"; sha256="0m3h0rkix48pr4jywvm0h1pbqlv62gdzq3safwgqpgb7m0pg6d08"; depends=[RTN]; };
   RTNsurvival = derive2 { name="RTNsurvival"; version="1.22.0"; sha256="00naywzamklldsvipyg3q2c16s84y8cw1bngdw2l1d8yra4qpq9r"; depends=[data_table dunn_test egg ggplot2 pheatmap RColorBrewer RTN RTNduals scales survival]; };
@@ -886,7 +886,7 @@ in with self; {
   Rtpca = derive2 { name="Rtpca"; version="1.8.0"; sha256="0n2k1pqba4fnf0mpkxywd93yzv9dk37c134pna3f25mgzgd84qj3"; depends=[Biobase dplyr fdrtool ggplot2 pROC tibble tidyr]; };
   Rtreemix = derive2 { name="Rtreemix"; version="1.60.0"; sha256="0pkc4xsqqfdvszbb0xwx3hbxl1f7kcx3vm9bhjd7zkwls1jvv2n8"; depends=[Biobase graph Hmisc]; };
   S4Vectors = derive2 { name="S4Vectors"; version="0.36.2"; sha256="131cg5fzrqgyp4kv260yn8hpr0zv5mxjhdnpl50ydgc2k0l43d38"; depends=[BiocGenerics]; };
-  SAIGEgds = derive2 { name="SAIGEgds"; version="1.12.4"; sha256="12cxrl47ka1h3b31f0i145shhxbiss976vzp78iw1ldh032sbdyh"; depends=[gdsfmt Rcpp RcppArmadillo RcppParallel SeqArray SPAtest]; };
+  SAIGEgds = derive2 { name="SAIGEgds"; version="1.12.5"; sha256="10cck00fc4wmj7iwzm0s5ddgm32rpw8f32fawqaigxxrb3r9yn20"; depends=[gdsfmt Rcpp RcppArmadillo RcppParallel SeqArray SPAtest]; };
   SANTA = derive2 { name="SANTA"; version="2.34.0"; sha256="1i99s33id75srjr0x3yfz1gdyxw6766pr9w4afs8varfq8gxyc48"; depends=[igraph Matrix]; };
   SBGNview = derive2 { name="SBGNview"; version="1.12.0"; sha256="0644hd9m4d1s9y000yh831pwyx7q1dzr69fjqf15bby78xkn70yn"; depends=[AnnotationDbi bookdown httr igraph KEGGREST knitr pathview Rdpack rmarkdown rsvg SBGNview_data SummarizedExperiment xml2]; };
   SBMLR = derive2 { name="SBMLR"; version="1.94.0"; sha256="1x7p27abv9yc9mxbnprlwh5ph50jkycmlb90qib0mj361g4sr72d"; depends=[deSolve XML]; };
@@ -896,7 +896,7 @@ in with self; {
   SCATE = derive2 { name="SCATE"; version="1.8.0"; sha256="1zxliw0q979jps5lrmwks5m39qjd827jbvax1ndkd8p6lp1pcm2h"; depends=[GenomicAlignments GenomicRanges mclust preprocessCore Rtsne SCATEData splines2 xgboost]; };
   SCArray = derive2 { name="SCArray"; version="1.6.0"; sha256="0crh2ddh87j5qbxnslr1f94nsf24rzqz61ng6v3g8zpsldkrw09b"; depends=[BiocGenerics DelayedArray DelayedMatrixStats gdsfmt IRanges S4Vectors SingleCellExperiment SummarizedExperiment]; };
   SCBN = derive2 { name="SCBN"; version="1.16.0"; sha256="1lan5anf451dmb19sra79d4w2qi9kk7xw3zijswlbhfnd4fv9kgz"; depends=[]; };
-  SCFA = derive2 { name="SCFA"; version="1.8.0"; sha256="02g7hzgg68y8ckwhdwlp86574x0ffjp86nwg11whyira80v5y97y"; depends=[BiocParallel cluster coro glmnet igraph Matrix matrixStats psych RhpcBLASctl survival torch]; };
+  SCFA = derive2 { name="SCFA"; version="1.8.1"; sha256="1839mh15wxn07nh2zx7ahs2nimgxczpvn11dcr113zimxibm1r5z"; depends=[BiocParallel cluster coro glmnet igraph Matrix matrixStats psych RhpcBLASctl survival torch]; };
   SCOPE = derive2 { name="SCOPE"; version="1.10.0"; sha256="1z9v27l8bs7gkbgp1kd1q9nyq77x46anc0x0c1as0m04qq7c5xbj"; depends=[BiocGenerics Biostrings BSgenome BSgenome_Hsapiens_UCSC_hg19 DescTools DNAcopy doParallel foreach GenomeInfoDb GenomicRanges gplots IRanges RColorBrewer Rsamtools S4Vectors]; };
   SCnorm = derive2 { name="SCnorm"; version="1.20.0"; sha256="0zv4pf650crwliby34cjv7kxkrbqhc7xvz15n39hz5d0fk7ablgd"; depends=[BiocGenerics BiocParallel cluster data_table forcats ggplot2 moments quantreg S4Vectors SingleCellExperiment SummarizedExperiment]; };
   SDAMS = derive2 { name="SDAMS"; version="1.18.0"; sha256="0i9i9w24qb66rbvkpjn2fin8x0mxd7g767i4ly0s75v9kbbp3ca6"; depends=[qvalue SummarizedExperiment trust]; };
@@ -956,7 +956,7 @@ in with self; {
   SimBindProfiles = derive2 { name="SimBindProfiles"; version="1.36.0"; sha256="12383rvcq7l2b3ik2gi741d33shrijj09gqpkbvbksj046j90swm"; depends=[Biobase limma mclust Ringo]; };
   SimBu = derive2 { name="SimBu"; version="1.0.2"; sha256="0w8aksmcs16d6zmczarni8vrkw5b5kmv7n495w0qhmy6ync197bx"; depends=[basilisk BiocParallel data_table dplyr ggplot2 Matrix phyloseq proxyC RColorBrewer RCurl reticulate sparseMatrixStats SummarizedExperiment tidyr]; };
   SimFFPE = derive2 { name="SimFFPE"; version="1.10.0"; sha256="1mlmlbnqqzxmjmir9lnqnqqb6hmj6wfxhy6wpmf6sv9y2vi2cvjz"; depends=[Biostrings doParallel dplyr foreach GenomicRanges IRanges Rsamtools truncnorm]; };
-  SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.20.0"; sha256="1y9c9wf3009w4qh03zpsmc0ff0nkzal673a4nql5c11cn55sza2g"; depends=[BiocGenerics DelayedArray GenomicRanges S4Vectors SummarizedExperiment]; };
+  SingleCellExperiment = derive2 { name="SingleCellExperiment"; version="1.20.1"; sha256="1xwa6ncmqp21a4zx1dbs9p9b9rqbxhdgq2279mj4yl0gnpyqr9d7"; depends=[BiocGenerics DelayedArray GenomicRanges S4Vectors SummarizedExperiment]; };
   SingleCellSignalR = derive2 { name="SingleCellSignalR"; version="1.10.0"; sha256="194gnss397wv3pxh1vf8gfikbz519l8hx3w4fm2hxvjs6q8k2234"; depends=[BiocManager circlize data_table edgeR foreach gplots igraph limma multtest pheatmap Rtsne scran SIMLR stringr]; };
   SingleMoleculeFootprinting = derive2 { name="SingleMoleculeFootprinting"; version="1.6.0"; sha256="0dqyx3w8mxhf04xczzdv49lc2jkyamv1vlbdvfj0556y54z45cgg"; depends=[BiocGenerics Biostrings BSgenome data_table GenomeInfoDb GenomicRanges IRanges plyr QuasR RColorBrewer]; };
   SingleR = derive2 { name="SingleR"; version="2.0.0"; sha256="05rw6l0d4n9m1dd7dp55zfripx036x1riwy83sx3aj5mw4r1awb6"; depends=[beachmat BiocNeighbors BiocParallel BiocSingular DelayedArray DelayedMatrixStats Matrix Rcpp S4Vectors SummarizedExperiment]; };
@@ -969,10 +969,10 @@ in with self; {
   SpatialExperiment = derive2 { name="SpatialExperiment"; version="1.8.1"; sha256="1kdsdk6n81n83bbbk4k8wqyj441d3xjbc4hqv1rpn8ny5mjcbpqg"; depends=[BiocFileCache BiocGenerics DropletUtils magick rjson S4Vectors SingleCellExperiment SummarizedExperiment]; };
   SpatialFeatureExperiment = derive2 { name="SpatialFeatureExperiment"; version="1.0.3"; sha256="1616qpg31cnahj42s4gz435jj4j3d4rprr3bzxy58bdi7l2f8gv6"; depends=[BiocGenerics BiocParallel rjson S4Vectors sf SingleCellExperiment SpatialExperiment spdep SummarizedExperiment]; };
   SpeCond = derive2 { name="SpeCond"; version="1.52.0"; sha256="09f5nz799ai7y4ig6y24xnldd37qvv7yd1k258z3s9ckc76cdgd4"; depends=[Biobase fields hwriter mclust RColorBrewer]; };
-  Spectra = derive2 { name="Spectra"; version="1.8.2"; sha256="0aj04f7lfs6fv34crxq49p98hvzvpggx3xlwic4s2227hswysfc0"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; };
+  Spectra = derive2 { name="Spectra"; version="1.8.3"; sha256="1qib5rdyhgcs657hjnvp9zfhj05z3lpd3ngybqw3pikmc93ssf0h"; depends=[BiocGenerics BiocParallel fs IRanges MsCoreUtils ProtGenerics S4Vectors]; };
   SpectralTAD = derive2 { name="SpectralTAD"; version="1.14.1"; sha256="1iml0by529cxhj6v82046l86affipar143ddk627b3p6a2sg35zr"; depends=[BiocParallel cluster dplyr GenomicRanges HiCcompare magrittr Matrix PRIMME]; };
   SpidermiR = derive2 { name="SpidermiR"; version="1.28.0"; sha256="13dbz24g7l25d26piq00cpyll4cf8ss5l1kih7nvp8lrb540h6df"; depends=[AnnotationDbi gdata httr igraph miRNAtap miRNAtap_db org_Hs_eg_db]; };
-  SpliceWiz = derive2 { name="SpliceWiz"; version="1.0.2"; sha256="0d3d95pkk75pd076i275azhd1s0r8hrhki9xr9s4biihfa3f86ws"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats DT fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array heatmaply IRanges magrittr matrixStats NxtIRFdata ompBAM pheatmap plotly progress R_utils RColorBrewer Rcpp RcppProgress rhandsontable rhdf5 rtracklayer S4Vectors shiny shinydashboard shinyFiles shinyWidgets SummarizedExperiment XML zlibbioc]; };
+  SpliceWiz = derive2 { name="SpliceWiz"; version="1.0.4"; sha256="1lf9rcqplp6zzq11zvd1barcr0a99hfw0rgxlc93sg9gi8vm5xbn"; depends=[AnnotationHub BiocFileCache BiocGenerics BiocParallel Biostrings BSgenome data_table DelayedArray DelayedMatrixStats DT fst genefilter GenomeInfoDb GenomicRanges ggplot2 HDF5Array heatmaply IRanges magrittr matrixStats NxtIRFdata ompBAM pheatmap plotly progress R_utils RColorBrewer Rcpp RcppProgress rhandsontable rhdf5 rtracklayer S4Vectors shiny shinydashboard shinyFiles shinyWidgets SummarizedExperiment XML zlibbioc]; };
