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909 Commits

Author SHA1 Message Date
Remy Goldschmidt
c473490524
osqp: init at 0.6.0 2020-08-08 13:32:51 -07:00
Daniël de Kok
57d4c67fb8
Merge pull request #93052 from danieldk/amd-blis-zen-only 
amd-blis: init at 2.2
 2020-08-08 20:01:24 +02:00
R. RyanTM
ca9c2e3548 petsc: 3.13.2 -> 3.13.3 2020-08-07 12:44:29 +10:00
Daniël de Kok
1474bfe27d
Merge pull request #93653 from danieldk/mkl-2020.2.254 
mkl: 2020.1.217 -> 2020.2.254
 2020-08-05 08:08:08 +02:00
Pavol Rusnak
7839270bb0
or-tools: 7.6 -> 7.7 2020-07-26 15:34:17 +02:00
Daniël de Kok
6a236f5410 mkl: 2020.1.217 -> 2020.2.254 2020-07-22 17:38:07 +02:00
markuskowa
533720caa9
Merge pull request #93031 from andrew-d/andrew/dsd 
dsd: init at 2018-07-01
 2020-07-18 23:18:23 +02:00
Jack Coughlin
8a65fe8da6 petsc: Fix install_name_tool patch 
The PETSc library's config/install.py script checks whether
/usr/bin/install_name_tool is an existing file:

https://gitlab.com/petsc/petsc/-/blob/master/config/install.py#L368

Therefore, it is not enough to replace it with something that we expect
to be on the PATH, as this will cause the linked if statement to be
silently skipped. The consequence is that applications linked against
this version of petsc will fail at runtime on MacOS with a dynamic
loading error.

Instead, we should replace install_name_tool with the absolute path of a
binary we know will be present at build time.

Note that this should be fixed upstream as well, but this is sufficient
to fix the runtime error.
 2020-07-18 08:47:24 -07:00
Andrew Dunham
f856cb8a9e it++: init at 4.3.1 2020-07-16 17:59:24 -07:00
Daniël de Kok
4fbe92df09 amd-blis: init at 2.2 
We compile specifically for Zen:

- Zen/Zen2 are not included in the x86_64 or amd64 configurations.
- Including them breaks AMD BLIS in other places, since some functions
  have Zen-specific definitions that fail on other platforms.

Non-Zen CI runners will succeed when they are Haswell or later, since
a Haswell kernel is compiled as a dependency.
 2020-07-13 13:16:37 +02:00
Benjamin Hipple
2ec5479689
Merge pull request #89299 from wucke13/petsc 
petsc: add fotran build argument
 2020-07-07 13:50:29 -04:00
wucke13
dc5113fb06 petsc: 3.13.1 -> 3.13.2 
+ add fortran build argument
 2020-07-07 09:34:43 +02:00
Matthew Bauer
8a525d6a2b arpack: add blas, lapack to library path 
Fixes #89215
 2020-07-06 01:30:10 -04:00
R. RyanTM
669b2ab244 suitesparse-graphblas: 3.2.2 -> 3.3.0 2020-06-30 16:21:46 +00:00
R. RyanTM
f79c05b113 openblas: 0.3.9 -> 0.3.10 2020-06-19 10:59:46 +02:00
Ryan Burns
92d7b38e89 openblas: enable on ppc64le 2020-10-02 18:10:44 -07:00
Doron Behar
60b4b396e5
Merge pull request #98501 from doronbehar/pkg/octave/arpack 2020-10-01 19:04:43 +03:00
Doron Behar
bd77df6d6f arpack: assert that blas and lapack are compatible 
Do it before buildInputs per:
https://github.com/NixOS/nixpkgs/pull/94892#discussion_r471110250

Remove unneed, BLAS_LIBS and LAPACK_LIBS from environment - the
libraries are detected just fine when in buildInputs.
 2020-09-23 00:57:31 +03:00
Doron Behar
e0d947c79c arpack: cosmetic changes 
Don't use `with stdenv.lib` at the top of the expression, per:
https://nix.dev/anti-patterns/language.html#with-attrset-expression

Use rec and version inside `mkDerivation`, like almost any other
derivation.
 2020-09-23 00:52:45 +03:00
Benjamin Hipple
4af635feff
Merge pull request #87866 from danieldk/validate-pkgconfig-hook 
validatePkgConfig: init
 2020-06-02 23:27:27 -04:00
Daniël de Kok
127cdd0cab mkl: use validatePkgConfig hook 2020-05-31 20:45:07 +02:00
Benjamin Hipple
f04a5af0cc
Merge pull request #82180 from bcdarwin/bppcore 
bppsuite: init at 2.4.1
 2020-05-26 21:07:25 -04:00
Ben Darwin
7f656f3ef6 bpp-popgen: init at 2.4.1 2020-05-25 21:12:17 -04:00
Ben Darwin
a53b27829c bpp-phyl: init at 2.4.1 2020-05-25 21:10:59 -04:00
Ben Darwin
8d712ccc16 bpp-seq: init at 2.4.1 2020-05-25 21:09:52 -04:00
Ben Darwin
adc7b4c979 bpp-core: init at 2.4.1 2020-05-25 21:08:31 -04:00
Daniël de Kok
e88673aa27 mkl: fix expectation of MKLROOT being set in pkg-config files 
The Intel MKL pkg-config files did not work, because they expect that
the MKLROOT environment variable is set. This change replaces
occurences by the actual path of MKL in the Nix store.

Since the pkg-config files seem to break quite frequently after
upgrades, add a post-install check to validate the pkg-config files.
 2020-05-14 19:40:18 +02:00
Timo Kaufmann
346de1fb8c
Merge pull request #87518 from r-ryantm/auto-update/sympow 
sympow: 2.023.5 -> 2.023.6
 2020-05-11 21:35:40 +00:00
R. RyanTM
f66d997a29 sympow: 2.023.5 -> 2.023.6 2020-05-10 16:42:21 +00:00
Frederik Rietdijk
303adc7697 Merge master into staging-next 2020-05-10 09:43:48 +02:00
Dmitry Kalinkin
e80302dc7d
Merge pull request #86142 from bcdarwin/itk-5.1.0 
Itk: 5.0.1 -> 5.1.0
 2020-05-09 15:03:28 -04:00
Frederik Rietdijk
d7cca0f356 Merge master into staging-next 2020-05-09 11:12:29 +02:00
R. RyanTM
c0e63bc87e petsc: 3.13.0 -> 3.13.1 2020-05-08 15:57:25 +00:00
Benjamin Hipple
706642091e mkl: include symlinks to versioned libblas.so.3 names 
Some build systems look for this specifically.
 2020-05-08 06:52:02 +02:00
Jonathan Ringer
c1e605dd6b openblas: also export unversioned libraries for linux 2020-05-08 06:52:02 +02:00
Mario Rodas
a340a9f4d8
Merge pull request #86755 from andersk/abseil-ortools 
abseil-cpp: 20191119 -> 20200225.2; or-tools: 7.5 -> 7.6
 2020-05-07 06:53:54 -05:00
Ben Darwin
5caa76705b elastix: update for ITK 5.1.0 
- fetch patches to build elastix 5.0 with ITK 5.1
- update 'platforms': builds on Darwin, fails on aarch64
 2020-05-05 00:08:04 -04:00
R. RyanTM
7a17b13b48 or-tools: 7.5 -> 7.6 2020-05-04 03:12:00 -07:00
Frederik Rietdijk
00bbfccecf Merge staging into staging-next 2020-05-01 09:28:45 +02:00
R. RyanTM
51b1533b37 suitesparse-graphblas: 3.2.1 -> 3.2.2 2020-05-01 09:06:34 +02:00
Markus Kowalewski
15cd0bd993 openblas: 0.3.8 -> 0.3.9 2020-05-01 09:02:51 +02:00
Benjamin Hipple
21be830522
Merge pull request #85799 from matthewbauer/blas-lapack-expand-docs 
BLAS/LAPACK fixup and expand docs
 2020-04-22 21:56:20 -04:00
Matthew Bauer
5a500ff0ba blas,lapack: use correct name for library 
To match the soname, we need to use libblas.so.3, liblapack.so.3.
 2020-04-22 12:37:04 -05:00
Frederik Rietdijk
ec21df329a
Merge pull request #85636 from matthewbauer/blas-lapack-fix-fallout-from-83888 
BLAS/LAPACK fix fallout from #83888
 2020-04-21 19:59:16 +02:00
Ben Darwin
fe07e2b2ac elastix: enable tests 2020-04-21 07:54:59 +02:00
Ben Darwin
30cafee8b6 elastix: python -> python3 2020-04-21 07:54:59 +02:00
Matthew Bauer
a6a502fca0 magma: remove mklSupport flag 
This now relies on the "blas" and "lapack" packages.
 2020-04-20 16:02:57 -05:00
Matthew Bauer
ff2f2644f8 blas,lapack: use isILP64 instead of is64bit 
This is a better name since we have multiple 64-bit things that could
be referred to.

