b12f/nixpkgs
1
0
Fork 0
Code Issues Pull requests Packages Projects Releases Wiki Activity
533279 commits 2 branches 0 tags 3.3 GiB
Commit graph

447 commits

Author SHA1 Message Date
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
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 9db967d700
rPackages.chebpol: fix fftw linking 2022-03-03 16:56:20 +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 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 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 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 f5cac4067c
rPackages: add maintainers to individual packages 2021-11-10 07:22:10 +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 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 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 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