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1052 Commits

Author SHA1 Message Date
Timo Kaufmann
a4c76b970c gap: use the check target for install checks 
As suggested by Max Horn.

This exists since gap 4.10 and will only run the install checks once
while also exiting with an appropriate exit code. This new check has
uncovered some test failures, which are harmless and actually disabled
in a future gap release. The error-detection code for the previous test
target was probably broken.
 2020-05-28 15:50:46 +02:00
Timo Kaufmann
b74991703a palp: fix hash 
The file was modified for the second time now. I'll try to contact
upstream about this. Maybe 2.11 is not actually a finished product yet.
 2020-05-28 00:20:30 +02:00
Mario Rodas
d30b7592c4
Merge pull request #88363 from r-ryantm/auto-update/clp 
clp: 1.17.5 -> 1.17.6
 2020-05-23 00:31:57 -05:00
Timo Kaufmann
b811d52b9c
Merge pull request #88428 from timokau/nauty-27r1 
nauty: 26r12 -> 27r1
 2020-05-20 13:22:15 +00:00
Timo Kaufmann
d0e171395a nauty: 26r12 -> 27r1 
Changes: http://pallini.di.uniroma1.it/changes24-27.txt
 2020-05-20 14:59:46 +02:00
Timo Kaufmann
a276c4485c nauty: add meta.changelog 2020-05-20 14:59:46 +02:00
R. RyanTM
d1b7e3f8cc clp: 1.17.5 -> 1.17.6 2020-05-20 10:04:01 +00:00
Timo Kaufmann
aae9af9632 palp: fix hash 
It looks like the upstream tarball was changed since I updated palp 3
days ago. Hopefully that won't happen again.
 2020-05-19 17:50:43 +02:00
Timo Kaufmann
d65850e975 palp: 2.1 -> 2.11 
According to the homepage[1]:

> Small change in Mori.h for compatibility with gcc_10 (thanks to J.
  Puydt) [May 15, 2020].

Disabling the strictoverflow seems to be no longer necessary (I'm
relying on the check phase here).

[1] http://hep.itp.tuwien.ac.at/~kreuzer/CY/CYpalp.html
 2020-05-16 15:07:57 +02:00
Timo Kaufmann
51de320353 palp: add meta.changelog 2020-05-16 15:05:45 +02:00
R. RyanTM
e07dfd38f1 wxmaxima: 20.02.4 -> 20.04.0 2020-05-12 22:12:53 -07:00
albakham
0c0f353d62 rofi-calc: 1.6 -> 1.7 2020-05-08 22:12:49 -04:00
Doron Behar
53effac040 mathematica: explicitly use opencv2 2020-05-05 13:48:55 +03:00
R. RyanTM
a930faab93 mxnet: 1.4.1 -> 1.6.0 2020-05-02 10:17:38 +02:00
Timo Kaufmann
7866440f12
Merge pull request #86274 from samlich/sage-matrix-double-dense 
sage: fix doctest matrix_double_dense is_unitary
 2020-05-01 22:12:10 +00:00
Peter Simons
205e4dffd5
Merge pull request #86081 from jabranham/update-r 
R: 3.6.3 --> 4.0.0 & update packages
 2020-05-01 20:25:14 +02:00
samlich
c0bd938e5c
sage: fix doctest matrix_double_dense is_unitary 2020-05-01 16:04:23 +00:00
Jan Tojnar
e89e2edc73
libusb-compat-0_1: rename from libusb 2020-04-28 05:33:41 +02:00
Alex Branham
8ce6552d64
R: 3.6.3 -> 4.0.0 2020-04-26 17:06:07 -04:00
Matthew Bauer
ff2f2644f8 blas,lapack: use isILP64 instead of is64bit 
This is a better name since we have multiple 64-bit things that could
be referred to.

LP64  : integer=32, long=64, pointer=64
ILP64 : integer=64, long=64, pointer=64
 2020-04-20 16:02:43 -05:00
Matthew Bauer
97fc083fd4 giac: broken on 64-bit blas 2020-04-17 16:24:31 -05:00
Matthew Bauer
1c8aba8334 treewide: use blas and lapack 
This makes packages use lapack and blas, which can wrap different
BLAS/LAPACK implementations.

treewide: cleanup from blas/lapack changes

A few issues in the original treewide:

- can’t assume blas64 is a bool
- unused commented code
 2020-04-17 16:24:09 -05:00
worldofpeace
433ea74af1 nasc: fix build 2020-04-15 17:19:47 -04:00
AndersonTorres
3b91c3de8f gp2c: 0.0.11pl2 -> 0.0.11pl3 2020-04-15 00:45:28 -03:00
Benjamin Hipple
17a1bf5dbd
Merge pull request #85069 from r-ryantm/auto-update/ginac 
ginac: 1.7.8 -> 1.7.9
 2020-04-12 11:18:43 -04:00
R. RyanTM
9b5aad0644 ginac: 1.7.8 -> 1.7.9 2020-04-12 12:04:38 +00:00
Michael Reilly
84cf00f980
treewide: Per RFC45, remove all unquoted URLs 2020-04-10 17:54:53 +01:00
Timo Kaufmann
b72fd98789
Merge pull request #84666 from jonringer/repofy-palp 
palp: correct metadata for repology
 2020-04-08 11:44:33 +00:00
Gabriel Ebner
e71c0d80a1
Merge pull request #84583 from r-ryantm/auto-update/qalculate-gtk 
qalculate-gtk: 3.8.0 -> 3.8.0a
 2020-04-08 11:01:33 +02:00
Jonathan Ringer
f89b76d9db
palp: correct metadata for repology 2020-04-07 14:08:03 -07:00
R. RyanTM
67ea5a0081 qalculate-gtk: 3.8.0 -> 3.8.0a 2020-04-07 10:29:32 +00:00
R. RyanTM
b43965986f gmsh: 4.5.4 -> 4.5.6 2020-04-05 19:28:16 +00:00
Timo Kaufmann
83fd89945d
Merge pull request #79661 from luc65r/pkg/cemu 
cemu: init at 1.3
 2020-03-31 15:17:33 +00:00
luc65r
8edd400bfb
rofi-calc: init at 1.6 (#83136) 
Also:
* maintainers: add albakhamj
* maintainers: add luc65r
* rofi: add plugins argument to wrapper

