Commit graph

1641 commits

Author SHA1 Message Date
Frederik Rietdijk
672bb6b4ab Merge remote-tracking branch 'upstream/master' into HEAD 2018-02-14 21:30:08 +01:00
Jörg Thalheim
6ec8fe0408 z3: also needs setuptools 2018-02-14 10:01:25 +00:00
Timo Kaufmann
0713bde50f sage: Don't build docs by default
This makes the HTML-docs an default-off option. Inline documentation
(`matrix-plot??`) is still available and HTML docs are available online.

Motivation: Get below the Hydra output size limit.
2018-02-13 17:52:41 +01:00
Will Dietz
2974ed9266 avy: fixes to work with clang and musl 2018-02-13 09:44:52 -06:00
Will Dietz
cbdd20878e cvc4: build in parallel 2018-02-13 09:44:45 -06:00
Will Dietz
12e60c232a cvc4: patch up fpu_control usage 2018-02-13 09:44:45 -06:00
Will Dietz
4c767417ea picosat: fix ar and ranlib usage for cross 2018-02-13 09:44:32 -06:00
Will Dietz
36b2706916 picosat: fixup include for unistd.h 2018-02-13 09:44:32 -06:00
Will Dietz
46cbded0de boolector: patch usage of ar and ranlib for cross
eep.
2018-02-13 09:44:32 -06:00
Will Dietz
9138d055bf boolector: fix missing stdint.h include 2018-02-13 09:44:31 -06:00
Jörg Thalheim
a0a3f674a7
Merge pull request #34094 from markuskowa/octopus-pr
octopus: init at 7.2
2018-02-10 14:14:01 +00:00
Jörg Thalheim
08d1400816
Merge pull request #34530 from unode/samtools-old
samtools-old: init at 0.1.19
2018-02-10 08:34:26 +00:00
Jörg Thalheim
80b096b2b3
Merge pull request #34531 from unode/raxml
RAxML: init at 8.2.11 (SSE3 & MPI)
2018-02-10 08:32:19 +00:00
Frederik Rietdijk
50a9d51a09 Merge commit '30d031b5d8d05422586043c3f105f4d9110e4f59' into HEAD 2018-02-08 12:14:07 +01:00
Peter Simons
fa23ff4a7d
Merge pull request #34651 from mnacamura/r-darwin-libcxx
R: add libcxx to default LDFLAGS and CPPFLAGS on Darwin
2018-02-07 08:31:10 +01:00
Tuomas Tynkkynen
4c6c919a31 Merge remote-tracking branch 'upstream/master' into HEAD
Conflicts:
	pkgs/os-specific/linux/kernel/generic.nix
2018-02-07 03:41:24 +02:00
Renato Alves
154d1d2f19
samtools: 1.6 -> 1.7 2018-02-06 15:38:00 +01:00
Mitsuhiro Nakamura
f4a031c63f R: add libcxx to default LDFLAGS and CPPFLAGS on Darwin 2018-02-06 18:57:12 +09:00
Tuomas Tynkkynen
9548028a22 Merge remote-tracking branch 'upstream/master' into staging
Conflicts:
	pkgs/os-specific/linux/cpupower/default.nix
2018-02-06 04:11:23 +02:00
Timo Kaufmann
272e930827 sage: fix non-deterministic build failures
The build was failing on some machines because of a `find` command that
touched files in different orders on different machines.

