Bruno Rodrigues
cee2b321f6
rPackages.TDA: fixed build
2024-02-18 20:32:52 +01:00
Bruno Rodrigues
bd37cac455
rPackages.GeneralizedWendland: added deps to fix build
2024-02-18 20:01:29 +01:00
Bruno Rodrigues
cc5deb282e
rPackages.bioacoustics: added deps to fix build
2024-02-18 19:37:45 +01:00
Bruno Rodrigues
4e61655eba
rPackages.poisbinom: added dep
2024-02-18 19:28:50 +01:00
Bruno Rodrigues
82cb3d3ca1
rPackages.vcfppR: fixed build
2024-02-16 16:16:36 +01:00
Bruno Rodrigues
bbd656149e
rPackages.vdiffr: fixed build
2024-02-16 15:49:42 +01:00
Bruno Rodrigues
d1d551370f
rPackages.zlib: fix build
2024-02-16 14:54:24 +01:00
Bruno Rodrigues
95623b60be
rPackages.highs: fix build
2024-02-16 10:36:13 +01:00
Bruno Rodrigues
4c1abf10d9
rPackages.MAGEE: fixed build
2024-02-16 10:23:00 +01:00
Bruno Rodrigues
252a17a97d
rPackages.LOMAR: added dependency
2024-02-16 10:11:31 +01:00
Bruno Rodrigues
be902cb365
rPackages.Cyclops: fixed build
2024-02-16 09:50:10 +01:00
Bruno Rodrigues
47281231f3
rPackages.GPBayes: added dependency
2024-02-16 09:27:32 +01:00
Justin Bedő
4a72b618e4
Merge pull request #288659 from b-rodrigues/fix_poissonmultinomial
...
rPackages.PoissonMultinomial: added dependency
2024-02-16 13:08:39 +11:00
Justin Bedő
53bdd2cb60
Merge pull request #288658 from b-rodrigues/fix_strawr
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rPackages.strawr: added dependency
2024-02-16 13:05:07 +11:00
Justin Bedő
e388752036
Merge pull request #288655 from b-rodrigues/fix_apcf
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rPackages.apcf: add dependency
2024-02-16 13:02:53 +11:00
Justin Bedő
2f3b27ae27
Merge pull request #287244 from b-rodrigues/rpackages.archive
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rPackages.archive: added dependency
2024-02-16 12:58:42 +11:00
László Kupcsik
d6778cb518
rPackages.CytoML: fix build failure
...
Adds libxml to the nativeBuildInputs
2024-02-13 22:21:41 +01:00
Bruno Rodrigues
3ee7340f3d
rPackages.PoissonMultinomial: added dependency
2024-02-13 21:41:08 +01:00
Bruno Rodrigues
f74cea2c6c
rPackages.strawr: added dependency
2024-02-13 21:31:26 +01:00
Bruno Rodrigues
cdc9b2e29c
rPackages.apcf: add dependency
2024-02-13 21:25:55 +01:00
Bruno Rodrigues
6b759628f4
rPackages.archive: added dependency
2024-02-13 09:20:47 +00:00
Justin Bedő
f02a2b73e0
Merge pull request #287327 from b-rodrigues/fix_cellbarcode
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rPackages.CellBarcode: added dependency
2024-02-13 09:48:17 +11:00
Justin Bedő
c5c37f5b0c
Merge pull request #287271 from b-rodrigues/fix_excursions
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rPackages.excursions: added dependency
2024-02-13 09:30:12 +11:00
Bruno Rodrigues
ef9135062b
rPackages.CellBarcode: added dependency
2024-02-08 23:33:00 +01:00
Bruno Rodrigues
2f47fb0831
rPackages.excursions: added dependency
2024-02-08 17:44:12 +01:00
Bruno Rodrigues
83c9e4e910
rPackages.SuperGauss: add dependencies
2024-02-08 10:22:47 +01:00
Derek Hansen
aa866f5189
rPackages.rhdf5: fix build on aarch64-darwin
2024-02-06 17:06:10 -05:00
Sandro Jäckel
653837881e
treewide: replace lib/${python.libPrefix}/site-packages with its shorthand ${python.sitePackages}
...
