Commit graph

4272 commits

Author SHA1 Message Date
Yuri Victorovich
71977f2651 science/pcmsolver: Update 1.2.1 -> 1.2.2
Reported by:	portscout
2019-01-31 04:57:30 +00:00
Yuri Victorovich
f8c9f79e5e science/py-spglib: Update 1.11.1 -> 1.12.0
Reported by:	portscout
2019-01-31 04:47:08 +00:00
Yuri Victorovich
5208f41bde New port: science/healpix: Software for pixelization, visualization, etc of data on the sphere
Approved by:	portmgr
Differential Revision:	D18548
2019-01-28 09:33:12 +00:00
Yuri Victorovich
e6fb77ce12 New port: science/nwchem-data: Data for NWChem, the computational chemistry software
Split out data from science/nwchem to facilitate flavor creation there.
2019-01-26 22:00:10 +00:00
Yuri Victorovich
6de3d6383a science/nwchem: Update 6.8.1.20181107 -> 6.8.1.20190125 2019-01-26 20:59:45 +00:00
Yuri Victorovich
a31cd20709 science/datawarrior: Update 4.7.2 -> 5.0.0
Reported by:	repology
2019-01-26 08:01:20 +00:00
Yuri Victorovich
e04f7171a8 science/py-pymatgen: Update 2018.9.30 -> 2018.10.18
Reported by:	repology
2019-01-26 06:27:42 +00:00
Yuri Victorovich
d75d088d54 science/py-gpaw: Update 1.5.0 -> 1.5.1
Reported by:	portscout
2019-01-26 05:31:44 +00:00
Yuri Victorovich
f96277716c science/cp2k: Remove contiguous blank lines 2019-01-26 05:23:51 +00:00
Yuri Victorovich
7a4ad01d7a science/cp2k: Add missing executables that should be installed 2019-01-26 05:20:14 +00:00
Mark Linimon
9d8de19218 Conditionalize the dependence of libunwind to x86-only to allow building
these ports on !x86.

libunwind is only available for x86; lang/ruby* already expresses this
correctly.  Some of the rubygems did not: for the ones that already had
USE_RUBY, the dependency was overspecified in the first place.

Tested for no-harm on amd64.

While here, pet portlint where appropriate.

Approved by:	portmgr (tier-2 blanket)
2019-01-24 05:09:48 +00:00
Mathieu Arnold
08c11c4978 Sort categories Makefiles. 2019-01-22 16:26:49 +00:00
Guido Falsi
41ff4e536e Clenup xfce ports:
- Add missing dependencies
- Remove unneeded patches
- Regenerate and rename legacy patches
- Add NLS option to ports providing such a knob, and missing the
  option
- Add INSTALL_TARGET=install-strip where missing
- Sort things
- Remove unneeded +=
- Cosmetic changes to OPTION related variables to improve readability
- Update WWW
- Silence portlint warnings about variables order
- Bump PORTREVISION where changing dependencies and/or adding
  install-strip
2019-01-22 14:44:38 +00:00
Yuri Victorovich
83536c685a science/agrum: Update 0.13.4 -> 0.13.6
Reported by:	repology
2019-01-22 03:06:25 +00:00
Yuri Victorovich
ed75b0b4f0 science/gromacs: Update 2018.4 -> 2019
Reported by:	repology
2019-01-22 02:02:15 +00:00
Yuri Victorovich
546c380f50 science/spglib: Update 1.11.2 -> 1.11.2.1
Reported by:	portscout
2019-01-21 09:26:33 +00:00
Yuri Victorovich
aa9ea3249e science/octopus: patches 2019-01-20 01:22:46 +00:00
Yuri Victorovich
37c3652c36 science/octopus: Unbundle spglib; Add OPENMP option that makes it parallelized by default 2019-01-20 01:04:39 +00:00
Tobias C. Berner
82cde37c81 science/mcstas-comps: fix RUN_DEPENDS
Approved by:	portmgr blanket
2019-01-19 09:48:16 +00:00
Antoine Brodin
b5b2da5598 Mark BROKEN: missing RUN_DEPENDS
===>   mcstas-comps-2.2a depends on file: /usr/local/mcstas/2.2a/bin/mcstas - not found

