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
71f1f4884b
("openssl: stop static binaries referencing libs"), which
was reverted in 195c7da07d
. One problem with my previous attempt is
that I moved OpenSSL's libraries to a lib output, but many dependent
packages were hardcoding the out output as the location of the
libraries. This patch fixes every such case I could find in the tree.
It won't have any effect immediately, but will mean these packages
will automatically use an OpenSSL lib output if it is reintroduced in
future.
This patch should cause very few rebuilds, because it shouldn't make
any change at all to most packages I'm touching. The few rebuilds
that are introduced come from when I've changed a package builder not
to use variable names like openssl.out in scripts / substitution
patterns, which would be confusing since they don't hardcode the
output any more.
I started by making the following global replacements:
${pkgs.openssl.out}/lib -> ${lib.getLib pkgs.openssl}/lib
${openssl.out}/lib -> ${lib.getLib openssl}/lib
Then I removed the ".out" suffix when part of the argument to
lib.makeLibraryPath, since that function uses lib.getLib internally.
Then I fixed up cases where openssl was part of the -L flag to the
compiler/linker, since that unambigously is referring to libraries.
Then I manually investigated and fixed the following packages:
- pycurl
- citrix-workspace
- ppp
- wraith
- unbound
- gambit
- acl2
I'm reasonably confindent in my fixes for all of them.
For acl2, since the openssl library paths are manually provided above
anyway, I don't think openssl is required separately as a build input
at all. Removing it doesn't make a difference to the output size, the
file list, or the closure.
I've tested evaluation with the OfBorg meta checks, to protect against
introducing evaluation failures.
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