Commit graph

291 commits

Author SHA1 Message Date
James D. Trotter 518fb60797 fenics: init at 2017.1.0 2017-08-15 16:19:45 +02:00
Frederik Rietdijk b14efb6a6c Merge pull request #28211 from mimadrid/update/samtools-1.5.0
samtools: 1.4.0 -> 1.5.0
2017-08-13 22:32:48 +02:00
mimadrid 302e7825fa
htslib: 1.4.0 -> 1.5.0 2017-08-13 00:16:42 +02:00
mimadrid 09e0cc7cc7
Update homepage attributes: http -> https
Homepage link "http://.../" is a permanent redirect to "https://.../" and should be updated
https://repology.org/repository/nix_stable/problems
2017-08-03 11:56:15 +02:00
Silvan Mosberger f5fa5fa4d6 pkgs: refactor needless quoting of homepage meta attribute (#27809)
* pkgs: refactor needless quoting of homepage meta attribute

A lot of packages are needlessly quoting the homepage meta attribute
(about 1400, 22%), this commit refactors all of those instances.

* pkgs: Fixing some links that were wrongfully unquoted in the previous
commit

* Fixed some instances
2017-08-01 22:03:30 +02:00
Frederik Rietdijk ec59e3b3f5 openblas: 0.2.19 -> 0.2.20 2017-07-28 18:08:06 +02:00
Nikolay Amiantov 5fdc1e763f ipopt: 3.12.6 -> 2.12.8 2017-07-27 17:07:44 +03:00
Ben Darwin d1d0824b2f elastix: change platforms to "linux" from "unix" 2017-07-19 17:41:14 -04:00
Ben Darwin b21805d972 elastix: init at 4.8 2017-05-23 18:25:15 -04:00
Tyson Whitehead 8fdbc828b9
clblas-cuda: requires ocl-icd now for libOpenCL.so.1 #25902 2017-05-18 18:32:09 -04:00
Jörg Thalheim be19ad150c Merge pull request #25594 from mimadrid/update/htslib-1.4
Update/htslib 1.4
2017-05-11 07:08:56 +01:00
mimadrid 295a23a2db
htslib: 1.3.2 -> 1.4 2017-05-07 23:15:42 +02:00
Daiderd Jordan f240276000
blas: fix darwin library id 2017-04-27 23:25:07 +02:00
Vladimír Čunát 6617c8bd87
A fixed version of commit eb750f9a7b
For detailed explanation see:
https://github.com/NixOS/nixpkgs/commit/24444513fb5#commitcomment-21767916
2017-04-14 18:59:36 +02:00
Joachim Fasting 540a6412e3
suitesparse_4_4: NIX_CFLAGS -> NIX_CFLAGS_COMPILE
Tested with nix-build -A suitesparse_4_4
2017-04-12 19:27:03 +02:00
Joachim Fasting a883581ddb
suitesparse_4_2: remove bogus NIX_CFLAGS
NIX_CFLAGS should be NIX_CFLAGS_COMPILE; since pic is the default, we
simply remove the bogus declaration.

