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2097 Commits

Author SHA1 Message Date
Markus Kowalewski
e5974ddaec
jonprl: update homepage 2018-09-02 00:36:01 +02:00
Vladimír Čunát
2d6179d1e8
Merge branch 'master' into staging 
A few trivial conflicts due to *Platforms mass replace.
 2018-09-01 17:38:18 +02:00
Vladimír Čunát
342d3db703
Merge branch 'staging-next' 
The failure diff seems good-enough on Hydra now.
 2018-09-01 17:02:15 +02:00
Sebastian Meric de Bellefon
93ce77af40 python.pkgs.snakemake: init at 5.2.2 2018-09-01 09:18:19 -04:00
Gabriel Ebner
da3326902a vampire: fix nondeterministic hash 
Probably related to #8567
 2018-09-01 15:03:31 +02:00
R. RyanTM
7fdaf76869 verilator: 3.924 -> 3.926 (#45797) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
verilator
 2018-09-01 12:14:00 +02:00
Robert Schütz
93550cbddf Merge branch 'master' into staging-next 2018-08-31 17:32:48 +02:00
John Ericson
2c2f1e37d4 reewide: Purge all uses stdenv.system and top-level system 
It is deprecated and will be removed after 18.09.
 2018-08-30 17:20:32 -04:00
Vladimír Čunát
8fc6472ace
gnome-documents, tlaplus: fix glib references 2018-08-30 19:47:41 +02:00
Vladimír Čunát
b71b222b4c
Merge #44910: cmake: 3.11.2 -> 3.12.1 2018-08-30 16:04:52 +02:00
Vladimír Čunát
19c68fe28c
Merge branch 'master' into staging 2018-08-30 12:25:43 +02:00
Frederik Rietdijk
6038628ea5 Merge master into staging-next 2018-08-29 20:54:55 +02:00
R. RyanTM
e301589013 gmsh: 3.0.6 -> 4.0.0 (#45592) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gmsh/versions.
 2018-08-27 16:06:28 +02:00
Frederik Rietdijk
7945295410 Merge master into staging 2018-08-27 08:21:50 +02:00
Timo Kaufmann
c614c15f93
Merge pull request #45257 from timokau/openblas-pc 
openblas: add pkg-config aliases
 2018-08-26 20:13:19 +02:00
Timo Kaufmann
0e4160a3a1 pythonPackages.sympy: 1.1.1 -> 1.2 2018-08-26 19:56:44 +02:00
Frederik Rietdijk
c71942eb7e
Merge pull request #44752 from costrouc/costrouc/lammps-update 
material science packages (init and update): lammps, python - ase, pymatgen-lammps, lammps-cython, dftfit
 2018-08-25 19:03:36 +02:00
wucke13
b7e695461e apmplanner2: fixed wrong path in .desktop file 
The `apmplanner2.desktop` file defaults to `/usr/share/...` regardless which out
prefix is given to make. So I chose to fix it manually.
 2018-08-25 00:39:58 +02:00
Vladimír Čunát
7db611f2af
Merge branch 'staging' 
Includes libX11 security update.
 2018-08-24 09:19:43 +02:00
Bignaux Ronan
70d5f16898 astrolabe-generator: init at 3.3 (#45429) 2018-08-23 22:35:05 +02:00
Joachim F
0d80f9659c
Merge pull request #45305 from wucke13/apmplanner2 
apmplanner2: init at 2.0.26
 2018-08-23 14:07:45 +00:00
Matthew Bauer
f7bc33abf0 Revert "treewide: fixup breakage due to absolute compiler path" 
This reverts commit d0888d150333a2c523cd1e46606d6219afe23dc2.
 2018-08-22 01:14:53 +02:00
xeji
6216f5da04
Merge pull request #45263 from r-ryantm/auto-update/bowtie2 
bowtie2: 2.3.4.1 -> 2.3.4.2
 2018-08-21 19:51:36 +02:00
Uli Baum
c47aafde87 bowtie2: broken on aarch64 
never built as far back as hydra logs go.
 2018-08-21 19:11:37 +02:00
Timo Kaufmann
26d5d030fe openblas: add pkg-config aliases 2018-08-21 16:39:57 +02:00
Vladimír Čunát
765d695b89
Merge branch 'staging-next' 
Security fixes for a few packages are included.
 2018-08-21 15:36:02 +02:00
Vladimír Čunát
d0888d1503
treewide: fixup breakage due to absolute compiler path 
Some packages just can't handle them #44767.  It was tempting to try
to abstract this in some way, but I didn't do that ATM.
 2018-08-21 12:34:33 +02:00
xeji
54ff14b6f3
Merge pull request #45399 from markuskowa/license-8 
Add licenses
 2018-08-21 12:05:10 +02:00
Jörg Thalheim
736db8db10
Merge pull request #44951 from rittelle/eagle 
eagle: 7.7 -> 9.1.2