That confused `make`s timestamp mechanism.
2018-02-05 15:03:24 +01:00
Austin Seipp
0e371a60a5 symbiyosys: 2018.01.10 -> 2018.02.04
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2018-02-04 11:59:35 -06:00
Frederik Rietdijk
c1d79509a0
Merge pull request #34553 from NixOS/python-unstable
Python package updates
2018-02-04 13:29:23 +00:00
Frederik Rietdijk
aaa50d506e python.pkgs.spyder: fix expression
Note I still get
```
This application failed to start because it could not find or load the
Qt platform plugin "xcb"
in "".
```
but that may be because I run it from the store which is not support for
Qt5 applications.
2018-02-04 10:17:35 +01:00
Bjørn Forsman
6b834384f6 bitscope: create derivations with version info
So far the store paths produced by the bitscope derivations have been
version-less. Fix it.
2018-02-03 21:14:50 +01:00
Frederik Rietdijk
c7f535c82d spyder: 3.2.4 -> 3.2.6 2018-02-03 17:43:30 +01:00
Renato Alves
65ea5f8857
samtools_0_1_19: init at 0.1.19
samtools-1.5 already exists but some software requires the older version
2018-02-02 21:49:50 +01:00
Renato Alves
05889c52b9
RAxML: init at 8.2.11 (SSE3 & MPI)
This can potentially be extended to cover all the other compilation
targets. SSE3-PTHREADS and MPI being the most commonly used.
2018-02-02 18:31:40 +01:00
Vladimír Čunát
c9171e5a4c
Merge branch 'master' into staging
Hydra: ?compare=1430035
2018-01-30 19:51:33 +01:00
Renato Alves
b22e4976cb
muscle: init at 3.8.31 2018-01-28 12:32:46 +01:00
Markus Kowalewski
ec6e7c6eeb
octopus: init at 7.2 2018-01-27 16:23:04 -08:00
Tuomas Tynkkynen
c3a658deb1 Merge remote-tracking branch 'upstream/master' into staging 2018-01-27 21:53:16 +02:00
Alexey Shmalko
38fbc93f46
Merge pull request #34156 from arcadio/star
star: init at 2.5.3a
2018-01-27 17:02:16 +02:00
Vladimír Čunát
2d2dbe083f
Merge branch 'master' into staging
Hydra: ?compare=1429281
2018-01-27 09:14:22 +01:00
Timo Kaufmann
b223662ad1 sage: 8.0 -> 8.1, fix sandbox build
The sandboxed build was failing, because it relied heavily on
/usr/bin/env. This is fixed with a lot of shebang patching (both
to system packages and to sage-internal packages).
2018-01-26 14:42:24 +01:00
adisbladis
7a2d35d9db
Merge pull request #34119 from arcadio/master
igv: 2.3.98 -> 2.4.6
2018-01-25 18:33:49 +08:00
Samuel Leathers
efdb0983da
Merge pull request #34199 from arcadio/kallisto
kallisto: init at 0.43.1
2018-01-24 20:43:24 -07:00
Arcadio Rubio García
a7333e9ced kallisto: init at 0.43.1 2018-01-24 16:16:46 +00:00
Arcadio Rubio García
72d675b23c star: init at 2.5.3a 2018-01-24 16:07:15 +00:00
Frederik Rietdijk
769342b37b Merge remote-tracking branch 'upstream/master' into HEAD 2018-01-24 14:17:49 +01:00
Daiderd Jordan
5569851745
R: fix dylib install_name on darwin 2018-01-24 00:23:16 +01:00
Frederik Rietdijk
8510550b77
Merge pull request #34169 from Infinisil/add/almonds
almonds: init at 2015-12-27
2018-01-23 17:37:54 +01:00
Silvan Mosberger
8e8a259df4
almonds: init at 2015-12-27 2018-01-23 14:16:28 +01:00
adisbladis
266979a360
Merge pull request #34125 from arcadio/bwa
bwa: 0.7.16a -> 0.7.17
2018-01-23 20:12:56 +08:00
adisbladis
b0603f514b
Merge pull request #34139 from arcadio/bedtools
bedtools: 2.26.0 -> 2.27.1
2018-01-23 12:56:01 +08:00
Will Dietz
a5a64cfcb1 lean: fixup nativeBuildInputs vs buildInputs 2018-01-22 17:19:02 -06:00
adisbladis
7490d4d698
Merge pull request #34140 from arcadio/picard
picard-tools: 2.7.1 -> 2.17.4
2018-01-22 23:57:10 +08:00
Arcadio Rubio García
612953567d bowtie2: 2.3.3.1 -> 2.3.4 2018-01-22 12:28:06 +00:00
Arcadio Rubio García
12c5dc343f picard-tools: 2.7.1 -> 2.17.4 2018-01-22 12:16:26 +00:00
Arcadio Rubio García
c75e91a374 bedtools: 2.26.0 -> 2.27.1 2018-01-22 12:09:44 +00:00
Arcadio Rubio García
0d05bcae8c bwa: 0.7.16a -> 0.7.17 2018-01-22 01:58:36 +00:00
Arcadio Rubio García
550e6146d4 igv: 2.3.98 -> 2.4.6 2018-01-21 21:07:44 +00:00
Sarah Brofeldt
adf80590ae
Merge pull request #33924 from markuskowa/molden-pr
molden: init at 5.7
2018-01-21 12:19:48 +01:00
Miguel Madrid Mencía
8fb2be6772
weka: 3.8.1 -> 3.8.2 2018-01-18 15:25:35 +01:00
Yegor Timoshenko
506c89c30a maintainers: remove mornfall from packages 2018-01-17 05:17:33 +00:00
Markus Kowalewski
1c1e49a5c5
molden: init at 5.7 2018-01-15 23:06:41 -08:00
Ashley Gillman
245a67df8b dcm2niix: cmake is native, style 2018-01-15 16:53:28 +10:00
Ashley Gillman
271d4a7ca0 dcm2niix: init at 1.0.20170130 2018-01-15 16:45:03 +10:00
David Asabina
b986078593 bitscope: refactored to pass nixpkgs-lint
The linter (nixpkgs-lint) was not able to find the bitscope packages
because `recurseIntoAttrs` was not applied to the suite's set.

