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Author SHA1 Message Date
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
Frederik Rietdijk e41154d1ab Merge master into staging-next 2018-11-24 10:43:33 +01:00
Gabriel Ebner 4e1323a0cf vampire: fix nondeterministic hash 
Probably related to #8567
 2018-11-22 14:15:55 +01:00
Michael Raskin 6fe39605df polymake: init at 3.2r4 2018-11-22 12:29:14 +03:00
Frederik Rietdijk 2219e2578e Merge staging-next into staging 2018-11-22 10:10:40 +01:00
Frederik Rietdijk c31cb577ae Merge master into staging-next 2018-11-22 09:57:08 +01:00
worldofpeace 2e70b40f58
Merge pull request #49376 from dpaetzel/package-netlogo 
NetLogo: init 6.0.4
 2018-11-21 21:37:01 -05:00
Frederik Rietdijk fed881e510 Merge staging-next into staging 2018-11-21 12:39:46 +01:00
Frederik Rietdijk 701375662b Merge master into staging-next 2018-11-21 12:39:20 +01:00
Gabriel Ebner f505340252 iprover: 2.5 -> 2018_Jul_24_11h 2018-11-21 12:15:48 +01:00
David Pätzel fa623ad828 netlogo: init 6.0.4 2018-11-21 09:38:22 +01:00
Matthew Bauer d492f53faf
Merge pull request #50527 from matthewbauer/ninja-check-phase 
Add check phase to ninja setup hook
 2018-11-20 16:55:12 -06:00
markuskowa 0e98312b72
Merge pull request #50734 from r-ryantm/auto-update/gromacs 
gromacs: 2018.3 -> 2018.4
 2018-11-20 22:14:05 +01:00
Frederik Rietdijk aabf1a93bc Merge staging-next into staging 2018-11-20 11:51:11 +01:00
Frederik Rietdijk fd26e7be2a Merge master into staging-next 2018-11-20 11:47:26 +01:00
Renaud 6550c0275e
Merge pull request #50703 from r-ryantm/auto-update/ltl2ba 
ltl2ba: 1.2b1 -> 1.2
 2018-11-19 22:21:52 +01:00
luzpaz 0ec2af3736
gmsh: 4.0.4 -> 4.0.5 
Manually updated
 2018-11-19 11:12:38 -05:00
R. RyanTM 08a0192340 gromacs: 2018.3 -> 2018.4 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gromacs/versions
 2018-11-19 06:47:47 -08:00
R. RyanTM 5648699f6c ltl2ba: 1.2b1 -> 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/ltl2ba/versions
 2018-11-19 02:28:38 -08:00
Frederik Rietdijk e343a85cfb Merge master into staging-next 2018-11-19 09:55:32 +01:00
Matthew Bauer 2c47a4229f treewide: remove ctest usages 
These are already in the generated makefiles!
 2018-11-18 19:31:02 -06:00
Matthew Bauer 2c1d3a9a82 Merge remote-tracking branch 'upstream/master' into staging 2018-11-18 19:02:09 -06:00
Jörg Thalheim 1282ba6ac4
Merge pull request #50554 from r-ryantm/auto-update/verilator 
verilator: 4.004 -> 4.006
 2018-11-18 12:18:45 +00:00
Frederik Rietdijk 0d0d7dcd06 Merge staging-next into staging 2018-11-18 10:41:34 +01:00
Frederik Rietdijk 63c6875f26 Merge master into staging-next 2018-11-18 10:32:12 +01:00
R. RyanTM ee521455da verilator: 4.004 -> 4.006 
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
 2018-11-18 00:14:21 -08:00
Renaud 44f24a1b8c
Merge pull request #50474 from Pneumaticat/boinc-update 
boinc: 7.8.0 -> 7.14.2
 2018-11-17 12:03:09 +01:00
Jörg Thalheim 131f2e93b6
sage: unpin nodePackage version 2018-11-16 21:24:25 +00:00
Kevin Liu c93b16829c
boinc: 7.8.0 -> 7.14.2 2018-11-16 15:52:22 -05:00
Ben Darwin cb6d819b93 niftyseg: init at 1.0.0 2018-11-16 12:29:29 -05:00
Ben Darwin 6aa3deeb50 niftyreg: init at 1.3.9 2018-11-16 12:24:53 -05:00
Jörg Thalheim 218f12db70
Merge pull request #50324 from asymmetric/solc 
solc: 0.4.25 -> 0.5.0
 2018-11-15 21:26:32 +00:00
Jörg Thalheim abb0c81190
z3: restrict to x86_64 
it uses x86-only header:

include <immintrin.h>
          ^~~~~~~~~~~~~
compilation terminated.
