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3152 Commits

Author SHA1 Message Date
Robert Scott dc6233b972 aiger: enable for darwin 2019-12-08 18:31:49 +00:00
Renato Alves e18fb092f1 kssd: init at 1.0 2019-12-08 16:48:59 +01:00
R. RyanTM b3262d2284 eagle: 9.5.0 -> 9.5.1 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/eagle/versions
 2019-12-08 15:16:53 +01:00
scalavision 3dfabd6eff svaba: init at 1.1.0 2019-12-08 14:51:05 +01:00
markuskowa 444256039c
Merge pull request #75245 from r-ryantm/auto-update/jmol 
jmol: 14.29.55 -> 14.30.0
 2019-12-08 14:19:56 +01:00
R. RyanTM b40940e9d6 jmol: 14.29.55 -> 14.30.0 2019-12-08 04:52:52 -08:00
Maximilian Bosch e16df73d30
geogebra: 5-0-560-0 -> 5-0-569-0 2019-12-08 03:50:02 +01:00
Jonathan Ringer 9dc8e77e4e giac-with-xcas: fix build 
remove libGLU_combined package and replace with libGL and libGLU
 2019-12-07 16:58:50 -08:00
Calvin Pritchard 1850d616ac NetLogo: 6.0.4 -> 6.1.1 2019-12-07 22:24:26 +01:00
R. RyanTM 8582e5a759 marvin: 19.1.0 -> 19.23.0 2019-12-07 20:41:41 +01:00
Mario Rodas 835705d11b
Merge pull request #75095 from tbenst/bftools 
bftools: 5.9.2 -> 6.3.0
 2019-12-07 03:06:00 -05:00
Vincent Laporte 2942490c2c
coq_8_11: init at 8.11+β1 2019-12-07 07:58:00 +00:00
Tyler Benster 2700559bdc bftools: 5.9.2 -> 6.3.0 2019-12-06 02:11:00 -08:00
Mateusz Kowalczyk 1451a52a38 Remove myself (fuuzetsu) from maintainer lists 
I haven't been doing any maintenance for a long time now and not only
do I get notified, it also creates a fake impression that all these
packages had at least one maintainer when in practice they had none.
 2019-12-05 16:29:48 +09:00
Matt Huszagh 9c7cd63b3d symbiyosys: add yices dependency 
Symbioyosys requires at least smt solver backend
to work out of the box.
 2019-12-04 14:29:31 -06:00
Sébastien Maret c108acaaaf gildas: 20191001_a -> 20191201_a (#73041) 
* gildas: 20191001_a -> 20191101_a

* gildas: 20191101_a -> 20191201_a
 2019-12-04 20:18:39 +01:00
Timo Kaufmann 5c9000014e
Merge pull request #74945 from timokau/sage-no-timeout 
sage: disable test timeout
 2019-12-04 09:55:34 +01:00
Vincent Laporte 3806eff9ca coq_8_10: 8.10.1 → 8.10.2 2019-12-03 13:51:52 +00:00
R. RyanTM 605e88517b paml: 4.9i -> 4.9j 2019-12-01 18:43:58 +01:00
Timo Kaufmann e371a02b6c sage: disable test timeout 
I already did that once in 359bf7f1e3.
That change mysteriously got lost somehow (presumably in some merge
commit).

