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2414 Commits

Author SHA1 Message Date
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
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
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
https://repology.org/metapackage/jmol/versions
 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
https://github.com/ryantm/nixpkgs-update tools. This update was made
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
https://github.com/ryantm/nixpkgs-update tools. This update was made
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
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
Timo Kaufmann
1b42a1ba1e sage: 8.4.beta1 -> 8.4.beta2 2018-08-26 13:09:22 +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 d0888d1503.
 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
Timo Kaufmann
52b9217b50 sage: 8.4.beta0 -> 8.4.beta1 2018-08-16 00:17:14 +02:00
Timo Kaufmann
df97127114 Merge remote-tracking branch 'upstream/master' into sage-8.4 2018-08-15 13:51:07 +02:00
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
Timo Kaufmann
a8b048c686 sage: 8.3 -> 8.4.beta0 2018-08-05 21:09:56 +02:00