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Author SHA1 Message Date
Timo Kaufmann 35896e3506 sage: replace flask-babel version pin by patch 2018-07-12 22:55:16 +02:00
Austin Seipp 54e9f7dcbe z3: move to multiple output packages
The Z3 source code is effectively compiled into two completely separate
objects: the z3 binary file, and the libz3.so library -- but the binary is not
linked against the shared library, it simply incorporates all of the object
files. The Z3 code base results in an ~25MB object on x86_64-linux. As a
result, splitting bin/ and lib/ results in a 50% reduction in closure size.

(The include/ directory is also surprisingly large at .5MB...)

This also splits the python API into a completely separate .python attribute,
as well.

Signed-off-by: Austin Seipp <aseipp@pobox.com>
2018-07-12 15:48:48 -05:00
Timo Kaufmann d37c23c699 jmol: 14.29.12 -> 14.29.17 (#43429) 2018-07-12 22:31:52 +02:00
Frederik Rietdijk 04cae0e5fb
Merge pull request #43333 from r-ryantm/auto-update/libpoly
libpoly: 0.1.4 -> 0.1.5
2018-07-11 19:01:02 +02:00
R. RyanTM 40e648b7ab yices: 2.5.4 -> 2.6.0
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/yices/versions.
2018-07-11 08:45:45 -05:00
R. RyanTM a89b538f0b libpoly: 0.1.4 -> 0.1.5
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/libpoly/versions.
2018-07-11 02:29:13 -07:00
R. RyanTM ade3e571a1 qalculate-gtk: 2.6.0 -> 2.6.1
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/qalculate-gtk/versions.
2018-07-11 00:45:08 -07:00
R. RyanTM 99cb9de551 fricas: 1.3.3 -> 1.3.4 (#43023)
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/fricas/versions.

These checks were done:

- built on NixOS
- /nix/store/zbmbsjm8mg6i7s6fm3zas1bndg24w91x-fricas-1.3.4/bin/fricas passed the binary check.
- /nix/store/zbmbsjm8mg6i7s6fm3zas1bndg24w91x-fricas-1.3.4/bin/efricas passed the binary check.
- 2 of 2 passed binary check by having a zero exit code.
- 0 of 2 passed binary check by having the new version present in output.
- found 1.3.4 with grep in /nix/store/zbmbsjm8mg6i7s6fm3zas1bndg24w91x-fricas-1.3.4
- directory tree listing: https://gist.github.com/75d751d9733f6b0a7b582ab838a71963
- du listing: https://gist.github.com/4c6fe5f342430a2b36568da3229d3dc4
2018-07-09 16:02:58 +02:00
R. RyanTM 6ec4be7ec5 igv: 2.4.10 -> 2.4.11 (#43003)
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/igv/versions.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/yc18a4s9rs8m6wjbsmi1lax5v0kkyl2i-igv-2.4.11/bin/igv had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.4.11 with grep in /nix/store/yc18a4s9rs8m6wjbsmi1lax5v0kkyl2i-igv-2.4.11
- directory tree listing: https://gist.github.com/ca4cf484aab1c1590806c47c4fdde1d7
- du listing: https://gist.github.com/f7ff80a2429cf0a942195db4944659b1
2018-07-09 16:02:34 +02:00
Silvan Mosberger 8e2c3b93ba
Merge pull request #43096 from jbedo/mosdepth
mosdepth: init 0.2.3
2018-07-09 04:55:24 +02:00
Dan Peebles 1dd7bc7dfc monosat: update build to use handy new environment variable 2018-07-08 22:04:05 -04:00
Dan Peebles 0372c87481 monosat: cbaf79cf -> 2deeadef
Upstream fixed a few things I needed to work around
2018-07-08 21:57:00 -04:00
Justin Bedo 59141de608
mosdepth: init 0.2.3 2018-07-09 08:51:49 +10:00
Dan Peebles 631dd7a4e9 monosat: init at 1nx3wh34
Also includes the python and java bindings (although java is only
currently enabled on Linux)
2018-07-08 12:43:29 -04:00
R. RyanTM cb85999b6b picard-tools: 2.18.7 -> 2.18.9 (#42967)
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.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.9 with grep in /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9
- directory tree listing: https://gist.github.com/0972acdc51fe8a1cde470e4ab5e87993
- du listing: https://gist.github.com/6a66b6723ce4887cd108678369b87360
2018-07-06 20:24:57 +02:00
Sebastien Maret 8ae9e7ef10 gildas: apply upstream fix and restore parallel building 2018-07-06 14:02:37 +02:00
Sebastien Maret 72dc6fdf47 gildas: disable parallel building 2018-07-06 10:35:53 +02:00
John Wiegley 56afc551f2
verilator: Allow building on Darwin as well as Linux 2018-07-05 15:17:17 -07:00
Matthew Bauer bb0febf575
Merge pull request #43079 from matthewbauer/rework-extra-pkgs
Rework stage.nix's extraPkgs
2018-07-05 18:05:57 -04:00
Matthew Bauer c491a99362 treewide: remove callPackage_i686
This has been replaced with pkgsi686Linux.callPackage
2018-07-05 14:04:52 -04:00
Will Dietz 67986382e4
Merge pull request #43071 from dtzWill/fix/vampire-portability
vampire: portability fixes
2018-07-05 11:13:42 -05:00
Gabriel Ebner bec83a2b9e cvc4: 1.5 -> 1.6 2018-07-05 17:57:06 +02:00
Will Dietz 7353d8396d vampire: enable parallel building 2018-07-05 10:13:40 -05:00
Will Dietz 600abbedc9 vampire: portability fixes
These have been submitted upstream,
but seconds before writing this message
so naturally no upstream response "yet" :).

Regardless of response, fetch patches
from the corresponding PR's for context
and of course hopefully they'll
be included in next version.
2018-07-05 10:13:32 -05:00
Will Dietz 8e6db30bb7 vampire: use CC/CXX from env, instead of always g++ 2018-07-05 10:11:32 -05:00
Gabriel Ebner 887b6fd793 qalculate-gtk: 2.5.0 -> 2.6.0 2018-07-05 12:33:27 +02:00
Gabriel Ebner 7c63a9cac2 eprover: 2.0 -> 2.1 2018-07-05 12:26:43 +02:00
Gabriel Ebner 57ae4e8d8e vampire: init at 4.2.2 2018-07-05 09:34:28 +02:00
R. RyanTM 5a859d9b10 stellarium: 0.18.0 -> 0.18.1 (#42949)
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.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/2c607ylvxs69nbr99ly1bgcb0bbk47xf-stellarium-0.18.1/bin/stellarium had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/2c607ylvxs69nbr99ly1bgcb0bbk47xf-stellarium-0.18.1/bin/.stellarium-wrapped had a zero exit code or showed the expected version
- 0 of 2 passed binary check by having a zero exit code.
- 0 of 2 passed binary check by having the new version present in output.
- found 0.18.1 with grep in /nix/store/2c607ylvxs69nbr99ly1bgcb0bbk47xf-stellarium-0.18.1
- directory tree listing: https://gist.github.com/dd98359fb1214ae24bd70e291c1bc33d
- du listing: https://gist.github.com/67baedda5ffc1ad0aa064239cb503c2b
2018-07-05 00:24:22 +02:00
Michael Raskin 04bd737062
Merge pull request #43026 from r-ryantm/auto-update/clingo
clingo: 5.2.2 -> 5.3.0
2018-07-04 21:01:39 +00:00
R. RyanTM a431e4f207 clingo: 5.2.2 -> 5.3.0
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.