src/sat/sat_probing.cpp
make: *** [Makefile:182: util/mpz.o] Error 1
make: *** Waiting for unfinished jobs....
src/sat/sat_parallel.cpp
builder for '/nix/store/vd2wkhic8g77izxv659ackh6hcaamic3-z3-4.8.1.drv' failed with exit code 2
cannot build derivation '/nix/store/h5imnjsf31c45l558gw66vyzb0ickc1m-solc-0.5.0.drv': 1 dependencies couldn't be built
error: build of '/nix/store/h5imnjsf31c45l558gw66vyzb0ickc1m-solc-0.5.0.drv' failed
 2018-11-15 21:25:53 +00:00
Piotr Bogdan 5d0eeeee38 coq2html: switch to default make 2018-11-15 17:41:25 +00:00
Gabriel Ebner b1c149d47a tptp: use urls instead of url 
nix-prefetch-url breaks if the url argument to fetchurl is a list.
 2018-11-15 15:56:18 +01:00
Gabriel Ebner b3844d00f6 tptp: 7.1.0 -> 7.2.0 2018-11-15 15:50:48 +01:00
Renaud 650036f022
Merge pull request #50359 from jfrankenau/gurobi-java 
gurobi: install Java library files
 2018-11-15 14:13:47 +01:00
Johannes Frankenau b4e13e6257 gurobi: install Java library files 2018-11-14 19:38:18 +01:00
Jörg Thalheim 987bd62232
Merge pull request #50232 from wucke13/master 
qgroundcontrol: fixes #49870
 2018-11-14 17:10:05 +00:00
Renaud 7ca9d67948
Merge pull request #50102 from r-ryantm/auto-update/gp2c 
gp2c: 0.0.11 -> 0.0.11pl1
 2018-11-14 16:07:49 +01:00
wucke13 c26b42be74 qgroundcontrol: fixes #49870 
The `.desktop` referenced a non existent script to run `QGroundControl`. This commits adds a `sed` command, which replaces the non existent script by the name of the `QGroundControl` binary in the relevant `.desktop` file.
 2018-11-14 13:12:20 +01:00
markuskowa f597a88542
Merge pull request #50101 from r-ryantm/auto-update/gmsh 
gmsh: 4.0.2 -> 4.0.4
 2018-11-14 12:46:48 +01:00
Markus Kowalewski 644ab709e7
gmsh: restrict platform to x86_64-linux 2018-11-14 12:33:37 +01:00
Markus Kowalewski ced40eabfd
gmsh: use openblas instead of atlas/lapack 
* openblas is properly recognized by cmake
* the cmake patch is no longer neccessary
 2018-11-14 11:41:46 +01:00
Matthew Bauer 2e18ba6c5a
Merge pull request #49776 from matthewbauer/atlas-remove 
atlas: remove
 2018-11-13 19:18:35 -06:00
markuskowa 2823b5e698
Merge pull request #46667 from costrouc/costrouc/lammps-update 
lammps: update, hoomd-blue, dl_poly: init
 2018-11-13 21:00:02 +01:00
Markus J. Ankenbrand bf05da0967 hmmer: 3.1b2 -> 3.2.1 (#50284) 
This version was released in June 2018 and has many bug fixes
and improvements compared to the previous version from 2015.
See: https://cryptogenomicon.org/2018/06/07/hmmer-3-2-release/
 2018-11-13 15:43:44 +01:00
Frederik Rietdijk 3b052406ea Merge staging-next into staging 2018-11-12 19:01:36 +01:00
Frederik Rietdijk daf3297cb4 Merge master into staging-next 2018-11-12 18:59:08 +01:00
Peter Simons 22a802584f
Merge pull request #50179 from Thra11/r-without-jdk 
R: Remove jdk dependency on aarch32/64
 2018-11-12 12:42:39 +01:00
Frederik Rietdijk 1d3bff25db Merge staging-next into staging 2018-11-11 14:28:08 +01:00
Frederik Rietdijk 7863aae5b2 Merge master into staging-next 2018-11-11 08:59:44 +01:00
markuskowa 45a4adb1b3
Merge branch 'master' into atlas-remove 2018-11-11 02:22:04 +01:00
Markus Kowalewski 6533d7588d
colpack: set platform to linux 2018-11-11 02:17:49 +01:00
Tom Hall b51018ed2e R: Remove jdk dependency on aarch32/64 
Add javaSupport as an argument for R. Default to false on arm as there is no free jdk on arm.