LP64  : integer=32, long=64, pointer=64
ILP64 : integer=64, long=64, pointer=64
 2020-04-20 16:02:43 -05:00
Matthew Bauer
fcf33e2499 scs: breaks on 64bit blas 2020-04-17 16:24:31 -05:00
Matthew Bauer
1c8aba8334 treewide: use blas and lapack 
This makes packages use lapack and blas, which can wrap different
BLAS/LAPACK implementations.

treewide: cleanup from blas/lapack changes

A few issues in the original treewide:

- can’t assume blas64 is a bool
- unused commented code
 2020-04-17 16:24:09 -05:00
Matthew Bauer
43873351ff blas/lapack: add wrapper for “alternative”s of BLAS/LAPACK provider 
This is based on previous work for switching between BLAS and LAPACK
implementation in Debian[1] and Gentoo[2]. The goal is to have one way
to depend on the BLAS/LAPACK libraries that all packages must use. The
attrs “blas” and “lapack” are used to represent a wrapped BLAS/LAPACK
provider. Derivations that don’t care how BLAS and LAPACK are
implemented can just use blas and lapack directly. If you do care what
you get (perhaps for some CPP), you should verify that blas and lapack
match what you expect with an assertion.

The “blas” package collides with the old “blas” reference
implementation. This has been renamed to “blas-reference”. In
addition, “lapack-reference” is also included, corresponding to
“liblapack” from Netlib.org.

Currently, there are 3 providers of the BLAS and LAPACK interfaces:

- lapack-reference: the BLAS/LAPACK implementation maintained by netlib.org
- OpenBLAS: an optimized version of BLAS and LAPACK
- MKL: Intel’s unfree but highly optimized BLAS/LAPACK implementation

By default, the above implementations all use the “LP64” BLAS and
LAPACK ABI. This corresponds to “openblasCompat” and is the safest way
to use BLAS/LAPACK. You may received some benefits from “ILP64” or
8-byte integer BLAS at the expense of breaking compatibility with some
packages.

This can be switched at build time with an override like:

    import <nixpkgs> {
        config.allowUnfree = true;
        overlays = [(self: super: {
          lapack = super.lapack.override {
            lapackProvider = super.lapack-reference;
          };
          blas = super.blas.override {
            blasProvider = super.lapack-reference;
          };
        })];
      }

or, switched at runtime via LD_LIBRARY_PATH like:

    $ LD_LIBRARY_PATH=$(nix-build -E '(with import <nixpkgs> {}).lapack.override { lapackProvider = pkgs.mkl; is64bit = true; })')/lib:$(nix-build -E '(with import <nixpkgs> {}).blas.override { blasProvider = pkgs.mkl; is64bit = true; })')/lib ./your-blas-linked-binary

By default, we use OpenBLAS LP64 also known in Nixpkgs as
openblasCompat.

[1]: https://wiki.debian.org/DebianScience/LinearAlgebraLibraries
[2]: https://wiki.gentoo.org/wiki/Blas-lapack-switch
 2020-04-17 16:23:55 -05:00
Matthew Bauer
90326ba624 lapack: enable shared libraries, cblas, and tests 2020-04-17 16:17:12 -05:00
R. RyanTM
1450740470 suitesparse: 5.7.1 -> 5.7.2 2020-04-10 11:55:20 -07:00
Benjamin Hipple
a1f6400fd5
Merge pull request #84451 from robertodr/update-mkl 
mkl: 2020.0.166 -> 2020.1.217 (Linux only)
 2020-04-10 13:54:49 -04:00
Michael Reilly
84cf00f980
treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
Mario Rodas
2f41064d86
Merge pull request #84455 from r-ryantm/auto-update/petsc 
petsc: 3.12.4 -> 3.13.0
 2020-04-08 21:35:27 -05:00
Niklas Hambüchen
df907c4786 openblas: Add singleThreaded option. Off by default. 
See https://github.com/xianyi/OpenBLAS/issues/2543
 2020-04-08 13:46:04 +02:00
Mario Rodas
ad15e4e8a0
petsc: fix build on darwin 2020-04-06 12:00:00 +00:00
R. RyanTM
758e81662f petsc: 3.12.4 -> 3.13.0 2020-04-06 11:46:40 +00:00
Roberto Di Remigio
488527eaa6
mkl: 2020.0.166 -> 2020.1.217 2020-04-06 11:57:22 +02:00
Roberto Di Remigio
335e097352
mkl: 2019.5.281 -> 2020.0.166 (Linux only) 2020-03-27 08:45:20 +01:00
Jan Tojnar
d951c534da
Merge pull request #82274 from jtojnar/suitesparese-5.6 
suitesparse: 5.4.0 → 5.7.1 + clean up
 2020-03-22 06:58:25 +01:00
Josef Kemetmüller
fbb273c5fe fenics: 2017.1.0 -> 2019.1.0 
Fixes: NixOS/nixpkgs#75886
 2020-03-19 21:48:27 -07:00
Timo Kaufmann
d8d0b60c22
Merge pull request #82766 from r-ryantm/auto-update/brial 
brial: 1.2.7 -> 1.2.8
 2020-03-17 14:29:02 +00:00
R. RyanTM
707e0b1e96 brial: 1.2.7 -> 1.2.8 2020-03-17 01:13:50 +00:00
Tom Hall
c6c753668d openblas: disable optimisation pending fix 
See https://github.com/xianyi/OpenBLAS/issues/2496
 2020-03-14 18:06:59 +00:00
wucke13
4f58c15ee6 petsc: 3.8.4 -> 3.12.4 
+ add cxx flag to configure, because getdp needs it
 2020-03-13 04:10:20 +00:00
Jan Tojnar
b552b84ae2
suitesparse: ultimate clean-up 
* Switch to default buildPhase & installPhase
* In preConfigure
	* Do not add -DNPARTITION to CHOLMOD_CONFIG. That would disable the use of Metis but we already have that.
	* Do not remove -lrt on Darwin, Darwin compiler can handle that and the code no longer exists anyway.
	* With CUDA enabled
		* Do not replace CUDA_ROOT. It does not exist any more. Instead we are setting CUDA_PATH in makeFlags.
		* Do not replace GPU_BLAS_PATH, it defaults to CUDA_PATH so it will end up with the same value.
		* Do not add -DCHOLMOD_OMP_NUM_THREADS to GPU_CONFIG. Why would be having the library use the same number of threads as the builder a good idea?
		* Do not replace CUDA_PATH, we are setting it in makeFlags now.
		* Do not replace CUDART_LIB and CUBLAS_LIB. They were being replaced incorrectly (cuda libs are located in lib directory, not lib64). Instead set the correct paths in makeFlags.
		* Do not replace CUDA_INC_PATH. Its default looks like it will end up with the same value.
		* Do not replace NV20, NV30, NV35 – not used any more.
		* Do not replace NVCC, defaults to the same.
		* Do not replace NVCCFLAGS, we just used the default from SourceSparse 4.4.7 with -gencode=arch=compute_60,code=compute_60 tacked on top. Current upstream default looks much better.
* Stop adding -DNTIMER to CFLAGS on Darwin – clock_gettime is supported by macOS 10.12 SDK.
* In buildPhase
	* Move the make arguments to makeFlags and library to buildFlags, allowing us to drop the manual make call. I did not verify all of these are still needed.
	* Remove the creation of libsuitesparse.so. As far as I could tell it is some kind of remnant of our old expression – perhaps due to past deficiencies of the build scripts, we created the individual libraries as symlinks to libsuitesparse.so: e36b3ec0a5 But since the build script can now build individual .so libraries, there should be no need for this abomination. No other distros do this either.
* In installPhase
	* No need to copy things manually, there is an install target. We just need to pass INSTALL=$out flag to make to let it know where to install the files.
	* I do not have means of verifying the darwin dylib name fix but it looks like it might be fixed in an upcoming release.
	* I dropped the rpath fixup as it does not seem to be needed any more (ldd does not report any unresolved libraries).
 2020-03-11 03:45:25 +01:00
Jan Tojnar
c16d5b6534
suitesparse: do not build Mongoose & GraphBLAS 
We already have package for them
 2020-03-11 02:33:06 +01:00
Jan Tojnar
306cf6091f
suitesparse: link against system metis 2020-03-10 21:16:28 +01:00
Jan Tojnar
e9d7774b7b
suitesparse: 5.4.0 → 5.7.1 2020-03-10 21:16:27 +01:00
Jan Tojnar
559f02e208
suitesparse-graphblas: init at 3.1.2 2020-03-10 21:16:27 +01:00
Jan Tojnar
b4e6293a8d
mongoose: init at 2.0.4 2020-03-10 20:35:44 +01:00
Jan Tojnar
40ae28791f
suitesparse: clean up 
* Split to multiple outputs
* Fetch source from GitLab (the only source for future releases)
* Re-order attrset to be more idiomatic
* Format with nixpkgs-fmt
 2020-03-10 20:35:44 +01:00
Josef Kemetmüller
1cc9b2501d suitesparse: Enable parallel building 2020-03-10 17:16:17 +01:00
Mario Rodas
99722af1d5
Merge pull request #81843 from OmnipotentEntity/cudnn-7.6.5 
cudnn_cudatoolkit_10_2: init at 7.6.5
 2020-03-10 07:19:50 -05:00
R. RyanTM
e04fab644f osi: 0.108.4 -> 0.108.6 2020-03-06 07:22:33 +01:00
Michael Reilly
972db874b3 cudnn_cudatoolkit_10_2: init at 7.6.5 2020-03-05 15:14:10 -05:00
Frederik Rietdijk
9d88ee08f6 Merge master into staging-next 2020-02-18 16:09:19 +01:00
Dylan Simon
e25f0b3e3d scalapack: 2.1 -> 2.1.0 
2.1 seems to have disappeared
 2020-02-17 18:31:13 -05:00
Frederik Rietdijk
ec1184f461 Merge master into staging-next 2020-02-17 15:12:28 +01:00
Drew Risinger
c71f63a337 ecos: 2.0.6 -> 2.0.7 
Bump ecos module.
 2020-02-16 19:12:52 -08:00
R. RyanTM
6222192872 openblas: 0.3.7 -> 0.3.8 2020-02-11 12:01:57 +00:00
Anders Kaseorg
1a32e383e6 or-tools: 7.3 -> 7.5 
Signed-off-by: Anders Kaseorg <andersk@mit.edu>
 2020-02-10 20:40:12 +01:00
R. RyanTM
5659946d6a m4ri: 20200115 -> 20200125 2020-02-08 16:16:48 +00:00
Drew Risinger
c13bf84d45 libraries.science.math.scs: 2.0.2 -> 2.1.1 2020-01-31 16:05:05 -05:00
Frederik Rietdijk
dce0ca29d9 Merge master into staging-next 2020-01-28 10:46:13 +01:00
Timo Kaufmann
e39e304638
Merge pull request #78496 from r-ryantm/auto-update/brial 
brial: 1.2.6 -> 1.2.7
 2020-01-26 23:28:02 +01:00
R. RyanTM
2d172e6403 brial: 1.2.6 -> 1.2.7 2020-01-26 02:39:07 +00:00
Timo Kaufmann
d62e410ccd
Merge pull request #78222 from r-ryantm/auto-update/m4ri 
m4ri: 20140914 -> 20200115
 2020-01-22 17:43:44 +01:00
R. RyanTM
813678058f m4ri: 20140914 -> 20200115 2020-01-21 23:46:57 +00:00
R. RyanTM
3937313195 m4rie: 20150908 -> 20200115 2020-01-21 23:24:43 +00:00
Anders Kaseorg
3cd8ce3bce treewide: Fix unsafe concatenation of $LD_LIBRARY_PATH 
Naive concatenation of $LD_LIBRARY_PATH can result in an empty
colon-delimited segment; this tells glibc to load libraries from the
current directory, which is definitely wrong, and may be a security
vulnerability if the current directory is untrusted.  (See #67234, for
example.)  Fix this throughout the tree.

