Commit graph

2075 commits

Author SHA1 Message Date
Orivej Desh 7545b7dcf3 platypus: 2017-03-07 -> 2018-07-22 2018-09-21 22:42:28 +00:00
Orivej Desh cefd38b721 samtools: 1.8 -> 1.9 2018-09-21 22:42:28 +00:00
Chris Ostrouchov a2bc529f22
siesta: init at 4.0.2 2018-09-14 15:40:25 -04:00
Chris Ostrouchov 2c7295ebe0
quantum-espresso: init at 6.3 2018-09-14 15:40:14 -04:00
Maximilian Bosch 2cfc0bb7ee tamarin-prover: fix ghc 8.4 build (#46597)
See https://hydra.nixos.org/build/81125645

`tamarin-prover' upstream has a patch to fix GHC 8.4 compilation (and
uses stack lts-12.1 now), but it's not released yet:

a08f6e4007

The build is divided in several derivations, therefore the patch had to
be splitted and rebased for `lib/term', `lib/theory' and `lib/utils' to
ensure that the patch applies properly during the `patchPhase'.

Addresses #45960
2018-09-13 14:11:09 +02:00
Markus J. Ankenbrand e2df8e7c0f seaview: init at 4.7 (#46595) 2018-09-13 14:10:44 +02:00
R. RyanTM e94947af0a gromacs: 2018.2 -> 2018.3 (#46275)
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
gromacs
2018-09-12 23:07:27 +02:00
R. RyanTM c4e8db3de0 star: 2.6.0c -> 2.6.1a (#46176)
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
star
2018-09-12 22:49:12 +02:00
Matthew Bauer 40d19d8e7c
Merge pull request #45102 from jbedo/hisat2
hisat2: init 2.1.0
2018-09-10 15:11:58 -05:00
Matthew Bauer 05d379f3cf
Merge pull request #46211 from r-ryantm/auto-update/picard-tools
picard-tools: 2.18.11 -> 2.18.12
2018-09-10 14:58:59 -05:00
Silvan Mosberger 10a412f251
almonds: update license 2018-09-09 02:04:34 +02:00
Markus Kowalewski 70e254d6bd
root: add license 2018-09-08 14:51:28 +02:00
Markus Kowalewski 1cff2dd135
pynac: add license 2018-09-08 14:48:19 +02:00
Markus Kowalewski 258c202565
prooftree: add license 2018-09-08 14:44:43 +02:00
Markus Kowalewski 2ed07fdb2b
drgeo: add license + homepage 2018-09-08 14:42:12 +02:00
Timo Kaufmann db784d883c sage: re-add pkg-config aliases
Those were removed because they were added to openblas itself. There was
an error with that however and it will take some time until the fix
makes its way through staging. For the time being, reverting this part
of 26d5d030fe will fix the sage build.
This commit should be reverted once
408eacbc89 is in master.
2018-09-07 21:55:41 +02:00
Timo Kaufmann 7521f2863d sage: fix numpy and scipy integration 2018-09-07 18:36:52 +02:00
Timo Kaufmann 759e495881
Merge pull request #46268 from r-ryantm/auto-update/jmol
jmol: 14.29.17 -> 14.29.19
2018-09-07 11:32:26 +02:00
R. RyanTM baf51804f0 jmol: 14.29.17 -> 14.29.19
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
jmol
2018-09-06 19:54:40 -07:00
R. RyanTM f72cba212c picard-tools: 2.18.11 -> 2.18.12
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
picard-tools
2018-09-06 14:22:26 -07:00
Profpatsch 3e45b61a99 lib/trivial: add a few examples of usage of assertMsg/assertOneOf 2018-09-06 18:14:27 +02:00
Sebastien Maret 5b58c6ac76 gildas: add alternative url for the source code (#46145)
For each new release, the upstream developers of Gildas move the
source code of the previous release to a different directory. Add this
directory to the list of url to avoid build failure at each new
release.
2018-09-06 15:10:21 +01:00
Renato Garcia 318c9296fa snakemake: add maintainers (#46117) 2018-09-05 21:46:17 +02:00
xeji bf2a90298a
Merge pull request #46053 from danieldk/mxnet-fixes
pythonPackages.mxnet: fix build
2018-09-05 16:07:56 +02:00
Sebastien Maret b76cf0b54c gildas: ignore clang warnings for unused command line arguments
See #46044
2018-09-05 12:17:05 +02:00
Daniël de Kok 590ce7d1ae mxnet: fix library dependencies.
- mxnet now builds the open source MKL DNN library. However, this
  was not included with the build.
- mxnet builds its own OpenMP library, even when OpenMP is provided
  by the system. This leads to problems, so remove the included
  OpenMP implementation:

  https://github.com/apache/incubator-mxnet/pull/12160
2018-09-04 20:27:25 +02:00
Sebastien Maret 3bc898035d gildas: fix makefile rule 2018-09-04 16:05:44 +02:00
Daniël de Kok 93a5947158 mxnet: 1.1.0 -> 1.2.1 (#46026)
Update and fix the build:

- Perl is a build-time requirement.
- Fix hardcoded /bin/bash invocation.
2018-09-04 11:37:54 +02:00
Ryan Mulligan 7b54a50e97
Merge pull request #45730 from Helkafen/snakemake
snakemake: init at 5.2.2
2018-09-02 07:54:13 -07:00
xeji a3434cf4e5
Merge pull request #45921 from markuskowa/homepages
Cleanup homepage links
2018-09-02 08:39:30 +02:00
Markus Kowalewski ee54f1f817
plm: remove dead homepage link, mark as broken 2018-09-02 01:46:25 +02:00
Markus Kowalewski 5cf25dded7
symmetrica: update homepage 2018-09-02 01:46:25 +02:00
Markus Kowalewski c184150a22
jags: update homepage + fix license 2018-09-02 01:46:18 +02:00
Markus Kowalewski e5974ddaec
jonprl: update homepage 2018-09-02 00:36:01 +02:00
Vladimír Čunát 342d3db703
Merge branch 'staging-next'
The failure diff seems good-enough on Hydra now.
2018-09-01 17:02:15 +02:00
Sebastian Meric de Bellefon 93ce77af40 python.pkgs.snakemake: init at 5.2.2 2018-09-01 09:18:19 -04:00
Gabriel Ebner da3326902a vampire: fix nondeterministic hash
Probably related to #8567
2018-09-01 15:03:31 +02:00
R. RyanTM 7fdaf76869 verilator: 3.924 -> 3.926 (#45797)
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
verilator
2018-09-01 12:14:00 +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
Frederik Rietdijk 6038628ea5 Merge master into staging-next 2018-08-29 20:54:55 +02:00
R. RyanTM e301589013 gmsh: 3.0.6 -> 4.0.0 (#45592)
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gmsh/versions.
2018-08-27 16:06:28 +02:00
Frederik Rietdijk 7945295410 Merge master into staging 2018-08-27 08:21:50 +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
Timo Kaufmann 0e4160a3a1 pythonPackages.sympy: 1.1.1 -> 1.2 2018-08-26 19:56:44 +02:00
Frederik Rietdijk c71942eb7e
Merge pull request #44752 from costrouc/costrouc/lammps-update
material science packages (init and update): lammps, python - ase, pymatgen-lammps, lammps-cython, dftfit
2018-08-25 19:03:36 +02:00
wucke13 b7e695461e apmplanner2: fixed wrong path in .desktop file
The `apmplanner2.desktop` file defaults to `/usr/share/...` regardless which out
prefix is given to make. So I chose to fix it manually.
2018-08-25 00:39:58 +02:00
Vladimír Čunát 7db611f2af
Merge branch 'staging'
Includes libX11 security update.
2018-08-24 09:19:43 +02:00
Bignaux Ronan 70d5f16898 astrolabe-generator: init at 3.3 (#45429) 2018-08-23 22:35:05 +02:00
Joachim F 0d80f9659c
Merge pull request #45305 from wucke13/apmplanner2
apmplanner2: init at 2.0.26
2018-08-23 14:07:45 +00:00