1
0
Fork 1
mirror of https://github.com/NixOS/nixpkgs.git synced 2024-12-25 03:17:13 +00:00
Commit graph

3892 commits

Author SHA1 Message Date
Matt Huszagh fc66192b37 fparser: init at 4.5.1 2020-04-09 11:28:21 -07:00
Jonathan Ringer 3238302827 libpoly: fix src 2020-04-09 11:22:53 -07:00
R. RyanTM f4a9fe36fa libpoly: 0.1.7 -> 0.1.8 2020-04-09 10:29:28 -07:00
Timo Kaufmann b72fd98789
Merge pull request #84666 from jonringer/repofy-palp
palp: correct metadata for repology
2020-04-08 11:44:33 +00:00
Gabriel Ebner e71c0d80a1
Merge pull request #84583 from r-ryantm/auto-update/qalculate-gtk
qalculate-gtk: 3.8.0 -> 3.8.0a
2020-04-08 11:01:33 +02:00
Vincent Laporte f4ff33cce6 alt-ergo: 2.3.1 → 2.3.2 2020-04-08 10:23:48 +02:00
Jonathan Ringer f89b76d9db
palp: correct metadata for repology 2020-04-07 14:08:03 -07:00
R. RyanTM 67ea5a0081 qalculate-gtk: 3.8.0 -> 3.8.0a 2020-04-07 10:29:32 +00:00
Mario Rodas c9ce292597
Merge pull request #84383 from r-ryantm/auto-update/gmsh
gmsh: 4.5.4 -> 4.5.6
2020-04-05 20:03:05 -05:00
R. RyanTM b43965986f gmsh: 4.5.4 -> 4.5.6 2020-04-05 19:28:16 +00:00
Vincent Laporte d6a8d0ca5b coq_8_11: 8.11.0 → 8.11.1 2020-04-05 15:32:32 +02:00
Frederik Rietdijk 866c5aa090 Merge master into staging-next 2020-04-05 08:33:39 +02:00
Jan Tojnar 418628e162
dsview: fix build
It was using libusb-compat instead of libusb1, and the former no longer propagates the latter.
2020-04-05 01:13:14 +02:00
Timo Kaufmann 02b1f2a2de
Merge pull request #83224 from shnarazk/cadical-pr
cadical: init at 1.2.1
2020-04-04 15:44:04 +00:00
Narazaki, Shuji c5a12e33d2 cadical: init at 1.2.1 2020-04-05 00:22:36 +09:00
Jan Tojnar 08cf27e5d9
libsigrok4dsl: fix build
It was using libusb-compat instead of libusb1, and the former no longer propagates the latter.
2020-04-04 10:50:34 +02:00
Dmitry Kalinkin 99a236b477
Merge pull request #83914 from cgevans/gwyddion-darwin
gwyddion: support darwin
2020-04-01 21:44:21 -04:00
Constantine Glen Evans cacbbe92bf
gwyddion: add darwin support
Gwyddion will build on Darwin, but gnome2.gtkglext is broken there,
and so I am disabling it as an optional dependency here when building
on Darwin.
2020-04-01 17:50:36 -07:00
R. RyanTM 92c8881358 picard-tools: 2.22.0 -> 2.22.2 2020-04-01 17:29:55 +00:00
Timo Kaufmann 83fd89945d
Merge pull request #79661 from luc65r/pkg/cemu
cemu: init at 1.3
2020-03-31 15:17:33 +00:00
R. RyanTM 3017e6989f deeptools: 3.3.1 -> 3.4.1 2020-03-30 21:47:32 -07:00
R. RyanTM cff5adc2fb
snakemake: 5.10.0 -> 5.13.0 (#83839) 2020-03-31 00:39:00 -04:00
R. RyanTM bd245a755f stacks: 2.41 -> 2.52 2020-03-30 16:13:02 -07:00
Ryan Mulligan d8c21cb4bc
Merge pull request #83746 from r-ryantm/auto-update/marvin
marvin: 20.6.0 -> 20.9.0
2020-03-30 06:14:11 -07:00
R. RyanTM 1d349b8512 marvin: 20.6.0 -> 20.9.0 2020-03-30 04:02:45 +00:00
luc65r 8edd400bfb
rofi-calc: init at 1.6 (#83136)
Also:
* maintainers: add albakhamj
* maintainers: add luc65r
* rofi: add plugins argument to wrapper

Co-authored-by: Maciej Krüger <mkg20001@gmail.com>
2020-03-30 01:18:56 +02:00
Maximilian Bosch 9e7c54325e
stellarium: 0.19.3 -> 0.20.0
https://github.com/Stellarium/stellarium/releases/tag/v0.20.0
2020-03-29 17:56:35 +02:00
Jörg Thalheim d04396da8b
Merge pull request #82852 from Mic92/cross-build-rust-package
[WIP] buildRustPackage: enable strictDeps
2020-03-29 14:07:07 +01:00
Guanpeng Xu d2702c915f mathematica: 12.0.0 -> 12.1.0 2020-03-29 14:38:33 +02:00
Jörg Thalheim e841dce44a
rink: fix strict deps build 2020-03-29 12:37:25 +01:00
Constantine Glen Evans 59fbc7acba gwyddion: 2.48 -> 2.55 (and add options)
Gwyddion has a large number of optional dependencies. In this update,
those dependencies have been added with options set mostly to true,
and an option (default false) for working Python 2.7 support in the
program and in Python has been added. I have also added myself as a
maintainer as no maintainer is currently set.
2020-03-27 10:56:00 -07:00
Ryan Mulligan c669d2991b
Merge pull request #83464 from r-ryantm/auto-update/last
last: 1047 -> 1060
2020-03-27 07:34:18 -07:00
R. RyanTM bd3fbef804 last: 1047 -> 1060 2020-03-27 04:12:41 +00:00
Ryan Mulligan 8c5f9d0200
Merge pull request #83390 from r-ryantm/auto-update/seaview
seaview: 5.0 -> 5.0.2
2020-03-26 03:10:56 -07:00
R. RyanTM 4a3ea14b5b seaview: 5.0 -> 5.0.2 2020-03-26 00:25:29 +00:00
Austin Seipp 517fd073fc
xcircuit: 3.9.73 -> 3.10.12, maintain
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2020-03-25 17:46:15 -05:00
Austin Seipp 765b2fd866
mcy: 2020.03.16 -> 2020.03.21
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2020-03-25 06:46:01 -05:00
Austin Seipp 4808bef486
symbiyosys: 2020.02.11 -> 2020.03.24
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2020-03-25 06:46:01 -05:00
Vincent Laporte 618bca7054 alt-ergo: 2.3.0 → 2.3.1 2020-03-24 20:43:06 -04:00
Mario Rodas b2df6d541d
lean: 3.7.0 -> 3.7.2 2020-03-22 04:20:00 -05:00
Mario Rodas baeb670ce2
Merge pull request #82610 from r-ryantm/auto-update/eagle
eagle: 9.5.2 -> 9.6.0
2020-03-20 06:21:30 -05:00
Vincent Laporte 8dddd8a07f ocamlPackages.camlp5: 7.10 → 7.11 2020-03-19 18:04:14 -07:00
Claudio Bley 39767f8ae5
foldingathome: Make FAHControl be able to start the FAHViewer (#82925)
The command to run when clicking the button is configurable, but by default it
tries to run `FAHViewer`.
2020-03-19 13:05:54 +00:00
Austin Seipp 2ef42e07fd
mcy: 2020.02.05 -> 2020.03.16
Now with working web UI dashboard -- but no working GUI (yet!)

Signed-off-by: Austin Seipp <aseipp@pobox.com>
2020-03-17 17:19:40 -05:00
Austin Seipp 5cd4fd5bc5
symbiyosys: 2020.02.08 -> 2020.02.11
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2020-03-17 17:19:40 -05:00
Austin Seipp 9b43cf3a00
yosys: 2020.02.25 -> 2020.03.16
- Bump `abc-verifier` (2020.03.05)
  - Install `yosys-abc` symlink for tool compatbility
  - Various `yosys` expression cleanups

Signed-off-by: Austin Seipp <aseipp@pobox.com>
2020-03-17 17:19:37 -05:00
Dmitry Kalinkin ebe5f10794
kicad: don't build versions with 3d on Hydra
The hydraPlatforms have to be set on the kicad package itself, that can be
checked using:

  echo ":p { inherit kicad kicad-small kicad-unstable; }" | nix repl ./pkgs/top-level/release.nix

This commit disables build of all kicad variants that require downloading
packages3d, which currently fail on hydra with the "Output limit exceeded"
status. This leaves Hydra with only building the kicad-small, which will allow
us to cache the build of kicad-base as well as all libraries except of
packages3d.
2020-03-16 19:45:04 -04:00
Dmitry Kalinkin 68db99ad97 snakemake: 5.9.1 -> 5.10.0 2020-03-14 15:58:24 -07:00
R. RyanTM bafbfc5a06 eagle: 9.5.2 -> 9.6.0 2020-03-14 20:19:26 +00:00
zimbatm 001be890f7 folding@home: 6.02 -> 7.5.1
The v7 series is very different.

This commit introduces the 3 packages: fahclient, fahcontrol and
fahviewer. It also rebuilds the NixOS module to map better with the new
client.
2020-03-14 13:01:26 -07:00
Frederik Rietdijk 5175c35a99
Merge pull request #81611 from r-ryantm/auto-update/R
R: 3.6.2 -> 3.6.3
2020-03-14 14:29:05 +01:00
Josef Kemetmüller 3a8d05747b qgroundcontrol: Fix build
This silences some warnings to not run into "Log limit exceeded" on
hydra.
2020-03-14 03:18:39 +00:00
Mario Rodas c935567de6 lean: 3.6.1 -> 3.7.0 2020-03-14 01:32:58 +00:00
wucke13 c24b9a57c4 getdp: 3.0.4 -> 3.3.0 2020-03-13 04:10:20 +00:00
R. RyanTM a58d091d8d verilator: 4.028 -> 4.030 2020-03-12 20:57:34 -05:00
Maximilian Bosch 76821e6f43
geogebra: 5-0-573-0 -> 5-0-574-0 2020-03-12 18:12:57 +01:00
Timo Kaufmann ba589e24c9 sage: patch for pari 2.11.3 2020-03-12 12:24:41 +01:00
Timo Kaufmann c4ab541443 pari: backport bug fix
https://trac.sagemath.org/ticket/29313#comment:4
2020-03-12 12:24:35 +01:00
xaverdh 5ac085c3cc
wxmaxima: 18.02.0 -> 20.02.4 (#82323)
The commit description is 18.02.0 -> 20.02.4, because in the last version bump (1c6a193b3e), the version string was changed, but the hash was not.

Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
2020-03-11 12:07:53 -04:00
Timo Kaufmann 1a6b1fb32a symmetrica: add timokau to maintainers 2020-03-10 18:10:28 +01:00
Timo Kaufmann 0c875c28c6 symmetrica: 2.0 -> 3.0.1
This switches to the sagemath fork, since the original upstream is no
longer maintained and sagemath has effectively maintained symmetrica
through patches for a while now. The update fixes one bug in particular
that has caused failures in the sagemath test suite:

https://github.com/NixOS/nixpkgs/issues/81449
https://trac.sagemath.org/ticket/15312
https://trac.sagemath.org/ticket/29061

Regarding the licensing change:

7cf91b3800
2020-03-10 18:10:25 +01:00
Timo Kaufmann e05e219b31
Merge pull request #82240 from timokau/sage-docutils-0.15-fix
sage: fix test suite with docutils 0.15
2020-03-10 15:25:22 +00:00
Timo Kaufmann 7133577405 sage: fix test suite with docutils 0.15
The better way to fix this would be to backport the upstream sphinx
patch:

faedcc48cc

Unfortunately it doesn't apply cleanly and isn't worth the effort
of backporting. Let's hope we can switch to python3 sage and the recent
sphinx version that comes with it before this becomes a problem.
2020-03-10 13:15:41 +01:00
Timo Kaufmann 63ed2bf3c3
Merge pull request #81950 from r-ryantm/auto-update/pari
pari: 2.11.2 -> 2.11.3
2020-03-09 17:31:14 +00:00
Michael Raskin bbab73266d
Merge pull request #80719 from mucaho/feature/clingcon_init
clingcon: init at 3.3.0
2020-03-09 07:42:38 +00:00
mucaho 202c2a8eff clingcon: init at 3.3.0 2020-03-08 19:21:55 +01:00
Maximilian Bosch 84f862ed91
Merge pull request #81796 from JohnAZoidberg/satallax-gcc9
satallax: Fix build with GCC9
2020-03-08 16:12:40 +01:00
Gabriel Ebner d7a68e9bce
Merge pull request #82028 from r-ryantm/auto-update/qalculate-gtk
qalculate-gtk: 3.7.0 -> 3.8.0
2020-03-08 13:31:00 +01:00
Frederik Rietdijk 0eb0ddc4db Merge staging-next into master 2020-03-08 08:11:01 +01:00
R. RyanTM e6f5bb8dc4 qalculate-gtk: 3.7.0 -> 3.8.0 2020-03-08 00:14:22 +00:00
Vincent Laporte dcfccdfc33
acgtk: 1.5.0 → 1.5.1 (#81539)
Co-authored-by: Jon <jonringer@users.noreply.github.com>
2020-03-07 09:56:18 +01:00
R. RyanTM 6528554396 pari: 2.11.2 -> 2.11.3 2020-03-07 02:43:40 +00:00
Gabriel Ebner 8428f5bb4a elan: v0.8.0 tag was force-pushed by upstream 2020-03-06 15:35:37 +01:00
Gabriel Ebner 70e5428d66 elan: 0.7.5 -> 0.8.0 2020-03-06 14:28:36 +01:00
Joachim Breitner 2d2a5a9b63
js_of_ocaml: 3.4.0 -> 3.5.2 (#75766)
drive-by contributions, as I was playing around with this (it has better
support for the `num` library, it seems.)

js_of_ocaml: 3.4.0 -> 3.5.2
ocamlPackages.js_of_ocaml-ppx_deriving_json: use ppxlib-0.12.0
ocamlPackages.eliom: 6.8.0 → 6.10.1
ocamlPackages.ocsigen-toolkit: 2.2.0 → 2.5.0
ocamlPackages.ocsigen-start: 2.7.0 → 2.16.1

Co-authored-by: Vincent Laporte <Vincent.Laporte@gmail.com>
2020-03-06 07:42:04 +01:00
Frederik Rietdijk 188c3a4d03 Merge staging-next into staging 2020-03-06 07:09:30 +01:00
Mario Rodas 7597bdd59b
Merge pull request #81783 from r-ryantm/auto-update/gmsh
gmsh: 4.5.2 -> 4.5.4
2020-03-05 08:31:38 -05:00
Mario Rodas 1196a5c7a7
Merge pull request #81722 from r-ryantm/auto-update/workcraft
workcraft: 3.2.5 -> 3.2.6
2020-03-05 07:42:25 -05:00
Daniel Schaefer bc56175034 satallax: Fix build with GCC9 2020-03-05 05:16:49 +01:00
R. RyanTM 9974067129 gmsh: 4.5.2 -> 4.5.4 2020-03-05 00:20:08 +00:00
R. RyanTM adcdd7b0a7 gromacs: 2020 -> 2020.1 2020-03-04 23:10:39 +00:00
Jan Tojnar 1a44e325d2
Merge branch 'staging-next' into staging 2020-03-04 21:24:05 +01:00
R. RyanTM 86e6080daf workcraft: 3.2.5 -> 3.2.6 2020-03-04 13:41:09 +00:00
Mario Rodas 5760e001ca
Merge pull request #81706 from r-ryantm/auto-update/picard-tools
picard-tools: 2.21.8 -> 2.22.0
2020-03-04 07:26:05 -05:00
R. RyanTM 343ec80712 picard-tools: 2.21.8 -> 2.22.0 2020-03-04 09:58:40 +00:00
Gabriel Ebner 0d470dc5ea
Merge pull request #81692 from r-ryantm/auto-update/lean
lean: 3.6.0 -> 3.6.1
2020-03-04 10:32:38 +01:00
R. RyanTM 5b833c08ef lean: 3.6.0 -> 3.6.1 2020-03-04 06:26:01 +00:00
Aiken Cairncross 3db82f6fc3 python3Packages.monosat: Fix hash
PR #81562 inadvertently broke these builds
2020-03-03 11:02:23 -08:00
markuskowa dbb9fab27f
Merge pull request #81604 from markuskowa/upd-octopus
octopus: 9.1 -> 9.2
2020-03-03 12:45:16 +01:00
R. RyanTM faa5c3bde3 R: 3.6.2 -> 3.6.3 2020-03-03 11:34:22 +00:00
markuskowa 4822d61252
Merge pull request #80977 from r-ryantm/auto-update/quantum-espresso
quantum-espresso: 6.4.1 -> 6.5
2020-03-03 11:09:30 +01:00
Markus Kowalewski eebd6fe75a
octopus: 9.1 -> 9.2 2020-03-03 10:54:23 +01:00
Aiken Cairncross 2148a154c6 python3Packages.monosat: Fix Python 3.8 build 2020-03-03 07:40:57 +01:00
Brenton Horne b07eb54048 marvin: 20.4.0 -> 20.6.0 2020-03-02 21:50:25 +01:00
Jan Tojnar f27031f48f
Merge pull request #81063 from NixOS/netpbm
netpbm: 10.82.01 → 10.89.1
2020-03-02 19:26:25 +01:00
scalavision dbb4826457 truvari:1.3.2->1.3.4 2020-03-02 09:15:58 +01:00
Jan Tojnar 9555834399
netpbm: split into multiple outputs 2020-03-01 15:13:03 +01:00
Frederik Rietdijk 21b808cd76 Merge staging-next into staging 2020-02-29 15:29:45 +01:00
Benjamin Hipple ad30a30488 rustPlatform.fetchCargo: handle custom Cargo.lock patchfiles with validation
Previously, we would asssert that the lockfiles are consistent during the
unpackPhase, but if the pkg has a patch for the lockfile itself then we must
wait until the patchPhase is complete to check.

This also removes an implicity dependency on the src attribute coming from
`fetchzip` / `fetchFromGitHub`, which happens to name the source directory
"source". Now we glob for it, so different fetchers will work consistently.
2020-02-28 18:54:23 -08:00
Matthieu Coudron 05b6836816 torchPackages, torch-repl: remove
See https://github.com/NixOS/nixpkgs/issues/71888
and https://github.com/NixOS/nixpkgs/issues/56398

To sump up, development has moved on to other technologies than lua:
https://github.com/torch/torch7#development-status
and the current packages are broken anyway.
2020-02-28 20:56:42 +01:00
Austin Seipp 7e66ce29bf
mcy: init at 2020.02.05
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2020-02-27 21:52:15 -06:00
Austin Seipp 3d8efecda1
symbiyosys: fix calls to external programs
48085826f broke symbiyosys when it needed to call `yosys-abc`: when
`ABCEXTERNAL` is set in the Makefile, then `yosys-abc` is not built.

But in general `sby` was just calling programs out of the ambient
environment. Fix that for most programs it can invoke: it now has a
direct dependency on boolector, aiger, abc, yosys, etc.

This also does some other minor clean up.

Signed-off-by: Austin Seipp <aseipp@pobox.com>
2020-02-27 21:52:15 -06:00
Mario Rodas 79f057e2eb
lean: 3.5.1 -> 3.6.0 2020-02-26 18:00:00 -05:00
Dmitry Kalinkin b9ee6cd85c
Merge pull request #80640 from smaret/gildas-20200201a
gildas: 20200101_a -> 20200201_a
2020-02-25 10:26:18 -05:00
R. RyanTM 56d58ecb24 quantum-espresso: 6.4.1 -> 6.5 2020-02-24 19:40:14 +00:00
R. RyanTM 4080e7976e gtkwave: 3.3.103 -> 3.3.104 2020-02-24 11:43:54 -06:00
Linus Heckemann 0cc83f884a
Merge pull request #80292 from bcdarwin/mrtrix
mrtrix: init at 3.0_RC3_latest
2020-02-24 13:52:38 +01:00
Timo Kaufmann f4dbf4402b
Merge pull request #80759 from Thra11/fix-r
Fix R
2020-02-23 23:48:21 +00:00
Tom Hall ae9e09a2e1 R: fix build on aarch64 by removing a failing test
I believe this test is currently incorrect on aarch64 and expects a
warning about loss of precision with much smaller numbers than the
platform's long doubles can handle.
2020-02-22 13:17:40 +00:00
Edward Tjörnhammar 9b6faedb18
shogun: 6.0.0 -> 6.1.4
Also migrate to opencv3 to address #72739, the PR didn't build for me.
Disable testing and ccache since they were broken.

Co-authored-by: Robert Scott <code@humanleg.org.uk>
2020-02-21 11:05:09 +01:00
Sébastien Maret 7667207f3d
gildas: 20200101_a -> 20200201_a
- Upgrade gildas to the latest version

 - Remove a patch that has been included upstream

 - Re-enable parallel building (fixed upstream)
2020-02-20 15:28:57 +01:00
Gabriel Ebner f098b0dd2c
Merge pull request #80576 from bhipple/u/rust-cargo-elan
elan: upgrade cargo fetcher and cargoSha256
2020-02-20 09:53:49 +01:00
Maximilian Bosch 7bdc103ac8
geogebra: 5-0-570-0 -> 5-0-573-0 2020-02-20 03:09:06 +01:00
Benjamin Hipple ed85c9981a elan: upgrade cargo fetcher and cargoSha256
Infra upgrade as part of #79975; ran `nixpkgs-review wip` successfully.
2020-02-19 18:17:27 -05:00
Tom Hall 4e5aeca90b R: Enable java support on all platforms 2020-02-19 22:57:41 +00:00
Ben Darwin 9a2cd20478 mrtrix: init at 3.0_RC3_latest
This package consists mostly of command-line tools, but there are also two qt5-based image viewers (`mrview` and `shview`). I have provided an option `withGui = true` to allow users to disable these viewers. They work on NixOS but unlikely to work out-of-the box on non-NixOS Linux (see #62169), but I've refrained from asserting that they shouldn't be built since a user might want to fiddle with runtime GL stuff.

Some programs rely on FSL and/or ANTs backends; I have somewhat heavy-handedly wrapped all binaries to point to ANTs, while FSL is not available in Nix at the moment and has a non-commercial license so would be convenient to disable by default for Hydra builds.
2020-02-16 22:25:25 -05:00
Daniel Schaefer 1e613230d2
Merge pull request #80122 from r-ryantm/auto-update/kallisto
kallisto: 0.46.1 -> 0.46.2
2020-02-15 22:41:15 +01:00
R. RyanTM 4c6c40d96a kallisto: 0.46.1 -> 0.46.2
Co-authored-by: Daniel Schaefer <git@danielschaefer.me>
2020-02-15 22:39:58 +01:00
Junyoung Clare Jang b71c03e483
lean: 3.4.2 -> 3.5.1
3.4.2 is not compilable with GCC >= 9.1
2020-02-15 02:29:12 -05:00
R. RyanTM d54a58a2cd verilator: 4.026 -> 4.028 2020-02-14 12:13:04 -06:00
Benjamin Hipple eb11feaa0b treewide: change fetchCargoTarball default to opt-out
Changes the default fetcher in the Rust Platform to be the newer
`fetchCargoTarball`, and changes every application using the current default to
instead opt out.

This commit does not change any hashes or cause any rebuilds. Once integrated,
we will start deleting the opt-outs and recomputing hashes.

