Commit graph

1577 commits

Author SHA1 Message Date
Roger Qiu 30ba063dc3 gpredict: Added hamlib to buildInputs to control radios, and wrapped with wrapGAppsHook to fix gnome errors 2018-03-04 16:30:21 +11:00
Timo Kaufmann 4f239f9d49 sage: Make build more platform independant 2018-03-04 01:36:31 +01:00
Austin Seipp 7270f2139a tlaplus: init at 1.5.6
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2018-03-02 21:20:54 -06:00
Ryan Mulligan a4809a57e1 root: 6.10.08 -> 6.12.06
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/genreflex -h` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/genreflex --help` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/pq2 -h` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/rootn.exe -h` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/rootn.exe --help` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/rootn.exe -h` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/rootn.exe --help` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/xpdtest -h` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/xpdtest --help` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/root.exe -h` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/root.exe --help` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/root.exe -h` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/root.exe --help` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/root-config --help` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/root-config --version` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/prepareHistFactory -h` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/prepareHistFactory --help` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/prepareHistFactory help` got 0 exit code
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/prepareHistFactory -V` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/prepareHistFactory -v` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/prepareHistFactory --version` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/prepareHistFactory version` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/prepareHistFactory -h` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/prepareHistFactory --help` and found version 6.12.06
- ran `/nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06/bin/prepareHistFactory help` and found version 6.12.06
- found 6.12.06 with grep in /nix/store/4gcl610xv4sj6vzwnksm825qp29f8ibx-root-6.12.06

cc "@veprbl"
2018-03-01 15:39:08 +01:00
Ryan Mulligan 75072efb4b tulip: 4.9.0 -> 5.1.0
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/z17wdp6l55y3b18875c9zj2pw1lywrqd-tulip-5.1.0/bin/tulip-config -h` got 0 exit code
- ran `/nix/store/z17wdp6l55y3b18875c9zj2pw1lywrqd-tulip-5.1.0/bin/tulip-config --help` got 0 exit code
- ran `/nix/store/z17wdp6l55y3b18875c9zj2pw1lywrqd-tulip-5.1.0/bin/tulip-config help` got 0 exit code
- ran `/nix/store/z17wdp6l55y3b18875c9zj2pw1lywrqd-tulip-5.1.0/bin/tulip-config --version` and found version 5.1.0
- found 5.1.0 with grep in /nix/store/z17wdp6l55y3b18875c9zj2pw1lywrqd-tulip-5.1.0

cc ""
2018-02-28 20:33:39 +00:00
Ryan Mulligan 0c69b50356 picard-tools: 2.17.4 -> 2.17.10
Semi-automatic update. These checks were performed:

- built on NixOS
- found 2.17.10 with grep in /nix/store/f74zildbrr99qmp5qkb579x9159n88c6-picard-tools-2.17.10
- found 2.17.10 in filename of file in /nix/store/f74zildbrr99qmp5qkb579x9159n88c6-picard-tools-2.17.10

cc "@jbedo"
2018-02-28 15:02:46 +00:00
Ryan Mulligan 2fe9ca05e4 pari: 2.9.3 -> 2.9.4
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/tex2mail help` got 0 exit code
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gphelp --help` got 0 exit code
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gphelp help` got 0 exit code
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 -h` got 0 exit code
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 --help` got 0 exit code
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 -V` and found version 2.9.4
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 -v` and found version 2.9.4
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 --version` and found version 2.9.4
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 -h` and found version 2.9.4
- ran `/nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4/bin/gp-2.9 --help` and found version 2.9.4
- found 2.9.4 with grep in /nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4
- found 2.9.4 in filename of file in /nix/store/v2rvjr4kl79kmn1w70lj7zf0dz00p3mf-pari-2.9.4

