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358 commits

Author SHA1 Message Date
Matthew Bauer 1c8aba8334 treewide: use blas and lapack 
This makes packages use lapack and blas, which can wrap different
BLAS/LAPACK implementations.

treewide: cleanup from blas/lapack changes

A few issues in the original treewide:

- can’t assume blas64 is a bool
- unused commented code
 2020-04-17 16:24:09 -05:00
Alex Branham f5afc20d06
R: Update CRAN and bioconductor packages 2020-04-08 10:01:19 -04:00
Edward Tjörnhammar d5b5ff5ae5
rPackages.ggbio: patch away spelling mistake 2020-02-26 09:45:23 +01:00
tricktron e97ac66410
r-modules/generic-builder: Add missing iconv library to fix build on darwin (#78965) 
Add missing iconv dependency to fix builds of several r-modules on darwin.
 2020-02-07 10:50:43 +01:00
Maximilian Bosch 3c525b702a
r-packages: update 
This update was primarily done to update rPackages.V8 to 3.0 which
doesn't depend on an ancient version of v8 anymore.

Also dropped the `-lv8_libplatform` linker flag. It seems as this now
part of `v8.so` as `v8_libplatform.so` doesn't exist anymore on recent
v8 versions in nixpkgs, but the headers are still there and there aren't
any "undefined reference to" errors while linking.
 2020-01-28 20:11:00 +01:00
Alex Branham e206c37550
R: Update CRAN and bioconductor packages 2020-01-23 21:22:55 -05:00
Linus Heckemann 1e840fc421 rgl: fix build 
It seems that the dev output of libGLU needs to be included explicitly
for this to work. I've also moved the libraries from nativeBuildInputs
to buildInputs to be more semantically correct (and maybe support
cross compilation, not tested though).
 2020-01-01 20:37:38 +01:00
Alex Branham b9a558aaa4 R: Update CRAN and bioconductor packages 
Closes https://github.com/NixOS/nixpkgs/pull/75010.
 2019-12-16 18:56:49 +01:00
Peter Simons 9be0d6d4ae
Merge pull request #75021 from mnacamura/r-websocket 
rPackages.websocket: fix build
 2019-12-10 11:00:16 +01:00
Mitsuhiro Nakamura 350d358dea rPackages.websocket: fix build 2019-12-05 13:00:19 +09:00
adisbladis c9d8624ccd
treewide: Get rid of libGLU_combined 2019-11-18 20:10:43 +00:00
Nick Partridge 4d54c9e368 rPackages.glmnet: Add missing dependency 
Fixes the error:
    ld: library not found for -liconv
 2019-11-01 08:14:25 +10:00
Nick Partridge f21ac0e4dc rPackages.ModelMetrics: fix darwin build 
This fixes the error:

	auc_.cpp:2:10: fatal error: 'omp.h' file not found
	#include <omp.h>
 2019-10-31 10:10:55 +10:00
Peter Simons 7deb982d6a r-systemfonts: fix shebang of configure script 
Closes https://github.com/NixOS/nixpkgs/pull/70813.
 2019-10-10 20:50:49 +02:00
Dylan Simon 13085f13aa r-systemfonts: fix package dependencies 2019-10-10 20:50:49 +02:00
Peter Simons ca05a50d83 r-data.table: add missing zlib dependency to fix the build 2019-10-06 14:38:07 +02:00
Alex Branham 24f0ef530e R: Update CRAN and bioconductor packages 2019-10-06 14:38:07 +02:00
Vladimír Čunát eab41878ac
Merge branch 'master' into staging-next 2019-09-24 08:14:34 +02:00
Jörg Thalheim c89df5544e
Merge pull request #69333 from mnacamura/r-ucminf 
r-ucminf: fix build on Darwin
 2019-09-24 03:36:25 +01:00
Jörg Thalheim b47d81393d
Merge pull request #69330 from mnacamura/r-rf 
r-randomForest: fix build on Darwin
 2019-09-24 03:24:06 +01:00
Jörg Thalheim adc066fec9
Merge pull request #69332 from mnacamura/r-minqa 
r-minqa: fix build on Darwin
 2019-09-24 03:23:19 +01:00
Mitsuhiro Nakamura 8d64b03b0c r-ucminf: fix build on Darwin 2019-09-24 09:36:22 +09:00
Mitsuhiro Nakamura aefe6bc2e1 r-minqa: fix build on Darwin 2019-09-24 08:06:26 +09:00
Mitsuhiro Nakamura 3001a1f3ff r-pan: fix build on Darwin 2019-09-24 07:59:04 +09:00
Mitsuhiro Nakamura 8df7139996 r-randomForest: fix build on Darwin 2019-09-24 07:23:25 +09:00
Vladimír Čunát 22a216849b
Re-Revert "Merge branch 'staging-next'" 
This reverts commit f8a8fc6c7c.
 2019-09-22 09:38:09 +02:00
Vladimír Čunát f8a8fc6c7c
Revert "Merge branch 'staging-next'" 
This reverts commit 41af38f372, reversing
changes made to f0fec244ca.

Let's delay this.  We have some serious regressions.
 2019-09-21 20:05:09 +02:00
Izorkin 329a88efa7 treewide: replace mysql.connector-c to libmysqlclient 2019-09-09 15:55:34 +03:00
volth 7b8fb5c06c treewide: remove redundant quotes 2019-09-08 23:38:31 +00:00
cfhammill 8e5aae5a19 Fix broken builds for rgdal and sf R packages 
Builds were failing to include PROJ, depending on proj.dev
appears to fix it.
 2019-09-02 16:23:24 +03:00
Peter Simons 8ac6b77eff
Merge pull request #66204 from jabranham/r-pkgs 
R: Update CRAN and bioconductor packages
 2019-08-07 10:24:37 +02:00
Alex Branham eab786451f
R: Update CRAN and bioconductor packages 2019-08-06 08:49:39 -05:00
Dominic Steinitz 4788c7eb28 Ensure sundialr builds on macos. 2019-08-06 13:45:44 +01:00
Frederik Rietdijk 7cf5909fad Merge staging-next into staging 2019-07-09 15:44:08 +02:00
Thomas Tuegel 51d78034a1
wrapQtAppsHook: Remove ad hoc Qt wrappers 2019-07-05 10:42:08 -05:00
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
c0bw3b 9cb260d091 [treewide] delete unused patches 2019-05-04 19:52:24 +02:00
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
Alex Branham 48541ab6b9 R: update CRAN and BIOC package sets 
Closes https://github.com/NixOS/nixpkgs/pull/53414.
 2019-01-08 09:34:37 +01:00
Alex Branham 6f7459b40b
R: update CRAN package set 2018-12-12 11:17:25 -06:00
Edmund Wu a898f88d57
rstudioWrapper: include desktop file 2018-12-07 16:44:01 -05:00
Joachim F f0dbbdf970
Merge pull request #51581 from joachifm/rWrapper-local-runCommand 
Implement R wrappers as local-only runCommand
 2018-12-07 09:17:44 +00:00
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