Reported by:	pkg-fallout
2019-01-19 07:17:55 +00:00
Yuri Victorovich
9fe291bb3c science/erkale: Update 0c285c1 -> 4bd3930 2019-01-18 16:25:43 +00:00
Yuri Victorovich
249fd7f792 science/py-rmsd: Fix CATEGORIES 2019-01-18 02:07:03 +00:00
Yuri Victorovich
6cee334b36 New port: science/py-rmsd: Calculate root-mean-square deviation (RMSD) between coordinate sets 2019-01-18 02:03:39 +00:00
Sunpoet Po-Chuan Hsieh
5542508c35 Add py-asdf 2.3.1
The Advanced Scientific Data Format (ASDF) is a next-generation interchange
format for scientific data. This package contains the Python implementation of
the ASDF Standard.

The ASDF format has the following features:
- A hierarchical, human-readable metadata format (implemented using YAML)
- Numerical arrays are stored as binary data blocks which can be memory mapped.
  Data blocks can optionally be compressed.
- The structure of the data can be automatically validated using schemas
  (implemented using JSON Schema)
- Native Python data types (numerical types, strings, dicts, lists) are
  serialized automatically
- ASDF can be extended to serialize custom data types

WWW: https://github.com/spacetelescope/asdf
2019-01-17 19:21:25 +00:00
Yuri Victorovich
f61a4ea522 New port: science/erkale-pseudopotentials: Pseudopotentials for Erkale, the quantum chemistry program 2019-01-17 09:42:53 +00:00
Yuri Victorovich
26eefa7fb5 science/erkale: Update 0927d8c -> 0c285c1
Port changes:
* Add the standard location for erkale's pseudopotentials.
* Add pkg-message suggesting to install erkale-pseudopotentials
2019-01-17 09:40:24 +00:00
Yuri Victorovich
7463d93b02 science/py-OpenFermion: Update 0.8 -> 0.9.0
Reported by:	portscout
2019-01-17 06:31:46 +00:00
Yuri Victorovich
a750ea6346 science/lm: Do not set VMD_VARS twice
PR:		234747
Reported by:	tobik
2019-01-17 06:24:51 +00:00
Yuri Victorovich
b3c58e4521 science/coot: Remove the unused CONFIGURE_ARGS line
PR:		234737
Reported by:	tobik
2019-01-17 05:59:38 +00:00
Yuri Victorovich
f0427f8df6 science/vipster: Update 1.14a -> 1.14.1a
This should fix build failures due to wrong STL headers.
2019-01-16 18:22:23 +00:00
Tijl Coosemans
1bf487d3e7 Fix Qt5 symbol version scripts to put the catch-all clause first. When
a symbol matches multiple clauses the last one takes precedence.  If the
catch-all is last it captures everything.  In the case of Qt5 libraries
this caused all symbols to have a Qt_5 label while some should have
Qt_5_PRIVATE_API.  This only affects lld because GNU ld always gives the
catch-all lowest priority.

Older versions of Qt5Webengine exported some memory allocation symbols from
the bundled Chromium.  Version 5.9 stopped exporting these [1] but the
symbols were kept as weak wrappers for the standard allocation functions to
maintain binary compatibility. [2][3]  The problem is that the call to the
standard function in these weak wrappers is only resolved to the standard
function if there's a call to this standard function in other parts of
Qt5Webengine, because only then is there a non-weak symbol that takes
precedence over the weak one.  If there's no such non-weak symbol the call
in the weak wrapper resolves to the weak wrapper itself creating an infinite
call loop that overflows the stack and causes a crash.  Some of the
allocation functions are variants of C++ new and delete and it probably
depends on the compiler whether these variants are used in other parts of
Qt5Webengine.

Remove the weak wrappers (make them Linux specific).  This isn't binary
compatible but we are already breaking that with the changes to the symbol
versions.

[1] 5c2cbfccf9
[2] 2ed5054e3a
[3] 009f5ebb4b

Bump all ports that depend on Qt5.

