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Author SHA1 Message Date
Aaron Andersen 063c82fd2f
Merge pull request #68773 from mimame/update/cytoscape-3.7.2 
cytoscape: 3.7.1 -> 3.7.2
 2019-09-15 09:43:11 -04:00
Vladimír Čunát b6c6e1f9e8
Merge branch 'master' into staging-next 2019-09-15 13:18:54 +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
Miguel Madrid Mencía 40b760e07c
cytoscape: 3.7.1 -> 3.7.2 2019-09-14 10:52:46 +02:00
Linus Heckemann f6182da2c6 ants: use itk 4.x 2019-09-13 11:54:21 +02:00
Jan Tojnar 9b6789de73
tree-wide: replace wrapProgram with wrapGApp 
where appropriate
 2019-09-10 17:54:57 +02:00
Izorkin 329a88efa7 treewide: replace mysql.connector-c to libmysqlclient 2019-09-09 15:55:34 +03:00
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
Michael Raskin 4149a662a7 petrinizer: fix build by pinning the neccessary library versions 2019-09-07 13:33:50 +03:00
Frederik Rietdijk 66bc7fc1b3 Merge master into staging-next 2019-09-06 22:46:05 +02:00
Justin Bedo 6beabe7d2c bedtools: 2.28.0 -> 2.29.0 2019-09-06 21:23:15 +02:00
Dmitry Kalinkin d6264f9094
Merge pull request #65726 from smaret/gildas-20190801_a 
gildas: 20190701_a -> 20190901_a
 2019-09-06 11:15:45 -04:00
Jan Tojnar cdf426488b
Merge branch 'master' into staging-next 
Fixed trivial conflicts caused by removing rec.
 2019-09-06 03:20:09 +02:00
Jan Tojnar ed54a5b51d
Merge branch 'gtk-no-plus' 2019-09-06 02:57:51 +02:00
Jan Tojnar 72e7d569a7
tree-wide: s/GTK+/GTK/g 
GTK was renamed.
 2019-09-06 02:54:53 +02:00
Aaron Andersen 11de7aa609
Merge pull request #64322 from jbedo/xenomapper 
xenomapper: init 1.0.2
 2019-09-05 12:08:10 -04:00
Justin Bedo 3f83cbf538
xenomapper: init 1.0.2 2019-09-05 20:50:22 +10:00
Sébastien Maret 4f3eacc2bf
gildas: 20190701_a -> 20190901_a 2019-09-05 12:30:46 +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
worldofpeace 59e68d3b74 treewide: don't use single quotes with placeholder 2019-09-03 13:01:42 -04:00
Timo Kaufmann 84578046aa sage: 8.9.beta7 -> 8.9.beta8 2019-09-03 15:34:28 +02:00
Ryan Mulligan 32f9c619f5
Merge pull request #67969 from petabyteboy/feature/remove-dobuild 
treewide: remove uses of doBuild and doConfigure
 2019-09-02 15:13:47 -07:00
Milan Pässler (work) 185fd61631 treewide: remove uses of doBuild and doConfigure 
doBuild and doConfigure are not actually used by any builders, they were
probably added by mistake and just confuse people.
 2019-09-02 23:42:12 +02:00
Vladimír Čunát f21211ebfe
Merge branch 'master' into staging 2019-09-02 23:25:24 +02:00
Emily d1dfaa79e3 symbiyosys: fix path to bash (again) 
/usr/bin/env works on NixOS normally, but previously sby would fail if
used from inside the Nix sandbox.
 2019-09-01 14:22:49 -05:00
Tadeo Kondrak 2aa9b655f4
kallisto: 0.43.1 -> 0.46.0 2019-08-31 14:06:31 -06:00
Frederik Rietdijk 98ef78326d Merge staging-next into staging 2019-08-31 18:07:33 +02:00
Frederik Rietdijk 96e5474329 Merge master into staging-next 2019-08-31 18:04:31 +02:00
Alyssa Ross 1da1a7a479 pari: 2.11.1 -> 2.11.2 2019-08-31 13:33:00 +00:00
Niklas Hambüchen 9e78f76ade treewide: Remove unnecessary --disable-static (#66759) 
* freetype: Remove unnecessary `--disable-static`.

The true-by-default `dontDisableStatic` already takes care of it.

Fixes freetype not being overridable to have static libs.

* treewide: Remove unnecessary `--disable-static`.

The true-by-default `dontDisableStatic` already takes care of it.

