Commit graph

447 commits

Author SHA1 Message Date
Justin Bedo 93168abf30
rPackages.rawrr: fix missing mono dependency 2021-11-04 09:29:41 +11:00
Justin Bedo a451b3441f
rPackages.arrow: fix build 2021-11-04 09:04:28 +11:00
Justin Bedo 803ae4b5f3
rPackages.{fixest,paxtoolsr}: fix new builds requiring home 2021-11-04 09:03:44 +11:00
Justin Bedo 9f69e37ccc
rPackages: fix builds requiring gsl 2021-11-01 19:39:52 +11:00
Justin Bedo ed24de47ab
rPackages: fix builds requiring home 2021-11-01 18:24:56 +11:00
Justin Bedo 92ed7e16b6
rPackages.RoBMA: fix missing dependency 2021-11-01 17:44:53 +11:00
Justin Bedo 1f0317cd5b
rPackages.BayesXsrc: fix build 2021-10-26 09:31:32 +11:00
Justin Bedo 69c284c3c0
rPackages: fix compression library dependencies 2021-10-25 18:12:13 +11:00
Justin Bedo 7aa68ac8ae
rPackages: fix packages requiring home during build 2021-10-25 18:12:12 +11:00
tpob e3a5f66a77 fix httpgd cairo dependency missing 2021-10-25 09:36:02 +08:00
Justin Bedo 71eeb7ee56
Merge remote-tracking branch 'origin/master' into r-updates 2021-10-17 21:41:51 +11:00
Justin Bedo b1d8a801a0
rPackages.mzR: fix aarch64-linux build 2021-10-16 07:44:35 +11:00
Justin Bedo e26f35b8ce
rPackages.h2o: disable JAR fetching while in nix build 2021-10-15 11:22:46 +11:00
Justin Bedo 4c96ee566d
rPackages.CNEr: fix build 2021-10-13 07:02:08 +11:00
Justin Bedo db5b03ba89
rPackages.EMCluster: fix build 2021-10-13 06:59:10 +11:00
Justin Bedo 0e6a38a1b0
rPackages.DiffBind: fix build 2021-10-13 06:56:35 +11:00
Justin Bedo a644e88ab4
rPackages.DirichletMultinomial: fix build 2021-10-13 06:51:43 +11:00
Justin Bedo 7af2111792
rPackages.proj4: mark as broken 2021-10-12 09:05:10 +11:00
Justin Bedo 09730dc399
rPackages.av: mark as broken 2021-10-12 08:37:18 +11:00
Justin Bedo 403bcccbb3
rPackages.R_cache: shift override to requiring home framework 2021-10-12 08:18:04 +11:00
Justin Bedo 83ada1edee
rPackages: mark R.cache depenencies as requiring home 2021-10-12 08:15:26 +11:00
Justin Bedo 6dbe815676
rPackages.keyring: fix build 2021-10-12 08:14:36 +11:00
Justin Bedo 95c7c9555a
rPackages.mzR: fix build 2021-10-12 08:14:36 +11:00
Justin Bedo 07bf8a26b7
rPackages.x13binary: mark broken 2021-10-11 22:26:11 +11:00
Justin Bedo a50b96d990
rPackages.ggiraph: fix build 2021-10-11 22:21:25 +11:00
Justin Bedo e6bf94c615
rPackages.OmnipathR: fix build 2021-10-11 22:11:22 +11:00
Justin Bedo 7f9e8c1d42
rPackages.NetLogoR: mark as broken 2021-10-11 22:10:41 +11:00
Justin Bedo 2ab8998641
rPackages.MatchIt: backport build patch 2021-10-11 22:10:41 +11:00
Justin Bedo 22e4ee209e
rPackages: unpin all GSL 1 dependencies
All packages now successfully build against current GSL.
2021-10-11 22:10:41 +11:00
Justin Bedo 5e49d8461a
rPackages.rgl: mark as broken 2021-10-11 22:10:40 +11:00
Thomas Churchman c417b44d83
rPackages: introduce packagesRequiringHome override
Some R packages require access to a home directory to pass install tests. Extend
r-modules to allow creating a temporary home directory for packages with
such requirements.
2021-10-11 18:23:42 +11:00
Justin Bedő 68f25d5a86
Merge pull request #140170 from marsam/r-hydra
R: don't restrict hydraPlatforms
2021-10-07 08:54:26 +11:00
Peter Simons d8e6e07af0 r-httpuv: add missing zlib.dev dependency to fix the build 2021-10-04 08:04:02 +02:00
Mario Rodas 4662abd3b4 R: don't restrict hydraPlatforms
The restriction of hydraPlatforms was added in [1: ef05fad51a], but
doesn't seem to be a real reason behind it. R is Free Software and it
take takes a few minutes to build so I believe it can be distributed by
Hydra.

