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277 Commits

Author SHA1 Message Date
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
mimadrid
afd1a4c933
r-modules: fix affyio package 2017-01-06 21:07:25 +01:00
mimadrid
4c0c3c7493
r-modules: fix BitSeq package 2017-01-06 21:07:24 +01:00
mimadrid
272b447ea7
r-modules: fix bamsignals package 2017-01-06 21:07:24 +01:00
mimadrid
c5e4754ca7
r-modules: fix affyPLM package 2017-01-06 21:07:24 +01:00
mimadrid
1d7fd8f3c4
r-modules: fix xml2 package 2017-01-06 21:07:24 +01:00
mimadrid
5b813c2ab0
r-modules: fix XBRL package 2017-01-06 21:07:24 +01:00
mimadrid
512be9e14a
r-modules: fix WhopGenome package 2017-01-06 21:07:24 +01:00
mimadrid
f9d84f8b65
r-modules: fix tkrplot package 2017-01-06 21:07:24 +01:00
mimadrid
0b3e62bb12
r-modules: fix tiff package 2017-01-06 21:07:23 +01:00
mimadrid
9420fa23c6
r-modules: fix TAQMNGR package 2017-01-06 21:07:23 +01:00
mimadrid
2303e63116
r-modules: fix spate package 2017-01-06 21:07:23 +01:00
mimadrid
fcbed4b654
r-modules: fix showtext package 2017-01-06 21:07:23 +01:00
mimadrid
8a6b58d51d
r-modules: fix seqminer package 2017-01-06 21:07:23 +01:00
mimadrid
e1a5eeef06
r-modules: fix seqinr package 2017-01-06 21:07:22 +01:00
mimadrid
1ef67b9e78
r-modules: fix RVowpalWabbit package 2017-01-06 21:05:54 +01:00
mimadrid
ae2723a144
r-modules: fix rtiff package 2017-01-06 21:05:54 +01:00
mimadrid
d7ac90dd0c
r-modules: fix rtfbs package 2017-01-06 21:05:53 +01:00
mimadrid
fd175e4084
r-modules: fix Rssa package 2017-01-06 21:05:52 +01:00
mimadrid
bd2aaada6e
r-modules: fix RSclient package 2017-01-06 21:05:52 +01:00
mimadrid
53235dbe14
r-modules: fix rphast package 2017-01-06 21:05:52 +01:00
mimadrid
780fb79e32
r-modules: fix Rmpfr package 2017-01-06 21:05:51 +01:00
mimadrid
a58db75ccb
r-modules: fix rmatio package 2017-01-06 21:05:51 +01:00
mimadrid
674a2077dd
r-modules: fix rJava package 2017-01-06 21:05:51 +01:00
mimadrid
13a582688f
r-modules: fix RJaCGH package 2017-01-06 21:05:51 +01:00
mimadrid
9922867fa8
r-modules: fix Rhtslib package 2017-01-06 21:05:50 +01:00
mimadrid
bb60f939ae
r-modules: fix Rhpc package 2017-01-06 21:05:50 +01:00
mimadrid
e1bc505da9
r-modules: fix rggobi package 2017-01-06 21:05:50 +01:00
mimadrid
9f2b5e0425
r-modules: fix RGtk2 package 2017-01-06 21:05:50 +01:00
mimadrid
3342f8bd59
r-modules: fix RcppOctave package 2017-01-06 21:05:50 +01:00
mimadrid
ba86a39645
r-modules: fix RcppCNPy package 2017-01-06 21:05:49 +01:00
mimadrid
dd159d06b6
r-modules: fix rcdd package 2017-01-06 21:05:49 +01:00
mimadrid
8b229baf33
r-modules: fix rbamtools package 2017-01-06 21:05:49 +01:00
mimadrid
558f67e85f
r-modules: fix R2SWF package 2017-01-06 21:05:48 +01:00
mimadrid
277efe9896
r-modules: fix sysfonts package 2017-01-06 21:05:48 +01:00
mimadrid
062c9037d1
r-modules: fix PopGenome package 2017-01-06 21:05:48 +01:00
mimadrid
c5ef08cc65
r-modules: fix PKI package 2017-01-06 21:05:48 +01:00
mimadrid
1e9071948f
r-modules: fix mwaved package 2017-01-06 21:05:48 +01:00
mimadrid