 2018-08-21 10:51:13 +01:00
wucke13
b4531605c3 apmplanner2: init at 2.0.26 
I would like to see more Ground Control Stations in the nixpkgs.
 2018-08-21 02:02:51 +02:00
Markus Kowalewski
a1129ef9cb
glsurf: add license 2018-08-20 21:15:16 +02:00
Markus Kowalewski
3c1819fcce
ginac: add license 2018-08-20 21:02:45 +02:00
Joachim F
6755ab8b34
Merge pull request #44250 from jbedo/strelka 
strelka: init 2.9.5
 2018-08-20 06:24:15 +00:00
Justin Bedo
27960b6acf
strelka: init 2.9.5 2018-08-20 08:58:22 +10:00
rittelle
9e4d2d723a
eagle: 7.7 -> 9.1.2 
Updated eagle to version to 9.1.2 while keeping version 7.7 as eagle7.
 2018-08-19 15:36:08 +02:00
Jörg Thalheim
4609e3abf2
Merge pull request #45303 from markuskowa/molden-up 
molden: 5.7 -> 5.8.2
 2018-08-19 13:32:28 +01:00
Markus Kowalewski
04d283ecda
molden: patch to deactivate extension installer script 2018-08-19 11:29:31 +02:00
Orivej Desh
65663f883c msgpack: rename from libmsgpack 
The project does not use the name "libmsgpack". It variously uses "msgpack" and
"msgpack-c", and "msgpackc" for the name of the library.
 2018-08-18 23:19:54 +00:00
Markus Kowalewski
79bf57ca23
molden: 5.7 -> 5.8.2 2018-08-18 14:24:39 +02:00
Vladimír Čunát
209730208a
Merge branch 'staging-next' 2018-08-17 20:51:31 +02:00
Jörg Thalheim
5cb9703a8f
Merge pull request #45173 from r-ryantm/auto-update/octopus 
octopus: 8.1 -> 8.2
 2018-08-17 16:10:43 +01:00
R. RyanTM
73f1448a1f bowtie2: 2.3.4.1 -> 2.3.4.2 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/bowtie2/versions.
 2018-08-17 06:50:10 -07:00
Justin Bedo
9bd7a4f520
hisat2: init 2.1.0 2018-08-17 23:03:42 +10:00
Vladimír Čunát
cbabebcc2e
Merge branch 'master' into staging-next 
Hydra: ?compare=1473892
 2018-08-17 13:45:21 +02:00
Jörg Thalheim
3dd311bde9
Merge pull request #45220 from r-ryantm/auto-update/gtkwave 
gtkwave: 3.3.92 -> 3.3.93
 2018-08-17 11:58:27 +01:00
Jörg Thalheim
0359c5eb65
Merge pull request #45217 from r-ryantm/auto-update/igv 
igv: 2.4.13 -> 2.4.14
 2018-08-17 11:56:26 +01:00
Peter Simons
a721bc4bf3
Merge pull request #45134 from r-ryantm/auto-update/stellarium 
stellarium: 0.18.1 -> 0.18.2
 2018-08-17 11:55:31 +02:00
R. RyanTM
190bd05de2 gtkwave: 3.3.92 -> 3.3.93 
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.
 2018-08-17 02:05:58 -07:00
R. RyanTM
33ebfbfcf8 igv: 2.4.13 -> 2.4.14 
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.
 2018-08-17 01:23:03 -07:00
R. RyanTM
ae846c0c03 octopus: 8.1 -> 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/octopus/versions.
 2018-08-16 20:04:53 -07:00
Jörg Thalheim
4e9b4a9ca7
Merge pull request #45158 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.10 -> 2.18.11
 2018-08-17 00:36:56 +02:00
R. RyanTM
ff7d82d405 picard-tools: 2.18.10 -> 2.18.11 
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.
 2018-08-16 14:33:38 -07:00
R. RyanTM
c274490146 stellarium: 0.18.1 -> 0.18.2 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/stellarium/versions.
 2018-08-16 12:03:22 -07:00
zimbatm
b7e50d52f0
caffe: add darwin support (#44616) 2018-08-16 12:46:51 +01:00
Gabriel Ebner
f207998d79 qalculate-gtk: 2.6.1 -> 2.6.2 2018-08-16 11:56:27 +02:00
Austin Seipp
d5e496a2bb boolector: 2.4.1 -> 3.0.0, relicensed to MIT 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2018-08-15 20:44:05 -05:00
Austin Seipp
9b64100add btor2tools: init at pre55_8c150b39 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2018-08-15 20:44:05 -05:00
Austin Seipp
68cc845295 lingeling: init at pre1_03b4860d 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2018-08-15 20:44:05 -05:00
Austin Seipp
6e910b2b3d aiger: clean up configurePhase, install multi-output objects/headers 
The library and header files are useful for other tools, such as
the upcoming 'lingeling'.

Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2018-08-15 20:44:05 -05:00
Michael Mercier
b8566965df Update simgrid 3.19.1 -> 3.20 + parallel tests + enable darwin (#42721) 
* simgrid: 3.19.1 -> 3.20

Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/simgrid/versions.

These checks were done:

- built on NixOS
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/smpicc passed the binary check.
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/smpicxx passed the binary check.
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/smpirun passed the binary check.
- Warning: no invocation of /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/tesh had a zero exit code or showed the expected version
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/simgrid-colorizer passed the binary check.
- Warning: no invocation of /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/simgrid_update_xml had a zero exit code or showed the expected version
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/simgrid_convert_TI_traces passed the binary check.
- Warning: no invocation of /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/smpimain had a zero exit code or showed the expected version
- /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20/bin/graphicator passed the binary check.
- 6 of 9 passed binary check by having a zero exit code.
- 4 of 9 passed binary check by having the new version present in output.
- found 3.20 with grep in /nix/store/cvyi6hvgc9rvgrnp7c028xrlzbl7jzb9-simgrid-3.20
- directory tree listing: https://gist.github.com/edefc2f1a2e81412484edc2e45986e03
- du listing: https://gist.github.com/a44f7d57537e93152a8e6c569f8ed1ae

* simgrid: 3.19.1 -> 3.20 + add darwin

- Fix dependencies to enable build on darwin
- Add ctest flag to enable parallel testing

* Use simpler parallel testing logic

because it is already done in nixpkgs/pkgs/stdenv/generic/setup.sh
 2018-08-15 19:54:41 -05:00
Bernard Fortz
22c15abe20 cplex: init at 12.8 (#44029) 
* cplex: init at 12.8

* Removed bundled java from bin directory

* Refactored

* More refactoring

* Added config option for releasePath

* Minor cleanup
 2018-08-15 19:46:09 -05:00
adisbladis
2937e7367f
Merge pull request #45009 from jbaum98/ratpoints-darwin 
ratpoints: 2.1.3 -> 2.1.3.p4; add darwin support
 2018-08-15 15:28:39 +08:00
Jörg Thalheim
0ee6d7e3ab
Merge pull request #45011 from jbaum98/symmetrica-darwin 
symmetrica: Add darwin support
 2018-08-15 07:54:56 +02:00
Jake Waksbaum
47aa6abe96 ratpoints: 2.1.3 -> 2.1.3.p4; add darwin support 2018-08-14 11:27:59 -04:00
Jake Waksbaum
8ae47fa81a symmetrica: Add darwin support 2018-08-14 11:23:21 -04:00
Jake Waksbaum
be81e1e29c gfan: Add darwin support 2018-08-14 00:16:46 -04:00
Vladimír Čunát
5b0398dc36
Merge branch 'master' into staging-next 
Conflicts: gobby and libinfinity - I took the hand-edited versions
instead of those resuting from the mass-replacement.

Hydra: ?compare=1473190
 2018-08-13 20:43:59 +02:00
Sebastien Maret
b4599987e3 gildas: 20180701_a -> 20180801_a 2018-08-13 15:17:15 +02:00
Gabriel Ebner
7478da5e84
Merge pull request #42885 from smaret/gildas 
gildas: 20180601_a -> 20180701_a
 2018-08-13 10:55:18 +02:00
Andrew Childs
07bd1d8737 kicad: use default cmake 2018-08-13 11:05:54 +09:00
Samuel Dionne-Riel
c9035c6e12
Merge pull request #44681 from r-ryantm/auto-update/vcftools 
vcftools: 0.1.15 -> 0.1.16
 2018-08-12 19:26:38 -04:00
Vladimír Čunát
00df25ee57
Merge branch 'master' into staging-next 
Hydra: ?compare=1472947
 2018-08-12 10:33:41 +02:00
Chris Ostrouchov
9745611ed6
lammps: 16Feb16 -> patch_2Aug2018 
Major changes and update to lammps build