Version release notes (from GitHub):
# Packages

- The easiest way to obtain Python enabled clingo packages is using [Anaconda][ana]. Packages are available in the [Potassco channel][pch]. First [install either Anaconda or Miniconda][ins] and then run: `conda install -c potassco clingo`.
- Packages for clingo are available in the Linux distributions [Debian][deb], [Ubuntu][ubu], and [Arch Linux (AUR)][aur].
- For Mac OS X, clingo packages are available in [homebrew][hbr] and [macports][mac].

# Changes

* change C API to use numeric instead of symbolic literals
  * affects assumptions and assigning/releasing externals (breaks backward compatibility)
  * added overloads to C++, python and lua API to support both numeric and symbolic version (preserves backward compatibility for most code)
* the python, C and C++ APIs now allow for customizing clingo by implementing a custom main function but reusing the rest of the application including the standard output
* add API function to detect conflicting programs
* add message logger to python and lua interface
* add support for primes in the beginning of identifiers and variable names
* add per solver registration of watches during propagator initialization
* add a directive to selectivel suppress undefined atom warnings
* add support for user defined statistics
* add _to_c functions for python API to be able to call C functions from python
* only create ground representations for requested program parts when grounding (#71)
* improve program observer (#19)
* support for binary, octal, and hexadecimal numbers (#65)
* the backend has to be opened/closed now
* release python's GIL while grounding (#82)
* TruthValue.{True,False} becomes TruthValue.{\_True,\_False} in python API
* improve API and it's documentation

[deb]: https://www.debian.org/
[ubu]: https://www.ubuntu.com/
[aur]: https://aur.archlinux.org/
[hbr]: https://brew.sh/
[mac]: https://www.macports.org/
[ana]: https://conda.io
[pch]: https://anaconda.org/potassco/clingo
[ins]: https://conda.io/docs/user-guide/install/index.html

These checks were done:

- built on NixOS
- /nix/store/484fg7w1fr5xh2avc4g7811mxq3v3p9x-clingo-5.3.0/bin/lpconvert passed the binary check.
- /nix/store/484fg7w1fr5xh2avc4g7811mxq3v3p9x-clingo-5.3.0/bin/clasp passed the binary check.
- /nix/store/484fg7w1fr5xh2avc4g7811mxq3v3p9x-clingo-5.3.0/bin/reify passed the binary check.
- /nix/store/484fg7w1fr5xh2avc4g7811mxq3v3p9x-clingo-5.3.0/bin/gringo passed the binary check.
- /nix/store/484fg7w1fr5xh2avc4g7811mxq3v3p9x-clingo-5.3.0/bin/clingo passed the binary check.
- 5 of 5 passed binary check by having a zero exit code.
- 0 of 5 passed binary check by having the new version present in output.
- found 5.3.0 with grep in /nix/store/484fg7w1fr5xh2avc4g7811mxq3v3p9x-clingo-5.3.0
- directory tree listing: https://gist.github.com/bba2eaf1d132fbdd88a2710a6030c419
- du listing: https://gist.github.com/230340bfa02557290a60cfc6d2e7e977
2018-07-04 11:23:33 -07:00
Silvan Mosberger fac943fc81
Merge pull request #42897 from fragamus/master
add bliss package
2018-07-04 13:59:41 +02:00
Michael Gough e3ea685957 bliss: init at 0.73 2018-07-04 11:33:10 +00:00
Timo Kaufmann dcc1013f6b pythonPackages.backports_shutil_get_terminal_size: 1.0 -> 2016-02-21 (#42840) 2018-07-02 18:03:05 +02:00
Sebastien Maret d46fde9eb1 gildas: 20180601_a -> 20180701_a 2018-07-02 17:16:25 +02:00
Sarah Brofeldt f06ce58323
Merge pull request #42843 from fragamus/master
hmetis: init at 1.5
2018-07-02 11:40:41 +02:00
Peter Simons cbc1a03ab8 R: update to version 3.5.1
(cherry picked from commit 7e2f2037ea6d6533492d407696f260e7b11df49d)
2018-07-02 11:33:50 +02:00
Michael Gough f180facaa0 hmetis: init at 1.5 2018-07-01 18:29:55 +00:00
Michael Raskin 055a29c4a1
Merge pull request #39981 from timokau/sage-on-nixos
Sage on nixos
2018-07-01 07:37:42 +00:00
Timo Kaufmann 70ba695777 sage: replace JUPYTER_PATH patch by upstream patch
The patch was replaced by a better upstream patch that doesn't mvoe the
jupyter dir to the user's home.
2018-06-30 22:30:30 +02:00
Timo Kaufmann 398dad270a sage, arb: update sage dependencies arb and pynac
Removes the version pinning for arb and pynac by backporting the
upstream (sage) package upgrades. This necessitates a new patch for arb,
which was however already proposed and accepted upstream.
2018-06-30 17:05:56 +02:00
Luz f6a2869031 librepcb-unstable: 2017-12-29 -> 2018-06-28 (#42786)
* Update: 2017-12-29 -> 2018-06-28

* Update libs also to qt5.9

* Add required default font file

* Switch back to default Qt version
2018-06-30 13:56:12 +02:00
Ryan Mulligan 1d54dc6841 treewide: http -> https 2018-06-29 17:18:27 -07:00
Timo Kaufmann 17e6b391eb sage: 8.1 -> 8.2, use system packages 2018-06-30 01:21:31 +02:00
Timo Kaufmann 424835acc8 symmetrica: add patches 2018-06-30 01:20:46 +02:00
Théo Zimmermann 314eb884ec
coq_8_8: 8.8.0 -> 8.8.1 2018-06-29 11:10:31 +02:00
Matthew Bauer 2171fc4d55
Merge pull request #42590 from TimPut/openmvsbuildfix
openmvs: build with CGAL 4.12
2018-06-28 22:33:40 -04:00
Matthew Bauer e714f85b2f
Merge pull request #41929 from smaret/gildas
gildas: init at 201806_a
2018-06-28 22:17:07 -04:00
Matthew Bauer 574883f665
Merge pull request #42571 from iimog/hmmer
hmmer: init at 3.1b2
2018-06-28 22:00:09 -04:00
Silvan Mosberger 57bccb3cb8 treewide: http -> https sources (#42676)
* treewide: http -> https sources

This updates the source urls of all top-level packages from http to
https where possible.