See #79975 for details.
2020-02-13 22:41:37 -08:00
Dmitry Kalinkin 5f2a3bef33
Merge pull request #79778 from jbedo/delly
delly: 0.8.1 -> 0.8.2
2020-02-11 03:54:02 -05:00
Justin Bedo a8fe9e7aff
delly: 0.8.1 -> 0.8.2
Backported patch required for htslib 1.10.2
2020-02-11 19:21:59 +11:00
Ryan Mulligan b99e12f4fe
Merge pull request #79534 from r-ryantm/auto-update/last
last: 1045 -> 1047
2020-02-10 18:10:08 -08:00
Brenton Horne 567be48707 marvin: 20.3.0 -> 20.4.0 2020-02-10 19:55:13 +01:00
Evils d3a9e634bf kicad-unstable: update update.sh && update
use /tmp instead of XDG_RUNTIME_DIR
  which is /run/user/1000, which defaults to 10% of RAM
  and kicad-packages3d needs ~6gb
2020-02-10 19:54:38 +01:00
Evils a9942b0226 kicad: simplify component names 2020-02-10 19:54:38 +01:00
Ben Darwin 39f0e3b32b minc_tools: enable building conversion tools 2020-02-10 19:53:25 +01:00
Ben Darwin bcad453bcf minc_tools: 2017-09-11 -> unstable-2019-12-04 2020-02-10 19:53:25 +01:00
luc65r 94c60990fc cemu: init at 1.3 2020-02-10 19:26:25 +01:00
R. RyanTM e988c072be clp: 1.17.3 -> 1.17.5 2020-02-10 13:24:22 +01:00
R. RyanTM 1d4fd7f5f2 verifast: 18.02 -> 19.12 2020-02-09 14:29:31 -06:00
R. RyanTM 3a1098e3e2 pcb: 4.2.1 -> 4.2.2 2020-02-09 16:49:13 +01:00
Frederik Rietdijk 3846896084 Merge pull request #79293 from NixOS/staging-next
Staging next (with glibc 2.30)
2020-02-09 16:40:16 +01:00
Ryan Mulligan c9cf351871 Merge pull request #79479 from r-ryantm/auto-update/workcraft
workcraft: 3.1.9 -> 3.2.5
2020-02-09 06:37:47 -08:00
Frederik Rietdijk 531a48ebdb Merge master into staging-next 2020-02-09 11:00:29 +01:00
Jannik Vierling 6ea5cd21ab iprover: 2018_Jul_24_11h -> 3.1 2020-02-09 09:38:57 +01:00
Frederik Rietdijk 03755ed59a Merge master into staging-next 2020-02-09 09:17:51 +01:00
Luz 0522b3347e librepcb: 0.1.2 -> 0.1.3 (#74786) 2020-02-09 01:07:31 -05:00
Dmitry Kalinkin 1872e69450
Merge pull request #79301 from Abdillah/patch-2
librepcb: Fix platform plugin xcb not found
2020-02-09 00:28:49 -05:00
Emily a14a32fd75 symbiyosys: 2019.10.11 -> 2020.02.08 2020-02-08 23:00:07 -06:00
Ryan Mulligan 537f07555f Merge pull request #79557 from r-ryantm/auto-update/marvin
marvin: 19.27.0 -> 20.3.0
2020-02-08 12:42:18 -08:00
R. RyanTM 20f22f681f marvin: 19.27.0 -> 20.3.0 2020-02-08 19:34:35 +00:00
markuskowa 8261fc4980
Merge pull request #79511 from r-ryantm/auto-update/gmsh
gmsh: 4.5.1 -> 4.5.2
2020-02-08 14:21:27 +01:00
R. RyanTM dae266aa66 last: 1045 -> 1047 2020-02-08 13:04:53 +00:00
R. RyanTM 7c58b6437b gmsh: 4.5.1 -> 4.5.2 2020-02-08 07:25:27 +00:00
Ryan Mulligan 555ca166ec
Merge pull request #79467 from r-ryantm/auto-update/picard-tools
picard-tools: 2.21.6 -> 2.21.8
2020-02-07 18:10:16 -08:00
R. RyanTM 5bf0de57ad workcraft: 3.1.9 -> 3.2.5 2020-02-07 21:09:41 +00:00
Frederik Rietdijk 30f0909e3a Merge master into staging-next 2020-02-07 19:27:52 +01:00
R. RyanTM d5404eebe9 picard-tools: 2.21.6 -> 2.21.8 2020-02-07 17:20:58 +00:00
R. RyanTM 78d6e74427 eagle: 9.5.1 -> 9.5.2 2020-02-06 20:17:53 +01:00
R. RyanTM ce5b0406db labelImg: 1.6.0 -> 1.8.1 2020-02-06 20:11:53 +01:00
Hernawan Faïz Abdillah 2d4ee40176
librepcb: Fix platform plugin xcb not found 2020-02-06 08:44:16 +07:00
Frederik Rietdijk 292fd97f67 Merge staging-next into staging 2020-02-05 20:48:28 +01:00
Frederik Rietdijk 419bc0a4cd Revert "Revert "Merge master into staging-next""
In 87a19e9048 I merged staging-next into master using the GitHub gui as intended.
In ac241fb7a5 I merged master into staging-next for the next staging cycle, however, I accidentally pushed it to master.
Thinking this may cause trouble, I reverted it in 0be87c7979. This was however wrong, as it "removed" master.

This reverts commit 0be87c7979.
2020-02-05 19:41:25 +01:00
Frederik Rietdijk 0be87c7979 Revert "Merge master into staging-next"
I merged master into staging-next but accidentally pushed it to master.
This should get us back to 87a19e9048.

This reverts commit ac241fb7a5, reversing
changes made to 76a439239e.
2020-02-05 19:18:35 +01:00
Ryan Mulligan 67143ec938
Merge pull request #79231 from r-ryantm/auto-update/SPAdes
SPAdes: 3.13.1 -> 3.14.0
2020-02-05 06:54:45 -08:00
Vladimír Čunát 48a997cd76
Merge #66528: glibc: 2.27 -> 2.30 (into staging)
Includes update of stdenv bootstap tools (for three main platforms)
and many package fixes with new glibc.
2020-02-05 13:41:09 +01:00
R. RyanTM 3c54ae5679 SPAdes: 3.13.1 -> 3.14.0 2020-02-04 16:40:50 +00:00
Millian Poquet 150f4a967c simgrid: 3.24 -> 3.25 2020-02-03 10:37:03 -08:00
Maximilian Bosch ea8ae88f04
Merge branch 'staging' into glibc230 2020-02-01 17:42:03 +01:00
Florian Klink 570afbcb5b abc-verifier: passthru rev
Some consumers of abc-verifier require certain abc versions.
For that reason, expose the exact rev via a passtrhru.
2020-02-01 12:49:45 +01:00
Florian Klink 351f47da57 abc-verifier: 2018-07-08 -> 2020-01-11 2020-02-01 12:49:45 +01:00
markuskowa d9209250e5
Merge pull request #78981 from r-ryantm/auto-update/jmol
jmol: 14.30.1 -> 14.30.2
2020-02-01 11:07:38 +01:00
Mario Rodas c8af1bef6e
Merge pull request #78833 from r-ryantm/auto-update/snakemake
snakemake: 5.8.1 -> 5.9.1
2020-02-01 04:11:11 -05:00
Mario Rodas 611971f9a5
Merge pull request #78849 from r-ryantm/auto-update/tetgen
tetgen: 1.5.0 -> 1.5.1
2020-02-01 04:10:16 -05:00
R. RyanTM 097737b5a4 jmol: 14.30.1 -> 14.30.2 2020-02-01 03:50:56 +00:00
Vincent Laporte 13dd5844fd coqPackages_8_11.coq: 8.11+β1 → 8.11.0 2020-01-31 14:09:51 +01:00
Vincent Laporte 659a7ae963 coq: disable CoqIDE on Darwin for Coq ≥ 8.10 2020-01-31 14:09:51 +01:00
Luka Blaskovic fd614a8e8f saw-tools: use default llvm 2020-01-30 18:35:30 -05:00
Jörg Thalheim 6eb23e0721
verilator: 4.024 -> 4.026 (#78891)
verilator: 4.024 -> 4.026
2020-01-30 20:43:40 +00:00
Jörg Thalheim 37286820f2
verilator: shebangs patch is not needed anymore 2020-01-30 20:42:51 +00:00
R. RyanTM ab63f72b23
sherpa: 2.2.6 -> 2.2.8 (#78852) 2020-01-30 13:08:47 -05:00
R. RyanTM cd526d844b verilator: 4.024 -> 4.026 2020-01-30 18:06:40 +00:00
Ryan Mulligan c179ec8a64
Merge pull request #78823 from r-ryantm/auto-update/seaview
seaview: 4.7 -> 5.0
2020-01-30 06:59:41 -08:00
Maximilian Bosch abefd4f78a
pspp: 1.0.1 -> 1.2.0, fix build w/glibc-2.30 2020-01-30 15:19:44 +01:00
R. RyanTM 53706054ba tetgen: 1.5.0 -> 1.5.1 2020-01-30 12:47:50 +00:00
R. RyanTM a94c66bc88 snakemake: 5.8.1 -> 5.9.1 2020-01-30 09:44:26 +00:00
R. RyanTM 42fff82421 seaview: 4.7 -> 5.0 2020-01-30 08:26:52 +00:00
Mario Rodas a20b7cff7c
Merge pull request #78521 from r-ryantm/auto-update/ott
ott: 0.29 -> 0.30
2020-01-29 21:47:20 -05:00
Frederik Rietdijk dce0ca29d9 Merge master into staging-next 2020-01-28 10:46:13 +01:00
Silvan Mosberger 80a2740991
Merge pull request #78265 from Synthetica9/https-homepages
treewide: fix redirected urls
2020-01-27 15:00:53 +01:00
Gabriel Ebner 3809627321
Merge pull request #78511 from r-ryantm/auto-update/libqalculate
libqalculate: 3.6.0 -> 3.7.0
2020-01-26 18:47:18 +01:00
Gabriel Ebner 8161fe21e0 qalculate-gtk: 3.6.0 -> 3.7.0 2020-01-26 18:43:29 +01:00
R. RyanTM f1085d02bb ott: 0.29 -> 0.30 2020-01-26 09:43:23 +00:00
samlich 3376628557
pymol: cleanup 2020-01-25 19:58:36 +00:00
samlich 77317774ce
pymol: link desktop icon 2020-01-24 19:51:08 +00:00
samlich 3638755ff3
pymol: add samlich as maintainer 2020-01-24 19:49:38 +00:00
samlich 97410b59f3
pymol: 2.1.0 -> 2.3.0 2020-01-24 19:42:59 +00:00
Justin Bedo 7f142260d3 manta: init 1.6.0 2020-01-24 02:02:19 -08:00
Ryan Mulligan a6dc361cae
Merge pull request #78261 from r-ryantm/auto-update/picard-tools
picard-tools: 2.21.3 -> 2.21.6
2020-01-22 16:18:57 -08:00
Patrick Hilhorst 593e11fd94
treewide: fix redirected urls
According to https://repology.org/repository/nix_unstable/problems, we have a
lot of packages that have http links that redirect to https as their homepage.
This commit updates all these packages to use the https links as their
homepage.

The following script was used to make these updates:

```

curl https://repology.org/api/v1/repository/nix_unstable/problems \
    | jq '.[] | .problem' -r \
    | rg 'Homepage link "(.+)" is a permanent redirect to "(.+)" and should be updated' --replace 's@$1@$2@' \
    | sort | uniq > script.sed

find -name '*.nix' | xargs -P4 -- sed -f script.sed -i
```
2020-01-22 11:26:22 +01:00
R. RyanTM fff7a7a862 picard-tools: 2.21.3 -> 2.21.6 2020-01-22 10:12:28 +00:00
DwarfMaster 227a3f4383 Renamed maintainer lucas8 -> dwarfmaster 2020-01-21 16:39:52 +10:00
Jonathan Ringer 4de137a77d samtools: 1.9 -> 1.10 2020-01-19 13:13:01 -08:00
Frederik Rietdijk bcd8c6b8dc Merge master into staging-next 2020-01-17 17:08:16 +01:00
Dmitry Kalinkin 430dfb8082
Merge pull request #77631 from smaret/gildas-202001a
gildas: 20191201_a -> 20200101_a
2020-01-17 10:23:28 -05:00
Anders Kaseorg 3cd8ce3bce treewide: Fix unsafe concatenation of $LD_LIBRARY_PATH
Naive concatenation of $LD_LIBRARY_PATH can result in an empty
colon-delimited segment; this tells glibc to load libraries from the
current directory, which is definitely wrong, and may be a security
vulnerability if the current directory is untrusted.  (See #67234, for
example.)  Fix this throughout the tree.

