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6372 Commits

Author SHA1 Message Date
github-actions[bot]
1ff1108cce
Merge master into staging-next 2022-06-11 12:01:21 +00:00
Sergei Trofimovich
1c838684de
Merge pull request #176437 from trofi/fix-fno-common-for-geda 
geda: pull upstream fixes for -fno-common toolchains
 2022-06-11 11:23:30 +00:00
Luflosi
0045581c23
boinc: 7.18.1 -> 7.20.0 
https://github.com/BOINC/boinc/releases/tag/client_release%2F7.20%2F7.20.0
 2022-06-11 11:26:45 +02:00
github-actions[bot]
3540574f91
Merge master into staging-next 2022-06-10 18:01:27 +00:00
R. Ryantm
acf23020f0 snakemake: 7.8.1 -> 7.8.2 2022-06-09 19:49:56 +00:00
Martin Weinelt
6451e9d4a5 Merge remote-tracking branch 'origin/staging-next' into staging 2022-06-08 22:22:26 +02:00
Martin Weinelt
351556ffac
Merge pull request #175805 from NixOS/python-updates 
Python Updates 2022-06-01 (was: python3: 3.9 -> 3.10)
 2022-06-08 20:28:39 +02:00
Pierre Roux
ecf2791d8b coq_8_16: init at 8.16+rc1 2022-06-08 18:42:10 +02:00
Sergei Trofimovich
2f9d125d58 gpredict: pull upstream fix for -fno-common toolchains 
Without the change build fails on upstream gcc-10 as:

    ld: save-pass.o:src/qth-data.h:36: multiple definition of
       `qth_data_type'; gtk-azel-plot.o:src/qth-data.h:36: first defined here
 2022-06-08 09:04:20 +01:00
Sergei Trofimovich
4c33f198e3 fped: add -fcommon workaround 
Workaround build failure on -fno-common toolchains like upstream
gcc-10. Otherwise build fails as:

    ld: postscript.o:postscript.h:29: multiple definition of
      `postscript_params'; fped.o:postscript.h:29: first defined here
 2022-06-08 08:32:57 +01:00
Sandro Jäckel
0f14467d44
MACS2: mark broken 2022-06-06 11:46:22 -07:00
Rick van Schijndel
3037752d1d
Merge pull request #175961 from helsinki-systems/rem/broken 
remove some packages marked broken for over 1.5 years
 2022-06-06 20:44:39 +02:00
Ben Siraphob
d6f311f306
zchaff: 2004.5.13 -> 2007.3.12 2022-06-05 23:22:06 -07:00
Sergei Trofimovich
8b7b76a612 geda: pull upstream fixes for -fno-common toolchains 
Without the change builda fails on upstream gcc-10 as:

    ld: gattrib/src/../include/globals.h:97:
      multiple definition of `window'; gattrib/src/../include/globals.h:97: first defined here
 2022-06-05 19:42:55 +01:00
Vincent Laporte
1b95daa381 alt-ergo: ensure compatibility with Menhir ≥ 20211215 2022-06-05 15:44:28 +02:00
Robert Scott
53573e4866
Merge pull request #176278 from risicle/ris-jar-source-provenance 
treewide: set `sourceProvenance` for packages containing downloaded jars
 2022-06-05 12:04:38 +01:00
Luz
a001dc6e37 ngspice: 36 -> 37 2022-06-05 12:58:26 +02:00
Robert Scott
3b6bc4b69c treewide: set sourceProvenance for packages containing downloaded jars 
these are the easily identifiable cases and will not be comprehensive
 2022-06-04 19:47:57 +01:00
Sergei Trofimovich
60ba187b0f gravit: pull fix pending upstream inclusion for -fno-common toolchains 
Without the change build fails on upstream gcc-10 as:

    ld: tool.o:(.bss+0x0): multiple definition of `view'; color.o:(.bss+0x0): first defined here
    ld: tool.o:(.bss+0x820): multiple definition of `video'; color.o:(.bss+0x820): first defined here
    ld: png_save.o:(.bss+0x0): multiple definition of `view'; color.o:(.bss+0x0): first defined here
 2022-06-04 07:02:41 +01:00
Vincent Laporte
442db9429b coq: 8.15.1 → 8.15.2 2022-06-03 10:45:45 +02:00
Sergei Trofimovich
fd48676596
Merge pull request #175259 from trofi/workaround-fno-common-for-svaba 
svaba: add -fcommon workaround
 2022-06-03 05:59:16 +00:00
ajs124
5d42a4bf7e scilab: remove after being marked broken for over 18 months 
It was marked in commit 2bc87d48f1 by Kirill Boltaev on 2016-09-19 (commited on 2016-09-26)
 2022-06-02 18:03:52 +02:00
Bobby Rong
e5fd1f69cf
Merge pull request #174881 from r-ryantm/auto-update/mavproxy 
mavproxy: 1.8.49 -> 1.8.50
 2022-06-02 22:48:45 +08:00
R. Ryantm
e9fb739e59 snakemake: 7.8.0 -> 7.8.1 2022-06-02 01:20:40 +00:00
Sandro
06e6b81e98
Merge pull request #175625 from collares/fpylll 
python3Packages.fpylll: unmark as broken on darwin
 2022-06-01 17:04:28 +02:00
Guillaume Girol
2f62b09ac8 giac-with-xcas: fix command to open help inside browser 2022-06-01 12:00:00 +00:00
Ben Siraphob
b5827f1033
Merge pull request #175700 from siraben/cvc4-darwin 
cvc4: fix build on darwin
 2022-06-01 08:09:45 +00:00
Ben Siraphob
583a2312e4
cvc4: fix build on darwin 
Dependency on cln is optional
 2022-05-31 23:56:18 -07:00
Ben Siraphob
eb33086520
Merge pull request #164779 from collares/lean2 2022-06-01 06:16:17 +00:00
Mauricio Collares
268d1c2826 pari: mark as broken on aarch64-darwin 2022-05-31 19:26:14 -06:00
Sandro
0950dcd37b
Merge pull request #174261 from LumiGuide/lumi-team 
picoscope, openrazer, it87, esptool: move maintainership to new LumiGuide team
 2022-05-31 15:40:04 +02:00
ckie
958fcfb4fa
Merge pull request #175477 from bzizou/astral 
astral: init at 5.7.1
 2022-05-31 14:55:37 +03:00
Bruno Bzeznik
376897ced3 astral: init at 5.7.1 2022-05-31 09:03:24 +02:00
R. RyanTM
7a54d237e0
snakemake: 7.7.0 -> 7.8.0 (#174592) 2022-05-30 10:51:36 -04:00
Janne Heß
bfc5086ae9
Merge pull request #173671 from Mindavi/treewide/broken-zhf 
treewide: start marking packages broken
 2022-05-30 14:10:43 +02:00
Rick van Schijndel
433701147a
treewide: pkgs/applications: mark broken for aarch64-linux 2022-05-30 13:42:58 +02:00
Rick van Schijndel
a0dd8198cd
speedcrunch: mark broken on darwin 2022-05-30 13:42:58 +02:00
Sergei Trofimovich
53591dcd4d
Merge pull request #173021 from trofi/fix-fno-common-for-gerbv 
gerbv: pull fix pending upstream inclusion for -fno-common toolchains
 2022-05-29 15:52:56 +00:00
Rick van Schijndel
37c633f7ae treewide: pkgs/applications: mark broken for darwin 2022-05-29 10:56:04 +02:00
Rick van Schijndel
90869787c5 boinc: mark broken for aarch64 2022-05-29 10:56:03 +02:00
Rick van Schijndel
5e1adacaf0 aspino: mark broken for x86_64 Darwin 
Been broken for a few years already too.
 2022-05-29 10:56:02 +02:00
Sergei Trofimovich
2f60be03bb svaba: add -fcommon workaround 
Workaround build failure on -fno-common toolchains like upstream
gcc-10. Otherwise build fails as:

    ld: ./libfml.a(rle.o):/build/source/SeqLib/fermi-lite/rle.h:33: multiple definition of
      `rle_auxtab'; ./libfml.a(misc.o):/build/source/SeqLib/fermi-lite/rle.h:33: first defined here
 2022-05-29 08:07:23 +01:00
Vincent Laporte
5637570f51 ocamlPackages: rename sedlex_2 into sedlex 2022-05-29 08:48:00 +02:00
Anderson Torres
1b2e9ca249
Merge pull request #175044 from collares/pari-2.13.4 
pari: 2.13.3 -> 2.13.4
 2022-05-28 18:45:26 -03:00
Rick van Schijndel
331e26b6ec
Merge pull request #173867 from trofi/fix-fno-common-for-kssd 
kssd: pull upstream fix for -fno-common tollchains
 2022-05-28 20:39:38 +02:00
Timo Kaufmann
4c45cec9e7
Merge pull request #175041 from collares/nauty-2.7r3 
nauty: 27r1 -> 2.7r3
 2022-05-28 20:05:57 +02:00
Mario Rodas
0f20a255ec
Merge pull request #174677 from r-ryantm/auto-update/gmsh 
gmsh: 4.9.5 -> 4.10.2
 2022-05-28 11:48:04 -05:00
Robert Scott
17b62c338f
Merge pull request #175039 from azahi/clingcon-fix 
clingcon: fix build
 2022-05-28 12:40:54 +01:00
Bobby Rong
4125f6cefb
Merge pull request #174552 from r-ryantm/auto-update/dcmtk 
dcmtk: 3.6.6 -> 3.6.7
 2022-05-28 19:02:58 +08:00
Jörg Thalheim
bcd2d6dc23
Merge pull request #152437 from Mic92/picoscope 
picoscope: fix sources
 2022-05-28 08:39:36 +01:00
Jörg Thalheim
a3a93502f1
picoscope: fix sources 2022-05-28 09:36:31 +02:00
7c6f434c
ae0bca4605
Merge pull request #174438 from r-ryantm/auto-update/clingo 
clingo: 5.5.1 -> 5.5.2
 2022-05-28 07:28:47 +00:00
Mauricio Collares
9e22a36080 pari: 2.13.3 -> 2.13.4 2022-05-27 16:42:28 -07:00
Mauricio Collares
82d40a0695 nauty: 27r1 -> 2.7r3 2022-05-27 16:31:14 -07:00
Azat Bahawi
aa8447dd0c
clingcon: fix build 
Fix build https://hydra.nixos.org/build/178237905
 2022-05-28 02:21:13 +03:00
Artturi
60a0871486
Merge pull request #172391 from Artturin/deprecate-stdenv-glibc 2022-05-27 17:56:19 +03:00
R. Ryantm
c762acd8f1 mavproxy: 1.8.49 -> 1.8.50 2022-05-27 07:52:03 +00:00
Artturin
c1fffdfffb treewide: change some glibc to stdenv.cc.libc 2022-05-27 05:57:43 +03:00
Timo Kaufmann
d6ed7b20f4
Merge pull request #174139 from collares/sage-kernelspec 
sage: fix passthru.kernelspec regression
 2022-05-26 21:06:26 +02:00
Doron Behar
0d4aa93b26
Merge pull request #174586 from alyaeanyx/qalculate-4.2.0 2022-05-26 09:15:51 +03:00
R. Ryantm
6f241e6555 gmsh: 4.9.5 -> 4.10.2 2022-05-26 05:47:28 +00:00
Sandro
b9c9593a88
Merge pull request #173304 from IvarWithoutBones/bump/dotnetmodule 2022-05-26 00:26:18 +02:00
Mauricio Collares
8711501e96 sage: fix passthru.kernelspec regression 2022-05-25 14:54:52 -07:00
alyaeanyx
7275bd17fd
libqalculate, qalculate-gtk: 4.1.1 -> 4.2.0 2022-05-25 21:05:36 +02:00
Cyril Cohen
d113661156 coqPackages: etc 
- put `findlib` in `buildInputs` of `mkCoqDerivation` to make sure `coq` packages find their ocaml plugin dependencies,
- use `propagatedBuildInputs` to make sure ocaml plugin dependencies are in path,
- updated `coqPackage.heq` (broken url),
- fixed use of `DESTDIR` and `COQMF_COQLIB` in mkCoqDerivation,
- adding `COQCORELIB` environement variable to put ocaml plugin files in the right place,
- make `metaFetch` available from `coqPackages`
 2022-05-25 20:00:25 +02:00
R. Ryantm
3ff99d8e4c dcmtk: 3.6.6 -> 3.6.7 2022-05-25 16:48:38 +00:00
Artturin
0c4d65b21e treewide: stdenv.glibc -> glibc 2022-05-25 15:51:20 +03:00
R. Ryantm
2582a1bfce nengo-gui: 0.4.8 -> 0.4.9 2022-05-25 09:22:12 +00:00
R. Ryantm
c1ab8c327a clingo: 5.5.1 -> 5.5.2 2022-05-25 07:48:30 +00:00
Sandro
3b9985498d
Merge pull request #174036 from trofi/workaround-fno-common-for-paml 
paml: add -fcommon workaround
 2022-05-25 00:35:00 +02:00
Sandro
9fd6278214
Merge pull request #173992 from trofi/workaround-fno-common-for-mni_autoreg 
mni_autoreg: pull upstream workaround for -fno-common toolchains
 2022-05-25 00:26:12 +02:00
Bobby Rong
d1c457d050
Merge pull request #173942 from lopsided98/qgroundcontrol-update 
qgroundcontrol: 4.2.0 -> 4.2.1
 2022-05-24 21:43:19 +08:00
Yorick van Pelt
0924b1863c
picoscope, openrazer, it87, esptool: move maintainership to LumiGuide 
I no longer work there, but I inherited a few package maintainerships.
 2022-05-24 12:16:25 +02:00
Sergei Trofimovich
8cba3775d8 paml: add -fcommon workaround 
Workaround build failure on -fno-common toolchains like upstream
gcc-10. Otherwise build fails as:

    ld: /build/ccKomtcd.o:(.bss+0x4544): multiple definition of `SeqTypes';
      /build/ccx7EsgU.o:(.bss+0x2a0dfdc): first defined here
 2022-05-22 20:23:12 +01:00
github-actions[bot]
107b6041bc
Merge master into staging-next 2022-05-22 18:01:20 +00:00
ajs124
7d66e93927
Merge pull request #173402 from imsofi/update/geogebra 
geogebra: 5-0-680-0 -> 5-0-706-0
 2022-05-22 16:14:06 +02:00
Sergei Trofimovich
94a5ae4f91 mni_autoreg: pull upstream workaround for -fno-common toolchains 
Without the change build fails on upstream gcc-10 as:

    ld: lib_minctracc.a(minctracclib.c.o):(.bss+0x78): multiple definition of
      `prog_name'; CMakeFiles/xfm2param.dir/Extra_progs/xfm2param.c.o:(.bss+0x18): first defined here
 2022-05-22 14:37:30 +01:00
Sofi
382f65bd30
geogebra: 5-0-680-0 -> 5-0-706-0 2022-05-22 15:04:08 +02:00
github-actions[bot]
deef19c9a1
Merge master into staging-next 2022-05-22 06:01:27 +00:00
Bobby Rong
3b468e68b7
Merge pull request #173017 from trofi/workaround-fno-common-for-freebayes 
freebayes: add -fcommon workaround
 2022-05-22 13:39:14 +08:00
Ben Wolsieffer
fde16aefa7 qgroundcontrol: 4.2.0 -> 4.2.1 2022-05-21 20:51:32 -04:00
github-actions[bot]
dbef850602
Merge master into staging-next 2022-05-22 00:02:20 +00:00
Ben Siraphob
519f0b9e58
zchaff: use clangStdenv 
Fixes build on Linux
 2022-05-21 16:55:37 -07:00
Ben Siraphob
3c31489f15
Merge pull request #173933 from siraben/zchaff-init 
zchaff: init at 2004.5.13
 2022-05-21 16:26:06 -07:00
Mauricio Collares
8fdfe10bcf lean2: 2017-07-22 -> 2018-10-01, unbreak 2022-05-21 16:06:51 -07:00
Ben Siraphob
a6aa08532c
zchaff: init at 2004.5.13 2022-05-21 15:12:08 -07:00
Justin Bedő
48a33d0bbe
Merge pull request #171597 from NixOS/r-updates 
R 4.2.0
 2022-05-22 07:20:19 +10:00
Jan Tojnar
b8b9f52393 Merge branch 'master' into staging-next 
Conflicts:
- pkgs/applications/networking/browsers/firefox/common.nix between 318fae87c0 and f6c5761935.
 2022-05-21 17:52:39 +02:00
Sergei Trofimovich
eb0590ec3d kssd: pull upstream fix for -fno-common tollchains 
Without the change build fails on upstream gcc-10 as:

    ld: ccD2iWhk.o:(.bss+0x8): multiple definition of `domain';
      ccgA4lYl.o:(.bss+0x8): first defined here
    ld: ccD2iWhk.o:(.bss+0x0): multiple definition of `long_domain';
      ccgA4lYl.o:(.bss+0x0): first defined here
 2022-05-21 11:22:53 +01:00
7c6f434c
91c498f0f2
Merge pull request #173543 from collares/sage-gdlib 
sageWithDoc: clean up sagedoc.nix
 2022-05-21 04:31:03 +00:00
Mauricio Collares
727e5a1473 sageWithDoc: cleanup sagedoc.nix 2022-05-20 11:03:25 -07:00
github-actions[bot]
77bded3c43
Merge master into staging-next 2022-05-20 18:02:18 +00:00
Sandro
9c03535bdd
Merge pull request #147486 from pmiddend/crystfel-init 
CrystFEL: init at 0.10.1
 2022-05-20 15:01:53 +02:00
github-actions[bot]
bd83e4cf98
Merge master into staging-next 2022-05-19 12:01:54 +00:00
Sandro
ed58443645
Merge pull request #173172 from Artturin/deprecatestringconf 
stdenv: start deprecating non-list configureFlags
 2022-05-19 11:25:24 +02:00
Sergei Trofimovich
68f3647eae
Merge pull request #172998 from trofi/workaround-fno-common-for-eukleides 
eukleides: add -fcommon workaround
 2022-05-19 07:09:54 +00:00
github-actions[bot]
17dfec3606
Merge master into staging-next 2022-05-19 00:02:14 +00:00
Mauricio Collares
21ae98f5f0 sageWithDoc: add sage-with-env to buildInputs 2022-05-18 15:53:02 -07:00
Vincent Laporte
4a87fcbc86
why3: 1.4.1 → 1.5.0 
easycrypt: fix build with why3-1.5.0
frama-c: build with why3 1.4.1
 2022-05-19 00:13:20 +02:00
Vincent Laporte
6e3a86f2f7
why3.withProvers: fix #168644 2022-05-19 00:09:30 +02:00
github-actions[bot]
925219f62b
Merge master into staging-next 2022-05-18 18:01:13 +00:00
Artturin
cf7476804a treewide: convert string configureFlags to list of strings 2022-05-18 20:32:33 +03:00
Gabriel Ebner
cc24423641
Merge pull request #170265 from collares/lean-3.42.1 
lean: 3.42.0 -> 3.43.0
 2022-05-18 17:24:31 +02:00
Mauricio Collares
4b37f16232 lean: 3.42.1 -> 3.43.0 2022-05-18 10:30:32 -04:00
Mauricio Collares
0a449d8fff lean: 3.42.0 -> 3.42.1 2022-05-18 10:27:18 -04:00
Shea Levy
7456be85db
Merge branch 'staging-next' into staging 2022-05-18 06:40:21 -04:00
Someone Serge
b96c7caea6
mxnet: mark cuda build as broken 2022-05-18 09:48:45 +03:00
Robert Scott
39369610f8
Merge pull request #173333 from veprbl/pr/xfitter_fix 
xfitter: fix for gfortran10+
 2022-05-17 23:02:47 +01:00
Fabian Affolter
44b8ec5ccb
Merge pull request #173416 from r-ryantm/auto-update/snakemake 
snakemake: 7.6.2 -> 7.7.0
 2022-05-17 20:39:48 +02:00
Ben Darwin
5cf446f41b ezminc: mark broken 
Package refuses to build with current GCC (11), but building with older
GCC causes error linking libminc and I don't want to pin a bunch of
deps.