Nix has its own timeout settings, so there is no risk in running
forever. At the same time, some tests can exceed the default timeout
(30minutes per file for --long tests) when run on many weak cores (like
the aarch64 community builder or some hydra builders).
 2019-12-01 13:23:54 +01:00
Jan Tojnar 8cbc862b83
dconf: move to top-level 2019-12-01 01:01:40 +01:00
R. RyanTM 9e52523747 verilator: 4.020 -> 4.022 2019-11-30 18:27:06 -05:00
R. RyanTM c41deafba3 gtkwave: 3.3.102 -> 3.3.103 2019-12-01 00:21:13 +01:00
R. RyanTM da09e1e772 kallisto: 0.46.0 -> 0.46.1 (#74430) 2019-11-30 21:12:54 +01:00
Jan Tojnar a69ad18da9
Merge branch 'master' into staging-next 2019-11-30 19:44:51 +01:00
R. RyanTM 98e0ead3ba picard-tools: 2.21.1 -> 2.21.3 (#74528) 2019-11-30 16:24:44 +01:00
Frederik Rietdijk d14baf7747 Merge master into staging-next 2019-11-30 08:57:28 +01:00
Ryan Mulligan bc6b377a86
Merge pull request #74412 from r-ryantm/auto-update/hmmer 
hmmer: 3.2.1 -> 3.3
 2019-11-28 06:14:56 -08:00
Jonathan Ringer 0c1c18ca44
Merge branch 'master' into staging-next 2019-11-27 22:57:50 -08:00
R. RyanTM 6563dd3351 hmmer: 3.2.1 -> 3.3 2019-11-27 18:40:23 -08:00
Matthew Bauer e010c1b031
Merge pull request #74092 from veprbl/pr/applgrid_fix 
applgrid: fix build
 2019-11-25 22:22:48 -06:00
John Ericson d60532bc71 coq: Fix setup hook 2019-11-25 14:20:10 +00:00
Dmitry Kalinkin bd0c4dd6ab
root: fix setupHook to work with "set -u" 2019-11-24 17:51:46 -05:00
Frederik Rietdijk 1d18c5a0fe Merge staging-next into staging 2019-11-24 10:13:31 +01:00
Michael Raskin c5e3aec122 golly: fix build 2019-11-22 17:41:46 +01:00
Kai Wohlfahrt 6b2504f9f2 freebayes: 2017-08-23 -> 1.3.1 (2019-06-03) 2019-11-20 09:10:31 -08:00
Frederik Rietdijk 5f8b0d7d99 Merge staging-next into staging 2019-11-19 14:53:29 +01:00
adisbladis c9d8624ccd
treewide: Get rid of libGLU_combined 2019-11-18 20:10:43 +00:00
Mario Rodas 9f9720a567
Merge pull request #73447 from yrashk/streamlit-0.50.2 
streamlit: 0.49.0 -> 0.50.2
 2019-11-16 14:51:06 -05:00
c0bw3b 9367367dfd Treewide: fix URL permanent redirects 
Permanent redirects on homepages and/or source URLs
as reported by Repology
 2019-11-16 01:41:23 +01:00
Jörg Thalheim d729fdcd6e
nifticlib and niftseg: change platform from linux to unix sinc… (#73442) 
nifticlib and niftseg: change platform from linux to unix since these…
 2019-11-15 11:57:17 +00:00
Yurii Rashkovskii a1a2d8d4c0
streamlit: 0.49.0 -> 0.50.2 2019-11-15 08:35:43 +01:00
Ben Darwin 736860d34b nifticlib and niftseg: change platform from linux to unix since these build on OSX 2019-11-14 21:25:10 -05:00
Guanpeng Xu 66d5277375 mathematica: fix version issue with zlib (#73425) 2019-11-14 17:19:30 -05:00
Dmitry Kalinkin 93ee8095b0 snakemake: 5.4.4 -> 5.7.4 (#72929) 
(#72929)
 2019-11-13 00:46:56 +01:00
Renaud 630380651d
Merge pull request #73215 from vbgl/why3-1.2.1 
why3: 1.2.0 → 1.2.1
 2019-11-13 00:12:05 +01:00
Dmitry Kalinkin a84607a0e9
eagle: use mkDerivation provided by qt5 2019-11-12 11:21:06 -05:00
Vincent Laporte a61354f262
why3: 1.2.0 → 1.2.1 2019-11-11 11:30:52 +00:00
Matthew Bauer 5ebd36403e
Merge pull request #70641 from maggesi/rename-z77z-into-maggesi 
Rename z77z into maggesi
 2019-11-07 17:18:20 -05:00
Matthew Bauer 551d9f632d
Merge pull request #72954 from nkpart/nkpart/R-darwin-enable-tcltk 
R: enable tcltk on darwin
 2019-11-07 16:49:46 -05:00
Yurii Rashkovskii 2e52f98ddb streamlit: init at 0.49.0 2019-11-06 11:01:06 -08:00
Timo Kaufmann afb9887dbd sage: backport fix for threejs r109 2019-11-06 14:40:16 +01:00
Timo Kaufmann f64885b9ca sage: fix pkgconfig errors in tests 
python.pkgs.pkgconfig raises an exception on missing packages since
version 1.5.0. Previously those errors were just silently ignored. That
worked fine, since the packages are only missing at runtime (when they
are not really needed) but present at buildtime.

