JakeHillion/nixpkgs
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212 Commits

Author SHA1 Message Date
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
Eelco Dolstra
2aa6f262cb Merge remote-tracking branch 'origin/master' into stdenv-updates 2013-02-15 13:36:34 +01:00
Peter Simons
83df975ba8 atlas: allow users to override the CPU configuration used to build ATLAS 2013-02-06 12:27:23 +01:00
Peter Simons
3334f33daf atlas: update to version 3.10.1 
This patch fixes issue #297.
 2013-02-06 11:31:49 +01:00
Eelco Dolstra
5bb548d2e4 Merge remote-tracking branch 'origin/master' into stdenv-updates 2013-01-17 14:19:14 +01:00
Eelco Dolstra
7fd42a8380 Get rid of the "sf" alias for "sourceforge" 2013-01-14 12:00:32 +01:00
Eelco Dolstra
ab3eeabfed Rename buildNativeInputs -> nativeBuildInputs 
Likewise for propagatedBuildNativeInputs, etc.  "buildNativeInputs"
sounds like an imperative rather than a noun phrase.
 2012-12-28 19:20:09 +01:00
Eelco Dolstra
5553546c21 Remove a bunch of unreferenced files 
Plus a small number of obsolete packages (like old versions of qemu).
 2012-11-29 13:43:37 +01:00
Ludovic Courtès
bf08f68ccb blas: really fix installation on FreeBSD 2012-10-18 17:35:00 +02:00
Ludovic Courtès
dc3fafe06d blas: `install -d' on FreeBSD 2012-10-18 10:21:24 +02:00
Michael Raskin
901574fe8a Julia language: update to a fresh version 
Update julia and some of its dependencies

Split PCRE because a lot of packages depend on it and I am not sure we
want to test them in a hurry (and Julia specifies exact version).
 2012-08-02 17:48:36 +04:00
Lluís Batlle i Rossell
8f50680a05 I hope now I guess fine how to tell ATLAS not to accept any simd for i686. 
svn path=/nixpkgs/trunk/; revision=33793
 2012-04-15 12:44:48 +00:00
Lluís Batlle i Rossell
2e753bc4cf Typo again in atlas. 
svn path=/nixpkgs/trunk/; revision=33791
 2012-04-15 08:11:12 +00:00
Lluís Batlle i Rossell
023cd3b7bd Oh, I removed -fPIC in my last atlas commit. I didn't mean to. 
svn path=/nixpkgs/trunk/; revision=33790
 2012-04-15 07:58:58 +00:00
Lluís Batlle i Rossell
30d7a7fbe1 I think we better disable SIMD for i686. Or it can detect whatever the machine has. 
svn path=/nixpkgs/trunk/; revision=33789
 2012-04-14 22:00:12 +00:00
Lluís Batlle i Rossell
60ecc500f9 Trying to fix atlas i686. I set Pentium II and having sse/sse2 at the same time for i686... 
I think Pentium II does not have sse.


svn path=/nixpkgs/trunk/; revision=33787
 2012-04-14 18:58:30 +00:00
Lluís Batlle i Rossell
4250dd8104 I made atlas build for fixed architectures. 
We saw a crash in many computers, in the octave check phase, where octave crashed.
It was due to atlas being built for AMD Family 10h, which has a special SSE
trick that others computer don't have.

For x86_64, atlas is for K7. And for i686, PII.


svn path=/nixpkgs/trunk/; revision=33780
 2012-04-13 18:46:24 +00:00
Michael Raskin
3c69bcf348 Support shared library build; tests do not currently work for shared build. 
svn path=/nixpkgs/trunk/; revision=33613
 2012-04-05 12:18:56 +00:00
Michael Raskin
2f97078c96 Support shared library build 
svn path=/nixpkgs/trunk/; revision=33612
 2012-04-05 12:18:08 +00:00
Peter Simons
e321903ff1 Atlas aborts the build some kind of CPU frequency scaling is detected on the 
build machine because that feature offsets the performance timings. We ignore
that check, however, because with binaries being pre-built on Hydra those
timings aren't accurate for the local machine in the first place. The build log
might show something such as the following:

 | It appears you have cpu throttling enabled, which makes timings
 | unreliable and an ATLAS install nonsensical.  Aborting.
 | See ATLAS/INSTALL.txt for further information
 | Ignoring CPU throttling by user override!

svn path=/nixpkgs/trunk/; revision=32506
 2012-02-23 11:33:26 +00:00
Lluís Batlle i Rossell
4d4d324776 Making liblapack do the check phase 
svn path=/nixpkgs/trunk/; revision=32494
 2012-02-22 22:41:27 +00:00
Lluís Batlle i Rossell
8f7485d784 Making atlas do the check phase. 
svn path=/nixpkgs/trunk/; revision=32493
 2012-02-22 22:40:35 +00:00
Lluís Batlle i Rossell
e4c4ab35e5 I think I fixed atlas for i686. It wants '-b 32'. Why, I don't know. 
svn path=/nixpkgs/trunk/; revision=32471
 2012-02-22 11:37:10 +00:00
Lluís Batlle i Rossell
5e2de19cc1 Fixing octave, so plot(1) works. 
Linking octave with clapack did not work.