Tested with nix-build -A suitesparse_4_2
2017-04-12 19:26:58 +02:00
Frederik Rietdijk 767e459200 Merge pull request #22726 from matthewbauer/openblas-closure-size
openblas: disable static libs
2017-04-10 16:11:19 +02:00
Matthew Daiter d712c04d25 suitesparse: refining CUDA support 2017-04-04 17:23:20 +02:00
Matthew Daiter 6f721ce534 suitesparse: add CUDA support 2017-03-29 15:47:51 +02:00
Matthew Bauer bd8654f45d openblas: disable static libs
Disable static on openblas. This should save about 57M from closure sizes.
2017-02-12 18:45:44 -06:00
Matthew Daiter 82835f7eb3 cudnn51_cudatoolkit80: hash change 2017-02-08 18:40:32 +01:00
Anthony Cowley 084a76ef6f atlas: change platforms to unix
The build succeeds on darwin and linux.
2017-01-10 21:02:04 -05:00
Robert Helgesson 2990cd8aea
clblas-cuda: use system gtest library
Without this the build attempts to download the library.
2016-12-28 12:21:07 +01:00
mimadrid 25c984f940
htslib: 1.3.1 -> 1.3.2 2016-12-23 19:31:44 -05:00
Thomas Tuegel bed668c051
openblas: refactor and set TARGET always 2016-12-10 16:49:45 -06:00
Nikolay Amiantov be95ceaff2 treewide: quote URLs in my packages 2016-11-24 01:17:52 +03:00
Matthew Daiter 3897b344f3 cudnn51_cudatoolkit80: Init at 5.1-8.0 2016-11-21 14:51:39 +01:00
Falco Peijnenburg 5f5f0614b0 Support for ARM in openblas
Attempting to build openblas on ARM resulted in the error "unsopported system: armv7l_linux". This PR resolves that issue and some other issues that pop up when trying to build openblas for ARM.
2016-11-18 12:44:49 +01:00
Matthew Daiter 541b3fc7d2 cudnn5_cudatoolkit80: adding to main repo 2016-11-07 12:07:29 +01:00
Daiderd Jordan 3187b01720 Merge pull request #19816 from veprbl/octave_fixes
octave: darwin fix
2016-11-05 10:49:33 +01:00
Frederik Rietdijk 7077a270bf Merge remote-tracking branch 'upstream/master' into HEAD 2016-10-26 13:06:43 +02:00
Dmitry Kalinkin a8eb57d953
openblas: silence warnings on darwin
Without this one gets a lot of build time warnings like:

ld: warning: object file (/tmp/strip.2OzFn8) was built for newer OSX
version (10.9) than being linked (10.7)
2016-10-23 21:19:14 -04:00
Thomas Tuegel a58ec829e4
openblas: disable some hardening flags 2016-10-22 12:57:40 -05:00
Frederik Rietdijk 9b66b5c2cc liblapack: use python2 2016-10-18 23:16:05 +02:00
Thomas Tuegel d94abcb157
openblas: 0.2.17 -> 0.2.19 2016-09-09 19:42:54 -05:00
Michael Raskin 6b075ee8b1 openlibm: 0.4.1 -> 0.5.4 2016-09-06 19:31:38 +02:00
obadz 0e8d2725dc Merge branch 'master' into staging 2016-08-23 18:50:06 +01:00
Tuomas Tynkkynen a18ee4acb7 treewide: Make explicit that 'dev' output of boost is used
Also fix one incorrect output in geant.
2016-08-23 04:32:21 +03:00
Tuomas Tynkkynen d3705faa56 treewide: Use makeLibraryPath in LD_LIBRARY_PATHs 2016-08-23 00:14:00 +03:00
Robin Gloster 33e1c78ae3 Merge remote-tracking branch 'upstream/master' into hardened-stdenv 2016-08-16 07:54:01 +00:00
Nikolay Amiantov 0464600859 ipopt: 3.12.4 -> 3.12.6 2016-08-14 22:37:08 +03:00
Robin Gloster 1b979d8384 Merge remote-tracking branch 'upstream/master' into hardened-stdenv 2016-08-03 13:34:44 +00:00
Tuomas Tynkkynen 21f17d69f6 treewide: Add lots of meta.platforms
Build-tested on x86_64 Linux & Mac.
2016-08-02 21:42:43 +03:00
Robin Gloster 1f04b4a566 Merge remote-tracking branch 'upstream/master' into hardened-stdenv 2016-07-21 00:56:43 +00:00
Josef Kemetmueller f3dc4d9ec3 superlu: init at 5.2.1 2016-07-19 12:37:08 +00:00
Franz Pletz f597e97236 atlas: Fix hardening 2016-07-13 19:30:52 +02:00
Franz Pletz 26dd9acba5 Merge remote-tracking branch 'origin/master' into hardened-stdenv 2016-07-09 13:21:28 +02:00
Joachim Fasting 46b07b335b Merge pull request #16379 from mimadrid/init/bcftools-1.3.1
bcftools: init at 1.3.1
2016-06-24 22:15:51 +02:00
mimadrid d3da5cbf44
htslib: init at 1.3.1 2016-06-24 21:08:16 +02:00
artuuge 465d6a2113 Theano-cuda: init at 0.8.2 2016-06-20 01:06:07 +02:00
Robin Gloster 8031cba2ab Merge remote-tracking branch 'upstream/master' into hardened-stdenv 2016-06-10 09:27:04 +00:00
artuuge 5b51f0bff9 clblas-cuda: init at git-20160505 2016-06-05 14:33:19 +02:00
Ian-Woo Kim ff8985e7ab cudnn: add cudatoolkit to propagatedBuildInputs 2016-06-02 19:33:03 +02:00
Robin Gloster 2d382f3d98 Merge remote-tracking branch 'upstream/master' into hardened-stdenv 2016-05-30 19:39:34 +00:00
Arseniy Seroka c6b3aca4e2 Merge pull request #15654 from wavewave/magma
magma: init at 2.0.2
2016-05-26 01:02:14 +03:00
Ian-Woo Kim e47070ad64 cudnn: init at 4.0 2016-05-25 18:26:57 +00:00
Ian-Woo Kim fd42fccd4c magma: init at 2.0.2 2016-05-25 18:14:41 +00:00
Franz Pletz f8d481754c
Merge remote-tracking branch 'origin/master' into hardened-stdenv 2016-05-18 17:10:02 +02:00
Peter Simons 8e462995ba Bring my stdenv.lib.maintainers user name in line with my github nick. 2016-05-16 22:49:55 +02:00
Evgeny Egorochkin 4b979eef29 atlas: put the name suffix where it belongs 2016-05-16 10:19:38 +03:00
Robin Gloster d020caa5b2 Merge remote-tracking branch 'upstream/master' into hardened-stdenv 2016-04-18 13:49:22 +00:00
= 9ec9da1a24 iSpike: init at 2.1.1 2016-04-12 14:36:20 +02:00
Robin Gloster 696d85a62d Merge remote-tracking branch 'upstream/master' into hardened-stdenv 2016-04-03 11:01:57 +00:00
Frederik Rietdijk 4bd01c5cbd openblas_2_14: remove
because we don't need it for numpy anymore.
2016-03-31 21:51:45 +02:00
Franz Pletz 2e08d8234e Merge remote-tracking branch 'origin/master' 2016-03-31 10:06:30 +02:00
Frederik Rietdijk c1abb1d404 openblas: 0.2.15 -> 0.2.17 2016-03-28 15:58:10 +02:00
Robin Gloster 3f45f0948d Merge remote-tracking branch 'upstream/master' into hardened-stdenv 2016-03-15 01:44:24 +00:00
Anthony Cowley f3a6f3e2f3 suitesparse: build dylibs on darwin
Makes the shared libraries usable on darwin so that, e.g., the Julia
compiler may be built.
2016-03-13 04:13:26 -04:00
Anthony Cowley 9d1053dc6d suitesparse: darwin compatibility
There is no librt on darwin, so it must be disabled.
2016-03-12 21:17:15 -05:00
Robin Gloster 5969a59052 Merge remote-tracking branch 'upstream/master' into hardened-stdenv 2016-02-09 16:28:44 +00:00
Frederik Rietdijk 3e476a73ef openblas_2_14: init at 0.2.14 2016-02-08 20:33:31 +01:00
Robin Gloster acb408646e remove local pic flags, now set by hardened stdenv 2016-01-30 16:36:57 +00:00