cc "@ertes @raskin @AndersonTorres"
2018-02-28 14:27:07 +00:00
Peter Simons 09f18d3baf
Merge pull request #36094 from ryantm/auto-update/wxmaxima-17.10.1-to-18.02.0
wxmaxima: 17.10.1 -> 18.02.0
2018-02-28 13:40:02 +01:00
Ryan Mulligan 9394e70b0d verilator: 3.900 -> 3.920
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator_bin -V` and found version 3.920
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator_bin --version` and found version 3.920
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator_bin_dbg -V` and found version 3.920
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator_bin_dbg --version` and found version 3.920
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator_coverage_bin_dbg -V` and found version 3.920
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator_coverage_bin_dbg --version` and found version 3.920
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator -V` and found version 3.920
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator --version` and found version 3.920
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator_coverage -V` and found version 3.920
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator_coverage --version` and found version 3.920
- ran `/nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920/bin/verilator_profcfunc help` got 0 exit code
- found 3.920 with grep in /nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920
- found 3.920 in filename of file in /nix/store/j0sz8wy56xhm5agjgjrzy3r35qzyrb5s-verilator-3.920

cc "@thoughtpolice"
2018-02-28 12:36:17 +01:00
Ryan Mulligan 84091451ec wxmaxima: 17.10.1 -> 18.02.0
Semi-automatic update. These checks were performed:

- built on NixOS
- found 18.02.0 with grep in /nix/store/q3pav5f98v0imlk0bsr295k8xf2w8njr-wxmaxima-18.02.0
- found 18.02.0 in filename of file in /nix/store/q3pav5f98v0imlk0bsr295k8xf2w8njr-wxmaxima-18.02.0

cc "@peti"
2018-02-27 19:05:41 -08:00
Frederik Rietdijk b45845f228
Merge pull request #35713 from ryantm/auto-update/fricas-1.3.1-to-1.3.2
fricas: 1.3.1 -> 1.3.2
2018-02-27 08:12:42 +00:00
Frederik Rietdijk 671e405332
Merge pull request #35720 from ryantm/auto-update/igv-2.4.6-to-2.4.8
igv: 2.4.6 -> 2.4.8
2018-02-27 08:09:50 +00:00
Ryan Mulligan be7cd20d3c lp_solve: 5.5.2.0 -> 5.5.2.5
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/n5jgpvmzaqdfxdfawfi5rf8vav1qgi7w-lp_solve-5.5.2.5/bin/lp_solve -h` got 0 exit code
- ran `/nix/store/n5jgpvmzaqdfxdfawfi5rf8vav1qgi7w-lp_solve-5.5.2.5/bin/lp_solve -h` and found version 5.5.2.5
- found 5.5.2.5 with grep in /nix/store/n5jgpvmzaqdfxdfawfi5rf8vav1qgi7w-lp_solve-5.5.2.5
- found 5.5.2.5 in filename of file in /nix/store/n5jgpvmzaqdfxdfawfi5rf8vav1qgi7w-lp_solve-5.5.2.5

cc "@smironov"
2018-02-26 21:57:53 -08:00
Ryan Mulligan d1dc4cae54 igv: 2.4.6 -> 2.4.8
Semi-automatic update. These checks were performed:

- built on NixOS
- found 2.4.8 with grep in /nix/store/3vwg5hpprkm3v345fy05gxdjicfakql7-igv-2.4.8
- found 2.4.8 in filename of file in /nix/store/3vwg5hpprkm3v345fy05gxdjicfakql7-igv-2.4.8

cc "@mimadrid"
2018-02-26 19:11:52 -08:00
Ryan Mulligan 4440d28fbd fricas: 1.3.1 -> 1.3.2
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/8zf9gq9g97prcmq27qln6vw7w4aqigw5-fricas-1.3.2/bin/fricas -h` got 0 exit code
- ran `/nix/store/8zf9gq9g97prcmq27qln6vw7w4aqigw5-fricas-1.3.2/bin/fricas -h` and found version 1.3.2
- ran `/nix/store/8zf9gq9g97prcmq27qln6vw7w4aqigw5-fricas-1.3.2/bin/efricas --help` got 0 exit code
- found 1.3.2 with grep in /nix/store/8zf9gq9g97prcmq27qln6vw7w4aqigw5-fricas-1.3.2