 - using fetchFromGitHub to get source instead of lammps mirror
 - configurable lammps packages included and includes for compilation
 - cleaner build script
 - preserving the executable, shared library names, and include headers
 2018-08-10 16:35:54 -04:00
Sebastien Maret
e3b42396c6 gildas: update source url 2018-08-10 10:13:31 +02:00
Sebastien Maret
170426510e gildas: patch perl interpreter path 2018-08-10 10:04:27 +02:00
Silvan Mosberger
68d3350433
Merge pull request #44837 from Infinisil/fix/sad 
sad: fix build
 2018-08-09 22:36:14 +02:00
Jake Waksbaum
3babbaaa47 palp: Add darwin support (#44829) 2018-08-09 22:28:27 +02:00
Silvan Mosberger
e710f80018
sad: fix build 2018-08-09 22:13:44 +02:00
Frederik Rietdijk
d9fa74ba78 Merge master into staging 2018-08-09 18:28:15 +02:00
Austin Seipp
752284680b symbiyosys: 2018.05.03 -> 2018.07.26 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2018-08-08 19:49:42 -05:00
R. RyanTM
f5f55e4727 vcftools: 0.1.15 -> 0.1.16 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/vcftools/versions.
 2018-08-08 00:48:04 -07:00
Timo Kaufmann
291018b34e arb: 2.13.0 -> 2.14.0 (#44600) 2018-08-07 16:38:34 +02:00
symphorien
0ca40a51c7 gwyddion, ripser: fix derivation name (#44577) 2018-08-07 01:21:53 +02:00
Michael Raskin
75cb04672f
Merge pull request #44508 from timokau/cddlib-0.94j 
cddlib: 0.94i -> 0.94j
 2018-08-05 19:03:47 +00:00
Timo Kaufmann
0a44ff7676 cddlib: 0.94i -> 0.94j 
cddlib was autotoolized, incorporated equivalents to the sage patches
and moved to GitHub.
 2018-08-05 19:02:45 +02:00
Michael Raskin
6b0234942b
Merge pull request #44501 from timokau/sage-native-pari 
sage: don't override pari
 2018-08-05 15:14:00 +00:00
Timo Kaufmann
30c822189d sage: don't override pari 
Sage assumes that pari does not use threads. However instead of
disabling them at compile time, we can diable them at runtime instead.
As a result, sage doesn't need its own version of pari anymore. That
means less rebuilds, less complexity and easier debugging.
 2018-08-05 13:48:14 +02:00
Michael Raskin
58384b1dd0 scilab-bin: 5.5.2 -> 6.0.1 2018-08-05 11:27:35 +03:00
Michael Raskin
b79dbfe482
Merge pull request #43281 from timokau/sage-8.3 
sage: 8.2 -> 8.3
 2018-08-04 13:02:06 +00:00
Timo Kaufmann
834a24e0ff sage: don't pin ntl 
Now possible because of the lcalc c++11 patch.
 2018-08-04 14:22:58 +02:00
Timo Kaufmann
e550e5d0c7 lcalc: apply c++11 patch 2018-08-04 14:22:29 +02:00
Timo Kaufmann
fa34f6d41c sage: don't pin pari 2018-08-04 14:22:28 +02:00
Timo Kaufmann
e82c26af9b sage: don't pin singular 2018-08-04 14:22:28 +02:00
Timo Kaufmann
289173366b singular: backport ntl error handling patch 2018-08-04 14:22:27 +02:00
Timo Kaufmann
840b64fdb8 sage: 8.2 -> 8.3 2018-08-04 14:22:21 +02:00
Tuomas Tynkkynen
008fd5fcf5 Merge remote-tracking branch 'upstream/master' into staging 2018-08-04 15:17:42 +03:00
John Ericson
db965063b3 treewide: Make configureFlags lists 2018-08-03 17:06:03 -04:00
John Ericson
85a9913edd treewide: Make more complicated configureFlags lists 2018-08-03 17:06:03 -04:00
John Ericson
632d24f11f scilab: Make configureFlags a list 2018-08-03 17:05:58 -04:00
Robert Schütz
ae3bbf2958 almonds: use python3 2018-08-03 18:04:46 +02:00