   SplicingFactory = derive2 { name="SplicingFactory"; version="1.6.0"; sha256="1l92i96n7pgwrrl4ywwmbpl1al5x3lamn9wrplclkh0l8yx8c033"; depends=[SummarizedExperiment]; };
   SplicingGraphs = derive2 { name="SplicingGraphs"; version="1.38.0"; sha256="0bqgn2lcmf6n188mj70cczwaps97dghmsililviq9sll91dj1gn8"; depends=[BiocGenerics BiocParallel GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph igraph IRanges Rgraphviz Rsamtools S4Vectors]; };
   SpotClean = derive2 { name="SpotClean"; version="1.0.1"; sha256="1sxmj1zgx7xf3f29l9qws4sf9k6v1wwh94brawqd6qq1plv79g51"; depends=[dplyr ggplot2 Matrix RColorBrewer readbitmap rhdf5 rjson rlang S4Vectors Seurat SpatialExperiment SummarizedExperiment tibble viridis]; };
@@ -1017,7 +1017,7 @@ in with self; {
   TSCAN = derive2 { name="TSCAN"; version="1.36.0"; sha256="0aqn1rxzbil9m9mpcdfc0k75s5k6ljy0k4bjrn0zq3492zz4x1qi"; depends=[combinat DelayedArray fastICA ggplot2 gplots igraph Matrix mclust mgcv plyr S4Vectors shiny SingleCellExperiment SummarizedExperiment TrajectoryUtils]; };
   TTMap = derive2 { name="TTMap"; version="1.20.0"; sha256="1vfj2zq4k4fzjnq48pckxkl3bwxwghhfwq8cz14hhwf10f735pq7"; depends=[Biobase colorRamps rgl SummarizedExperiment]; };
   TVTB = derive2 { name="TVTB"; version="1.24.0"; sha256="16lhbbisgxmvp86qfkp0cdd8akjld0ryklw41hi3k4ndimzax6hf"; depends=[AnnotationFilter BiocGenerics BiocParallel Biostrings ensembldb ensemblVEP GenomeInfoDb GenomicRanges GGally ggplot2 Gviz IRanges limma reshape2 Rsamtools S4Vectors SummarizedExperiment VariantAnnotation]; };
-  TarSeqQC = derive2 { name="TarSeqQC"; version="1.27.0"; sha256="0iiv7c3jd1iw7i5nn65370zbvi11s9qn72zig9rw1gz8nvnmdgpq"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; };
+  TarSeqQC = derive2 { name="TarSeqQC"; version="1.28.0"; sha256="14ima8ymdb91lpkhdnsg6q7ajxs5p1xzzcsjfhixxkm341k45j35"; depends=[BiocGenerics BiocParallel Biostrings cowplot GenomeInfoDb GenomicAlignments GenomicRanges ggplot2 Hmisc IRanges openxlsx plyr reshape2 Rsamtools S4Vectors]; };
   TargetDecoy = derive2 { name="TargetDecoy"; version="1.4.0"; sha256="1xx9y5faf5ic14h7cnxpb83nr34mqzz0c846g1z28f3x9d0kg9kz"; depends=[ggplot2 ggpubr miniUI mzID mzR shiny]; };
   TargetScore = derive2 { name="TargetScore"; version="1.36.0"; sha256="00z2zv5yhxriagvcz3bwkpr9ii0r9lw4vcf7kjp7x5pjzcc6q6wq"; depends=[Matrix pracma]; };
   TargetSearch = derive2 { name="TargetSearch"; version="2.0.0"; sha256="1m5v2d67w0hi3x1b6nlsq97z197djnr23d6lj9krib1im70cclwy"; depends=[assertthat ncdf4]; };
@@ -1090,7 +1090,7 @@ in with self; {
   agilp = derive2 { name="agilp"; version="3.30.0"; sha256="15cw004g1vxfwvf939018vmlv9gym4r473jissamkygqdv78hcr0"; depends=[]; };
   airpart = derive2 { name="airpart"; version="1.6.0"; sha256="07zxv0sjhlajaw4gxpjni14qyyqn70ar8ph5cpibzcky1lx6pmkl"; depends=[apeglm clue ComplexHeatmap dplyr dynamicTreeCut emdbook forestplot ggplot2 lpSolve matrixStats mclust pbapply plyr RColorBrewer rlang S4Vectors scater SingleCellExperiment smurf SummarizedExperiment]; };
   alevinQC = derive2 { name="alevinQC"; version="1.14.0"; sha256="0rd64j4hkdk2d6mlld6qkv2m96lqc93807xjdf05xm8qkyx8g8y2"; depends=[cowplot dplyr DT GGally ggplot2 Rcpp rjson rlang rmarkdown shiny shinydashboard tximport]; };
-  alpine = derive2 { name="alpine"; version="1.24.0"; sha256="0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors speedglm stringr SummarizedExperiment]; };
+  alpine = derive2 { name="alpine"; version="1.24.0"; sha256="0rjnwljh4c2f7ml0m14pllns4pvyjwwf23qsn6zjygm5x04bapf0"; depends=[Biostrings GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges graph IRanges RBGL Rsamtools S4Vectors stringr SummarizedExperiment]; };
   altcdfenvs = derive2 { name="altcdfenvs"; version="2.60.0"; sha256="0fm4l93j6nm1w1w57zzryc1hkzapp8l16pkwjzdzllvwvsnsg8r0"; depends=[affy Biobase BiocGenerics Biostrings hypergraph makecdfenv S4Vectors]; };
   amplican = derive2 { name="amplican"; version="1.20.0"; sha256="1c990i6gxbarcpbdpkz017x94spwzap95l95synlizbkyif4z8ij"; depends=[BiocGenerics BiocParallel Biostrings data_table dplyr GenomeInfoDb GenomicRanges ggplot2 ggthemes gridExtra gtable IRanges knitr Matrix matrixStats Rcpp rmarkdown S4Vectors ShortRead stringr waffle]; };
   animalcules = derive2 { name="animalcules"; version="1.14.0"; sha256="1alpsamrglgvzhcibkaf7m3gyiv61wbj1gvsq4lw6vjka100j9qr"; depends=[ape assertthat biomformat caret covr DESeq2 dplyr DT forcats ggplot2 glmnet GUniFrac lattice limma magrittr Matrix MultiAssayExperiment plotly plotROC rentrez reshape2 S4Vectors scales shiny shinyjs SummarizedExperiment tibble tsne umap vegan XML]; };
@@ -1155,7 +1155,7 @@ in with self; {
   biodbNcbi = derive2 { name="biodbNcbi"; version="1.2.0"; sha256="0bjw5q9ls7p5pi13rzmax4iqfi5l7b0inga9b96bz18mcq071pqp"; depends=[biodb chk R6 XML]; };
   biodbNci = derive2 { name="biodbNci"; version="1.2.0"; sha256="18kjpc71gis82hkg6h7jn0qqwc3m2dlc6ddmyr9cfmm1wvr3fdc6"; depends=[biodb chk R6 Rcpp testthat]; };
   biodbUniprot = derive2 { name="biodbUniprot"; version="1.4.0"; sha256="1xg4f72maczqm2srscnzj3fhibnsya49d9a00d5r6qg1avc3g33v"; depends=[biodb R6]; };
-  biomaRt = derive2 { name="biomaRt"; version="2.54.0"; sha256="0c6agi652kbffqwd1r3c22ncisqaiy3gqbc9fz13767rr71im6lq"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
+  biomaRt = derive2 { name="biomaRt"; version="2.54.1"; sha256="13nhp97cklaimc3cd931hz584nc58szk2gyxrkfhp7knfli6jbpi"; depends=[AnnotationDbi BiocFileCache digest httr progress rappdirs stringr XML xml2]; };
   biomformat = derive2 { name="biomformat"; version="1.26.0"; sha256="0728fpj05bvna5lpm29pdbn4slfmq16nz35as086ddbl2hhc9ni1"; depends=[jsonlite Matrix plyr rhdf5]; };
   biomvRCNS = derive2 { name="biomvRCNS"; version="1.38.0"; sha256="0n026b744ah5kcnipsyiqqs7vlz5n5im1kgv35i2pgxyzvf7a8sn"; depends=[GenomicRanges Gviz IRanges mvtnorm]; };
   biosigner = derive2 { name="biosigner"; version="1.26.0"; sha256="11ncmxy4wqdg30w8a6dgcsywyzda49f9al435fz3pfj5rmlbbrlj"; depends=[Biobase e1071 MultiAssayExperiment MultiDataSet randomForest ropls SummarizedExperiment]; };
@@ -1333,7 +1333,7 @@ in with self; {
   dittoSeq = derive2 { name="dittoSeq"; version="1.10.0"; sha256="0sxpwg2cjw70pzdxbdw68nic521w65ryn83mj0pb2m1ncpimin4b"; depends=[colorspace cowplot ggplot2 ggrepel ggridges gridExtra pheatmap reshape2 S4Vectors SingleCellExperiment SummarizedExperiment]; };
   divergence = derive2 { name="divergence"; version="1.14.0"; sha256="1khxmngdqsvn77hfiyz732q4z268qwk0r9ydmipz25lnddb25p7m"; depends=[SummarizedExperiment]; };
   dks = derive2 { name="dks"; version="1.44.0"; sha256="1vg6xlw5ia6r1xycd5hrh6s2nxrkrgi34dsd1kfzhkf11d40ydfh"; depends=[cubature]; };
-  dmrseq = derive2 { name="dmrseq"; version="1.18.0"; sha256="1zx62lbj0am85p0c1vk06s7qf8294vk8yyh67nkiqc7xgqqwybyk"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
+  dmrseq = derive2 { name="dmrseq"; version="1.18.1"; sha256="0djd2r0xzjcyw496wdw2gwzk4wjf3jp639b198x4pc0g0mmgw245"; depends=[AnnotationHub annotatr BiocParallel bsseq bumphunter DelayedMatrixStats GenomeInfoDb GenomicRanges ggplot2 IRanges locfit matrixStats nlme outliers RColorBrewer rtracklayer S4Vectors]; };
   doppelgangR = derive2 { name="doppelgangR"; version="1.26.0"; sha256="1qfgfvxj44zyqfcj57lphrqgh7yb3lv807bl9xhg7k2gc3rmy5n1"; depends=[Biobase BiocParallel digest impute mnormt SummarizedExperiment sva]; };
   doseR = derive2 { name="doseR"; version="1.14.0"; sha256="0cpjy8whi7nhpyhyz8k2g70l7rhfpg2xcgclxdasbrj695qy79f0"; depends=[digest edgeR lme4 matrixStats mclust RUnit S4Vectors SummarizedExperiment]; };
   dpeak = derive2 { name="dpeak"; version="1.10.0"; sha256="1cnbvi8x3zjfvbsc71gz8pk7x7fglydhnc8msp6c10sd06blpibs"; depends=[BSgenome IRanges MASS Rcpp]; };
@@ -1360,7 +1360,7 @@ in with self; {
