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9246 Commits

Author SHA1 Message Date
R. Ryantm
f4a362ed25 eigenmath: unstable-2024-02-25 -> unstable-2024-03-06 2024-03-07 17:49:19 +00:00
Robert Hensing
7d2a83e6c2 Merge branch 'master' into HEAD 2024-03-07 18:39:12 +01:00
Samuel Ainsworth
a417c4b9ec
Merge pull request #293773 from GaetanLepage/mujoco 
mujoco: 3.1.2 -> 3.1.3
 2024-03-07 11:03:32 -05:00
Weijia Wang
13a97affb1
Merge pull request #291880 from r-ryantm/auto-update/pari 
pari: 2.15.4 -> 2.15.5
 2024-03-07 16:56:45 +01:00
Gaetan Lepage
d62f208672 mujoco: 3.1.2 -> 3.1.3 
Diff: https://github.com/google-deepmind/mujoco/compare/refs/tags/3.1.2...3.1.3

Changelog: https://github.com/google-deepmind/mujoco/releases/tag/3.1.3
 2024-03-07 15:41:37 +01:00
Weijia Wang
dba4cc979f
Merge pull request #287372 from r-ryantm/auto-update/cryptominisat 
cryptominisat: 5.11.15 -> 5.11.21
 2024-03-07 15:23:07 +01:00
7c6f434c
40ddcd77cf
Merge pull request #293918 from r-ryantm/auto-update/opensmt 
opensmt: 2.5.2 -> 2.6.0
 2024-03-07 11:22:39 +00:00
Weijia Wang
b2a57ed0b9
Merge pull request #285423 from r-ryantm/auto-update/diamond 
diamond: 2.1.8 -> 2.1.9
 2024-03-07 11:24:20 +01:00
Weijia Wang
c02fcb5130
Merge pull request #287668 from r-ryantm/auto-update/igv 
igv: 2.17.1 -> 2.17.2
 2024-03-07 09:31:05 +01:00
Weijia Wang
05bdea1c17
Merge pull request #291482 from r-ryantm/auto-update/verilator 
verilator: 5.020 -> 5.022
 2024-03-07 08:08:34 +01:00
Weijia Wang
cbf8d3d567
Merge pull request #292044 from r-ryantm/auto-update/mavproxy 
mavproxy: 1.8.66 -> 1.8.70
 2024-03-07 07:58:16 +01:00
Mario Rodas
66e4e61595 elan: revert temporary directory creation 2024-03-07 04:20:00 +00:00
R. Ryantm
08a8c74c4b opensmt: 2.5.2 -> 2.6.0 2024-03-07 01:36:53 +00:00
github-actions[bot]
8534fb2f53
Merge master into haskell-updates 2024-03-07 00:10:05 +00:00
Weijia Wang
d83c961db0
Merge pull request #289177 from r-ryantm/auto-update/clingcon 
clingcon: 5.2.0 -> 5.2.1
 2024-03-06 23:48:05 +01:00
Weijia Wang
aac102629b
Merge pull request #290917 from r-ryantm/auto-update/magic-vlsi 
magic-vlsi: 8.3.460 -> 8.3.463
 2024-03-06 22:24:44 +01:00
R. Ryantm
9bb1834bfa cadical: 1.9.4 -> 1.9.5 2024-03-06 15:23:48 +00:00
R. Ryantm
6473b3f6b7 getdp: 3.5.0 -> 3.6.0 2024-03-06 02:37:46 +00:00
R. Ryantm
66d4364107 magic-vlsi: 8.3.460 -> 8.3.463 2024-03-05 20:26:29 +00:00
Markus Kowalewski
d73e602b44 gromacs: 2024 -> 2024.1 2024-03-05 14:38:54 +01:00
github-actions[bot]
1ad8409e69
Merge master into haskell-updates 2024-03-05 00:12:06 +00:00
Mario Rodas
4ca2b298cc lean4: 4.6.0 -> 4.6.1 
Diff: https://github.com/leanprover/lean4/compare/v4.6.0...v4.6.1