Signed-off-by: Anders Kaseorg <andersk@mit.edu>
 2020-01-15 09:47:03 +01:00
Niklas Hambüchen
de1e61f34d
Merge pull request #77104 from r-ryantm/auto-update/htslib 
htslib: 1.9 -> 1.10.2
 2020-01-13 01:51:32 +01:00
Mario Rodas
5ab4676d88
Merge pull request #77194 from r-ryantm/auto-update/primesieve 
primesieve: 7.4 -> 7.5
 2020-01-09 05:02:21 -05:00
R. RyanTM
e28fe589d9 primesieve: 7.4 -> 7.5 2020-01-07 00:22:48 -08:00
R. RyanTM
940d12bf5d htslib: 1.9 -> 1.10.2 2020-01-06 09:16:51 -08:00
Mario Rodas
e11aab8340
Merge pull request #76356 from r-ryantm/auto-update/openlibm 
openlibm: 0.6.0 -> 0.7.0
 2020-01-06 09:58:54 -05:00
Frederik Rietdijk
17ab5f9d88 Merge master into staging-next 2020-01-06 10:38:20 +01:00
Ryan Mulligan
f8cd096aad
Merge pull request #54967 from volhovm/volhovm/clmagma 
clmagma: init at 1.3
 2020-01-05 08:18:12 -08:00
Frederik Rietdijk
828f93a326 Merge master into staging-next 2020-01-05 16:00:21 +01:00
markuskowa
1c55261574
Merge pull request #75526 from robertodr/more-mkl 
Add GNU threading and Fortran libraries to MKL package
 2020-01-04 20:36:43 +01:00
Frederik Rietdijk
867552957f openblas: fix static musl build 2020-01-03 12:50:47 +01:00
Frederik Rietdijk
960c24a996
Merge pull request #75798 from tobim/pkgsStatic/arrow 
arrow-cpp: add pkgsStatic support
 2020-01-03 10:13:31 +01:00
Frederik Rietdijk
f08e3e38d4 Merge master into staging-next 2020-01-02 21:41:13 +01:00
Tobias Mayer
db5d3cdfe2 openblas: partially fix static build 2019-12-31 15:05:13 +01:00
Robin Gloster
313da176d3
treewide: NIX_*_FLAGS -> string 2019-12-31 00:16:46 +01:00
Robin Gloster
5f2b92e3ec
treewide: NIX_*_COMPILE -> string 2019-12-31 00:13:29 +01:00
Robin Gloster
2157dcd141
treewide: installFlags is a list 2019-12-30 13:22:43 +01:00
Merijn Broeren
133103d709
treewide: replace make/build/configure/patchFlags with nix lists 2019-12-30 12:58:11 +01:00
Linus Heckemann
2c19725202 mirtk: enable tbb support for multithreading 2019-12-30 01:16:08 +01:00
R. RyanTM
a2a56df6f8 openlibm: 0.6.0 -> 0.7.0 2019-12-23 20:42:29 -08:00
Roberto Di Remigio
153597a320
mkl: filter static libs in installPhase 2019-12-19 10:23:26 +01:00
Roberto Di Remigio
6cc9bbe2fd
mkl: extract static libraries optionally 2019-12-19 10:12:00 +01:00
Roberto Di Remigio
e0605b3174
mkl: add GNU threading and Fortran libraries 
Signed-off-by: Roberto Di Remigio <roberto.diremigio@gmail.com>
 2019-12-19 10:12:00 +01:00
Timo Kaufmann
135081a538 brial: 1.2.5 -> 1.2.6 
Motivation is mostly https://github.com/BRiAl/BRiAl/pull/37, which is a
pre-requiste for getting the sage tests to pass with python3.
 2019-12-13 20:31:31 +01:00
Mateusz Kowalczyk
1451a52a38 Remove myself (fuuzetsu) from maintainer lists 
I haven't been doing any maintenance for a long time now and not only
do I get notified, it also creates a fake impression that all these
packages had at least one maintainer when in practice they had none.
 2019-12-05 16:29:48 +09:00
Dmitry Kalinkin
aa7efea848
Merge pull request #73958 from markuskowa/upd-lapack 
liblapack: 3.8.0 -> 3.9.0
 2019-11-24 20:06:04 -05:00
John Ericson
d0d5136cce Merge remote-tracking branch 'upstream/master' into wrapper-pname-support 2019-11-24 17:25:07 +00:00
John Ericson
9b090ccbca treewide: Get rid of most parseDrvName without breaking compat 
That is because this commit should be merged to both master and
release-19.09.
 2019-11-24 17:22:28 +00:00
Markus Kowalewski
7e44c6dee6
liblapack: 3.8.0 -> 3.9.0 2019-11-24 11:47:50 +01:00
Markus Kowalewski
8419bb2a20
scalapack: 2.0.2 -> 2.1 2019-11-20 22:44:33 +01:00
Renaud
5411dbda33
Merge pull request #71710 from bcdarwin/fix-elastix 
elastix: 4.9.0 -> 5.0.0 (and mark unbroken)
 2019-11-18 23:23:16 +01:00
Ben Darwin
b618730708 elastix: 4.9.0 -> 5.0.0 (and mark unbroken) 2019-11-18 13:29:02 -05:00
markuskowa
7d728faea5
Merge pull request #73227 from markuskowa/fix-mkl 
mkl: add scalapack libraries to output
 2019-11-18 10:46:33 +01:00
Markus Kowalewski
d817a49faa
mkl: add scalapack libraries to output 2019-11-18 09:05:03 +01:00
Ben Darwin
736860d34b nifticlib and niftseg: change platform from linux to unix since these build on OSX 2019-11-14 21:25:10 -05:00
Andreas Rammhold
1e72fa5158
Merge pull request #68954 from dguibert/dg/cudatoolkit_10_1 
cudatoolkit: add 10.1.243
 2019-11-06 08:58:30 +01:00
Benjamin Hipple
fa1e275f31 mkl: 2019.3 -> 2019.5 (#71476) 
Includes bugfixes, new features, and performance improvements.

