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Author SHA1 Message Date
Timo Kaufmann
95909d4fb6 Revert "sage: preload openblasCompat" 
This reverts commit 4900bbee17.

The issue that was supposed to fix is now fixed by lazy-loading rpy2 and
makign sure scipy is loaded before that.
That is not quite as nice, but preloading is now causing its own issues
with openblas 0.3.4:
https://github.com/xianyi/OpenBLAS/issues/1936
 2018-12-28 23:06:05 +01:00
Timo Kaufmann
360eddd3a3 sage: remove outdated patch files 2018-12-28 23:06:05 +01:00
Timo Kaufmann
6f0f06ec89 sage: 8.5.rc1 -> 8.5 2018-12-28 23:06:05 +01:00
Andrey Komarov
bc7aa5d202 iverilog: 2017.08.12 -> 2018.12.15 2018-12-28 07:53:36 -06:00
Frederik Rietdijk
10afccf145 Merge staging-next into staging 2018-12-27 18:11:34 +01:00
R. RyanTM
338cf1a7fc igv: 2.4.15 -> 2.4.16 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/igv/versions
 2018-12-26 10:44:01 +01:00
Jan Tojnar
c45e9d0fac
Merge branch 'master' into staging 2018-12-25 17:03:57 +01:00
Alexey Shmalko
a5306b311b
Merge pull request #52768 from r-ryantm/auto-update/stellarium 
stellarium: 0.18.2 -> 0.18.3
 2018-12-24 16:38:24 +02:00
Jan Tojnar
ef935fa101
Merge branch 'master' into staging 2018-12-24 15:02:29 +01:00
R. RyanTM
c6cc68a510 stellarium: 0.18.2 -> 0.18.3 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/stellarium/versions
 2018-12-24 04:42:47 -08:00
Jörg Thalheim
5bae6dea20
Merge pull request #52669 from r-ryantm/auto-update/verilator 
verilator: 4.006 -> 4.008
 2018-12-22 12:51:50 +01:00
R. RyanTM
d4021ad9e4 verilator: 4.006 -> 4.008 
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
 2018-12-22 03:33:41 -08:00
Dmitry Kalinkin
62aea9510c
Merge pull request #51796 from bachp/dsview-0.99 
dsview: init at 0.99
 2018-12-21 17:40:40 -05:00
Alex Branham
a5fc513079 R: 3.5.1 -> 3.5.2 
Closes https://github.com/NixOS/nixpkgs/pull/52571.
 2018-12-21 13:59:36 +01:00
Pascal Bach
3facb3bf79 dsview: init at 0.99 2018-12-21 10:24:16 +01:00
Samuel Dionne-Riel
3c38cc8058
Merge pull request #51813 from samueldr/aarch64/disable-non-arm-builds-part-1 
aarch64: ZHF for aarch64 (1/??)
 2018-12-20 21:06:52 -05:00
Renaud
6f5ec9d889
Merge pull request #52134 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.17 -> 2.18.20
 2018-12-19 17:53:47 +01:00
Frederik Rietdijk
9ab61ab8e2 Merge staging-next into staging 2018-12-19 09:00:36 +01:00
volth
fed7914539
Merge branch 'staging' into make-perl-pathd 2018-12-18 17:13:27 +00:00
Renaud
921caad16d
Merge pull request #52284 from r-ryantm/auto-update/gtkwave 
gtkwave: 3.3.95 -> 3.3.97
 2018-12-17 16:23:56 +01:00
Gabriel Ebner
21597583f9
Merge pull request #52067 from r-ryantm/auto-update/qalculate-gtk 
qalculate-gtk: 2.8.1 -> 2.8.2
 2018-12-17 09:46:32 +01:00
markuskowa
96b0a38f07
Merge pull request #52015 from r-ryantm/auto-update/star 
star: 2.6.1c -> 2.6.1d
 2018-12-16 23:38:37 +01:00
Timo Kaufmann
b09967d812 sage: 8.5.rc0 -> 8.5.rc1 2018-12-16 21:33:28 +01:00
Jörg Thalheim
33c227c23b
Merge pull request #52392 from r-ryantm/auto-update/calc 
calc: 2.12.7.1 -> 2.12.7.2
 2018-12-16 17:33:43 +00:00
R. RyanTM
ae22d3dc85 cubicle: 1.1.1 -> 1.1.2 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/cubicle/versions