Changelog: https://github.com/leanprover/lean4/blob/v4.6.1/RELEASES.md
 2024-03-04 04:20:00 +00:00
github-actions[bot]
153ed76492
Merge master into haskell-updates 2024-03-04 00:13:07 +00:00
Alois Wohlschlager
aecaeee645
geogebra: fix 3D view again 2024-03-03 20:05:36 +01:00
github-actions[bot]
b74f04cf79
Merge master into haskell-updates 2024-03-03 00:13:21 +00:00
R. Ryantm
16d5b925a8 lammps-mpi: 2Aug2023_update2 -> 2Aug2023_update3 2024-03-02 20:33:42 +00:00
Doron Behar
bef4ada0eb
Merge pull request #292584 from r-ryantm/auto-update/wxmaxima 
wxmaxima: 24.02.1 -> 24.02.2
 2024-03-02 18:21:28 +02:00
R. Ryantm
b4acd43269 cvc5: 1.1.1 -> 1.1.2 2024-03-02 04:58:08 +00:00
Mario Rodas
37d0669466
Merge pull request #287403 from trofi/graphia-gcc-13-fix-update 
graphia: 3.2 -> 4.2
 2024-03-01 23:26:37 -05:00
github-actions[bot]
38eff76eca
Merge master into haskell-updates 2024-03-02 00:11:53 +00:00
R. Ryantm
3f388279f7 nnpdf: 4.0.8 -> 4.0.9 2024-03-01 12:36:01 -05:00
R. Ryantm
39b24670d7 wxmaxima: 24.02.1 -> 24.02.2 2024-03-01 13:40:14 +00:00
Mario Rodas
7767a0f22d
Merge pull request #292202 from marsam/update-lean4 
lean4: 4.5.0 -> 4.6.0
 2024-02-29 20:49:17 -05:00
github-actions[bot]
a1ed79952d
Merge master into haskell-updates 2024-03-01 00:14:10 +00:00
Justin Bedő
5deb2a3b18
Merge pull request #289911 from r-ryantm/auto-update/last 
last: 1541 -> 1542
 2024-03-01 08:59:19 +11:00
github-actions[bot]
47e7b83fd1
Merge master into haskell-updates 2024-02-29 00:12:06 +00:00
R. Ryantm
93030f9ff7 mavproxy: 1.8.66 -> 1.8.70 2024-02-28 09:50:10 +00:00
R. Ryantm
c2338e336f eigenmath: unstable-2024-02-04 -> unstable-2024-02-25 2024-02-28 07:51:09 +00:00
Mario Rodas
468b7bae7f lean4: 4.5.0 -> 4.6.0 
Diff: https://github.com/leanprover/lean4/compare/v4.5.0...v4.6.0

Changelog: https://github.com/leanprover/lean4/blob/v4.6.0/RELEASES.md
 2024-02-28 04:20:00 +00:00
R. Ryantm
9b570f04bc pari: 2.15.4 -> 2.15.5 2024-02-27 15:53:35 +00:00
R. Ryantm
a8a2cc301b verilator: 5.020 -> 5.022 2024-02-26 05:26:02 +00:00
github-actions[bot]
70706e07ef
Merge master into haskell-updates 2024-02-26 00:12:47 +00:00
Nick Cao
c063b9b052
Merge pull request #291307 from trofi/sortmerna-gcc-13-fix 
sortmerna: fix `gcc-13` build
 2024-02-25 11:12:12 -05:00
Sergei Trofimovich
0c544b0f0f sortmerna: fix gcc-13 build 
Without the change the build on `master` fails as
https://hydra.nixos.org/build/249070958:

    In file included from /build/source/src/sortmerna/kseq_load.cpp:38:
    /build/source/include/kseq_load.hpp:61:12: error: 'uint64_t' has not been declared
       61 |            uint64_t number_total_read,
          |            ^~~~~~~~
 2024-02-25 07:49:10 +00:00
github-actions[bot]
257171f024
Merge master into haskell-updates 2024-02-25 00:13:49 +00:00
Sergei Trofimovich
b4e6152dc5 starspace: mark broken 
THe build fails against `zlib-1.3` in `master` as
https://hydra.nixos.org/build/249158742:

    3rdparty/zlib.h:1468:32: error: expected initializer before 'Z_ARG'
     1468 | ZEXTERN int ZEXPORTVA gzprintf Z_ARG((gzFile file, const char *format, ...));
          |                                ^~~~~