Full release notes here:
https://software.intel.com/en-us/articles/intel-math-kernel-library-release-notes-and-new-features

Leave Darwin on 2019.3 pending resolution of DMG issues
 2019-10-27 15:34:16 -04:00
Sam Stites
f12199614d magma: use cudatoolkit 2019-10-23 10:57:43 -07:00
markuskowa
f6d7f8ae16
Merge pull request #68927 from danieldk/mkl 
mkl: include pkgconfig files
 2019-10-13 19:16:49 +02:00
Linus Heckemann
5aa4b19946 treewide: mark some broken packages as broken 
Refs:
e6754980264fe927320d5ff2dbd24ca4fac9a160
1e9cc5b9844ef603fe160e9f671178f96200774f
793a2fe1e8bb886ca2096c5904e1193dc3268b6d
c19cf65261639f749012454932a532aa7c681e4b
f6544d618f30fae0bc4798c4387a8c7c9c047a7c
 2019-10-08 17:14:26 +02:00
Orivej Desh
2455b2e309 or-tools: 7.0 -> 7.3 2019-10-04 05:17:48 +00:00
Nikolay Amiantov
1c429acbff tensorflow: add OpenGL path to find libcudart 2019-10-02 10:33:31 +03:00
Timo Kaufmann
7a7e9c1b27
Merge pull request #64193 from timokau/sage-8.9 
sage: 8.8 -> 8.9
 2019-09-30 11:13:46 +00:00
Joachim F
ad773d31e2
Merge pull request #69345 from joachifm/feat/split-version 
Replace uses of splitString for splitting version strings
 2019-09-27 06:19:18 +00:00
Joachim Fasting
bad07dfac5
tree-wide: replace uses of splitString "." with lib.versions 
Quoting from the splitString docstring:

   NOTE: this function is not performant and should never be used.

This replaces trivial uses of splitString for splitting version
strings with the (potentially builtin) splitVersion.
 2019-09-26 17:42:49 +02:00
Timo Kaufmann
1797c9c295 sage: 8.9.beta9 -> 8.9.rc0 
Sage now by default expects the lcalc library to be named Lfunction
(instead of libLfunction). This could be changed by an environment
variable (https://trac.sagemath.org/ticket/28224), but various distros
seem to agree on this standard
(https://groups.google.com/forum/#!topic/sage-packaging/xvh55IxHTZg) so
it's best just to follow it. The old standard was set by sage anyway and
sage is the only consumer of lcalc in nixpkgs.
 2019-09-24 17:51:09 +02:00
Matthieu Coudron
d70eba7ab3 ns-3: 3.29 -> 3.30 
Fixes python bindings.
 2019-09-24 00:30:12 +09:00
Daniël de Kok
9f25e95576 mkl: include pkgconfig files 2019-09-22 20:07:34 +02:00
David Guibert
92690a8937 cuddn: add 10.1 (version 7.6.3) 2019-09-17 15:19:41 +02:00
Markus Kowalewski
ecd20d2166
liblapack: remove optimized blas flag. 
This cmake flag has no effect since no external blas
library is provided in the build inputs.
 2019-09-15 11:39:58 +02:00
Markus Kowalewski
fc7374176f
liblapack: build LAPACKE C api 2019-09-15 11:39:58 +02:00
Vladimír Čunát
991c0e1618
treewide: mark packages as buildable on darwin (PR #45364) 
vcunat amended the commit a bit; see the PR for details/discussion.
 2019-09-15 10:50:08 +02:00
Miguel Madrid Mencía
148c82e07e
maintainer: mimadrid: update github username and personal data 2019-09-14 12:15:46 +02:00
volth
7b8fb5c06c treewide: remove redundant quotes 2019-09-08 23:38:31 +00:00
Frederik Rietdijk
5f4734b1dd Merge remote-tracking branch 'upstream/gcc-8' into staging-next 
Earlier the gcc8 branch was merged instead of the gcc-8 branch (note the dash)...
 2019-09-08 20:44:26 +02:00
Frederik Rietdijk
66bc7fc1b3 Merge master into staging-next 2019-09-06 22:46:05 +02:00
tbenst
6d7282d74a magma: 2.0.2 -> 2.5.0 2019-09-06 20:15:10 +02:00
Vladimír Čunát
4aad2947f8
Merge branch 'master' into staging-next 2019-09-04 11:00:56 +02:00
Franz Pletz
de85797565
Merge remote-tracking branch 'origin/master' into gcc-8 2019-09-03 22:15:07 +02:00
idontgetoutmuch
739cdb368e Ensure blas produces pkg config files (#67629) 
blas: produce pkgconfig file
 2019-09-03 16:34:45 +02:00
Mikhail Volkhov
58dffa3459
clmagma: init at 1.3 2019-08-30 22:40:04 +02:00
volth
08f68313a4 treewide: remove redundant rec 2019-08-28 11:07:32 +00:00
Frederik Rietdijk
5061fe0c2c Merge staging-next into staging 2019-08-28 08:26:42 +02:00
volth
35d68ef143 treewide: remove redundant quotes 2019-08-26 21:40:19 +00:00
Robin Gloster
616b8343c4
Merge remote-tracking branch 'upstream/master' into gcc-8 2019-08-25 18:55:46 +02:00
Vladimír Čunát
2e6bf42a22
Merge branch 'master' into staging-next 
There ver very many conflicts, basically all due to
name -> pname+version.  Fortunately, almost everything was auto-resolved
by kdiff3, and for now I just fixed up a couple evaluation problems,
as verified by the tarball job.  There might be some fallback to these
conflicts, but I believe it should be minimal.

Hydra nixpkgs: ?compare=1538299
 2019-08-24 08:55:37 +02:00
R. RyanTM
0ff0c288a8 sympow: 2.023.4 -> 2.023.5 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/sympow/versions
 2019-08-20 21:06:37 -07:00
Markus Kowalewski
6ff8958bef openblas: 0.3.6 -> 0.3.7 2019-08-18 11:49:24 +02:00
volth
c814d72b51 treewide: name -> pname 2019-08-17 10:54:38 +00:00
Frederik Rietdijk
fe9a3e3e63 Merge staging-next into staging 2019-08-17 09:39:23 +02:00
volth
46420bbaa3 treewide: name -> pname (easy cases) (#66585) 
treewide replacement of

stdenv.mkDerivation rec {
  name = "*-${version}";
  version = "*";

to pname
 2019-08-15 13:41:18 +01:00
Gabriel Ebner
a736d87393 spooles: init at 2.2 2019-08-14 19:09:39 +02:00
Timo Kaufmann
5e58c5f900 sympow: 1.018.1 -> 2.023.4 
Maintenance taken over by debian package maintainer jgmbenoit:
https://trac.sagemath.org/ticket/3360#comment:17

This moves sympow to his fork, since there is no offical
version-controlled source repository from the original author and they
do not seem to maintain sympow anymore. We had already accumulated quite
some patches from debian, who have effectively maintained sympow for a
while now.
 2019-08-09 17:45:08 +02:00
Nikolay Amiantov
0a1bf4734f libtensorflow: add binary build and add automatic generation 2019-07-31 13:28:44 +03:00
Orivej Desh
b5d1d50aa9 google-gflags: move to aliases.nix 
google-gflags were renamed to gflags in 2012:
https://github.com/gflags/gflags/#25-january-2012

gflags.name will be updated in staging.
 2019-07-25 09:18:32 +00:00
Orivej Desh
5d86f9a9ce nccl: 2.4.2-1 -> 2.4.8-1 2019-07-18 17:04:43 +00:00
Ryan Mulligan
508ae42a0f treewide: fix redirect URLs 2019-07-10 12:52:51 -07:00
Nikolay Amiantov
08b1d81089 osi: init at 0.108.4 2019-06-24 15:59:57 +03:00
R. RyanTM
069f2235af brial: 1.2.4 -> 1.2.5 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/brial/versions
 2019-06-17 13:23:05 +02:00
Franz Pletz
146f9fda2b
papi: fix build with gcc8 2019-06-17 07:25:57 +02:00
volth
f3282c8d1e treewide: remove unused variables (#63177) 
* treewide: remove unused variables

* making ofborg happy
 2019-06-16 19:59:05 +00:00
Dmitry Kalinkin
cbaa9a7ab9
Merge pull request #57947 from smaret/fix-mkl 
mkl: fix install_name on Darwin
 2019-06-06 18:27:30 -04:00
Sébastien Maret
fb883a58df
mkl: fix install_name on Darwin 
Closes #57697

Co-Authored-By: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
 2019-06-04 22:08:48 +02:00
Niklas Hambüchen
8d5864eb47 openblas: Add enableStatic flag 2019-05-28 08:57:23 +02:00
Niklas Hambüchen
43fda1c96d openblas: 0.3.5 -> 0.3.6 2019-05-28 08:57:23 +02:00
Silvan Mosberger
16c66f66ae
scalapack: Increase individual test timeout to prevent hydra failures 2019-05-27 20:08:32 +02:00
Florian Klink
2ed6903da5
libglvnd, ocl-icd, vulkan-loader: Add /run/opengl-driver(-32) to RUNPATH. (#60985) 
libglvnd, ocl-icd, vulkan-loader: Add /run/opengl-driver(-32) to RUNPATH.
 2019-05-22 23:36:01 +02:00
Ambroz Bizjak
28a0918916 Add driver library path to some packages to find CUDA libraries. 
This is to avoid relying on LD_LIBRARY_PATH for finding the CUDA driver libraries.
 2019-05-22 18:34:09 +02:00
Frederik Rietdijk
f137783927 Merge master into staging-next 2019-05-01 11:45:46 +02:00
R. RyanTM
16e1d009e0 ipopt: 3.12.12 -> 3.12.13 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ipopt/versions
 2019-05-01 11:11:28 +02:00
Markus Kowalewski
6968c4f305 openblas: turn off AVX512 optimizations 
The AVX512 optimization has a bug in openblas-0.3.5
and can also lead to slower code on Xeon Silver CPUs.