A newer version is available upstream but it only works with ITK 5.0
(see https://github.com/BIC-MNI/EZminc/issues/15),
but we have 4.x and 5.2.x in tree and I'm reluctant to add 5.0 just for
one package (even ITK 4.x is only used by ants and ezminc and should be
removed as soon as ants is upgraded).
 2022-05-17 10:24:07 -07:00
R. Ryantm
a52b64015a snakemake: 7.6.2 -> 7.7.0 2022-05-17 16:18:18 +00:00
Justin Bedo
e052be0a84
Merge remote-tracking branch 'origin/master' into r-updates 2022-05-17 20:57:40 +10:00
Dmitry Kalinkin
1c78ce70fa
xfitter: fix for gfortran10+ 2022-05-16 22:07:39 -04:00
Robert Scott
4f7d4241c2
Merge pull request #173279 from veprbl/pr/root5_fix 
root5: fix build with recent gcc
 2022-05-16 22:18:29 +01:00
Ivar Scholten
402cfbf73c formula: update for dotnet 6 2022-05-16 21:39:47 +02:00
Dmitry Kalinkin
fdf0806386
root5: fix build with recent gcc 2022-05-16 11:53:42 -04:00
github-actions[bot]
add75748e2
Merge staging-next into staging 2022-05-16 12:03:45 +00:00
7c6f434c
1d4c47ea08
Merge pull request #171511 from collares/sage-9.6 
sage: 9.5 -> 9.6
 2022-05-16 09:51:47 +00:00
github-actions[bot]
e2602ad62e
Merge staging-next into staging 2022-05-16 00:04:11 +00:00
Mauricio Collares
26a87ada65 sage: 9.5 -> 9.6 2022-05-15 19:23:40 -04:00
Dmitry Kalinkin
8e24a6db2e nnpdf: init at 4.0.4 2022-05-15 16:00:00 -07:00
Mauricio Collares
10b16ea5e7 sageWithDoc: make jupyter-sphinx available for docbuild 2022-05-15 12:45:25 -04:00
Mauricio Collares
09ab2aba13 lrcalc: 1.2 -> 2.1 2022-05-15 12:45:24 -04:00
Jan Tojnar
d1b77f990f Merge branch 'staging-next' into staging 
Conflicts:
	pkgs/applications/networking/browsers/firefox/common.nix between f6c5761935 and a373324120.
 2022-05-15 07:08:29 +02:00
Jörg Thalheim
3d4109f3a4
Merge pull request #172588 from res0Nanz/patch-1 
wolfram-engine: fix quotes in installation script
 2022-05-14 19:27:38 +01:00
AndersonTorres
91621176e0 primecount: 7.2 -> 7.3 2022-05-14 11:01:08 -03:00
AndersonTorres
d488388cfc primesieve: 7.8 -> 7.9 2022-05-14 10:56:13 -03:00
Sergei Trofimovich
0b3eecc56f gerbv: pull fix pending upstream inclusion for -fno-common toolchains 
Without the change build fails on upstream gcc-10 as:

    ld: interface.o:/build/gerbv/src/callbacks.h:50: multiple definition of
      `toggle_layer'; callbacks.o:/build/gerbv/src/callbacks.h:50: first defined here
    ld: interface.o:/build/gerbv/src/callbacks.h:44: multiple definition of
      `CALLBACKS_SAVE_FILE_TYPE'; callbacks.o:/build/gerbv/src/callbacks.h:44: first defined here
    ld: render.o:/build/gerbv/src/callbacks.h:44: multiple definition of
      `CALLBACKS_SAVE_FILE_TYPE'; callbacks.o:/build/gerbv/src/callbacks.h:44: first defined here
 2022-05-14 13:41:11 +01:00
Sergei Trofimovich
deaab56289 freebayes: add -fcommon workaround 
Workaround build failure on -fno-common toolchains like upstream
gcc-10. Otherwise build fails as:

    ld: foomatic_rip-options.o:/build/foomatic-filters-4.0.17/options.c:49: multiple definition of `cupsfilter';
      foomatic_rip-foomaticrip.o:/build/foomatic-filters-4.0.17/foomaticrip.c:158: first defined here
 2022-05-14 13:19:17 +01:00
Sergei Trofimovich
d45dfee2d6 eukleides: add -fcommon workaround 
Workaround build failure on -fno-common toolchains like upstream
gcc-10. Otherwise build fails as:

    ld: eukleides_build/triangle.o:(.bss+0x28): multiple definition of `A';
        eukleides_build/quadrilateral.o:(.bss+0x18): first defined here
 2022-05-14 10:28:22 +01:00
tomberek
ca885c3ac1
Merge pull request #172933 from armeenm/bump-alliance 
alliance: unstable-2021-09-15 -> unstable-2022-01-13
 2022-05-14 00:25:21 -04:00
Armeen Mahdian
d912addd5a alliance: unstable-2021-09-15 -> unstable-2022-01-13 2022-05-13 17:18:09 -05:00
Sergei Trofimovich
ff22bc1ff6 chemtool: add -fcommon workaround 
Workaround build failure on -fno-common toolchains like upstream
gcc-10. Otherwise build fails as:

    ld: inout.o:/build/chemtool-1.6.14/ct1.h:279: multiple definition of
      `outtype'; draw.o:/build/chemtool-1.6.14/ct1.h:279: first defined here
 2022-05-13 21:30:28 +01:00
github-actions[bot]
fe71877bbd
Merge staging-next into staging 2022-05-13 18:03:04 +00:00
Gabriel Ebner
d04ae3049e
Merge pull request #172885 from armeenm/fix-aspino 
aspino: 2017-03-09 -> 2018-03-24
 2022-05-13 18:39:20 +02:00
markuskowa
78075c4443
Merge pull request #172868 from markuskowa/upd-molcas 
openmolcas: 21.10 -> 22.02
 2022-05-13 18:07:39 +02:00
Armeen Mahdian
f779b60d20 aspino: 2017-03-09 -> 2018-03-24 2022-05-13 10:53:37 -05:00
Markus Kowalewski
45083c5d1d
openmolcas: 21.10 -> 22.02 
* make MPI optional instead of default
* allow optional MKL build/switch wrapped BLAS interface
 2022-05-13 17:06:11 +02:00
Sandro
741d2d2578
Merge pull request #172846 from LeSuisse/bayescan-c++14-zhf 
bayescan: fix the build
 2022-05-13 17:03:05 +02:00
Guanpeng Xu
cefda1c7ca
Mathematica: refactored (#172136) 2022-05-13 14:16:50 +00:00
github-actions[bot]
814126147f
Merge staging-next into staging 2022-05-13 12:02:03 +00:00
Thomas Gerbet
44c1590f1f bayescan: fix the build 
Moved back to C++14 to avoid the new errors and warnings introduced with
C++17.
 2022-05-13 12:00:08 +02:00
Philipp Middendorf
93332c2779 CrystFEL: init at 0.10.1 2022-05-13 07:09:53 +02:00
Vincent Laporte
1f11888116 Revert "coqPackages: etc" 
This reverts commit 7e589a45ef.
 2022-05-13 06:47:14 +02:00
Vincent Laporte
215235cce5 Revert "moving findlib to propagedNativeBuildInputs" 
This reverts commit 82440c9374.
 2022-05-13 06:47:14 +02:00
github-actions[bot]
d79af4efe4
Merge staging-next into staging 2022-05-13 00:03:35 +00:00
Thiago Kenji Okada
5c5187646d
Merge pull request #172366 from ncfavier/wrappers-cleanup 
make{,Binary}Wrapper: some cleanups
 2022-05-12 22:17:34 +01:00
Thiago Kenji Okada
eae1669de5
Merge pull request #171836 from ncfavier/escape-wrapper-args 
Fix wrapper arguments escaping
 2022-05-12 21:55:06 +01:00
Thomas Gerbet
1ba72de384 ripser: 1.0.0 -> 1.2.1 
https://github.com/Ripser/ripser/releases/tag/v1.0.1
https://github.com/Ripser/ripser/releases/tag/v1.1
https://github.com/Ripser/ripser/releases/tag/v1.2
https://github.com/Ripser/ripser/releases/tag/v1.2.1
 2022-05-12 08:26:44 -07:00
Naïm Favier
3c77d361b5
makeShellWrapper: add explicitly named attribute 
So that things that use the makeShellWrapper/wrapProgramShell
functions can depend on makeShellWrapper explicitly, which should ease
migration in the future.
 2022-05-12 11:01:23 +02:00
Thiago Kenji Okada
1919e181fb
Merge pull request #172641 from WolfangAukang/monosat-fix 
python3Packages.monosat: disable failing tests
 2022-05-12 10:01:16 +01:00
Rick van Schijndel
716bc55f98
Merge pull request #172443 from a-m-joseph/pr/zhf/vhd2vl 
vhd2vl: fix the tests
 2022-05-12 10:06:04 +02:00
Adam Joseph
5d44c9a222 vhd2vl: fix the tests 
The testing scheme for vhd2vl is sensitive to subtle shifts in
iverilog's parenthesization choices, meaning that the golden test
outputs require constant maintenance.

