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370 Commits

Author SHA1 Message Date
Alex Branham
0a80d3dc82 R: update CRAN and Bioconductor package sets 
Closes https://github.com/NixOS/nixpkgs/pull/59186.
 2019-04-11 20:37:18 +02:00
Peter Simons
3c9ff308e7
Merge pull request #58467 from mnacamura/r-sys 
r-sys: remove obsolete dependency
 2019-03-28 12:42:19 +01:00
Mitsuhiro Nakamura
157921f2e7 rPackages: fix missing dependency to libiconv 2019-03-28 12:11:47 +09:00
Mitsuhiro Nakamura
d07c3139ed r-sys: remove obsolete dependency 2019-03-28 11:20:04 +09:00
Alex Branham
8dcba2b842 R: update CRAN and Bioconductor package sets 
Closes https://github.com/NixOS/nixpkgs/pull/57423.
 2019-03-14 19:50:37 +01:00
Markus Ankenbrand
7fcfbcdbc9 rPackages.phytools: fix installation 2019-03-06 11:39:48 +01:00
Alex Branham
ec03ed450c update R package set 
Closes https://github.com/NixOS/nixpkgs/pull/55462.
 2019-02-10 11:16:19 +01:00
Alex Branham
48541ab6b9 R: update CRAN and BIOC package sets 
Closes https://github.com/NixOS/nixpkgs/pull/53414.
 2019-01-08 09:34:37 +01:00
Alex Branham
6f7459b40b
R: update CRAN package set 2018-12-12 11:17:25 -06:00
Edmund Wu
a898f88d57
rstudioWrapper: include desktop file 2018-12-07 16:44:01 -05:00
Joachim F
f0dbbdf970
Merge pull request #51581 from joachifm/rWrapper-local-runCommand 
Implement R wrappers as local-only runCommand
 2018-12-07 09:17:44 +00:00
Christian Kauhaus
3b445042ac rPackages.littler: fix build (#51282) 
littler gives a wrapped called `r` (or `lr` for non-case-preserving
systems like Darwin) which works as shebang or pipe target.

The build was completely broken before (missing deps).