   epialleleR = derive2 { name="epialleleR"; version="1.6.1"; sha256="0b416ibi9y81h7xycj1sxmq344ami3a5mcqac3rzbn3l380kl5ms"; depends=[BH BiocGenerics data_table GenomeInfoDb GenomicRanges Rcpp Rhtslib stringi SummarizedExperiment VariantAnnotation zlibbioc]; };
   epidecodeR = derive2 { name="epidecodeR"; version="1.6.0"; sha256="0qfb912xsyp4cvblhpwpa22iziwqz39hfnf8x68d23pnfwnb1v74"; depends=[dplyr EnvStats GenomicRanges ggplot2 ggpubr IRanges rstatix rtracklayer]; };
   epigenomix = derive2 { name="epigenomix"; version="1.38.0"; sha256="0vdrnn2qmcy3znz534m5iynvzw208whcyypw7mhdqvrfzkzb4m4a"; depends=[beadarray Biobase BiocGenerics GenomeInfoDb GenomicRanges IRanges MCMCpack Rsamtools S4Vectors SummarizedExperiment]; };
-  epigraHMM = derive2 { name="epigraHMM"; version="1.6.3"; sha256="1qnh135gzz7fq73ryqg3bax0bw6krghpyf05b9xp5py1fk9ic9d3"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
+  epigraHMM = derive2 { name="epigraHMM"; version="1.6.4"; sha256="137qs09idwrc40379dvl3gmy2dcfhmp2x09rzzslkzkh0nj4ikcn"; depends=[bamsignals csaw data_table GenomeInfoDb GenomicRanges ggplot2 ggpubr GreyListChIP IRanges limma magrittr MASS Matrix pheatmap Rcpp RcppArmadillo rhdf5 Rhdf5lib Rsamtools rtracklayer S4Vectors scales SummarizedExperiment]; };
   epihet = derive2 { name="epihet"; version="1.13.0"; sha256="1p5sgb438yj6h0fv0v17dhz1pl32vai5zcbmgpgagrd5829a6a7r"; depends=[data_table doParallel foreach GenomicRanges ggplot2 igraph IRanges pheatmap qvalue ReactomePA Rtsne S4Vectors WGCNA]; };
   epimutacions = derive2 { name="epimutacions"; version="1.2.0"; sha256="1anpx122fcrwldkv5bz5c1cmf6a7y1ai8pc5wjpch7c0nim4a8xg"; depends=[AnnotationDbi AnnotationHub BiocGenerics BiocParallel biomaRt bumphunter ensembldb epimutacionsData ExperimentHub GenomeInfoDb GenomicFeatures GenomicRanges ggplot2 ggrepel gridExtra Gviz Homo_sapiens IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b2_hg19 IlluminaHumanMethylationEPICmanifest IRanges isotree matrixStats minfi purrr reshape2 robustbase rtracklayer S4Vectors SummarizedExperiment tibble TxDb_Hsapiens_UCSC_hg18_knownGene TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
   epistack = derive2 { name="epistack"; version="1.4.0"; sha256="06z380js0hgnps8nkfrk2ay7s8fyqbndipavk5ipihbp80yzmgpx"; depends=[BiocGenerics GenomicRanges IRanges plotrix S4Vectors SummarizedExperiment viridisLite]; };
@@ -1378,7 +1378,7 @@ in with self; {
   eudysbiome = derive2 { name="eudysbiome"; version="1.28.0"; sha256="0q6x3nlvarhgc1fq5j4h7hxq5dcmfm0fgm3lmgz63bcbpsf60n5g"; depends=[Biostrings plyr R_utils Rsamtools]; };
   evaluomeR = derive2 { name="evaluomeR"; version="1.14.0"; sha256="0wjmm2wzqprn0v0vn90cc3b3wsa274b305p661fdpsql4714jmrq"; depends=[class cluster corrplot flexmix fpc ggdendro ggplot2 kableExtra MASS matrixStats mclust MultiAssayExperiment plotrix prabclus randomForest Rdpack reshape2 SummarizedExperiment]; };
   exomeCopy = derive2 { name="exomeCopy"; version="1.44.0"; sha256="11a95rpqzc5502s75ar703bv9hisgfx7yqdf03n0q1qh6ykil35g"; depends=[GenomeInfoDb GenomicRanges IRanges Rsamtools]; };
-  exomePeak2 = derive2 { name="exomePeak2"; version="1.10.0"; sha256="1j8l3q5bq3yb1889vjpk8l9qzrmg7lv38m7jb57cb9q67sflqjzs"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magrittr mclust Rsamtools rtracklayer S4Vectors speedglm SummarizedExperiment]; };
+  exomePeak2 = derive2 { name="exomePeak2"; version="1.10.0"; sha256="1j8l3q5bq3yb1889vjpk8l9qzrmg7lv38m7jb57cb9q67sflqjzs"; depends=[BiocGenerics BiocParallel Biostrings BSgenome DESeq2 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 IRanges magrittr mclust Rsamtools rtracklayer S4Vectors SummarizedExperiment]; };
   extraChIPs = derive2 { name="extraChIPs"; version="1.2.4"; sha256="1jhpzw7ps8bknf3b1pjcpsf5kncm3ia7q5niygvrw3idkbszz2c2"; depends=[BiocIO BiocParallel broom ComplexUpset csaw dplyr edgeR EnrichedHeatmap forcats GenomeInfoDb GenomicInteractions GenomicRanges ggforce ggplot2 ggrepel ggside glue Gviz InteractionSet IRanges limma patchwork RColorBrewer rlang Rsamtools rtracklayer S4Vectors scales stringr SummarizedExperiment tibble tidyr tidyselect vctrs VennDiagram]; };
   fCCAC = derive2 { name="fCCAC"; version="1.24.0"; sha256="1r4rdbv1xv8rwsna8w89fzd76hzspf825fxzcn475ll31gmsxsrv"; depends=[ComplexHeatmap fda genomation GenomicRanges ggplot2 IRanges RColorBrewer S4Vectors]; };
   fCI = derive2 { name="fCI"; version="1.28.0"; sha256="1jiws5q3ppq0z0s71nhb6fs63470v2di45y0gdf7anjnpxgjcjq9"; depends=[FNN gtools psych rgl VennDiagram zoo]; };
@@ -1405,7 +1405,7 @@ in with self; {
   flowCHIC = derive2 { name="flowCHIC"; version="1.32.0"; sha256="18mcywl4857wmka63rcnvp2xvh8wj5r8gvbsri9a3f4190wg8yn9"; depends=[EBImage flowCore ggplot2 hexbin vegan]; };
   flowCL = derive2 { name="flowCL"; version="1.35.0"; sha256="1jxr0zn3fgm5nqishssxh332mmxfz3fc9zgshn0lbq4avxc2x128"; depends=[graph Rgraphviz]; };
   flowClean = derive2 { name="flowClean"; version="1.36.0"; sha256="1wqwq8fw0dk78l43p4cjzll3psc0d4mg7gjckddvpmzlg6w4ha3k"; depends=[bit changepoint flowCore sfsmisc]; };
-  flowClust = derive2 { name="flowClust"; version="3.36.0"; sha256="1l1lfgm6x06gyzda36m6gvqmb91zbrz8m83b1fnfzpxkhqha20yq"; depends=[Biobase BiocGenerics flowCore graph]; };
+  flowClust = derive2 { name="flowClust"; version="3.36.1"; sha256="1r27nm5dxlhl5rk96dkjfx8326bvdgx55xg4w2zji3m49x9db2gs"; depends=[Biobase BiocGenerics flowCore graph]; };
   flowCore = derive2 { name="flowCore"; version="2.10.0"; sha256="0j0ryyz3vcih964is5gdm2jp39ssdli9q6r03q6rj9nwzplq5asj"; depends=[BH Biobase BiocGenerics cpp11 cytolib matrixStats Rcpp RProtoBufLib S4Vectors]; };
   flowCut = derive2 { name="flowCut"; version="1.8.0"; sha256="0p66wcr940m5nvl024izqn3w0x6zmp0n7j43xj70arfcxrxp9gxd"; depends=[Cairo e1071 flowCore flowDensity]; };
   flowCyBar = derive2 { name="flowCyBar"; version="1.34.0"; sha256="1nbg49s18mxvr5pzv4lx4hvdrwxn5spagxn71zid5kgk13f142a6"; depends=[gplots vegan]; };
@@ -1442,7 +1442,7 @@ in with self; {
   gcapc = derive2 { name="gcapc"; version="1.22.0"; sha256="1n3g6fvj86q9n6q3ccmj6ns0gdd4sqfdm43sh1hpxkid9v88209y"; depends=[BiocGenerics Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicRanges IRanges MASS matrixStats Rsamtools S4Vectors]; };
   gcatest = derive2 { name="gcatest"; version="1.28.2"; sha256="1f2bp16x7ji9sh5kk150w57gqpbrisrb0xlkjv8wnd63j0vnng3l"; depends=[lfa]; };
   gcrma = derive2 { name="gcrma"; version="2.70.0"; sha256="0a3wjwjgjkpmfvgg0b4jc1rkwzsqrjbaziydjfnkll4rw9xcavy1"; depends=[affy affyio Biobase BiocManager Biostrings XVector]; };
-  gdsfmt = derive2 { name="gdsfmt"; version="1.34.0"; sha256="1ck3qq4vhjp6vvicpldr7d2rkpspp5albjkbqjbshnbq11fhrk06"; depends=[]; };
+  gdsfmt = derive2 { name="gdsfmt"; version="1.34.1"; sha256="1sx7yw44djrnc6km8fip3w3vclkgz5s0w6ibp8lpvmjcay8nv2sx"; depends=[]; };
   geNetClassifier = derive2 { name="geNetClassifier"; version="1.38.0"; sha256="1ahlml1ssjmg126ki1phdprq4v0nawzbbfq8jray5ypaj32qx3r2"; depends=[Biobase e1071 EBarrays minet]; };
   gemini = derive2 { name="gemini"; version="1.12.0"; sha256="12p44p3nzn32am2m609k64iy4lfj42dygdxmb770ld8lpihhrkmz"; depends=[dplyr ggplot2 magrittr mixtools pbmcapply scales]; };
   gemma_R = derive2 { name="gemma.R"; version="1.0.1"; sha256="0m6mmv55ghvwqw462ym335bcng61c52d84irkn5xwq6yzr2dgxsa"; depends=[Biobase bit64 data_table glue httr jsonlite lubridate magrittr memoise rappdirs rlang S4Vectors stringr SummarizedExperiment tibble tidyr]; };
@@ -1479,7 +1479,7 @@ in with self; {
   glmGamPoi = derive2 { name="glmGamPoi"; version="1.10.2"; sha256="1ihjqzdhx6k99gdd4556xxn9822sblg6vmblcmbzml01bhv6xzar"; depends=[beachmat BiocGenerics DelayedArray DelayedMatrixStats HDF5Array MatrixGenerics matrixStats Rcpp RcppArmadillo rlang SingleCellExperiment SummarizedExperiment]; };
   glmSparseNet = derive2 { name="glmSparseNet"; version="1.16.0"; sha256="1573cclc2qn4mhw24k7ab75a9inc7z205b0j85favmvv1zcyqal4"; depends=[biomaRt digest dplyr forcats futile_logger futile_options ggplot2 glmnet glue httr Matrix MultiAssayExperiment readr reshape2 stringr SummarizedExperiment survminer]; };