Signed-off-by: Anders Kaseorg <andersk@mit.edu>
2020-01-15 09:47:03 +01:00
Frederik Rietdijk 2a88c3c302 Merge staging-next into staging 2020-01-15 09:23:28 +01:00
Will Dietz afe905246d nota: init at 1.0
Fixes #77590.
2020-01-14 15:16:21 -08:00
Sébastien Maret 0956fcab16
gildas: 20191201_a -> 20200101_a 2020-01-14 11:22:53 +01:00
Luka Blaskovic 991a7e041f pcalc: build with bison3 2020-01-13 21:35:19 +00:00
lewo 4ea7d13c5c
Merge pull request #77041 from filalex77/rink-0.4.5
rink: 0.4.4 -> 0.4.5
2020-01-11 09:35:16 +01:00
Jonathan Ringer 5961f211f3 python.pkgs wide: fix problematic urls 2020-01-10 21:02:12 -08:00
Jörg Thalheim 01d93cbbe1
kicad: split version.nix & add update.sh (#77003)
kicad: split version.nix & add update.sh
2020-01-10 14:19:14 +00:00
Bruno Bzeznik f7a4e4a93a bayescan: init at 2.1 (#68191)
Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
2020-01-09 12:38:53 -05:00
markuskowa 2aecfca22c
Merge pull request #77083 from r-ryantm/auto-update/gmsh
gmsh: 4.4.1 -> 4.5.1
2020-01-09 12:27:11 +01:00
Mario Rodas 2148e53664
Merge pull request #77160 from r-ryantm/auto-update/ngspice
ngspice: 30 -> 31
2020-01-09 05:13:15 -05:00
Mario Rodas 6f79952429
Merge pull request #77169 from r-ryantm/auto-update/pcb
pcb: 4.2.0 -> 4.2.1
2020-01-09 05:09:50 -05:00
Daniel Albert d5dc2cc7ba xflr5: init at 6.47 2020-01-08 23:35:11 +01:00
Evils 2607c4b9f9 kicad: split version.nix & add update.sh
update.sh generates version.nix
  by default only updates kicad-unstable
  several options (can be combined)
    all, update to latest tag and master
    clean, generate versions.sh from scratch
    commit, make a git commit
2020-01-08 23:04:54 +01:00
Maximilian Bosch 8a6baaecb5
geogebra: 5-0-569-0 -> 5-0-570-0 2020-01-07 23:26:31 +01:00
Luis Pedro Coelho fdfebafc10 blast: init at 2.10.0 (#61430)
Co-authored-by: Pavel Chuprikov <pschuprikov@gmail.com>
2020-01-07 20:14:18 +01:00
Markus Kowalewski a74b248f06
openmolcas: 18.09 -> 19.11 2020-01-07 15:36:59 +01:00
R. RyanTM cc98c9fbb2 pcb: 4.2.0 -> 4.2.1 2020-01-06 19:47:54 -08:00
Ryan Mulligan 8e0b0d08c2
Merge pull request #77125 from r-ryantm/auto-update/last
last: 1042 -> 1045
2020-01-06 18:51:09 -08:00
R. RyanTM 501f79aa9b ngspice: 30 -> 31 2020-01-06 17:40:29 -08:00
R. RyanTM 4bc4c70bc6 last: 1042 -> 1045 2020-01-06 11:46:28 -08:00
R. RyanTM 66156e04d5 gmsh: 4.4.1 -> 4.5.1 2020-01-06 06:33:28 -08:00
R. RyanTM 60fd879921 gromacs: 2019.4 -> 2020 2020-01-06 04:30:02 -08:00
Oleksii Filonenko bc8dc2bd0a
rink: add filalex77 to maintainers 2020-01-06 12:41:19 +02:00
Oleksii Filonenko 8d8ce109cb
rink: 0.4.4 -> 0.4.5 2020-01-06 12:39:32 +02:00
markuskowa b06114f078
Merge pull request #76311 from r-ryantm/auto-update/marvin
marvin: 19.23.0 -> 19.27.0
2020-01-04 12:24:48 +01:00
Gabriel Ebner 3604ae8394
Merge pull request #74259 from Evils-Devils/kicad-unstable
kicad: cleanup, fix and update
2020-01-03 20:14:07 +01:00
Frederik Rietdijk 7aa2b0215b Merge master into staging-next 2020-01-03 10:25:14 +01:00
Ryan Mulligan ec29bb50bf
Merge pull request #76208 from r-ryantm/auto-update/bcftools
bcftools: 1.9 -> 1.10.2
2020-01-02 16:42:27 -08:00
Evils e4786f3a1c kicad: update & cleanup
minor simplification, fix base version

split i18n and get from gitlab

correct wrapper pythonpath, cleanup build output

update & fake git describe

correct base.nix to fit contributing.md
2020-01-02 03:45:34 +01:00
Evils 6119ca27bb kicad: split wrapping and building 2020-01-02 03:45:34 +01:00
Evils d96992a21b kicad: unite unstable.nix with default.nix
use latest libraries for unstable
move all revs and hashes to default.nix

thanks TQ for getting me through this blockage
2020-01-02 03:45:34 +01:00
Evils 958d745fec kicad: use separated libraries
switch source to gitlab as that's the new upstream source

use wrapper variables for everything but i18n
  add sym and fp templates to template path

update meta to reflect kicad's own language
  set license to AGPLv3, according to the source's LICENSE.README

reduce diff between default and unstable in preparation of merging

on debian gets "no module named 'math'"
  pcbnew 3d viewer is unusable (at least on my T410)
2020-01-02 03:45:34 +01:00
Evils c61170168d kicad: switch to best try from unstable and 5.1.5
make unstable use kicad-libraries
  still using a link in $out..., not sure that's a bad thing
  this allows setting that path in makeWrapperArgs
    can't use $out there

kicad-with-packages3d -> kicad and kicad-small

default to OCCT, OCE is outdated
  enforce OCCT on aarch64, where OCE is broken
  withOCE flag allows using OCE on non-aarch64
2020-01-02 03:45:34 +01:00
Evils 6477f717e3 kicad-unstable: wrap
use wxGTK31
  brings hiDPI support
  no python shell...
2020-01-02 03:45:34 +01:00
Matt Huszagh d40747ed2c kicad: add python six package as dep
This is needed for python scripting support.
2020-01-02 03:45:34 +01:00
Matt Huszagh 1eb1b067dd kicad: python2 -> python3 2020-01-02 03:45:34 +01:00
Robin Gloster 95526382be
polymake: fix for structured attrs 2019-12-31 00:49:42 +01:00
Robin Gloster 5f2b92e3ec
treewide: NIX_*_COMPILE -> string 2019-12-31 00:13:29 +01:00
Robin Gloster ab0cfd9e03
treewide: NIX_*_COMPILE -> string 2019-12-31 00:10:18 +01:00
Frederik Rietdijk 6d059becd3 Merge gcc-9 into staging (#68029) 2019-12-30 16:38:38 +01:00
Robin Gloster 65395a7105
treewide: installTargets is a list 2019-12-30 13:29:27 +01:00
Merijn Broeren 133103d709
treewide: replace make/build/configure/patchFlags with nix lists 2019-12-30 12:58:11 +01:00
Robin Gloster 1065d80dd3
simgrid: *Flags are lists 2019-12-30 12:15:25 +01:00
Jan Tojnar ea4da9b5fa
Merge pull request #76674 from jtojnar/structured-attrs-masterable
treewide: structured-attrs fixes
2019-12-30 04:52:45 +01:00
Robin Gloster ac8eaa8507
treewide: fix *Flags 2019-12-30 04:50:37 +01:00
Franz Pletz 1a871b4382
minisat: 2.2.0 -> 2.2.1 2019-12-30 03:50:35 +01:00
Franz Pletz a88fc6be6d
strelka: fix build w/ gcc9 2019-12-30 03:18:19 +01:00
R. RyanTM 3d740ef586 verilator: 4.022 -> 4.024 2019-12-29 15:48:39 -06:00
Frederik Rietdijk eda01862c4
Merge pull request #75900 from jbedo/tebreak
Tebreak, minia, last, bx-python, python-lzo
2019-12-29 10:24:31 +01:00
Justin Bedo 11460d4cac
tebreak: init at 1.0 2019-12-29 17:16:10 +11:00
Ben Wolsieffer 660345d9fe mavproxy: 1.8.17 -> 1.8.18 2019-12-27 16:23:20 -08:00
Franz Pletz 81248e703c
xfitter: 2.0.0 -> 2.0.1, fix build w/ gcc9 2019-12-27 03:48:21 +01:00
Dmitry Kalinkin 984ceb1092
Merge pull request #76541 from veprbl/pr/root_python_wrap
root: wrap python executables
2019-12-26 12:29:12 -05:00
Dmitry Kalinkin 0b28198f23
root: wrap python executables
In normal use of ROOT the PYTHONPATH is intended to be set when user
sources the thisroot.{,s}sh. We do that in the setupHook. This covers
the case when thisroot.sh was not sourced.
2019-12-26 11:49:12 -05:00
Maximilian Bosch 9842c4b107
treewide: update which packages I'm currently maintaining
Idea shamelessly stolen from 4e60b0efae.

I realized that I don't really know anymore where I'm listed as maintainer and what
I'm actually (co)-maintaining which means that I can't proactively take
care of packages I officially maintain.

As I don't have the time, energy and motivation to take care of stuff I
was interested in 1 or 2 years ago (or packaged for someone else in the
past), I decided that I make this explicit by removing myself from several
packages and adding myself in some other stuff I'm now interested in.

I've seen it several times now that people remove themselves from a
package without removing the package if it's unmaintained after that
which is why I figured that it's fine in my case as the affected pkgs
are rather low-prio and were pretty easy to maintain.
2019-12-26 15:27:47 +01:00
Franz Pletz 77b6c3cd06
Merge remote-tracking branch 'origin/master' into gcc-9 2019-12-26 14:17:36 +01:00
Timo Kaufmann 8ac53ed0b1 python.pkgs.sympy: 1.4 -> 1.5
Sage needs some doctest changes. The patch was included upstream.
Modelled after https://trac.sagemath.org/ticket/28911.
2019-12-26 11:46:42 +01:00
Markus Kowalewski 63d62699e0
marvin: 19.25.0 -> 19.27.0 2019-12-25 15:11:16 +01:00
Jan Tojnar b1b26f8cf6
Merge pull request #76412 from jtojnar/pangox-compat-drop
pangox_compat: drop
2019-12-24 20:04:10 +01:00
Jan Tojnar aee453e5c9
openmodelica: remove pangox dependency
It was probably just a dependency of `gtkglext` since I cannot find any reference to `pangox` in the repo.

