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276 commits

Author SHA1 Message Date
Peter Simons 74c2af4ca7
Merge pull request #110050 from PhDyellow/master_plus_patches_3 
r-modules: fix gert build
 2021-01-20 09:05:51 +01:00
Jonathan Ringer 9bb3fccb5b treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix 
continuation of #109595

pkgconfig was aliased in 2018, however, it remained in
all-packages.nix due to its wide usage. This cleans
up the remaining references to pkgs.pkgsconfig and
moves the entry to aliases.nix.

python3Packages.pkgconfig remained unchanged because
it's the canonical name of the upstream package
on pypi.
 2021-01-19 01:16:25 -08:00
Peter Simons a15e4b69e7
Merge pull request #93590 from lblasc/r-packages 
R: remove qtbase.patch and fix few CRAN packages
 2021-01-18 21:22:57 +01:00
Phil Dyer a10b00e080 r-modules: fix gert build 
gert requires pkgs.libgit2 to build.
 2021-01-18 20:49:27 +10:00
Phil Dyer 364de6ddd2 r-modules: fix clustermq and rzmq build 
rzmq uses pkgconfig.

clustermq now incorporates ZMQ libs directly, rather than using
the rzmq package. clustermq now uses zeromq and pkgconfig.

Both packages needed patchShebangs, due to pkgconfig.
 2021-01-18 15:30:28 +10:00
Tikhon Jelvis 4203a4dabc Added suggested macOS fix and fixed data.table package. 
`data.table` had a `postInstall` step to rename `data.table.so` to `datatable.so`, but after the package bump the file was already called `datatable.so` and `mv` command would fail.
 2021-01-04 18:20:10 -08:00
Tikhon Jelvis 70cd2cb336 r-modules: update cran and bioc packages 
The last snapshot was 4 months ago (2020-08-19). I also found that I needed newer definitions when I was trying to fix the R arrow package.

This update required a couple of manual changes:

  1. Removing a few deleted packages from default.nix
  2. Renaming the "assert" package to "r_assert" in generate-r-packages.R because "assert" is a keyword in Nix
 2021-01-02 15:03:06 -08:00
Sandro a3f9335ed2
Merge pull request #101451 from moritzschaefer/fix-r-mirror-path 
fix package path for bioc server
 2020-11-27 01:58:30 +01:00
Luka Blaskovic 0601f34356 R: remove qtbase.patch and fix few CRAN packages 2020-11-05 06:42:38 +00:00
Moritz Schaefer dfba5e1c9b Fixes missing configure script 2020-10-23 14:40:18 +02:00
Moritz Schaefer 2eda0fbc5b fix package path for bioc server (http://mirrors.ustc.edu.cn/bioc/3.11/bioc/src/contrib/Archive/) 2020-10-23 11:46:53 +02:00
Justin Bedo 6bec22ee40
r-modules: bioc and cran update 2020-08-20 16:46:22 +10:00
Michele Guerini Rocco bb395a9a47
Merge pull request #91288 from rnhmjoj/zeromq 
Remove old zeromq 3.x packages
 2020-07-26 17:37:10 +02:00
cfhammill 3c503aa733 rpackages.RcppParallel: Patch shebang 
Fixes hydra build error
 2020-07-13 14:21:34 -04:00
rnhmjoj c7b3e54dff
rzmq: use default zeromq 2020-06-22 15:37:36 +02:00
Matt Wittmann 5b3f0c4f4a
r-statmod: Add libiconv to buildInputs 2020-05-14 20:00:58 -07:00
Peter Simons ec5d1a79d1
Merge pull request #82504 from mcwitt/fix/r-mvtnorm 
r-mvtnorm: add libiconv to buildInputs
 2020-05-11 20:38:42 +02:00
Alex Branham cb1a13ad98
R: Update CRAN and bioconductor packages 2020-04-26 17:16:34 -04:00
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
Matt Wittmann dcda9df724
r-mvtnorm: add libiconv to buildInputs 
Fixes build failure with `ld: library not found for -liconv`
 2020-03-13 10:33:27 -07:00
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
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
Dominic Steinitz 4788c7eb28 Ensure sundialr builds on macos. 2019-08-06 13:45:44 +01:00
Alex Branham 46bca1d643
R: Update CRAN and bioconductor packages 2019-07-02 15:48:06 -05:00