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356 Commits

Author SHA1 Message Date
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
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
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
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
Peter Simons
701251e435 r-modules: update from CRAN state at 2015-03-21T20:01:16+0100) 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
a591dbac3b r-modules: update from CRAN state at 2015-03-09T16:32:24+0100 2015-03-09 16:37:05 +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
2397f96d92 CRAN MASS_7.3-39 was uploaded twice, so use the newer checksum 
The two dates are:

Packaged: 2015-02-20 08:29:38 UTC; ripley
Packaged: 2015-02-24 10:34:20 UTC; ripley

There were with changes to tests/Examples/MASS-Ex.Rout.save,
but the rest of the code seems unaffected.
 2015-02-26 19:16:55 -05:00
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
Adam Vogt
f8d0a412d6 update cran packages 2015-02-25 17:50:42 -05:00
Adam Vogt
8365753a43 let generate-cran-packages.R read checksums from cran-packages.nix 
this lets "Rscript generate-cran-packages.R > cran-packages.nix"
complete much quicker, because we only have to download packages
with new versions.
 2015-02-25 17:43:43 -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
Nikolay Amiantov
3e6531c174 rPackages: add packagesWithRDepends 2015-02-19 23:51:24 +03:00
Nikolay Amiantov
88ab59eb73 rPackages: nicer override* functions 2015-02-19 23:50:42 +03:00
Nikolay Amiantov
0f9c0348af rPackages: remove Xvfb where it's not needed 2015-02-19 23:49:41 +03:00
Nikolay Amiantov
6c2a607112 R: update archive url 2015-02-18 15:41:46 +03:00
Nikolay Amiantov
75ce44a95c r-modules: regenerate 2015-02-18 15:41:46 +03:00
Peter Simons
6b261cc4d4 rPackages: allow users to override the version of R to be used for building 2015-01-27 14:04:54 +01:00
Peter Simons
282fd58c85 r-curl: help the package find curl's headers 2015-01-26 10:23:34 +01:00
Peter Simons
7fa0fa6450 r-modules: fix evaluation and minor cleanups 2015-01-22 11:39:00 +01:00
Michel Kuhlmann
4a3be6c787 rPackages: overall update and cleaning default.nix 2015-01-21 11:15:38 +01:00
Peter Simons
1b50c50432 r-modules: enable packages that were broken by the missing gdal dependency 2015-01-14 11:24:28 +01:00
Peter Simons
9489dac1d3 r-modules: update list of broken packages 2015-01-13 12:44:11 +01:00
Peter Simons
844828afad r-caret: update hash 2015-01-13 12:44:11 +01:00
Peter Simons
f09fec34e9 r-skmeans: update hash 2015-01-13 12:44:11 +01:00
Peter Simons
d2d868534f r-OceanView: update hash 2015-01-13 12:44:11 +01:00
Peter Simons
1f49c1cef7 Mark R packages h2o, jvmr, and qtbase as broken. 
This also breaks dependent packages qtutils, qtpaint, and bamboo.
 2014-12-04 15:00:54 +01:00
Peter Simons
7ee70a1644 R-defaults: add obsolete package temporarily 2014-12-04 14:45:09 +01:00
Peter Simons
1897946daf r-selectspm: cannot be built because it depends on the broken package ecespa 2014-12-03 16:28:29 +01:00
Peter Simons
d9f1968cab r-modules: always set meta.platforms when meta.hydraPlatforms is set, too 
By default, we take both values from the R derivation.
 2014-12-03 16:28:28 +01:00
Peter Simons
1c15a4122b r-modules: fix reference to cran-packages.nix 2014-12-03 16:28:28 +01:00
taku0
2d3dd68d27 cran-packages: combined packages definition files further 2014-12-03 16:28:28 +01:00
taku0
916e36940b cran-packages: combined packages definition files 2014-12-03 16:28:28 +01:00
taku0
4647743ed7 cran-packages: updated sources 2014-12-03 16:28:28 +01:00
taku0
2532844fb5 cran-packages: marks broken packages broken instead of removeing them 2014-12-03 16:28:28 +01:00
taku0
8f0d6091bb cran-packages: uses common variable names, doCheck and installFlags 2014-12-03 16:28:28 +01:00
taku0
dc1a3ed9b2 cran-packages: makes packages overridable 2014-12-03 16:28:28 +01:00
taku0
ea3c59907f cran-packages: sets hydraPlatforms of rpud and CARramps to none since those packages require non-free NVidia drivers 2014-12-03 16:28:28 +01:00
taku0
a28a6999b4 cran-packages: renamed the files from camelCase to kebab-case 2014-12-03 16:28:28 +01:00
taku0
2a1d9ddbf2 cran-packages: restructured 2014-12-03 16:28:28 +01:00
Peter Simons
7bc300570b r-RcmdrPlugin.ROC: disable broken build 2014-11-02 17:09:54 +01:00
Peter Simons
