Justin Bedo
9db967d700
rPackages.chebpol: fix fftw linking
2022-03-03 16:56:20 +11:00
Justin Bedo
763671ce96
rPackages: CRAN and BioC update
2022-02-09 10:25:30 +11:00
Justin Bedo
145172b2c4
Merge remote-tracking branch 'origin/master' into r-updates
2022-02-09 10:25:07 +11:00
Naïm Favier
59be16611c
rPackages: fix evaluation
...
Removes uses of aliases
2022-02-08 11:29:12 -08:00
Justin Bedo
cb13e4e96d
rPackages.nloptr: fix build
...
Unnecessary to remove bundled source as it is unused during build.
2022-02-07 19:04:40 +11:00
Justin Bedo
dc636edd74
rPackages: CRAN and BioC update
2022-02-01 21:38:19 +11:00
cfhammill
fd51177e5c
rstudio-server, rstudioServerWrapper: init at rstudio.version (1.4.1717)
...
Co-authored-by: Justin Bedo <cu@cua0.org>
Co-authored-by: Jonathan Ringer <jonringer@users.noreply.github.com>
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
Co-authored-by: Benjamin Darwin <bcdarwin@gmail.com>
2022-01-17 10:24:37 +11:00
Justin Bedo
16216b2e04
rPackages.geomorph: fix build
2022-01-07 14:17:54 +11:00
Justin Bedo
cad7decdd2
rPackages.ragg: fix build
2022-01-07 14:10:44 +11:00
Justin Bedo
18b3b8e2a7
rPackages: CRAN and BioC update
2022-01-06 08:27:03 +11:00
Justin Bedo
02c59ff6e0
rPackages: CRAN and BioC update
2021-12-09 09:20:47 +11:00
Justin Bedo
13ab11bf60
rPackages: fix whitespace
2021-12-07 19:18:05 +11:00
Justin Bedo
03df8c8b88
rPackages.flowClust: x86 only
2021-12-07 09:23:21 +11:00
Justin Bedo
bd49665b8f
rPackages.x13binary: remove double occurance in broken list
2021-12-07 09:23:20 +11:00
Justin Bedo
bedc496dde
rPackages.RMariaDB: fix build
2021-12-07 09:23:14 +11:00
Justin Bedo
717914f31f
rPackages.DropletUtils: fix build
2021-12-07 09:20:31 +11:00
Justin Bedo
f4c82e0d62
rPackages.textshaping: fix build
2021-12-07 09:20:20 +11:00
Justin Bedo
8541b1178c
rPackages.RandomFieldsUtils: x86 only
2021-12-07 09:04:29 +11:00
Justin Bedo
ef010a832e
rPackages.V8: fix build on aarch64-linux
2021-12-05 07:43:22 +11:00
Justin Bedo
35fbf7a709
rPackages.{HiveR,HIBAG}: mark broken
2021-12-02 13:24:05 +11:00
Justin Bedo
aa8c9a8183
rPackages.MatchIt: fix build
...
patch no-longer applicable
2021-12-02 13:23:34 +11:00
Justin Bedo
10feaddf41
rPackages.HilbertVisGUI: fix build
2021-12-02 13:23:16 +11:00
Justin Bedo
f223a2b84d
rPackages.RcppBigIntAlgos: fix build
2021-12-02 13:22:50 +11:00
Justin Bedo
2d8306ef9d
rPackages.RcppAlgos: fix build
2021-12-02 13:22:17 +11:00
Justin Bedo
248f05a120
rPackages.PING: fix build
2021-12-02 13:21:55 +11:00
Justin Bedo
08b77f3886
rPackages.RcppMeCab: fix build
2021-12-02 13:21:30 +11:00
Justin Bedo
c520de648b
rPackages.Rrdrand: restrict to x86 architecture
2021-12-02 13:20:51 +11:00
Justin Bedo
e4a127c171
rPackages: allow overriding of platforms
2021-12-02 13:20:21 +11:00
Justin Bedo
b9adefed54
rPackages: CRAN and BioC update
2021-12-01 13:13:40 +11:00
Justin Bedo
113c1e3574
rPackages.rgl: fix build
2021-11-22 19:17:46 +11:00
Justin Bedo
502b9e7a1d
rPackages.ChIPXpress: disable hydra
...