* buildtorrent: fix url and tab -> spaces
2018-06-28 20:43:35 +02:00
Ryan Mulligan fce8f26af6 treewide: http -> https (#42665) 2018-06-27 22:12:57 +02:00
R. RyanTM d4f62f651f gromacs: 2018.1 -> 2018.2 (#42504)
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.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/GMXRC had a zero exit code or showed the expected version
- /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/GMXRC.bash passed the binary check.
- /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/GMXRC.zsh passed the binary check.
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/GMXRC.csh had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/demux.pl had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/xplor2gmx.pl had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/gmx-completion.bash had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/gmx-completion-gmx.bash had a zero exit code or showed the expected version
- /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2/bin/gmx passed the binary check.
- 3 of 9 passed binary check by having a zero exit code.
- 0 of 9 passed binary check by having the new version present in output.
- found 2018.2 with grep in /nix/store/illh3rp28ipz35z0wipsfc18z4m03sah-gromacs-2018.2
- directory tree listing: https://gist.github.com/1679f0362dfcc7299a6d5b8d9e76c14e
- du listing: https://gist.github.com/2f848bb0fe181676c17b61a9d5a94953
2018-06-27 19:02:19 +02:00
Timo Kaufmann 9ce041a8c7 pynac: 0.7.21 -> 0.7.22 (#42650) 2018-06-27 15:41:29 +02:00
Timo Kaufmann 2b22ecf01e palp: restrict platforms to linux (#42651) 2018-06-27 15:28:39 +02:00
Timo Kaufmann 08a59bb10d palp: fix runtime error introduced by #28029 (#42633)
After #28029 it is necessary to add "strictoverflow" to the disabled
hardening flags. That probably has something to do with the `-O3` option
in palps makefile.

This commit also adds a test to check for this regression (as it only
occured at runtime).
2018-06-27 09:42:26 +02:00
tim put 385114da68 openmvs: fix CGAL 4.12 dependency
patch executables with openMVS library path
2018-06-26 21:55:15 -06:00
Sebastien Maret 7b01e2b7d6 gildas: use internal LAPACK instead of OpenBLAS
Gildas' uv_fit task segfaults when it uses OpenBLAS. Use internal
LAPACK version instead.
2018-06-26 17:15:51 +02:00
Sebastien Maret ba2f45c182 gildas: use the standard installPhase 2018-06-26 11:09:45 +02:00
Sebastien Maret 8603f343a3 gildas: init at 201806_a 2018-06-26 11:09:45 +02:00
tim put a47a16a887 openmvg: 1.1 -> 1.3 2018-06-25 16:12:26 -06:00
Markus Ankenbrand 851ab7f323 hmmer: init at 3.1b2 2018-06-25 16:56:21 +02:00
xeji c51ac5eb33
Merge pull request #42423 from ryantm/repology-problems
treewide: http -> https
2018-06-24 20:44:50 +02:00
Maximilian Bosch 8cf8c4bac2 stellarium: 0.16.1 -> 0.18.0 (#42357) 2018-06-24 20:26:58 +02:00
Matthew Justin Bauer e09861f11f
gravit: fix eval 2018-06-23 17:35:31 -04:00
Matthew Justin Bauer 9bfd3ade2e
gravit: only build on linux 2018-06-23 17:33:25 -04:00
Ryan Mulligan 0d5eb901ad treewide: http -> https 2018-06-23 04:34:55 -07:00
R. RyanTM b75e083c69 verilator: 3.922 -> 3.924
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.

These checks were done:

- built on NixOS
- /nix/store/gnmapahqvab762fi885bwhlfhxvpfs81-verilator-3.924/bin/verilator_bin passed the binary check.
- /nix/store/gnmapahqvab762fi885bwhlfhxvpfs81-verilator-3.924/bin/verilator_bin_dbg passed the binary check.
- /nix/store/gnmapahqvab762fi885bwhlfhxvpfs81-verilator-3.924/bin/verilator_coverage_bin_dbg passed the binary check.
- /nix/store/gnmapahqvab762fi885bwhlfhxvpfs81-verilator-3.924/bin/verilator passed the binary check.
- /nix/store/gnmapahqvab762fi885bwhlfhxvpfs81-verilator-3.924/bin/verilator_coverage passed the binary check.
- Warning: no invocation of /nix/store/gnmapahqvab762fi885bwhlfhxvpfs81-verilator-3.924/bin/verilator_profcfunc had a zero exit code or showed the expected version
- 5 of 6 passed binary check by having a zero exit code.
- 0 of 6 passed binary check by having the new version present in output.
- found 3.924 with grep in /nix/store/gnmapahqvab762fi885bwhlfhxvpfs81-verilator-3.924
- directory tree listing: https://gist.github.com/eebd214973454154b716fc6a9556b922
- du listing: https://gist.github.com/cb78abec038b5abdae8004ea1edcefc0
2018-06-19 10:14:47 -05:00
Timothée Jourde cb597c229b openspace: init at 0.11.1
This adds a new package: OpenSpace, an open source astrovisualization
project, and one of its dependencies: SOIL (Simple OpenGL Image
Library).

This kind of works for me, but please note that this build is not very
usable for now. This is a first attempt. Also, Linux doesn't seem to
be well supported upstream, hence the various patches (I will open an
issue upstream to discuss them).

Squashed commits:
openspace: fetch upstream glm "patch"
openspace: add missing dependency (libXxf86vm)
soil: mesa -> mesa_noglu
2018-06-19 02:59:23 +02:00
R. RyanTM b3052440f6 picard-tools: 2.18.5 -> 2.18.7 (#41975)
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.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.7 with grep in /nix/store/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7
- directory tree listing: https://gist.github.com/a49ed5f2ff312ce6180174183901e38f
- du listing: https://gist.github.com/243f4d89d2100ef27d332e3562d5f173
2018-06-18 22:41:49 +02:00
R. RyanTM d97f7d3b89 raxml: 8.2.11 -> 8.2.12 (#41964)
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/RAxML/versions.