   globalSeq = derive2 { name="globalSeq"; version="1.26.0"; sha256="0l4n755v8gxxrxqgzhks4yz06rr3m703zaaavh0fyryk2mnijpip"; depends=[]; };
-  globaltest = derive2 { name="globaltest"; version="5.52.0"; sha256="1qcrs7dasb1aaws3zkiipznlc1z6i7zijhcsfv6hw3d9wpb0np9k"; depends=[annotate AnnotationDbi Biobase survival]; };
+  globaltest = derive2 { name="globaltest"; version="5.52.1"; sha256="1g5dv3bw0fj8sq0hsr8c7nh6n1rzvx1bisqlyqjqq3f8lsyb51kb"; depends=[annotate AnnotationDbi Biobase survival]; };
   gmapR = derive2 { name="gmapR"; version="1.40.0"; sha256="03fi4ld4f102xch75z6s67kb27mvyg5zik5n59ni4zdiipi9i2cl"; depends=[Biobase BiocGenerics BiocParallel Biostrings BSgenome GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges IRanges Rsamtools rtracklayer S4Vectors VariantAnnotation]; };
   gmoviz = derive2 { name="gmoviz"; version="1.10.0"; sha256="0vafsa3i8z08bfl4x0adlg3bf0jdw4a7zb459cw7bfdkkw8g4850"; depends=[BiocGenerics Biostrings circlize colorspace ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges gridBase IRanges pracma Rsamtools rtracklayer S4Vectors]; };
   goProfiles = derive2 { name="goProfiles"; version="1.60.0"; sha256="0wkvb79lb309ff6iv8p23z9rwrrv7qha86ngs0ag670mpm9yra5j"; depends=[AnnotationDbi Biobase CompQuadForm GO_db stringr]; };
@@ -1531,7 +1531,7 @@ in with self; {
   iSEE = derive2 { name="iSEE"; version="2.10.0"; sha256="1l2bwqk7ivj79xxjzc0hc3x5v5h19zpk9pa0vbpb5p64z1pshnjn"; depends=[BiocGenerics circlize colourpicker ComplexHeatmap DT ggplot2 ggrepel igraph mgcv rintrojs S4Vectors shiny shinyAce shinydashboard shinyjs shinyWidgets SingleCellExperiment SummarizedExperiment vipor viridisLite]; };
   iSEEhex = derive2 { name="iSEEhex"; version="1.0.0"; sha256="06n9ls71rg2kilr3kjlwwk5rnj8v68svjmzcr2hg0gwwyaxcyk9w"; depends=[ggplot2 hexbin iSEE shiny SummarizedExperiment]; };
   iSEEhub = derive2 { name="iSEEhub"; version="1.0.0"; sha256="1ggkm7931axcl0464h0d5cnf5lbd6nx3fbac1zrlkwyb2lym7wi8"; depends=[AnnotationHub BiocManager DT ExperimentHub iSEE rintrojs S4Vectors shiny shinydashboard shinyjs SingleCellExperiment SummarizedExperiment]; };
-  iSEEu = derive2 { name="iSEEu"; version="1.10.0"; sha256="0040k9p1bmlg2065s3a124qvx5qgqqs4kgbkkz0k9vsdvr3z87zs"; depends=[colourpicker DT ggplot2 IRanges iSEE iSEEhex S4Vectors shiny shinyAce SingleCellExperiment SummarizedExperiment]; };
+  iSEEu = derive2 { name="iSEEu"; version="1.10.1"; sha256="04c2ha4s4fvk30qm65shzzvymiilj0y85qdjc3lw4c90jfvnf44q"; depends=[colourpicker DT ggplot2 IRanges iSEE iSEEhex S4Vectors shiny shinyAce SingleCellExperiment SummarizedExperiment]; };
   iSeq = derive2 { name="iSeq"; version="1.50.0"; sha256="1h0da0298g2lvvqbys3jh2acjjzh1dvivfpl07g319nafxkfsi1q"; depends=[]; };
   iasva = derive2 { name="iasva"; version="1.16.0"; sha256="192cpnpyyjf16pqnzj70nsqkzv6wp4acia7fciz1zvz5jhncrsva"; depends=[BiocParallel cluster irlba SummarizedExperiment]; };
   ibh = derive2 { name="ibh"; version="1.46.0"; sha256="0kxqpb9711yxg5xz2mhpwjw9nwixmfzzy6qql1sifi4mp6bh2fzf"; depends=[simpIntLists]; };
@@ -1672,7 +1672,7 @@ in with self; {
   minfi = derive2 { name="minfi"; version="1.44.0"; sha256="15989zilgy2j4k4nw046qg8wli7ynjh2b1yzfv7cwgn87mp618lc"; 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="1.28.0"; sha256="0662jsrw745973kf3f95l3n6i5s9h2nk2ap6alv8sb5rkykva2in"; depends=[AnnotationDbi ggplot2 graph org_Hs_eg_db Rgraphviz ROntoTools]; };
   mirTarRnaSeq = derive2 { name="mirTarRnaSeq"; version="1.6.0"; sha256="07lfh8c7ks9lbnskvqjhjrssp0wk1kpp7mbh7c7cg6q1kxcxpqyx"; depends=[assertthat caTools corrplot data_table dplyr ggplot2 MASS pheatmap pscl purrr R_utils reshape2]; };
-  missMethyl = derive2 { name="missMethyl"; version="1.32.0"; sha256="10r3yvamkd1h291lmbas66mshrmy7djkz6pldh8lpqngm0rpgdr6"; depends=[AnnotationDbi BiasedUrn Biobase BiocGenerics GenomicRanges GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest IRanges limma methylumi minfi org_Hs_eg_db ruv S4Vectors statmod stringr SummarizedExperiment]; };
+  missMethyl = derive2 { name="missMethyl"; version="1.32.1"; sha256="1rrm8m68kgjkrw1wdli5lrwqlavhbm490zgnj5vafzpvx7xajfma"; depends=[AnnotationDbi BiasedUrn Biobase BiocGenerics GenomicRanges GO_db IlluminaHumanMethylation450kanno_ilmn12_hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno_ilm10b4_hg19 IlluminaHumanMethylationEPICmanifest IRanges limma methylumi minfi org_Hs_eg_db ruv S4Vectors statmod stringr SummarizedExperiment]; };
   missRows = derive2 { name="missRows"; version="1.18.0"; sha256="0kwbmhz80an07fcp6skv4bik0ncszxcllfi7jv9h0k814qciij0y"; depends=[ggplot2 gtools MultiAssayExperiment plyr S4Vectors]; };
   mistyR = derive2 { name="mistyR"; version="1.6.1"; sha256="0kcqcr1bmmhxngmygr64ca5kl8gsc7z9qwq2ivcc97f78xs3p6p8"; depends=[assertthat caret deldir digest distances dplyr filelock furrr ggplot2 purrr R_utils ranger readr ridge rlang rlist stringr tibble tidyr tidyselect withr]; };
   mitch = derive2 { name="mitch"; version="1.10.0"; sha256="174hiq8xzbvdkfxdgm742sjs7qcmnkb9shcid1p8x8ci6fk9vs61"; depends=[beeswarm echarts4r GGally ggplot2 gplots gridExtra knitr MASS plyr reshape2 rmarkdown]; };
@@ -1694,12 +1694,12 @@ in with self; {
   msPurity = derive2 { name="msPurity"; version="1.24.0"; sha256="1w998i5lv1c2485cmdzk31inykhl64s7njaj725cs1r3gzi4l7h4"; depends=[DBI dbplyr doSNOW dplyr fastcluster foreach ggplot2 magrittr mzR plyr Rcpp reshape2 RSQLite stringr]; };
   msa = derive2 { name="msa"; version="1.30.1"; sha256="064hmry0zhmpchxgjsw0krsybr9v9gbsz26zmj2a39pg1nggwbq4"; depends=[BiocGenerics Biostrings IRanges Rcpp S4Vectors]; };
   msgbsR = derive2 { name="msgbsR"; version="1.22.0"; sha256="0g6d0gx5af61svxjdzx438vz24sd81qml7f755kq8nrr89pacvh0"; depends=[BSgenome easyRNASeq edgeR GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggbio ggplot2 IRanges plyr R_utils Rsamtools S4Vectors SummarizedExperiment]; };
-  mslp = derive2 { name="mslp"; version="1.0.1"; sha256="01w9lzfl1vci4z63yzcjk9fn7yzkcxiw6ms528qbg3nmfq08kx5a"; depends=[data_table doRNG fmsb foreach magrittr org_Hs_eg_db pROC randomForest RankProd]; };
+  mslp = derive2 { name="mslp"; version="1.0.2"; sha256="0sv6a9vjrgi4cd2mvb88jvr8wdwf6hr3570zpq3w3072m8m8gj4v"; depends=[data_table doRNG fmsb foreach magrittr org_Hs_eg_db pROC randomForest RankProd]; };
   msmsEDA = derive2 { name="msmsEDA"; version="1.36.0"; sha256="17xklsg483zd205q5hyxy6b3cgrb53pplb1wc7pmv5638y7nsq2v"; depends=[gplots MASS MSnbase RColorBrewer]; };
   msmsTests = derive2 { name="msmsTests"; version="1.36.0"; sha256="10frsvqhi3i0v2w4q4q9xz1ykyf6s3nrjlmn94x3kd06p3s839k3"; depends=[edgeR msmsEDA MSnbase qvalue]; };
   msqrob2 = derive2 { name="msqrob2"; version="1.6.1"; sha256="1cv7i2n8a470jzpldlwyrx12d8my2al2522vilyyfr9j74xgi0ln"; depends=[BiocParallel codetools limma lme4 MASS Matrix MultiAssayExperiment purrr QFeatures SummarizedExperiment]; };
   multiClust = derive2 { name="multiClust"; version="1.28.0"; sha256="0mw48jm154c0k9nhal56xc4jv0n3ms0s1770g2i2lxkr37905swq"; depends=[amap cluster ctc dendextend mclust survival]; };
-  multiGSEA = derive2 { name="multiGSEA"; version="1.8.1"; sha256="1y43nf7c3zyqjsdpx7g5xfdy53qwzzbynb9lhhyj6rbbirrpj48b"; depends=[AnnotationDbi dplyr fgsea graphite magrittr metap rappdirs rlang]; };
+  multiGSEA = derive2 { name="multiGSEA"; version="1.8.2"; sha256="1s8rdrzpvnscdisv1ld31aiv5vbddvr7f523sc9ngv2nsmisxdq8"; depends=[AnnotationDbi dplyr fgsea graphite magrittr metap rappdirs rlang]; };
   multiHiCcompare = derive2 { name="multiHiCcompare"; version="1.16.0"; sha256="0mwb61c6yqq1frnsgp3nafmlrl1zi8sxckp5yw7z083805y3fbyr"; depends=[aggregation BiocParallel data_table dplyr edgeR GenomeInfoDb GenomeInfoDbData GenomicRanges HiCcompare pbapply pheatmap qqman]; };
   multiMiR = derive2 { name="multiMiR"; version="1.20.0"; sha256="1zfjr1cw1qpi70wxrkw32y3dmwhbsdzd2522cgkj4x97g4d5cn99"; depends=[AnnotationDbi BiocGenerics dplyr purrr RCurl tibble XML]; };