I updated lapack, and additionally I build it with atlas, instead of blas. That should give
better performance. I don't know if atlas builds everywhere though.

On the other hand, maybe some programs linking with liblapack will fail. We'll have to check
the hydra reports.

I plan to remove clapack; liblapack provides a C interface too.


svn path=/nixpkgs/trunk/; revision=32464
 2012-02-21 21:43:44 +00:00
Lluís Batlle i Rossell
2847a37fa9 Updating atlas to 3.9.67, the latest development version 
svn path=/nixpkgs/trunk/; revision=32458
 2012-02-21 14:49:36 +00:00
Eelco Dolstra
6609710409 * Get rid of many instances of "args: with args;", and other coding 
guidelines violations.
* Updated libsamplerate to 0.1.7.

svn path=/nixpkgs/trunk/; revision=22782
 2010-07-28 11:55:54 +00:00
David Guibert
3563194637 compile static libraries for blas and lapack 
svn path=/nixpkgs/trunk/; revision=22549
 2010-07-09 13:15:56 +00:00
Eelco Dolstra
0a882d423b * Fix stdenv evaluation - use ${stdenv.shell} instead of 
${stdenv.bash}/bin/bash.

svn path=/nixpkgs/trunk/; revision=19723
 2010-01-29 00:17:59 +00:00
Peter Simons
30bbff2b68 pkgs/development/libraries/science/math/liblapack: fixed license tag 
Thanks to Ludovic Courtès for pointing that out.

svn path=/nixpkgs/trunk/; revision=19687
 2010-01-26 19:28:09 +00:00
Peter Simons
6a61d675bb pkgs/development/libraries/science/math/blas: set license to "public domain" 
It's not entirely clear whether BLAS is in the public domain, but according to
<87636orixx.fsf@gnu.org> Debian did classify it that way, and the license text
sure feels like the authors intend the package to be in the public domain. So
here we are.

svn path=/nixpkgs/trunk/; revision=19686
 2010-01-26 19:28:03 +00:00
Peter Simons
8cb6ced793 pkgs/development/libraries/science/math/liblapack: fixed build and updated to version 3.2.1 
svn path=/nixpkgs/trunk/; revision=19672
 2010-01-26 14:53:13 +00:00
Peter Simons
a5030f06df pkgs/development/libraries/science/math/blas: added BLAS version 20070405 
svn path=/nixpkgs/trunk/; revision=19671
 2010-01-26 14:53:08 +00:00
Marc Weber
94ba737704 fix atlas by Tobias Neumann 
svn path=/nixpkgs/trunk/; revision=15685
 2009-05-21 17:39:17 +00:00
Lluís Batlle i Rossell
645279d544 Updating atlas 
svn path=/nixpkgs/trunk/; revision=14957
 2009-04-08 22:08:05 +00:00
Marc Weber
d97a7e08bc make atlas build again (tested on amd64) 
svn path=/nixpkgs/trunk/; revision=13560
 2008-12-02 22:55:33 +00:00
Pjotr Prins
3ce5cba9c7 Added pkgMaintainer info to these 'biology' section packages. 
svn path=/nixpkgs/trunk/; revision=12987
 2008-10-07 15:12:06 +00:00
Pjotr Prins
b3aa5d6bfc Added meta.pkgMaintainer to biology packages - a claim to fame, or 
you know who to blame!

svn path=/nixpkgs/trunk/; revision=12986
 2008-10-07 15:12:01 +00:00
Pjotr Prins
2391d84867 Two math packages 
svn path=/nixpkgs/trunk/; revision=12955
 2008-10-05 09:01:59 +00:00
Pjotr Prins
73d2e4f49d - Some Ruby interpreter bumped version 
- Kernel headers 2.6.18 added (XEN virtual images)
- unifdef package added for kernel headers 2.6.18
- Python Zope and 4suite added
- Trying bioconductor packages with R-lang (still failing)
- Bumped gmp version
- Added rq cluster runner - still requires extra gems (installs, but does not run)


svn path=/nixpkgs/trunk/; revision=12766
 2008-08-29 13:53:28 +00:00
Pjotr Prins
07595b0397 Introduced biolib package 
svn path=/nixpkgs/trunk/; revision=12535
 2008-08-07 15:01:21 +00:00
Pjotr Prins
289da88ccc Moved NCBI-tools to applications 
svn path=/nixpkgs/trunk/; revision=12004
 2008-06-07 06:34:02 +00:00
Pjotr Prins
d78d018ad8 Added ncbi-tools 
svn path=/nixpkgs/trunk/; revision=12003
 2008-06-06 19:42:00 +00:00