Since this fails the tests now, we just add the packages to
PKG_CONFIG_PATH at runtime. This does not add additional runtime
dependencies. Still, it would be nicer if the sage testssuite would not
test the buildsystem at runtime in the first place.

The breakage was originally caused by the pkgconfig update in
1efa71616f.
 2019-11-06 14:40:13 +01:00
Timo Kaufmann da7ec1c139 sage: ignore werkzeug immutable dict deprecation 2019-11-06 14:40:13 +01:00
Timo Kaufmann f85ce834ce sage: ignore deprecation warnings in rst2sws 
Needs to be fixed upstream (by werkzeug, twisted). Doesn't impact the
functionality and the tests are soon to be removed with the py3 update
anyway.
 2019-11-06 14:40:13 +01:00
Timo Kaufmann af480796c9 sage: ignore cmp deprecation in sagenb 2019-11-06 14:40:13 +01:00
Nick Partridge 22d0ccbd2d R: enable tcltk on darwin 2019-11-06 13:14:11 +10:00
R. RyanTM b7f151df70 yacas: 1.6.1 -> 1.8.0 2019-11-04 23:49:42 -08:00
Franz Pletz 18ab125e83
minisatUnstable: fix build with gcc9 2019-11-05 02:01:18 +01:00
Franz Pletz 8dca8b9ccb
Merge remote-tracking branch 'origin/master' into gcc-9 2019-11-05 01:07:22 +01:00
Franz Pletz 6c3f824540
minisat: fix build with gcc9 2019-11-04 23:07:58 +01:00
scalavision d9b40f6397 deeptools: init at 3.3.1 2019-11-04 02:42:36 -08:00
Franz Pletz 6b10b78872
Merge remote-tracking branch 'origin/master' into gcc-9 2019-11-03 14:44:12 +01:00
Franz Pletz 8e63a6cd13
niftyreg: fix build with gcc9 2019-11-03 14:43:37 +01:00
Franz Pletz dffcb87383
colmap: fix build with gcc9 2019-11-03 14:43:33 +01:00
R. RyanTM 28b0a6a9e0 star: 2.7.2b -> 2.7.3a 2019-11-03 10:23:05 +01:00
R. RyanTM 1faee87692 dcmtk: 3.6.4 -> 3.6.5 2019-11-02 11:12:28 -07:00
Franz Pletz e39773fe5b
megahit: 1.1.4 -> 1.2.9 2019-11-02 15:53:57 +01:00
Gabriel Ebner ac24901d17
libqalculate: 3.4.0 -> 3.5.0 (#72550) 
libqalculate: 3.4.0 -> 3.5.0
 2019-11-02 10:59:06 +01:00
Gabriel Ebner a4f0bfdc87 qalculate-gtk: 3.4.0 -> 3.5.0 2019-11-02 10:54:10 +01:00
Jörg Thalheim 04a079082c
Merge pull request #72539 from r-ryantm/auto-update/jmol 
jmol: 14.29.54 -> 14.29.55
 2019-11-02 07:49:50 +00:00
R. RyanTM b3799c5627 jmol: 14.29.54 -> 14.29.55 2019-11-02 00:16:58 -07:00
R. RyanTM 7f919914bf eprover: 2.3 -> 2.4 2019-11-01 14:00:31 -07:00
Timo Kaufmann f7c1e8f274
Merge pull request #72328 from timokau/sage-ignore-cmp-deprecation 
sage: ignore attrs deprecation warning
 2019-10-30 23:14:07 +01:00
Timo Kaufmann 32827e35d8 sage: ignore attrs deprecation warning 
cmp is deprecated since attrs 19.2.0:
http://www.attrs.org/en/19.2.0/changelog.html

