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266 commits

Author SHA1 Message Date
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
6f3e071755 rPackages: try to unbreak reverse dependencies of cudatoolkit 2017-02-28 17:22:06 +03:00
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
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
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
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
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
Tuomas Tynkkynen
555292017e treewide: Mass replace 'xorg.libXft}/lib' to refer the 'out' output 2016-01-24 10:03:37 +02:00
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
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
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
Vladimír Čunát
333d69a5f0 Merge staging into closure-size 
The most complex problems were from dealing with switches reverted in
the meantime (gcc5, gmp6, ncurses6).
It's likely that darwin is (still) broken nontrivially.
 2015-11-20 14:32:58 +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
Vladimír Čunát
99e4371526 curl: split into multiple outputs 
Also use pkgconfig to be safer and fix (some) referrers.
 2015-10-13 20:18:48 +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
Vladimír Čunát
38313d5d87 libxml2,libxslt: split into multiple outputs 
Fixed all references, hopefully.
libxml2Python is slightly hacky now, but it seems to work.
 2015-10-05 13:44:16 +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
7a0fa8f898 r-modules: fix evaluation errors 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
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
Michel Kuhlmann
aabee7eb46 r-modules: regenerate 2015-05-11T14:48:00+0100 2015-05-12 07:47:41 +02:00
Peter Simons
e313cd711e r-modules: disable broken builds on Hydra 2015-04-20 17:38:46 +02:00
Peter Simons
0b088ce581 r-modules: revert "disable builds that depend on broken gdal library" 
This reverts commit 9e9b5e6e69. gdal has
been fixed in 1645795c53.
 2015-04-19 17:52:50 +02:00
Peter Simons
9e9b5e6e69 r-modules: disable builds that depend on broken gdal library 2015-04-17 20:02:46 +02:00
Michel Kuhlmann
cc5f5f0fd3 r-modules: update from CRAN state at 2015-04-16T11:23:00+0100 
Closes https://github.com/NixOS/nixpkgs/pull/7411.
 2015-04-17 15:38:12 +02:00
William A. Kennington III
758319f67f One more mysql fix 2015-04-01 16:52:38 -07:00
Peter Simons
aed1895643 r-modules: remedy remaining Hydra failures 2015-03-29 00:17:55 +01:00
Peter Simons
f6886c62dc r-modules: disable broken builds on Hydra 2015-03-28 10:36:54 +01:00
Michel Kuhlmann
c96bc1e507 r-modules: fixing rggobi by adding initial expression for ggobi 2015-03-26 12:20:07 +01:00
Peter Simons
5238bfb73f r-modules: fix evaluation errors 2015-03-21 23:33:50 +01:00
Joachim Fasting
0e52c562b5 RAppArmor: use AppArmor 2.9 2015-03-19 14:14:28 +01:00
Peter Simons
d388855731 r-SID: mark broken 2015-03-09 21:14:00 +01:00
Peter Simons
e8b33876af r-Cell: drop obsolete package 2015-03-09 16:43:37 +01:00
Peter Simons
eaf728c3d3 r-modules: fix git2r, TAQMNGR, and WhopGenome 2015-03-06 11:21:21 +01:00
Peter Simons
030bd26af3 r-modules: mark daff and rjade broken 2015-03-04 12:51:43 +01:00
Adam Vogt
5adab4cbc9 remove some packages marked broken for cran-packages.nix 
those packages were removed from cran (and cran-packages.nix)
 2015-02-26 16:17:15 -05:00
Peter Simons
80101c8329 Disable some broken R packages. 2015-02-22 18:22:35 +01:00
Peter Simons
7afe039842 pkgs/development/r-modules: fix evaluation errors 2015-02-20 15:08:18 +01:00
Nikolay Amiantov
8450ff3ab8 rPackages: fix broken packages 2015-02-19 23:53:36 +03:00