These checks were done:

- built on NixOS
- /nix/store/w8iy7fvdwhjw7zx1dkga3v56fz59s7r8-RAxML-8.2.12/bin/raxmlHPC-PTHREADS-SSE3 passed the binary check.
- 1 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 8.2.12 with grep in /nix/store/w8iy7fvdwhjw7zx1dkga3v56fz59s7r8-RAxML-8.2.12
- directory tree listing: https://gist.github.com/8a2b70b299e53bfee9f18d2ab8cd5f9f
- du listing: https://gist.github.com/02803409663f19671adc6be233a327fd
2018-06-18 22:40:49 +02:00
Maximilian Bosch 0dbfa47ed1 geogebra: 5-0-444-0 -> 5-0-472-0 (#41990)
Bumped to the latest version available.

Also tested the `web.archive.org` backup to avoid broken downloads when
the tarball is removed from the official download mirror.
2018-06-17 18:04:14 +02:00
spacefrogg 0b475d300c ngspice: Fix regression due to missing X libs (#41890) 2018-06-13 13:48:15 +02:00
spacefrogg 0cc4396818 xcircuit: init at 3.9.73 (#41891) 2018-06-13 13:21:34 +02:00
Ben Gamari f4d4f5e65a kicad-unstable: 2018-03-10 -> 2018-06-12 2018-06-12 20:15:51 -04:00
Matthew Justin Bauer cc42186614
Merge pull request #41668 from r-ryantm/auto-update/ngspice
ngspice: 27 -> 28
2018-06-10 19:08:30 -04:00
R. RyanTM d50e65b346 pynac: 0.7.19 -> 0.7.21 (#41662)
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/pynac/versions.

These checks were done:

- built on NixOS

- 0 of 0 passed binary check by having a zero exit code.
- 0 of 0 passed binary check by having the new version present in output.
- found 0.7.21 with grep in /nix/store/883yhmfc1k4vz1dd37l73v7clvnyaa3v-pynac-0.7.21
- directory tree listing: https://gist.github.com/a0f53cebb1c4cae07c81edef938ac632
- du listing: https://gist.github.com/78800724710d0766e4add7ed1847c3fc
2018-06-08 19:02:38 +02:00
Jörg Thalheim 2e26c117eb
Merge pull request #41689 from r-ryantm/auto-update/gromacs
gromacs: 2018 -> 2018.1
2018-06-08 17:17:52 +01:00
R. RyanTM bab8aee740 gromacs: 2018 -> 2018.1
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/gromacs/versions.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/GMXRC had a zero exit code or showed the expected version
- /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/GMXRC.bash passed the binary check.
- /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/GMXRC.zsh passed the binary check.
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/GMXRC.csh had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/demux.pl had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/xplor2gmx.pl had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/gmx-completion.bash had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/gmx-completion-gmx.bash had a zero exit code or showed the expected version
- /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1/bin/gmx passed the binary check.
- 3 of 9 passed binary check by having a zero exit code.
- 0 of 9 passed binary check by having the new version present in output.
- found 2018.1 with grep in /nix/store/a0ab5ixcsgcj9pzkmysfa46dydbbzsyy-gromacs-2018.1
- directory tree listing: https://gist.github.com/4d089bde03168c17ad10db514f47d339
- du listing: https://gist.github.com/5dd10f02ed60d442ec148efcf18c7661
2018-06-08 06:30:20 -07:00
R. RyanTM 8195e37c14 ngspice: 27 -> 28
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/ngspice/versions.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/7mjpw971bh37wil41hin4ssn290wr3ad-ngspice-28/bin/cmpp had a zero exit code or showed the expected version
- /nix/store/7mjpw971bh37wil41hin4ssn290wr3ad-ngspice-28/bin/ngspice passed the binary check.
- 1 of 2 passed binary check by having a zero exit code.
- 0 of 2 passed binary check by having the new version present in output.
- found 28 with grep in /nix/store/7mjpw971bh37wil41hin4ssn290wr3ad-ngspice-28
- directory tree listing: https://gist.github.com/890c9d6d1b1aa9e86b2f4c8ddf86a36d
- du listing: https://gist.github.com/099b236d47fee839749355d18a841493
2018-06-08 02:31:16 -07:00
Matthew Justin Bauer d6a97a524a
Merge pull request #41576 from MarcFontaine/xearth
xearth : init at 1.1
2018-06-06 21:27:09 -04:00
R. RyanTM 517d5ff6e1 cryptoverif: 1.28 -> 2.00
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/cryptoverif/versions.

These checks were done:

- built on NixOS
- /nix/store/449i03imd329g3yi4gbmcbq9pv5ijpib-cryptoverif-2.00/bin/cryptoverif passed the binary check.
- 1 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.00 with grep in /nix/store/449i03imd329g3yi4gbmcbq9pv5ijpib-cryptoverif-2.00
- directory tree listing: https://gist.github.com/b4cdf4e1befb51addd9b1dc1c39d78d9
- du listing: https://gist.github.com/18190fb11f51471790dcc668635aba6a
2018-06-06 14:40:27 -05:00
R. RyanTM ff92e43a17 gtkwave: 3.3.90 -> 3.3.91
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.

These checks were done:

- built on NixOS
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/evcd2vcd passed the binary check.
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/fst2vcd passed the binary check.
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/vcd2fst passed the binary check.
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/fstminer passed the binary check.
- Warning: no invocation of /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/ghwdump had a zero exit code or showed the expected version
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/lxt2miner passed the binary check.
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/lxt2vcd passed the binary check.
- Warning: no invocation of /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/shmidcat had a zero exit code or showed the expected version
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/vcd2lxt passed the binary check.
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/vcd2lxt2 passed the binary check.
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/vcd2vzt passed the binary check.
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/vzt2vcd passed the binary check.
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/vztminer passed the binary check.
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/gtkwave passed the binary check.
- Warning: no invocation of /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/twinwave had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/rtlbrowse had a zero exit code or showed the expected version
- /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91/bin/vermin passed the binary check.
- 13 of 17 passed binary check by having a zero exit code.
- 0 of 17 passed binary check by having the new version present in output.
- found 3.3.91 with grep in /nix/store/saxwlbm10w3r18rlj0svnfbrf5crwr4w-gtkwave-3.3.91
- directory tree listing: https://gist.github.com/3ce8b90b2a4e815255bced6a94d99818
- du listing: https://gist.github.com/8571bbab590243bbfadf05271e188f20
2018-06-06 14:40:12 -05:00
MarcFontaine 220d2637c1 xearth : init at 1.1 2018-06-06 14:34:00 +02:00
Will Dietz edbebe7214 z3: 4.6.0 -> 4.7.1 2018-05-30 16:54:21 -05:00
Sarah Brofeldt b7c524f006
Merge pull request #41178 from ryantm/simgrid
simgrid: 3.17 -> 3.19.1
2018-05-28 22:40:05 +02:00
Ben Darwin de897bacea celf: init at 2013-07-25 (#41141) 2018-05-28 21:27:53 +02:00
Ryan Mulligan e094cda74f simgrid: 3.17 -> 3.19.1 2018-05-28 06:01:17 -07:00
Ryan Mulligan af9d10a91b treewide: fix derivation names 2018-05-28 05:59:57 -07:00
Frederik Rietdijk b22cc53db1 Merge staging into master 2018-05-27 17:44:08 +02:00
R. RyanTM e33eacbc1d picard-tools: 2.18.4 -> 2.18.5
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.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.5 with grep in /nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5
- directory tree listing: https://gist.github.com/1938ad634fa882d94e8d28fd1625547c
- du listing: https://gist.github.com/4b51e89646327900f6ef6f2242f5d0bd
2018-05-26 10:42:37 -07:00
Jan Malakhovski ad35019501 Merge branch 'master' into staging
Fixed conflicts:
- lib/systems/for-meta.nix: in favor of staging
- pkgs/os-specific/darwin/xcode/default.nix: in favor of master
2018-05-26 00:20:17 +00:00
Matthew Justin Bauer 98f2f08b4b
Merge pull request #41009 from matthewbauer/normalize-names
Add versions to packages missing it
2018-05-25 16:32:48 -05:00
Yegor Timoshenko 4e049b2fd4 simgrid: cleanup 2018-05-25 15:48:28 -05:00
Matthew Bauer 02297beade treewide: add version to packages
Lots of packages are missing versions in their name. This adds them
where appropriate. These were found with this command:

 $ nix-env -qa -f. | grep -v '\-[0-9A-Za-z.-_+]*$' | grep -v '^hook$'

See issue #41007.
2018-05-25 15:48:05 -05:00
Jörg Thalheim f7650ebd5f python.pkgs.spyder: fix setup.py patch 2018-05-25 11:00:14 +01:00
Gabriel Ebner d96cc05a60 qalculate-gtk: 2.3.0 -> 2.5.0 2018-05-24 18:19:55 +02:00
Sarah Brofeldt 6ea941d3fd gmsh: gfortran -> nativeBuildInputs (fix #40976) (#40984) 2018-05-23 17:32:43 +02:00
Dmitry Kalinkin 65c3273250 form: init at 4.2.0 (#40693) 2018-05-22 20:17:32 +02:00
Vincent Laporte ae23bb2bcc
proverif: 1.97pl1 -> 2.00 2018-05-22 06:58:10 +00:00
R. RyanTM b34f0a11dc pari: 2.9.4 -> 2.9.5
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/pari/versions.

These checks were done:

- built on NixOS
- /nix/store/18hjz56shfnp00r1pgslfy3zci2wk6m9-pari-2.9.5/bin/gp passed the binary check.
- /nix/store/18hjz56shfnp00r1pgslfy3zci2wk6m9-pari-2.9.5/bin/tex2mail passed the binary check.
- /nix/store/18hjz56shfnp00r1pgslfy3zci2wk6m9-pari-2.9.5/bin/gphelp passed the binary check.
- /nix/store/18hjz56shfnp00r1pgslfy3zci2wk6m9-pari-2.9.5/bin/gp-2.9 passed the binary check.
- 4 of 4 passed binary check by having a zero exit code.
- 0 of 4 passed binary check by having the new version present in output.
- found 2.9.5 with grep in /nix/store/18hjz56shfnp00r1pgslfy3zci2wk6m9-pari-2.9.5
- directory tree listing: https://gist.github.com/63c5da24ace1d863b434a462fc0d0123
- du listing: https://gist.github.com/d275cd2f3b274f52576dbab1bf9ebc9c
2018-05-21 08:53:00 +00:00
R. RyanTM 364f922cbf gtkwave: 3.3.89 -> 3.3.90
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.

These checks were done:

- built on NixOS
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/evcd2vcd passed the binary check.
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/fst2vcd passed the binary check.
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/vcd2fst passed the binary check.
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/fstminer passed the binary check.
- Warning: no invocation of /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/ghwdump had a zero exit code or showed the expected version
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/lxt2miner passed the binary check.
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/lxt2vcd passed the binary check.
- Warning: no invocation of /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/shmidcat had a zero exit code or showed the expected version
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/vcd2lxt passed the binary check.
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/vcd2lxt2 passed the binary check.
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/vcd2vzt passed the binary check.
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/vzt2vcd passed the binary check.
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/vztminer passed the binary check.
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/gtkwave passed the binary check.
- Warning: no invocation of /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/twinwave had a zero exit code or showed the expected version
- Warning: no invocation of /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/rtlbrowse had a zero exit code or showed the expected version
- /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90/bin/vermin passed the binary check.
- 13 of 17 passed binary check by having a zero exit code.
- 0 of 17 passed binary check by having the new version present in output.
- found 3.3.90 with grep in /nix/store/hhpifj7x2j4nr80kiksdhqyfny1hlyvh-gtkwave-3.3.90
- directory tree listing: https://gist.github.com/cf30f5f6dd398a3083156aed84f02f36
- du listing: https://gist.github.com/6d77f0a1fdfe06cfe325c3873fdfd97c
2018-05-18 08:59:50 -05:00
Pascal Wittmann 97ab2d40cb
Merge pull request #40614 from symphorien/ries
ries: init at 2018-04-11
2018-05-17 21:30:47 +02:00
Symphorien Gibol ea7404dcd7 ries: init at 2018-04-11 2018-05-17 14:09:33 +02:00
R. RyanTM de49ba6c3f nauty: 26r7 -> 26r10
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.

These checks were done:

- built on NixOS
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/dreadnaut passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/copyg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/listg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/labelg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/dretog passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/amtog passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/geng passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/complg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/showg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/NRswitchg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/biplabg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/addedgeg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/deledgeg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/countg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/pickg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/genrang passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/newedgeg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/catg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/genbg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/directg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/gentreeg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/genquarticg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/ranlabg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/multig passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/planarg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/gentourng passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/linegraphg passed the binary check.
- Warning: no invocation of /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/watercluster2 had a zero exit code or showed the expected version
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/dretodot passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/subdivideg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/vcolg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/delptg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/cubhamg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/twohamg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/hamheuristic passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/converseg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/genspecialg passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/genbgL passed the binary check.
- /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/shortg passed the binary check.
- Warning: no invocation of /nix/store/f2icw60ljw5s4nkj8hlgwxz83szfi1m7-nauty-26r10/bin/configure had a zero exit code or showed the expected version
- 38 of 40 passed binary check by having a zero exit code.
- 0 of 40 passed binary check by having the new version present in output.
- directory tree listing: https://gist.github.com/3bca602211d416ba58097f4f8880b6d0
- du listing: https://gist.github.com/4ac19efe14e18aae8fece0ec1a500bf1
2018-05-17 03:57:50 -07:00
Matthew Bauer e0d6edddd7 pspp: provide default icons & settings
psppire needs to be wrapped so that it will work outside of GNOME
desktop. We provide hicolor-icon-theme & gsettings-desktop-schemas.

