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1582 Commits

Author SHA1 Message Date
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