which should be always preferred
2024-01-30 19:56:57 +01:00
TomaSajt
eea9674ac5
rPackages.bsts: 0.9.9 -> 0.9.10
2024-01-18 08:34:56 +01:00
Justin Bedo
9941724e23
rPackages.rhdf5filters: simplify patch
2024-01-17 09:34:31 +11:00
Justin Bedo
a947ea124a
rPackages.rhdf5filters: fix build
2024-01-15 16:07:47 +11:00
Justin Bedo
1030e1fc2d
rPackages.httr2: fix build
2024-01-15 16:07:47 +11:00
Vladimír Čunát
671c34fdc4
Merge branch 'master' into r-updates
2024-01-12 20:18:05 +01:00
TomaSajt
e6fb2723aa
rPackages.multibridge: fix build
2024-01-10 02:21:46 +01:00
Justin Bedo
41fb6ea81b
rPackages: CRAN and BioC update
2024-01-10 11:53:53 +11:00
Justin Bedo
f1ea01f944
rPackages.tesseract: fix build
2023-12-13 13:22:43 +11:00
Justin Bedő
0ec1ec8d76
Merge pull request #269991 from TomaSajt/fix-r-xlconnect
...
rPackages.XLConnect: fix build
2023-11-26 15:48:18 +11:00
TomaSajt
7474a2f4f7
rPackages.XLConnect: fix build
2023-11-25 22:18:29 +01:00
TomaSajt
53014d2701
rPackages.redux: fix build
2023-11-25 19:39:12 +01:00
Justin Bedő
3367c3b552
Merge pull request #263039 from NixOS/r-updates
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rPackages: CRAN and BioC update
2023-11-07 10:02:17 +11:00
Vincenzo Mantova
2a0440c2a4
rPackages: replace texlive.combined.scheme-medium with texliveMedium
2023-11-05 11:56:03 +00:00
Justin Bedo
b0a0f9856d
rPackages.httpuv: fix build
2023-10-26 21:24:21 +11:00
Justin Bedo
af63e7a15d
rPackages: CRAN and BioC update
2023-10-24 09:21:33 +11:00
nviets
bcbe587526
rPackages.quarto: add quarto to propagatedBuildInputs
2023-10-18 14:44:33 -05:00
Dominic Steinitz
f6e9496176
Make rPackage.sf build fixes 257221
2023-09-25 09:39:56 +01:00
Justin Bedo
6e903b7b7e
rPackages.pandoc: fix pandoc linking
2023-09-15 14:08:30 +10:00
Savyasachee Jha
953b2d706b
python310Packages.radian: 0.6.6 -> 0.6.7
2023-08-21 22:28:53 +05:30
Justin Bedo
1441d0080a
rPackages.spaMM: fix build
2023-08-14 09:20:19 +10:00
Justin Bedo
7befcff38e
rPackages.webp: fix build
2023-08-14 09:13:22 +10:00
Justin Bedo
5a0314fb3d
rPackages.ijtiff: fix build
2023-08-14 09:12:09 +10:00
Justin Bedo
11a5b1a80e
rPackages.xslt: fix build
2023-08-14 09:10:06 +10:00
Justin Bedo
7215aa7e36
rPackages.symengine: disable vendoring
2023-08-14 09:07:57 +10:00
Justin Bedo
9c648710b9
rPackages.redland: fix build
2023-08-13 13:08:37 +10:00
Justin Bedo
720895e124
rPackages: CRAN and BioC update
2023-08-11 09:12:08 +10:00
Justin Bedo
95f039acd7
rPackages.ROracle: add dependency
2023-08-04 14:37:33 +10:00
fortuneteller2k
7a1ff1ae89
rPackages.pbdZMQ: use zeromq from nixpkgs instead of vendored copy
...