 2018-11-10 20:53:26 +00:00
R. RyanTM 2fd0c31673 calc: 2.12.6.8 -> 2.12.7.1 (#50173) 
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
 2018-11-10 15:32:06 +01:00
Gabriel Ebner 698ad2dd4d nasc: 0.5.0 -> 0.5.1 2018-11-10 14:18:31 +01:00
Gabriel Ebner 5f2a7607fa qalculate-gtk: 2.6.2 -> 2.8.1 2018-11-10 13:17:17 +01:00
Frederik Rietdijk 53d00c3351 Merge master into staging-next 2018-11-10 11:08:54 +01:00
Timo Kaufmann ea8d794026
Merge pull request #50092 from r-ryantm/auto-update/jmol 
jmol: 14.29.26 -> 14.29.28
 2018-11-10 10:13:35 +01:00
R. RyanTM 37f01d5bf8 igv: 2.4.14 -> 2.4.15 (#50087) 
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
 2018-11-09 22:42:04 -05:00
R. RyanTM f5b4eb63f3 gp2c: 0.0.11 -> 0.0.11pl1 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gp2c/versions
 2018-11-09 17:56:17 -08:00
R. RyanTM 6f2bb3c275 gmsh: 4.0.2 -> 4.0.4 
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
 2018-11-09 17:41:49 -08:00
R. RyanTM 3902a47bed jmol: 14.29.26 -> 14.29.28 
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
 2018-11-09 16:17:35 -08:00
Jörg Thalheim c44e7b2e1c
Merge pull request #50024 from r-ryantm/auto-update/ngspice 
ngspice: 28 -> 29
 2018-11-09 14:35:44 +00:00
R. RyanTM 791286efd9 ngspice: 28 -> 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/ngspice/versions
 2018-11-09 06:07:46 -08:00
Renaud 5810df24a7
Merge pull request #49834 from smaret/gildas-update 
gildas: 20181001_b -> 20181101_a
 2018-11-09 10:20:32 +01:00
Matthew Bauer 3dcb8c10f5 shogun: remove liblapack 
not needed anymore
 2018-11-08 14:42:29 -06:00
Gabriel Ebner 155595b0c7 eprover: 2.1 -> 2.2 2018-11-07 22:33:25 +01:00
Matthew Bauer 349f3dfe25 shogun: use openblas 
shogun needs the cblas.h header file to be available. It used to get
it from liblapack, but that is not available anymore. Instead we can
use openblasCompat to get it.
 2018-11-07 13:18:33 -06:00
Timo Kaufmann efe6322ce4 pythonPackages.networkx: 2.1 -> 2.2 2018-11-07 20:15:37 +01:00
Timo Kaufmann 72e6e792f6 sage: add fetchSageDiff utility function 2018-11-07 20:15:37 +01:00
Sebastien Maret 1048a7349e gildas: 20181001_b -> 20181101_a 2018-11-06 17:00:10 +01:00
Patrick Hilhorst 9ec40cc3bf
treewide: Fix overrides having wrong versions 2018-11-06 00:06:21 +01:00
John Ericson 48caae5045 Merge remote-tracking branch 'upstream/master' into HEAD 2018-11-05 15:19:33 -05:00
Matthew Bauer 95373d3634 atlas: remove 
atlas is broken and can apparently be removed.