The patch previously applied in order to deal with this situation is
no longer sufficient, so a patch which is sufficient has been added.

Also, the `buildTargets` and `checkTarget` attributes have been set,
so future benign failures of this sort can be dealt with through
`doCheck=false` in a pinch.
 2022-05-11 23:59:59 -07:00
Cyril Cohen
82440c9374 moving findlib to propagedNativeBuildInputs 2022-05-12 06:11:43 +02:00
Cyril Cohen
7e589a45ef coqPackages: etc 
- use propagatedBuildInputs to make sure ocaml plugin stuff is in path
- updated coqPackage.heq (broken url)
- fixed use of `DESTDIR` and `COQMF_COQLIB` in mkCoqDerivation
- adding `COQCORELIB` environement variable to put ocaml plugin files in the right place
- make metaFetch available from `coqPackages`
 2022-05-12 06:11:43 +02:00
P. R. d. O
17be6f75ce
python3Packages.monosat: disable failing tests 2022-05-11 18:29:58 -06:00
Sandro
324a5be95c
Merge pull request #172580 from collares/singular-osx 
singular: fix darwin build
 2022-05-12 01:33:52 +02:00
Yu-Chen Ding
e98f71d477
wolfram-engine: fix quotes in installation script 2022-05-12 01:29:53 +08:00
Mauricio Collares
15cf12c0ac singular: fix darwin build 2022-05-11 12:08:20 -04:00
Markus Kowalewski
1e2065983e
octopus: 11.3 -> 11.4 2022-05-11 14:01:02 +02:00
Theodore Ni
81046b393b
bowtie: fix build on case insensitive file systems 
Add a patch that removes the current source directory from the include
search path during compilation so that #include <version> does not end
up picking the VERSION source code file.
 2022-05-11 03:20:03 -05:00
Theodore Ni
802a8416b6
bowtie: add arm64 patch to build on M1 Macs 
This does not fix the build on Macs, but it brings the build on M1 Macs
to parity with non-M1 Macs.
 2022-05-11 02:36:56 -05:00
davidak
7dd05c6052
Merge pull request #171662 from Hexadecimaaal/wolfram-engine 
wolfram-engine: infinite loop on `WolframKernel`; `wolframscript` available in package but not installed
 2022-05-11 02:53:23 +02:00
Artturi
6c7e0653c2
Merge pull request #172356 from zaninime/nanovna-zhf 
nanovna-saver: 0.3.8 -> 0.4.0
 2022-05-11 03:35:13 +03:00
Naïm Favier
62245943aa
makeWrapper,makeBinaryWrapper: introduce explicitly named functions 
Because both versions might end up in a derivation's build inputs, it
might be useful to be able to explicitly select which function to use.
 2022-05-10 22:07:56 +02:00
Mustafa Çalışkan
f24cf4422d maintainers: change musfay to muscaln 2022-05-10 21:34:19 +03:00
Francesco Zanini
d404697e7c nanovna-saver: 0.3.8 -> 0.4.0 2022-05-10 18:18:55 +02:00
Thiago Kenji Okada
c4956c85b4
Merge pull request #172320 from xaverdh/binary-wrapper-fixes 
treewide: use non-binary wrapper for wrapGAppsHook where appropriate
 2022-05-10 17:07:26 +01:00
Markus Kowalewski
5fd7f4ef82
molden: unbreak build, make compatible with gcc-10 2022-05-10 17:01:35 +02:00
Dominik Xaver Hörl
86e7fa945e tlaplusToolbox: use non-binary wrapper for wrapGAppsHook 
The use of --add-flags in this derivation does not work with binary
    wrappers, which wrapGAppsHook uses since #164163.
 2022-05-10 15:13:58 +02:00
Markus Kowalewski
de869f039d
siesta: fix hardcoded path to rm 2022-05-10 12:53:22 +02:00
Lassulus
d369c0c118
Merge pull request #163869 from r-ryantm/auto-update/gurobi 
gurobi: 9.5.0 -> 9.5.1
 2022-05-10 11:46:25 +02:00
Lassulus
5ed1d2ff8f
Merge pull request #163885 from r-ryantm/auto-update/ott 
ott: 0.31 -> 0.32
 2022-05-10 11:45:47 +02:00
Artturi
6d007b2ce4
Merge pull request #172250 from Artturin/ridofnulls 
remove some useless null asserts
 2022-05-10 04:24:31 +03:00
Artturin