1: 2014-05-04 ef05fad51a
   R: don't restrict meta.platforms to Linux; other architectures should build fine
2021-10-01 04:20:00 +00:00
Justin Bedo 831fa2f7b9
rPackages.csaw: fix build 2021-09-27 18:17:57 +10:00
Justin Bedo 5ed5a62cae
rPackages.Rhtslib: passthrough libcurl to dependents correctly 2021-09-27 18:17:52 +10:00
Justin Bedo a0802ef5a5
rPackages.gaston: fix build 2021-09-27 18:17:45 +10:00
Justin Bedo ff0b840c6c
rPackages.Rbowtie: fix build 2021-09-27 18:17:40 +10:00
Justin Bedo c60aa79a64
rPackages.spp: fix build 2021-09-27 18:17:35 +10:00
Justin Bedo 2bed59ab86
rPackages.loon: fix build 2021-09-27 18:17:30 +10:00
Justin Bedo 17ffaf2a07
rPackages.arrangements: fix build 2021-09-27 18:17:24 +10:00
Justin Bedo 1af3c32897
rPackages.sodium: fix build 2021-09-27 18:17:19 +10:00
Justin Bedo e1c796341a
rPackages.bio3d: fix build 2021-09-27 18:17:12 +10:00
Justin Bedo ff6652c17c
rPackages.vcfR: fix build 2021-09-27 18:17:07 +10:00
Justin Bedo d17b097899
rPackages.ggbio: fix build 2021-09-27 18:17:00 +10:00
Justin Bedo fcd7af4a53
rPackages.qpdf: fix build 2021-09-27 18:16:54 +10:00
Justin Bedo 6df27f3109
rPackages.writexl: add zlib dependency 2021-09-27 18:16:48 +10:00
Justin Bedo 353fea8792
rPackages.bbl: add missing gsl dependency 2021-09-27 18:16:39 +10:00
Justin Bedo 3f72620275
rPackages.ArrayExpressHTS: add missing buildInputs 2021-09-27 18:16:32 +10:00
Justin Bedo 85f963caca
rPackages.s2: add missing buildInput 2021-09-27 18:16:25 +10:00
Justin Bedő 6f333e8723
Merge pull request #136964 from jbedo/rPackages-RclusTool
rPackages.RclusTool: add to packges requiring X
2021-09-25 22:33:42 +10:00
Justin Bedő 29595eba18
Merge pull request #127790 from PhDyellow/r_bioc_updater_revised
r-modules: R bioc updater revised
2021-09-16 09:36:18 +00:00
Phil Dyer 96eb04ef7a rPackages: improve formatting in default.nix 2021-09-15 11:17:41 +10:00
Maciej Krüger a286dc9ef2
rPackages.RMySQL: fix package 2021-09-13 13:50:35 +02:00
Justin Bedo 006c32f161
rPackages.RclusTool: add to packges requiring X 2021-09-07 16:34:43 +10:00
Justin Bedo 6af74c9ff8
rPackages.ssh: include missing libssh buildInput 2021-09-07 11:32:15 +10:00
Phil Dyer 174c5e166e r-modules: revert changes to lwgeom 2021-08-24 21:16:51 +10:00
Phil Dyer d7ac07cdbb r-modules: fix r package build failures
r-modules: fix r package system dependencies

r-modules: fix terra package dependencies

r-modules: fix edge case for R package import

The R package "import" has a name that clashes
with the nix function "import". The package
name in nixpkgs is correctly modified to
avoid the clash, but the name of the
R package was also being changed in
cran-packages.nix, which broke downloading
of the package.

cran-packages.nix has been manually patched,
and genreate-r-packages.R has been fixed so
future automatic updates will succeed.

r-modules: fix repeated `pkgs.` and svglite
2021-08-24 09:11:14 +10:00
Josh Moller-Mara f787c0b130 rPackages.rsvg: fix build
rsvg needs pkg-config and development headers from librsvg to build
2021-08-17 22:59:19 -07:00
Artturi 1f8e01479b
Merge pull request #125556 from ivan-tkatchev/rhdf5
rhdf5: fix build (#125101)
2021-08-07 02:29:52 +03:00
Manuel Bärenz 4e75706a46 rPackages.svglite: Fix nativeBuildInputs 2021-06-30 00:03:02 -07:00
Peter Simons 53b797c185
Merge pull request #121819 from Jake-Gillberg/bump-r-cran
bump R packages
2021-06-24 16:41:01 +02:00
Ivan Tkatchev 2854b52437
rPackages.hdf5r: add missing depedency on pkgs.hdf5 (#125549)
Co-authored-by: Ivan Tkatchev <tkatchev@gmail.com>
2021-06-06 02:12:22 +02:00
Ivan Tkatchev 634ac0e565 rhdf5: fix build (#125101) 2021-06-03 22:29:59 +03:00
Alvar Penning 8bf4f7e2f3 rPackages.lwgeom: fix build 2021-05-24 19:09:06 +02:00
Florian Beeres 7ee9a6642b rPackages.RcppArmadillo: fix darwin
RcppArmadillo requires libiconv on darwin to build successfully
2021-05-17 17:40:04 +02:00
Jake Gillberg dbe770ed1e remove references to archived CRAN packages 2021-05-06 23:16:20 -04:00
Sandro Jäckel 3453b89f4b
lzma: deprecate alias 2021-04-04 19:49:52 +02:00
Samuel Gräfenstein 819ab46fe7
treewide: pkgconfig -> pkg-config
Fix building with `config.allowAliases = false;`.
2021-03-17 00:00:19 +01:00
Peter Simons 64b5504939 r-arrow: add missing arrow-cpp dependency to the build
See https://github.com/NixOS/nixpkgs/issues/81761 for further details.
2021-02-16 12:47:21 +01:00
Markus Kowalewski 6dba41fbcb
mpi: use mpi attribute consistently as the default MPI implementations
Use the attribute mpi to provide a system wide default MPI
implementation. The default is openmpi (as before).
This now allows for overriding the MPI implentation by using
the overlay mechanism. Build all packages with mpich instead
of the default openmpi can now be achived like this:
self: super:
 {
   mpi = super.mpich;
 }

All derivations that have been using "mpi ? null" to provide optional
building with MPI have been change in the following way to allow for
optional builds with MPI:
{ ...
, mpi
, useMpi ? false
}
2021-01-23 12:15:13 +01:00
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
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 1eb1fec3aee1f1d1084779acec001e13ee9cbd71)
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