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455 commits

Author SHA1 Message Date
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