also fixes aarch64-darwin in the process
2023-07-04 18:27:28 +08:00
Justin Bedo
bc592fb843
rPackages.torch: fix build
2023-06-27 23:28:33 +10:00
Justin Bedo
4ef0369ff2
rPackages: CRAN and BioC update
2023-06-26 18:51:26 +10:00
Justin Bedo
f5e7c1c474
rPackages.data_table: add required pkg-config dependency
2023-06-08 09:21:23 +10:00
Justin Bedo
8ac4225a0e
rPackages.rvg: add dependency
2023-06-02 16:12:10 +10:00
Justin Bedo
63d60675b2
rPackages.rhdf5filters: update patch
2023-06-01 08:28:33 +10:00
Justin Bedo
7798454aae
rPackages: CRAN and BioC update
2023-05-30 17:51:17 +10:00
Justin Bedő
9fed7877db
Merge pull request #226447 from savyajha/radian-wrapper-fix
...
radianWrapper: Explicitly set R_HOME and always have R in buildInputs
2023-04-30 08:18:09 +10:00
Savyasachee Jha
e7c6fb0f86
radianWrapper: Explicitly set R_HOME and always have R in buildInputs
...
Before this commit, `wrapR = false` (the default) would lead to
situations where the `RHOME` variable would not be found. Adding `--set
R_HOME ${R}/lib/R` so that the wrapper explicitly exports `R_HOME` fixes
this issue. In addition, R is also made part of `buildInputs` by default
so that package loading works correctly.
2023-04-29 18:24:06 +05:30
Weijia Wang
19b7602cbd
rPackages.textshaping: fix build on darwin
2023-04-26 10:48:33 +03:00
Justin Bedo
0963a3a36b
rPackages: CRAN and BioC update
2023-04-06 09:11:41 +10:00
Justin Bedo
bb87f24392
rPackages: regenerate CRAN hashes
2023-04-05 13:25:07 +10:00
Justin Bedo
3e6b47a007
rPackages: switch to official CRAN mirrors
2023-04-05 13:25:06 +10:00
Justin Bedo
d8d5d73bac
rPackages.Rhdf5lib: enable cxx bindings
2023-03-24 09:47:44 +11:00
Justin Bedo
445df9ef48
rPackages.Rhdflib: patch linking flags
2023-03-23 15:19:58 +11:00
Justin Bedo
14db22f868
rPackages.rhdf5: fix build
...
use nixpkgs provided hdf5 instead of vendored library
2023-03-22 09:48:06 +11:00
Justin Bedo
442e1b87d1
rPackages.rhdf5filters: fix build
...
- use hdf5-blosc from nixpkgs to fix failing vendored build
- add missing build dependencies
2023-03-22 09:47:58 +11:00
Justin Bedo
ccfbc19630
rPackages.Rhdf5lib: fix build
...
use nixpkgs provided hdf5 and libaec to resolve failing vendored code
2023-03-22 09:47:48 +11:00
Justin Bedo
a10887cb3f
rPackages.purrr: patch configure shebang
2023-03-16 22:10:42 +11:00
Justin Bedo
0c0c6908b9
rPackages: CRAN and BioC update
2023-03-16 21:32:06 +11:00
Sandro
46e5d1e231
Merge pull request #217517 from savyajha/radian
2023-03-10 23:11:26 +01:00
Justin Bedő
4f4a054dd2
Merge pull request #219439 from nviets/sparklyr
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rPackages: sparklyr environment variables
2023-03-08 03:52:05 +00:00
Nathan Viets
2f430da1c6
Replacing MRAN mirror with posit
2023-03-07 18:23:26 +01:00
nviets
7939447527
Update pkgs/development/r-modules/default.nix
...
Co-authored-by: Justin Bedő <cu@cua0.org>
2023-03-07 11:08:38 +01:00
nviets
62821edd2e
This PR sets default SPARK_HOME and JAVA_HOME for R's sparklyr package using a patch in .onload. Preset value take precedence. SPARK_HOME points to python3Packages.pyspark rather than pkgs.spark because the former is actively maintained.
2023-03-06 12:03:04 +01:00
Savyasachee Jha
e730867dc0
python310Packages.radian: init at 0.6.4 and provide radianWrapper
2023-03-05 19:12:32 +05:30
K900
3dccc7c365
r-modules: fix eval
...