PR:		234070
Exp-run by:	antoine
Approved by:	kde (adridg)
2019-01-16 11:13:44 +00:00
Yuri Victorovich
98b078ed4d science/tinker: Update 8.4.4 -> 8.5.3
Reported by:	portscout
2019-01-16 04:36:12 +00:00
Yuri Victorovich
1b54784efc science/py-gpaw: Update 1.4.0 -> 1.5.0
Reported by:	portscout
2019-01-15 18:29:45 +00:00
Yuri Victorovich
d9430feacb science/bagel: Update 1.2.1 -> 1.2.2 2019-01-15 18:27:47 +00:00
Jose Alonso Cardenas Marquez
49e853cd3d - Add LLD_UNSAFE
PR:		214864
2019-01-15 05:44:58 +00:00
Jose Alonso Cardenas Marquez
846470de89 - Add LLD_UNSAFE
PR:		214864
2019-01-15 05:43:59 +00:00
Tobias Kortkamp
2e3378cde0 Cleanup RLN usage
RLN is based on install(1) and -s means "run strip(1) on the installed
binary".  install(1) ignores -s when it makes a link, so it "works"
now instead of failing when it links non-binaries.
2019-01-14 14:05:39 +00:00
Steve Wills
0dfb1596dd science/mcstas: update to 2.5
While here, update LICENSE, clean up, pet portlint

PR:		234589
Submitted by:	Erik B Knudsen <erkn@fysik.dtu.dk> (maintainer)
2019-01-14 13:02:57 +00:00
Wen Heping
eb55bf7954 - Update to 0.9.3
- Take maintainership
2019-01-14 03:26:29 +00:00
Sunpoet Po-Chuan Hsieh
8634eafdb9 Remove outdated document
- Bump PORTREVISION for package change
2019-01-13 20:25:41 +00:00
Sunpoet Po-Chuan Hsieh
988707b887 Update to 4.4.5
Changes:	https://github.com/Unidata/netcdf-fortran/releases
2019-01-13 20:08:15 +00:00
Sunpoet Po-Chuan Hsieh
dd30bd4544 Change MASTER_SITES 2019-01-13 20:08:10 +00:00
Sunpoet Po-Chuan Hsieh
f983c40255 Update to 4.6.2
Changes:	https://github.com/Unidata/netcdf-c/releases
		https://github.com/Unidata/netcdf-c/blob/master/RELEASE_NOTES.md
2019-01-13 20:08:05 +00:00
Ruslan Makhmatkhanov
555634eec2 science/py-lifelines: update to 0.17.0 2019-01-13 18:19:07 +00:00
Mark Linimon
901513498c USES=compiler:c++11-lang is necessary to build this port on GCC-based
architectures.

PR:		234373
Submitted by:	Piotr Kubaj
Approved by:	maintainer
2019-01-13 02:18:22 +00:00
Mark Linimon
0fc750a4ce This port requires USES=compiler:c++11-lang to build on GCC-based
architectures.

PR:		234355
Submitted by:	Piotr Kubaj
Approved by:	maintainer
2019-01-12 23:32:09 +00:00
Tobias C. Berner
7ee9c5458d Update KDE Applications to 18.12.1
Release Announcement:
	https://www.kde.org/announcements/announce-applications-18.12.1.php

Today KDE released the first stability update for KDE Applications 18.12.
This release contains only bugfixes and translation updates, providing a
safe and pleasant update for everyone.

About 20 recorded bugfixes include improvements to Kontact, Cantor, Dolphin,
JuK, Kdenlive, Konsole, Okular, among others.

Improvements include:
  *  Akregator now works with WebEngine from Qt 5.11 or newer
  *  Sorting columns in the JuK music player has been fixed
  *  Konsole renders box-drawing characters correctly again

You can find the full list of changes here:
	https://www.kde.org/announcements/fulllog_applications-aether.php?version=18.12.1
2019-01-10 19:52:57 +00:00
Yuri Victorovich
73e341e267 science/agrum: Simplify PLIST_SUB
Reported by:	mat
2019-01-09 19:42:50 +00:00
Yuri Victorovich
6a66c47692 science/agrum: Simplify PLIST_SUB 2019-01-09 11:11:01 +00:00
Yuri Victorovich
2324f72911 science/agrum: Fix build for python 3.x
PR:		234780
Reported by:	antoine
2019-01-09 11:04:37 +00:00