Fixes #49594
 2018-11-04 20:23:12 -06:00
Jörg Thalheim b3ed2b4c18
Merge pull request #49728 from vbgl/acgtk-1.5.0 
acgtk: 1.3.1 -> 1.5.0
 2018-11-04 17:09:34 +00:00
Frederik Rietdijk cb4ff927a1 Merge master into staging-next 2018-11-04 08:49:24 +01:00
Théo Zimmermann dd21f83950 coq_8_9: init at 8.9+beta1 2018-11-04 07:26:29 +00:00
Vincent Laporte 08ac103970
acgtk: 1.3.1 -> 1.5.0 2018-11-04 06:29:27 +00:00
Renaud 848f2f3d0d
Merge pull request #49559 from ikarulus/librepcb 
bump version librepcb-unstable: 2018-06-28 -> 2018-10-31
 2018-11-03 14:38:39 +01:00
Ikarulus f5af5b19f4 librepcb-unstable: 2018-06-28 -> 2018-10-31 2018-11-03 13:01:41 +01:00
Matthew Bauer 7f4b26681d
Merge pull request #49417 from matthewbauer/disallow-native-build-inputs 
Disallow references to nativeBuildInputs
 2018-11-02 20:26:48 -05:00
Kevin Quick 411c665f33
yices: 2.6.0 -> 2.6.1 2018-11-02 15:49:09 -07:00
Jan Tojnar 3493f44727
Merge pull request #49560 from worldofpeace/eos-third-update 
update some elementary thirdparty apps
 2018-11-02 21:29:57 +01:00
worldofpeace 0a2420bccd nasc: 0.4.7 -> 0.5.0 2018-11-02 16:01:05 -04:00
Austin Seipp 3378db6adf Merge branch 'master' into staging 2018-11-02 14:01:15 -05:00
Michael Raskin 722476273c
Merge pull request #49547 from fadenb/simgrid_3.21 
simgrid: 3.20 -> 3.21
 2018-11-02 14:22:47 +00:00
Vladimír Čunát a92a2c8e15
Merge branch 'master' into staging 
Conflict: rename of pythondaemon -> python-daemon.
 2018-11-02 14:40:14 +01:00
Tristan Helmich (omniIT) 4f8cac02c6 simgrid: 3.20 -> 3.21 2018-11-02 14:23:39 +01:00
ikarulus 7bd8805408 kicad 5.0.0 -> 5.0.1 (#49561) 2018-11-02 10:32:32 +01:00
Gabriel Ebner 5de50f8fa3
Merge pull request #49250 from royneary/nim-0.19 
nim: 0.18.0 -> 0.19.0
 2018-11-02 10:20:13 +01:00
Will Dietz c417342cd2
Merge pull request #48579 from dtzWill/update/z3-4.8.1 
z3: 4.7.1 -> 4.8.1
 2018-11-02 04:02:24 -05:00
royneary bb2bae6986 mosdeph: fix compilation with nim 0.19 2018-10-31 22:03:27 +01:00
Frederik Rietdijk 1d196d99be Merge staging-next into staging 2018-10-30 20:35:15 +01:00
Jörg Thalheim 8df0ca2bbc
coq_8_4: remove 
verasco was its only user
 2018-10-30 13:31:11 +00:00
Tuomas Tynkkynen 067d1cf330 Merge remote-tracking branch 'upstream/master' into staging 
Conflicts:
	pkgs/applications/science/math/sage/sage-src.nix
 2018-10-27 19:58:03 +03:00
Timo Kaufmann 2513747356 sage: fix attrname 
This is a minimal change mainly to make sure repology recognizes this
package as sage. I plan a bit more refactoring later, but this is
intentionally kept minimally invasive so that it won't break anything
and can be backported to 18.09.
 2018-10-27 14:18:08 +02:00
Timo Kaufmann 7970a5a475
Merge pull request #49225 from timokau/arb-2.15.1 
arb: 2.14.0 -> 2.15.1
 2018-10-27 12:36:51 +02:00
Timo Kaufmann fbea2cd77a arb: 2.14.0 -> 2.15.1 2018-10-27 11:27:03 +02:00
Timo Kaufmann 2ce2fcfc30 pythonPackages.cython: 0.28.5 -> 0.29 
Needs a sage patch from
https://trac.sagemath.org/ticket/25292
 2018-10-24 20:05:44 +02:00
Joachim F b6a5cd8970
Merge pull request #48812 from mpickering/cedille 
cedille bug fixes
 2018-10-24 15:29:47 +00:00
R. RyanTM c759273e2e star: 2.6.1a -> 2.6.1c 
Semi-automatic update generated by
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based on information from
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 2018-10-24 15:22:22 +02:00
Timo Kaufmann db75fe7313 sage: fix doctest 
The test is depending on the "py2" tag always being added. I patched
that recently to make it possible to test sagedoc individually. Somehow
I missed this doctest.
 2018-10-22 14:52:19 +02:00
Matthew Pickering 08e5ef20d8 cedille: Make a seperate output for the base library 
For now, for normal usage you need to add `${cedille.lib}` to
the `~/.cedille/options` file so that cedille will find the base
libraries. There is no option to pass options by the command line.