See https://github.com/xianyi/OpenBLAS/issues/1955
and https://github.com/xianyi/OpenBLAS/issues/2029
 2019-04-27 07:07:49 +02:00
Matthew Bauer
87944c3125
Merge pull request #56744 from matthewbauer/macos-10-12 
Update macOS to 10.12
 2019-04-26 22:20:03 -04:00
Matthew Bauer
63831c398a python-fenics: put pytest in nativeBuildInputs 2019-04-26 21:55:10 -04:00
Renaud
6186a6f012
Merge pull request #58484 from sveitser/cudnn-v7.4.2 
cudnn_cudatoolkit_10: 7.3.1 -> 7.4.2
 2019-04-24 22:40:17 +02:00
Daniel Schaefer
bac4d95aa2 treewide: Change URLs to HTTPS 
Lots of URLs were HTTP redirect to HTTPS. Changed those and checked them
if there's actual content. Inspired by
https://github.com/NixOS/nixpkgs/issues/60004
 2019-04-22 10:19:54 +02:00
Mateusz Kowalczyk
575d6a4826
Merge pull request #58417 from andersk/ortools-7.0 
or-tools: 6.10 -> 7.0, add Python bindings
 2019-04-20 17:39:23 +09:00
Matthew Bauer
f475aeaf29
Merge pull request #59535 from matthewbauer/homepage-fixes 
treewide: update homepages to https where available
 2019-04-15 20:47:30 -04:00
Matthew Bauer
290a5d916e treewide: update homepages to https where available 
Based on "problems" from repology:

https://repology.org/repository/nix_unstable/problems

Mostly simple changes to reflect redirects.
 2019-04-15 10:10:05 -04:00
Dmitry Kalinkin
59c81160e7
Merge pull request #58504 from symphorien/static-proot 
Static proot, wafHook cross compilation
 2019-04-13 12:04:32 -04:00
Matthew Bauer
a79a8f29bc waf: use wafConfigureFlags for waf flags 
This avoids the potential conflict between autoconf flags and the waf
flags. There is some overlap between the two but waf errors when it
doesn’t recognize the flag.
 2019-04-09 23:44:37 -04:00
Frederik Rietdijk
d108b49168 Merge master into staging-next 2019-04-09 16:38:35 +02:00
Vladimír Čunát
e1f55599cc
Merge #58589: openblas: fix aarch64 build 2019-04-07 16:58:42 +02:00
Jan Tojnar
cb1a20499a
Merge branch 'master' into staging 2019-04-05 11:37:15 +02:00
Markus Kowalewski
70867a92f6
arpack: fix tests on darwin 2019-04-03 10:48:52 +02:00
Markus Kowalewski
9a60a65249
arpack: 3.6.3 -> 3.7.0 
* switch to FetchFromGitHub
* switch from autotools to cmake
* add eigen to input (is now required)
 2019-04-03 10:48:52 +02:00
Markus Kowalewski
734c6c21cb
mkl: 2019.0.117 -> 2019.3.199 2019-04-01 21:50:23 +02:00
Markus Kowalewski
fa28a838f3
openblas: fix aarch64 build 2019-03-31 12:19:41 +02:00
Markus Kowalewski
4c74ee948e
clblas: turn of gtest, fix build 
clblas does not work anymore with gmock 1.8.1.
Turning off the test suite fixes the build.
 2019-03-29 13:59:45 +01:00
sveitser
e29e315c5f
cudnn_cudatoolkit_10: 7.3.1 -> 7.4.2 2019-03-28 21:49:13 +08:00
Anders Kaseorg
ae6b9dcb0e or-tools: 6.10 -> 7.0 
Signed-off-by: Anders Kaseorg <andersk@mit.edu>
 2019-03-26 17:04:03 -07:00
Anders Kaseorg
08e9273e29 or-tools: Add Python bindings 
Signed-off-by: Anders Kaseorg <andersk@mit.edu>
 2019-03-26 17:04:03 -07:00
Wael M. Nasreddine
5af0780492
Merge remote-tracking branch 'origin/master' into staging 
* origin/master: (693 commits)
  buildGoModule: use go_1_12 instead of go_1_11 (#58103)
  gitAndTools.lab: 0.15.2 -> 0.15.3 (#58091)
  signal-desktop: 1.22.0 -> 1.23.0
  added missing semicolon to documentation
  terminus_font_ttf: 4.46.0 -> 4.47.0
  buildGoModule: remove SSL env vars in favor of cacert in buildInputs (#58071)
  dav1d: init at 0.2.1
  dropbox-cli: 2018.11.28 -> 2019.02.14
  atlassian-confluence: 6.14.1 -> 6.14.2
  maintainers: update email for dywedir
  python.pkgs.hglib: use patch to specify hg path (#57926)
  chkrootkit: 0.52 -> 0.53
  radare2-cutter: 1.7.2 -> 1.8.0
  autorandr: 1.7 -> 1.8
  pythonPackages.pyhepmc: fix build
  llvm-polly/clang-polly: use latest llvm
  apulse: 0.1.11.1 -> 0.1.12, cleanup
  factorio: experimental 0.17.14 → 0.17.16 (#58000)
  sequeler: 0.6.7 -> 0.6.8
  nasc: 0.5.1 -> 0.5.2
  ...
 2019-03-21 21:01:25 -07:00
R. RyanTM
e14d70d955 primesieve: 7.3 -> 7.4 (#57375) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/primesieve/versions
 2019-03-12 22:43:56 +01:00
Matthew Bauer
37eba81c7b
Merge pull request #56391 from matthewbauer/cmake-treewide 
Add more CMake flags
 2019-03-11 12:43:46 -04:00
Matthew Bauer
6ed49262f5 treewide: remove BUILD_TESTING flag 
This is now set by CMake
 2019-03-11 10:11:28 -04:00
R. RyanTM
cac06fc53d ipopt: 3.12.11 -> 3.12.12 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ipopt/versions
 2019-03-03 20:47:42 +01:00
Averell Dalton
d7806fe4ed openblas: adjust makeFlags handling 2019-02-23 09:13:57 +01:00
Markus Kowalewski
dbf5135385
scalapack: update meta data 
* Set platform from linux -> x86_64-linux
  Scalapack does not seem to run properly on ARM (failing tests)

* Add markuskowa as maintainer
 2019-02-21 15:08:33 +01:00
Markus Kowalewski
4aa90ac089
scalapack: add openmpi4 compatibility patch 2019-02-21 15:08:32 +01:00
Will Dietz
32322da1a6 openblas: fix config breakage introduced for configs using 'false' 
My earlier change mistakenly expected `toString false` to produce '0'
instead of the empty string, leading to unexpected config changes.

Intended to address issue mentioned here and in following discussion:

https://github.com/NixOS/nixpkgs/pull/53972#issuecomment-459981602

Sorry, folks!

(special-case handling of bools here makes this "cleanup" a bit
 less of an obvious win but hopefully still preferable overall :))

-----------

makeFlags in resulting derivation, according to this one-liner:

$ nix show-derivation -f . openblas|jq ".[].env.makeFlags"

before:
"BINARY=64 CC=cc CROSS= DYNAMIC_ARCH=1 FC=gfortran HOSTCC=cc INTERFACE64=1 NO_BINARY_MODE= NO_STATIC=1 NUM_THREADS=64 PREFIX=/1rz4g4znpzjwh1xymhjpm42vipw92pr73vdgl6xs1hycac8kf2n9 TARGET=ATHLON USE_OPENMP=1"

after:
"BINARY=64 CC=cc CROSS=0 DYNAMIC_ARCH=1 FC=gfortran HOSTCC=cc INTERFACE64=1 NO_BINARY_MODE=0 NO_STATIC=1 NUM_THREADS=64 PREFIX=/1rz4g4znpzjwh1xymhjpm42vipw92pr73vdgl6xs1hycac8kf2n9 TARGET=ATHLON USE_OPENMP=1"

Without knowing how `placeholder` works, it seems interesting if
entirely unrelated that the `PREFIX` is same for both! :). TIL.
 2019-02-17 19:51:55 +01:00
Dylan Simon
e69fdc1715 sympow: fix patch url to working revision (#55778) 
fix_pointer_initialization2.patch no longer exists on trunk -- download
from a fixed older revision where it did.
 2019-02-14 21:10:37 +01:00
Matthew Bauer
2433c575f0 openblas: fix on linux 
This reverse changes made cfc4313 which broke builds on linux. Still
not sure why this broke Linux, but we can investigate it later.
“buildPackages.stdenv.cc” shouldn’t be put in nativeBuildInputs in
general. Either way, this restores hashes to before that commit.

thanks to @jethrokuan
 2019-02-10 20:16:16 -05:00
Matthew Bauer
cfc43138cb openblas: fix on darwin 
The openblas script relies on CC=clang for succesfully compiling on
Darwin systems. This seems like bad behavior, but we get things like
https://hydra.nixos.org/build/87657058 otherwise.

