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
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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
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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
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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
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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
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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