But cannot verify build since it is broken.
2019-12-24 16:13:13 +01:00
markuskowa 64b6fa927e
Merge pull request #76285 from r-ryantm/auto-update/jmol
jmol: 14.30.0 -> 14.30.1
2019-12-24 02:05:48 +01:00
R. RyanTM cf6d80a89d marvin: 19.23.0 -> 19.25.0 2019-12-23 13:15:32 -08:00
R. RyanTM 398f11945e jmol: 14.30.0 -> 14.30.1 2019-12-23 09:16:44 -08:00
R. RyanTM c905a6da5a bcftools: 1.9 -> 1.10.2 2019-12-22 20:00:29 -08:00
Maximilian Bosch 65061ab2ae
stellarium: 0.19.2 -> 0.19.3
https://github.com/Stellarium/stellarium/releases/tag/v0.19.3
2019-12-22 13:57:13 +01:00
Alyssa Ross 7887a81193
treewide: fix cargoSha256 (again)
cargo-vendor output was changed in a4fc84de44.
2019-12-20 20:08:53 +00:00
Justin Bedo 2191912274
minia: init at 3.2.1 2019-12-20 11:27:04 +11:00
Justin Bedo 6741cff527
last: init at 1042 2019-12-20 11:27:02 +11:00
Jan Tojnar 048faed66a
pcb: 20140316 → 4.2.0
* Long overdue update
* Clean up the expression
* Drop unneeded pangox_compat – it was probably needed before gtkglext propagated it.
2019-12-19 00:47:20 +01:00
Justin Bedo 28a057a56b
bedtools: 2.29.1 -> 2.29.2 2019-12-18 10:39:25 +11:00
Mario Rodas 5e5ce79db4
Merge pull request #75807 from jbedo/strelka
strelka: fix broken build
2019-12-16 23:52:35 -05:00
Justin Bedo c3f09c33eb
strelka: fix broken build 2019-12-17 11:20:32 +11:00
Alex Branham 7af84afa2a R: 3.6.1 -> 3.6.2
Closes https://github.com/NixOS/nixpkgs/pull/75587.
2019-12-16 18:56:49 +01:00
Florian Klink 0380ed20db
Merge pull request #75657 from flokli/gtkwave-gtk3
gtkwave: build with gtk3
2019-12-15 15:07:07 +01:00
Renaud 2a1a4cad38
Merge pull request #75388 from Lassulus/xplanet
xplanet: 1.3.0 -> 1.3.1
2019-12-15 14:57:48 +01:00
lassulus 3772d04e1c xplanet: 1.3.0 -> 1.3.1 2019-12-15 14:02:36 +01:00
Florian Klink ac1a5ac2db gtkwave: build with gtk3
gtkwave ships a gtk3 flavour on sourceforge. let's use that one.
2019-12-15 03:54:35 +01:00
Austin Seipp 367676ce82
z3: 4.8.5 -> 4.8.7
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2019-12-14 20:33:59 -06:00
Ben Wolsieffer bd9549baa9 mavproxy: init at 1.8.17 2019-12-14 11:00:34 -08:00
Vincent Laporte 856d0a44ec
Merge pull request #75141 from vbgl/coq-8.11β1
coq_8_11: init at 8.11+β1
2019-12-14 19:13:40 +01:00
Dmitry Kalinkin b6d8873825 root: 6.12.06 -> 6.18.04
Also switch to python3.
2019-12-14 01:28:27 -08:00
Timo Kaufmann ce013bb430
Merge pull request #75613 from timokau/brial-1.2.6
brial: 1.2.5 -> 1.2.6, pybrial: use brial src
2019-12-13 21:47:50 +01:00
Timo Kaufmann 6a800927bb pybrial: 1.2.3 -> 1.2.5, directly use the brial src
The pybrial package is a bit awkward. It doesn't have its own top-level
attribute, since it has a cyclic dependency with sage. That's one of the
reasons why it rarely gets updated. Its distributed along with brial, so
its best to keep the versions synchronized. The easiest way to do this
is to just re-use the source of brial.
2019-12-13 20:29:16 +01:00
Robert Scott c676063047 btor2tools: correct meta information 2019-12-12 10:37:02 -06:00
Robert Scott b9185a96be boolector: add patch for CVE-2019-7560 2019-12-12 10:37:02 -06:00
markuskowa 3922a30090
Merge pull request #75416 from jbedo/bedtools
bedtools: 2.29.0 -> 2.29.1
2019-12-10 23:58:03 +01:00
Justin Bedo 50fbca4bfc
bedtools: fix clang builds 2019-12-11 09:27:57 +11:00
Gabriel Ebner 5f1790101f Merge branch 'auto-update/libqalculate' 2019-12-10 17:38:25 +01:00
Gabriel Ebner 12d9b6929c qalculate-gtk: 3.5.0 -> 3.6.0 2019-12-10 17:34:29 +01:00
Justin Bedo 592d288aa2
bedtools: 2.29.0 -> 2.29.1 2019-12-10 13:24:27 +11:00
R. RyanTM 13c757e69c snakemake: 5.7.4 -> 5.8.1 (#74637) 2019-12-09 20:47:24 +01:00
Robert Scott 2611887c2e lingeling: enable for darwin 2019-12-08 18:32:04 +00:00
Robert Scott dc6233b972 aiger: enable for darwin 2019-12-08 18:31:49 +00:00
Renato Alves e18fb092f1 kssd: init at 1.0 2019-12-08 16:48:59 +01:00
R. RyanTM b3262d2284 eagle: 9.5.0 -> 9.5.1
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/eagle/versions
2019-12-08 15:16:53 +01:00
scalavision 3dfabd6eff svaba: init at 1.1.0 2019-12-08 14:51:05 +01:00
markuskowa 444256039c
Merge pull request #75245 from r-ryantm/auto-update/jmol
jmol: 14.29.55 -> 14.30.0
2019-12-08 14:19:56 +01:00
R. RyanTM b40940e9d6 jmol: 14.29.55 -> 14.30.0 2019-12-08 04:52:52 -08:00
Maximilian Bosch e16df73d30
geogebra: 5-0-560-0 -> 5-0-569-0 2019-12-08 03:50:02 +01:00
Jonathan Ringer 9dc8e77e4e giac-with-xcas: fix build
remove libGLU_combined package and replace with libGL and libGLU
2019-12-07 16:58:50 -08:00
Calvin Pritchard 1850d616ac NetLogo: 6.0.4 -> 6.1.1 2019-12-07 22:24:26 +01:00
R. RyanTM 8582e5a759 marvin: 19.1.0 -> 19.23.0 2019-12-07 20:41:41 +01:00
Mario Rodas 835705d11b
Merge pull request #75095 from tbenst/bftools
bftools: 5.9.2 -> 6.3.0
2019-12-07 03:06:00 -05:00
Vincent Laporte 2942490c2c
coq_8_11: init at 8.11+β1 2019-12-07 07:58:00 +00:00
Tyler Benster 2700559bdc bftools: 5.9.2 -> 6.3.0 2019-12-06 02:11:00 -08:00
Mateusz Kowalczyk 1451a52a38 Remove myself (fuuzetsu) from maintainer lists
I haven't been doing any maintenance for a long time now and not only
do I get notified, it also creates a fake impression that all these
packages had at least one maintainer when in practice they had none.
2019-12-05 16:29:48 +09:00
Matt Huszagh 9c7cd63b3d symbiyosys: add yices dependency
Symbioyosys requires at least smt solver backend
to work out of the box.
2019-12-04 14:29:31 -06:00
Sébastien Maret c108acaaaf gildas: 20191001_a -> 20191201_a (#73041)
* gildas: 20191001_a -> 20191101_a

* gildas: 20191101_a -> 20191201_a
2019-12-04 20:18:39 +01:00
Timo Kaufmann 5c9000014e
Merge pull request #74945 from timokau/sage-no-timeout
sage: disable test timeout
2019-12-04 09:55:34 +01:00
Vincent Laporte 3806eff9ca coq_8_10: 8.10.1 → 8.10.2 2019-12-03 13:51:52 +00:00
R. RyanTM 605e88517b paml: 4.9i -> 4.9j 2019-12-01 18:43:58 +01:00
Timo Kaufmann e371a02b6c sage: disable test timeout
I already did that once in 359bf7f1e3.
That change mysteriously got lost somehow (presumably in some merge
commit).

Nix has its own timeout settings, so there is no risk in running
forever. At the same time, some tests can exceed the default timeout
(30minutes per file for --long tests) when run on many weak cores (like
the aarch64 community builder or some hydra builders).
2019-12-01 13:23:54 +01:00
Jan Tojnar 8cbc862b83
dconf: move to top-level 2019-12-01 01:01:40 +01:00
R. RyanTM 9e52523747 verilator: 4.020 -> 4.022 2019-11-30 18:27:06 -05:00
R. RyanTM c41deafba3 gtkwave: 3.3.102 -> 3.3.103 2019-12-01 00:21:13 +01:00
R. RyanTM da09e1e772 kallisto: 0.46.0 -> 0.46.1 (#74430) 2019-11-30 21:12:54 +01:00
Jan Tojnar a69ad18da9
Merge branch 'master' into staging-next 2019-11-30 19:44:51 +01:00
R. RyanTM 98e0ead3ba picard-tools: 2.21.1 -> 2.21.3 (#74528) 2019-11-30 16:24:44 +01:00
Frederik Rietdijk d14baf7747 Merge master into staging-next 2019-11-30 08:57:28 +01:00
Ryan Mulligan bc6b377a86
Merge pull request #74412 from r-ryantm/auto-update/hmmer
hmmer: 3.2.1 -> 3.3
2019-11-28 06:14:56 -08:00
Jonathan Ringer 0c1c18ca44
Merge branch 'master' into staging-next 2019-11-27 22:57:50 -08:00
R. RyanTM 6563dd3351 hmmer: 3.2.1 -> 3.3 2019-11-27 18:40:23 -08:00
Matthew Bauer e010c1b031
Merge pull request #74092 from veprbl/pr/applgrid_fix
applgrid: fix build
2019-11-25 22:22:48 -06:00
John Ericson d60532bc71 coq: Fix setup hook 2019-11-25 14:20:10 +00:00
Dmitry Kalinkin bd0c4dd6ab
root: fix setupHook to work with "set -u" 2019-11-24 17:51:46 -05:00
Frederik Rietdijk 1d18c5a0fe Merge staging-next into staging 2019-11-24 10:13:31 +01:00
Michael Raskin c5e3aec122 golly: fix build 2019-11-22 17:41:46 +01:00
Kai Wohlfahrt 6b2504f9f2 freebayes: 2017-08-23 -> 1.3.1 (2019-06-03) 2019-11-20 09:10:31 -08:00
Frederik Rietdijk 5f8b0d7d99 Merge staging-next into staging 2019-11-19 14:53:29 +01:00
adisbladis c9d8624ccd
treewide: Get rid of libGLU_combined 2019-11-18 20:10:43 +00:00
Mario Rodas 9f9720a567
Merge pull request #73447 from yrashk/streamlit-0.50.2
streamlit: 0.49.0 -> 0.50.2
2019-11-16 14:51:06 -05:00
c0bw3b 9367367dfd Treewide: fix URL permanent redirects
Permanent redirects on homepages and/or source URLs
as reported by Repology
2019-11-16 01:41:23 +01:00
Jörg Thalheim d729fdcd6e
nifticlib and niftseg: change platform from linux to unix sinc… (#73442)
nifticlib and niftseg: change platform from linux to unix since these…
2019-11-15 11:57:17 +00:00
Yurii Rashkovskii a1a2d8d4c0
streamlit: 0.49.0 -> 0.50.2 2019-11-15 08:35:43 +01:00
Ben Darwin 736860d34b nifticlib and niftseg: change platform from linux to unix since these build on OSX 2019-11-14 21:25:10 -05:00
Guanpeng Xu 66d5277375 mathematica: fix version issue with zlib (#73425) 2019-11-14 17:19:30 -05:00
Dmitry Kalinkin 93ee8095b0 snakemake: 5.4.4 -> 5.7.4 (#72929)
(#72929)
2019-11-13 00:46:56 +01:00
Renaud 630380651d
Merge pull request #73215 from vbgl/why3-1.2.1
why3: 1.2.0 → 1.2.1
2019-11-13 00:12:05 +01:00
Dmitry Kalinkin a84607a0e9
eagle: use mkDerivation provided by qt5 2019-11-12 11:21:06 -05:00
Vincent Laporte a61354f262
why3: 1.2.0 → 1.2.1 2019-11-11 11:30:52 +00:00
Matthew Bauer 5ebd36403e
Merge pull request #70641 from maggesi/rename-z77z-into-maggesi
Rename z77z into maggesi
2019-11-07 17:18:20 -05:00
Matthew Bauer 551d9f632d
Merge pull request #72954 from nkpart/nkpart/R-darwin-enable-tcltk
R: enable tcltk on darwin
2019-11-07 16:49:46 -05:00
Yurii Rashkovskii 2e52f98ddb streamlit: init at 0.49.0 2019-11-06 11:01:06 -08:00
Timo Kaufmann afb9887dbd sage: backport fix for threejs r109 2019-11-06 14:40:16 +01:00
Timo Kaufmann f64885b9ca sage: fix pkgconfig errors in tests
python.pkgs.pkgconfig raises an exception on missing packages since
version 1.5.0. Previously those errors were just silently ignored. That
worked fine, since the packages are only missing at runtime (when they
are not really needed) but present at buildtime.