The upstream repository did not see updates for past 5 years and is
archived. Let's schedule it for removal.
 2024-02-24 22:44:20 +00:00
github-actions[bot]
57bbe4245f
Merge master into haskell-updates 2024-02-24 00:11:45 +00:00
Fabián Heredia Montiel
db1ee6dfe6 Merge remote-tracking branch 'origin/master' into staging-next 
fastcdr was moved to by-name

Related to:

- https://github.com/NixOS/nixpkgs/pull/290836
 2024-02-23 16:47:01 -06:00
Pol Dellaiera
6c2979370b
Merge pull request #290850 from raboof/gnucap-by-name 
gnucap: move to by-name
 2024-02-23 22:58:44 +01:00
github-actions[bot]
b67dbe0ff1
Merge master into staging-next 2024-02-23 18:01:06 +00:00
R. Ryantm
6643d56edb snakemake: 8.4.8 -> 8.4.12 2024-02-23 12:38:33 -05:00
github-actions[bot]
d08f9b5833
Merge master into staging-next 2024-02-23 12:01:18 +00:00
Luke Granger-Brown
ed88887f50
Merge pull request #290693 from simonhollingshead/boolector-3.2.3-plus-cpp14 
boolector: 3.2.2 -> 3.2.3 + upstream patch for C++14 compatibility.
 2024-02-23 11:19:22 +00:00
Mario Rodas
03c08e4262
Merge pull request #290735 from marsam/update-elan 
elan: 3.1.0 -> 3.1.1
 2024-02-23 06:11:10 -05:00
Arnout Engelen
68d9ecff4c
gnucap: move to by-name 
tested gnucap-full still works as well
 2024-02-23 12:01:37 +01:00
github-actions[bot]
c1d60ca8ac
Merge master into haskell-updates 2024-02-23 00:12:05 +00:00
Justin Bedő
26037c1a65
Merge pull request #290162 from trofi/octopus-caller-gcc-13-fix 
octopus-caller: fix `gcc-13` build failure (drop `-Werror`)
 2024-02-23 09:38:42 +11:00
markuskowa
b665514a11
Merge pull request #290665 from markuskowa/fix-gromacs 
gromacs: fix CUDA build
 2024-02-22 22:01:26 +01:00
Simon Hollingshead
f0b157a764 boolector: 3.2.2 -> 3.2.3 + upstream patch for C++14 compatibility. 
https://github.com/Boolector/boolector/compare/3.2.2...3.2.3
cc13f371c0
 2024-02-22 19:48:14 +00:00
Markus Kowalewski
f6616d2e3a gromacs: require single precssion when building with CUDA 2024-02-22 17:47:11 +01:00
Markus Kowalewski
eb93eb95ac gromacs: fix CUDA build 2024-02-22 17:39:02 +01:00
Mauricio Collares
464832df1d
Merge pull request #290040 from r-ryantm/auto-update/primesieve 
primesieve: 11.2 -> 12.0
 2024-02-22 10:21:06 +01:00
Fabian Affolter
85611f8249
Merge pull request #290454 from fabaff/strictdoc-fix 
strictdoc: refactor
 2024-02-22 08:33:27 +01:00
Mario Rodas
e4de5ceffd elan: 3.1.0 -> 3.1.1 
Diff: https://github.com/leanprover/elan/compare/v3.1.0...v3.1.1

