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597 Commits

Author SHA1 Message Date
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 
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
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