 2018-12-16 17:24:47 +01:00
R. RyanTM
67536060ac calc: 2.12.7.1 -> 2.12.7.2 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/calc/versions
 2018-12-16 07:44:09 -08:00
R. RyanTM
b26ba90c34 jmol: 14.29.28 -> 14.29.29 (#52275) 
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
 2018-12-16 09:22:07 +01:00
R. RyanTM
54ece098fd gtkwave: 3.3.95 -> 3.3.97 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gtkwave/versions
 2018-12-15 18:07:39 -08:00
Michael Raskin
2f0cbb34cf
Merge pull request #52171 from r-ryantm/auto-update/pari 
pari: 2.11.0 -> 2.11.1
 2018-12-15 12:08:50 +00:00
markuskowa
feb0aba969
Merge pull request #52153 from r-ryantm/auto-update/octopus 
octopus: 8.2 -> 8.3
 2018-12-15 11:46:44 +01:00
R. RyanTM
943e6fa283 pari: 2.11.0 -> 2.11.1 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/pari/versions
 2018-12-14 22:17:15 -08:00
volth
bb9557eb7c lib.makePerlPath -> perlPackages.makePerlPath 2018-12-15 03:50:31 +00:00
R. RyanTM
b8e09ad0b5 octopus: 8.2 -> 8.3 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/octopus/versions
 2018-12-14 19:45:56 -08:00
R. RyanTM
b261fb0474 picard-tools: 2.18.17 -> 2.18.20 
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
 2018-12-14 16:27:07 -08:00
R. RyanTM
a7e1717d4b qalculate-gtk: 2.8.1 -> 2.8.2 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/qalculate-gtk/versions
 2018-12-14 07:37:22 -08:00
luz.paz
ab9532b1fe gmsh: 4.0.5 -> 4.0.7 2018-12-14 08:01:20 -05:00
R. RyanTM
87481c2ff1 star: 2.6.1c -> 2.6.1d 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
 2018-12-14 01:07:34 -08:00
Samuel Dionne-Riel
5e1dfd3025 avy: Disable build on aarch64-linux 2018-12-10 14:55:20 -05:00
Samuel Dionne-Riel
7aabdea1ca aspino: Disable build on aarch64-linux 
This is due to glucose not building.
 2018-12-10 14:55:20 -05:00
Samuel Dionne-Riel
516f436614 glucose: Disable build on aarch64-linux 2018-12-10 14:55:20 -05:00
Timo Kaufmann
90bc5ce04d sage: 8.5.beta5 -> 8.5.beta6 2018-12-10 19:36:24 +01:00
Timo Kaufmann
f0ea741a9a
Merge pull request #51786 from symphorien/giac-1.5 
giac: 1.4.9 -> 1.5.0
 2018-12-10 13:40:03 +01:00
Maximilian Bosch
de02111a51
Merge pull request #51534 from jbedo/bowtie2 
bowtie2: fix missing dependencies
 2018-12-10 00:58:51 +01:00
Symphorien Gibol
29242e472e giac: build with nauty support 2018-12-09 23:18:58 +01:00
Symphorien Gibol
2253b3e760 nauty: also install libs 2018-12-09 23:18:53 +01:00
Symphorien Gibol
8b4f885264 giac: add missing optional dependencies 2018-12-09 23:18:53 +01:00
Symphorien Gibol
e7801461e0 giac: don't split in multiple outputs for when gui enabled 
This breaks the Phys and Turtle menu, among other things.
 2018-12-09 23:18:53 +01:00
Symphorien Gibol
b5435d0551 giac: 1.4.9 -> 1.5.0 2018-12-09 23:18:46 +01:00
Frederik Rietdijk
e0950ae9ad Merge master into staging-next 2018-12-08 12:40:13 +01:00
Sebastien Maret
da314a44ea gildas: 20181101_a -> 20181201_a 2018-12-06 12:02:05 +01:00
Justin Bedo
8c5251e3c0
bowtie2: fix missing dependencies 2018-12-05 10:51:30 +11:00
Frederik Rietdijk
a510aa2672 Merge master into staging-next 2018-12-03 12:18:43 +01:00
Timo Kaufmann
5f2b8de75c
Revert "pythonPackages.cypari2: 1.3.1 -> 2.0.1 (#49446)" (#51414) 
This reverts commit d9b650f4cc.