   multiOmicsViz = derive2 { name="multiOmicsViz"; version="1.22.0"; sha256="0g28ksb9vf2lpv15s9s64nnz6smhxrf9cbsw4kba0dlyrrzzha4a"; depends=[doParallel foreach SummarizedExperiment]; };
@@ -1742,7 +1742,7 @@ in with self; {
   nuCpos = derive2 { name="nuCpos"; version="1.16.3"; sha256="14anlg6a7b3qw2k39q273p5396v3nqlask0gz92h170z24gjyc1s"; depends=[]; };
   nucleR = derive2 { name="nucleR"; version="2.30.0"; sha256="0j8g0lf6pzqzak259fp6xckgcjrabqgd28bwy9fbx3pd1qj5yrh0"; depends=[Biobase BiocGenerics Biostrings dplyr GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr Rsamtools S4Vectors ShortRead]; };
   nucleoSim = derive2 { name="nucleoSim"; version="1.26.0"; sha256="0cgljwk9car3s5ncslx0j0bya6hchfv1zk09q8r0y6258mim4qy6"; depends=[IRanges S4Vectors]; };
-  nullranges = derive2 { name="nullranges"; version="1.4.0"; sha256="01f7x99nzgi0si02p5bsjvf0mybl52kxnkm2j1f1s2rai5srkca4"; depends=[data_table GenomeInfoDb GenomicRanges ggplot2 ggridges InteractionSet IRanges ks plyranges progress rlang S4Vectors scales speedglm]; };
+  nullranges = derive2 { name="nullranges"; version="1.4.0"; sha256="01f7x99nzgi0si02p5bsjvf0mybl52kxnkm2j1f1s2rai5srkca4"; depends=[data_table GenomeInfoDb GenomicRanges ggplot2 ggridges InteractionSet IRanges ks plyranges progress rlang S4Vectors scales]; };
   occugene = derive2 { name="occugene"; version="1.58.0"; sha256="13hv71w25jzlf0fs5wx400m1zh4l4vxlvv42vidiyggj894ky5a3"; depends=[]; };
   octad = derive2 { name="octad"; version="1.0.0"; sha256="0qa407rhi9z1n2hif40j27vbfsy222wi2hh26qn4s0s7f2fnfyfl"; depends=[AnnotationHub Biobase data_table DESeq2 dplyr EDASeq edgeR ExperimentHub foreach ggplot2 GSVA htmlwidgets httr limma magrittr octad_db plotly reshape2 Rfast rhdf5 RUVSeq S4Vectors]; };
   odseq = derive2 { name="odseq"; version="1.26.0"; sha256="0p51lay3xasqg55j99gdx1gpk93p4m2czvbw912h559v2s4hnzqq"; depends=[kebabs mclust msa]; };
@@ -1799,6 +1799,7 @@ in with self; {
   periodicDNA = derive2 { name="periodicDNA"; version="1.8.0"; sha256="03wdxbgsrj2c7j3fgxigjbq349y5c8cw80xvb5ja7lbi1isfb785"; depends=[BiocParallel Biostrings BSgenome cowplot GenomeInfoDb GenomicRanges ggplot2 IRanges magrittr rtracklayer S4Vectors zoo]; };
   pgca = derive2 { name="pgca"; version="1.22.0"; sha256="0bcq1qks87jjgd2bwpds6xvcvidcvl9pq53mi0dafihgd0s2ycfn"; depends=[]; };
   phantasus = derive2 { name="phantasus"; version="1.18.4"; sha256="0rjn66xjkr57w4nsjczxrw3hw90r9zfwqbmhs8pw4y1hd7j1alhi"; depends=[AnnotationDbi assertthat Biobase ccaPP curl data_table DESeq2 fgsea GEOquery ggplot2 gtable htmltools httpuv httr jsonlite limma Matrix opencpu pheatmap protolite rhdf5 Rook scales stringr svglite]; };
+  phemd = derive2 { name="phemd"; version="1.14.1"; sha256="18i2qps2r8h9fqln9gm0wz373xg3lfkgb3my8wk4w944h3an6280"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; };
   phenoTest = derive2 { name="phenoTest"; version="1.46.0"; sha256="0rcgbnqglfs9asyrssnhy7h99kikmnr7s1827y8q2agq3pl96q13"; depends=[annotate AnnotationDbi Biobase biomaRt BMA Category ellipse genefilter ggplot2 gplots GSEABase Heatplus hgu133a_db Hmisc hopach limma mgcv survival xtable]; };
   phenomis = derive2 { name="phenomis"; version="1.0.2"; sha256="15lk3wapaaqqrlp02b2cvdlx8dgcvc3vjsfv8i70qh89rljialf8"; depends=[Biobase biodb biodbChebi data_table futile_logger ggplot2 ggrepel htmlwidgets igraph limma MultiAssayExperiment MultiDataSet plotly PMCMRplus ranger RColorBrewer ropls SummarizedExperiment tibble tidyr VennDiagram]; };
   phenopath = derive2 { name="phenopath"; version="1.22.0"; sha256="0p2lh858ykhqz0zj4h1vmjd27szwkrlswanapz4shhmvb4plrlbv"; depends=[dplyr ggplot2 Rcpp SummarizedExperiment tibble tidyr]; };
@@ -1832,7 +1833,7 @@ in with self; {
   primirTSS = derive2 { name="primirTSS"; version="1.16.0"; sha256="00h9m37ga3wsbcafg4c338457xqjlmgmhhkcrvm38x39h20kxrqy"; 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]; };
   proActiv = derive2 { name="proActiv"; version="1.8.0"; sha256="150n6nglbji1510g6kkq6b7i0nix70c6zahdrr4a6p1dpg15gfgv"; depends=[AnnotationDbi BiocParallel data_table DESeq2 dplyr GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 gplots IRanges rlang S4Vectors scales SummarizedExperiment tibble]; };
   proBAMr = derive2 { name="proBAMr"; version="1.32.0"; sha256="1pn48pmiz6cgc3hjczhpzgld69my7xk37d1k7k37gm0dwzpd85c3"; depends=[AnnotationDbi Biostrings GenomicFeatures GenomicRanges IRanges rtracklayer]; };
-  proBatch = derive2 { name="proBatch"; version="1.13.0"; sha256="1z55rbgjzxkj0i9gwwbh3wa82w9xflnipkkx58bgnni1nfnbia9k"; depends=[Biobase corrplot data_table dplyr ggfortify ggplot2 lazyeval lubridate magrittr pheatmap preprocessCore purrr pvca RColorBrewer reshape2 rlang scales sva tibble tidyr viridis wesanderson WGCNA]; };
+  proBatch = derive2 { name="proBatch"; version="1.14.0"; sha256="079dh61v1dmsasrh5sn6sn1rgi34mavxa1sc1y8x6wqjwabm4w1j"; depends=[Biobase corrplot data_table dplyr ggfortify ggplot2 lazyeval lubridate magrittr pheatmap preprocessCore purrr pvca RColorBrewer reshape2 rlang scales sva tibble tidyr viridis wesanderson WGCNA]; };
   proDA = derive2 { name="proDA"; version="1.12.0"; sha256="1b1p8sh80x5967rakyq75cj0sz01303w7p05b9irfr69yvfvlj45"; depends=[BiocGenerics extraDistr S4Vectors SummarizedExperiment]; };
   proFIA = derive2 { name="proFIA"; version="1.23.0"; sha256="0y08vj401f45dvgxjwjx94hvd0rk1wljk8n1irpkdafg24gv4fvj"; depends=[Biobase BiocParallel minpack_lm missForest pracma ropls xcms]; };
   procoil = derive2 { name="procoil"; version="2.26.0"; sha256="1ncls2bgdaaq1kc728p5ay95ypm5byyhpzjck34hfpq867lp7x7m"; depends=[Biostrings kebabs S4Vectors]; };
@@ -1851,7 +1852,7 @@ in with self; {
   pvca = derive2 { name="pvca"; version="1.38.0"; sha256="1cpyxgw1ynq3dms5yvcwaqd3s55ky80dgy811nl226mji278v9cl"; depends=[Biobase lme4 Matrix vsn]; };
   pwOmics = derive2 { name="pwOmics"; version="1.30.0"; sha256="1mklwy9p6miwzvcjzin5q0qcg9625bmbj5hi9dvm6cq48r0x5gwp"; depends=[AnnotationDbi AnnotationHub Biobase BiocGenerics biomaRt data_table GenomicRanges gplots graph igraph rBiopaxParser STRINGdb]; };
   pwrEWAS = derive2 { name="pwrEWAS"; version="1.12.0"; sha256="1y8knyl0axnbidkg1z9n1dmchdb79ixr7d6m1g2zhlzp10kmi4pk"; depends=[abind BiocManager CpGassoc doParallel doSNOW foreach genefilter ggplot2 limma pwrEWAS_data shiny shinyBS shinyWidgets truncnorm]; };
-  qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.16.0"; sha256="18hswwff9smiz9dr28mmh7fh58wknb8cfzxvg5xdw4fw09cb48m9"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer readr rlang scales stringr tibble tidyr tidyselect]; };
+  qPLEXanalyzer = derive2 { name="qPLEXanalyzer"; version="1.16.1"; sha256="0jzk0h6lll7yxmiplrk0rhx5pvhq8jjifhi2fj4nyskx1brsnnfh"; depends=[assertthat Biobase BiocGenerics Biostrings dplyr ggdendro ggplot2 IRanges limma magrittr MSnbase preprocessCore purrr RColorBrewer readr rlang scales stringr tibble tidyr tidyselect]; };
   qckitfastq = derive2 { name="qckitfastq"; version="1.14.0"; sha256="0220r27adgm8mj348602hzgrbj8f94d0xbcrfg9r5sjaajqbmf8w"; depends=[data_table dplyr ggplot2 magrittr Rcpp reshape2 rlang RSeqAn seqTools zlibbioc]; };
   qcmetrics = derive2 { name="qcmetrics"; version="1.36.0"; sha256="1ab6w3ghalgjarkq91ci85dwpwp1dqdsj2m9adlmx05wpljg9qc4"; depends=[Biobase knitr pander S4Vectors xtable]; };
   qmtools = derive2 { name="qmtools"; version="1.2.0"; sha256="19zn0q493vn45wllzbzqfgnazr5x6ik2hvh7pay3s95421vls1bd"; depends=[ggplot2 heatmaply igraph MsCoreUtils patchwork rlang scales SummarizedExperiment VIM]; };
@@ -1878,7 +1879,7 @@ in with self; {
   rScudo = derive2 { name="rScudo"; version="1.14.0"; sha256="1bk7w1rb87j6c3280r6bwnvfhfzdv0ck9g96y0a8k1g297gvyvcc"; depends=[Biobase BiocGenerics igraph S4Vectors stringr SummarizedExperiment]; };
   rTRM = derive2 { name="rTRM"; version="1.36.0"; sha256="11dp7vz1343hmaa7lly5m9h9fx94cpqqhsrvbb6vy57bh8nb6v4v"; depends=[AnnotationDbi DBI igraph RSQLite]; };
   rTRMui = derive2 { name="rTRMui"; version="1.36.0"; sha256="1gindmnq5vkapmfjpy9hglbk79g0s1sgzdljmhn3m5925h2al4k0"; depends=[MotifDb org_Hs_eg_db org_Mm_eg_db rTRM shiny]; };