Thomas Tuegel 36a08ce5a0 arpack: 3.2.0 -> 3.3.0 2015-12-28 11:44:03 -06:00
Thomas Tuegel cd7cfcc9a2 arpack: include OpenBLAS path in pkgconfig file 2015-12-22 14:22:19 -06:00
Vladimír Čunát ffb72182a6 blas: fix remains of hardcoded version
Thanks to @knedlsepp for pointing out
2b71fdbbc3 (commitcomment-14919659)
2015-12-11 10:25:40 +01:00
Pascal Wittmann 7fd2796e99 Replace 'with plaforms; platform' with 'platforms.platform' 2015-11-17 21:30:43 +01:00
Thomas Tuegel 9a2d5cb4d5 openblas: include which on all platforms
The `f_check` script uses `which` to check that the Fortran compiler is
available. `which` is a shell built-in on NixOS, but not on Darwin or
other Linuxes.
2015-11-07 14:00:04 -06:00
Thomas Tuegel 841df2cd7a openblas: use packaged LAPACK
Upstream began shipping OpenBLAS with LAPACK 3.4.1. This is the version
we were using in Nixpkgs anyway, so there is no reason to continue
copying the LAPACK sources into the build tree.
2015-11-07 14:00:04 -06:00
Thomas Tuegel 3d87c5f9c3 openblas: 0.2.14 -> 0.2.15 2015-11-05 10:24:31 -06:00
Thomas Tuegel b3bb609b96 atlas: build on Linux only
Fixes #10808.
2015-11-04 12:36:23 -06:00
Jude Taylor 9da6517c36 atlas: patch out usage of deprecated tmpnam on darwin 2015-10-30 20:15:26 -07:00
Vladimír Čunát 2b71fdbbc3 blas: fix by updating, fixes #10420, close #10545
The new URL also looks more stable.
2015-10-22 20:13:33 +02:00
Nikolay Amiantov d54a459063 ipopt: 3.12.3 -> 3.12.4 2015-10-15 17:06:23 +03:00
Thomas Tuegel 0daee71b1c suitesparse: link shared library against openblas 2015-10-11 09:16:34 -05:00
Thomas Tuegel eb300443f0 openblas: run tests 2015-10-11 09:16:27 -05:00
Thomas Tuegel cd2c0e4e86 openspecfun: init at 0.4 2015-10-10 12:55:30 -05:00
Thomas Tuegel f9e7011626 fixup! openlibm: init at 0.4.1 2015-10-10 12:55:08 -05:00
Thomas Tuegel 3436c78fc3 openlibm: init at 0.4.1 2015-10-09 19:02:01 -05:00
Thomas Tuegel aa4efac850 arpack: update homepage 2015-09-16 11:08:39 -05:00
danshapero 8885889b48 metis: init at 5.1.0 2015-08-13 16:53:18 +02:00
Thomas Tuegel 74e4f6befa ipopt: build with openblas 2015-06-12 07:26:47 -05:00
Thomas Tuegel 71b848b45d openblas: build with USE_OPENMP=0 on Darwin
Darwin's clang does not support OpenMP yet. OpenMP is required on other
platforms for e.g. Julia.
2015-06-09 06:34:52 -05:00
Thomas Tuegel fff0191f48 arpack: build with openblas 2015-06-04 17:42:03 -05:00
Thomas Tuegel e36b3ec0a5 suitesparse: build shared libraries 2015-06-04 17:42:03 -05:00
Thomas Tuegel a17d8bcc4b suitesparse_4_4: update to 4.4.4 2015-06-04 17:42:02 -05:00
Thomas Tuegel e5ee1a0577 suitesparse: remove unnecessary patches 2015-06-04 17:42:02 -05:00
Thomas Tuegel b02f300c44 suitesparse_4_4_1: build with openblas
Compared to ATLAS, OpenBLAS offers better performance, faster builds,
and dynamic architecture detection.
2015-06-04 17:42:01 -05:00
Thomas Tuegel 982aabc561 suitesparse_4_2: build with openblas
Compared to ATLAS, OpenBLAS offers better performance, faster builds,
and dynamic architecture detection.
2015-06-04 17:42:01 -05:00
Thomas Tuegel b4eb8a5bc3 openblas: remove old expressions 2015-06-04 17:42:01 -05:00
Thomas Tuegel 86fb034008 openblas: build with native-width integers by default 2015-06-04 17:42:01 -05:00
Thomas Tuegel 14ee766024 openblas: set NUM_THREADS and USE_OPENMP 2015-06-04 17:42:00 -05:00
Peter Simons d3073741a3 Merge pull request #8042 from adnelson/liblapack_atlas_dependency_optional
Liblapack atlas dependency optional
2015-05-30 19:25:54 +02:00
Allen Nelson e001340cf6 returned to two-file structure for liblapack 2015-05-28 21:49:06 -05:00
Peter Simons 99273a6716 Merge pull request #8047 from nckx/master
Don't use "with licenses;" for single licences
2015-05-28 22:14:53 +02:00
Peter Simons bcd5dc6bac Merge pull request #8023 from thinkpad20/pure_liblapack
added cmake flag to prevent autodetection of SDK directory
2015-05-28 21:44:07 +02:00
Allen Nelson 2c125cf37a removed default dependency of liblapack on ATLAS. was causing an unnecessary double-build of atlas 2015-05-28 12:39:49 -05:00
Tobias Geerinckx-Rice 158e1cfdd0 Don't use "with licenses;" for single licences
And don't use square brackets on such lines.
2015-05-28 19:20:29 +02:00
Tobias Geerinckx-Rice b2d7f4b1ba Use common licence attributes from lib/licenses.nix
Many (less easily automatically converted) old-style strings
remain.

