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2101 Commits

Author SHA1 Message Date
Jörg Thalheim
a24cf5c4f7
Merge pull request #47845 from r-ryantm/auto-update/bowtie2 
bowtie2: 2.3.4.2 -> 2.3.4.3
 2018-10-04 20:19:35 +01:00
Gabriel Ebner
0a7e258012 elan: 0.5.0 -> 0.7.1 2018-10-04 16:33:36 +02:00
R. RyanTM
269efba0aa bowtie2: 2.3.4.2 -> 2.3.4.3 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/bowtie2/versions
 2018-10-03 21:49:10 -07:00
R. RyanTM
98092f7a67 nauty: 26r10 -> 26r11 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/nauty/versions
 2018-10-03 05:54:07 -07:00
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