 2018-10-22 08:43:07 +00:00
Matthew Pickering f7d4bc2c71 cedille: Apply patch which unbreaks the options file 
See https://github.com/cedille/cedille/issues/29
 2018-10-22 08:42:01 +00:00
Timo Kaufmann b39142cd1f sage: fix dochtml tests 2018-10-21 19:17:07 +02:00
Timo Kaufmann 38c2be5ffe sage: fix docbuild 
This is only a hotfix without really knowing the issue. See
https://groups.google.com/forum/#!msg/sage-packaging/VU4h8IWGFLA/mrmCMocYBwAJ
 2018-10-21 14:16:06 +02:00
Timo Kaufmann a413dedde1
Merge pull request #44527 from timokau/sage-8.4 
[WIP] sage: 8.3 -> 8.4
 2018-10-20 01:34:34 +02:00
Vincent Laporte c091e93b99
Merge pull request #48617 from Zimmi48/passthru-ocamlPackages-in-coq-package 
coq: add ocamlPackages in passthru
 2018-10-19 09:38:07 +00:00
Jörg Thalheim a595b872c8
Merge pull request #48509 from r-ryantm/auto-update/gtkwave 
gtkwave: 3.3.94 -> 3.3.95
 2018-10-19 09:29:23 +01:00
Jörg Thalheim 02405cfe83
Merge pull request #48565 from rprospero/sasview-4.2.0 
Sasview: unstable -> 4.2.0
 2018-10-18 21:44:25 +01:00
Jörg Thalheim 84890ac196
Merge pull request #48653 from vbgl/why3-1.1.0 
why3: 1.0.0 -> 1.1.0
 2018-10-18 18:55:10 +01:00
Timo Kaufmann 7ca1c31dfa sage: 8.4.rc1 -> 8.4 2018-10-18 09:58:36 +02:00
Vincent Laporte bc8d25c1ef
why3: 1.0.0 -> 1.1.0 2018-10-18 05:43:36 +00:00
Jörg Thalheim 4057f2107a
Merge pull request #48511 from r-ryantm/auto-update/gmsh 
gmsh: 4.0.1 -> 4.0.2
 2018-10-17 16:02:01 +01:00
Adam Washington 6be90bf8d7
sasmodels: unstable -> 4.2.0 2018-10-17 14:36:46 +01:00
Théo Zimmermann fa12476755
coq: add ocamlPackages in passthru 
We might need OCaml packages that are not the one Coq is depending on
but they still need to come from the same package set (same OCaml version).
 2018-10-17 13:26:43 +02:00
Will Dietz 51e511130a z3: 4.7.1 -> 4.8.1 2018-10-16 12:28:06 -05:00
Timo Kaufmann d2b5518e1e
Merge pull request #48507 from r-ryantm/auto-update/jmol 
jmol: 14.29.22 -> 14.29.26
 2018-10-16 10:36:39 +02:00
R. RyanTM eeb2ee296c gmsh: 4.0.1 -> 4.0.2 
Semi-automatic update generated by
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based on information from
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 2018-10-15 21:54:45 -07:00
R. RyanTM a721411239 gtkwave: 3.3.94 -> 3.3.95 
Semi-automatic update generated by
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 2018-10-15 21:21:29 -07:00
R. RyanTM fedc17a99d jmol: 14.29.22 -> 14.29.26 
Semi-automatic update generated by
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 2018-10-15 21:05:03 -07:00
Chris Ostrouchov 397e15f89e
lammps: patch_2Aug2018 -> stable_22Aug2018 
nix derivation was cleaned significantly to follow nixpkgs better
 2018-10-15 08:43:57 -04:00
Chris Ostrouchov 7717a2b844
dl-poly-classic: init 1.10 
only mpi version provided
 2018-10-15 08:43:50 -04:00
Matthew Pickering 43ae33728b cedille: init at 1.0.0 2018-10-14 19:17:23 +00:00
R. RyanTM d074fb1940 verilator: 4.002 -> 4.004 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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 2018-10-14 09:01:56 +02:00
Moritz Kiefer 6738033727
alt-ergo: 1.30->2.2.0, ocplib-simplex: 0.3->0.4 2018-10-13 17:45:45 +00:00
Timo Kaufmann f89df0b556 sage: 8.4.rc0 -> 8.4.rc1 2018-10-13 13:27:10 +02:00
Sebastien Maret 4f3c13b84f gildas: 20181001_a -> 20181001_b (#48200) 2018-10-11 11:37:38 +02:00
Vincent Laporte 6113d95235
prooftree: cleaning 2018-10-11 05:59:21 +00:00
Théo Zimmermann 2fdd38ed2d
camlp5_transitional: remove in favor of camlp5 (strict) 2018-10-10 19:44:54 +02:00
Théo Zimmermann 7ac0a23194
prooftree: 0.12 -> 0.13 2018-10-10 19:42:50 +02:00
Théo Zimmermann c76ffb9253
matita: remove broken package 
As requested by Vincent Laporte.