The deprecation warning breaks the doctests.  Fortunately they have a
rather long deprecation window, so we can just wait until upstream(s)
fix this.
 2019-10-30 22:27:00 +01:00
Peter Simons 3bc76218a3
Merge pull request #72058 from nh2/r-static-library 
R: Add enableShared/enableStatic arguments
 2019-10-30 13:31:52 +01:00
Niklas Hambüchen edbe2d8145 R: Add static argument. 
R's autoconf does not use the normal configure flags for that.
 2019-10-30 11:44:02 +01:00
Ben Darwin ddc2955ad9 EZminc: 2017-08-29 -> 2019-07-25; mark unbroken 2019-10-26 09:55:30 -07:00
Alexey Shmalko 140d402cb5
Merge pull request #71991 from iimog/dcmtk 
DCMTK: init at 3.6.4
 2019-10-26 15:15:50 +03:00
Markus Ankenbrand 905245b32c dcmtk: init at 3.6.4 2019-10-26 13:02:50 +02:00
Vincent Laporte a8892b0d76
coq_8_10: 8.10.0 → 8.10.1 2019-10-25 07:58:47 +00:00
Vincent Laporte d56582eb2b coq_8_10: enable CoqIDE 2019-10-25 07:58:02 +00:00
scalavision 535a7006ea truvari: init at 1.3.2 (#70877) 
pythonPackages.pyvcf: init at 0.6.8
 2019-10-24 17:06:42 -04:00
R. RyanTM c6af1f6e03 verilator: 4.018 -> 4.020 
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
 2019-10-24 14:02:00 -05:00
R. RyanTM c300055e11 ott: 0.28 -> 0.29 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ott/versions
 2019-10-23 11:44:13 -07:00
R. RyanTM b8acb48b24 picard-tools: 2.20.8 -> 2.21.1 (#71748) 
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
 2019-10-23 09:34:40 +02:00
R. RyanTM a9551de99a dcm2niix: 1.0.20190410 -> 1.0.20190902 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/dcm2niix/versions
 2019-10-22 16:31:19 -07:00
Timo Kaufmann ed145e8f22
Merge pull request #71694 from r-ryantm/auto-update/nauty 
nauty: 26r11 -> 26r12
 2019-10-22 23:33:48 +02:00
R. RyanTM d93659ffa0 nauty: 26r11 -> 26r12 
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
 2019-10-22 10:14:36 -07:00
R. RyanTM dbab6b7994 jmol: 14.29.53 -> 14.29.54 
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
 2019-10-22 10:06:52 +02:00
Mario Rodas e8e1f42499
Merge pull request #71590 from r-ryantm/auto-update/ginac 
ginac: 1.7.7 -> 1.7.8
 2019-10-21 20:21:31 -05:00
R. RyanTM bf30d5d6f6 ginac: 1.7.7 -> 1.7.8 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ginac/versions
 2019-10-21 15:21:33 -07:00
Michael Raskin a35022aa80
Merge pull request #71566 from r-ryantm/auto-update/golly 
golly: 3.2 -> 3.3
 2019-10-21 19:41:50 +00:00
R. RyanTM b73b9399ba golly: 3.2 -> 3.3 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/golly/versions
 2019-10-21 11:24:52 -07:00
Renaud 410d794f05
Merge pull request #71073 from nyanloutre/betaflight_configurator_10_6_0 
betaflight-configurator: 10.5.1 -> 10.6.0
 2019-10-20 20:01:00 +02:00
Ben Wolsieffer 8d04355d87 qgroundcontrol: 3.3.0 -> 3.5.5, fix build (#71308) 
* qgroundcontrol: 3.3.0 -> 3.5.4, fix build

* qgroundcontrol: 3.5.4 -> 3.5.5
 2019-10-20 19:27:23 +02:00
Emily fecfbe18bd symbiyosys: 2019.08.13 -> 2019.10.11 2019-10-19 12:26:49 -05:00
Daniel Frank b4136a8f5b kicad: 5.1.2 -> 5.1.4, fix ngspice, mark broken on aarch64 (#69584) 2019-10-16 02:02:49 -04:00
Vincent Laporte b4db381443 coq_8_10: 8.10+β3 → 8.10.0 
coqPackages.coq-elpi: master → 1.1.0
 2019-10-16 02:43:46 +00:00
Vincent Laporte 0cc70b5697 coq: do not build CoqIDE for Coq 8.10 
GTK3 at version 3.24.11 has broken pkg-config files
 2019-10-16 02:43:46 +00:00