The update is causing segfaults. See
https://trac.sagemath.org/ticket/26442.
 2018-12-03 00:44:33 +01:00
markuskowa
506d4c7e44
Merge pull request #51329 from c0bw3b/cleanup/gnu-https 
Favor HTTPS URLs - the GNU edition
 2018-12-02 16:52:33 +01:00
c0bw3b
0498ccd076 Treewide: use HTTPS on GNU domains 
HTTP -> HTTPS for :
- http://gnu.org/
- http://www.gnu.org/
- http://elpa.gnu.org/
- http://lists.gnu.org/
- http://gcc.gnu.org/
- http://ftp.gnu.org/ (except in fetchurl mirrors)
- http://bugs.gnu.org/
 2018-12-02 15:51:59 +01:00
c0bw3b
0f868d8116 Treewide: use HTTPS on SourceForge 2018-12-02 15:33:08 +01:00
Jan Tojnar
a51a99c690
gobject-introspection: rename package 
camelCase package name was a huge inconsistency in GNOME package set.
 2018-12-02 12:42:29 +01:00
Brenton Horne
10f40f3ac6 scilab-bin: adding application launchers 
Moving the desktop configuration files from
opt/scilab-$ver/share/applications to share/applications, making the
required changes, and moving the icons in opt/scilab-$ver/share/icons to
share/icons. Moving locales, appdata and mime out of there
opt/scilab-${ver} too. Also removing unneeded scilab-${ver} and
scilab-${majorVer} symlinks from bin/.
 2018-12-02 17:53:40 +10:00
Brenton Horne
7041972128 scilab-bin: adding bin/scilab symlink (#51346) 
Should fix #51343, merely adding a scilab symlink within the bin/ directory, so that it can be detected by SageMath.
 2018-12-01 23:25:40 +01:00
Timo Kaufmann
88b69a0d40
Merge pull request #51337 from timokau/sagenb-matplotlib-fix 
sage: misc fixes
 2018-12-01 22:04:48 +01:00
Timo Kaufmann
0e570199de sage: fix jmol integration 2018-12-01 21:31:29 +01:00
Timo Kaufmann
cb73495f02 sagenb: fix matplotlib path 2018-12-01 20:41:40 +01:00
Timo Kaufmann
d9b650f4cc
pythonPackages.cypari2: 1.3.1 -> 2.0.1 (#49446) 2018-12-01 12:57:55 +01:00
Jan Tojnar
c5881ec2c9
Merge remote-tracking branch 'upstream/master' into staging 2018-11-30 20:09:45 +01:00
Frederik Rietdijk
1828a5c5ba Merge master into staging-next 2018-11-30 17:46:21 +01:00
Matthew Bauer
76c7a8bac0
Merge pull request #51205 from matthewbauer/more-setup-hooks 
Add premake & imake setup hook
 2018-11-29 19:36:25 -06:00
Frederik Rietdijk
9b81c7e455 Merge staging-next into staging 2018-11-29 09:18:35 +01:00
Frederik Rietdijk
9db2421d1f Merge master into staging-next 2018-11-29 08:12:56 +01:00
Matthew Bauer
c0a804c747 treewide: add dontUseImakeConfigure where needed 
We need to set dontUseImakeConfigure in a few places to prevent imake
from overriding the default configure phase. This packages all have a
configure script that needs to get run:

- Xaw3d
- R
- tkgate
- ssvnc
 2018-11-28 20:14:45 -06:00
Matthew Bauer
8a4da41849 xearth: use imake setup hook 2018-11-28 20:14:36 -06:00
Will Dietz
d7a0e03cfa
Merge pull request #51162 from dtzWill/update/z3-4.8.3 
z3: 4.8.1 -> 4.8.3
 2018-11-28 18:15:31 -06:00
Timo Kaufmann
aa053197de
Merge pull request #51191 from timokau/sage-fixes 
sage: fix test timeout and downgraded R tests
 2018-11-28 23:10:32 +01:00
Timo Kaufmann
d6376bca6d sage: don't test the downgraded R 
Fails transiently. See https://github.com/NixOS/nixpkgs/pull/49249. The
failures look harmless and are fixed with R 3.5 which will be used in
sage 8.5.
