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4529 Commits

Author SHA1 Message Date
Guido Falsi
ad1ecbc81b - Simplify XFCE MASTER_SITES usage 
- Update XFCE Master sites list

Submitted by:		olivierd
Reviewed by:		mat
Approved by:		portmgr (mat)
Differential Revision:	https://reviews.freebsd.org/D8416
 2019-06-19 16:14:27 +00:00
Yuri Victorovich
e77c7663ca science/py-qcengine: Update 0.6.4 -> 0.7.1 
Reported by:	portscout
 2019-06-19 08:15:53 +00:00
Yuri Victorovich
4de4161b08 science/py-qcelemental: Update 0.4.1 -> 0.4.2 
Reported by:	portscout
 2019-06-19 08:14:24 +00:00
Jason W. Bacon
6be8fa3bb2 science/afni: Upgrade to 19.1.20 
Upstreamed FreeBSD patches, other minor fixes and enhancements

Reported by:    portscout, Rick Reynolds (NIH)
 2019-06-18 19:00:55 +00:00
Mark Linimon
4b97875495 Add compiler:c++11-lang to USES to fix the following on GCC-based systems: 
/usr/local/lib/libgraphite2.so.3: undefined reference to `__cxa_throw_bad_array_new_length@CXXABI_1.3.8'

Approved by:	portmgr (tier-2 blanket)
 2019-06-17 11:39:30 +00:00
Antoine Brodin
e19903f0ae Clean up LIB_DEPENDS 2019-06-16 16:05:28 +00:00
Yuri Victorovich
1d0afd2ae4 science/gromacs: Update 2019.2 -> 2019.3 
Reported by:	portscout
 2019-06-15 19:35:27 +00:00
Yuri Victorovich
d90385ba3c science/qbox: Update 1.67.1 -> 1.67.2 
Reported by:	portscout
 2019-06-13 09:04:51 +00:00
Pietro Cerutti
ac5da5db90 science/jstrack: remove meaningless 85+ from USES tk 2019-06-12 16:16:10 +00:00
Sunpoet Po-Chuan Hsieh
7352189e45 Update to 1.9.7 
Changes:	https://code.mpimet.mpg.de/news/445
 2019-06-11 20:19:26 +00:00
Sunpoet Po-Chuan Hsieh
46e9786119 Update to 4.1.2 
Changes:	https://bitbucket.org/levitsky/pyteomics/src/default/CHANGELOG
		https://pyteomics.readthedocs.io/en/latest/changelog.html
 2019-06-09 16:52:36 +00:00
Yuri Victorovich
9e7fd269f9 science/lammps: Add the PORTSCOUT=ignore line 2019-06-09 04:22:37 +00:00
Yuri Victorovich
de69d47ef7 New port: science/smoldyn: Biochemical simulator for molecular diffusion, surface interactions 2019-06-09 03:26:15 +00:00
Piotr Kubaj
4842639ea0 science/nifticlib: fix build 
Add MAKE_JOBS_UNSAFE=yes to fix build:
nifti_stats.c:2:22: error: nifticdf.h: No such file or directory
nifti_stats.c: In function 'main':
nifti_stats.c:30: error: 'inam' undeclared (first use in this function)
nifti_stats.c:30: error: (Each undeclared identifier is reported only once
nifti_stats.c:30: error: for each function it appears in.)