Changelog: https://github.com/leanprover/elan/blob/v3.1.1/CHANGELOG.md
 2024-02-22 04:20:00 +00:00
github-actions[bot]
3508418a67
Merge master into haskell-updates 2024-02-22 00:12:14 +00:00
Nikolay Korotkiy
ca4179166e
Merge pull request #290031 from voidIess/master 
geogebra: linked icon to archive.org
 2024-02-22 00:56:29 +04:00
Fabian Affolter
ec4408d8b4 strictdoc: refactor 2024-02-21 17:33:31 +01:00
github-actions[bot]
f694e31ceb
Merge master into haskell-updates 2024-02-21 00:12:23 +00:00
Arnout Engelen
8b1ad909bd
Merge pull request #256087 from raboof/gnucap-update 
gnucap: update to 20240130-dev and add gnucap-modelgen-verilog
 2024-02-20 23:43:07 +01:00
markuskowa
a39a9ee214
Merge pull request #288514 from sheepforce/avogadro2 
avogadro2: 1.98.1 -> 1.99.0
 2024-02-20 14:25:01 +01:00
Phillip Seeber
2a876140a8 openmolcas: 23.10 -> 24.02 2024-02-20 10:41:51 +01:00
Sergei Trofimovich
75f093fed6 octopus-caller: fix gcc-13 build failure (drop -Werror) 
Without the change the build on `master` fails as
https://hydra.nixos.org/build/249090788:

    /build/source/src/config/option_collation.cpp: In function 'auto octopus::options::make_variant_generator_builder(const OptionMap&, boost::optional<const octopus::ReadSetProfile&>)':
    /build/source/src/config/option_collation.cpp:1298: error: redundant move in initialization [-Werror=redundant-move]
     1298 |                 throw ConflictingSourceVariantFile {std::move(source_path), *output_path};
          |

Blanket `-Werror` frequently causes build failures unless upstream is
quick at addressing build failures.
 2024-02-20 09:39:27 +00:00
github-actions[bot]
ec769627e0
Merge master into haskell-updates 2024-02-20 00:12:32 +00:00
Julius Schmitt
a18382a83b geogebra: linked icon to archive.org 2024-02-19 22:27:53 +01:00
R. Ryantm
929ed3cde7 primesieve: 11.2 -> 12.0 2024-02-19 21:11:46 +00:00
Fabian Affolter
4646a0c7db sasview: add changelog to meta 2024-02-19 16:02:14 +01:00
Fabian Affolter
711d382967 sasview: 5.0.4 -> 5.0.6 
Diff: https://github.com/SasView/sasview/compare/refs/tags/v5.0.4...v5.0.6
 2024-02-19 16:01:09 +01:00
Mario Rodas
e27d391266
Merge pull request #289941 from marsam/update-elan 
elan: 3.0.0 -> 3.1.0
 2024-02-19 09:25:45 -05:00
OTABI Tomoya
9e52c50c55
Merge pull request #289381 from r-ryantm/auto-update/snakemake 
snakemake: 8.4.4 -> 8.4.8
 2024-02-19 23:16:21 +09:00
R. Ryantm
acb4c80843 clingo: 5.7.0 -> 5.7.1 2024-02-19 09:11:09 +00:00
R. Ryantm
c8ee33f26e last: 1541 -> 1542 2024-02-19 07:08:37 +00:00
Mario Rodas
41dd647a85 elan: 3.0.0 -> 3.1.0 
Diff: https://github.com/leanprover/elan/compare/v3.0.0...v3.1.0

