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2969 commits

Author SHA1 Message Date
Bruno Bzeznik 1ba3f3f00f SPAdes: init at 3.13.1 (#63082) 2019-10-03 09:18:48 +00:00
R. RyanTM eca416c469 verilator: 4.016 -> 4.018 
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
 2019-10-01 21:09:12 -05:00
Timo Kaufmann 7a7e9c1b27
Merge pull request #64193 from timokau/sage-8.9 
sage: 8.8 -> 8.9
 2019-09-30 11:13:46 +00:00
Timo Kaufmann d9176bee70 sage: 8.9.rc1 -> 8.9 2019-09-30 11:10:10 +02:00
Ryan Mulligan 8519cd1aa0
Merge pull request #69735 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.20.5 -> 2.20.8
 2019-09-29 15:44:33 -07:00
Emily b2c482b700 verilog: extend platforms 2019-09-28 16:55:21 -05:00
Vladimír Čunát fda4a08d4a
Merge branch 'staging-next' 
There are several security fixes - again, as it consists mainly of the
previously reverted staging-next merge.
 2019-09-28 07:43:04 +02:00
R. RyanTM 8c397c2bc2 picard-tools: 2.20.5 -> 2.20.8 
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
 2019-09-27 18:25:22 -07:00
Aaron Andersen af5176b430
Merge pull request #63117 from bzizou/macse 
macse: init at 2.03
 2019-09-27 17:26:07 -04:00
Vladimír Čunát 217cf982c7
Merge branch 'master' into staging-next 2019-09-27 22:13:02 +02:00
Marek Mahut 5c116916d6
Merge pull request #69575 from r-ryantm/auto-update/ginac 
ginac: 1.7.6 -> 1.7.7
 2019-09-27 22:04:49 +02:00
Michael Raskin 2213e53fcf
Merge pull request #69477 from r-ryantm/auto-update/clingo 
clingo: 5.3.0 -> 5.4.0
 2019-09-27 10:12:24 +00:00
Timo Kaufmann 6181a20ab2
Merge pull request #69609 from r-ryantm/auto-update/jmol 
jmol: 14.29.49 -> 14.29.53
 2019-09-27 09:22:11 +00:00
Joachim F ad773d31e2
Merge pull request #69345 from joachifm/feat/split-version 
Replace uses of splitString for splitting version strings
 2019-09-27 06:19:18 +00:00
R. RyanTM 0826d695de jmol: 14.29.49 -> 14.29.53 
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
 2019-09-26 16:35:12 -07:00
R. RyanTM b7f156625e ginac: 1.7.6 -> 1.7.7 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ginac/versions
 2019-09-26 12:09:29 -07:00
Timo Kaufmann 4a863fa567
Merge pull request #69519 from r-ryantm/auto-update/eclib 
eclib: 20190226 -> 20190909
 2019-09-26 17:27:41 +00:00
Joachim Fasting bad07dfac5
tree-wide: replace uses of splitString "." with lib.versions 
Quoting from the splitString docstring:

   NOTE: this function is not performant and should never be used.

This replaces trivial uses of splitString for splitting version
strings with the (potentially builtin) splitVersion.
 2019-09-26 17:42:49 +02:00
R. RyanTM faf9a73e2f eclib: 20190226 -> 20190909 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/eclib/versions

Relevant sage upstream ticket: https://trac.sagemath.org/ticket/28472
 2019-09-26 16:41:50 +02:00
Jörg Thalheim 9a1b767a55
treewide: remove empty buildInputs 2019-09-26 09:17:23 +01:00
R. RyanTM f54eb7f159 clingo: 5.3.0 -> 5.4.0 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/clingo/versions
 2019-09-26 01:07:35 -07:00
Dmitry Kalinkin c455adcc42
Merge branch 'master' into staging-next 
Fixes eval on darwin after #69072

Resolved conflict in pkgs/tools/security/thc-hydra/default.nix
Basically had to revert a1c0e10564 which
adapts #69210 to master that doesn't yet have
329a88efa7

