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3058 Commits

Author SHA1 Message Date
Kai Wohlfahrt
6b2504f9f2 freebayes: 2017-08-23 -> 1.3.1 (2019-06-03) 2019-11-20 09:10:31 -08:00
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
scalavision
d9b40f6397 deeptools: init at 3.3.1 2019-11-04 02:42:36 -08:00
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
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