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533 Commits

Author SHA1 Message Date
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: 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 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, but if clang needs help
  finding lld when it is used we should just pass it flags / put in the
  resource dir. Providing it at build time increases critical path
  length for no good reason.

----

A note on `nativeCC`:

`stdenv` takes tools from the previous stage, so:

1. `pkgsBuildBuild`: `(?1, x, x)`
2. `pkgsBuildBuild.stdenv.cc`: `(?0, ?1, x)`

while:

1. `pkgsBuildBuild`: `(?1, x, x)`
2. `pkgsBuildBuild.targetPackages`: `(x, x, ?2)`
3. `pkgsBuildBuild.targetPackages.stdenv.cc`: `(?1, x, x)`
 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