Tested using maintainers/scripts/eval-release.sh before and after to see
that the fix works
 2019-09-25 19:21:46 -04:00
Timo Kaufmann 78741fc409 sage: 8.9.rc0 -> 8.9.rc1 2019-09-25 10:19:04 +02:00
Timo Kaufmann 1797c9c295 sage: 8.9.beta9 -> 8.9.rc0 
Sage now by default expects the lcalc library to be named Lfunction
(instead of libLfunction). This could be changed by an environment
variable (https://trac.sagemath.org/ticket/28224), but various distros
seem to agree on this standard
(https://groups.google.com/forum/#!topic/sage-packaging/xvh55IxHTZg) so
it's best just to follow it. The old standard was set by sage anyway and
sage is the only consumer of lcalc in nixpkgs.
 2019-09-24 17:51:09 +02:00
Kierán Meinhardt 815d940e52 tamarin-prover: mark as broken because upstream is broken 2019-09-24 15:25:43 +02:00
Bruno Bzeznik e4108becbe macse: init at 2.03 2019-09-24 08:24:07 +02:00
Vladimír Čunát eab41878ac
Merge branch 'master' into staging-next 2019-09-24 08:14:34 +02:00
Timo Kaufmann ba9e5a2785 Merge remote-tracking branch 'upstream/master' into sage-8.9 2019-09-23 23:58:37 +02:00
Timo Kaufmann 995a728684 pynac: 0.7.25 -> 0.7.26 2019-09-23 22:08:23 +02:00
Timo Kaufmann 5aba3be6f9 sage: 8.9.beta8 -> 8.9.beta9 2019-09-23 18:50:59 +02:00
Timo Kaufmann 8593d468ae Merge remote-tracking branch 'upstream/master' into sage-8.9 2019-09-23 17:11:15 +02:00
Timo Kaufmann cbe12344ca sage: add pager to environment 
Temporary fixup while waiting for an upstream fix.
 2019-09-23 15:14:43 +02:00
Vladimír Čunát 22a216849b
Re-Revert "Merge branch 'staging-next'" 
This reverts commit f8a8fc6c7c.
 2019-09-22 09:38:09 +02:00
Vladimír Čunát f8a8fc6c7c
Revert "Merge branch 'staging-next'" 
This reverts commit 41af38f372, reversing
changes made to f0fec244ca.

Let's delay this.  We have some serious regressions.
 2019-09-21 20:05:09 +02:00
Vladimír Čunát 41af38f372
Merge branch 'staging-next' 2019-09-21 13:14:09 +02:00
Matthew Bauer 566796ab13
Merge pull request #69038 from matthewbauer/ncurses5 
treewide: use libtinfo.so.5 where needed
 2019-09-20 23:00:04 -04:00
Bjørn Forsman 5af0d0b5da kicad: fix build 
Fix configure time error:
  ...
  ImportError: No module named wx
  CMake Error at CMakeModules/FindwxPython.cmake:52 (message):
    wxPython/Phoenix does not appear to be installed on the system

Only build tested.

Fixes: f7e28bf5d8 ("Split buildPythonPackage into setup hooks")
 2019-09-20 08:17:58 +02:00
Will Dietz 6429696f43
libqalculate,qalculate-gtk: 3.3.0 -> 3.4.0 2019-09-18 17:05:59 -05:00
Matthew Bauer 4c85abae94 treewide: use libtinfo.so.5 where needed 
This was originally added in

https://github.com/NixOS/nixpkgs/pull/21350

best to use this name for clarity.
 2019-09-18 13:57:20 -04:00
Vladimír Čunát fa4a3af5a7
Merge branch 'master' into staging-next 2019-09-16 19:24:52 +02:00
Vincent Laporte 8288301636 coq_8_10: 8.10+β2 → 8.10+β3 2019-09-16 11:41:43 -05:00
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