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1544 commits

Author SHA1 Message Date
Vladimír Čunát
b5aaaf87a7
Merge staging and PR #35021 
It's the last staging commit (mostly) built on Hydra,
and a minimal fix for Darwin regression in pysqlite.
 2018-02-16 09:13:12 +01:00
John Wiegley
90252481bf coq: 8.7.1 -> 8.7.2 2018-02-15 23:12:43 -08:00
Vincent Laporte
e75009ecdc
eprover: fix build in non-GCC environments 2018-02-14 22:46:12 +00:00
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