-  rWikiPathways = derive2 { name="rWikiPathways"; version="1.18.0"; sha256="0vk6j07xxkpdaybsiip41xavsiwc8qr165sxab5fy1r13w3ya4d3"; depends=[data_table httr RCurl rjson tidyr XML]; };
+  rWikiPathways = derive2 { name="rWikiPathways"; version="1.18.1"; sha256="1zh6yz49s4jdpgg17dkkjv32fkp4zvdrcljfpbysbvc9lplrlj65"; depends=[data_table httr RCurl rjson tidyr XML]; };
   rain = derive2 { name="rain"; version="1.32.0"; sha256="0zlb52z0wk6057ph12lj7313bfkpbn502568cgdwify8s6q9g8ms"; depends=[gmp multtest]; };
   rama = derive2 { name="rama"; version="1.72.0"; sha256="0i6crxnzhwxnc55xh2rv36jfwh4bd30alw1f05ixdrxwqwsslbpy"; depends=[]; };
   ramr = derive2 { name="ramr"; version="1.6.0"; sha256="1rn5jvrcl3823124iwwbrjx89yyp3yflhlvjwnf6jldvm5bwqwpz"; depends=[BiocGenerics doParallel doRNG EnvStats ExtDist foreach GenomicRanges ggplot2 IRanges matrixStats reshape2 S4Vectors]; };
@@ -1893,7 +1894,7 @@ in with self; {
   reconsi = derive2 { name="reconsi"; version="1.10.0"; sha256="1hzwjmnbkdb4v8nvsk06vmyh5hm1snjn1a2q21jingppjs0dzvik"; depends=[ggplot2 ks Matrix matrixStats phyloseq reshape2]; };
   recount = derive2 { name="recount"; version="1.24.1"; sha256="0ryxz7kf52rwwri1bbpfpn67ivcx3fxrnym430d4nv6j1qfb1kh4"; depends=[BiocParallel derfinder downloader GenomeInfoDb GenomicRanges GEOquery IRanges RCurl rentrez rtracklayer S4Vectors SummarizedExperiment]; };
   recount3 = derive2 { name="recount3"; version="1.8.0"; sha256="1syfy713ybsl8vlvfag6i85icv34k1y0f6g6v168snc2z1xq4yrd"; depends=[BiocFileCache data_table GenomicRanges Matrix R_utils RCurl rtracklayer S4Vectors sessioninfo SummarizedExperiment]; };
-  recountmethylation = derive2 { name="recountmethylation"; version="1.8.3"; sha256="04xcj58wdsbz4ibx030br2d27lvld4aqvj1j7686r7jcjj2s92kq"; depends=[BiocFileCache HDF5Array IlluminaHumanMethylation450kmanifest minfi R_utils RCurl rhdf5 S4Vectors]; };
+  recountmethylation = derive2 { name="recountmethylation"; version="1.8.6"; sha256="1nrav24pq3jwi9jmy7b0h799q6bnw1sjd8a0gca3c1pn9zvg8xqn"; depends=[basilisk BiocFileCache DelayedMatrixStats HDF5Array minfi R_utils RCurl reticulate rhdf5 S4Vectors]; };
   recoup = derive2 { name="recoup"; version="1.26.0"; sha256="00ia9a9kqmcn329pvipaz15xfci6rw4377hpf7gnxhjkxx4b1rna"; depends=[BiocGenerics biomaRt Biostrings circlize ComplexHeatmap GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 httr IRanges Rsamtools RSQLite rtracklayer S4Vectors stringr]; };
   regionReport = derive2 { name="regionReport"; version="1.32.0"; sha256="0ilqm51dnhv5bhda7ljdn1x4hwr4infpngsvwn7wvssvsgp1pcz0"; depends=[BiocStyle DEFormats derfinder DESeq2 GenomeInfoDb GenomicRanges knitr knitrBootstrap RefManageR rmarkdown S4Vectors SummarizedExperiment]; };
   regioneR = derive2 { name="regioneR"; version="1.30.0"; sha256="01anwhz0axdl0g2zsaqz1qdxswxrryarbw6pmn5kmlpz4ipiq049"; depends=[Biostrings BSgenome GenomeInfoDb GenomicRanges IRanges memoise rtracklayer S4Vectors]; };
@@ -1908,7 +1909,7 @@ in with self; {
   rgsepd = derive2 { name="rgsepd"; version="1.30.0"; sha256="1bk6i336x2ng1kvgywcs18v6sn47cndahfbpcagl17x77pcna7by"; depends=[AnnotationDbi biomaRt DESeq2 GO_db goseq gplots org_Hs_eg_db SummarizedExperiment]; };
   rhdf5 = derive2 { name="rhdf5"; version="2.42.0"; sha256="1vxs227d1295fz8irr6fsv603cw96a801j8njhblvs0cry38d087"; depends=[rhdf5filters Rhdf5lib]; };
   rhdf5client = derive2 { name="rhdf5client"; version="1.20.0"; sha256="0wf0mv1kc3gd7vpazdip9253c1727ns9xysqfipg9lf1ydjny1fq"; depends=[DelayedArray httr R6 rjson S4Vectors]; };
-  rhdf5filters = derive2 { name="rhdf5filters"; version="1.10.0"; sha256="17x2a3122mm3z9qnalw25am2x08cfpm17nwhigabid3ha3d2mgz1"; depends=[Rhdf5lib]; };
+  rhdf5filters = derive2 { name="rhdf5filters"; version="1.10.1"; sha256="14rkr0fisy7qrvjikpnwxwag79205hdxy6nkpwz501li4fr1rbnp"; depends=[Rhdf5lib]; };
   riboSeqR = derive2 { name="riboSeqR"; version="1.32.0"; sha256="0la8kmxxh5jnqsrmmvyhi313bjdbqkiq16hcxar6mgyjhxlsm610"; depends=[abind baySeq GenomeInfoDb GenomicRanges IRanges Rsamtools seqLogo]; };
   ribor = derive2 { name="ribor"; version="1.10.0"; sha256="16ikb3815cmwagjjjcv8rmshybpjl0vfc20mpl5xr92dzbnn7jj2"; depends=[dplyr ggplot2 hash rhdf5 rlang S4Vectors tidyr yaml]; };
   ribosomeProfilingQC = derive2 { name="ribosomeProfilingQC"; version="1.10.0"; sha256="04r0nhjfm659i5n2351f67dghjm9jrfvcnzbf7ylqgnhym4ibzrn"; depends=[AnnotationDbi BiocGenerics Biostrings BSgenome cluster EDASeq GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggfittext ggplot2 ggrepel IRanges motifStack Rsamtools Rsubread rtracklayer RUVSeq S4Vectors scales XVector]; };
@@ -1930,7 +1931,7 @@ in with self; {
   rtracklayer = derive2 { name="rtracklayer"; version="1.58.0"; sha256="1qxr0ffmmkbfkbijz7pbks3kvms9k4a5rmma4j9p7ar477fxvlmk"; depends=[BiocGenerics BiocIO Biostrings GenomeInfoDb GenomicAlignments GenomicRanges IRanges RCurl restfulr Rsamtools S4Vectors XML XVector zlibbioc]; };
   runibic = derive2 { name="runibic"; version="1.20.0"; sha256="0g7hqgsq7h0338fmlb4ipv1kwiijcrfajhgwchn5akhspvsch269"; depends=[biclust Rcpp SummarizedExperiment testthat]; };
   sRACIPE = derive2 { name="sRACIPE"; version="1.14.0"; sha256="079lmgi6az5ri05lvca58msh678r7k1xwk3xhq8iffqh87wy6cmj"; depends=[BiocGenerics ggplot2 gplots gridExtra htmlwidgets MASS RColorBrewer Rcpp reshape2 S4Vectors SummarizedExperiment umap visNetwork]; };
-  sSNAPPY = derive2 { name="sSNAPPY"; version="1.2.4"; sha256="0ja3hbsfhmwibc8mj4192kcwcp4bj2lish1nsy7kd6hdv28i5nm8"; depends=[BiocParallel dplyr edgeR ggforce ggnewscale ggplot2 ggraph graphite igraph magrittr org_Hs_eg_db pheatmap purrr Rcpp RcppArmadillo reshape2 rlang SummarizedExperiment tibble]; };
+  sSNAPPY = derive2 { name="sSNAPPY"; version="1.2.5"; sha256="17z0iz6jr0nx14s4d80j94jdk78af4i1zkin24z56fas28sm2ka8"; depends=[BiocParallel dplyr edgeR ggforce ggnewscale ggplot2 ggraph graphite igraph magrittr org_Hs_eg_db pheatmap purrr Rcpp RcppArmadillo reshape2 rlang SummarizedExperiment tibble]; };
   sSeq = derive2 { name="sSeq"; version="1.36.0"; sha256="1w0iq7pih9z8662wj2lj1xbg66n752mx4g2q33ck5vwdxg10ry4c"; depends=[caTools RColorBrewer]; };
   safe = derive2 { name="safe"; version="3.38.0"; sha256="1gza1liz0y2i6f5nnnwbwl99fjp3cr1aknxiy3rmbjydfq8yxbrw"; depends=[AnnotationDbi Biobase SparseM]; };
   sagenhaft = derive2 { name="sagenhaft"; version="1.68.0"; sha256="0hh9gkv07qrlnarrj7h579dhisyq01c5jjl3rvq5w086wfy9154m"; depends=[SparseM]; };
@@ -1940,7 +1941,7 @@ in with self; {
   sarks = derive2 { name="sarks"; version="1.10.0"; sha256="1f3yypn7dzjq58jnkv3jc0330mddpapzn1wlvq2crjbh161mxaym"; depends=[binom Biostrings cluster IRanges rJava]; };
   satuRn = derive2 { name="satuRn"; version="1.6.0"; sha256="1gldcdnpbxc2bgi5sr3g0cgkfx8gx2jmyadnxzm07zcmi724nsyx"; depends=[BiocParallel boot ggplot2 limma locfdr Matrix pbapply SummarizedExperiment]; };
   savR = derive2 { name="savR"; version="1.36.0"; sha256="1b7kjgj2r6lgkdnrq91wcwvwb5an0gfdsbyp7j0pvn2byfm4lply"; depends=[ggplot2 gridExtra reshape2 scales XML]; };
-  scAlign = derive2 { name="scAlign"; version="1.11.0"; sha256="01gy9p07nyx42i0phgc89yhjavpykzgh1mwr11358ddbwz41hxnr"; depends=[FNN ggplot2 irlba purrr Rtsne Seurat SingleCellExperiment tensorflow]; };
+  scAlign = derive2 { name="scAlign"; version="1.12.0"; sha256="1mlhxwsfrmhysa5mcyx7vf2jn49snf41yb7xqmyi40wilj9h8qlb"; depends=[FNN ggplot2 irlba purrr Rtsne Seurat SingleCellExperiment tensorflow]; };
   scAnnotatR = derive2 { name="scAnnotatR"; version="1.4.0"; sha256="0rc035kzbzrxvlcpphzg0yg7q82jvlxpi9xjq8q59hvbpyg1sz93"; depends=[AnnotationHub ape caret data_tree dplyr e1071 ggplot2 kernlab pROC ROCR Seurat SingleCellExperiment SummarizedExperiment]; };
   scBFA = derive2 { name="scBFA"; version="1.12.0"; sha256="0884s9laa63yf2p9wf66a67ipkc2x075c432x8p96vr326p4h8nf"; depends=[copula DESeq2 ggplot2 MASS Matrix Seurat SingleCellExperiment SummarizedExperiment zinbwave]; };