5007ea281d gwyddion: remove useless nulls 2022-05-10 00:56:23 +03:00
davidak
0bc16c7f2b
Merge pull request #172182 from markuskowa/fix-siesta 
siesta: fix build for gcc/gfortran-10/11
 2022-05-09 15:16:40 +02:00
Markus Kowalewski
a5e2f0f410
siesta: fix build for gcc/gfortran-10/11 2022-05-09 14:31:16 +02:00
Sandro
c1daf2ae36
Merge pull request #170792 from grindhold/elmerfix 
elmerfem: make elmerfem-9.0 run properly
 2022-05-09 12:00:52 +02:00
grindhold
865d79bb5b elmerfem: make elmerfem-9.0 properly 
0) ElmerGUI displays things in the Model tree on the
     left screen side again
  1) Enable the import of STEP- and other opencascade-
     based formats
  2) Patch the source to enable builds with gcc-11
  3) Build the Qt5 version instead of the Qt4 version
 2022-05-09 10:41:56 +02:00
Sandro
20b3e2f83d
Merge pull request #172079 from lschuermann/dev/horizon-eda-2.3.0 
horizon-eda: 2.2.0 -> 2.3.0
 2022-05-09 01:16:46 +02:00
Sandro
5c1adf9ffd
Merge pull request #168576 from evils/kicad-unstable 2022-05-08 23:50:51 +02:00
Sandro
a0aeb0dc1e
Merge pull request #171765 from evils/kicad-6.0.5 
kicad: 6.0.4 -> 6.0.5
 2022-05-08 23:50:32 +02:00
Leon Schuermann
c353f171b9 horizon-eda: 2.2.0 -> 2.3.0 
Signed-off-by: Leon Schuermann <leon@is.currently.online>
 2022-05-08 20:57:06 +02:00
Bobby Rong
0542fa89a7
Merge pull request #171479 from tpwrules/fix-qgroundcontrol-build 
qgroundcontrol: fix build
 2022-05-08 20:26:58 +08:00
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
Hexadecimal
94c5433df2
wolfram-engine: fix wrappers 2022-05-07 10:13:57 +08:00
Naïm Favier
76f93323f2
qucs-s: fix wrapper arguments escaping 2022-05-06 18:29:50 +02:00
Evils
3592ccf6cc kicad-unstable: 2022-03-19 -> 2022-05-06 2022-05-06 06:20:03 +02:00
Evils
64436e0df5 kicad: 6.0.4 -> 6.0.5 2022-05-06 04:48:05 +02:00
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
Thomas Watson
8030981007 qgroundcontrol: fix build 
Fixes build problems on x86_64 caused by a bug in their vendored version of
gst-plugins-good. Unfortunately I can't `fetchpatch` the fix because it just
changes a submodule pointer. The patch I added was generated from the fix at
https://github.com/mavlink/qgroundcontrol/issues/10140 .
 2022-05-03 20:57:46 -05:00
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
Justin Bedo
5eb9f35c44
R: 4.1.3 -> 4.2.0 
Patch needed to past test, as there are extra warnings
in a sandbox build due to lack of internet access.
x
 2022-04-27 09:55:00 +10:00
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
Sandro
f37f0ad4e1
Merge pull request #168969 from SuperSandro2000/staging-next-sandro 
Staging next fixes
 2022-04-17 00:35:09 +02:00
Dmitry Kalinkin
81f9e28844
root5: fix for glibc 2022-04-16 17:20:16 -04:00
Martin Weinelt
fa1bb283d8 Merge remote-tracking branch 'origin/master' into staging-next 2022-04-16 23:14:55 +02:00
Sandro Jäckel
f1189d812e
fast-downward: substitute version, fix buildInputs, minor cleanup 2022-04-16 22:46:45 +02:00
veprbl
bb5678ef5f
Merge pull request #168733 from veprbl/pr/xfitter_2_2_0 
xfitter: 2.0.1 -> 2.2.0
 2022-04-16 16:01:10 -04:00
Ben Siraphob
259fa13d53 treewide: remove nativeBuildInputs that are in stdenv 2022-04-16 21:46:46 +03:00
Fabián Heredia Montiel
5275050ab0 fityk: add -std=c++11 flag for gcc11 and later 2022-04-16 11:11:46 -05:00
Fabián Heredia Montiel
8c5a58144d fast-downward: 19.12 → 21.12.0 2022-04-16 11:11:46 -05:00
Dmitry Kalinkin
cdc17db882
xfitter: 2.0.1 -> 2.2.0 2022-04-15 22:24:52 -04:00
Fabián Heredia Montiel
8a9d5e296b cmtk: add -std=c++11 to fix build on gcc11 2022-04-15 11:15:30 -05:00