JakeHillion/nixpkgs
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2936 Commits

Author SHA1 Message Date
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
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
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
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
Jörg Thalheim
eddd2f88bc
verilog: 2019.03.27 -> 2019.08.1 (#65730) 
verilog: 2019.03.27 -> 2019.08.1
 2019-08-02 11:20:17 +01:00
Daniel Schaefer
9c50ec6189 verilog: Add optional dependencies 
Increases the closure size by just 4MB.
 2019-08-02 10:34:39 +02:00
Daniel Schaefer
8b3274178f verilog: 2019.03.27 -> 2019.08.1 
Fixes the build, see: https://github.com/steveicarus/iverilog/issues/247
 2019-08-02 10:31:30 +02:00
Frederik Rietdijk
6f723b9bad Merge master into staging-next 2019-08-02 09:18:37 +02:00
Robin Gloster
c6f1c9044b
Merge pull request #63282 from jbedo/strelka 
strelka: 2.9.5 -> 2.9.10
 2019-08-01 23:44:58 +00:00
Orivej Desh
32fbbc6f9b Merge master into staging 2019-07-25 09:23:21 +00:00
Orivej Desh
b5d1d50aa9 google-gflags: move to aliases.nix 
google-gflags were renamed to gflags in 2012:
https://github.com/gflags/gflags/#25-january-2012

gflags.name will be updated in staging.
 2019-07-25 09:18:32 +00:00
R. RyanTM
a47962010d cryptoverif: 2.01 -> 2.01pl1 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/cryptoverif/versions
 2019-07-23 19:32:45 -05:00
Guanpeng Xu
6988b0b929 mathematica: 11.3.0 -> 12.0.0 (#65031) 
* mathematica: archive version 11

* mathematica: 11.3.0 -> 12.0.0
 2019-07-23 22:23:00 +02:00
worldofpeace
b1bc0645ea gdk-pixbuf: rename from gdk_pixbuf 2019-07-22 18:50:57 -04:00
lewo
481bb449a2
Merge pull request #64897 from bzizou/est-sfs 
est-sfs: init at 2.03
 2019-07-22 22:52:16 +02:00
Robin Gloster
dbfcfe495e
Merge pull request #65183 from r-ryantm/auto-update/scilab-bin 
scilab-bin: 6.0.1 -> 6.0.2
 2019-07-22 17:49:05 +00:00
R. RyanTM
7251e3a2af scilab-bin: 6.0.1 -> 6.0.2 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/scilab-bin/versions
 2019-07-20 09:33:18 -07:00
Justin Bedo
11ed86d873 bedtools: 2.27.1 -> 2.28.0 2019-07-20 14:15:38 +02:00
avitex
44324bdd7c caffe: add python package requirements 2019-07-20 13:17:17 +02:00
avitex
955ed925e5 caffe: fix python build 2019-07-20 13:17:17 +02:00
R. RyanTM
9a6f0ca8b7 stacks: 2.4 -> 2.41 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/stacks/versions
 2019-07-17 09:34:10 +02:00
Ryan Mulligan
e7920cbcfc
Merge pull request #64862 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.20.2 -> 2.20.3
 2019-07-16 20:04:43 -07:00
Bruno Bzeznik
9a22c8c697 est-sfs: init at 2.03 2019-07-16 13:55:59 +02:00
Frederik Rietdijk
a28a9ac156 Merge master into staging-next 2019-07-16 11:15:46 +02:00
R. RyanTM
b7fc14d8e6 picard-tools: 2.20.2 -> 2.20.3 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
 2019-07-15 21:46:51 -07:00
Frederik Rietdijk
800da69c8a
Merge pull request #64551 from jonringer/update-pyproj 
proj: 5.2.0 -> 6.1.1
 2019-07-15 21:14:04 +02:00
Ryan Mulligan
6e03fdd341
Merge pull request #64811 from r-ryantm/auto-update/gp2c 
gp2c: 0.0.11pl1 -> 0.0.11pl2
 2019-07-15 11:30:01 -05:00
R. RyanTM
3ef3712313 gp2c: 0.0.11pl1 -> 0.0.11pl2 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gp2c/versions
 2019-07-15 08:14:30 -07:00
Vladimír Čunát
3686036e02
Merge branch 'master' into staging-next 
Hydra nixpkgs: ?compare=1530372
 2019-07-15 09:39:03 +02:00
Jonathan Ringer
e6223c022b openspace: mark as broken 
Fails to build with GL error
 2019-07-14 09:59:31 -07:00
Théo Zimmermann
3bc04b576a coq: 8.10+beta1 -> 8.10+beta2 2019-07-14 14:58:49 +00:00
worldofpeace
7ce0cc0a6a
Merge pull request #64324 from jbedo/hisat2 
hisat2: fix missing perl dependency
 2019-07-13 13:21:11 -04:00
Frederik Rietdijk
54065ae20d Merge master into staging-next 2019-07-13 09:45:40 +02:00
Daniël de Kok
3a4ba91b4a fasttext: 0.2.0 -> 0.9.1 
Changes:

- Refactoring of internal classes.
- Better unicode handling.

https://github.com/facebookresearch/fastText/releases/tag/v0.9.1
 2019-07-12 02:13:23 +02:00
Frederik Rietdijk
22cb7f25f2 Merge master into staging-next 2019-07-11 09:40:10 +02:00
Ryan Mulligan
508ae42a0f treewide: fix redirect URLs 2019-07-10 12:52:51 -07:00
Frederik Rietdijk
79a03641d5 Merge staging-next into staging 2019-07-09 15:46:26 +02:00
Frederik Rietdijk
74c24385cb Merge master into staging-next 2019-07-09 15:46:00 +02:00
Frederik Rietdijk
7cf5909fad Merge staging-next into staging 2019-07-09 15:44:08 +02:00
Millian Poquet
0513ae77ff simgrid: 3.22.2 -> 3.23 2019-07-08 14:00:14 +02:00
Vladimír Čunát
0746c4dbb4
Merge branch 'master' into staging-next 
There are several thousand rebuilds from master already.
Hydra nixpkgs: ?compare=1528940
 2019-07-06 13:44:40 +02:00
Thomas Tuegel
56d5963382
Merge pull request #54525 from ttuegel/feature/qt-5/wrap-qt-apps 
Wrap Qt applications
 2019-07-05 14:38:10 -05:00
Thomas Tuegel
51d78034a1
wrapQtAppsHook: Remove ad hoc Qt wrappers 2019-07-05 10:42:08 -05:00