   scBubbletree = derive2 { name="scBubbletree"; version="1.0.0"; sha256="0ivyp3zf7clr4zbdv2srjv42dx2zvlaq4yprccxb3yimrnmihks6"; depends=[ape future future_apply ggplot2 ggtree patchwork reshape2 scales Seurat]; };
@@ -2096,8 +2097,8 @@ in with self; {
   ternarynet = derive2 { name="ternarynet"; version="1.42.0"; sha256="01z262509vka2sfhzccwlmgi5frf56x07gbsan762hgvrcscg8jb"; depends=[BiocParallel igraph]; };
   terraTCGAdata = derive2 { name="terraTCGAdata"; version="1.2.0"; sha256="1yfvqdsgd3apan43cbjin95mwnbym1m0f1c8x212k277cc3rm22r"; depends=[AnVIL BiocFileCache dplyr GenomicRanges MultiAssayExperiment RaggedExperiment readr S4Vectors TCGAutils tidyr]; };
   tidySingleCellExperiment = derive2 { name="tidySingleCellExperiment"; version="1.8.0"; sha256="0kkxd64rlksw7l0hw53ckc9mhsvsb0yj8w078bh4rd16iqk3jnnc"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors SingleCellExperiment stringr SummarizedExperiment tibble tidyr tidyselect ttservice]; };
-  tidySummarizedExperiment = derive2 { name="tidySummarizedExperiment"; version="1.8.0"; sha256="0y7k0svcjx0lvxn3jw8g7vkrvwhvj9b7mhb0igavad1rc5pc54f3"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect vctrs]; };
-  tidybulk = derive2 { name="tidybulk"; version="1.10.0"; sha256="1n31wqad7wdfyfy1mcjsq68rlyyyd15srcrvz6ylp2pi8nbwxfly"; depends=[crayon dplyr GenomicRanges lifecycle magrittr preprocessCore purrr readr rlang S4Vectors scales stringi stringr SummarizedExperiment tibble tidyr tidyselect]; };
+  tidySummarizedExperiment = derive2 { name="tidySummarizedExperiment"; version="1.8.1"; sha256="1sry782zf2sisjwlhgdh1vfr0ljbw2rrwwb907jxmafg6jm96rxq"; depends=[cli dplyr ellipsis fansi ggplot2 lifecycle magrittr pillar plotly purrr rlang S4Vectors stringr SummarizedExperiment tibble tidyr tidyselect vctrs]; };
+  tidybulk = derive2 { name="tidybulk"; version="1.10.1"; sha256="100xnjz73wl48a93gv4361pllyb96nbhg5q8spgq131wp0i0zjzz"; depends=[crayon dplyr GenomicRanges lifecycle magrittr preprocessCore purrr readr rlang S4Vectors scales stringi stringr SummarizedExperiment tibble tidyr tidyselect]; };
   tigre = derive2 { name="tigre"; version="1.52.0"; sha256="1cj4yqdad1xs8k682qx92b03nbyx51qdqsf7y90bll3z51xhwvdq"; depends=[annotate AnnotationDbi Biobase BiocGenerics DBI gplots RSQLite]; };
   tilingArray = derive2 { name="tilingArray"; version="1.76.0"; sha256="19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd"; depends=[affy Biobase genefilter pixmap RColorBrewer strucchange vsn]; };
   timeOmics = derive2 { name="timeOmics"; version="1.10.0"; sha256="1szhdd29gfa7ah7yf683d69s2w0w6r8nh3kc7fii3vnyqspspb19"; depends=[dplyr ggplot2 ggrepel lmtest magrittr mixOmics plyr purrr stringr tibble tidyr]; };
@@ -2136,11 +2137,11 @@ in with self; {
   tximeta = derive2 { name="tximeta"; version="1.16.1"; sha256="15qf8s9akl5qp5wklph5i61d96d9ifr5ijl796v1vafwrj4f3wpa"; depends=[AnnotationDbi AnnotationHub BiocFileCache Biostrings ensembldb GenomeInfoDb GenomicFeatures GenomicRanges IRanges jsonlite Matrix S4Vectors SummarizedExperiment tibble tximport]; };
   tximport = derive2 { name="tximport"; version="1.26.1"; sha256="1r67q4nb2bx9nqycyr2gnfmh4gizl0c7l510vmlcdvplv3yi73yn"; depends=[]; };
   uSORT = derive2 { name="uSORT"; version="1.24.0"; sha256="1fhhl00qdj7ihvb3ia2nd215m1ylbaszpyq1w7bmgv89v5ghhsgf"; depends=[Biobase BiocGenerics cluster fpc gplots igraph Matrix monocle plyr RANN RSpectra VGAM]; };
-  uncoverappLib = derive2 { name="uncoverappLib"; version="1.7.0"; sha256="1fsn5wpknx1f6sj12x9q456iqi68kwgcqzkk3343hfg185rnn8sh"; depends=[BiocFileCache BSgenome_Hsapiens_UCSC_hg19 BSgenome_Hsapiens_UCSC_hg38 condformat DT EnsDb_Hsapiens_v75 EnsDb_Hsapiens_v86 GenomicRanges Gviz Homo_sapiens markdown openxlsx org_Hs_eg_db OrganismDbi processx rappdirs rlist Rsamtools S4Vectors shiny shinyBS shinycssloaders shinyjs shinyWidgets stringr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
+  uncoverappLib = derive2 { name="uncoverappLib"; version="1.8.1"; sha256="196xw6m69ld6nnbgqyyr7vd9qgqlczybgs7phvm7g36q4rywsnkm"; depends=[BiocFileCache condformat DT EnsDb_Hsapiens_v75 EnsDb_Hsapiens_v86 GenomicRanges Gviz Homo_sapiens markdown openxlsx org_Hs_eg_db OrganismDbi processx rappdirs rlist Rsamtools S4Vectors shiny shinyBS shinycssloaders shinyjs shinyWidgets stringr TxDb_Hsapiens_UCSC_hg19_knownGene TxDb_Hsapiens_UCSC_hg38_knownGene]; };
   unifiedWMWqPCR = derive2 { name="unifiedWMWqPCR"; version="1.34.0"; sha256="0zkqr1s8gagwsh33kzp0n2n7ff5jhfn6a60gvab5spk7vr76j442"; depends=[BiocGenerics HTqPCR]; };
   universalmotif = derive2 { name="universalmotif"; version="1.16.0"; sha256="1vfg703wxbgxw2cwqqz3kfyqj4za5n3skxxzi8c31azamg4hxs18"; depends=[BiocGenerics Biostrings ggplot2 IRanges MASS Rcpp RcppThread rlang S4Vectors yaml]; };
   updateObject = derive2 { name="updateObject"; version="1.2.0"; sha256="13rq1hv0rg8cj3z8d2b9mfih5sybicb4razv8vaic1i7c7sbypwf"; depends=[BiocGenerics digest S4Vectors]; };
-  variancePartition = derive2 { name="variancePartition"; version="1.28.7"; sha256="0iv5c5p0g4axhanc62mmk0c43qcwdsxzslxh5qdck0v1kb7bd1d9"; depends=[aod Biobase BiocParallel doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS Matrix pbkrtest progress Rdpack remaCor reshape2 RhpcBLASctl rlang scales]; };
+  variancePartition = derive2 { name="variancePartition"; version="1.28.9"; sha256="1al7wkbv26gldba61gq80c3mznsxwr7z5njv2s0lb7hnll9bscar"; depends=[aod Biobase BiocParallel doParallel foreach ggplot2 gplots iterators limma lme4 lmerTest MASS Matrix pbkrtest progress Rdpack remaCor reshape2 RhpcBLASctl rlang scales]; };
   vbmp = derive2 { name="vbmp"; version="1.66.0"; sha256="1gfvk1g9q73p9z91zasblya1w218yhzawp6dgyf0lnldx36kpvc9"; depends=[]; };
   velociraptor = derive2 { name="velociraptor"; version="1.8.0"; sha256="07nwx9cahia4a6g15xhccdlwxnhvwq46dy2hqcqqzydgpsapa6wv"; depends=[basilisk BiocGenerics BiocParallel BiocSingular DelayedArray Matrix reticulate S4Vectors scuttle SingleCellExperiment SummarizedExperiment zellkonverter]; };
   veloviz = derive2 { name="veloviz"; version="1.4.0"; sha256="01f2d28h0gnh38g50yphmg3aqy1ya2ysj1xabs2a6y3wnqzrahzk"; depends=[igraph Matrix mgcv Rcpp RSpectra]; };
@@ -2228,7 +2229,6 @@ in with self; {
   methyAnalysis = derive2 { name="methyAnalysis"; version="1.34.0"; sha256="05k3n7iy5ijidbnblbqqas8dsj8drwzbhyrbs8wl1ypkg51havi0"; depends=[annotate AnnotationDbi Biobase BiocGenerics biomaRt genefilter GenomeInfoDb GenomicFeatures GenomicRanges Gviz IRanges lumi methylumi org_Hs_eg_db rtracklayer SummarizedExperiment VariantAnnotation]; broken = true; };
   networkBMA = derive2 { name="networkBMA"; version="2.35.0"; sha256="0xa0b977apbr6p9kqk38582af635kp99csj32bsn2bf8pjsmd4d2"; depends=[BH BMA leaps Rcpp RcppArmadillo RcppEigen]; broken = true; };
   perturbatr = derive2 { name="perturbatr"; version="1.13.0"; sha256="0ssk8cr42hibn917s2z2nzcdan54c7xiydypbi8f3g4w68q4ly31"; depends=[assertthat diffusr doParallel dplyr foreach formula_tools ggplot2 igraph lazyeval lme4 magrittr rlang scales tibble tidyr]; broken = true; };
-  phemd = derive2 { name="phemd"; version="1.12.0"; sha256="0nn0qgb0rz4j2xsjq0wydjhg5pmf2ra67rm9fdm4m1izmzwa0nhs"; depends=[Biobase BiocGenerics cluster cowplot destiny ggplot2 igraph maptree monocle phateR pheatmap pracma RANN RColorBrewer reticulate Rtsne S4Vectors scatterplot3d Seurat SingleCellExperiment SummarizedExperiment transport VGAM]; broken = true; };
   ppiStats = derive2 { name="ppiStats"; version="1.62.0"; sha256="0w5gkfah2y50x4wj5fn8i6ycx1x013mn9w4bs8r2vfqabpws1a81"; depends=[Biobase Category graph lattice RColorBrewer]; broken = true; };
   predictionet = derive2 { name="predictionet"; version="1.40.0"; sha256="1f3ghlcfnls9mx2hbs923rdz7kn0wdhy2csp1y1286c5q5dybrgh"; depends=[catnet igraph MASS penalized RBGL]; broken = true; };
   pulsedSilac = derive2 { name="pulsedSilac"; version="1.9.1"; sha256="1zb8xzs9h4rcrnmsfvrwb1qixn3jbnzxdwqgdrb82hgmxabmajlb"; depends=[cowplot ggplot2 ggridges MuMIn R_utils robustbase S4Vectors SummarizedExperiment UpSetR]; broken = true; };

