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3193 Commits

Author SHA1 Message Date
Franz Pletz
81248e703c
xfitter: 2.0.0 -> 2.0.1, fix build w/ gcc9 2019-12-27 03:48:21 +01:00
Dmitry Kalinkin
984ceb1092
Merge pull request #76541 from veprbl/pr/root_python_wrap 
root: wrap python executables
 2019-12-26 12:29:12 -05:00
Dmitry Kalinkin
0b28198f23
root: wrap python executables 
In normal use of ROOT the PYTHONPATH is intended to be set when user
sources the thisroot.{,s}sh. We do that in the setupHook. This covers
the case when thisroot.sh was not sourced.
 2019-12-26 11:49:12 -05:00
Maximilian Bosch
9842c4b107
treewide: update which packages I'm currently maintaining 
Idea shamelessly stolen from 4e60b0efae.

I realized that I don't really know anymore where I'm listed as maintainer and what
I'm actually (co)-maintaining which means that I can't proactively take
care of packages I officially maintain.

As I don't have the time, energy and motivation to take care of stuff I
was interested in 1 or 2 years ago (or packaged for someone else in the
past), I decided that I make this explicit by removing myself from several
packages and adding myself in some other stuff I'm now interested in.

I've seen it several times now that people remove themselves from a
package without removing the package if it's unmaintained after that
which is why I figured that it's fine in my case as the affected pkgs
are rather low-prio and were pretty easy to maintain.
 2019-12-26 15:27:47 +01:00
Franz Pletz
77b6c3cd06
Merge remote-tracking branch 'origin/master' into gcc-9 2019-12-26 14:17:36 +01:00
Timo Kaufmann
8ac53ed0b1 python.pkgs.sympy: 1.4 -> 1.5 
Sage needs some doctest changes. The patch was included upstream.
Modelled after https://trac.sagemath.org/ticket/28911.
 2019-12-26 11:46:42 +01:00
Markus Kowalewski
63d62699e0
marvin: 19.25.0 -> 19.27.0 2019-12-25 15:11:16 +01:00
Jan Tojnar
b1b26f8cf6
Merge pull request #76412 from jtojnar/pangox-compat-drop 
pangox_compat: drop
 2019-12-24 20:04:10 +01:00
Jan Tojnar
aee453e5c9
openmodelica: remove pangox dependency 
It was probably just a dependency of `gtkglext` since I cannot find any reference to `pangox` in the repo.