Not sure how this worked before. Now it at least evals.
2023-02-24 22:45:28 +03:00
Artturin
5110d8b6fb
rPackages: s/overrideDerivation/overrideAttrs
...
and attrs.NIX_CFLAGS_COMPILE to attrs.env.NIX_CFLAGS_COMPILE
https://nixos.org/manual/nixpkgs/stable/#sec-pkg-overrideDerivation
> Do not use this function in Nixpkgs as it evaluates a Derivation before modifying it, which breaks package abstraction and removes error-checking of function arguments
2023-02-23 18:45:41 +02:00
Artturin
f9fdf2d402
treewide: move NIX_CFLAGS_COMPILE to the env attrset
...
with structuredAttrs lists will be bash arrays which cannot be exported
which will be a issue with some patches and some wrappers like cc-wrapper
this makes it clearer that NIX_CFLAGS_COMPILE must be a string as lists
in env cause a eval failure
2023-02-22 21:23:04 +02:00
nviets
dcd759fe65
rPackages.quarto: add quarto dependency
2023-02-17 03:25:35 +00:00
Justin Bedő
d92d0a1e54
Merge pull request #212537 from nviets/nanonext
...
nng: 1.5.2 -> 1.6.0-prerelease and to rPackages.nanonext dependencies
2023-02-07 02:07:00 +00:00
Nathan Viets
67e898c12e
nng: 1.5.2 -> 1.6.0-prerelease and rPackages.nanonext dependency
2023-02-06 18:49:06 -06:00
Nathan Viets
3f5c9df651
rPackages: added libiconv to darwin builds and removed redundant package level calls
2023-02-07 09:39:53 +11:00
Chris Warburton
802527baa2
rPackages.classInt: add libiconv dependency to fix build on darwin
...
Avoids 'ld: library not found for -liconv' on x86_64-darwin
2023-01-06 12:05:12 +00:00
Justin Bedo
7ed992a3fb
rPackages: CRAN and BioC update
2022-12-15 08:51:33 +11:00
Justin Bedő
e442f93a8c
Merge pull request #204684 from trofi/rPackages.devEMF-without-xlibsWrapper
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rPackages.devEMF: use xorg.* packages directly instead of xlibsWrappe…
2022-12-06 07:22:53 +00:00
Justin Bedő
43f39630df
Merge pull request #204550 from trofi/rPackages.imager-without-xlibsWrapper
...
rPackages.imager: use xorg.* packages directly instead of xlibsWrappe…
2022-12-06 07:16:01 +00:00
Sergei Trofimovich
b2b5c4db0b
rPackages.Cairo: use xorg.* packages directly instead of xlibsWrapper indirection
...
Validated as no change in `out` output with `diffoscope`.
2022-12-05 21:22:13 +00:00
Sergei Trofimovich
a2fbaae04a
rPackages.devEMF: use xorg.* packages directly instead of xlibsWrapper indirection
...
Validated as no change in `out` output with `diffoscope`.
2022-12-05 21:16:38 +00:00
Sergei Trofimovich
c5b0d1ec8e
rPackages.imager: use xorg.* packages directly instead of xlibsWrapper indirection
...
Validated as no change in `out` output with `diffoscope`.
2022-12-04 22:36:36 +00:00
Sergei Trofimovich
2d36d576f8
rPackages.rgl: use xorg.* packages directly instead of xlibsWrapper indirection
...
Validated as no change in `out` output with `diffoscope`.
2022-12-04 18:44:31 +00:00
Mario Rodas
e76e9ed99c
rPackages.bigmemory: fix evaluation on darwin
...
On Darwin pkgs.libuuid is null, hence evaluating `.dev` fails.
2022-11-24 01:46:29 -05:00
Justin Bedo
1249b08676
rPackages.RNifti: fix build
2022-11-02 10:14:57 +11:00
Justin Bedo
644b5a7ac7
rPackages.bigmemory: add missing dependency
2022-11-02 10:11:53 +11:00
Justin Bedo
3f86920ae8
rPackages: CRAN and BioC update
2022-10-31 13:46:43 +11:00
Justin Bedő
abe366dd5c
Merge pull request #196979 from Et7f3/fix-deldir
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deldir: specify iconv library for darwin.
