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277 commits

Author SHA1 Message Date
Alex Branham 46bca1d643
R: Update CRAN and bioconductor packages 2019-07-02 15:48:06 -05:00
Alex Branham 00b202e34a
rPackages.git2r: Use system libgit2 
Otherwise git2r builds a bundled libgit2
 2019-06-14 10:05:07 -05:00
Alex Branham 0a80d3dc82 R: update CRAN and Bioconductor package sets 
Closes https://github.com/NixOS/nixpkgs/pull/59186.
 2019-04-11 20:37:18 +02:00
Peter Simons 3c9ff308e7
Merge pull request #58467 from mnacamura/r-sys 
r-sys: remove obsolete dependency
 2019-03-28 12:42:19 +01:00
Mitsuhiro Nakamura 157921f2e7 rPackages: fix missing dependency to libiconv 2019-03-28 12:11:47 +09:00
Mitsuhiro Nakamura d07c3139ed r-sys: remove obsolete dependency 2019-03-28 11:20:04 +09:00
Alex Branham 8dcba2b842 R: update CRAN and Bioconductor package sets 
Closes https://github.com/NixOS/nixpkgs/pull/57423.
 2019-03-14 19:50:37 +01:00
Markus Ankenbrand 7fcfbcdbc9 rPackages.phytools: fix installation 2019-03-06 11:39:48 +01:00
Alex Branham ec03ed450c update R package set 
Closes https://github.com/NixOS/nixpkgs/pull/55462.
 2019-02-10 11:16:19 +01:00
Christian Kauhaus 3b445042ac rPackages.littler: fix build (#51282) 
littler gives a wrapped called `r` (or `lr` for non-case-preserving
systems like Darwin) which works as shebang or pipe target.

The build was completely broken before (missing deps).