Fixes #55536.
 2019-02-10 18:49:04 -05:00
Vladimír Čunát
c40f211499
Merge branch 'staging-next' 
It's not completely without regressions, but ATM it seems to bring more
upsides than downsides and the iteration is too long already.
 2019-02-10 14:20:49 +01:00
Orivej Desh
59cd3ee895 nccl: 2.1.4 -> 2.4.2-1 (#55292) 2019-02-10 01:20:04 +00:00
Vladimír Čunát
ff101946a8
Merge branch 'master' into staging-next 
Hydra nixpkgs: ?compare=1503899
 2019-02-06 14:24:46 +01:00
Guillaume Bouchard
9f0ee6c606 primesieve: init at 7.3 2019-02-04 13:03:50 +01:00
Vladimír Čunát
5effa4e0f9
Merge branch 'master' into staging-next 
Comments on conflicts:
- llvm: d6f401e1 vs. 469ecc70 - docs for 6 and 7 say the default is
  to build all targets, so we should be fine
- some pypi hashes: they were equivalent, just base16 vs. base32
 2019-02-01 09:22:29 +01:00
Markus Kowalewski
57c37456db
openblas: make the optimazation target overridable 2019-01-29 14:34:02 +01:00
Will Dietz
1f0467005d openblas: 0.3.4 -> 0.3.5, rework a bit (#53972) 
* openblas: simplify a bit, fix doCheck so tests are enabled non-cross.

* doCheck should be 'true' in (at least) the non-cross case,
  this looks like an inverted check that's largely benign
* doCheck will be set to 'false' in the cross case anyway,
  makeDerivation does this IIRC
* targetPrefix can be used without checking, probably by design

Derivation hash does change but no "real" functionality change intended.

* openblas: nix types for config attrs (hash-preserving)

* openblas: more nix-ification, merge in cross attrs, prefer to always set

(but set appropriately for cross and non-cross cases both)

* I'm not sure what NO_BINARY_MODE does,
  this change now sets explicitly false in the non-cross scenario
  (previously unset unless cross).
* Drop musl NO_AFFINITY case, will be removed in upgrade shortly

* openblas: 0.3.4 -> 0.3.5
 2019-01-15 16:36:07 +01:00
Frederik Rietdijk
05ee1015bb openblas: fix cross-compilation 2019-01-15 10:11:33 +01:00
Timo Kaufmann
04ba895ecd
suitesparse: 5.3.0 -> 5.4.0 (#53128) 2019-01-01 15:47:55 +01:00
Silvan Mosberger
eb864397a0
Merge pull request #52508 from tkonolige/fix_suitesparse_darwin 
suitesparse: Fix darwin support
 2018-12-31 03:24:48 +01:00
agracie
a3fc481b76 mkl: fix hash on Darwin 2018-12-26 20:57:08 -05:00
Bas van Dijk
72eae72223 openblas: fix build on x86_64-darwin 
See: https://github.com/xianyi/OpenBLAS/issues/1926
 2018-12-20 13:25:44 +01:00
Benjamin Hipple
6206a342e0 mkl: include Intel's libiomp.so in the MKL RPM unpack 
Since Intel's default openmp implementation is available in the same src
tarball, we can just include it in the package. This means that `mkl` now "just
works" without any environment variables, fragile setup-hooks, or forced
propagation.

Since the openmp implementation is only needed at runtime (and for test cases),
users can substitute a different one if they prefer by exporting it with
`LD_PRELOAD`, which is how Intel recommends handling this. If they do not do so,
`libiomp.so` lives next to `libmkl_rt.so` and thus will be in the RPATH as a
sane default.

Since this still comes from the same src tarball, we can ship it without losing
the fixed-output derivation; likewise, since Hydra is not building or caching
these, shipping these proprietary packages costs no bandwidth for the nix
community.
 2018-12-19 22:05:22 +01:00
Tristan Konolige
00005ce0bd suitesparse: Fix darwin support 
Suitesparse libraries would end up containing references to the build
directory. fixDarwinDylibNames appears to not fix this problem. We
manually use intall_name_tool to set the library paths correctly.
 2018-12-18 18:08:17 -07:00
Frederik Rietdijk
4deb04a97a openblas: 0.3.3 -> 0.3.4 2018-12-07 15:21:25 +01:00
Frederik Rietdijk
a510aa2672 Merge master into staging-next 2018-12-03 12:18:43 +01:00
Will Dietz
cd14ad53c3 or-tools: appease warning re:python3, try testing 2018-12-01 13:38:16 -06:00
Will Dietz
046e7980f9 or-tools: parallel 2018-12-01 13:38:16 -06:00
Will Dietz
70c2e88c96 or-tools: touchup 2018-12-01 13:38:16 -06:00
Will Dietz
c4feda8b01 or-tools: v6.9.1 -> v6.10 
https://github.com/google/or-tools/releases/tag/v6.10
 2018-12-01 13:38:16 -06:00
Frederik Rietdijk
fed881e510 Merge staging-next into staging 2018-11-21 12:39:46 +01:00
Matthew Bauer
d492f53faf
Merge pull request #50527 from matthewbauer/ninja-check-phase 
Add check phase to ninja setup hook
 2018-11-20 16:55:12 -06:00
Timo Kaufmann
6059bf842a
Merge pull request #49994 from r-ryantm/auto-update/python3.6-cvxopt 
python36Packages.cvxopt: 1.2.1 -> 1.2.2
 2018-11-20 14:25:43 +01:00
Matthew Bauer
285eb9a894 cmake: set CTEST_OUTPUT_ON_FAILURE globally 
We should always use this.
 2018-11-19 16:16:16 -06:00
Frederik Rietdijk
e343a85cfb Merge master into staging-next 2018-11-19 09:55:32 +01:00
Matthew Bauer
2c47a4229f treewide: remove ctest usages 
These are already in the generated makefiles!
 2018-11-18 19:31:02 -06:00
Matthew Bauer
2c1d3a9a82 Merge remote-tracking branch 'upstream/master' into staging 2018-11-18 19:02:09 -06:00
Orivej Desh
e66d263f6b eigen3_3: move version overrides to all-packages.nix 2018-11-18 10:53:25 +00:00
Frederik Rietdijk
63c6875f26 Merge master into staging-next 2018-11-18 10:32:12 +01:00
Renaud
cde945a165
Merge pull request #48044 from schneefux/pkg/fetchfromgithub 
treewide: Use fetchFromGitHub instead of fetchurl
 2018-11-14 09:48:22 +01:00
Matthew Bauer
f2a20b6e52 treewide: use wafHook 
Replace "waf" phases with wafHook that manages everything
automatically. Should make things more modular.

Packages affected here are:

- a2jmidid
- ams-lv2
- ardour
- fomp
- guitarix
- ingen
- jalv
- mda-lv2
- non
- patchage
- hamster-time-tracker
- kupfer
- xiphos
- xfce4-dockbarx-plugin
- xfce4-namebar-plugin
- dropbox
- clasp
- aubio
- liliv
- lv2
- lvtk
- ntk
- raul
- sratom
- suil
- ganv
- ndn-cxx
- ns3
- serd
- sord
- termbox
- wxmupen64plus
- jackaudio
- pflask
- blockhash
- glmark2
- weighttp
 2018-11-13 19:13:48 -06:00
Daiderd Jordan
5b8c4b0646
suitesparse: fixup darwin libraries 
The build created libraries with an install_name that points to the
build directory instead of the installation prefix.  Causing errors like
this when other packages try to link against it's libraries.

    Library not loaded: /private/tmp/nix-build-suitesparse-5.3.0.drv-0/SuiteSparse/lib/libcholmod.3.0.12.dylib
 2018-11-13 00:25:32 +01:00
markuskowa
45a4adb1b3
Merge branch 'master' into atlas-remove 2018-11-11 02:22:04 +01:00
Markus Kowalewski
06f3676770
scalapack: set platform to linux 2018-11-11 02:17:20 +01:00
markuskowa
bf8c031074
Merge pull request #49199 from markuskowa/fet-scalapack 
scalapack: switch to openblas and add test
 2018-11-05 21:12:01 +01:00
Matthew Bauer
95373d3634 atlas: remove 
atlas is broken and can apparently be removed.

