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Author SHA1 Message Date
R. RyanTM 609f9198f2 verilator: 3.926 -> 4.002 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/verilator/versions
 2018-10-02 09:56:10 -05:00
Sebastien Maret 34ac35dfc6 gildas: 20180901_a -> 20181001_a (#47657) 
- Update gildas to the latest version
 - Remove a patch that has been applied upstream
 2018-10-02 12:49:33 +02:00
Austin Seipp 919a3b7f9c symbiyosys: 2018.07.26 -> 2018.09.12 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2018-10-01 22:32:54 -05:00
R. RyanTM 77f8e10fed picard-tools: 2.18.12 -> 2.18.14 (#46978) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
 2018-09-29 21:03:17 +02:00
R. RyanTM 7ecc7c9220 gtkwave: 3.3.93 -> 3.3.94 (#47048) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gtkwave/versions
 2018-09-28 23:47:58 +02:00
R. RyanTM b65fbe8fcd gmsh: 4.0.0 -> 4.0.1 (#47060) 
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
 2018-09-28 22:17:32 +02:00
Will Dietz eb91037e7b tree-wide: patchelf used during build -> nativeBuildInputs 
In a few cases it wasn't clear so I left them as-is.

While visiting these moved other things to nativeBuildInputs
when it was clear they were one of these cases:

* makeWrapper
* archive utilities (in order to unpack src)
  * a few of these might no longer be needed but leaving for another day
 2018-09-28 11:43:16 -05:00
Timo Kaufmann 87ca34b895
Merge pull request #47043 from r-ryantm/auto-update/jmol 
jmol: 14.29.19 -> 14.29.22
 2018-09-27 12:09:01 +02:00
markuskowa 6f6222c40f openmolcas: 20180529 -> 18.09 (#47410) 2018-09-27 10:47:02 +02:00
Vincent Laporte 23900febe7 coq: 8.8.1 -> 8.8.2 (#47388) 2018-09-26 22:26:39 +02:00
Sebastien Maret 1e67ff3f05 gildas: 20180801_a -> 20180901_a (#46159) 
* gildas: 20180801_a -> 20180801_b

  - Update gildas
  - Remove a patch that has been applied upstream

* gildas: 20180801_b -> 20180901_a
 2018-09-25 16:18:53 +02:00
Frederik Rietdijk 56853dc6d8
Merge pull request #45941 from NixOS/staging-next 
Staging next
 2018-09-23 09:31:28 +02:00
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
R. RyanTM 730eb9f5f2 jmol: 14.29.19 -> 14.29.22 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/jmol/versions
 2018-09-20 12:30:18 -07:00
Frederik Rietdijk de419917a3 Merge master into staging-next 2018-09-18 18:44:48 +02:00
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
Uli Baum 1df2560dde Merge branch 'master' into staging-next 2018-09-13 10:08:53 +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
Vladimír Čunát 1428d00aa4
Merge branch 'master' into staging-next 
Hydra: ?compare=1477053
 2018-09-04 13:06:45 +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
Frederik Rietdijk b910b697f6 Merge master into staging 2018-09-02 12:10:33 +02:00
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