Commit graph

3423 commits

Author SHA1 Message Date
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
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:
e6754980264fe927320d5ff2dbd24ca4fac9a160
1e9cc5b9844ef603fe160e9f671178f96200774f
793a2fe1e8bb886ca2096c5904e1193dc3268b6d
c19cf65261639f749012454932a532aa7c681e4b
f6544d618f30fae0bc4798c4387a8c7c9c047a7c
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