pkgs/development/r-modules/default.nix

@@ -68,9 +68,10 @@ let
     hydraPlatforms = [];
   };
   deriveCran = mkDerive {
-    mkHomepage = {name, snapshot, ...}: "https://cran.r-project.org/${snapshot}/web/packages/${name}/";
-    mkUrls = {name, version, snapshot}: [
-      "https://packagemanager.rstudio.com/cran/${snapshot}/src/contrib/${name}_${version}.tar.gz"
+    mkHomepage = {name, ...}: "https://cran.r-project.org/web/packages/${name}/";
+    mkUrls = {name, version}: [
+      "mirror://cran/${name}_${version}.tar.gz"
+      "mirror://cran/Archive/${name}/${name}_${version}.tar.gz"
     ];
   };
 

pkgs/development/r-modules/generate-r-packages.R

@@ -1,6 +1,5 @@
 #!/usr/bin/env Rscript
 library(data.table)
-library(jsonlite)
 library(parallel)
 library(BiocManager)
 cl <- makeCluster(10)
@@ -12,13 +11,11 @@ if ("release" %in% biocVersion$BiocStatus) {
 } else {
   biocVersion <-  max(as.numeric(as.character(biocVersion$Bioc)))
 }
-dates <- stream_in(url("https://packagemanager.rstudio.com/__api__/repos/2/transaction-dates"), verbose = FALSE)
-snapshotDate <- as.Date(dates[nrow(dates), "alias"])
 
 mirrorUrls <- list( bioc=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/bioc/src/contrib/")
                   , "bioc-annotation"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/annotation/src/contrib/")
                   , "bioc-experiment"=paste0("http://bioconductor.statistik.tu-dortmund.de/packages/", biocVersion, "/data/experiment/src/contrib/")
-                  , cran=paste0("https://packagemanager.rstudio.com/cran/", snapshotDate, "/src/contrib/")
+                  , cran="https://cran.r-project.org/src/contrib/"
                   )
 
 mirrorType <- commandArgs(trailingOnly=TRUE)[1]
@@ -44,6 +41,10 @@ nixPrefetch <- function(name, version) {
     url <- paste0(mirrorUrl, name, "_", version, ".tar.gz")
     tmp <- tempfile(pattern=paste0(name, "_", version), fileext=".tar.gz")
     cmd <- paste0("wget -q -O '", tmp, "' '", url, "'")
+    if(mirrorType == "cran"){
+      archiveUrl <- paste0(mirrorUrl, "Archive/", name, "/", name, "_", version, ".tar.gz")
+      cmd <- paste0(cmd, " || wget -q -O '", tmp, "' '", archiveUrl, "'")
+    }
     cmd <- paste0(cmd, " && nix-hash --type sha256 --base32 --flat '", tmp, "'")
     cmd <- paste0(cmd, " && echo >&2 '  added ", name, " v", version, "'")
     cmd <- paste0(cmd, " ; rm -rf '", tmp, "'")
@@ -74,9 +75,8 @@ formatPackage <- function(name, version, sha256, depends, imports, linkingTo) {
     paste0("  ", attr, " = derive2 { name=\"", name, "\"; version=\"", version, "\"; sha256=\"", sha256, "\"; depends=[", depends, "]; };")
 }
 
-clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "knownPackages"))
+clusterExport(cl, c("nixPrefetch","readFormatted", "mirrorUrl", "mirrorType", "knownPackages"))
 
-pkgs <- as.data.table(available.packages(mirrorUrl, filters=c("R_version", "OS_type", "duplicates"), method="libcurl"))
 pkgs <- pkgs[order(Package)]
 
 write(paste("updating", mirrorType, "packages"), stderr())
@@ -102,7 +102,7 @@ cat(paste("# Rscript generate-r-packages.R", mirrorType, ">new && mv new", packa
 cat("\n\n")
 cat("{ self, derive }:\n")
 cat("let derive2 = derive ")
-if (mirrorType == "cran") { cat("{ snapshot = \"", paste(snapshotDate), "\"; }", sep="")
+if (mirrorType == "cran") { cat("{  }")
 } else if (mirrorType == "irkernel") { cat("{}")
 } else { cat("{ biocVersion = \"", biocVersion, "\"; }", sep="") }
 cat(";\n")

pkgs/development/r-modules/generate-shell.nix

@@ -15,7 +15,6 @@ stdenv.mkDerivation {
     (rWrapper.override {
       packages = with rPackages; [
         data_table
-        jsonlite
         parallel
         BiocManager
       ];

pkgs/development/tools/analysis/checkov/default.nix

@@ -6,16 +6,15 @@
 let
   py = python3.override {
     packageOverrides = self: super: {
-
-      dpath = super.dpath.overridePythonAttrs (oldAttrs: rec {
-        version = "1.5.0";
-        src = oldAttrs.src.override {
-          inherit version;
-          hash = "sha256-SWYVtOqEI20Y4NKGEi3nSGmmDg+H4sfsZ4f/KGxINhs=";
+      cyclonedx-python-lib = super.cyclonedx-python-lib.overridePythonAttrs (oldAttrs: rec {
+        version = "2.7.1";
+        src = fetchFromGitHub {
+          owner = "CycloneDX";
+          repo = "cyclonedx-python-lib";
+          rev = "v${version}";
+          hash = "sha256-c/KhoJOa121/h0n0GUazjUFChnUo05ThD+fuZXc5/Pk=";
         };
-        doCheck = false;
       });
-
     };
   };
 in
@@ -23,14 +22,14 @@ with py.pkgs;
 
 buildPythonApplication rec {
   pname = "checkov";
-  version = "2.3.96";
+  version = "2.3.150";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "bridgecrewio";
     repo = pname;
     rev = "refs/tags/${version}";
-    hash = "sha256-jQ5VaOvJkxhZ0fHrNmkuFK+qmRUNdzR5XCWqWv1iBs4=";
+    hash = "sha256-AgYI3V5xJT6LEZYrJV8nO/86MMp5deuTdLhnUHdrge4=";
   };
 
   patches = [
@@ -38,17 +37,19 @@ buildPythonApplication rec {
   ];
 
   pythonRelaxDeps = [
+    "dpath"
+    "bc-detect-secrets"
     "bc-python-hcl2"
     "pycep-parser"
     "networkx"
   ];
 
-  nativeBuildInputs = with py.pkgs; [
+  nativeBuildInputs = [
     pythonRelaxDepsHook
     setuptools-scm
   ];
 
-  propagatedBuildInputs = with py.pkgs; [
+  propagatedBuildInputs = [
     aiodns
     aiohttp
     aiomultiprocess
@@ -74,6 +75,7 @@ buildPythonApplication rec {
     jsonschema
     junit-xml
     networkx
+    openai
     packaging
     policyuniverse
     prettytable
@@ -87,7 +89,7 @@ buildPythonApplication rec {
     update_checker
   ];
 
-  nativeCheckInputs = with py.pkgs; [
+  nativeCheckInputs = [
     aioresponses
     mock
     pytest-asyncio

pkgs/development/tools/build-managers/rocm-cmake/default.nix

@@ -7,7 +7,7 @@
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "rocm-cmake";
-  version = "5.4.3";
+  version = "5.4.4";
 
   src = fetchFromGitHub {
     owner = "RadeonOpenCompute";