4e7de52c26
r-module: fix kza package 2017-01-06 21:05:47 +01:00
mimadrid
debb12ce1a
r-module: fix jpeg package 2017-01-06 21:05:47 +01:00
mimadrid
e3a2c97c7b
r-modules: fix gmp package 2017-01-06 21:05:47 +01:00
mimadrid
72eb6a8644
r-modules: fix fftwtools package 2017-01-06 21:05:47 +01:00
mimadrid
427c4d954a
r-modules: fix fftw package 2017-01-06 21:05:47 +01:00
mimadrid
b88b8ea05b
r-modules: fix devEMF package 2017-01-06 21:05:47 +01:00
mimadrid
6c6aab3e5b
r-modules: fix cairoDevice package 2017-01-06 21:05:47 +01:00
mimadrid
f717538866
r-modules: fix git2r package 2017-01-06 21:05:47 +01:00
mimadrid
88fcfafafe
r-modules: fix BayesXsrc package 2017-01-06 21:05:46 +01:00
mimadrid
6f9124e118
r-modules: fix Cairo package 2017-01-06 21:05:46 +01:00
mimadrid
321d5a01b6
r-modules: fix seewave package 2017-01-06 16:31:30 +01:00
Mike Sperber
6c226b1e7a rPackages.DescTools: unbreak build outside of Linux. (#20787) 
DescTools does not require X during build, so remove it from that list.
 2016-12-13 16:25:44 +01:00
Andreas Herrmann
98fce78cb3 r-modules: Fix png package 
The package requires the `dev` output of `libpng`.
 2016-12-12 10:53:10 +01:00
Langston Barrett
2b300c9bef r-modules: add more environment documentation 
Use nix-shell with a `default.nix` rather than using
config.nix
 2016-10-13 22:18:16 +00:00
Andreas Herrmann
cf3a2e99ad r-modules: edgeR is broken due to broken url 2016-09-27 17:47:16 +02:00
Andreas Herrmann
54915ecf0d r-modules: Fix h5 and rhdf5 
and some packages that depend on them.
 2016-09-27 17:46:06 +02:00
Peter Simons
23c122d277 r-openssl: fix build some more 2016-09-10 12:28:13 +02:00
Peter Simons
1196540a1d r-openssl: fix build 2016-09-09 15:13:07 +02:00
Peter Simons
fe0256cd01 r-curl: fix build 2016-09-09 15:12:54 +02:00
Peter Simons
b2113f7893 r-XML: fix build 2016-09-09 14:36:49 +02:00
Thomas Tuegel
787875c287
r-stringi: fix build by including icu.dev output 2016-09-07 17:19:20 -05:00
Tuomas Tynkkynen
2258b21e4b treewide: Add lots of platforms to packages with no meta 
Build-tested on x86_64 Linux and on Darwin.
 2016-08-02 21:17:44 +03:00
Michael Stone
c1d24efd6a darwin: R: provide gettext and gfortran as buildInputs on Darwin. 
As discussed in #10623, many R modules fail to build on Darwin without the
libraries and compilers provided by these packages.

For more detail, please see comment:

  https://github.com/NixOS/nixpkgs/pull/10623#issuecomment-172375342
 2016-07-22 13:31:40 -04:00
Ben Darwin
a896233396 jags: 3.4.0 -> 4.1.0 (#16804) 
* jags: 3.4.0 -> 4.1.0
* unbreak rjags and dependent packages
 2016-07-18 13:11:18 +02:00
Tuomas Tynkkynen
2a73de6e6c treewide: Make explicit that 'dev' output of openssl is used 2016-05-19 10:02:23 +02:00
Tuomas Tynkkynen
3f8b08f506 treewide: Make explicit that 'dev' output of mpfr is used 2016-05-19 10:00:49 +02:00
Tuomas Tynkkynen
b465dc202f boost: Kill unnecessary 'lib' output 
This was split in somewhere pre-2014 without the current infra which
automates parts of this, in particular the output propagation.
