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533 commits

Author SHA1 Message Date
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