Fixes these packages not being overridable to have static libs.
 2019-08-31 08:10:53 -04:00
Alexander 35ac3344e7 colmap: init at 3.5 (#67759) 
* colmap: init at 3.5
 2019-08-31 08:06:46 -04:00
volth 7bb6b373ab treewide: name -> pname (#67513) 2019-08-31 07:41:22 -04:00
Lassulus a8d26fc34a
Merge pull request #63127 from bzizou/trimal 
trimal: init at 1.4.1
 2019-08-31 13:04:41 +02:00
Frederik Rietdijk ad1d58c622 Merge staging-next into staging 2019-08-31 10:04:20 +02:00
Frederik Rietdijk fc74ba8291 Merge master into staging-next 2019-08-31 09:50:38 +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
Léo Gaspard 8a4721d606
Merge pull request #64669 from luispedro/add_sortmerna 
sortmerna: init at 3.0.3
 2019-08-27 17:19:53 +02:00
Frederik Rietdijk 98640fd482 Merge master into staging-next 2019-08-27 16:36:47 +02:00
Luis Pedro Coelho bc22c2e07f sortmerna: init at 3.0.3 
This is a useful package in bioinformatics, namely in processing
short-read sequencing data from metagenomes
 2019-08-27 00:37:43 +02:00
volth 35d68ef143 treewide: remove redundant quotes 2019-08-26 21:40:19 +00:00
Jonathan Ringer 6f279584fd stp: 2.2.0 -> 2.3.3 2019-08-26 14:00:48 -07:00
Robin Gloster 616b8343c4
Merge remote-tracking branch 'upstream/master' into gcc-8 2019-08-25 18:55:46 +02:00
Vladimír Čunát 985d1ac425
Merge branch 'master' into staging-next 
There were several more conflicts from name -> pname+version;
all auto-solved by kdiff3, hopefully OK.

Hydra nixpkgs: ?compare=1538611
 2019-08-25 14:57:11 +02:00
Gabriel Ebner 440c63a38a vampire: 4.2.2 -> 4.4 2019-08-25 14:43:51 +02:00
Nikolay Amiantov 9015d7a4f1 sumorobot-manager: init at 0.9.0 2019-08-24 19:11:27 +03:00
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
Emily 05c54717f8 symbiyosys: extend platforms 2019-08-23 02:14:40 -05:00
Marek Mahut 44d43368cb
Merge pull request #67155 from r-ryantm/auto-update/tulip 
tulip: 5.1.0 -> 5.2.1
 2019-08-21 21:40:06 +02:00
R. RyanTM 187ec1a8c6 tulip: 5.1.0 -> 5.2.1 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/tulip/versions
 2019-08-20 19:45:43 -07:00
Marek Mahut 51980d6830
Merge pull request #67019 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.20.4 -> 2.20.5
 2019-08-20 20:15:31 +02:00
R. RyanTM 41571dc81a picard-tools: 2.20.4 -> 2.20.5 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
 2019-08-19 21:40:40 -07:00
Marek Mahut b8a9d33bcd
Merge pull request #66884 from markuskowa/upd-octopus 
octopus: 9.0 -> 9.1
 2019-08-19 11:53:01 +02:00
Marek Mahut 22aa7eadf1
Merge pull request #66871 from peterhoeg/f/apmplanner 
apmplanner2: fix build against qt 5.12
 2019-08-19 11:43:40 +02:00
Markus Kowalewski a81bb36249
octopus: 9.0 -> 9.1 
* switch to GitLab download
* cleanup fftw dependence
 2019-08-19 10:24:44 +02:00
Peter Hoeg 374e0ad0a8 pulseview: use mkDerivation 2019-08-19 08:14:21 +02:00
Peter Hoeg abbac2334b apmplanner2: fix build against qt 5.12 2019-08-19 14:01:55 +08:00
Timo Kaufmann 071a4db33e sage: 8.9.beta6 -> 8.9.beta7 2019-08-19 00:16:06 +02:00
Timo Kaufmann e8436f5e23 sage: 8.9.beta5 -> 8.9.beta6 2019-08-18 21:52:27 +02:00
Frederik Rietdijk f65aa21bb2 Merge master into staging-next 2019-08-18 12:53:44 +02:00
Vladimír Čunát 8ed485c67b
Merge #65948: tlaplusToolbox: 1.5.7 -> 1.6.0 2019-08-18 10:11:50 +02:00
Frederik Rietdijk 113dbfeb27
Merge pull request #66596 from emilazy/update-pypy-and-eda-tools 
Update PyPy and FOSS EDA tools
 2019-08-17 17:48:21 +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
Timo Kaufmann 192197dc6c
Merge pull request #65802 from timokau/sage-transient-debug 
sage: add patch to debug transient issue
 2019-08-17 00:33:05 +02:00
Timo Kaufmann 41bb319462 sage: avoid running out of memory during tests 2019-08-16 23:50:55 +02:00
markuskowa 8f5ce70861
Merge pull request #66665 from markuskowa/upd-molden 
molden: 6.1 -> 6.2
 2019-08-15 18:59:50 +02:00
Matthew Bauer ae15177ade calc: don’t include glibc headers in closure 2019-08-15 23:31:14 +09:00
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
Markus Kowalewski 5b0bbcbb6e
molden: 6.1 -> 6.2 2019-08-15 09:35:34 +02:00
Gabriel Ebner 0a1e131077 gmsh: opencascade support 2019-08-14 19:09:40 +02:00
Gabriel Ebner f91904a889 calculix: init at 2.15 2019-08-14 19:09:40 +02:00
Emily a51e3987ad symbiyosys: 2019.04.18 -> 2019.08.13 2019-08-14 00:14:22 -07:00
Dmitry Kalinkin 34224c7ba0
Merge pull request #66117 from veprbl/pr/hepmc_2_06_10 
hepmc: 2.06.09 -> 2.06.10
 2019-08-11 22:16:16 -04:00
Timo Kaufmann 3541df594e
Merge pull request #66396 from timokau/sage-undo-short 
sage: default to long tests again
 2019-08-10 13:16:00 +02:00
Lancelot SIX 8137a78adc
Merge pull request #66063 from lsix/drop_motu_client 
motu_client: drop
 2019-08-10 00:02:12 +02:00
Timo Kaufmann f6265b0da5 sage: default to long tests again 
Changed by accident in 5e58c5f900.
 2019-08-09 18:42:14 +02:00
Timo Kaufmann 9ef44b3431 sage: move sympow cache to .sage 2019-08-09 17:45:14 +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
Timo Kaufmann ddd3faf08e sage: 8.9.beta4 -> 8.9.beta5 2019-08-07 15:33:15 +02:00
Ryan Mulligan 423e09b3b5
Merge pull request #66018 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.20.3 -> 2.20.4
 2019-08-06 21:44:53 -07:00
Gabriel Ebner ef3b016545 Merge branch 'qalc330' 2019-08-06 09:08:58 +02:00
Gabriel Ebner ca1895ace3 qalculate-gtk: 3.2.0 -> 3.3.0 2019-08-06 09:03:45 +02:00
Dmitry Kalinkin ecef988054
hepmc: rename to hepmc2 2019-08-05 17:47:43 -04:00
Lancelot SIX 2e955ca4c5
motu_client: drop 
This fork of cls-motu is unmaintained. Remove it from nixpkgs.
 2019-08-05 14:32:25 +02:00
R. RyanTM 3bfd09b76d picard-tools: 2.20.3 -> 2.20.4 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
 2019-08-04 23:04:42 -07:00
R. RyanTM 5bb58479d7 jmol: 14.29.46 -> 14.29.49 (#65951) 
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
 2019-08-04 22:09:13 +02:00
Badi Abdul-Wahid 40b53a5d0d
tla+ toolbox: 1.5.7 -> 1.6.0 
Bumps to new release of TLA+ Toolbox.