Symlink executables and manpage into standard locations so that this
packages also works in `environment.systemPackages`.
 2018-12-06 17:22:31 +01:00
Averell Dalton 25e68e3048 r-ps: patchShebangs in ./configure to fix build 2018-11-02 23:02:04 +01:00
Peter Simons c9e1380626 r-nloptr: fix build by adding pkgconfig 2018-11-02 17:50:18 +01:00
Peter Simons 9b63cc6313 r-rlang: patch shebang in configure script to fix the build 2018-11-02 17:50:18 +01:00
Tom McLaughlin cac5c9401e R: update CRAN and BIOC package sets 
Closes https://github.com/NixOS/nixpkgs/pull/49430.
 2018-11-02 17:50:18 +01:00
Rob Vermaas 3f719b0fad Fix build for rPackages.units 
(cherry picked from commit 1eb1fec3ae)
 2018-10-08 12:53:43 +02:00
ivanbrennan 989f24befc
git2r: add SSH support 
When building the devtools R module, which depends on git2r, it reports
that libssh2 cannot be found, and falls back to building without SSH
support. Adding libssh2.dev to git2r's native build inputs fixes this.
 2018-09-11 16:39:20 -04:00
Ryan Mulligan 73ae8e53e2 rPackages.RPostgres: fix configure paths and includes 
closes #46208
 2018-09-09 14:37:28 -07:00
Mitsuhiro Nakamura 5e42a081a3 r-jqr: fix build (#45333) 2018-08-20 00:08:28 +02:00
volth e6d3c65442
r-packages: fix regression 2018-08-04 06:19:08 +00:00
Mitsuhiro Nakamura 559997179d rPackages: export buildRPackage 2018-08-03 01:08:07 +09:00
volth 52f53c69ce pkgs/*: remove unreferenced function arguments 2018-07-21 02:48:04 +00:00
Markus Ankenbrand 775fd4bfba rPackages.haven: fix installation 2018-07-12 11:07:27 +02:00
Mitsuhiro Nakamura c072024409 rPackages.reprex: fix build 2018-07-11 23:16:49 +09:00
Markus Ankenbrand 89f44c1314 rPackages.rhdf5: fix installation 
Fix #43285
 2018-07-10 16:38:11 +02:00
Peter Simons 03476783a5 R: fix evaluation errors 2018-07-07 12:10:46 +02:00
Markus Ankenbrand 9eeea0b9ef rPackages.rhdf5: fix installation 
Fix #42878
 2018-07-02 18:51:18 +02:00
Daiderd Jordan 654960c1cd
Merge pull request #42290 from mnacamura/r-igraph-darwin 
rPackages.igraph: fix Darwin build
 2018-06-20 19:52:36 +02:00
Mitsuhiro Nakamura f972a30f16 rPackages.igraph: fix Darwin build 2018-06-20 11:08:29 +09:00
Mitsuhiro Nakamura dada18527a rPackages.RcppEigen: fix Darwin build 2018-06-20 10:59:18 +09:00
Josef Kemetmüller aeda45821d rPackages.mgcv: fix darwin build 
This fixes the error:
    ld: library not found for -liconv
 2018-06-07 00:00:42 +02:00
Josef Kemetmüller 0275562a12 rPackages.Matrix: fix darwin build 
This fixes the error:
    ld: library not found for -liconv
 2018-06-07 00:00:07 +02:00
Josef Kemetmüller d8ad2ad916 rPackages.nlme: fix darwin build 
This fixes the error:
    ld: library not found for -liconv
 2018-06-06 23:59:09 +02:00
Josef Kemetmüller e023f117f8 rPackages.KernSmooth: fix darwin build 
This fixes the error:
    ld: library not found for -liconv
 2018-06-06 23:58:46 +02:00
Josef Kemetmüller 5d092b3052 rPackages.cluster: fix darwin build 
This fixes the error:
    ld: library not found for -liconv
 2018-06-06 23:57:08 +02:00
Mitsuhiro Nakamura 89a5e6db55 rPackages.JuniperKernel: fix non-Darwin build 2018-05-15 17:50:11 +09:00
Mitsuhiro Nakamura d35604d910 rPackages: fix binutils path on Darwin 2018-05-12 20:51:43 +09:00
Peter Simons 94295e3cee R: update CRAN and BIOC package sets 2018-04-24 09:19:38 +02:00
Peter Simons 9c207cd922 R: fix evaluation errors 2018-03-15 21:14:29 +01:00
Averell Dalton 028e67abce rPackages.mongolite: fix build 2018-03-10 04:01:49 +01:00
Vladimír Čunát 565bd805e6
Merge branch 'master' 2018-03-05 14:53:27 +01:00
Peter Simons a06b81b8ad
Merge pull request #35651 from mnacamura/r-xml2-darwin 
rPackages.xml2: fix darwin build
 2018-02-26 20:16:16 +01:00
Mitsuhiro Nakamura 4b1627d313 rPackages.xml2: fix darwin build 2018-02-26 10:47:57 +09:00
Mitsuhiro Nakamura 671e3f5c4d rPackages.JuniperKernel: fix darwin build 2018-02-26 10:00:00 +09:00
Alexander V. Nikolaev 0acec7e984 treewide: transition mesa to libGLU_combined 2018-02-24 17:06:49 +02:00
Justin Bedo 8d03d9b9af
rPackages: add bioconductor archive url 2018-02-21 09:58:17 +11:00
Justin Bedo cfc07bcf0e
bioconductor: 3.4 -> 3.6 2018-02-21 09:58:17 +11:00
Mitsuhiro Nakamura c4658ac0a4 rPackages.pbdZMQ: fix package loading on Darwin 2018-02-10 00:54:28 +09:00
Mitsuhiro Nakamura 2533720976 rPackages.data_table: OpenMP support on Darwin 2018-01-19 19:30:55 +09:00
Daiderd Jordan 5a02143c20
Merge pull request #33010 from LnL7/cacert-hook 
cacert: add hook that sets SSL_CERT_FILE
 2018-01-07 09:55:15 +01:00
Robin Gloster ee1c85aee9 mariadb: lib -> connector-c 2017-12-29 02:18:35 +01:00
Daiderd Jordan 091c2b9f04
cacert: cleanup exporting SSL_CERT_FILE 2017-12-27 21:36:32 +01:00
Peter Simons 65b15c40f1 R: update package set 2017-12-01 13:48:26 +01:00
Peter Simons 458331408e r-openssl: fix build 2017-11-30 18:45:47 +01:00
Matthew Justin Bauer 24e38f3075
r-modules: fix eval 
Fixes #31508
 2017-11-12 21:49:41 -06:00
Hamish Mackenzie 8870d1a67d r-modules: Fix a number of popular R packages 
The R V8 package still depends on V8 3.14 so this is also included.
 2017-10-21 11:29:21 +01:00
Mitsuhiro Nakamura c5fe03ace2 r-pbdZMQ: fix Darwin install 2017-07-14 14:32:51 +09:00
Peter Simons b1ebe7a72c r-modules: update package set 2017-07-02 09:51:42 +02:00
Peter Simons 85a9e6dcdf R: update list of broken packages (and some cosmetic) 2017-04-24 15:39:54 +02:00
Peter Simons 430cbcfd2b R: update CRAN and BIOC package sets 2017-04-24 15:39:08 +02:00
Chris Hodapp 80beb55cfc imager (r-modules): add pkgs.x11 to fix build, unmark imager/ForestTools as broken 2017-04-20 14:18:01 -04:00
Peter Simons add394d8f1 r-modules: update CRAN package set 2017-03-07 14:56:46 +01:00
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