Symlink executables and manpage into standard locations so that this
packages also works in `environment.systemPackages`.
 2018-12-06 17:22:31 +01:00
Joachim Fasting
21d83e5b11
rstudioWrapper: use runCommand, local build only 
This seems more appropriate for a wrapper generator.
 2018-12-05 20:59:41 +01:00
Joachim Fasting
d2b467a2de
rWrapper: use runCommand, local build only 
This seems more appropriate for a wrapper generator.
 2018-12-05 20:59:35 +01:00
Timo Kaufmann
63b39af496
pythonPackages.rpy2: various fixes (#51084) 
- make sure libreadline is found at runtime
- make sure python libraries are found at runtime
- add libraries necessary to pass the testsuite and standard libraries
 2018-11-27 18:24:37 +01:00
Massimo Redaelli
5afe1e7c70 rstudio: fix qt plugins not found 2018-11-23 23:10:29 +01:00
Averell Dalton
25e68e3048 r-ps: patchShebangs in ./configure to fix build 2018-11-02 23:02:04 +01:00
Peter Simons
c9e1380626 r-nloptr: fix build by adding pkgconfig 2018-11-02 17:50:18 +01:00
Peter Simons
9b63cc6313 r-rlang: patch shebang in configure script to fix the build 2018-11-02 17:50:18 +01:00
Tom McLaughlin
cac5c9401e R: update CRAN and BIOC package sets 
Closes https://github.com/NixOS/nixpkgs/pull/49430.
 2018-11-02 17:50:18 +01:00
Rob Vermaas
3f719b0fad Fix build for rPackages.units 
(cherry picked from commit 1eb1fec3ae)
 2018-10-08 12:53:43 +02:00
ivanbrennan
989f24befc
git2r: add SSH support 
When building the devtools R module, which depends on git2r, it reports
that libssh2 cannot be found, and falls back to building without SSH
support. Adding libssh2.dev to git2r's native build inputs fixes this.
 2018-09-11 16:39:20 -04:00
Ryan Mulligan
73ae8e53e2 rPackages.RPostgres: fix configure paths and includes 
closes #46208
 2018-09-09 14:37:28 -07:00
Mitsuhiro Nakamura
5e42a081a3 r-jqr: fix build (#45333) 2018-08-20 00:08:28 +02:00
volth
e6d3c65442
r-packages: fix regression 2018-08-04 06:19:08 +00:00
Mitsuhiro Nakamura
0a541aa38c rPackages.buildRPackage: fix error if requireX is missing 2018-08-03 01:08:35 +09:00
Mitsuhiro Nakamura
559997179d rPackages: export buildRPackage 2018-08-03 01:08:07 +09:00
volth
52f53c69ce pkgs/*: remove unreferenced function arguments 2018-07-21 02:48:04 +00:00
Markus Ankenbrand
775fd4bfba rPackages.haven: fix installation 2018-07-12 11:07:27 +02:00
Mitsuhiro Nakamura
c072024409 rPackages.reprex: fix build 2018-07-11 23:16:49 +09:00
Markus Ankenbrand
89f44c1314 rPackages.rhdf5: fix installation 
Fix #43285
 2018-07-10 16:38:11 +02:00
Peter Simons
03476783a5 R: fix evaluation errors 2018-07-07 12:10:46 +02:00
Peter Simons
49c649d573 R: update CRAN package set to snapshot 2018-07-06 2018-07-07 12:10:46 +02:00
Peter Simons
d984656a2a R: update package set 
The CRAN snapshot is at "2018-07-03". Bioc is now at 3.8.
 2018-07-07 12:10:46 +02:00
Markus Ankenbrand
9eeea0b9ef rPackages.rhdf5: fix installation 
Fix #42878
 2018-07-02 18:51:18 +02:00
Daiderd Jordan
654960c1cd
Merge pull request #42290 from mnacamura/r-igraph-darwin 
rPackages.igraph: fix Darwin build
 2018-06-20 19:52:36 +02:00
Mitsuhiro Nakamura
f972a30f16 rPackages.igraph: fix Darwin build 2018-06-20 11:08:29 +09:00
Mitsuhiro Nakamura
dada18527a rPackages.RcppEigen: fix Darwin build 2018-06-20 10:59:18 +09:00
Josef Kemetmüller
aeda45821d rPackages.mgcv: fix darwin build 
This fixes the error:
    ld: library not found for -liconv
 2018-06-07 00:00:42 +02:00
Josef Kemetmüller
0275562a12 rPackages.Matrix: fix darwin build 
This fixes the error:
    ld: library not found for -liconv
 2018-06-07 00:00:07 +02:00
Josef Kemetmüller
d8ad2ad916 rPackages.nlme: fix darwin build 
This fixes the error:
    ld: library not found for -liconv
 2018-06-06 23:59:09 +02:00
Josef Kemetmüller
e023f117f8 rPackages.KernSmooth: fix darwin build 
This fixes the error:
    ld: library not found for -liconv
 2018-06-06 23:58:46 +02:00
Josef Kemetmüller
5d092b3052 rPackages.cluster: fix darwin build 
This fixes the error:
    ld: library not found for -liconv
 2018-06-06 23:57:08 +02:00
Mitsuhiro Nakamura
89a5e6db55 rPackages.JuniperKernel: fix non-Darwin build 2018-05-15 17:50:11 +09:00
Mitsuhiro Nakamura
d35604d910 rPackages: fix binutils path on Darwin 2018-05-12 20:51:43 +09:00
Peter Simons
94295e3cee R: update CRAN and BIOC package sets 2018-04-24 09:19:38 +02:00
Shea Levy
05e375d710
Merge remote-tracking branch 'origin/master' into staging 2018-03-28 09:36:47 -04:00
Graham Christensen
92d53362d4
Move all nixpkgs doc files in to the doc directory 
This makes a makefile-driven developer workflow nicer.
 2018-03-25 19:52:00 -04:00
Matthew Bauer
9109a90479 treewide: remove some more gettext references 2018-03-22 16:50:14 -05:00
Peter Simons
9c207cd922 R: fix evaluation errors 2018-03-15 21:14:29 +01:00
Peter Simons
52dce0fb38 R: update the CRAN and BIOC package sets 2018-03-15 19:39:55 +01:00
Averell Dalton
028e67abce rPackages.mongolite: fix build 2018-03-10 04:01:49 +01:00
Vladimír Čunát
565bd805e6
Merge branch 'master' 2018-03-05 14:53:27 +01:00
Peter Simons
a06b81b8ad
Merge pull request #35651 from mnacamura/r-xml2-darwin 
rPackages.xml2: fix darwin build
 2018-02-26 20:16:16 +01:00
Mitsuhiro Nakamura
4b1627d313 rPackages.xml2: fix darwin build 2018-02-26 10:47:57 +09:00
Mitsuhiro Nakamura
671e3f5c4d rPackages.JuniperKernel: fix darwin build 2018-02-26 10:00:00 +09:00
Alexander V. Nikolaev
0acec7e984 treewide: transition mesa to libGLU_combined 2018-02-24 17:06:49 +02:00
Justin Bedo
8d03d9b9af
rPackages: add bioconductor archive url 2018-02-21 09:58:17 +11:00
Justin Bedo
cfc07bcf0e
bioconductor: 3.4 -> 3.6 2018-02-21 09:58:17 +11:00
Mitsuhiro Nakamura
c4658ac0a4 rPackages.pbdZMQ: fix package loading on Darwin 2018-02-10 00:54:28 +09:00
Mitsuhiro Nakamura
2533720976 rPackages.data_table: OpenMP support on Darwin 2018-01-19 19:30:55 +09:00
Daiderd Jordan
5a02143c20
Merge pull request #33010 from LnL7/cacert-hook 
cacert: add hook that sets SSL_CERT_FILE
 2018-01-07 09:55:15 +01:00
Robin Gloster
ee1c85aee9 mariadb: lib -> connector-c 2017-12-29 02:18:35 +01:00
Daiderd Jordan
091c2b9f04
cacert: cleanup exporting SSL_CERT_FILE 2017-12-27 21:36:32 +01:00
Peter Simons
65b15c40f1 R: update package set 2017-12-01 13:48:26 +01:00
Peter Simons
458331408e r-openssl: fix build 2017-11-30 18:45:47 +01:00
John Ericson
405412dfd9
Merge pull request #31775 from obsidiansystems/stdenv-both-propagated-files 
stdenv setup: Always use both propagated files
 2017-11-22 15:23:37 -05:00
John Ericson
da19c34d0f stdenv setup: Always use both propagated files 
This continues #23374, which always kept around both attributes, by
always including both propagated files: `propgated-native-build-inputs`
and `propagated-build-inputs`. `nativePkgs` and `crossPkgs` are still
defined as before, however, so this change should only barely
observable.