Main change:
- toolbox now includes JRE so those external dependencies are no
longer needed.

Testing:
- nix-build -A tlaplusToolbox
- ./result/bin/tla-toolbox
- pdf generation
- validation of a simple pluscal model
 2019-08-04 09:27:13 -05:00
markuskowa ad0ad1dc71
Merge pull request #65929 from r-ryantm/auto-update/gmsh 
gmsh: 4.4.0 -> 4.4.1
 2019-08-04 15:14:29 +02:00
R. RyanTM 5f3787932f gmsh: 4.4.0 -> 4.4.1 
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
 2019-08-04 04:16:21 -07:00
WilliButz 3d4942c731
Merge pull request #65906 from r-ryantm/auto-update/eagle 
eagle: 9.4.1 -> 9.4.2
 2019-08-04 12:51:29 +02:00
R. RyanTM ea9bff4c0c eagle: 9.4.1 -> 9.4.2 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/eagle/versions
 2019-08-03 22:38:20 -07:00
Jake Waksbaum 3ab32ee8f6 framac: 18 -> 19 and update why3 2019-08-03 14:03:22 +00:00
Timo Kaufmann f6a1fe64eb sage: 8.9.beta3 -> 8.9.beta4 2019-08-02 23:50:45 +02:00
Frederik Rietdijk d20a59d2e5 Merge master into staging-next 2019-08-02 23:27:18 +02:00
Timo Kaufmann 69d9700c61 sage: add list of past test failures 2019-08-02 18:09:18 +02:00
Timo Kaufmann dac4719e0b sage: add patch to debug transient issue 2019-08-02 18:09:15 +02:00