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8932 Commits

Author SHA1 Message Date
7c6f434c
9abbc21589
Merge pull request #286922 from r-ryantm/auto-update/jmol 
jmol: 16.1.51 -> 16.1.53
 2024-02-11 10:23:53 +00:00
Weijia Wang
c00ace12ae
Merge pull request #287814 from trofi/openboardview-gcc-13-fix 
openboardview: fix `gcc-13` build failure
 2024-02-10 21:36:37 +01:00
Weijia Wang
9d579087ef
Merge pull request #287718 from trofi/mcrl2-update 
mcrl2: 202206 -> 202307
 2024-02-10 21:35:55 +01:00
Weijia Wang
7c66bc81f0
Merge pull request #287641 from wegank/jogl-rename 
javaPackages.jogl_2_4_0: rename to jogl
 2024-02-10 21:34:56 +01:00
Weijia Wang
b95f9bd48c javaPackages.jogl_2_4_0: rename to jogl 2024-02-10 18:00:38 +01:00
Sergei Trofimovich
9684e352a8 openboardview: fix gcc-13 build failure 
Without the change build fails on `master` as
https://hydra.nixos.org/build/247580552:

    /build/source/src/openboardview/FileFormats/FZFile.h:69:40: error: 'uint32_t' has not been declared
       69 |         FZFile(std::vector<char> &buf, uint32_t fzkey[44]);
          |                                        ^~~~~~~~
 2024-02-10 16:23:29 +00:00
Sergei Trofimovich
d952b5884c mcrl2: 202206 -> 202307 
Among other things fixes `gcc-13` build fix as
https://hydra.nixos.org/build/247554470:

    In file included from /build/mcrl2-202206.1/libraries/utilities/source/bitstream.cpp:10:
    /build/mcrl2-202206.1/libraries/utilities/include/mcrl2/utilities/bitstream.h:56:25: error: 'uint8_t' in namespace 'std' does not name a type; did you mean 'wint_t'?
       56 |   void write(const std::uint8_t* buffer, std::size_t size);
          |                         ^~~~~~~
          |                         wint_t
 2024-02-10 10:14:43 +00:00
Cosima Neidahl
47072d1003
Merge pull request #259629 from vifino/sigrok-nightly 
sigrok and friends: Update to nightly
 2024-02-10 11:01:36 +01:00
Manuel Frischknecht
14a19fa225 hh-suite: fix build on GCC 13 
The build of `hh-suite` stopped working with GCC 13 because
GCC stopped transitively including a couple of headers like
`cstdint` in various scenarios.

There already is an upstream PR proposed that fixes this issue [1]
but hasn't been merged yet. This change pulls in this correction
using `fetchpatch`, fixing the build for now.

[1]: https://github.com/soedinglab/hh-suite/pull/357
 2024-02-08 21:54:47 +00:00
Adrian Pistol
8b712406e6 pulseview: 0.4.2 -> 0.4.2-unstable-2024-01-26 2024-02-08 21:45:11 +01:00
Robert Scott
005f312ae9
Merge pull request #286257 from risicle/ris-hal-hardware-analyzer-darwin-2024-02 
hal-hardware-analyzer: fix build on darwin
 2024-02-07 19:45:27 +00:00
Gaetan Lepage
ddb3833217 mujoco: 3.1.1 -> 3.1.2 
Diff: https://github.com/google-deepmind/mujoco/compare/refs/tags/3.1.1...3.1.2