This is an incremental step to fully keeping the dependencies separate
in all cases.
 2017-11-21 10:44:44 -05:00
Matthew Justin Bauer
24e38f3075
r-modules: fix eval 
Fixes #31508
 2017-11-12 21:49:41 -06:00
Maciej Kazulak
42b70ae5ed nixpkgs manual: add rstudio shell.nix example 
Provide an example of a self-contained shell.nix for rstudio with
additional packages.
 2017-11-04 12:26:08 +01:00
Hamish Mackenzie
8870d1a67d r-modules: Fix a number of popular R packages 
The R V8 package still depends on V8 3.14 so this is also included.
 2017-10-21 11:29:21 +01:00
Peter Simons
11131d5fc1 R: update package set 2017-09-29 15:21:09 +02:00
Peter Simons
aa9bebf261 R: update package set 2017-08-31 21:59:06 +02:00
Mitsuhiro Nakamura
c5fe03ace2 r-pbdZMQ: fix Darwin install 2017-07-14 14:32:51 +09:00
Peter Simons
b1ebe7a72c r-modules: update package set 2017-07-02 09:51:42 +02:00
Chris Hodapp
29969a5ec7 rstudio: Fix recompilation issue with custom package set 
This attempts to fix the issue described at
https://github.com/NixOS/nixpkgs/pull/22219#issuecomment-291801133.
Any change to the custom packages passed to RStudio causes this to
completely rebuild RStudio, which is completely unnecessary and also a
bit of a hindrance as it's a fairly slow build.