 2016-04-28 00:41:28 +03:00
Peter Simons
a6978ded09 Merge pull request #14144 from jefdaj/r-bioc-data-packages 
r-modules: update CRAN, add Bioconductor data packages
 2016-04-15 14:46:19 +02:00
Jeffrey David Johnson
2291885f9e mark bioc packages broken; should match hydra now 2016-04-14 14:34:11 -07:00
Jeffrey David Johnson
f88843f545 mark bioc packages broken; should match hydra now 2016-04-14 09:54:46 -07:00
Jeffrey David Johnson
2f6581df00 r-modules: mark mzR broken 2016-04-12 14:16:43 -07:00
Jeffrey David Johnson
2ceec79ad5 work on fixing up bioconductor packages 2016-03-31 16:16:34 -07:00
Jeffrey David Johnson
3c0fb5ede1 work on fixing up bioconductor packages 2016-03-31 11:36:39 -07:00
Jeffrey David Johnson
c9934bbcb8 work on fixing up bioconductor packages 2016-03-31 11:17:21 -07:00
Jeffrey David Johnson
518fd135ed work on fixing up bioconductor packages 2016-03-27 23:14:24 -07:00
Jeffrey David Johnson
e98a231af8 work on fixing up bioconductor packages 2016-03-26 11:26:29 -07:00
Jeffrey David Johnson
05fc143451 work on fixing up bioconductor packages 2016-03-25 09:15:02 -07:00
Jeffrey David Johnson
1911d4925e work on fixing up bioconductor package 2016-03-25 00:30:20 -07:00
Jeffrey David Johnson
4cd2202918 work on fixing up bioconductor packages 2016-03-24 14:51:21 -07:00
Jeffrey David Johnson
66bcbfb93d r-modules: update CRAN, add Bioconductor data pkgs 2016-03-22 22:50:54 -07:00
Vladimír Čunát
09af15654f Merge master into closure-size 
The kde-5 stuff still didn't merge well.
I hand-fixed what I saw, but there may be more problems.
 2016-03-08 09:58:19 +01:00
Michel Kuhlmann
312494180d nixpkgs manual: add basic R documentation, fixes #13362 
also fixes #13243
 2016-02-22 10:16:06 +01:00
Vladimír Čunát
ae74c356d9 Merge recent 'staging' into closure-size 
Let's get rid of those merge conflicts.
 2016-02-03 16:57:19 +01:00
Tuomas Tynkkynen
555292017e treewide: Mass replace 'xorg.libXft}/lib' to refer the 'out' output 2016-01-24 10:03:37 +02:00
Tobias Geerinckx-Rice
32d40f0f98 Remove no longer (or never) referenced patches 
55 files changed, 6041 deletions. Tested with `nix-build -A tarball`.
 2016-01-24 02:02:21 +01:00
Vladimír Čunát
716aac2519 Merge branch 'staging' into closure-size 2016-01-19 09:55:31 +01:00
Asko Soukka
a225a650bf R: fix Darwin build 
Merged manually from https://github.com/NixOS/nixpkgs/pull/10623.
 2016-01-06 22:20:40 +01:00
Michel Kuhlmann
26f80d7a6f r-modules: update list of broken packages 
Closes https://github.com/NixOS/nixpkgs/pull/12181.
 2016-01-06 21:50:36 +01:00
Michel Kuhlmann
4c3d76d3c8 r-modules: regenerate CRAN packages 2016-01-04 09:19:24 +01:00
Vladimír Čunát
f9f6f41bff Merge branch 'master' into closure-size 
TODO: there was more significant refactoring of qtbase and plasma 5.5
on master, and I'm deferring pointing to correct outputs to later.
 2015-12-31 09:53:02 +01:00
Peter Simons
3a8112f7da r-modules: prefer gsl 1.x since 2.x is unsupported by r-gsl-1.9.x 2015-12-29 21:22:59 +01:00
Luca Bruno
a412927924 Merge remote-tracking branch 'origin/master' into closure-size 2015-11-25 21:37:30 +01:00
Peter Simons
de02462a36 r-modules: update list of broken packages 2015-11-25 11:39:28 +01:00
Nikolay Amiantov
bd4297dc4d r-modules: regenerate CRAN, BIOC and IRKernel 2015-11-25 11:39:28 +01:00
Nikolay Amiantov
287f99bada r-modules: use HTTPS, allow passing args from generated set, use MRAN 2015-11-25 11:39:28 +01:00
Peter Simons
fa5de61315 r-tikzDevice: update to new texlive 2015-11-24 17:30:28 +01:00