 2018-10-09 09:47:31 +02:00
Théo Zimmermann 34394a38ef
ocamlPackages_3_11_2: remove 
This requires removing also the Coq 8.3 and Matita 0.5.8 packages.

Coq 8.3 was released 8 years ago (2010) and there is no trace left
of users of this version (contrary to Coq 8.4, released 2012).
It is well over time to remove it.

Matita 0.5.8 was released in 2010 and because this version was still
used for teaching according to the official website, a legacy release
(0.5.9) was released in 5 years later to compile with more recent
OCaml libraries.
Updating to 0.5.9 (or a more recent version like 0.99.3) should allow
getting rid of the dependency on older OCaml but it is hard to test
given that the package is already broken before this update.
 2018-10-08 21:10:05 +02:00
Dmitry Kalinkin 5828821b1e
xfitter: extend UB patch to fix all -Wreturn-type issues 2018-10-08 10:59:17 -04:00
Timo Kaufmann 27919e06f1 sage: 8.4.beta7 -> 8.4.rc0 2018-10-07 12:23:10 +02:00
Marco Maggesi 9a5f7b1630 hol_light: 2017-07-06 -> 2018-09-30 
Also handle compatibility with newer version of OCaml (depend on num
library as needed).
 2018-10-06 15:49:09 +00:00
Matthew Bauer c4f344ac44
Merge pull request #47291 from veprbl/pr/xfitter_init 
xfitter: init at 2.0.0
 2018-10-05 22:38:09 -05:00
Jörg Thalheim 5200167f12
Merge pull request #47831 from r-ryantm/auto-update/calc 
calc: 2.12.6.6 -> 2.12.6.8
 2018-10-04 23:31:38 +01:00
Jörg Thalheim a24cf5c4f7
Merge pull request #47845 from r-ryantm/auto-update/bowtie2 
bowtie2: 2.3.4.2 -> 2.3.4.3
 2018-10-04 20:19:35 +01:00
Gabriel Ebner 0a7e258012 elan: 0.5.0 -> 0.7.1 2018-10-04 16:33:36 +02:00
R. RyanTM 269efba0aa bowtie2: 2.3.4.2 -> 2.3.4.3 
Semi-automatic update generated by
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based on information from
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 2018-10-03 21:49:10 -07:00
R. RyanTM 904fd99bb4 calc: 2.12.6.6 -> 2.12.6.8 
Semi-automatic update generated by
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 2018-10-03 16:01:08 -07:00
R. RyanTM 98092f7a67 nauty: 26r10 -> 26r11 
Semi-automatic update generated by
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 2018-10-03 05:54:07 -07:00
R. RyanTM 609f9198f2 verilator: 3.926 -> 4.002 
Semi-automatic update generated by
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 2018-10-02 09:56:10 -05:00
Sebastien Maret 34ac35dfc6 gildas: 20180901_a -> 20181001_a (#47657) 
- Update gildas to the latest version
 - Remove a patch that has been applied upstream
 2018-10-02 12:49:33 +02:00
Austin Seipp 919a3b7f9c symbiyosys: 2018.07.26 -> 2018.09.12 
Signed-off-by: Austin Seipp <aseipp@pobox.com>
 2018-10-01 22:32:54 -05:00
Timo Kaufmann a13eb29485 sage: 8.4.beta6 -> 8.4.beta7 2018-10-01 17:38:20 +02:00
Timo Kaufmann bcc066b569 Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-10-01 14:20:33 +02:00
R. RyanTM 77f8e10fed picard-tools: 2.18.12 -> 2.18.14 (#46978) 
Semi-automatic update generated by
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 2018-09-29 21:03:17 +02:00
R. RyanTM 7ecc7c9220 gtkwave: 3.3.93 -> 3.3.94 (#47048) 
Semi-automatic update generated by
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based on information from
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 2018-09-28 23:47:58 +02:00