Since this fails the tests now, we just add the packages to
PKG_CONFIG_PATH at runtime. This does not add additional runtime
dependencies. Still, it would be nicer if the sage testssuite would not
test the buildsystem at runtime in the first place.

The breakage was originally caused by the pkgconfig update in
1efa71616f.
2019-11-06 14:40:13 +01:00
Timo Kaufmann da7ec1c139 sage: ignore werkzeug immutable dict deprecation 2019-11-06 14:40:13 +01:00
Timo Kaufmann f85ce834ce sage: ignore deprecation warnings in rst2sws
Needs to be fixed upstream (by werkzeug, twisted). Doesn't impact the
functionality and the tests are soon to be removed with the py3 update
anyway.
2019-11-06 14:40:13 +01:00
Timo Kaufmann af480796c9 sage: ignore cmp deprecation in sagenb 2019-11-06 14:40:13 +01:00
Nick Partridge 22d0ccbd2d R: enable tcltk on darwin 2019-11-06 13:14:11 +10:00
R. RyanTM b7f151df70 yacas: 1.6.1 -> 1.8.0 2019-11-04 23:49:42 -08:00
Franz Pletz 18ab125e83
minisatUnstable: fix build with gcc9 2019-11-05 02:01:18 +01:00
Franz Pletz 8dca8b9ccb
Merge remote-tracking branch 'origin/master' into gcc-9 2019-11-05 01:07:22 +01:00
Franz Pletz 6c3f824540
minisat: fix build with gcc9 2019-11-04 23:07:58 +01:00
scalavision d9b40f6397 deeptools: init at 3.3.1 2019-11-04 02:42:36 -08:00
Franz Pletz 6b10b78872
Merge remote-tracking branch 'origin/master' into gcc-9 2019-11-03 14:44:12 +01:00
Franz Pletz 8e63a6cd13
niftyreg: fix build with gcc9 2019-11-03 14:43:37 +01:00
Franz Pletz dffcb87383
colmap: fix build with gcc9 2019-11-03 14:43:33 +01:00
R. RyanTM 28b0a6a9e0 star: 2.7.2b -> 2.7.3a 2019-11-03 10:23:05 +01:00
R. RyanTM 1faee87692 dcmtk: 3.6.4 -> 3.6.5 2019-11-02 11:12:28 -07:00
Franz Pletz e39773fe5b
megahit: 1.1.4 -> 1.2.9 2019-11-02 15:53:57 +01:00
Gabriel Ebner ac24901d17
libqalculate: 3.4.0 -> 3.5.0 (#72550)
libqalculate: 3.4.0 -> 3.5.0
2019-11-02 10:59:06 +01:00
Gabriel Ebner a4f0bfdc87 qalculate-gtk: 3.4.0 -> 3.5.0 2019-11-02 10:54:10 +01:00
Jörg Thalheim 04a079082c
Merge pull request #72539 from r-ryantm/auto-update/jmol
jmol: 14.29.54 -> 14.29.55
2019-11-02 07:49:50 +00:00
R. RyanTM b3799c5627 jmol: 14.29.54 -> 14.29.55 2019-11-02 00:16:58 -07:00
R. RyanTM 7f919914bf eprover: 2.3 -> 2.4 2019-11-01 14:00:31 -07:00
Timo Kaufmann f7c1e8f274
Merge pull request #72328 from timokau/sage-ignore-cmp-deprecation
sage: ignore attrs deprecation warning
2019-10-30 23:14:07 +01:00
Timo Kaufmann 32827e35d8 sage: ignore attrs deprecation warning
cmp is deprecated since attrs 19.2.0:
http://www.attrs.org/en/19.2.0/changelog.html

The deprecation warning breaks the doctests.  Fortunately they have a
rather long deprecation window, so we can just wait until upstream(s)
fix this.
2019-10-30 22:27:00 +01:00
Peter Simons 3bc76218a3
Merge pull request #72058 from nh2/r-static-library
R: Add enableShared/enableStatic arguments
2019-10-30 13:31:52 +01:00
Niklas Hambüchen edbe2d8145 R: Add static argument.
R's autoconf does not use the normal configure flags for that.
2019-10-30 11:44:02 +01:00
Ben Darwin ddc2955ad9 EZminc: 2017-08-29 -> 2019-07-25; mark unbroken 2019-10-26 09:55:30 -07:00
Alexey Shmalko 140d402cb5
Merge pull request #71991 from iimog/dcmtk
DCMTK: init at 3.6.4
2019-10-26 15:15:50 +03:00
Markus Ankenbrand 905245b32c dcmtk: init at 3.6.4 2019-10-26 13:02:50 +02:00
Vincent Laporte a8892b0d76
coq_8_10: 8.10.0 → 8.10.1 2019-10-25 07:58:47 +00:00
Vincent Laporte d56582eb2b coq_8_10: enable CoqIDE 2019-10-25 07:58:02 +00:00
scalavision 535a7006ea truvari: init at 1.3.2 (#70877)
pythonPackages.pyvcf: init at 0.6.8
2019-10-24 17:06:42 -04:00
R. RyanTM c6af1f6e03 verilator: 4.018 -> 4.020
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/verilator/versions
2019-10-24 14:02:00 -05:00
R. RyanTM c300055e11 ott: 0.28 -> 0.29
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ott/versions
2019-10-23 11:44:13 -07:00
R. RyanTM b8acb48b24 picard-tools: 2.20.8 -> 2.21.1 (#71748)
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-10-23 09:34:40 +02:00
R. RyanTM a9551de99a dcm2niix: 1.0.20190410 -> 1.0.20190902
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/dcm2niix/versions
2019-10-22 16:31:19 -07:00
Timo Kaufmann ed145e8f22
Merge pull request #71694 from r-ryantm/auto-update/nauty
nauty: 26r11 -> 26r12
2019-10-22 23:33:48 +02:00
R. RyanTM d93659ffa0 nauty: 26r11 -> 26r12
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/nauty/versions
2019-10-22 10:14:36 -07:00
R. RyanTM dbab6b7994 jmol: 14.29.53 -> 14.29.54
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/jmol/versions
2019-10-22 10:06:52 +02:00
Mario Rodas e8e1f42499
Merge pull request #71590 from r-ryantm/auto-update/ginac
ginac: 1.7.7 -> 1.7.8
2019-10-21 20:21:31 -05:00
R. RyanTM bf30d5d6f6 ginac: 1.7.7 -> 1.7.8
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ginac/versions
2019-10-21 15:21:33 -07:00
Michael Raskin a35022aa80
Merge pull request #71566 from r-ryantm/auto-update/golly
golly: 3.2 -> 3.3
2019-10-21 19:41:50 +00:00
R. RyanTM b73b9399ba golly: 3.2 -> 3.3
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/golly/versions
2019-10-21 11:24:52 -07:00
Renaud 410d794f05
Merge pull request #71073 from nyanloutre/betaflight_configurator_10_6_0
betaflight-configurator: 10.5.1 -> 10.6.0
2019-10-20 20:01:00 +02:00
Ben Wolsieffer 8d04355d87 qgroundcontrol: 3.3.0 -> 3.5.5, fix build (#71308)
* qgroundcontrol: 3.3.0 -> 3.5.4, fix build

* qgroundcontrol: 3.5.4 -> 3.5.5
2019-10-20 19:27:23 +02:00
Emily fecfbe18bd symbiyosys: 2019.08.13 -> 2019.10.11 2019-10-19 12:26:49 -05:00
Daniel Frank b4136a8f5b kicad: 5.1.2 -> 5.1.4, fix ngspice, mark broken on aarch64 (#69584) 2019-10-16 02:02:49 -04:00
Vincent Laporte b4db381443 coq_8_10: 8.10+β3 → 8.10.0
coqPackages.coq-elpi: master → 1.1.0
2019-10-16 02:43:46 +00:00
Vincent Laporte 0cc70b5697 coq: do not build CoqIDE for Coq 8.10
GTK3 at version 3.24.11 has broken pkg-config files
2019-10-16 02:43:46 +00:00
Vincent Laporte 1292f49a37 coq_8_10: do not take “camlp5” as input 2019-10-16 02:43:46 +00:00
Vincent Laporte 325f89ef19 coq_8_10: fix CoqIDE on darwin 2019-10-16 02:43:46 +00:00
worldofpeace 4bcef38f24
Merge pull request #63827 from acairncross/fix-monosat
monosat: Fix Linux build
2019-10-15 20:55:28 +00:00
Aiken Cairncross 15dbd8de7c monosat: 60528a3 -> 1.8.0
This fixes the broken Linux build by only building the dynamic library/
executable (an option that was only added in the latest tagged version).
2019-10-15 16:52:25 -04:00
Aiken Cairncross b4da391ade monosat: Add self as maintainer 2019-10-15 12:20:55 +01:00
Millian Poquet 5b9cbeb75c simgrid: 3.23 -> 3.24 2019-10-14 16:08:43 +02:00
Marco Maggesi 24d0bd37b5
Merge branch 'master' into rename-z77z-into-maggesi 2019-10-13 18:06:23 +02:00
Renaud e6f99fa3b1
Merge pull request #69961 from r-ryantm/auto-update/star
star: 2.7.1a -> 2.7.2b
2019-10-13 17:10:23 +02:00
nyanloutre d849c213ba
betaflight-configurator: 10.5.1 -> 10.6.0 2019-10-13 11:58:00 +02:00
Renaud 94500c93dc
Merge pull request #69515 from r-ryantm/auto-update/eagle
eagle: 9.4.2 -> 9.5.0
2019-10-12 15:09:07 +02:00
Renaud a12f3ebee7
Merge pull request #69488 from r-ryantm/auto-update/clp
clp: 1.17.2 -> 1.17.3
2019-10-12 14:15:31 +02:00
scalavision 3d860972ee delly: init at 0.8.1 (#70871) 2019-10-10 22:08:45 -04:00
worldofpeace dfe338e464
Merge pull request #70890 from worldofpeace/pantheon-no-lts-vala
pantheon: use latest vala
2019-10-10 15:18:38 +00:00
Marek Mahut 19610dce34
Merge pull request #70790 from r-ryantm/auto-update/stellarium
stellarium: 0.19.1 -> 0.19.2
2019-10-10 11:21:55 +02:00
worldofpeace bdb851ee2d pantheon: use latest vala
elementary OS's ecosystem is curated around Ubuntu's LTS releases.
This means the development platform for their curated applications
always includes a LTS version of vala (in 18.04 it's 0.40).
Because of how vala development works it suspect some of these
applications to have serious issues if complied with the latest vala.
However in the past year or so, for Pantheon at least, I don't think
their applications will have much issues with latest vala, and if there
is I don't think they'd be difficult to fix. In this single regard they've
become more responsive since their preferred language is vala.