Fixes #49594
 2018-11-04 20:23:12 -06:00
Patrick Hilhorst
4cfeb9da53
cudatoolkit, cudnn: many updates 
cudatoolkit_9_1: 9.1.85.1 -> 9.1.85.3
cudatoolkit_9_2: init at 9.2.148.1
cudatoolkit_9: 9.1.85.1 -> 9.2.148.1
cudatoolkit_10, cudatoolkit_10_0: init at 10.0.130

cudnn_cudatoolkit_9_0: 7.0.5 -> 7.3.0
cudnn_cudatoolkit_9_1: init at 7.1.3
cudnn_cudatoolkit_9_2: init at 7.2.1
cudnn_cudatoolkit_9: 7.0.5 (9.1) -> 7.3.1 (9.2)
cudnn_cudatoolkit_10, cudnn_cudatoolkit_10_0: init at 7.3.1
 2018-10-30 19:09:20 +01:00
Markus Kowalewski
41a579aa68
scalapack: switch to openblas + add test 
* change from blas,lapack to openblas
* add check phase
* enable parallel building
* fix license
 2018-10-27 01:06:07 +02:00
Mateusz Kowalczyk
02fb26136c or-tools: new package (v6.9.1) 2018-10-25 14:15:13 +09:00
Mateusz Kowalczyk
b41f8936b9 QuadProgpp: Add new package. 
Necessary for #48895.
 2018-10-24 09:19:26 +09:00
Michael Raskin
acb7d85993 lrs: init at 7.0 2018-10-23 11:41:29 +03:00
Renaud
0cc07aeee6
Merge pull request #48172 from jluttine/cholmod-extra-1.2.0 
cholmod-extra: init at 1.2.0
 2018-10-21 17:28:30 +02:00
Thomas Tuegel
2e4397f631
Merge pull request #35213 from jluttine/suitesparse-5.1.2 
suitesparse: 4.4.4 -> 5.3.0
 2018-10-20 08:07:27 -05:00
Jörg Thalheim
351319e557
Merge pull request #48419 from r-ryantm/auto-update/ipopt 
ipopt: 3.12.10 -> 3.12.11
 2018-10-15 21:36:42 +01:00
Matthew Bauer
0b298d516a
Merge pull request #47182 from bhipple/add/mkl 
mkl: init at 2019.0.117
 2018-10-15 15:17:57 -05:00
R. RyanTM
ab050719ba ipopt: 3.12.10 -> 3.12.11 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ipopt/versions
 2018-10-14 08:11:02 -07:00
Jaakko Luttinen
f065de344d
cholmod-extra: init at 1.2.0 2018-10-10 22:08:25 +03:00
Jaakko Luttinen
8fb27604fb
suitesparse: 4.4.4 -> 5.3.0 2018-10-10 07:36:00 +03:00
schneefux
d81a96e601 mirtk: use fetchFromGitHub instead of fetchgit 2018-10-08 14:33:55 +02:00
Timo Kaufmann
65589faa2f zn_poly: 0.9 -> 0.9.1 
Sage has taken over maintenance since the original author no longer
maintains the project.
 2018-10-05 15:50:30 +02:00
Benjamin Hipple
0b82df8dbe Convert entire mkl package to a fixed-output derivation 2018-10-04 13:16:20 +00:00
Benjamin Hipple
ba02a2c371 Add Darwin as a supported platform 2018-10-02 22:53:48 -04:00
Daiderd Jordan
1383c08f2c
Merge branch 'master' into staging-next 2018-10-01 19:42:07 +02:00
R. RyanTM
0e5e4aed06 arpack: 3.5.0 -> 3.6.3 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/arpack/versions
 2018-09-26 11:28:59 +02:00
John Ericson
c701d6cb21 Merge remote-tracking branch 'upstream/master' into staging 2018-09-25 14:20:27 -04:00
Will Dietz
8a0a34f766 openblas: try leaving openmp enabled w/musl 2018-09-25 00:08:17 -05:00
Dmitry Vyal
81caec3568 openblas-0.3.1 -> 0.3.3 2018-09-23 09:35:29 +02:00
Frederik Rietdijk
14673d61ed Merge master into staging 2018-09-23 09:33:09 +02:00
Benjamin Hipple
d7c1d04af4 mkl: init at 2019.0.117 
This packags the Intel Math Kernel library on x86-64 platforms, which is a
dependency for many data science and machine learning packages.

Upstream, Intel provides proprietary binary RPMs with a permissive
redistribution license. These have been repackaged in both Debian and Anaconda,
so we are not the first distribution to redistribute.
 2018-09-22 15:28:39 -04:00
Orivej Desh
f0c0e2acc6 htslib: 1.7 -> 1.9 2018-09-21 22:42:28 +00:00
John Ericson
7319013ea1 Merge remote-tracking branch 'upstream/master' into staging 2018-09-18 16:55:42 -04:00
Christopher Ostrouchov
9ef31b2f96 papi: init at 5.6.0 (#46619) 
papi is a high resolution performance counter.
 2018-09-13 23:35:06 +02:00
Christopher Ostrouchov
e34a9fff1f scalapack: init at 2.0.2 (#46610) 
Added scalapack with flexibility to choose blas, lapack, and mpi
implementation.
 2018-09-13 21:27:47 +02:00
Uli Baum
79d9145469 parmetis: set license to unfree 
generic unfree license fits best
 2018-09-13 21:10:40 +02:00
Christopher Ostrouchov
3c2a74719a parmetis: init at 4.0.3 (#46615) 2018-09-13 21:02:17 +02:00
Daiderd Jordan
89e52157c8
Merge pull request #46584 from LnL7/darwin-broken-a 
broken darwin packages (a)
 2018-09-13 00:05:42 +02:00
Josef Kemetmüller
d726c0ff1d scs: Fix darwin build 
Additionally we make the unit-test deterministic by specifying a seed
instead of using something random.
 2018-09-12 20:58:26 +02:00
Daiderd Jordan
f1542f612b
atlas: mark broken on darwin 
Started to fail since 3.10.3.

    /private/tmp/nix-build-atlas-3.10.3.drv-0/ATLAS/build/bin/ATLrun.sh: line 4: 31119 Segmentation fault: 11  $atldir/$*
    make[3]: *** [Makefile:1695: ssanity_test] Error 139

/cc ZHF #45961
 2018-09-12 20:50:54 +02:00
Timo Kaufmann
408eacbc89 openblas: fix pkg-config alias name 
Turns out the filename is important. It should be `cblas`, not
`openblas-cblas`.
 2018-09-03 23:57:45 +02:00
Robert Schütz
93550cbddf Merge branch 'master' into staging-next 2018-08-31 17:32:48 +02:00
John Ericson
2c2f1e37d4 reewide: Purge all uses stdenv.system and top-level system 
It is deprecated and will be removed after 18.09.
 2018-08-30 17:20:32 -04:00
Robert Schütz
a9780a095b Merge branch 'master' into staging-next 2018-08-30 21:56:13 +02:00
Jan Tojnar
c1e53166ad
Revert "sympow: don't use placeholder" 
This reverts commit bae15c811f.
 2018-08-30 18:18:30 +02:00
Timo Kaufmann
c614c15f93
Merge pull request #45257 from timokau/openblas-pc 
openblas: add pkg-config aliases
 2018-08-26 20:13:19 +02:00
Benjamin Hipple
291de70ed6 scs: init at 2.0.2 (#45294) 2018-08-23 23:26:41 +02:00
Timo Kaufmann
26d5d030fe openblas: add pkg-config aliases 2018-08-21 16:39:57 +02:00
Vladimír Čunát
153a19df05
Merge branch 'master' into staging-next 
Hydra: ?compare=1474536
 2018-08-20 09:15:33 +02:00
Timo Kaufmann
8014c7f186
Merge pull request #45013 from jbaum98/fflas-ffpack_darwin 
fflas-ffpack: Add darwin support
 2018-08-19 16:24:52 +02:00
Jake Waksbaum
8374400cec fflas-ffpack: Add darwin support 2018-08-18 20:28:06 +00:00
Benjamin Hipple
65bb0b23b9 Add platforms.all 2018-08-18 12:11:06 -04:00
Benjamin Hipple
460029cf94 ecos: init at 2.0.6 2018-08-18 03:38:50 +00:00
Vladimír Čunát
14aa936ec5
Merge branch 'staging-next' into staging 2018-08-17 20:53:27 +02:00
Vladimír Čunát
cbabebcc2e
Merge branch 'master' into staging-next 
Hydra: ?compare=1473892
 2018-08-17 13:45:21 +02:00
Sarah Brofeldt
692c02ff4b
Merge pull request #44993 from bcdarwin/MIRTK 
mirtk: init at 2.0.0
 2018-08-16 10:51:12 +02:00
Jake Waksbaum
c0c854da95 zn_poly: Add darwin support 2018-08-14 00:49:42 -04:00
Ben Darwin
0adc6f4d8f mirtk: init at 2.0.0 2018-08-13 15:55:04 -04:00
Vladimír Čunát
ded9a4b1aa
Merge branch 'staging-next' into staging 
Commits from master, conflict resolutions, etc.
 2018-08-13 20:57:50 +02:00
Vladimír Čunát
00df25ee57
Merge branch 'master' into staging-next 
Hydra: ?compare=1472947
 2018-08-12 10:33:41 +02:00
Jan Malakhovski
b2563a55b7 nifticlib: disable tests 2018-08-11 09:35:38 +00:00
Jake Waksbaum
6385e5ffda lcalc: Add darwin support (#44850) 2018-08-10 09:53:52 +02:00
Frederik Rietdijk
d9fa74ba78 Merge master into staging 2018-08-09 18:28:15 +02:00
Timo Kaufmann
aabc55e154 libhomfly: init at 1.02r5 
libhomfly is a new standard package for sage. See
https://trac.sagemath.org/ticket/25705
 2018-08-05 16:50:33 +02:00
Timo Kaufmann
34c2f4150b libbraiding: init at 1.0 
libbraiding is a new standard package for sage. See
https://trac.sagemath.org/ticket/25705
 2018-08-05 16:50:32 +02:00
Timo Kaufmann
e550e5d0c7 lcalc: apply c++11 patch 2018-08-04 14:22:29 +02:00
John Ericson
db965063b3 treewide: Make configureFlags lists 2018-08-03 17:06:03 -04:00
Frederik Rietdijk
ad47d658d1 Merge master into staging-next 2018-07-21 19:43:53 +02:00
Jörg Thalheim
218298b30f
Merge branch 'master' into unused5 2018-07-21 15:41:22 +01:00
volth
52f53c69ce pkgs/*: remove unreferenced function arguments 2018-07-21 02:48:04 +00:00
volth
6d2857a311 [bot] treewide: remove unused 'inherit' in let blocks 2018-07-20 19:38:19 +00:00
Frederik Rietdijk
8213ff161c Merge master into staging-next 2018-07-19 18:24:24 +02:00
Luke Adams
eba8679bc5 cudnn*_cudatoolkit*: use public NVIDIA mirror (#31551) 
* cudnn*_cudatoolkit*: use NVIDIA mirror instead of requireFile