Changelog: https://github.com/leanprover/elan/blob/v3.1.0/CHANGELOG.md
 2024-02-19 04:20:00 +00:00
github-actions[bot]
2198036532
Merge master into haskell-updates 2024-02-19 00:13:13 +00:00
Mario Rodas
9c3d856bed
Merge pull request #289312 from r-ryantm/auto-update/qucs-s 
qucs-s: 2.1.0 -> 24.1.0
 2024-02-18 17:57:27 -05:00
github-actions[bot]
743ad436a7
Merge master into haskell-updates 2024-02-18 00:13:34 +00:00
Dmitry Kalinkin
cb6f36e8ff
xrootd: fix plugin loading on Linux (#289140) 2024-02-17 15:38:01 -05:00
Mario Rodas
99b92cf3e0
Merge pull request #288000 from trofi/timeloop-gcc-13-fix 
timeloop: unstable-2022-11-29 -> 3.0.3, fix `gcc-13` build failure
 2024-02-17 07:19:06 -05:00
github-actions[bot]
2f576c19f7
Merge master into haskell-updates 2024-02-17 00:12:14 +00:00
R. Ryantm
2444fc7fa5 snakemake: 8.4.4 -> 8.4.8 2024-02-16 21:15:11 +00:00
R. Ryantm
fd5be7589c qucs-s: 2.1.0 -> 24.1.0 2024-02-16 15:39:58 +00:00
OTABI Tomoya
dbbd7412af
Merge pull request #289197 from r-ryantm/auto-update/qtrvsim 
qtrvsim: 0.9.6 -> 0.9.7
 2024-02-16 21:24:57 +09:00
7c6f434c
330ab32380
Merge pull request #289178 from r-ryantm/auto-update/clingo 
clingo: 5.6.2 -> 5.7.0
 2024-02-16 07:43:56 +00:00
R. Ryantm
e2351c1c52 qtrvsim: 0.9.6 -> 0.9.7 2024-02-16 02:36:23 +00:00
R. Ryantm
ac0579e7c9 clingo: 5.6.2 -> 5.7.0 2024-02-16 01:36:49 +00:00
R. Ryantm
e9db8c4c77 clingcon: 5.2.0 -> 5.2.1 2024-02-16 01:36:32 +00:00
Justin Bedő
db83508472
Merge pull request #288810 from r-ryantm/auto-update/last 
last: 1540 -> 1541
 2024-02-16 12:26:05 +11:00
github-actions[bot]
02be936be3
Merge master into haskell-updates 2024-02-16 00:12:20 +00:00
Pol Dellaiera
a53894b556
Merge pull request #288470 from McSinyx/stp-u8 
stp: fix build failure
 2024-02-15 23:07:44 +01:00
Weijia Wang
11a28beb53 openmolcas: bump boost version 2024-02-15 07:57:44 +01:00
Mario Rodas
46a93d0751
Merge pull request #287601 from trofi/stp-gcc-13-fix 
stp: fix the build against `gcc-13`
 2024-02-14 20:17:23 -05:00
github-actions[bot]
82277a5b63
Merge master into haskell-updates 2024-02-15 00:12:24 +00:00
Dmitry Kalinkin
3b27f2ac6e
xfitter: fix for recent clang (#288816) 2024-02-14 18:51:35 -05:00
Dmitry Kalinkin
419da635c6
Merge pull request #285505 from GaetanLepage/xroot 
xrootd: 5.5.5 -> 5.6.6, python311Packages.xrootd: init at 5.6.6
 2024-02-14 11:15:22 -05:00
R. Ryantm
55fab6dfd9 last: 1540 -> 1541 2024-02-14 15:51:25 +00:00
Nick Cao
a42f5c6d1a
Merge pull request #256126 from bouk/openmvg-use-nixpkgs-libraries 
openmvg: unstable-2022-12-30 -> 2.1
 2024-02-14 09:31:01 -05:00
Bouke van der Bijl
91414c639f openmvg: unstable-2022-12-30 -> 2.1 
* Use the nixpkgs libraries instead of the vendored ones
* Add updateScript

Co-authored-by: Nick Cao <nickcao@nichi.co>
 2024-02-14 11:23:46 +01:00
Phillip Seeber
06a5108a6c avogadro2: 1.98.1 -> 1.99.0 2024-02-14 10:46:01 +01:00
kirillrdy
399d51fba7
Merge pull request #287721 from trofi/megahit-gcc-13-fix 
megahit: fix `gcc-13` build failure
 2024-02-14 20:22:18 +11:00
kirillrdy
cd54cfb658
Merge pull request #287985 from trofi/svaba-gcc-13-fix 
svaba: fix `gcc-13` build failure
 2024-02-14 20:07:39 +11:00
github-actions[bot]
319f251f5c
Merge master into haskell-updates 2024-02-14 00:12:36 +00:00
Gaetan Lepage
7b9e11995d xrootd: 5.5.5 -> 5.6.6 
Changelog: https://github.com/xrootd/xrootd/releases/tag/v5.6.6

Structured attrs don't work with cmakeFlags - only first item is passed.

Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
 2024-02-13 16:45:54 -05:00
Sergei Trofimovich
3bbdc26df2 timeloop: unstable-2022-11-29 -> 3.0.3 
Changes:
- https://github.com/NVlabs/timeloop/releases/tag/v3.0
- https://github.com/NVlabs/timeloop/releases/tag/v3.0.1
- https://github.com/NVlabs/timeloop/releases/tag/v3.0.2
- https://github.com/NVlabs/timeloop/releases/tag/v3.0.3
 2024-02-13 08:19:21 +00:00
Nguyễn Gia Phong
b63babd55d
stp: fix build failure 2024-02-13 16:41:23 +09:00
Vincent Laporte
8601deaed1 cryptoverif: 2.07 → 2.08pl1 2024-02-13 06:23:27 +01:00
github-actions[bot]
ed9046f8aa
Merge master into haskell-updates 2024-02-13 00:13:09 +00:00
Doron Behar
4f78d8564d
Merge pull request #288127 from r-ryantm/auto-update/wxmaxima 
wxmaxima: 24.02.0 -> 24.02.1
 2024-02-12 10:32:54 +02:00
Bruno Bzeznik
f9b6960581 kstars: 3.6.7 -> 3.6.9 2024-02-12 08:00:53 +01:00
github-actions[bot]
04663e9026
Merge master into haskell-updates 2024-02-12 00:12:56 +00:00
Sandro
4b96fcd46b
Merge pull request #279656 from risicle/ris-degate-2.0.0 
degate: init at 2.0.0
 2024-02-11 23:39:17 +01:00
Mario Rodas
f9d39fb9af
Merge pull request #287604 from trofi/lean3-mark-broken 
lean3: fix gcc-13 build failure
 2024-02-11 17:04:38 -05:00
R. Ryantm
3ea21a4ea9 wxmaxima: 24.02.0 -> 24.02.1 2024-02-11 19:53:05 +00:00
Sergei Trofimovich
016be1d8b3 lean3: fix gcc-13 build failure) 
Without the change the build fails on `master` as https://hydra.nixos.org/build/247665202:

    /build/source/src/shell/lean_js.h:11:32: error: 'uintptr_t' was not declared in this scope
       11 | int emscripten_process_request(uintptr_t msg);
          |                                ^~~~~~~~~
 2024-02-11 19:47:22 +00:00
Robert Scott
36631d8171
Merge pull request #288090 from r-ryantm/auto-update/openrefine 
openrefine: 3.7.7 -> 3.7.9
 2024-02-11 19:11:41 +00:00
Nick Cao
175126c839
Merge pull request #287282 from r-ryantm/auto-update/magic-vlsi 
magic-vlsi: 8.3.459 -> 8.3.460
 2024-02-11 13:04:10 -05:00
Nick Cao
2d8077c394
Merge pull request #286906 from ashgillman/master 
dcm2niix: 1.0.20211006 -> 1.0.20230411
 2024-02-11 12:43:56 -05:00
R. Ryantm
1128be2775 openrefine: 3.7.7 -> 3.7.9 2024-02-11 17:18:59 +00:00
Nick Cao
dc4db874a0
Merge pull request #288017 from trofi/vowpal-wabbit-gcc-13-fix 
vowpal-wabbit: fix `gcc-13` build failure
 2024-02-11 10:18:31 -05:00
Sergei Trofimovich
14f9faadd0 vowpal-wabbit: fix gcc-13 build failure 
Without the change build fails on `master as
https://hydra.nixos.org/build/248985028:

    In file included from /build/source/vowpalwabbit/core/src/named_labels.cc:5:
    /build/source/vowpalwabbit/core/include/vw/core/named_labels.h:28:3: error: 'uint32_t' does not name a type
       28 |   uint32_t getK() const;
          |   ^~~~~~~~
 2024-02-11 12:03:38 +00:00
Sergei Trofimovich
a74b1732a7 timeloop: fix gcc-13 build failure 
Without the change build fails on `master` as
https://hydra.nixos.org/build/248973743:

    include/compound-config/compound-config.hpp:149:8: error: ‘uint64_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’?
      149 |   std::uint64_t parseElementSize(std::string name);
          |        ^~~~~~~~
          |        wint_t
 2024-02-11 10:44:44 +00:00
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
Sergei Trofimovich
a59d5e3028 svaba: fix gcc-13 build failure 
Without the change build fails on `master` as
https://hydra.nixos.org/build/249164637:

    In file included from Histogram.cpp:1:
    Histogram.h:104:61: error: 'uint32_t' does not name a type
      104 |   Histogram(const int32_t& start, const int32_t& end, const uint32_t& width);
          |                                                             ^~~~~~~~
 2024-02-11 09:59:19 +00:00
github-actions[bot]
cf96a5e9ad
Merge master into haskell-updates 2024-02-11 00:13:59 +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
90a5d1b931 megahit: fir gcc-13 build failure 
Without the change build fails on `master` against `gcc-13` as
https://hydra.nixos.org/build/247673319:

    In file included from /build/source/src/main_local_assemble.cpp:27:
    /build/source/src/localasm/local_assemble.h:31:3: error: 'uint32_t' does not name a type
       31 |   uint32_t kmin{11};
          |   ^~~~~~~~
    /build/source/src/localasm/local_assemble.h:1:1: note: 'uint32_t' is defined in header '<cstdint>'; did you forget to '#include <cstdint>'?
      +++ |+#include <cstdint>
 2024-02-10 10:26:43 +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
R. Ryantm
5ca14e22c6 igv: 2.17.1 -> 2.17.2 2024-02-10 06:01:14 +00:00
github-actions[bot]
63f3a9268c
Merge master into haskell-updates 2024-02-10 00:12:04 +00:00
Sergei Trofimovich
b531de72bf stp: fix the build against gcc-13 
Without the change the build fails on `master` as
https://hydra.nixos.org/build/247636021:

    /build/source/include/stp/AST/ASTNode.h:77:3: error: 'uint8_t' does not name a type
       77 |   uint8_t getIteration() const;
          |   ^~~~~~~
 2024-02-09 22:43:16 +00:00
R. Ryantm
cc15000690 cryptominisat: 5.11.15 -> 5.11.21 2024-02-09 04:52:13 +00:00
Sergei Trofimovich
e006445420 graphia: 3.2 -> 4.2 
The main change is the build fis against `gcc-13`
https://hydra.nixos.org/build/247540136:

    /build/source/source/thirdparty/breakpad/src/client/linux/handler/minidump_descriptor.h:115:3: error: 'uintptr_t' does not name a type
      115 |   uintptr_t address_within_principal_mapping() const {
          |   ^~~~~~~~~

Changes:
- https://github.com/graphia-app/graphia/releases/tag/4.0
- https://github.com/graphia-app/graphia/releases/tag/4.1
- https://github.com/graphia-app/graphia/releases/tag/4.2
 2024-02-08 23:30:17 +00:00
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
R. Ryantm
4f45c92f1a magic-vlsi: 8.3.459 -> 8.3.460 2024-02-08 17:49:42 +00:00
github-actions[bot]
1e13dfffc6
Merge master into haskell-updates 2024-02-08 00:12:04 +00:00
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
Ashley Gillman
18eeabfe73 dcm2niix: 1.0.20211006 -> 1.0.20230411 2024-02-07 16:11:03 +10:00
github-actions[bot]
28d39db400
Merge master into haskell-updates 2024-02-07 00:12:13 +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
github-actions[bot]
0e09aea96c
Merge master into haskell-updates 2024-02-06 00:12:25 +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
github-actions[bot]
3a0aae25fa
Merge master into haskell-updates 2024-02-05 00:13:15 +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
github-actions[bot]
e93379ba64
Merge master into haskell-updates 2024-02-04 00:13:37 +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
github-actions[bot]
f7af6d355f
Merge master into haskell-updates 2024-02-03 00:12:45 +00:00
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
github-actions[bot]
34dab68635
Merge master into haskell-updates 2024-02-02 00:12:11 +00:00
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
Mario Rodas
3ada8a22ba
Merge pull request #285422 from marsam/update-lean4 
lean4: 4.4.0 -> 4.5.0
 2024-02-01 05:39:59 -05:00
Markus Kowalewski
e7ea94137c gromacs: 2023.3 -> 2024 2024-02-01 10:55:43 +01:00
Mario Rodas
dbf625d8d7
Merge pull request #284969 from marsam/update-z3_4_12 
z3_4_12: 4.12.4 -> 4.12.5
 2024-01-31 23:50:04 -05:00
R. Ryantm
bfb42a9bbc seqkit: 2.6.1 -> 2.7.0 2024-02-01 04:24:02 +00:00