Co-authored-by: Maciej Krüger <mkg20001@gmail.com>
 2020-03-30 01:18:56 +02:00
Guanpeng Xu
d2702c915f mathematica: 12.0.0 -> 12.1.0 2020-03-29 14:38:33 +02:00
Frederik Rietdijk
5175c35a99
Merge pull request #81611 from r-ryantm/auto-update/R 
R: 3.6.2 -> 3.6.3
 2020-03-14 14:29:05 +01:00
wucke13
c24b9a57c4 getdp: 3.0.4 -> 3.3.0 2020-03-13 04:10:20 +00:00
Maximilian Bosch
76821e6f43
geogebra: 5-0-573-0 -> 5-0-574-0 2020-03-12 18:12:57 +01:00
Timo Kaufmann
ba589e24c9 sage: patch for pari 2.11.3 2020-03-12 12:24:41 +01:00
Timo Kaufmann
c4ab541443 pari: backport bug fix 
https://trac.sagemath.org/ticket/29313#comment:4
 2020-03-12 12:24:35 +01:00
xaverdh
5ac085c3cc
wxmaxima: 18.02.0 -> 20.02.4 (#82323) 
The commit description is 18.02.0 -> 20.02.4, because in the last version bump (1c6a193b3e), the version string was changed, but the hash was not.

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

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

Regarding the licensing change:

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

faedcc48cc

Unfortunately it doesn't apply cleanly and isn't worth the effort
of backporting. Let's hope we can switch to python3 sage and the recent
sphinx version that comes with it before this becomes a problem.
 2020-03-10 13:15:41 +01:00
Timo Kaufmann
63ed2bf3c3
Merge pull request #81950 from r-ryantm/auto-update/pari 
pari: 2.11.2 -> 2.11.3
 2020-03-09 17:31:14 +00:00
R. RyanTM
e6f5bb8dc4 qalculate-gtk: 3.7.0 -> 3.8.0 2020-03-08 00:14:22 +00:00
R. RyanTM
6528554396 pari: 2.11.2 -> 2.11.3 2020-03-07 02:43:40 +00:00
R. RyanTM
9974067129 gmsh: 4.5.2 -> 4.5.4 2020-03-05 00:20:08 +00:00
R. RyanTM
faa5c3bde3 R: 3.6.2 -> 3.6.3 2020-03-03 11:34:22 +00:00
Timo Kaufmann
f4dbf4402b
Merge pull request #80759 from Thra11/fix-r 
Fix R
 2020-02-23 23:48:21 +00:00
Tom Hall
ae9e09a2e1 R: fix build on aarch64 by removing a failing test 
I believe this test is currently incorrect on aarch64 and expects a
warning about loss of precision with much smaller numbers than the
platform's long doubles can handle.
 2020-02-22 13:17:40 +00:00
Maximilian Bosch
7bdc103ac8
geogebra: 5-0-570-0 -> 5-0-573-0 2020-02-20 03:09:06 +01:00
Tom Hall
4e5aeca90b R: Enable java support on all platforms 2020-02-19 22:57:41 +00:00
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
Frederik Rietdijk
03755ed59a Merge master into staging-next 2020-02-09 09:17:51 +01:00
R. RyanTM
7c58b6437b gmsh: 4.5.1 -> 4.5.2 2020-02-08 07:25:27 +00:00
Maximilian Bosch
abefd4f78a
pspp: 1.0.1 -> 1.2.0, fix build w/glibc-2.30 2020-01-30 15:19:44 +01:00
Frederik Rietdijk
dce0ca29d9 Merge master into staging-next 2020-01-28 10:46:13 +01:00
Gabriel Ebner
8161fe21e0 qalculate-gtk: 3.6.0 -> 3.7.0 2020-01-26 18:43:29 +01:00
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
Luka Blaskovic
991a7e041f pcalc: build with bison3 2020-01-13 21:35:19 +00:00
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
Maximilian Bosch
8a6baaecb5
geogebra: 5-0-569-0 -> 5-0-570-0 2020-01-07 23:26:31 +01:00
R. RyanTM
66156e04d5 gmsh: 4.4.1 -> 4.5.1 2020-01-06 06:33:28 -08:00
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
Merijn Broeren
133103d709
treewide: replace make/build/configure/patchFlags with nix lists 2019-12-30 12:58:11 +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
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
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
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
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
Timo Kaufmann
5c9000014e
Merge pull request #74945 from timokau/sage-no-timeout 
sage: disable test timeout
 2019-12-04 09:55:34 +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
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
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
Guanpeng Xu
66d5277375 mathematica: fix version issue with zlib (#73425) 2019-11-14 17:19:30 -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
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
Gabriel Ebner
a4f0bfdc87 qalculate-gtk: 3.4.0 -> 3.5.0 2019-11-02 10:54:10 +01:00
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
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
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
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
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