* cudnn_cudatoolkit7: update hash since public mirror is different
 2018-07-18 03:21:57 +00:00
Will Dietz
1b3d8eefe3 openblas: backport another patch, fix crash w/Go and Octave 
Also fixes numpy crashing during tests w/musl.
 2018-07-12 12:03:26 -05:00
Timo Kaufmann
d2f0fc1f41 openblas: backport fix 
https://github.com/xianyi/OpenBLAS/issues/1666

Causing test failures in cvxopt and (according to an openblas issue) numpy.
 2018-07-11 22:06:32 +02:00
aszlig
c8ed322b04
openblas: 0.3.0 -> 0.3.1 
Since the exposure of the version attribute done in
892a0e8ff4, the OpenBLAS build fails for
i686-linux:

https://nix-cache.s3.amazonaws.com/log/wi79zyfmwdpwx7bm29dzqh4vglx3x550-openblas-0.3.0.drv

According to @edolstra the build slaves of Hydra updated to a new
kernel, which seems to be the real cause for this issue. The latter is
already tracked upstream[1] and a fix[2] is already included in version
0.3.1.

This very update cases 4795 rebuilds across all architectures we
support, so it's still not significant enough to go through staging. In
addition the number of rebuilds doesn't include the amount of builds
that are currently failing.

My original idea was to add a patch just for fixing this on i686-linux
and do the real update via staging, but the amount of rebuilds still is
in an acceptable range IMO and @edolstra agreed on that on IRC.

[1]: https://github.com/xianyi/OpenBLAS/issues/1575
[2]: https://github.com/xianyi/OpenBLAS/pull/1583

Signed-off-by: aszlig <aszlig@nix.build>
Cc: @ttuegel
 2018-07-01 18:46:36 +02:00
Timo Kaufmann
5d78baa37a sympow: actually install datafiles 2018-06-30 01:20:46 +02:00
Timo Kaufmann
082169ab02 fetchurl: add sageupstream mirror 2018-06-30 01:20:44 +02:00
Timo Kaufmann
892a0e8ff4 openblas: expose version attribute 2018-06-30 01:20:44 +02:00
Matthew Bauer
753544ab52
Merge pull request #42471 from r-ryantm/auto-update/openlibm 
openlibm: 0.5.5 -> 0.6.0
 2018-06-28 22:06:11 -04:00
Silvan Mosberger
57bccb3cb8 treewide: http -> https sources (#42676) 
* treewide: http -> https sources

This updates the source urls of all top-level packages from http to
https where possible.

* buildtorrent: fix url and tab -> spaces
 2018-06-28 20:43:35 +02:00
R. RyanTM
b9137d6bce openlibm: 0.5.5 -> 0.6.0 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/openlibm/versions.

These checks were done:

- built on NixOS

- 0 of 0 passed binary check by having a zero exit code.
- 0 of 0 passed binary check by having the new version present in output.
- found 0.6.0 with grep in /nix/store/crnh2jiksr0b3sq5v6fc9x7zrrsjgirg-openlibm-0.6.0
- directory tree listing: https://gist.github.com/c287196625881e2d6c72af761704718e
- du listing: https://gist.github.com/ac9a45900fb2ba4ff48120c343677dec
 2018-06-23 18:48:17 -07:00
R. RyanTM
12a554dc31 brial: 1.2.3 -> 1.2.4 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/brial/versions.

These checks were done:

- built on NixOS

- 0 of 0 passed binary check by having a zero exit code.
- 0 of 0 passed binary check by having the new version present in output.
- found 1.2.4 with grep in /nix/store/d80z046q8l3rhi7zwbcxzaydfrqxvzq9-brial-1.2.4
- directory tree listing: https://gist.github.com/73a4fe4d778faacdf1c17f40a83e3884
- du listing: https://gist.github.com/23202c35b020ea0976f7c4ff9e23ca2c
 2018-06-19 16:52:22 -07:00
Vladimír Čunát
31530c185e
Merge a subset of staging (security) 
In particular, this contains Firefox-related and libgcrypt updates.
Other larger rebuilds would apparently need lots of time to catch up
on Hydra, due to nontrivial rebuilds in other branches than staging.
 2018-06-15 08:48:02 +02:00
R. RyanTM
cc9fc2bdcd ipopt: 3.12.9 -> 3.12.10 (#41555) 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/ipopt/versions.

These checks were done:

- built on NixOS

- 0 of 0 passed binary check by having a zero exit code.
- 0 of 0 passed binary check by having the new version present in output.
- found 3.12.10 with grep in /nix/store/6748l35g9dz7z77wqwal99ylrhn87liv-ipopt-3.12.10
- directory tree listing: https://gist.github.com/5da4bb4853af0913caca26e8cbc87666
- du listing: https://gist.github.com/c4d8373c7d9a61f39479151fdffa99cb
 2018-06-09 23:33:17 +02:00
Will Dietz
912b58a2c1 openblas: workaround mass-rebuilds 
Thanks for the suggestion:
https://github.com/NixOS/nixpkgs/pull/41639#issuecomment-395509669
 2018-06-07 13:38:08 -05:00
Will Dietz
b1d54822e4 openblas: remove patch that's no longer needed (PR merged) 2018-06-07 12:20:08 -05:00
Frederik Rietdijk
4dc7cc8cc7
Merge pull request #41259 from jyp/tf-1.7.1-bin 
python.pkgs.tensorflow: wheel version
 2018-06-07 11:27:39 +02:00
R. RyanTM
9d1d274928 openblas: 0.2.20 -> 0.3.0 (#41054) 2018-06-03 13:23:38 +00:00
Jean-Philippe Bernardy
397c4b7748 cudatoolkit: add 9.0 
This version is a dependency of tensorflow binaries
 2018-05-31 22:21:54 +02:00
Jean-Philippe Bernardy
9e730ee254 renaming cudatoolkit version numbers 2018-05-31 22:21:53 +02:00
Orivej Desh
0159beb89c ns-3: fix build after #28029 2018-05-30 02:37:40 +00:00
Ben Darwin
7a64b0726a bicgl: init at 2017-09-10 2018-05-09 14:05:29 -04:00
Robert Schütz
6e6005c2af
Merge pull request #38794 from timokau/brial-init 
brial: init at 1.2.3
 2018-05-08 08:08:15 +02:00
Timo Kaufmann
8b5ecf9141 brial: init at 1.2.3 2018-05-08 01:27:35 +02:00
Timo Kaufmann
ca9ea31ae1 liblapack: 3.4.1 -> 3.8.0 2018-05-06 21:12:01 +02:00
Matthew Justin Bauer
8e6684ca32
Merge pull request #39795 from r-ryantm/auto-update/atlas 
atlas: 3.10.2 -> 3.10.3
 2018-05-04 17:18:23 -05:00
R. RyanTM
24761ef5d4 atlas: 3.10.2 -> 3.10.3 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/atlas/versions.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 3.10.3 with grep in /nix/store/bgqampvgm3zdncg3206n7qnvyvl0jipj-atlas-3.10.3
- directory tree listing: https://gist.github.com/a7dd287df10b13796423e3c2df0850eb
 2018-04-30 23:08:21 -07:00
Timo Kaufmann
a0076a4fb6 rubiks: fix build 2018-04-27 17:53:58 +02:00
Daiderd Jordan
bae15c811f
sympow: don't use placeholder 2018-04-26 22:50:36 +02:00
Matthew Justin Bauer
7ebb6212a2
Merge pull request #38805 from timokau/zn_poly-init 
zn_poly: init at 0.9
 2018-04-24 09:28:27 -05:00
Timo Kaufmann
28c023e246 zn_poly: init at 0.9 2018-04-22 20:44:06 +02:00
Timo Kaufmann
0c9aaf0814 rankwidth: init at 0.7 2018-04-22 20:11:49 +02:00
Timo Kaufmann
b74e884aab flintqs: init at 1.0 2018-04-21 20:43:56 -05:00
Timo Kaufmann
d0d7894f75 rubiks: init at 20070917 2018-04-21 20:42:58 -05:00
Timo Kaufmann
10124a4743 lcalc: init at 1.23 (#38796) 2018-04-21 20:38:40 -05:00
Jörg Thalheim
f7785dd61c
Merge branch 'master' into minc_ecosystem 2018-04-21 20:18:27 +01:00