Where there was any possible ambiguity about the exact version or
variant intended, nothing was changed. IANAL, nor a search robot.

Use `with stdenv.lib` wherever it makes sense.
2015-05-27 22:00:06 +02:00
Allen Nelson 6eb8ff878d added cmake flag to prevent autodetection of SDK directory 2015-05-27 12:42:40 -07:00
Allen Nelson 2a0a5c697e added clang dependency, using unix platform 2015-05-18 17:47:03 -05:00
Allen Nelson b4b6215523 added flags/switches necessary to get openblas to compile on osx 2015-05-18 17:01:43 -05:00
Nikolay Amiantov f1b51945bc ti-rpc: update package 2015-05-18 17:21:08 +03:00
Pascal Wittmann f99d5cf2fc Fixed some descriptions 2015-04-28 10:55:20 +02:00
Thomas Tuegel 8ed9f847b1 openblas: update to 0.2.14 2015-04-24 18:21:20 -05:00
Thomas Tuegel c90744fcb5 openblas: downgrade to 0.2.12, build generic target 2015-04-17 07:35:19 -05:00
Nikolay Amiantov d5d8efa0b8 ipopt: update 2015-03-29 13:05:27 +03:00
Thomas Tuegel b692340441 openblas: fix build on i686 2015-02-26 06:44:03 -06:00
Nikolay Amiantov d6363498e0 ipopt: update package 2015-02-03 14:27:51 +03:00
Domen Kožar de9f27b07d remove biolib 2015-01-18 11:52:00 +01:00
Raffael Mancini 3878472f02 ipopt: fix build after minor gcc update (close #5519)
The configure script only checks for a specific version to enable a fix in
finding cstdlib and cstring.
2015-01-01 11:12:19 +01:00
Thomas Tuegel d582090a15 suitesparse: add version 4.4.1 2014-12-27 13:47:53 -06:00
Thomas Tuegel 81c0f94d74 arpack: build against atlasWithLapack 2014-12-27 13:40:40 -06:00
Thomas Tuegel 893f277bd7 arpack: version bump to 3.2.0 2014-12-27 13:40:40 -06:00
Thomas Tuegel 3ce76d4dd0 atlas: optionally build with full lapack 2014-12-27 13:40:40 -06:00
Thomas Tuegel 91657e30ca atlas: fix generic options
Build atlas with the generic options recommended by the upstream
documentation for distributions. The expression now takes the parameter
'threads' which configures the number of threads atlas will use. The
default is to build serial atlas ('threads = "0"'). The expression also
takes the parameter 'cacheEdge' which is the L2 cache per core, in
bytes. This reduces build time because the cache size doesn't need to be
detected. It also reduces impurity, since different build nodes on Hydra
may have different hardware. It is set to 256k by default, which is
recommended for distributions by the upstream documentation.
2014-12-27 13:40:40 -06:00
Thomas Tuegel 8a5d7e7944 openblas: version bump to 0.2.13 2014-12-27 13:40:40 -06:00
Nikolay Amiantov bfbb46ea92 ipopt: add package 2014-11-12 03:43:35 +03:00
Mateusz Kowalczyk 007f80c1d0 Turn more licenses into lib.licenses style
Should eval cleanly, as far as -A tarball tells me.