The name supplied to `buildFHSUserEnv` produces a binary that
corresponds to the binary names in the deb packages (e.g.: bitscope-dso,
bitscope-chart, bitscope-logic, etc), however; this name does not
constitute a valid nixpkgs name. Valid nixpkgs names satisfy the
`/(.*)(-[0-9].*)$/` pattern, therefore a valid name is merged into the
derivation produced by `buildFHSUserEnv`.
2018-01-14 20:00:10 +01:00
adisbladis
ff94fbc416
Merge pull request #33851 from vbgl/why3-0.88.3
why3: 0.88.1 -> 0.88.3
2018-01-15 01:27:45 +08:00
adisbladis
a41d7b9ea1
Merge pull request #33839 from mimadrid/update/gephi-0.9.2
gephi: 0.9.1 -> 0.9.2
2018-01-15 01:10:52 +08:00
Vincent Laporte
aee1cebda7
why3: 0.88.1 -> 0.88.3 2018-01-14 05:51:06 +00:00
Miguel Madrid Mencía
eb21bf3d99
cytoscape: 3.5.1 -> 3.6.0 2018-01-13 23:21:49 +01:00
Miguel Madrid Mencía
111d4dbc06
gephi: 0.9.1 -> 0.9.2 2018-01-13 23:18:26 +01:00
adisbladis
5f232de6cd
qgroundcontrol: 2.9.4 -> 3.2.7, unbreak build 2018-01-13 04:03:38 +08:00
Luz
e056315a3e librepcb-unstable: init at 2017-12-29 (#33630) 2018-01-11 09:20:00 +00:00
Austin Seipp
4d4340805b symbiyosys: 2017.12.06 -> 2018.01.10
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2018-01-10 14:00:58 -06:00
Symphorien Gibol
bf49c616ee giac: fix build
giac was broken somewhere between 310ad4 and b33b4a, see
https://hydra.nixos.org/build/67137469
libgfortran.so.3 was not found
2018-01-10 18:42:38 +01:00
Samuel Dionne-Riel
7b97c8c0c8 treewide: homepage+src updates (found by repology, #33263) 2018-01-05 20:42:46 +01:00
Austin Seipp
ebeb95d18b z3: 4.5.0-2017-11-06 -> 4.6.0
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2018-01-03 21:44:56 -06:00
Vladimír Čunát
1fcd92ce92
Merge branch 'master' into staging
A few thousand rebuilds from master, again.
Hydra: ?compare=1422362
2017-12-31 09:53:49 +01:00
Orivej Desh
e87a82b010 cntk: mark as broken
It never succeeded to build.  @abbradar did not respond at
94dc37d622
2017-12-31 08:14:14 +00:00
John Ericson
4d2b763817
Merge pull request #26805 from obsidiansystems/cross-elegant
Make cross compilation elegant
2017-12-30 22:58:02 -05:00
John Ericson
046f091e0d treewide: Don't use envHook anymore
This commits needs a MAJOR audit as I oftentimes just guessed which of
`$hostOffset`, `$targetOffset`, or a fixed offset should be used.
2017-12-30 22:04:22 -05:00
Austin Seipp
ff555bdaeb tamarin-prover: enable tests
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2017-12-30 19:39:38 -06:00
Austin Seipp
bae2e7ceb3 nixpkgs: add sapic as a dependency to tamarin-prover
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2017-12-30 19:01:29 -06:00
Austin Seipp
3813ab2589 nixpkgs: init sapic 0.9
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2017-12-30 19:01:29 -06:00
Austin Seipp
a31bdc0739 nixpkgs: add 'graphviz' to tamarin-prover dependencies
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2017-12-30 19:01:29 -06:00
Austin Seipp
abcfa6f608 nixpkgs: add tamarin-prover 1.3.0 (dev) tool
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2017-12-30 18:23:15 -06:00
David Asabina
810ec3f8bd bitscope: init at 2017-12-28 2017-12-30 21:58:27 +01:00
Frederik Rietdijk
2d0bead714 Merge remote-tracking branch 'upstream/master' into HEAD 2017-12-30 17:04:54 +01:00
Orivej Desh
77cc63950a wxmaxima: build with cmake
Fixes reported version number: see
https://github.com/NixOS/nixpkgs/pull/31657#issuecomment-354414642

