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428045f39b
Commit Graph

5976 Commits

Author SHA1 Message Date
Sergei Trofimovich
428045f39b bwa: pull upstream fix for -fno-common tollchains 
Without the change build fails on -fno-common toolchains like upstream
gcc-10 as:

    $ nix build -L --impure --expr 'with import ./. {}; bwa.overrideAttrs (oa: {   NIX_CFLAGS_COMPILE = (oa.NIX_CFLAGS_COMPILE or "") + "-fno-common"; })'
    ...
    ld: ./libbwa.a(rope.o):/build/bwa-0.7.17/rle.h:33:
      multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/build/bwa-0.7.17/rle.h:33: first defined here
    ld: ./libbwa.a(rle.o):/build/bwa-0.7.17/rle.h:33:
      multiple definition of `rle_auxtab'; ./libbwa.a(bwtindex.o):/build/bwa-0.7.17/rle.h:33: first defined here
 2022-05-08 08:56:43 +01:00
R. Ryantm
5b55f851ac snakemake: 7.6.1 -> 7.6.2 2022-05-07 16:16:09 +00:00
Bernardo Meurer
e6b94ad07e
Merge pull request #171602 from malob/treewide-mainProgram 
treewide: add meta.mainProgram to many packages
 2022-05-05 18:16:09 -07:00
Will Dietz
4b79fa29a6 verilator: 4.220 -> 4.222 2022-05-05 12:15:54 -05:00
Fabian Affolter
ad619e60da
Merge pull request #171548 from r-ryantm/auto-update/snakemake 
snakemake: 7.5.0 -> 7.6.1
 2022-05-05 09:06:17 +02:00
Vincent Laporte
c777cdf5c5 easycrypt-runtest: init at 2022.04 2022-05-05 06:57:50 +02:00
Vincent Laporte
b20934a65c easycrypt: init at 2022.04 2022-05-05 06:57:50 +02:00
Malo Bourgon
16e15fa68f treewide: add meta.mainProgram to many packages 2022-05-04 18:08:19 -07:00
R. Ryantm
166b1378fe snakemake: 7.5.0 -> 7.6.1 2022-05-04 16:06:44 +00:00
Luis Pedro Coelho
596c5e7ea2 Static bwa 
AR needs to be passed specifically on the command line
 2022-05-04 02:20:50 +02:00
Luis Pedro Coelho
4758873378 Static build for samtools 
Curses is not supported (it may be possible to support it)
 2022-05-04 02:16:17 +02:00
Luis Pedro Coelho
0b1c28d5a1 Static build for megahit 2022-05-04 02:13:31 +02:00
Fabian Affolter
b10e012588
Merge pull request #171121 from fabaff/pathy-clean 
python310Packages.smart-open: 5.2.1 -> 6.0.0, python39Packages.spacy: 3.2.4 -> 3.3.0, snakemake: 6.15.5 -> 7.5.0
 2022-05-02 12:33:22 +02:00
Fabian Affolter
8b176291d7 snakemake: 6.15.5 -> 7.5.0 2022-05-01 13:02:10 +02:00
Vladimír Čunát
c480cc2895
Merge branch 'master' into staging-next-2022-04-23 2022-04-30 23:02:28 +02:00
Guillaume Girol
03e1b22740
Merge pull request #170413 from jdupak/master 
QtRVSim: 0.9.2 -> 0.9.3
 2022-04-29 18:42:50 +00:00
Bruno Bzeznik
5661ca1a2d adolc: init at 2.7.2 2022-04-29 10:38:40 -05:00
R. Ryantm
a82b1b63c3 blast: 2.12.0 -> 2.13.0 2022-04-29 09:39:10 -05:00
Vladimír Čunát
8caa1418f6
Merge branch 'master' into staging-next-2022-04-23 2022-04-28 18:04:16 +02:00
Serge K
1248ea16e1
colmap: fix for cuda11.6/gcc11 (#169623) 
* colmap: force nvcc std=c++14 after gcc11 bump

* colmap: optional -> optionals

* colmap: sha256 -> hash

* colmapWithCuda: force CUDA_ENABLED=ON safeguard

* colmapWithCuda: add opengl runpath
 2022-04-27 16:09:30 -07:00
github-actions[bot]
8261a7aaba
Merge master into staging-next 2022-04-27 00:02:17 +00:00
Ryan Mulligan
9fc849704f
Merge pull request #169916 from r-ryantm/auto-update/mavproxy 
mavproxy: 1.8.48 -> 1.8.49
 2022-04-26 16:31:50 -07:00
github-actions[bot]
f8c265f433
Merge master into staging-next 2022-04-26 06:01:08 +00:00
Rick van Schijndel
4586388f85
Merge pull request #170320 from andersk/negated-version 
treewide: Simplify negated uses of versionAtLeast, versionOlder
 2022-04-26 07:50:15 +02:00
Sandro
7deb7b084d
Merge pull request #170020 from Ma27/bump-stellarium 
stellarium: 0.22.0 -> 0.22.1
 2022-04-26 02:37:56 +02:00
Anders Kaseorg
00e66f10fa coq: Rename internal versionAtLeast helper to coqAtLeast 
To avoid potential confusion with lib.versionAtLeast.