c573e2d97b r-PoweR: fix build 2014-11-02 14:09:53 +01:00
Peter Simons
9707459112 r-nloptr: add missing dependency on nlopt library 2014-11-02 14:05:40 +01:00
Peter Simons
fdee0ec8e7 r-RcppArmadillo: fix download URL 2014-11-02 14:05:40 +01:00
Peter Simons
e1d2e1dd6f r-Defaults: add version 1.1-1 again 
The package is obsolete, but I still need it. :-(
 2014-11-01 21:39:12 +01:00
Peter Simons
f773ebc016 cran-packages: update all packages to their respecitve latest version 2014-11-01 16:30:57 +01:00
Aristid Breitkreuz
71806b7cba Merge pull request #4368 from michelk/r-XML 
r-XML: adding system-dependency libxml2
 2014-10-04 19:56:18 +02:00
Michel Kuhlmann
29b2a1fbd3 r-XML: adding system-dependency libxml2 2014-10-02 08:03:50 +02:00
Michel Kuhlmann
03ca349691 rJava: adding missing dependencies and JAVA-env-variables 2014-09-23 11:28:57 +02:00
Michel Kuhlmann
911d0d5b12 rPackages: prefixing package-system-dependencies with 'pkgs.' 
Closes #4217
 2014-09-23 07:47:37 +01:00
Peter Simons
bbca3a51a7 Merge pull request #4090 from michelk/r-jsonlite 
r-jsonlite: update to 0.9.11
 2014-09-19 12:41:00 +02:00
Michel Kuhlmann
cb152d9ed0 r-rgdal/rgeos: adding gdal geos and proj as dependency 2014-09-15 11:15:51 +02:00
Michel Kuhlmann
67ba8bbbf9 r-jsonlite: update to 0.9.11 2014-09-15 10:22:17 +02:00
Justin Bedo
28af151e1a Added missing curl dependency to RCurl package 2014-09-03 15:48:33 +10:00
Peter Simons
610f31fe92 RcmdrPlugin_ROC: remove broken package 
This build goes into an endless loop and produces gigabytes of useless
output. :-(
 2014-08-15 18:51:47 +02:00
Peter Simons
d612cbdccf cran-packages.nix: drop trailing whitespace 2014-08-15 14:36:58 +02:00
Peter Simons
d306fdd88e cran-packages.nix: added missing sha256 fields 2014-08-15 14:36:58 +02:00
Peter Simons
4669d7ca61 r-RcppArmadillo: update to version 0.4.300.0 2014-08-15 14:36:58 +02:00
Adam Vogt
4402eb3061 manually fix dplyr and png cran-packages 2014-08-15 14:36:58 +02:00
Adam Vogt
371c8dd0bb update cran packages 2014-08-15 14:36:58 +02:00
Justin Bedo
57f1baa66d Added CRAN archive to R package derivation to prevent R expressions from 
breaking when any package is updated.
 2014-07-08 11:02:05 +10:00
Peter Simons
977d43f6c5 cran-packages.nix: fix a couple of builds 2014-06-09 12:58:48 +02:00
Peter Simons
36e6eda5fc r-modules: set meta.hydraPlatforms for all R packages 2014-06-07 12:28:54 +02:00
Justin Bedo
3c4b9b26cf Updated some CRAN packages and fixed dependencies 2014-05-15 09:05:09 +10:00
Peter Simons
cdf7d6a66f r-RcppArmadillo: fix build (and update to 0.4.300.0) 2014-05-07 12:30:29 +02:00
Peter Simons
262aecef74 r-generic-builder.nix: build packages from the extracted $srcdir so that we have a chance to patch them 2014-05-07 12:30:29 +02:00
Peter Simons
c8f4775b8b r-curl: fix build 2014-05-05 10:22:10 +02:00
Peter Simons
97262a59b5 cran-packages.nix: provide meta.homepage links for all modules 2014-05-05 00:33:51 +02:00
Peter Simons
f31f57c32d r-generic-builder: don't let derivation override the naming scheme 2014-05-05 00:33:51 +02:00
Peter Simons
66bcd77f0e R: simplify the generic builder 2014-05-04 23:54:11 +02:00
Peter Simons
4e1e248cf1 r-generic-builder: clean up the expression 2014-05-04 22:24:57 +02:00
Peter Simons
a9258080b1 R: don't install the "recommended packages" 
These packages come with R, but if we install them as part of this build, then
we cannot update them without re-building R as well. Instead, we add those
packages to the R environment through the r-wrapper. This means that
recommended packages can be updated in cran-packgaes.nix, and those updates
have an effect on the installation without re-building R itself.
 2014-05-04 21:12:34 +02:00
Peter Simons
a329900977 Move r-packages.nix into the r-modules directory. 2014-05-04 21:09:38 +02:00
Peter Simons
ac6bcc7836 cosmetic: move the R-wrapper into its own directory 2014-05-04 21:07:54 +02:00
Peter Simons
7c6a730e0b R: added wrapper script that provides "R" and "Rscript" binaries that know about extra libraries 
Configure an override in ~/.nixpkgs/config.nix as follows:

  {
    packageOverrides = pkgs: {

      rWrapper = pkgs.rWrapper.override {
        packages = with pkgs.rPackages; [ Defaults dataTable foreach xtable ];
      };

    };
  }
 2014-05-04 15:33:15 +02:00
Justin Bedo
fdc6e4372f Wrapped R's package system similarly to perlPackages 2013-09-28 13:19:43 +02:00