Relevant: issue #2999, issue #739
2014-11-06 00:48:16 +00:00
Thomas Tuegel 16901dcae2 atlas: add ttuegel as maintainer 2014-09-21 11:00:24 -05:00
Thomas Tuegel 1d8d3d8bbe atlas: version bump to 3.10.2 2014-09-21 11:00:24 -05:00
Thomas Tuegel 634b9ae6d4 openblas: add ttuegel as maintainer 2014-08-29 10:06:24 -05:00
Thomas Tuegel 9ade2dfa3c openblas: add local build preference to pinned versions 2014-08-29 10:06:24 -05:00
Thomas Tuegel df731f151f openblas: add version 0.2.11 2014-08-29 10:06:24 -05:00
Thomas Tuegel 40ccaa2b4c openblas: pin all the versions julia requires 2014-08-29 10:06:24 -05:00
Bjørn Forsman c9baba9212 Fix many package descriptions
(My OCD kicked in today...)

Remove repeated package names, capitalize first word, remove trailing
periods and move overlong descriptions to longDescription.

I also simplified some descriptions as well, when they were particularly
long or technical, often based on Arch Linux' package descriptions.

I've tried to stay away from generated expressions (and I think I
succeeded).

Some specifics worth mentioning:
 * cron, has "Vixie Cron" in its description. The "Vixie" part is not
   mentioned anywhere else. I kept it in a parenthesis at the end of the
   description.

 * ctags description started with "Exuberant Ctags ...", and the
   "exuberant" part is not mentioned elsewhere. Kept it in a parenthesis
   at the end of description.

 * nix has the description "The Nix Deployment System". Since that
   doesn't really say much what it is/does (especially after removing
   the package name!), I changed that to "Powerful package manager that
   makes package management reliable and reproducible" (borrowed from
   nixos.org).

 * Tons of "GNU Foo, Foo is a [the important bits]" descriptions
   is changed to just [the important bits]. If the package name doesn't
   contain GNU I don't think it's needed to say it in the description
   either.
2014-08-24 22:31:37 +02:00
Michael Raskin 33ef69390b Fix Julia 0.3.0 build (for most purposes). Not making default yet because it is unclear if I missed something important. Failed to make it use external openblas and lapack correctly… 2014-08-24 00:24:55 +04:00
Michael Raskin d2539c6ff5 Adding Julia 0.3.0: some progress, but doesn't work yet 2014-08-21 22:09:55 +04:00
Michael Raskin 9fe10c90fa Properly mark platform support for arpack in relation to its openblas dependency 2014-08-10 16:36:48 +04:00
Eelco Dolstra 8a7f3c3618 Mark a bunch of packages as broken or not supported on Darwin 2014-08-08 17:59:02 +02:00
Mateusz Kowalczyk 7a45996233 Turn some license strings into lib.licenses values 2014-07-28 11:31:14 +02:00
Rob Vermaas 1a6a797ec3 Add liblbfgs 1.10 2014-05-07 14:22:04 +02:00
Thomas Tuegel df5639183c Claim maintainership of recently added packages
Also set platforms for some packages where it was missing.
2014-03-07 11:23:30 -06:00
Thomas Tuegel 2bd2747a50 arpack: version 3.1.5, fix pkgconfig 2014-03-01 18:46:53 -06:00
Thomas Tuegel bcd9f04226 add arpack-3.1.4 2014-01-26 08:57:11 -06:00
Michael Raskin 4dad238bab Fix forced CPU choice according to current openblas documentation 2014-01-05 16:34:05 +04:00
Jonas Hoersch 5ddefd6155 blas: update to version 20110419 2013-09-17 16:40:34 +02:00
Peter Simons a940651968 liblapack: add myself as a maintainer and enable Hydra builds (in stdenv-updates) 2013-08-16 22:45:30 +02:00
Peter Simons 400d4a03b0 Update references to 'rLang' to the new name 'R'. 2013-07-04 23:41:22 +02:00
Peter Simons 3df0409cb6 liblapack: propagate the 'shared' flag to atlas 2013-07-04 13:42:47 +02:00
Evgeny Egorochkin 9c6f7cc9c1 Add package versions to some of the packages or fix existing ones to conform to nixpkgs conventions. 2013-06-07 03:15:45 +03:00