Note that at runtime, I still get this error:

- Cannot create a converter for `IBM864' to `UTF-8': Invalid argument

Possibly a locale issue.

Fixes #40558
2018-05-15 15:42:13 -05:00
Arcadio Rubio García 699fa7e953 star: 2.5.3a -> 2.6.0c (#40518) 2018-05-15 15:09:06 +02:00
Arcadio Rubio García e4a2b70f91 minimap2: init at 2.10 2018-05-14 21:26:07 +01:00
Timo Kaufmann 053d1e0339 giac: re-add lapack without atlas (#40 (#40458)
giac: re-add lapack without atlas
2018-05-14 12:47:45 +02:00
Gabriel Ebner 0db951db83 elan: 0.3.2 -> 0.5.0 2018-05-14 09:40:13 +02:00
Timo Kaufmann 5550015b20 giac: remove liblapackWithAtlas dependency (#40430) 2018-05-13 18:33:51 +02:00
Maximilian Bosch be53a0f2ef sasview: fix build (#40433)
The package breaks currently breaks with the following message:

```
fixed-output derivation produced path '/nix/store/5dh1mdj027ad8sprk12fqa5h5bpdxs5n-sasview' with sha256 hash '12k1w4yq1mzjxcp2cqb562c7cbwzhi54rsbmgi0fax0i1660q167' instead of the expected hash '05la54wwzzlkhmj8vkr0bvzagyib6z6mgwqbddzjs5y1wd48vpcx'
```

To fix the build the following changes were applied:

* Switched to latest master for now as the older releases have a broken
  `py.test` configuration and altering hashes.

* Added `checkPhase` which invokes `py.test` directly and drops
  duplicated files from `dist/tmpbuild`.

* Rebased the patches `pyparsing-fix.patch` and `local_config.patch` for
  the latest master revision.

Additionally refer to the discussion in #40381 for further reference.
2018-05-13 17:25:18 +02:00
R. RyanTM 47c672b4b1 picard-tools: 2.18.3 -> 2.18.4
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/picard-tools/versions.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.4 with grep in /nix/store/k62ym9i08d0w9sgmdjjfyy4lf2n9ig7p-picard-tools-2.18.4
- directory tree listing: https://gist.github.com/4d9e3062e701681d9b53033dc9511663
2018-05-12 13:58:09 +02:00
John Ericson ae429f8e55 yacas: 1.2.2 -> 1.6.1
They switched to cmake and talk about mingw cross, so I can kill
crossAttrs too.
2018-05-10 11:42:08 -04:00
Austin Seipp 04002e2b71 tamarin-prover: 1.3.1 -> 1.4.0
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2018-05-07 11:17:49 -05:00
Jörg Thalheim d1ad5bf95d
Merge pull request #40113 from wchresta/tamarin/fix
tamarin-prover: Fix compile issues
2018-05-07 13:49:50 +01:00
Wanja Chresta ee95ed11ca tamarin-prover: Fix compile issues 2018-05-07 12:18:06 +02:00
Gabriel Ebner 5347d89420
Merge pull request #40093 from r-ryantm/auto-update/lean
lean: 3.3.0 -> 3.4.1
2018-05-07 11:31:23 +02:00
R. RyanTM 639376aff6 lean: 3.3.0 -> 3.4.1
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/lean/versions.

These checks were done:

- built on NixOS
- ran ‘/nix/store/kdbjdracd2m6fv18k9kc5bcmr0p60glx-lean-3.4.1/bin/lean -h’ got 0 exit code
- ran ‘/nix/store/kdbjdracd2m6fv18k9kc5bcmr0p60glx-lean-3.4.1/bin/lean --help’ got 0 exit code
- ran ‘/nix/store/kdbjdracd2m6fv18k9kc5bcmr0p60glx-lean-3.4.1/bin/leanpkg help’ got 0 exit code
- found 3.4.1 with grep in /nix/store/kdbjdracd2m6fv18k9kc5bcmr0p60glx-lean-3.4.1
- directory tree listing: https://gist.github.com/198504c00746718749b3019653fe78fd
2018-05-07 02:24:49 -07:00
Matthew Justin Bauer 4f08e5902f
Merge pull request #39972 from ikervagyok/mathematica
mathematica: add mesa, fix `libGL.so.1 not found` messages
2018-05-05 00:07:23 -05:00
Matthew Justin Bauer a733bbfb07
Merge pull request #39740 from r-ryantm/auto-update/picard-tools
picard-tools: 2.18.2 -> 2.18.3
2018-05-04 17:21:50 -05:00
Lengyel Balazs 1f1e16af73 mathematica: add mesa, fix libGL.so.1 not found messages 2018-05-04 13:10:26 +02:00
Austin Seipp 301f14e993 symbiyosys: 2018.03.21 -> 2018.05.03
Signed-off-by: Austin Seipp <aseipp@pobox.com>
2018-05-03 20:06:20 -05:00
Matthew Justin Bauer b45ef79b74
Merge pull request #39907 from matthewbauer/work
Miscellaneous cleanups
2018-05-03 13:33:42 -05:00
Matthew Bauer 143978a477 treewide: remove platform assertions
linux: readd assertion
2018-05-03 13:09:20 -05:00
R. RyanTM ef01f17c2d paml: 4.9g -> 4.9h
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/paml/versions.

