Commit Graph

274 Commits

Author SHA1 Message Date
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