Output is too large.
2021-11-21 11:27:34 +11:00
Justin Bedo
69bf9264a8
rPackages.{canceR,RcmdrPlugin_FuzzyClust,RcmdrPlugin_PcaRobust,uHMM}: fix build
2021-11-21 11:27:33 +11:00
Justin Bedo
257f13b85f
rPackages: disable hydra on annotations/experiments
2021-11-21 11:27:33 +11:00
Justin Bedo
5a7000ff27
rPackages.buildRPackage: set built-timestamp to epoch
2021-11-17 22:10:51 +11:00
Justin Bedo
31eccf77fd
rPackages: CRAN and BioC update
2021-11-15 22:12:32 +11:00
Justin Bedo
f5cac4067c
rPackages: add maintainers to individual packages
2021-11-10 07:22:10 +11:00
Justin Bedo
20de18c0a6
rPackages: CRAN and BioC update
2021-11-07 08:28:17 +11:00
Justin Bedo
e2c1e04a75
rPackages.HDF5Array: remove duplicate zlib dependency
2021-11-07 08:17:21 +11:00
Justin Bedő
7016c7df1c
Merge pull request #144820 from NixOS/r-updates
...
R,rPackages: R 4.1.1 -> 4.1.2, rPackages BioC 3.13 -> 3.14
2021-11-07 08:12:10 +11:00
coolneng
6220ede045
HDF5Array: fix build
2021-11-05 12:29:05 +01:00
Justin Bedo
30e8835d5c
rPackages.{HierO,tiledb,x13binary,switchr}: mark broken
2021-11-04 21:20:04 +11:00
Justin Bedo
9523357453
rPackages.systemPipeShiny: requires home
2021-11-04 21:19:29 +11:00
Justin Bedo
23b57f2e6a
rPackages.flowWorkspace: fix missing zlib dependency
2021-11-04 21:18:44 +11:00
Justin Bedo
40ff9b267f
rPackages.PoissonBionomial: fix missing dependency
2021-11-04 21:18:21 +11:00
Justin Bedo
a71c0e1615
rPackages.RmecabKo: fix missing dependency
2021-11-04 21:18:05 +11:00
Justin Bedo
6611a558d3
rPackages.{trackViewer,themetagenomics,NanoMethViz}: fix missing zlib dependencies
2021-11-04 21:17:35 +11:00
Justin Bedo
71723e1f68
rPackages.rrd: fix build
2021-11-04 21:16:51 +11:00
Justin Bedo
7264b569ac
rPackages.RcppCWB: fix build
2021-11-04 21:16:26 +11:00
Justin Bedo
ab946b5113
rPackages.{scModels,multibridge}: add mpfr dependency
2021-11-04 16:39:04 +11:00
Justin Bedo
c9ce16ee69
rPackages.valse: mark broken
2021-11-04 16:04:12 +11:00
Justin Bedo
cad71004f7
rPackages: fix builds requiring gsl
2021-11-04 16:04:03 +11:00
Justin Bedo
8920d6bce7
rPackages.nullrangesData: mark as broken
2021-11-04 09:30:20 +11:00
Justin Bedo
2b786e821c
rPackages.proj4: fix build
2021-11-04 09:30:11 +11:00
Justin Bedo
74aa5fc758
rPackages.{HDF5Array,FLAMES,ncdfFlow}: fix missing zlib dependency
2021-11-04 09:29:55 +11:00
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
3c6769b975
rPackages: CRAN and BioC update
2021-11-02 17:49:26 +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
7f8ec07897
rPackages: update CRAN and BIOC package sets
2021-10-22 14:35:36 +11:00
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: ef05fad51aef05fad51a
2021-10-01 04:20:00 +00:00
Justin Bedő
0bd43d11cc
Merge pull request #139609 from jbedo/r-updates
...
rPackages: update package set and fix some builds
2021-09-28 17:24:16 +10:00
Matthieu Coudron
639df4e23a
Merge pull request #139312 from jbedo/r-broken
...
rPackages: mark packages as broken when generating package sets
2021-09-27 10:32:30 +02:00
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 Bedo
f9067c45f1
rPackages: update package set
2021-09-27 18:14:08 +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 Bedo
9bc37bff1a
rPackages: mark packages as broken when generating package sets
...