As for the curated applications I have less of this confidence in.
So I'd have to be accept less applications, but that's something
I'm willing to compromise on. And this is easily reversible or
could be done on a per-application basis. And nix already makes
this trivial.
2019-10-09 22:47:37 -04:00
Robin Gloster d6d4a6b456
Merge pull request #70845 from BenBals/master
Geogebra: 5.0.535 -> 5.0.560
2019-10-09 17:36:35 +02:00
Luz ec13398cdf librepcb: 0.1.0 -> 0.1.2 (#70538)
* Update to new source

* Fix message 'xcb plugin not found'
2019-10-09 14:59:48 +02:00
Ben Justus Bals 911d5d59ec
Geogebra: 5.0.535 -> 5.0.560 2019-10-09 11:59:46 +02:00
Marco Maggesi bf56c15695
hol_light: 2019-03-27 -> 2019-10-06 2019-10-09 06:13:48 +00:00
R. RyanTM a174411c3c stellarium: 0.19.1 -> 0.19.2
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/stellarium/versions
2019-10-08 14:17:20 -07:00
Linus Heckemann 5aa4b19946 treewide: mark some broken packages as broken
Refs:
e675498026
1e9cc5b984
793a2fe1e8
c19cf65261
f6544d618f
2019-10-08 17:14:26 +02:00
R. RyanTM 9ac905e03f gtkwave: 3.3.101 -> 3.3.102
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gtkwave/versions
2019-10-07 12:18:42 -05:00
Marco Maggesi ff1ed720e2 Rename z77z into maggesi
Make the "handle" of the maintainer match the name of the github account.
Also update the email address.
2019-10-07 17:05:25 +02:00
markuskowa 86d97bb02c
Merge pull request #70602 from r-ryantm/auto-update/gromacs
gromacs: 2019.3 -> 2019.4
2019-10-07 14:43:39 +02:00
Markus Kowalewski ea45dc1053
gromacs: add perl to buildInputs 2019-10-07 13:03:13 +02:00
R. RyanTM 8c6ee4fe16 gromacs: 2019.3 -> 2019.4
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/gromacs/versions
2019-10-07 02:48:46 -07:00
Dmitry Kalinkin cfd881dce0
Merge pull request #70161 from smaret/gildas-20191001_a
gildas: 20190901_a -> 20191001_a
2019-10-06 17:46:41 -04:00
Nikolay Amiantov de171ba0c6 cntk: partially unbreak
* Use GCC 7 to unbreak the build;
* Mark CUDA build as broken due to cub incompatibility.
2019-10-05 16:18:20 +03:00
Orivej Desh 3dc70841d3 cbc: 2.10.2 -> 2.10.3 2019-10-04 05:17:48 +00:00
Bruno Bzeznik 1ba3f3f00f SPAdes: init at 3.13.1 (#63082) 2019-10-03 09:18:48 +00:00
R. RyanTM eca416c469 verilator: 4.016 -> 4.018
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/verilator/versions
2019-10-01 21:09:12 -05:00
Sébastien Maret b444b2e956
gildas: 20190901_a -> 20191001_a 2019-10-01 10:52:50 +02:00
Timo Kaufmann 7a7e9c1b27
Merge pull request #64193 from timokau/sage-8.9
sage: 8.8 -> 8.9
2019-09-30 11:13:46 +00:00
Timo Kaufmann d9176bee70 sage: 8.9.rc1 -> 8.9 2019-09-30 11:10:10 +02:00
Ryan Mulligan 8519cd1aa0
Merge pull request #69735 from r-ryantm/auto-update/picard-tools
picard-tools: 2.20.5 -> 2.20.8
2019-09-29 15:44:33 -07:00
R. RyanTM de95a92384 star: 2.7.1a -> 2.7.2b
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
2019-09-28 21:09:40 -07:00
Emily b2c482b700 verilog: extend platforms 2019-09-28 16:55:21 -05:00
Vladimír Čunát fda4a08d4a
Merge branch 'staging-next'
There are several security fixes - again, as it consists mainly of the
previously reverted staging-next merge.
2019-09-28 07:43:04 +02:00
R. RyanTM 8c397c2bc2 picard-tools: 2.20.5 -> 2.20.8
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-09-27 18:25:22 -07:00
Aaron Andersen af5176b430
Merge pull request #63117 from bzizou/macse
macse: init at 2.03
2019-09-27 17:26:07 -04:00
Vladimír Čunát 217cf982c7
Merge branch 'master' into staging-next 2019-09-27 22:13:02 +02:00
Marek Mahut 5c116916d6
Merge pull request #69575 from r-ryantm/auto-update/ginac
ginac: 1.7.6 -> 1.7.7
2019-09-27 22:04:49 +02:00
Michael Raskin 2213e53fcf
Merge pull request #69477 from r-ryantm/auto-update/clingo
clingo: 5.3.0 -> 5.4.0
2019-09-27 10:12:24 +00:00
Timo Kaufmann 6181a20ab2
Merge pull request #69609 from r-ryantm/auto-update/jmol
jmol: 14.29.49 -> 14.29.53
2019-09-27 09:22:11 +00:00
Joachim F ad773d31e2
Merge pull request #69345 from joachifm/feat/split-version
Replace uses of splitString for splitting version strings
2019-09-27 06:19:18 +00:00
R. RyanTM 0826d695de jmol: 14.29.49 -> 14.29.53
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/jmol/versions
2019-09-26 16:35:12 -07:00
R. RyanTM b7f156625e ginac: 1.7.6 -> 1.7.7
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/ginac/versions
2019-09-26 12:09:29 -07:00
Timo Kaufmann 4a863fa567
Merge pull request #69519 from r-ryantm/auto-update/eclib
eclib: 20190226 -> 20190909
2019-09-26 17:27:41 +00:00
Joachim Fasting bad07dfac5
tree-wide: replace uses of splitString "." with lib.versions
Quoting from the splitString docstring:

   NOTE: this function is not performant and should never be used.

This replaces trivial uses of splitString for splitting version
strings with the (potentially builtin) splitVersion.
2019-09-26 17:42:49 +02:00
R. RyanTM faf9a73e2f eclib: 20190226 -> 20190909
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/eclib/versions

Relevant sage upstream ticket: https://trac.sagemath.org/ticket/28472
2019-09-26 16:41:50 +02:00
R. RyanTM 24db075c5c eagle: 9.4.2 -> 9.5.0
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/eagle/versions
2019-09-26 05:34:41 -07:00
R. RyanTM 7653ff45cb clp: 1.17.2 -> 1.17.3
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/clp/versions
2019-09-26 01:49:26 -07:00
Jörg Thalheim 9a1b767a55
treewide: remove empty buildInputs 2019-09-26 09:17:23 +01:00
R. RyanTM f54eb7f159 clingo: 5.3.0 -> 5.4.0
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/clingo/versions
2019-09-26 01:07:35 -07:00
Dmitry Kalinkin c455adcc42
Merge branch 'master' into staging-next
Fixes eval on darwin after #69072

Resolved conflict in pkgs/tools/security/thc-hydra/default.nix
Basically had to revert a1c0e10564 which
adapts #69210 to master that doesn't yet have
329a88efa7

Tested using maintainers/scripts/eval-release.sh before and after to see
that the fix works
2019-09-25 19:21:46 -04:00
Timo Kaufmann 78741fc409 sage: 8.9.rc0 -> 8.9.rc1 2019-09-25 10:19:04 +02:00
Timo Kaufmann 1797c9c295 sage: 8.9.beta9 -> 8.9.rc0
Sage now by default expects the lcalc library to be named Lfunction
(instead of libLfunction). This could be changed by an environment
variable (https://trac.sagemath.org/ticket/28224), but various distros
seem to agree on this standard
(https://groups.google.com/forum/#!topic/sage-packaging/xvh55IxHTZg) so
it's best just to follow it. The old standard was set by sage anyway and
sage is the only consumer of lcalc in nixpkgs.
2019-09-24 17:51:09 +02:00
Kierán Meinhardt 815d940e52 tamarin-prover: mark as broken because upstream is broken 2019-09-24 15:25:43 +02:00
Bruno Bzeznik e4108becbe macse: init at 2.03 2019-09-24 08:24:07 +02:00
Vladimír Čunát eab41878ac
Merge branch 'master' into staging-next 2019-09-24 08:14:34 +02:00
Timo Kaufmann ba9e5a2785 Merge remote-tracking branch 'upstream/master' into sage-8.9 2019-09-23 23:58:37 +02:00
Timo Kaufmann 995a728684 pynac: 0.7.25 -> 0.7.26 2019-09-23 22:08:23 +02:00
Timo Kaufmann 5aba3be6f9 sage: 8.9.beta8 -> 8.9.beta9 2019-09-23 18:50:59 +02:00
Timo Kaufmann 8593d468ae Merge remote-tracking branch 'upstream/master' into sage-8.9 2019-09-23 17:11:15 +02:00
Timo Kaufmann cbe12344ca sage: add pager to environment
Temporary fixup while waiting for an upstream fix.
2019-09-23 15:14:43 +02:00
Vladimír Čunát 22a216849b
Re-Revert "Merge branch 'staging-next'"
This reverts commit f8a8fc6c7c.
2019-09-22 09:38:09 +02:00
Vladimír Čunát f8a8fc6c7c
Revert "Merge branch 'staging-next'"
This reverts commit 41af38f372, reversing
changes made to f0fec244ca.

Let's delay this.  We have some serious regressions.
2019-09-21 20:05:09 +02:00
Vladimír Čunát 41af38f372
Merge branch 'staging-next' 2019-09-21 13:14:09 +02:00
Matthew Bauer 566796ab13
Merge pull request #69038 from matthewbauer/ncurses5
treewide: use libtinfo.so.5 where needed
2019-09-20 23:00:04 -04:00
Bjørn Forsman 5af0d0b5da kicad: fix build
Fix configure time error:
  ...
  ImportError: No module named wx
  CMake Error at CMakeModules/FindwxPython.cmake:52 (message):
    wxPython/Phoenix does not appear to be installed on the system

Only build tested.

Fixes: f7e28bf5d8 ("Split buildPythonPackage into setup hooks")
2019-09-20 08:17:58 +02:00
Will Dietz 6429696f43
libqalculate,qalculate-gtk: 3.3.0 -> 3.4.0 2019-09-18 17:05:59 -05:00
Matthew Bauer 4c85abae94 treewide: use libtinfo.so.5 where needed
This was originally added in

