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Author SHA1 Message Date
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
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