 2018-11-28 22:52:15 +01:00
Timo Kaufmann
359bf7f1e3 sage: disable test timeout 
Hydra build failed due to timeout:
https://hydra.nixos.org/build/84870983
 2018-11-28 22:37:24 +01:00
Timo Kaufmann
4900bbee17 sage: preload openblasCompat 2018-11-28 20:44:09 +01:00
Renaud
d209180c78
Merge pull request #51087 from Luz/librepcb 
librepcb: 20181031 -> 0.1.0
 2018-11-28 08:19:13 +01:00
Will Dietz
a034d90e3b z3: 4.8.1 -> 4.8.3 
https://github.com/Z3Prover/z3/releases/tag/z3-4.8.3
 2018-11-27 22:00:19 -06:00
Timo Kaufmann
7ca2915a50 sage: 8.5.beta4 -> 8.5.beta5 2018-11-27 18:26:16 +01:00
Timo Kaufmann
2dd9a0ed72 Merge remote-tracking branch 'upstream/master' into sage-8.5 2018-11-27 18:25:39 +01:00
R. RyanTM
36a0335d02 picard-tools: 2.18.14 -> 2.18.17 (#50647) 
* picard-tools: 2.18.14 -> 2.18.16

Changelog: https://github.com/broadinstitute/picard/releases/tag/2.18.16
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

* picard-tools: 2.18.16 -> 2.18.17

Changelog: https://github.com/broadinstitute/picard/releases/tag/2.18.17
 2018-11-27 14:31:09 +01:00
Nick Hu
583911a0b2 quantomatic: init at 0.7 2018-11-26 21:51:58 +00:00
Luz
021b6e86fa librepcb: 20181031 -> 0.1.0 2018-11-26 22:33:39 +01:00
Vladimír Čunát
a5de78b7d7
Merge branch 'master' into staging-next 2018-11-26 10:28:00 +01:00
Timo Kaufmann
90cebaf828 sage: 8.5.beta3 -> 8.5.beta4 2018-11-25 19:39:18 +01:00
Timo Kaufmann
2a87caa892 sage: 8.5.beta2 -> 8.5.beta3 2018-11-25 19:39:17 +01:00
Timo Kaufmann
3370247f7f sage: 8.5.beta1 -> 8.5.beta2 2018-11-25 19:39:17 +01:00
Timo Kaufmann
883aa99226 sage: add short tests 2018-11-25 19:39:13 +01:00
Timo Kaufmann
8e7da1b8a4 sage: 8.5.beta0 -> 8.5.beta1 2018-11-25 19:36:21 +01:00
Timo Kaufmann
6138f5d5eb sage: 8.4 -> 8.5.beta0 2018-11-25 19:36:21 +01:00
Timo Kaufmann
2fbde72556
sage: add tkinter as matplotlib backend (#51032) 
Fixes #50959.
 2018-11-25 17:38:45 +01:00
Timo Kaufmann
98c94d3d7d sage: add jupyter notebook support 
Fixes #48544.
 2018-11-25 15:54:31 +01:00
Timo Kaufmann
0c23fa9aaf
Merge pull request #50998 from timokau/sage-refactor 
Sage refactor
 2018-11-24 23:59:28 +01:00
Timo Kaufmann
a0723f1285 sage: don't fix node version 2018-11-24 23:14:38 +01:00
Timo Kaufmann
e28a8ed287 sage: add some flexibility to the test runner 
Make it possible to run individual tests. This is very useful while
git-bisecting.
 2018-11-24 23:14:38 +01:00
Timo Kaufmann
21f9123ea6 sage: remove openblas hack 
The pc files have since been included into the openblas package.
 2018-11-24 23:14:38 +01:00
Timo Kaufmann
3832ddedb9 sage: refactor 2018-11-24 23:14:33 +01:00
c0bw3b
0ea604ac1d Treewide: use https for SourceForge 2018-11-24 19:58:03 +01:00
Timo Kaufmann
9b4a518465 sage: drop known-padics-failure patch 
The failure was not observed for a while and is probably fixed now.
 2018-11-24 19:01:57 +01:00
Timo Kaufmann
ca6475b5e8 sage: drop unused patches 2018-11-24 19:01:57 +01:00
Frederik Rietdijk
c1792242ef Merge staging-next into staging 2018-11-24 10:44:50 +01:00