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Author SHA1 Message Date
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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
 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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gmsh/versions
 2018-10-15 21:54:45 -07:00
R. RyanTM a721411239 gtkwave: 3.3.94 -> 3.3.95 
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
 2018-10-15 21:21:29 -07:00
R. RyanTM fedc17a99d jmol: 14.29.22 -> 14.29.26 
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
 2018-10-15 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
https://repology.org/metapackage/verilator/versions
 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
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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/bowtie2/versions
 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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/calc/versions
 2018-10-03 16:01:08 -07:00
R. RyanTM 98092f7a67 nauty: 26r10 -> 26r11 
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
 2018-10-03 05:54:07 -07:00
R. RyanTM 609f9198f2 verilator: 3.926 -> 4.002 
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
 2018-10-02 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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
 2018-09-29 21:03:17 +02:00
R. RyanTM 7ecc7c9220 gtkwave: 3.3.93 -> 3.3.94 (#47048) 
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
 2018-09-28 23:47:58 +02:00
R. RyanTM b65fbe8fcd gmsh: 4.0.0 -> 4.0.1 (#47060) 
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
 2018-09-28 22:17:32 +02:00
Will Dietz eb91037e7b tree-wide: patchelf used during build -> nativeBuildInputs 
In a few cases it wasn't clear so I left them as-is.

While visiting these moved other things to nativeBuildInputs
when it was clear they were one of these cases:

* makeWrapper
* archive utilities (in order to unpack src)
  * a few of these might no longer be needed but leaving for another day
 2018-09-28 11:43:16 -05:00
Timo Kaufmann 87ca34b895
Merge pull request #47043 from r-ryantm/auto-update/jmol 
jmol: 14.29.19 -> 14.29.22
 2018-09-27 12:09:01 +02:00
Timo Kaufmann 0be6ca9e71 sage: 8.4.beta5 -> 8.4.beta6 2018-09-27 12:08:15 +02:00
Timo Kaufmann 2f6b13950e Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-09-27 12:07:37 +02:00
markuskowa 6f6222c40f openmolcas: 20180529 -> 18.09 (#47410) 2018-09-27 10:47:02 +02:00
Vincent Laporte 23900febe7 coq: 8.8.1 -> 8.8.2 (#47388) 2018-09-26 22:26:39 +02:00
Sebastien Maret 1e67ff3f05 gildas: 20180801_a -> 20180901_a (#46159) 
* gildas: 20180801_a -> 20180801_b

  - Update gildas
  - Remove a patch that has been applied upstream

* gildas: 20180801_b -> 20180901_a
 2018-09-25 16:18:53 +02:00
Dmitry Kalinkin 39c85c3bf9 xfitter: init at 2.0.0 2018-09-24 14:34:49 -04:00
Dmitry Kalinkin 3187db6e8d root5: init at 5.34.36 2018-09-24 14:34:49 -04:00
Frederik Rietdijk 56853dc6d8
Merge pull request #45941 from NixOS/staging-next 
Staging next
 2018-09-23 09:31:28 +02:00
Orivej Desh 7545b7dcf3 platypus: 2017-03-07 -> 2018-07-22 2018-09-21 22:42:28 +00:00
Orivej Desh cefd38b721 samtools: 1.8 -> 1.9 2018-09-21 22:42:28 +00:00
R. RyanTM 730eb9f5f2 jmol: 14.29.19 -> 14.29.22 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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 2018-09-20 12:30:18 -07:00
Frederik Rietdijk de419917a3 Merge master into staging-next 2018-09-18 18:44:48 +02:00
Timo Kaufmann 1217882907 sage: 8.4.beta4 -> 8.4.beta5 2018-09-15 17:23:14 +02:00
Timo Kaufmann c3f652d5a8 Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-09-15 17:22:11 +02:00
Chris Ostrouchov a2bc529f22
siesta: init at 4.0.2 2018-09-14 15:40:25 -04:00
Chris Ostrouchov 2c7295ebe0
quantum-espresso: init at 6.3 2018-09-14 15:40:14 -04:00
Maximilian Bosch 2cfc0bb7ee tamarin-prover: fix ghc 8.4 build (#46597) 
See https://hydra.nixos.org/build/81125645

`tamarin-prover' upstream has a patch to fix GHC 8.4 compilation (and
uses stack lts-12.1 now), but it's not released yet:

a08f6e4007

The build is divided in several derivations, therefore the patch had to
be splitted and rebased for `lib/term', `lib/theory' and `lib/utils' to
ensure that the patch applies properly during the `patchPhase'.