2022-10-23 23:57:56 +00:00
Et7f3
e8327603e1
rPackages.interp: specify iconv library for darwin
2022-10-21 21:21:34 +02:00
Et7f3
a88371fb6d
rPackages.deldir: specify iconv library for darwin
2022-10-20 23:45:16 +02:00
Nicolas Benes
7396451d6c
rPackages.mzR: unpin boost
...
`mzR` currently ships and builds its own copy of boost-176, see
https://github.com/sneumann/mzR/blob/master/src/README.updateboost
2022-10-20 17:41:35 +02:00
Matthieu Coudron
8e7161ed80
rPackages.rmarkdown: add pandoc as buildInput
...
https://github.com/rstudio/rmarkdown/blob/main/DESCRIPTION#L91 requires pandoc from system
2022-09-30 12:40:07 +02:00
Theodore Ni
e0a5a1c3a0
rPackages: reenable stackprotector on aarch64-darwin
...
The original error that required disabling the stack protector on
aarch64-darwin has been fixed in GCC.
2022-09-04 11:47:02 -07:00
Justin Bedo
ba3564f74b
rPackages.s2: fix openssl linking
2022-08-22 11:41:09 +10:00
Justin Bedo
d7bf754c96
rPackages: CRAN and BioC update
2022-08-18 07:11:43 +10:00
Justin Bedo
09528e6db8
rPackages: CRAN and BioC update
2022-07-02 22:36:01 +10:00
hqurve
1fc4712f15
rPackages.gifski: fix build
2022-06-18 20:37:09 -04:00
Justin Bedo
f07c969b8d
rPackages: CRAN and BioC update
2022-05-17 13:34:56 +10:00
Justin Bedo
42caad601b
rPackages.Rhdf5lib: propagate hdf5 dependency
...
Packages that depend on Rhdf5lib also require the dev hdf5 outputs
for correct functionality.
2022-05-15 08:49:46 +10:00
Justin Bedo
72c388eed4
rPackages.Rhdf5lib: fix build
...
Patch is no-longer necessary; HDF5 no-longer vendored
2022-05-06 10:54:43 +10:00
Justin Bedo
db5e7f7a92
rPackages: CRAN and BioC update
2022-04-27 09:56:24 +10:00
Justin Bedo
6675a16146
rPackages: CRAN and BioC update
2022-04-11 11:31:14 +10:00
Ben Siraphob
0d95d03c98
Merge pull request #165765 from ConnorBaker/patch-1
2022-04-04 16:56:52 -05:00
Alyssa Ross
fd78240ac8
treewide: use lib.getLib for OpenSSL libraries
...
At some point, I'd like to make another attempt at
71f1f4884b195c7da07d
2022-03-30 15:10:00 +00:00
Connor Baker
f50e41bfd6
rPackages: nloptr requires libiconv
2022-03-25 14:36:43 -04:00
Connor Baker
78a439e514
rPackages: Disable stackprotector on aarch64-darwin
...
Some derivations, like `rPackages.KernSmooth`, fail to build on `aarch64-darwin` because `stackprotector` is enabled.
This is similar to the fix required to get R itself working on `aarch64-darwin`: https://github.com/NixOS/nixpkgs/pull/158992 .
2022-03-25 11:35:37 -04:00
Justin Bedo
e599d1ce98
rPackages.qqconf: add missing FFTW and pkg-config dependencies
2022-03-14 13:50:38 +11:00
Justin Bedo
95d69d32d9
rPackages.RNifti: use nixpkgs zlib
...
Build was failing due to incorrect zlib macro expansion.
Patch to use nixpkgs zlib rather than vendored copy.
2022-03-14 13:50:02 +11:00
Justin Bedo
f67c61e0d5
rPackages: CRAN and BioC update
2022-03-11 09:32:17 +11:00
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
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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
...
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
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
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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
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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