But cannot verify build since it is broken.
 2019-12-24 16:13:13 +01:00
markuskowa
64b6fa927e
Merge pull request #76285 from r-ryantm/auto-update/jmol 
jmol: 14.30.0 -> 14.30.1
 2019-12-24 02:05:48 +01:00
R. RyanTM
cf6d80a89d marvin: 19.23.0 -> 19.25.0 2019-12-23 13:15:32 -08:00
R. RyanTM
398f11945e jmol: 14.30.0 -> 14.30.1 2019-12-23 09:16:44 -08:00
R. RyanTM
c905a6da5a bcftools: 1.9 -> 1.10.2 2019-12-22 20:00:29 -08:00
Maximilian Bosch
65061ab2ae
stellarium: 0.19.2 -> 0.19.3 
https://github.com/Stellarium/stellarium/releases/tag/v0.19.3
 2019-12-22 13:57:13 +01:00
Alyssa Ross
7887a81193
treewide: fix cargoSha256 (again) 
cargo-vendor output was changed in a4fc84de44.
 2019-12-20 20:08:53 +00:00
Justin Bedo
2191912274
minia: init at 3.2.1 2019-12-20 11:27:04 +11:00
Justin Bedo
6741cff527
last: init at 1042 2019-12-20 11:27:02 +11:00
Jan Tojnar
048faed66a
pcb: 20140316 → 4.2.0 
* Long overdue update
* Clean up the expression
* Drop unneeded pangox_compat – it was probably needed before gtkglext propagated it.
 2019-12-19 00:47:20 +01:00
Justin Bedo
28a057a56b
bedtools: 2.29.1 -> 2.29.2 2019-12-18 10:39:25 +11:00
Mario Rodas
5e5ce79db4
Merge pull request #75807 from jbedo/strelka 
strelka: fix broken build
 2019-12-16 23:52:35 -05:00
Justin Bedo
c3f09c33eb
strelka: fix broken build 2019-12-17 11:20:32 +11:00
Alex Branham
7af84afa2a R: 3.6.1 -> 3.6.2 
Closes https://github.com/NixOS/nixpkgs/pull/75587.
 2019-12-16 18:56:49 +01:00
Florian Klink
0380ed20db
Merge pull request #75657 from flokli/gtkwave-gtk3 
gtkwave: build with gtk3
 2019-12-15 15:07:07 +01:00
Renaud
2a1a4cad38
Merge pull request #75388 from Lassulus/xplanet 
xplanet: 1.3.0 -> 1.3.1
 2019-12-15 14:57:48 +01:00
lassulus
3772d04e1c xplanet: 1.3.0 -> 1.3.1 2019-12-15 14:02:36 +01:00
Florian Klink
ac1a5ac2db gtkwave: build with gtk3 
gtkwave ships a gtk3 flavour on sourceforge. let's use that one.
 2019-12-15 03:54:35 +01:00
Austin Seipp
367676ce82
z3: 4.8.5 -> 4.8.7 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2019-12-14 20:33:59 -06:00
Ben Wolsieffer
bd9549baa9 mavproxy: init at 1.8.17 2019-12-14 11:00:34 -08:00
Vincent Laporte
856d0a44ec
Merge pull request #75141 from vbgl/coq-8.11β1 
coq_8_11: init at 8.11+β1
 2019-12-14 19:13:40 +01:00
Dmitry Kalinkin
b6d8873825 root: 6.12.06 -> 6.18.04 
Also switch to python3.
 2019-12-14 01:28:27 -08:00
Timo Kaufmann
ce013bb430
Merge pull request #75613 from timokau/brial-1.2.6 
brial: 1.2.5 -> 1.2.6, pybrial: use brial src
 2019-12-13 21:47:50 +01:00
Timo Kaufmann
6a800927bb pybrial: 1.2.3 -> 1.2.5, directly use the brial src 
The pybrial package is a bit awkward. It doesn't have its own top-level
attribute, since it has a cyclic dependency with sage. That's one of the
reasons why it rarely gets updated. Its distributed along with brial, so
its best to keep the versions synchronized. The easiest way to do this
is to just re-use the source of brial.
 2019-12-13 20:29:16 +01:00
Robert Scott
c676063047 btor2tools: correct meta information 2019-12-12 10:37:02 -06:00
Robert Scott
b9185a96be boolector: add patch for CVE-2019-7560 2019-12-12 10:37:02 -06:00
markuskowa
3922a30090
Merge pull request #75416 from jbedo/bedtools 
bedtools: 2.29.0 -> 2.29.1
 2019-12-10 23:58:03 +01:00
Justin Bedo
50fbca4bfc
bedtools: fix clang builds 2019-12-11 09:27:57 +11:00
Gabriel Ebner
5f1790101f Merge branch 'auto-update/libqalculate' 2019-12-10 17:38:25 +01:00
Gabriel Ebner
12d9b6929c qalculate-gtk: 3.5.0 -> 3.6.0 2019-12-10 17:34:29 +01:00
Justin Bedo
592d288aa2
bedtools: 2.29.0 -> 2.29.1 2019-12-10 13:24:27 +11:00
R. RyanTM
13c757e69c snakemake: 5.7.4 -> 5.8.1 (#74637) 2019-12-09 20:47:24 +01:00
Robert Scott
2611887c2e lingeling: enable for darwin 2019-12-08 18:32:04 +00:00
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