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138 commits

Author SHA1 Message Date
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
Michel Kuhlmann 312494180d nixpkgs manual: add basic R documentation, fixes #13362 
also fixes #13243
 2016-02-22 10:16:06 +01:00
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
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
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
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
Peter Simons d7e6a46770 r-modules: update list of broken builds to avoid Hydra errors 2015-11-18 15:23:46 +01:00
Michel Kuhlmann cab1f3de5e R: regenerate CRAN packages 2015-11-17 14:34:27 +01:00
Asko Soukka d8e3a981c5 r-modules: init IRkernel packages 2015-10-30 03:48:23 +02:00
Michel Kuhlmann ec8f31d26c R: fix some modules with configure-shebang-error 
- xml2: fix configure script
- rversion, devtools: mark as unbroken
  dependency R-curl was fixed in 513e31185b
 2015-10-12 10:02:48 +02:00
Peter Simons 7c516259e7 r-modules: update list of broken packages 2015-10-05 14:15:41 +02:00
Karn Kallio 94629aa57d R: regenerate CRAN and BIOC packages 2015-10-04 20:06:49 +02:00
Nikolay Amiantov 513e31185b R-curl: fix configure script 2015-10-04 20:06:49 +02:00
Vladimír Čunát 88c9f8b574 xlibs: replace occurrences by xorg 
This seems to have been confusing people, using both xlibs and xorg, etc.
- Avoided renaming local (and different) xlibs binding in gcc*.
- Fixed cases where both xorg and xlibs were used.
Hopefully everything still works as before.
 2015-09-15 12:54:34 +02:00
Vladimír Čunát 21e3ff658a x11: replace its usage by xlibsWrapper directly 
Scilab note: the parameters already had pointed to nonexistent dirs
before this set of refactoring. But that config wasn't even used by
default.
 2015-09-15 12:08:24 +02:00
Bjørn Forsman 22321f2e58 cudatoolkit: don't move $out/include to $out/usr_include 
This effectively reverts 86c283824f
("If cuda headers are presented to nix [...]") and all the following
workarounds that was added due to that commit.

As far as I can tell[1] this hack isn't needed anymore. And moving
includes to $out/usr_include causes pain for cudatoolkit users, so
better get rid of it.

In patches that did more than the $out/usr_include workaround, I only
changed the line back to $out/include instead of re-generating the
patches and fully removing the changed line.

[1]: I build tested blender and caffe, and temporarily added
recurseIntoAttrs to rPackages and haskellPackages so that nox-review
could get proper coverage. However, many of the packages do not build
even before this patch. I also built CUDA samples with cudatoolkit7
that ran fine.
 2015-09-10 10:35:40 +02:00
Peter Simons 5d1bcf2f4e R: fix Hydra build & evaluation errors 2015-08-06 20:13:50 +02:00
Peter Simons 36fc26c0fc R: regenerate CRAN and BIOC packages 2015-08-06 20:13:50 +02:00
Peter Simons 7a0fa8f898 r-modules: fix evaluation errors 2015-08-06 20:13:49 +02:00
Michel Kuhlmann 18cff91fb7 R: regenerate CRAN and BIOC packages 
Closes https://github.com/NixOS/nixpkgs/pull/9037.
 2015-08-06 20:13:49 +02:00
Peter Simons 73ad191afb r-modules: fix Hydra evaluation errors 2015-08-06 20:13:49 +02:00
Nikolay Amiantov e3461ce259 rPackages.stringi: add ICU data tables 2015-07-28 12:33:29 +03:00
Peter Simons b59685de83 r-stringi: fix build 2015-07-12 02:38:42 +02:00
Michel Kuhlmann bb2b683e63 R: regenerate CRAN and BIOC packages 2015-07-09 14:52:17 +02:00
Peter Simons bb42c215e2 R: improve support for CRAN and Bioconductor package sets 
- Update the instructions for re-generating each of the package set files.
 - Provide test-evaluation.nix expression to verify that the package sets evaluates.
 - Update list of known broken packages.
 2015-06-17 23:19:56 +02:00
Jeffrey David Johnson 93a742fd28 R: add support for Bioconductor packages 2015-06-17 23:19:56 +02:00
Peter Simons 362e60a5dc r-modules: fix rapportools 2015-06-16 12:48:50 +02:00
Peter Simons 21c18c4f0a r-modules: fix rapport 2015-06-16 12:48:50 +02:00
Peter Simons ccd6988b3d r-modules: fix xml2 2015-06-16 12:48:50 +02:00
Peter Simons 8ac6350ce7 r-modules: fix pander 2015-06-16 12:48:50 +02:00
Peter Simons 9fc5317055 r-modules: fix curl 2015-06-16 12:48:50 +02:00
Peter Simons d4c810cccd r-modules: disable broken packages to avoid Hydra evaluation errors 2015-06-16 12:48:49 +02:00
Peter Simons b667cb6163 Merge pull request #8298 from abbradar/r-updates 
R updates
 2015-06-15 20:31:57 +02:00
Nikolay Amiantov 29779ae642 R: regenerate CRAN packages 2015-06-12 03:44:39 +03:00
Nikolay Amiantov 9bb5e7edbd generate-cran-packages: make executable 2015-06-12 03:44:38 +03:00
Thomas Tuegel 8245caedf1 rPackages.SamplerCompare: build with openblas 2015-06-09 11:47:40 -05:00
Thomas Tuegel 58754130cc rPackages.slfm: build with openblas 2015-06-09 11:47:26 -05:00
Thomas Tuegel 77aa1c990e rPackages.Mposterior: build with openblas 2015-06-09 11:47:12 -05:00
Thomas Tuegel b120a737fd rPackages.BayesLogit: build with openblas 2015-06-09 11:43:00 -05:00
Peter Simons 949746f9f5 r-modules: disable broken builds 2015-05-15 13:48:38 +02:00
Peter Simons 278df52729 r-xml2: fix build 2015-05-15 13:47:27 +02:00
Peter Simons aaa9f837a9 r-modules: fix Hydra evaluation errors 2015-05-13 11:31:39 +02:00