https://github.com/NixOS/nixpkgs/pull/21350

best to use this name for clarity.
2019-09-18 13:57:20 -04:00
Vladimír Čunát fa4a3af5a7
Merge branch 'master' into staging-next 2019-09-16 19:24:52 +02:00
Vincent Laporte 8288301636 coq_8_10: 8.10+β2 → 8.10+β3 2019-09-16 11:41:43 -05:00
Aaron Andersen 063c82fd2f
Merge pull request #68773 from mimame/update/cytoscape-3.7.2
cytoscape: 3.7.1 -> 3.7.2
2019-09-15 09:43:11 -04:00
Vladimír Čunát b6c6e1f9e8
Merge branch 'master' into staging-next 2019-09-15 13:18:54 +02:00
Vladimír Čunát 991c0e1618
treewide: mark packages as buildable on darwin (PR #45364)
vcunat amended the commit a bit; see the PR for details/discussion.
2019-09-15 10:50:08 +02:00
Miguel Madrid Mencía 148c82e07e
maintainer: mimadrid: update github username and personal data 2019-09-14 12:15:46 +02:00
Miguel Madrid Mencía 40b760e07c
cytoscape: 3.7.1 -> 3.7.2 2019-09-14 10:52:46 +02:00
Linus Heckemann f6182da2c6 ants: use itk 4.x 2019-09-13 11:54:21 +02:00
Jan Tojnar 9b6789de73
tree-wide: replace wrapProgram with wrapGApp
where appropriate
2019-09-10 17:54:57 +02:00
Izorkin 329a88efa7 treewide: replace mysql.connector-c to libmysqlclient 2019-09-09 15:55:34 +03:00
volth 7b8fb5c06c treewide: remove redundant quotes 2019-09-08 23:38:31 +00:00
Frederik Rietdijk 5f4734b1dd Merge remote-tracking branch 'upstream/gcc-8' into staging-next
Earlier the gcc8 branch was merged instead of the gcc-8 branch (note the dash)...
2019-09-08 20:44:26 +02:00
Michael Raskin 4149a662a7 petrinizer: fix build by pinning the neccessary library versions 2019-09-07 13:33:50 +03:00
Frederik Rietdijk 66bc7fc1b3 Merge master into staging-next 2019-09-06 22:46:05 +02:00
Justin Bedo 6beabe7d2c bedtools: 2.28.0 -> 2.29.0 2019-09-06 21:23:15 +02:00
Dmitry Kalinkin d6264f9094
Merge pull request #65726 from smaret/gildas-20190801_a
gildas: 20190701_a -> 20190901_a
2019-09-06 11:15:45 -04:00
Jan Tojnar cdf426488b
Merge branch 'master' into staging-next
Fixed trivial conflicts caused by removing rec.
2019-09-06 03:20:09 +02:00
Jan Tojnar ed54a5b51d
Merge branch 'gtk-no-plus' 2019-09-06 02:57:51 +02:00
Jan Tojnar 72e7d569a7
tree-wide: s/GTK+/GTK/g
GTK was renamed.
2019-09-06 02:54:53 +02:00
Aaron Andersen 11de7aa609
Merge pull request #64322 from jbedo/xenomapper
xenomapper: init 1.0.2
2019-09-05 12:08:10 -04:00
Justin Bedo 3f83cbf538
xenomapper: init 1.0.2 2019-09-05 20:50:22 +10:00
Sébastien Maret 4f3eacc2bf
gildas: 20190701_a -> 20190901_a 2019-09-05 12:30:46 +02:00
Vladimír Čunát 4aad2947f8
Merge branch 'master' into staging-next 2019-09-04 11:00:56 +02:00
Franz Pletz de85797565
Merge remote-tracking branch 'origin/master' into gcc-8 2019-09-03 22:15:07 +02:00
worldofpeace 59e68d3b74 treewide: don't use single quotes with placeholder 2019-09-03 13:01:42 -04:00
Timo Kaufmann 84578046aa sage: 8.9.beta7 -> 8.9.beta8 2019-09-03 15:34:28 +02:00
Ryan Mulligan 32f9c619f5
Merge pull request #67969 from petabyteboy/feature/remove-dobuild
treewide: remove uses of doBuild and doConfigure
2019-09-02 15:13:47 -07:00
Milan Pässler (work) 185fd61631 treewide: remove uses of doBuild and doConfigure
doBuild and doConfigure are not actually used by any builders, they were
probably added by mistake and just confuse people.
2019-09-02 23:42:12 +02:00
Vladimír Čunát f21211ebfe
Merge branch 'master' into staging 2019-09-02 23:25:24 +02:00
Emily d1dfaa79e3 symbiyosys: fix path to bash (again)
/usr/bin/env works on NixOS normally, but previously sby would fail if
used from inside the Nix sandbox.
2019-09-01 14:22:49 -05:00
Tadeo Kondrak 2aa9b655f4
kallisto: 0.43.1 -> 0.46.0 2019-08-31 14:06:31 -06:00
Frederik Rietdijk 98ef78326d Merge staging-next into staging 2019-08-31 18:07:33 +02:00
Frederik Rietdijk 96e5474329 Merge master into staging-next 2019-08-31 18:04:31 +02:00
Alyssa Ross 1da1a7a479 pari: 2.11.1 -> 2.11.2 2019-08-31 13:33:00 +00:00
Niklas Hambüchen 9e78f76ade treewide: Remove unnecessary --disable-static (#66759)
* freetype: Remove unnecessary `--disable-static`.

The true-by-default `dontDisableStatic` already takes care of it.

Fixes freetype not being overridable to have static libs.

* treewide: Remove unnecessary `--disable-static`.

The true-by-default `dontDisableStatic` already takes care of it.

Fixes these packages not being overridable to have static libs.
2019-08-31 08:10:53 -04:00
Alexander 35ac3344e7 colmap: init at 3.5 (#67759)
* colmap: init at 3.5
2019-08-31 08:06:46 -04:00
volth 7bb6b373ab treewide: name -> pname (#67513) 2019-08-31 07:41:22 -04:00
Lassulus a8d26fc34a
Merge pull request #63127 from bzizou/trimal
trimal: init at 1.4.1
2019-08-31 13:04:41 +02:00
Frederik Rietdijk ad1d58c622 Merge staging-next into staging 2019-08-31 10:04:20 +02:00
Frederik Rietdijk fc74ba8291 Merge master into staging-next 2019-08-31 09:50:38 +02:00
volth 08f68313a4 treewide: remove redundant rec 2019-08-28 11:07:32 +00:00
Frederik Rietdijk 5061fe0c2c Merge staging-next into staging 2019-08-28 08:26:42 +02:00
Léo Gaspard 8a4721d606
Merge pull request #64669 from luispedro/add_sortmerna
sortmerna: init at 3.0.3
2019-08-27 17:19:53 +02:00
Frederik Rietdijk 98640fd482 Merge master into staging-next 2019-08-27 16:36:47 +02:00
Luis Pedro Coelho bc22c2e07f sortmerna: init at 3.0.3
This is a useful package in bioinformatics, namely in processing
short-read sequencing data from metagenomes
2019-08-27 00:37:43 +02:00
volth 35d68ef143 treewide: remove redundant quotes 2019-08-26 21:40:19 +00:00
Jonathan Ringer 6f279584fd stp: 2.2.0 -> 2.3.3 2019-08-26 14:00:48 -07:00
Robin Gloster 616b8343c4
Merge remote-tracking branch 'upstream/master' into gcc-8 2019-08-25 18:55:46 +02:00
Vladimír Čunát 985d1ac425
Merge branch 'master' into staging-next
There were several more conflicts from name -> pname+version;
all auto-solved by kdiff3, hopefully OK.

Hydra nixpkgs: ?compare=1538611
2019-08-25 14:57:11 +02:00
Gabriel Ebner 440c63a38a vampire: 4.2.2 -> 4.4 2019-08-25 14:43:51 +02:00
Nikolay Amiantov 9015d7a4f1 sumorobot-manager: init at 0.9.0 2019-08-24 19:11:27 +03:00
Vladimír Čunát 2e6bf42a22
Merge branch 'master' into staging-next
There ver very many conflicts, basically all due to
name -> pname+version.  Fortunately, almost everything was auto-resolved
by kdiff3, and for now I just fixed up a couple evaluation problems,
as verified by the tarball job.  There might be some fallback to these
conflicts, but I believe it should be minimal.

Hydra nixpkgs: ?compare=1538299
2019-08-24 08:55:37 +02:00
Emily 05c54717f8 symbiyosys: extend platforms 2019-08-23 02:14:40 -05:00
Marek Mahut 44d43368cb
Merge pull request #67155 from r-ryantm/auto-update/tulip
tulip: 5.1.0 -> 5.2.1
2019-08-21 21:40:06 +02:00
R. RyanTM 187ec1a8c6 tulip: 5.1.0 -> 5.2.1
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/tulip/versions
2019-08-20 19:45:43 -07:00
Marek Mahut 51980d6830
Merge pull request #67019 from r-ryantm/auto-update/picard-tools
picard-tools: 2.20.4 -> 2.20.5
2019-08-20 20:15:31 +02:00
R. RyanTM 41571dc81a picard-tools: 2.20.4 -> 2.20.5
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-08-19 21:40:40 -07:00
Marek Mahut b8a9d33bcd
Merge pull request #66884 from markuskowa/upd-octopus
octopus: 9.0 -> 9.1
2019-08-19 11:53:01 +02:00
Marek Mahut 22aa7eadf1
Merge pull request #66871 from peterhoeg/f/apmplanner
apmplanner2: fix build against qt 5.12
2019-08-19 11:43:40 +02:00
Markus Kowalewski a81bb36249
octopus: 9.0 -> 9.1
* switch to GitLab download
* cleanup fftw dependence
2019-08-19 10:24:44 +02:00
Peter Hoeg 374e0ad0a8 pulseview: use mkDerivation 2019-08-19 08:14:21 +02:00
Peter Hoeg abbac2334b apmplanner2: fix build against qt 5.12 2019-08-19 14:01:55 +08:00
Timo Kaufmann 071a4db33e sage: 8.9.beta6 -> 8.9.beta7 2019-08-19 00:16:06 +02:00
Timo Kaufmann e8436f5e23 sage: 8.9.beta5 -> 8.9.beta6 2019-08-18 21:52:27 +02:00
Frederik Rietdijk f65aa21bb2 Merge master into staging-next 2019-08-18 12:53:44 +02:00
Vladimír Čunát 8ed485c67b
Merge #65948: tlaplusToolbox: 1.5.7 -> 1.6.0 2019-08-18 10:11:50 +02:00
Frederik Rietdijk 113dbfeb27
Merge pull request #66596 from emilazy/update-pypy-and-eda-tools
Update PyPy and FOSS EDA tools
2019-08-17 17:48:21 +02:00
volth c814d72b51 treewide: name -> pname 2019-08-17 10:54:38 +00:00
Frederik Rietdijk fe9a3e3e63 Merge staging-next into staging 2019-08-17 09:39:23 +02:00
Timo Kaufmann 192197dc6c
Merge pull request #65802 from timokau/sage-transient-debug
sage: add patch to debug transient issue
2019-08-17 00:33:05 +02:00
Timo Kaufmann 41bb319462 sage: avoid running out of memory during tests 2019-08-16 23:50:55 +02:00
markuskowa 8f5ce70861
Merge pull request #66665 from markuskowa/upd-molden
molden: 6.1 -> 6.2
2019-08-15 18:59:50 +02:00
Matthew Bauer ae15177ade calc: don’t include glibc headers in closure 2019-08-15 23:31:14 +09:00
volth 46420bbaa3 treewide: name -> pname (easy cases) (#66585)
treewide replacement of

stdenv.mkDerivation rec {
  name = "*-${version}";
  version = "*";

to pname
2019-08-15 13:41:18 +01:00
Markus Kowalewski 5b0bbcbb6e
molden: 6.1 -> 6.2 2019-08-15 09:35:34 +02:00
Gabriel Ebner 0a1e131077 gmsh: opencascade support 2019-08-14 19:09:40 +02:00
Gabriel Ebner f91904a889 calculix: init at 2.15 2019-08-14 19:09:40 +02:00
Emily a51e3987ad symbiyosys: 2019.04.18 -> 2019.08.13 2019-08-14 00:14:22 -07:00
Dmitry Kalinkin 34224c7ba0
Merge pull request #66117 from veprbl/pr/hepmc_2_06_10
hepmc: 2.06.09 -> 2.06.10
2019-08-11 22:16:16 -04:00
Timo Kaufmann 3541df594e
Merge pull request #66396 from timokau/sage-undo-short
sage: default to long tests again
2019-08-10 13:16:00 +02:00
Lancelot SIX 8137a78adc
Merge pull request #66063 from lsix/drop_motu_client
motu_client: drop
2019-08-10 00:02:12 +02:00
Timo Kaufmann f6265b0da5 sage: default to long tests again
Changed by accident in 5e58c5f900.
2019-08-09 18:42:14 +02:00
Timo Kaufmann 9ef44b3431 sage: move sympow cache to .sage 2019-08-09 17:45:14 +02:00
Timo Kaufmann 5e58c5f900 sympow: 1.018.1 -> 2.023.4
Maintenance taken over by debian package maintainer jgmbenoit:
https://trac.sagemath.org/ticket/3360#comment:17

This moves sympow to his fork, since there is no offical
version-controlled source repository from the original author and they
do not seem to maintain sympow anymore. We had already accumulated quite
some patches from debian, who have effectively maintained sympow for a
while now.
2019-08-09 17:45:08 +02:00
Timo Kaufmann ddd3faf08e sage: 8.9.beta4 -> 8.9.beta5 2019-08-07 15:33:15 +02:00
Ryan Mulligan 423e09b3b5
Merge pull request #66018 from r-ryantm/auto-update/picard-tools
picard-tools: 2.20.3 -> 2.20.4
2019-08-06 21:44:53 -07:00
Gabriel Ebner ef3b016545 Merge branch 'qalc330' 2019-08-06 09:08:58 +02:00
Gabriel Ebner ca1895ace3 qalculate-gtk: 3.2.0 -> 3.3.0 2019-08-06 09:03:45 +02:00