These checks were done:

- built on NixOS
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 -h’ got 0 exit code
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 --help’ got 0 exit code
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 help’ got 0 exit code
- found 4.9h with grep in /nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h
- directory tree listing: https://gist.github.com/b2a37e7cd2b4b41178f0698f3aac69e2
2018-05-03 15:13:15 +02:00
Matthew Justin Bauer 5e6f1abfd3
Merge pull request #39790 from matthewbauer/gnu-on-darwin
GNUs on Darwin
2018-05-01 13:56:54 -05:00
Matthew Justin Bauer 63666bf1d5
Merge pull request #37855 from Mounium/chem3
jmol init, pymol -> 2.1.0 and tidied up all-packages.nix
2018-05-01 11:01:21 -05:00
Matthew Justin Bauer ea458f3bd7
Merge pull request #39630 from bcdarwin/conglomerate
conglomerate: init at 2017-09-10
2018-05-01 10:31:44 -05:00
Matthew Justin Bauer 278f59af49
Merge pull request #39586 from MatrixAI/labelImg
labelImg: init at 1.6.0
2018-05-01 10:24:18 -05:00
Matthew Bauer 57a4db2449 pspp: supports darwin 2018-05-01 00:45:05 -05:00
Will Dietz 4b7b083bcb treewide: stdenv.lib.platforms.gnu -> ... gnu ++ linux
Include all linux platforms.
2018-04-30 18:12:10 -05:00
R. RyanTM 4ea3841d7f picard-tools: 2.18.2 -> 2.18.3
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/picard-tools/versions.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.3 with grep in /nix/store/q67hqz7716nf3c4f8rjmlpf2dqbb06rz-picard-tools-2.18.3
- directory tree listing: https://gist.github.com/6b71ce718f18ef6a48c05457cd0e583b
2018-04-30 11:43:21 -07:00
Jörg Thalheim 68e75fbb53
Merge pull request #39577 from veprbl/pr/pythia_8.235
pythia: 8.226 -> 8.235, enable lhapdf6 plugin
2018-04-28 11:44:37 +01:00
Ben Darwin fa850e8fda conglomerate: init at 2017-09-10 2018-04-27 18:57:17 -04:00
Matthew Justin Bauer 914cc793e1
Merge pull request #39119 from veprbl/pr/sherpa_2.2.5
sherpa: 2.2.4 -> 2.2.5
2018-04-27 15:01:45 -05:00
Roger Qiu ff3b88713c labelImg: init at 1.6.0 2018-04-27 12:01:24 +10:00
Dmitry Kalinkin 2f47c93ec8
sacrifice: set LD_LIBRARY_PATH for pythia plugins to work 2018-04-26 18:19:14 -04:00
Jörg Thalheim 838db3b85d
Merge pull request #39529 from r-ryantm/auto-update/ott
ott: 0.27 -> 0.28
2018-04-26 09:14:36 +01:00
R. RyanTM 769093b867 ott: 0.27 -> 0.28
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.

These checks were done:

- built on NixOS
- ran ‘/nix/store/2lbl8zpp2lrrh9pgh2gnyhimq6i86rl1-ott-0.28/bin/ott --help’ got 0 exit code
- ran ‘/nix/store/2lbl8zpp2lrrh9pgh2gnyhimq6i86rl1-ott-0.28/bin/ott.opt --help’ got 0 exit code
- found 0.28 with grep in /nix/store/2lbl8zpp2lrrh9pgh2gnyhimq6i86rl1-ott-0.28
- directory tree listing: https://gist.github.com/177f63b8c23bae6301ced29fb0e617c4
2018-04-26 00:52:29 -07:00
Michiel Derhaeg 189a4f3656 verifast: 14.5 -> 18.02 (#39480) 2018-04-25 22:54:57 +01:00
Jörg Thalheim 18da50d8d3
Merge pull request #39503 from veprbl/pr/sacrifice_darwin_fix
sacrifice: fix runtime on darwin
2018-04-25 22:22:19 +01:00
Katona László 329d1ba69a jmol: made it runnable 2018-04-25 22:42:07 +02:00
Katona László 75d8c81868 pymol: 1.8.4 -> 2.1.0 2018-04-25 22:15:51 +02:00
Dmitry Kalinkin c1f45f76ad
sacrifice: fix runtime on darwin 2018-04-25 14:58:23 -04:00
Lancelot SIX 8d58b1a0a0
Merge pull request #39360 from lsix/update_motu
motuclient: 1.4.00 -> 1.5.00
2018-04-25 11:46:19 +02:00
Michael Raskin 1f909a8dfc
Merge pull request #39403 from timokau/maxima-exl-testfailures-2
maxima-ecl: Disable more failing tests
2018-04-24 15:44:04 +00:00
Matthew Justin Bauer d57e6466e0
Merge pull request #39377 from timokau/pari-pthread
pari: Make pthread optional, remove unstable
2018-04-24 10:03:01 -05:00
Timo Kaufmann 396b5d9c65 maxima-ecl: Disable more failing tests 2018-04-24 13:38:44 +02:00
Timo Kaufmann 75b0866d0c pari: Make pthread optional, remove unstable 2018-04-24 12:54:59 +02:00
Michael Raskin bc6f7a9ccf
Merge pull request #39370 from timokau/singular-ntl
singular: Fix ntl dependency
2018-04-24 10:54:23 +00:00
Timo Kaufmann ba389086de singular: Fix ntl dependency 2018-04-24 12:04:28 +02:00
Timo Kaufmann b707c91814 maxima-ecl: Disable failing tests 2018-04-24 11:16:55 +02:00
Peter Simons 6799fcb42b R: 3.4.4 -> 3.5.0
Unfortunately, the new version fails its test suite AGAIN when the recommended
packages are not build. Makes one wonder whether maybe we should offer the R
developers CI builds that check this. I've reported the issue upstream, let's
see what happens.
2018-04-24 09:19:13 +02:00
Matthew Justin Bauer a02d6c99af
Merge pull request #34014 from mnacamura/mathematica-l10n
mathematica: enable installation of localized editions
2018-04-23 11:58:34 -05:00
Lancelot SIX 9b5793790e
motuclient: 1.4.00 -> 1.5.00 2018-04-23 10:50:45 +02:00
Jörg Thalheim c7d278ad07
Merge pull request #39351 from matthewbauer/calc-on-darwin
calc: cleanup expression
2018-04-23 08:07:13 +01:00
Matthew Bauer 63507ada7d calc: cleanup expression
Fixes #39321

