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1519 commits

Author SHA1 Message Date
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
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
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
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
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
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