The current behaviour for generate-r-packages.R is to delete
packages that have been remove upstream. This patch changes the
behaviour to mark packages as broken rather than removing them.
This has the advantage of never breaking expressions, which
previously occured when a package with overrides in default.nix
was deleted. As a result, the update procedure is simplified,
allowing automated updates to the package tree to run, and
additionally if a package is re-established upstream the previous
overrides still exist.
2021-09-24 21:25:53 +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
Phil Dyer
8b565e95a4
rPackages: generate-shell.nix works with --pure
...
generate-R-packages.R fails without these changes.
Without `cacert`, all wget/curl calls will fail
with an error about no valid certificates.
Without `nix`, calling `nix-hash` fails.
An impure nix-shell can get away with not adding
these if the system NIXPKGS version is the same
as the version of NIXPKGS used
with `nix-shell generate-shell.nix`
2021-09-15 11:12:17 +10:00
Phil Dyer
29fdc0ce2d
rPackages: autoset bioconductor ver to match R ver
...
BioConductor releases are tied to specific R releases.
Updating the package set now automatically selects the
correct version of bioconductor to match the current version of
R.
2021-09-15 11:09:17 +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
github-actions[bot]
6d46d8a9b9
Merge master into staging-next
2021-05-08 18:22:46 +00:00
Robert Hensing
8e3c5eb501
treewide: xvfb_run -> xvfb-run
2021-05-08 15:48:41 +02:00
Jake Gillberg
dbe770ed1e
remove references to archived CRAN packages
2021-05-06 23:16:20 -04:00
Jake Gillberg
0ec4668924
run generate-r-packages.R (cran and bioc*)
2021-05-06 11:27:08 -04:00
Jake Gillberg
758b17a0f5
bump bioc in generate-r-packages
2021-05-06 08:47:56 -04:00
Jake Gillberg
f695a3eb1c
bump cran
2021-05-05 12:56:44 -04:00
Andrew Childs
7869d16545
llvmPackages: Multuple outputs for everythting
...
Also begin to start work on cross compilation, though that will have to
be finished later.
The patches are based on the first version of
https://reviews.llvm.org/D99484 . It's very annoying to do the
back-porting but the review has uncovered nothing super major so I'm
fine sticking with what I've got.
Beyond making the outputs work, I also strove to re-sync the packages,
as they have been drifting pointlessly apart for some time.
----
Other misc notes, highly incomplete
- lvm-config-native and llvm-config are put in `dev` because they are
tools just for build time.
- Clang no longer has an lld dep. That was introduced in
db29857eb3
2021-04-30 05:41:00 +00:00
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
c4d8bd324f
r-arrow: update the library to version 3.0.0 to match the version of arrow-cpp
...
See https://github.com/NixOS/nixpkgs/issues/81761 for further details.
2021-02-16 12:47:21 +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
Peter Simons
39cb2244ff
Merge pull request #109717 from teto/fix-r-wrapper
...
rWrapper: use symlinkJoin instead of runCommand
2021-01-18 19:25:59 +01:00
Phil Dyer
a10b00e080
r-modules: fix gert build
...
gert requires pkgs.libgit2 to build.
2021-01-18 20:49:27 +10:00
Matthieu Coudron
ef156fb8ed
rWrapper: use symlinkJoin instead of runCommand
...
While trying to build a haskell-project I got:
Configuring library for inline-r-0.10.4..
cabal: The pkg-config package 'libR' version ==3.0 || >3.0 is required but it
could not be found.
the rWrapper was only bringing the R binary without its companion
library: this fixes it.
