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269 commits

Author SHA1 Message Date
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
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