Signed-off-by: Anders Kaseorg <andersk@mit.edu>
 2022-04-25 13:35:06 -07:00
github-actions[bot]
073cad8fd6
Merge master into staging-next 2022-04-25 12:04:02 +00:00
markuskowa
b656483a05
Merge pull request #170240 from r-ryantm/auto-update/gromacs 
gromacs: 2022 -> 2022.1
 2022-04-25 13:54:46 +02:00
Jakub Dupak
773f7905b9 QtRVSim: 0.9.2 -> 0.9.3 2022-04-25 14:38:39 +03:00
R. Ryantm
0d56b692fa gromacs: 2022 -> 2022.1 2022-04-25 11:09:40 +00:00
Gabriel Ebner
5838726cb9 calculix: 2.17 -> 2.19 2022-04-25 12:56:36 +02:00
Gabriel Ebner
94f1225197 calculix: fix build with gfortran 10 2022-04-25 12:51:12 +02:00
Sandro
2f517412c4
Merge pull request #165477 from rbreslow/dcm2niix-optional-modules 2022-04-25 11:59:49 +02:00
github-actions[bot]
6a14b5834e
Merge master into staging-next 2022-04-25 00:02:35 +00:00
Ryan Mulligan
f05a748058
Merge pull request #169246 from r-ryantm/auto-update/bada-bib 
bada-bib: 0.6.1 -> 0.6.2
 2022-04-24 13:58:11 -07:00
R. Ryantm
e66cf9c6c8 elan: 1.4.0 -> 1.4.1 2022-04-24 14:14:48 -04:00
Maximilian Bosch
7c2fd0ae5d
stellarium: 0.22.0 -> 0.22.1 
ChangeLog: https://github.com/Stellarium/stellarium/releases/tag/v0.22.1
 2022-04-23 23:46:33 +02:00
Vladimír Čunát
82ec893b68
Merge branch 'staging' into staging-next 2022-04-23 18:10:57 +02:00
R. Ryantm
8914714916 mavproxy: 1.8.48 -> 1.8.49 2022-04-23 08:24:30 +00:00
Artturi
785373a76f
Merge pull request #166605 from siraben/remove-redundant-stdenv 2022-04-22 20:25:38 +03:00
Artturin
f1c7f19e49 treewide: testVersion -> testers.testVersion 2022-04-22 16:24:27 +03:00
Mauricio Collares
0f29ab871f sage: update test expectations 2022-04-21 09:08:41 +02:00
Mauricio Collares
5029df7737 giac: 1.6.0-47 -> 1.9.0-5 2022-04-21 09:08:40 +02:00
Jan van Brügge
9aa4c5dbfc
isabelle: Make closer to upstream 
This makes isabelle use the versions of polyml and z3 that are also used
upstream. Additionally it packages the sha1 library that isabelle uses.

Co-authored-by: 1000teslas <47207223+1000teslas@users.noreply.github.com>
 2022-04-20 11:22:43 +02:00
Jan van Brügge
2e52d5c892
naproche: 0.1.0.0 -> 2022-04-19 
This fixes the build with GHC 9
 2022-04-20 09:14:24 +02:00
veprbl
2511bad8aa
Merge pull request #168973 from veprbl/pr/root5_glibc_fix 
root5: fix for glibc
 2022-04-19 14:56:09 -04:00
ajs124
7d59bd47d2
Merge pull request #165341 from r-ryantm/auto-update/verilator 
verilator: 4.218 -> 4.220
 2022-04-19 17:52:10 +01:00
R. Ryantm
9919952421 bada-bib: 0.6.1 -> 0.6.2 2022-04-19 00:53:01 +00:00
Rocky Breslow
d1c3fea7ec
dcm2niix: support usage of suggested Cloudflare zlib 2022-04-18 15:00:45 -04:00
Rocky Breslow
9019ce0106
dcm2niix: add maintainer 
Also, fix grammatical error in long description.
 2022-04-18 15:00:16 -04:00