2021-01-18 10:35:35 +01:00
Phil Dyer
364de6ddd2
r-modules: fix clustermq and rzmq build
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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
Pavol Rusnak
cf2a67fef3
pkgs/development: stdenv.lib -> lib
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this takes care of the following folders in pkgs/development:
* arduino
* chez-modules
* go-packages
* guile-modules
* idris-modules
* perl-modules
* r-modules
* ruby-modules
2021-01-17 19:11:59 +01:00
Tikhon Jelvis
4203a4dabc
Added suggested macOS fix and fixed data.table package.
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`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
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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
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fix package path for bioc server
2020-11-27 01:58:30 +01:00
Graham Christensen
bc49a0815a
utillinux: rename to util-linux
2020-11-24 12:42:06 -05:00
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
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Remove old zeromq 3.x packages
2020-07-26 17:37:10 +02:00
cfhammill
3c503aa733
rpackages.RcppParallel: Patch shebang
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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
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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
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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
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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 )
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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'"
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This reverts commit f8a8fc6c7c
2019-09-22 09:38:09 +02:00
Vladimír Čunát
f8a8fc6c7c
Revert "Merge branch 'staging-next'"
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This reverts commit 41af38f372f0fec244ca
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
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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
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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
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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
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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
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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
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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
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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
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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
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Implement R wrappers as local-only runCommand
2018-12-07 09:17:44 +00:00
Christian Kauhaus
3b445042ac
rPackages.littler: fix build ( #51282 )
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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
Joachim Fasting
21d83e5b11
rstudioWrapper: use runCommand, local build only
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This seems more appropriate for a wrapper generator.
2018-12-05 20:59:41 +01:00
Joachim Fasting
d2b467a2de
rWrapper: use runCommand, local build only
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This seems more appropriate for a wrapper generator.
2018-12-05 20:59:35 +01:00
Timo Kaufmann
63b39af496
pythonPackages.rpy2: various fixes ( #51084 )
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- make sure libreadline is found at runtime
- make sure python libraries are found at runtime
- add libraries necessary to pass the testsuite and standard libraries
2018-11-27 18:24:37 +01:00
Massimo Redaelli
5afe1e7c70
rstudio: fix qt plugins not found
2018-11-23 23:10:29 +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
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Closes https://github.com/NixOS/nixpkgs/pull/49430 .
2018-11-02 17:50:18 +01:00
Rob Vermaas
3f719b0fad
Fix build for rPackages.units
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(cherry picked from commit 1eb1fec3aee1f1d1084779acec001e13ee9cbd71)
2018-10-08 12:53:43 +02:00
ivanbrennan
989f24befc
git2r: add SSH support
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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
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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
0a541aa38c
rPackages.buildRPackage: fix error if requireX is missing
2018-08-03 01:08:35 +09:00
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
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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
Peter Simons
49c649d573
R: update CRAN package set to snapshot 2018-07-06
2018-07-07 12:10:46 +02:00
Peter Simons
d984656a2a
R: update package set
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The CRAN snapshot is at "2018-07-03". Bioc is now at 3.8.
2018-07-07 12:10:46 +02:00
Markus Ankenbrand
9eeea0b9ef
rPackages.rhdf5: fix installation
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Fix #42878
2018-07-02 18:51:18 +02:00
Daiderd Jordan
654960c1cd
Merge pull request #42290 from mnacamura/r-igraph-darwin
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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
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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
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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
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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
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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
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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
Shea Levy
05e375d710
Merge remote-tracking branch 'origin/master' into staging
2018-03-28 09:36:47 -04:00
Graham Christensen
92d53362d4
Move all nixpkgs doc files in to the doc directory
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This makes a makefile-driven developer workflow nicer.
2018-03-25 19:52:00 -04:00
Matthew Bauer
9109a90479
treewide: remove some more gettext references
2018-03-22 16:50:14 -05:00
