ilyakooo0/nixpkgs
1
0
Fork 0
mirror of https://github.com/ilyakooo0/nixpkgs.git synced 2024-11-16 06:47:09 +03:00
Code Issues Projects Releases Wiki Activity
118,782 Commits 96 Branches 102 Tags 4.5 GiB
b676aa045f
Commit Graph

250 Commits

Author SHA1 Message Date
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