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6118 Commits

Author SHA1 Message Date
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
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