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Author SHA1 Message Date
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
Martin Weinelt a7fc5aaa76 Merge remote-tracking branch 'origin/master' into staging-next 2022-04-15 13:30:48 +02:00
Lassulus 92734ac395
Merge pull request #166865 from malob/treewide-mainProgram 
treewide: add meta.mainProgram to many packages
 2022-04-15 09:28:00 +01:00
Malo Bourgon 0e802eafad treewide: add meta.mainProgram to many packages 2022-04-14 10:24:01 -07:00
Vladimír Čunát d5d94127fd
Merge branch 'staging-next' into staging 
Minor conflicts; I hope I didn't mess up:
	pkgs/development/tools/misc/binutils/default.nix
	pkgs/games/openjk/default.nix
 2022-04-14 09:53:21 +02:00
R. Ryantm ae6932e7b9 elan: 1.3.1 -> 1.4.0 2022-04-13 20:56:11 -04:00
Luflosi 0a2f8109f4 abc-verifier: 2022.03.04 -> 2022.03.22 2022-04-12 08:38:25 -05:00
Lassulus 8ca12e04fe
Merge pull request #162172 from grnnja/init-jflap 
jflap: init at 7.1
 2022-04-12 12:08:26 +01:00
ajs124 9aa337095c
Merge pull request #164699 from r-ryantm/auto-update/mavproxy 
mavproxy: 1.8.46 -> 1.8.48
 2022-04-11 20:13:29 +01:00
Sandro ab1640b19b
Merge pull request #166909 from fedeinthemix/wolfram-engine-2 2022-04-11 13:53:05 +02:00
Federico Beffa 55a070a616 wolfram-for-jupyter-kernel: init at 0.9.2 
Also, add a script 'wolfram-notebook' to easily start a jupyter
notebook for working with the Wolfram Engine.

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-04-11 11:54:09 +02:00
Federico Beffa 2055f85304 wolfram-engine: init at 13.0.1 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-04-11 11:54:03 +02:00
Sandro 9b0ef251b3
Merge pull request #167729 from yuuyins/brmodelo 2022-04-10 21:19:44 +02:00
Fabian Affolter 394c9ba5e4
Merge pull request #168132 from r-ryantm/auto-update/calc 
calc: 2.14.0.14 -> 2.14.1.0
 2022-04-10 20:56:16 +02:00
github-actions[bot] bf63dd7434
Merge staging-next into staging 2022-04-10 18:01:38 +00:00
Vladimír Čunát 5e845236f2
Merge branch 'staging-next' into staging 2022-04-10 17:11:36 +02:00
Doron Behar 357ca2e62c
Merge pull request #168130 from alyaeanyx/qalculate-gtk-4.1.1 2022-04-10 16:39:23 +03:00
Lassulus 973fa1917c
Merge pull request #162300 from r-ryantm/auto-update/cwltool 
cwltool: 3.1.20220221074232 -> 3.1.20220224085855
 2022-04-10 13:37:54 +01:00
R. Ryantm 6ebcd043e2 calc: 2.14.0.14 -> 2.14.1.0 2022-04-10 12:33:50 +00:00
alyaeanyx 0fc77bcb21
qalculate-gtk: 4.1.0 -> 4.1.1 2022-04-10 13:59:30 +02:00
Artturi ebf6f84ea2
Merge pull request #164722 from armeenm/bump-eggnog-mapper 
eggnog-mapper: 1.0.3 -> 2.1.7
 2022-04-10 14:37:21 +03:00