"make check" did not run any tests with autotools, and is not defined with
cmake. ("make test" is not defined too.)
2017-12-29 21:00:03 +00:00
Vladimír Čunát
f29000b002
Merge branch 'master' into staging
Hydra: ?compare=1421760
2017-12-29 10:13:33 +01:00
Robin Gloster
ee1c85aee9 mariadb: lib -> connector-c 2017-12-29 02:18:35 +01:00
Nick Hu
8640e286b4 fdr: 4.2.0 -> 4.2.3 2017-12-29 02:01:31 +01:00
Vincent Laporte
b320538f4c
coq: lablgtk is only needed for coqide 2017-12-23 11:11:56 +00:00
John Wiegley
f962f33593 Specify the coq version in a more consistent location 2017-12-21 01:24:35 -08:00
Justin Bedo
a49c91f655
snpeff: 4.3p -> 4.3t 2017-12-21 10:52:26 +11:00
Vincent Laporte
4c454a3208
coq: minor cleaning 2017-12-18 15:30:36 +00:00
Orivej Desh
c13c93f03b drat-trim: fix build on darwin 2017-12-17 13:19:34 +00:00
Orivej Desh
fe9bf3ed23
Merge pull request #32648 from berce/upstream-kicad
kicad: init unstable at version 2017-12-11
2017-12-17 05:03:29 +00:00
Orivej Desh
c780dba59c kicad: show version 2017-12-17 05:02:51 +00:00
Orivej Desh
f314157041 kicad-unstable: set version 2017-12-17 04:49:00 +00:00
Orivej Desh
d8f668c7b3
Merge pull request #32643 from kini/drat-trim
drat-trim: init at 2017-08-31
2017-12-17 00:31:25 +00:00
Keshav Kini
7b6b074829 drat-trim: init at 2017-08-31
DRAT-trim is a tool which can be used to make SAT solvers (such as
glucose and glucose-syrup, which are in nixpkgs) more useful by
checking their work.  It has become well-accepted in the SAT solver
development community and has been used in the annual SAT competitions
for the last few years.
2017-12-17 00:27:52 +00:00
Bert Moens
5e0344dce9 kicad: add support for oce, ngspice and scripting 2017-12-17 00:20:45 +00:00
Bert Moens
af5272f599 kicad: add unstable version 2017-12-17 00:10:28 +00:00
Vincent Laporte
12c5fe3e2d ocamlPackages.cairo2: 0.4.6 -> 0.5 2017-12-16 12:14:35 +01:00
John Wiegley
40627000f7 coq_8_7: 8.7.0 -> 8.7.1 2017-12-15 22:09:15 -08:00
John Wiegley
2e93f93b2a z3_4_5_0: New expression, to access the release version's API 2017-12-14 23:32:37 -08:00
Pascal Wittmann
aacf756ed0
Merge pull request #32538 from vbgl/ott-0.27
ott: 0.25 -> 0.27
2017-12-14 09:07:46 +01:00
Vincent Laporte
b212125b54
Merge pull request #32250 from vbgl/coq-clean
coq_HEAD, coqPackages_8_4: remove
2017-12-11 18:13:24 +01:00
Vincent Laporte
1ccd3b9755
ott: 0.25 -> 0.27 2017-12-10 11:49:05 +00:00
Vladimír Čunát
2309acf723
Merge branch 'master' into staging 2017-12-09 21:00:07 +01:00
markuskowa
66da9b9f8f gpredict: init at 1.3 (#32436) 2017-12-09 09:45:29 +00:00
Vladimír Čunát
6f5d989478
treewide: checkMeta fixes for x86_64-linux 2017-12-07 07:50:47 -05:00
Orivej Desh
9f8ec7e4d3 stp: disable parallel building 2017-12-07 08:52:42 +00:00
Orivej Desh
812e0bced1 shogun: fix parallel building 2017-12-07 08:52:42 +00:00
Austin Seipp
520fa67746 nixpkgs: symbiyosys 2017.11.05 -> 2017.12.06
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2017-12-06 22:07:57 -06:00
Vincent Laporte
e36cb93283
coq_HEAD: remove 2017-12-02 08:38:58 +00:00
Keshav Kini
2d91801242 glucose-syrup: Remove unused fetchurl argument 2017-12-01 21:13:21 -08:00
Jörg Thalheim
ae096444a2
simgrid: 3.15 -> 3.17 (#32114)
* simgrid: 3.15 -> 3.17 + clean + add options