Changelog: https://github.com/google-deepmind/mujoco/releases/tag/3.1.2
 2024-02-07 09:58:51 +01:00
Gaetan Lepage
62da9ca239 mujoco: mark as broken on darwin 2024-02-07 09:58:46 +01:00
R. Ryantm
469c60a3f5 jmol: 16.1.51 -> 16.1.53 2024-02-07 06:40:55 +00:00
Justin Bedő
6b0d1402d7
Merge pull request #286653 from r-ryantm/auto-update/last 
last: 1519 -> 1540
 2024-02-07 11:04:57 +11:00
R. Ryantm
0b9427cf71 snakemake: 8.3.2 -> 8.4.4 2024-02-06 18:59:24 -05:00
Robert Scott
d5af553b62
Merge pull request #286741 from das-g/openrefine-mainprogram 
openrefine: set meta.mainProgram
 2024-02-06 19:14:07 +00:00
R. Ryantm
8e285cb208 eigenmath: unstable-2024-01-23 -> unstable-2024-02-04 2024-02-06 18:13:08 +00:00
Raphael Das Gupta
13f6915775 openrefine: set meta.mainProgram 2024-02-06 13:49:34 +01:00
R. Ryantm
ad308afcd0 last: 1519 -> 1540 2024-02-06 06:07:25 +00:00
Nikolay Korotkiy
3ca762663e
Merge pull request #286427 from r-ryantm/auto-update/gnuastro 
gnuastro: 0.21 -> 0.22
 2024-02-05 19:53:53 +04:00
Nikolay Korotkiy
6d544c6ff1
gnuastro: add meta.changelog 2024-02-05 18:44:12 +04:00
Doron Behar
99f1454341
Merge pull request #286230 from r-ryantm/auto-update/wxmaxima 
wxmaxima: 23.12.0 -> 24.02.0
 2024-02-05 16:23:09 +02:00
R. Ryantm
5727c18299 gnuastro: 0.21 -> 0.22 2024-02-05 05:41:57 +00:00
Robert Scott
8904ea5c84
Merge pull request #285426 from r-ryantm/auto-update/seqkit 
seqkit: 2.6.1 -> 2.7.0
 2024-02-04 22:59:49 +00:00
Weijia Wang
ab45f7963c
Merge pull request #282757 from r-ryantm/auto-update/bada-bib 
bada-bib: 0.8.0 -> 0.8.1
 2024-02-04 23:44:55 +01:00
Weijia Wang
0b8abd7798
Merge pull request #281847 from r-ryantm/auto-update/eggnog-mapper 
eggnog-mapper: 2.1.10 -> 2.1.12
 2024-02-04 22:48:27 +01:00
Weijia Wang
c92f88b5e3
Merge pull request #281665 from r-ryantm/auto-update/bowtie2 
bowtie2: 2.5.2 -> 2.5.3
 2024-02-04 22:35:03 +01:00
Weijia Wang
d1cf8f73a8
Merge pull request #281484 from r-ryantm/auto-update/gama 
gama: 2.27 -> 2.28
 2024-02-04 22:26:51 +01:00
Weijia Wang
cca77236b0
Merge pull request #283967 from r-ryantm/auto-update/magic-vlsi 
magic-vlsi: 8.3.456 -> 8.3.459
 2024-02-04 20:45:02 +01:00
Weijia Wang
612a107ae5
Merge pull request #284008 from r-ryantm/auto-update/workcraft 
workcraft: 3.4.1 -> 3.4.2
 2024-02-04 20:35:45 +01:00
Weijia Wang
f46ad549e2
Merge pull request #286265 from r-ryantm/auto-update/nvc 
nvc: 1.11.2 -> 1.11.3
 2024-02-04 19:31:51 +01:00
Nick Cao
b2d58dc9da
Merge pull request #286155 from risicle/ris-hal-hardware-analyzer-gcc-13 
hal-hardware-analyzer: fix build with gcc 13
 2024-02-04 09:42:55 -05:00
Doron Behar
cb6c4d8ac0
wxmaxima.src: use hash instead of sha256 
Co-authored-by: Muhammad Falak R Wani <falakreyaz@gmail.com>
 2024-02-04 14:21:06 +00:00
arthsmn
4ee1815267 gplates: 2.3.0 -> 2.4 2024-02-04 14:19:31 +01:00
Weijia Wang
aeaed88f33 nvc: drop libelf on darwin 2024-02-04 14:04:24 +01:00
R. Ryantm
db2a3483c0 nvc: 1.11.2 -> 1.11.3 2024-02-04 12:06:27 +00:00
Robert Scott
a9efe8b635 hal-hardware-analyzer: fix build on darwin 
allow old igraph to build on modern clang by ignoring some new
warnings, and build with sdk 11 to avoid memstream problems
 2024-02-04 11:35:35 +00:00
Felix Bühler
bfda12002a
Merge pull request #285982 from herberteuler/fix/284736-mathematica 
mathematica: minor fixes
 2024-02-04 10:14:33 +01:00
R. Ryantm
07d74035fa wxmaxima: 23.12.0 -> 24.02.0 2024-02-04 07:15:47 +00:00
Robert Scott
ce60e31cbd hal-hardware-analyzer: fix build with gcc 13 2024-02-03 21:29:44 +00:00
Ben Darwin
d6d8fd86dd abella: update url, refactor to finalAttrs style 2024-02-03 14:58:27 -05:00
Robert Scott
e5e19d75c0
Merge pull request #265959 from risicle/ris-openrefine 
openrefine: init at 3.7.7
 2024-02-03 14:28:55 +00:00
Robert Scott
272f7bb1f4 openrefine: init at 3.7.7 2024-02-03 13:37:59 +00:00
Guanpeng Xu
446a6771a6 mathematica: minor fixes 
This change includes two fixes:

1. add the directory containing dbus' libraries to LD_LIBRARY_PATH
   (#284736)

2. avoid creating conflicting `libcuda.so` in the CUDA environment
 2024-02-02 23:20:29 -08:00
Markus Kowalewski
13eb3a2abe gromacs: fix build on Darwin, add OpenMP for Darwin 
Gromacs enables OpenMP by default and fails its configure
if it can not build with OpenMP.
 2024-02-02 11:02:55 +01:00
h7x4
51c3e2b494
Merge pull request #285171 from r-ryantm/auto-update/boinc 
boinc: 7.24.2 -> 7.24.3
 2024-02-01 20:17:27 +01:00
Weijia Wang
a07361dd1c
Merge pull request #285382 from wegank/gplates-fix 
gplates: fix runtime error
 2024-02-01 19:42:53 +01:00
markuskowa
cced9bc060
Merge pull request #285516 from markuskowa/upd-gromacs 
gromacs: 2023.3 -> 2024
 2024-02-01 14:56:20 +01:00
Rolf Schröder
f835df35c7
igv: use jdk17 instead of jdk11 (#285521) 2024-02-01 14:42:34 +01:00