This rolls back most of that old PR, and instead implements something
more like rWrapper.  Existing configurations with the old useRPackages
will break.
 2017-05-01 09:46:40 -04:00
Peter Simons
85a9e6dcdf R: update list of broken packages (and some cosmetic) 2017-04-24 15:39:54 +02:00
Peter Simons
430cbcfd2b R: update CRAN and BIOC package sets 2017-04-24 15:39:08 +02:00
Chris Hodapp
80beb55cfc imager (r-modules): add pkgs.x11 to fix build, unmark imager/ForestTools as broken 2017-04-20 14:18:01 -04:00
Peter Simons
add394d8f1 r-modules: update CRAN package set 2017-03-07 14:56:46 +01:00
Peter Simons
f4595fa555 r-modules: drop broken irkernel package set 
We can no longer update that package set since, apparently, it has moved
to a different packaging scheme.
 2017-03-07 14:56:46 +01:00
Peter Simons
3dc4e12ff0 r-modules: remove weird version assertion 2017-03-07 14:56:46 +01:00
Nikolay Amiantov
477b507a4f rPackages: remove old cuda-related patches 
gputools doesn't build but because of unrelated linking issues.
 2017-02-28 17:31:07 +03:00
Nikolay Amiantov
6f3e071755 rPackages: try to unbreak reverse dependencies of cudatoolkit 2017-02-28 17:22:06 +03:00
Domen Kožar
ffe935ee86 Merge pull request #23104 from dtzWill/fix/generate-shell 
R/generate-shell: Use R from current tree, fix missing wget dep.
 2017-02-27 14:06:17 +01:00
Domen Kožar
a7dc912460 Merge pull request #23069 from lukego/R-packages-readme 
r-modules/README.md: mention generate-shell.nix
 2017-02-27 14:04:35 +01:00
Domen Kožar
4ccb553b70 Merge pull request #22817 from jbedo/r 
R: 3.2.4 -> 3.3.2
 2017-02-27 14:02:13 +01:00
Domen Kožar
7ed28a0b78
R: fix bio3d build 2017-02-27 13:51:55 +01:00
Justin Bedo
4c2d75f58c
R: unmark edgeR and limma as broken 2017-02-24 15:52:10 +11:00
Justin Bedo
4bb8727284
R: 3.2.4 -> 3.3.2 2017-02-24 15:22:12 +11:00
Will Dietz
2f303bc10e R/generate-shell: Use R from current tree, fix missing wget dep. 
Without this change, the 'R' version used might be the wrong
one which changes the package lists used.

Fixes #19530.
 2017-02-23 07:46:20 -06:00
Luke Gorrie
a000ec038e r-modules/README.md: mention generate-shell.nix 2017-02-22 04:48:50 +00:00
Eelco Dolstra
9d6a55aefd
~/.nixpkgs -> ~/.config/nixpkgs 
The former is still respected as a fallback for config.nix for
backwards compatibility (but not for overlays because they're a new
feature).
 2017-02-01 16:07:55 +01:00
Chris Hodapp
7638578342 RStudio: Optionally allow packages from custom R environment 
https://nixos.org/nixpkgs/manual/#r-packages contains a method for
setting up an R environment with a specific set of libraries, and it
creates an R wrapper which points R to those libraries.

The package RStudio relies on the standard R package, which then
cannot access any of the libraries specified in a custom R
environment.  While one may easily use pkgs.rstudio.override to change
rstudio's R dependency to the custom R environment, this accomplishes
nothing because while RStudio runs the correct R wrapper it clears out
the environment variable R_LIBS_SITE - and so it is still unable to
use any of those packages.

In order to work around this problem, these changes allow the user to
optionally modify rstudio's wrapper to set environment variable
R_PROFILE_USER to an R script which sets R's .libPaths(..) to point to
the same libraries; that script is generated from R_LIBS_SITE in the R
wrapper.

By default, this change has no effect.  If R is overridden to
something else, and if useRPackages is changed from its default of
false, then the change described above is made; for instance:

{
  packageOverrides = pkgs: let self = pkgs.pkgs; in
  rec {
    rEnv = pkgs.rWrapper.override {
      packages = with self.rPackages; [
        dplyr ggplot2 e1071 rpart reshape
      ];
    };
    rstudioEnv = pkgs.rstudio.override { R = rEnv; useRPackages = true; };
  };
}
 2017-01-27 18:54:50 -05:00
mimadrid
8954412fcc
r-modules: fix snpStats package 2017-01-06 21:07:25 +01:00
mimadrid
b5a0925663
r-modules: fix VariantAnnotation package 2017-01-06 21:07:25 +01:00
mimadrid
6540b6507d
r-modules: fix rtracklayer package 2017-01-06 21:07:25 +01:00
mimadrid
baf65d5000
r-modules: fix Rsubread package 2017-01-06 21:07:25 +01:00
mimadrid
9ebab25442
r-modules: fix gmapR package 2017-01-06 21:07:25 +01:00
mimadrid
286e86f3a5
r-modules: fix oligo package 2017-01-06 21:07:25 +01:00