* Add myself as maintainer

* Fix typo
2017-12-01 22:14:24 +00:00
Orivej Desh
1f99fd6965 libminc: fix build after hdf5 upgrade by using hdf5_1_8 2017-12-01 00:37:29 +00:00
Peter Simons
b0f82f0f2d R: update to 3.4.3 2017-11-30 18:45:48 +01:00
MERCIER Michael
42ec4556bd Fix typo 2017-11-28 13:13:01 +01:00
Vincent Laporte
a8da423332
acgtk: fix for yojson ≥ 1.4 2017-11-27 17:00:15 +00:00
MERCIER Michael
8fa00adf1a Add myself as maintainer 2017-11-27 17:58:49 +01:00
MERCIER Michael
0cace1fbd2 simgrid: 3.15 -> 3.17 + clean + add options 2017-11-27 17:50:25 +01:00
Orivej Desh
4f73b3162b treewide: preset windres missing to fix builds on Linux
https://github.com/NixOS/nixpkgs/pull/30484#issuecomment-345899910
2017-11-21 04:27:10 +00:00
Maximilian Bosch
38af8ec720
stellarium: 0.15.0 -> 0.16.1
The 0.16-releases contain several useful new features:
https://launchpad.net/stellarium/0.16/0.16.1

I also added myself as maintainer to have more people available if the
package breaks a release.
2017-11-19 12:01:15 +01:00
rybern
ef0486b1f9 vcftools: init at 0.1.15 (#31339) 2017-11-16 09:52:56 +02:00
Orivej Desh
089e0aaf72 pulseview: fix build 2017-11-16 00:40:16 +00:00
Joerg Thalheim
67092ffd43 spyder: 2.3.8 -> 3.2.4 2017-11-15 15:49:05 +00:00
Moritz Kiefer
c0f08557b9 why3: 0.87.3 -> 0.88.1 2017-11-15 10:15:12 +01:00
Dan Haraj
bdce7d3a04 sc2-headless: add pysc2 minigame map pack 2017-11-14 14:37:53 -05:00
Peter Simons
d70a021b95 maxima: 5.40.0 -> 5.41.0 2017-11-14 13:23:48 +01:00
Joerg Thalheim
21423521e6 wxmaxima: 15.04.0 -> 17.10.1
also fix crash at start-up due missing icons