Addresses #45960
 2018-09-13 14:11:09 +02:00
Markus J. Ankenbrand e2df8e7c0f seaview: init at 4.7 (#46595) 2018-09-13 14:10:44 +02:00
Uli Baum 1df2560dde Merge branch 'master' into staging-next 2018-09-13 10:08:53 +02:00
R. RyanTM e94947af0a gromacs: 2018.2 -> 2018.3 (#46275) 
Semi-automatic update generated by
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based on information from
gromacs
 2018-09-12 23:07:27 +02:00
R. RyanTM c4e8db3de0 star: 2.6.0c -> 2.6.1a (#46176) 
Semi-automatic update generated by
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based on information from
star
 2018-09-12 22:49:12 +02:00
Matthew Bauer 40d19d8e7c
Merge pull request #45102 from jbedo/hisat2 
hisat2: init 2.1.0
 2018-09-10 15:11:58 -05:00
Matthew Bauer 05d379f3cf
Merge pull request #46211 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.11 -> 2.18.12
 2018-09-10 14:58:59 -05:00
Silvan Mosberger 10a412f251
almonds: update license 2018-09-09 02:04:34 +02:00
Markus Kowalewski 70e254d6bd
root: add license 2018-09-08 14:51:28 +02:00
Markus Kowalewski 1cff2dd135
pynac: add license 2018-09-08 14:48:19 +02:00
Markus Kowalewski 258c202565
prooftree: add license 2018-09-08 14:44:43 +02:00
Markus Kowalewski 2ed07fdb2b
drgeo: add license + homepage 2018-09-08 14:42:12 +02:00
Timo Kaufmann db784d883c sage: re-add pkg-config aliases 
Those were removed because they were added to openblas itself. There was
an error with that however and it will take some time until the fix
makes its way through staging. For the time being, reverting this part
of 26d5d030fe will fix the sage build.
This commit should be reverted once
408eacbc89 is in master.
 2018-09-07 21:55:41 +02:00
Timo Kaufmann 770c5b8a69 sage: 8.4.beta3 -> 8.4.beta4 2018-09-07 20:56:37 +02:00
Timo Kaufmann 4ab832d6e7 Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-09-07 20:54:09 +02:00
Timo Kaufmann 7521f2863d sage: fix numpy and scipy integration 2018-09-07 18:36:52 +02:00
Timo Kaufmann 759e495881
Merge pull request #46268 from r-ryantm/auto-update/jmol 
jmol: 14.29.17 -> 14.29.19
 2018-09-07 11:32:26 +02:00
R. RyanTM baf51804f0 jmol: 14.29.17 -> 14.29.19 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
jmol
 2018-09-06 19:54:40 -07:00
R. RyanTM f72cba212c picard-tools: 2.18.11 -> 2.18.12 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
picard-tools
 2018-09-06 14:22:26 -07:00
Profpatsch 3e45b61a99 lib/trivial: add a few examples of usage of assertMsg/assertOneOf 2018-09-06 18:14:27 +02:00
Sebastien Maret 5b58c6ac76 gildas: add alternative url for the source code (#46145) 
For each new release, the upstream developers of Gildas move the
source code of the previous release to a different directory. Add this
directory to the list of url to avoid build failure at each new
release.
 2018-09-06 15:10:21 +01:00
Renato Garcia 318c9296fa snakemake: add maintainers (#46117) 2018-09-05 21:46:17 +02:00
xeji bf2a90298a
Merge pull request #46053 from danieldk/mxnet-fixes 
pythonPackages.mxnet: fix build
 2018-09-05 16:07:56 +02:00
Sebastien Maret b76cf0b54c gildas: ignore clang warnings for unused command line arguments 
See #46044
 2018-09-05 12:17:05 +02:00
Daniël de Kok 590ce7d1ae mxnet: fix library dependencies. 
- mxnet now builds the open source MKL DNN library. However, this
  was not included with the build.
- mxnet builds its own OpenMP library, even when OpenMP is provided
  by the system. This leads to problems, so remove the included
  OpenMP implementation:

  https://github.com/apache/incubator-mxnet/pull/12160
 2018-09-04 20:27:25 +02:00
Sebastien Maret 3bc898035d gildas: fix makefile rule 2018-09-04 16:05:44 +02:00
Vladimír Čunát 1428d00aa4
Merge branch 'master' into staging-next 
Hydra: ?compare=1477053
 2018-09-04 13:06:45 +02:00
Daniël de Kok 93a5947158 mxnet: 1.1.0 -> 1.2.1 (#46026) 
Update and fix the build:

- Perl is a build-time requirement.
- Fix hardcoded /bin/bash invocation.
 2018-09-04 11:37:54 +02:00
Ryan Mulligan 7b54a50e97
Merge pull request #45730 from Helkafen/snakemake 
snakemake: init at 5.2.2
 2018-09-02 07:54:13 -07:00
Timo Kaufmann 46e653673e sage: 8.4.beta2 -> 8.4.beta3 2018-09-02 12:42:44 +02:00
Frederik Rietdijk b910b697f6 Merge master into staging 2018-09-02 12:10:33 +02:00
xeji a3434cf4e5
Merge pull request #45921 from markuskowa/homepages 
Cleanup homepage links
 2018-09-02 08:39:30 +02:00
Markus Kowalewski ee54f1f817
plm: remove dead homepage link, mark as broken 2018-09-02 01:46:25 +02:00
Markus Kowalewski 5cf25dded7
symmetrica: update homepage 2018-09-02 01:46:25 +02:00
Markus Kowalewski c184150a22
jags: update homepage + fix license 2018-09-02 01:46:18 +02:00
Markus Kowalewski e5974ddaec
jonprl: update homepage 2018-09-02 00:36:01 +02:00