(Still needs testing on Linux)
2018-04-22 19:01:25 -05:00
Joachim F 36d58a2cd2
Merge pull request #39332 from markuskowa/octopus-up
octopus: 7.2 -> 7.3
2018-04-22 17:47:26 +00:00
Markus Kowalewski 1d0267b2e7
octopus: 7.2 -> 7.3 2018-04-22 08:43:19 -07:00
Timo Kaufmann b93e1fbbfb jmol: init at 14.29.12 2018-04-21 20:41:21 -05:00
Timo Kaufmann be0b8f2cf6 palp: init at 2.1 2018-04-21 20:40:59 -05:00
Timo Kaufmann 7dc6b2e3c3 pynac: init at 0.7.19 2018-04-21 20:40:22 -05:00
Jörg Thalheim f7785dd61c
Merge branch 'master' into minc_ecosystem 2018-04-21 20:18:27 +01:00
Jörg Thalheim 39e94277ba
Merge pull request #39197 from r-ryantm/auto-update/picard-tools
picard-tools: 2.18.1 -> 2.18.2
2018-04-21 19:21:15 +01:00
Matthew Justin Bauer 0d8e415d6b
Merge pull request #38969 from vbgl/coq-findlib
coq: fix installation of OCaml libraries
2018-04-20 18:02:52 -05:00
R. RyanTM 7d22bbe671 picard-tools: 2.18.1 -> 2.18.2
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/picard-tools/versions.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.2 with grep in /nix/store/sp6gc6c6knpvpsmfdx8074qclcsgs931-picard-tools-2.18.2
- directory tree listing: https://gist.github.com/114857d15222eccda94501b5a871fb24
2018-04-20 00:44:45 -07:00
xeji b3d50c7afa shogun: disable paralllel building
... to avoid sporadic failures
2018-04-19 12:27:00 -05:00
Matthew Justin Bauer 1bb28f26e8
Merge pull request #38810 from timokau/giac-improvements
giac: enable checks, separate outputs
2018-04-19 12:03:53 -05:00
Timo Kaufmann ddb7c0e930 lrcalc: init at 1.2 (#38755) 2018-04-19 08:42:06 +02:00
Matthew Justin Bauer 853529b2ea
Merge pull request #38740 from r-ryantm/auto-update/cytoscape
cytoscape: 3.6.0 -> 3.6.1
2018-04-18 22:20:04 -05:00
Dmitry Kalinkin 3b69e6ef1a
sherpa: 2.2.4 -> 2.2.5 2018-04-18 15:34:23 -04:00
Vincent Laporte 76a43d765c coq: 8.8+beta1 -> 8.8.0 2018-04-18 14:37:04 +02:00
Matthew Justin Bauer 88098d58f2
Merge pull request #38701 from r-ryantm/auto-update/samtools
samtools: 1.7 -> 1.8
2018-04-17 12:03:42 -05:00
Matthew Justin Bauer 1ec5b0389d
Merge pull request #36582 from ryantm/auto-update/gromacs
gromacs: 4.6.7 -> 2018
2018-04-17 10:38:06 -05:00
Jörg Thalheim 5dc7a70f65
Merge pull request #38589 from badi/tlatools
Add TLAPS and TLA+ Toolbox
2018-04-17 14:51:35 +01:00
Vladimír Čunát db071c4d1d
Merge #38702: Mark packages as broken (ZHF) 2018-04-17 13:36:20 +02:00
Badi Abdul-Wahid c4ef846c92
tlaplusToolbox: init at 1.5.6 2018-04-16 22:18:47 -04:00
Badi Abdul-Wahid d14a476054
tlaps: init at 1.4.3 2018-04-16 21:18:42 -04:00
Vincent Laporte dc4a8435f0
symbiyosys: larger meta.platforms 2018-04-16 11:47:48 +00:00
Jan Tojnar cee2c50748
celestia: clean up 2018-04-15 17:21:23 +02:00
Vincent Laporte caec7dbb9f
coq: fix installation of OCaml libraries 2018-04-15 11:24:17 +00:00
Vincent Laporte 5f97adccdc
coq: move some attributes inside passthru 2018-04-15 11:24:17 +00:00
Gabriel Ebner 9df0c12cde elan: 0.3.0 -> 0.3.2 2018-04-13 09:28:28 +02:00
xeji 6866542751 torchPackages.{sundown,lbase64}: mark as broken 2018-04-12 23:04:04 +02:00
xeji d63702a473 openmvg: mark as broken 2018-04-12 23:04:02 +02:00
Michael Raskin 783204bdbc
Merge pull request #38768 from timokau/singular-4.1.1
singular: 3.1.7 -> 4.1.1
2018-04-12 11:40:06 +00:00
Peter Simons 722d8226f4
Merge pull request #38812 from timokau/maxima-ecl
maxima: add various fixes, re-add ecl support
2018-04-12 11:43:15 +02:00
Timo Kaufmann eb119b045a maxima: add various fixes, re-add ecl support 2018-04-12 00:46:40 +02:00
Timo Kaufmann 32cf225ad9 giac: enable checks, separate outputs 2018-04-11 22:56:21 +02:00
Gabriel Ebner 99ee7fd311 elan: add leanchecker proxy 2018-04-11 19:08:22 +02:00
Gabriel Ebner a378389ac2 elan: 0.1.0 -> 0.3.0 2018-04-11 18:05:15 +02:00
Guillaume Maudoux b7dbff3aac gap-minimal: fix ofBorg evaluation 2018-04-11 17:08:54 +02:00
Timo Kaufmann fa3d0cef67 singular: 3.1.7 -> 4.1.1 2018-04-11 17:00:20 +02:00
Timo Kaufmann 6dc287802a gap: 4r8p3 -> 4r8p10 2018-04-11 15:22:03 +02:00
R. RyanTM 65e18bd38f cytoscape: 3.6.0 -> 3.6.1
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/cytoscape/versions.

These checks were done:

- built on NixOS
- ran ‘/nix/store/87clhargb10b1aps6nq86k0xz6yqyydz-cytoscape-3.6.1/bin/cytoscape -h’ got 0 exit code
- ran ‘/nix/store/87clhargb10b1aps6nq86k0xz6yqyydz-cytoscape-3.6.1/bin/cytoscape --help’ got 0 exit code
- found 3.6.1 with grep in /nix/store/87clhargb10b1aps6nq86k0xz6yqyydz-cytoscape-3.6.1
- directory tree listing: https://gist.github.com/8bad808238fc034c5394a80d8a5c1554
2018-04-11 01:12:34 -07:00
R. RyanTM c478b6217f samtools: 1.7 -> 1.8
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/samtools/versions.

These checks were done:

- built on NixOS
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/novo2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl help’ got 0 exit code
- found 1.8 with grep in /nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8
- directory tree listing: https://gist.github.com/4673ea3645eb509035dcb386c4ad1da2
2018-04-10 13:04:09 -07:00
Gabriel Ebner a14ae55c04 elan: init at 0.1.0 2018-04-10 18:38:45 +02:00
Ben Darwin de2f36982b ezminc: init at 2017-08-29 2018-04-09 18:07:15 -04:00
Ben Darwin cf2aac6a04 address license/version issues for PR #29782 2018-04-09 18:06:54 -04:00
Ben Darwin e90d1e8631 inormalize: init at 1.0.20 (develop branch) 2018-04-09 18:06:54 -04:00