fixes #18479
2017-11-14 11:28:00 +00:00
Renaud
2d8d35e342
Merge pull request #31564 from Mounium/aliza
aliza: 1.29.2->1.36.3
2017-11-12 22:07:01 +01:00
Katona László
c2d9871823 aliza: 1.29.2->1.36.3 2017-11-12 17:46:37 +01:00
Michael Raskin
eaaaebe00a golly: 2.8 -> 3.1 2017-11-11 15:31:37 +01:00
Michael Raskin
563b08c7c4 pari: 2.9.1 -> 2.9.3 2017-11-11 15:31:36 +01:00
Michael Raskin
20b6b3cf0e clingo: init at 5.2.2
Note that clasp (included in clingo) is already packaged separately, but
only an earlier version. As it is used by OPAM, but will stop being used
by OPAM later (and I want to grab the name for Clasp the Common Lisp
implementation), I decided to package clingo as a whole (as recommended),
but to leave clasp until OPAM stops needing it.
2017-11-10 14:04:32 +01:00
Austin Seipp
063e4dca79 z3: update to latest git
This has some nice improvements, like new string and real arithmetic solvers.

Signed-off-by: Austin Seipp <aseipp@pobox.com>
2017-11-09 13:20:01 -06:00
Michael Raskin
27f7999280 glucose, glucose-syrup: 4.0 -> 4.1 2017-11-08 09:55:29 +01:00
Michael Raskin
6475fa9b25
Merge pull request #31298 from timokau/sage-fix
sage: 6.8 -> 8.0
2017-11-06 01:25:28 +00:00
Michael Raskin
85eac6ff73
Restrict platforms to what is known to work. 2017-11-06 01:25:04 +00:00
Timo Kaufmann
fe68ba81d2 sage: 6.8 -> 8.0
This "un-breaks" sage while also updating it to 8.0.

It compiles sage with its dependencies as one big pile, which is not
the best approach but definately better than nothing for now.

To be able to shrink the huge output pile a little, it also splits
docs from the rest of the output.
2017-11-05 17:37:40 -06:00
Austin Seipp
5fc4f17862 yices: 2.5.3 -> 2.5.4
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2017-11-05 12:49:38 -06:00
Austin Seipp
e27e0ebe48 cvc4: unstable-2017-05-18 -> 1.5
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2017-11-05 12:49:38 -06:00
Austin Seipp
9cb5201d33 yosys/symbiyosys: 2017.10.16 -> 2017.11.05
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2017-11-05 12:49:38 -06:00
Ben Gamari
7eecac6f46 ngspice: Build shared library
This builds the libngspice shared library which is used by development
versions of kicad.
2017-11-02 19:26:06 -04:00
Piotr Bogdan
8904ce343a fix source root locations.
These have changed following commit
c3255fe8ec.

See also:

- https://github.com/NixOS/nixpkgs/pull/31004
- https://github.com/NixOS/nixpkgs/pull/31106
2017-11-02 13:53:36 +00:00
Daiderd Jordan
b93df24078 pari: enable darwin build 2017-10-30 18:24:22 +01:00
Edward Tjörnhammar
9acbfbc7b7
shogun: init at 6.0.0 2017-10-29 10:20:55 +01:00
Edward Tjörnhammar
77d3869f27
colpack: init at 1.0.10 2017-10-29 10:20:54 +01:00
John Wiegley
89720d851a
coqPackages_8_7: New expression, but don't make it the default yet 2017-10-22 12:43:27 -07:00
Tuomas Tynkkynen
a4833730c4 cntk: Disable parallel building
https://hydra.nixos.org/build/62781346
2017-10-22 18:19:03 +03:00
Ryan Bernstein
941014ffff bowtie2: init at 2.3.3.1 2017-10-22 00:11:49 +02:00
Dmitry Kalinkin
ef2fc289a6
root: 6.10.04 -> 6.10.08 2017-10-20 00:59:21 -04:00
Nikolay Amiantov
94dc37d622 cntk: init at 2.2 2017-10-19 13:24:24 +03:00
Nikolay Amiantov
57f82de364 caffe: 1.0-rc5 -> 1.0
Fix build with cudatoolkit9.
2017-10-19 12:47:30 +03:00