cc "@sprock"
2018-02-26 06:28:48 -08:00
adisbladis e046d8bc08
Merge pull request #35555 from ryantm/auto-update/bcftools-1.6-to-1.7
bcftools: 1.6 -> 1.7
2018-02-26 17:39:46 +08:00
Ryan Mulligan 72a22296dd cryptoverif: 1.22 -> 1.28
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/p13fvkr38qrak3ng6lpmj4z1palhr2in-cryptoverif-1.28/bin/cryptoverif --help` got 0 exit code
- found 1.28 with grep in /nix/store/p13fvkr38qrak3ng6lpmj4z1palhr2in-cryptoverif-1.28
- found 1.28 in filename of file in /nix/store/p13fvkr38qrak3ng6lpmj4z1palhr2in-cryptoverif-1.28
2018-02-26 08:32:20 +01:00
Jan Tojnar c65cd765f6
gpredict: 1.3 → 2.2.1 2018-02-26 05:26:41 +01:00
adisbladis e8d0563638
Merge pull request #35566 from ryantm/auto-update/bowtie2-2.3.4-to-2.3.4.1
bowtie2: 2.3.4 -> 2.3.4.1
2018-02-26 09:47:03 +08:00
adisbladis 780e1a34e1
Merge pull request #35583 from ryantm/auto-update/cbc-2.9.5-to-2.9.9
cbc: 2.9.5 -> 2.9.9
2018-02-26 09:33:53 +08:00
Ryan Mulligan 79795b44f9 cbc: 2.9.5 -> 2.9.9
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/clp help` got 0 exit code
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/clp version` and found version 2.9.9
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/clp help` and found version 2.9.9
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/cbc help` got 0 exit code
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/cbc version` and found version 2.9.9
- ran `/nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9/bin/cbc help` and found version 2.9.9
- found 2.9.9 with grep in /nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9
- found 2.9.9 in filename of file in /nix/store/7q93md698w3bnl212mk38rq2l6k7wav6-cbc-2.9.9
2018-02-25 14:03:37 -08:00
Nikolay Amiantov 7f1b8d744f cntk: fix build without CUDA 2018-02-25 22:50:20 +03:00
Nikolay Amiantov 3179002f61 mxnet: 0.11.0 -> 1.1.0 2018-02-25 22:24:09 +03:00
Nikolay Amiantov 6f96122d5b caffe: add nccl support 2018-02-25 22:24:09 +03:00
Nikolay Amiantov 25079ad238 caffe: depend on opencv3
openblas is used since it's propagated from OpenCV and ATLAS compiled without
architecture-specific optimizations is generally slower than OpenBLAS as I
heard.
2018-02-25 22:24:09 +03:00
Nikolay Amiantov 1bfca90bf7 cntk: 2.2 -> 2.4
Comment for `broken` indicates that it never worked at all, which is strange
since on my machine it did. Anyway it works now for me.
2018-02-25 22:24:09 +03:00
Nikolay Amiantov 08f8ad26b3 treewide: unquote homepage in my packages
I don't like this personally but we have #27809 as a precedent.
2018-02-25 22:24:08 +03:00
Ryan Mulligan bc730862d5 bowtie2: 2.3.4 -> 2.3.4.1
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -V` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -v` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -V` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -v` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --help` and found version 2.3.4.1
- found 2.3.4.1 with grep in /nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1
- found 2.3.4.1 in filename of file in /nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1
2018-02-25 09:45:04 -08:00
Ryan Mulligan 9af7602b8a bcftools: 1.6 -> 1.7
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -h` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --help` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools help` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -v` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --version` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools version` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -h` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --help` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools help` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/plot-vcfstats -h` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/plot-vcfstats --help` got 0 exit code
- found 1.7 with grep in /nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7
2018-02-25 09:02:06 -08:00
Jan Tojnar a31d98f312
tree-wide: autorename gnome packages to use dashes 2018-02-25 17:41:16 +01:00
Gabriel Ebner f5b173ffbc qalculate-gtk: 2.1.0 -> 2.2.1 2018-02-24 11:54:53 +01:00
Timo Kaufmann 89162cdd29 sage: explicitly use gfortran6
The recent change from gfortran=gfortran6 to gfortran=gfortran7 broke
the build.
2018-02-23 17:00:21 +01:00
Johannes Frankenau 74029a21bf bcal: init at 1.7 2018-02-21 00:05:16 +01:00
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