Approved by:	mat (mentor)
Differential Revision:	https://reviews.freebsd.org/D20500
 2019-06-08 19:24:18 +00:00
Jason W. Bacon
97b12f97b4 science/afni: Upgrade to 19.1.18 
Minor bugfixes/enhancements
 2019-06-08 19:14:18 +00:00
Yuri Victorovich
100912bdfb science/nwchem: Update 6.8.1.20190509 -> 6.8.1.20190606 2019-06-08 07:54:52 +00:00
Sunpoet Po-Chuan Hsieh
7100b05254 Update to 0.9.1 
Changes:	https://github.com/ecmwf/eccodes-python/blob/master/CHANGELOG.rst
 2019-06-07 23:04:38 +00:00
Yuri Victorovich
7f98aa57a0 science/lammps: Update 31May2019 -> 5Jun2019 
Approved by:	portscout
 2019-06-07 06:08:02 +00:00
Yuri Victorovich
0585d1c554 science/jmol: Update 14.29.42 -> 14.29.46 
Reported by:	portscout
 2019-06-07 05:59:51 +00:00
Tobias C. Berner
f240baeb83 Update KDE Applications to 19.04.2 
https://kde.org/announcements/announce-applications-19.04.2.php
 2019-06-07 04:08:25 +00:00
TAKATSU Tomonari
2885da0f8f - Update to 1.7-1 2019-06-02 07:44:51 +00:00
Stephen Montgomery-Smith
6685c898dd - Update devel/gdcm to 3.0.0. 
- Bump portrevision of dependent ports.
 2019-06-01 21:59:13 +00:00
Jason W. Bacon
144c4feb7d science/afni: Upgrade to 19.1.14 
Minor bug fixes and enhancements, some FreeBSD patches upstreamed
 2019-06-01 12:59:52 +00:00
Yuri Victorovich
0e443ebe39 science/py-qcelemental: Update 0.4.0 -> 0.4.1 
Reported by:	portscout
 2019-06-01 06:01:52 +00:00
Yuri Victorovich
f474e5deed science/lammps: Update 15May2019 -> 31May2019 
Reported by:	GitHub release notification
 2019-05-31 19:32:00 +00:00
Antoine Brodin
1f01284469 Chase devel/openmp expiration 2019-05-27 20:55:56 +00:00
Yuri Victorovich
7af6138dd6 science/py-rmsd: Fix license 
PR:		238134
Reported by:	tobik
 2019-05-26 18:17:15 +00:00
Yuri Victorovich
62e00b1db5 New port: science/opensph: Library and graphical tools for running SPH and N-body simulations 2019-05-26 04:08:09 +00:00
Sunpoet Po-Chuan Hsieh
218bf57515 Update to 4.1.1 
Changes:	https://pyteomics.readthedocs.io/en/latest/changelog.html
 2019-05-25 22:03:25 +00:00
Sunpoet Po-Chuan Hsieh
70d0371995 Update to 2.12.5 
Changes:	https://confluence.ecmwf.int/display/ECC/Latest+news
 2019-05-25 22:02:44 +00:00
Sunpoet Po-Chuan Hsieh
b4a96957bc Add py-eccodes-python 0.9.0 
Python 3 interface to encode and decode GRIB and BUFR files via the ECMWF
ecCodes library.

Features:
- reads and writes GRIB 1 and 2 files,
- reads and writes BUFR 3 and 4 files,
- supports all modern versions of Python 3.7, 3.6, 3.5 and PyPy3,
- works on most Linux distributions and MacOS, the ecCodes C-library is the only
  system dependency,
- PyPI package with no install time build (binds with CFFI ABI level, in-line
  mode),
- supports writing the index of a GRIB file to disk, to save a full-file scan on
  open.

WWW: https://github.com/ecmwf/eccodes-python
 2019-05-25 22:02:27 +00:00
Yuri Victorovich
e0b5281b58 science/py-GPy: Fix build by explicitly setting the path to libomp.so in xx_DEPENDS lines 
Reported by:	fallout
 2019-05-23 21:21:49 +00:00
Jason W. Bacon
73eb992926 science/afni: Upgrade to 19.1.10 
Rapid response from upstream on reported issue.  Additional patches to be
upstreamed in next release.
 2019-05-22 12:44:17 +00:00
Piotr Kubaj
9b1f148f09 science/wxmacmolplt: fix build with GCC-based architectures 
Add USES=compiler:c++11-lang to fix linking:
checking for wxWidgets libraries... not found

Approved by:	mentors (implicit approval)
 2019-05-20 20:09:32 +00:00
Jason W. Bacon
ade7919150 science/afni: Upgrade to 19.1.08 
Switch from personal dist snapshots to Github releases
Improve staging procedure to preserve results of build phase
Temporarily use bundled GLw pending fix of libglw port
 2019-05-20 19:35:57 +00:00
Thierry Thomas
b3a0da2461 Switch to Python 3.6 and upgrade to v5.3.3. 
Note: Code_Saturne does not run with Qt5 in combination with Python 2.7.
See <https://github.com/code-saturne/code_saturne/issues/44>.
 2019-05-19 19:22:45 +00:00
Yuri Victorovich
a60337fb4e science/py-phono3py: Fix build on 12/13 (broken due to missing libgomp.so); Add USES=blaslapack:openblas 
libgomp.so was found in gcc8, which this ports doesn't explicitly depend on,
and openmp wasn't installed but the build was failing later on 12 due to the
lack of libgomp.so.

Solution: Move openmp dependency from LIB_DEPENDS to BUILD_DEPENDS/RUN_DEPENDS.

Reported by:	Gleb Popov <6yearold@gmail.com> (USES=blaslapack:openblas)
 2019-05-19 16:48:08 +00:00
Yuri Victorovich
749b46c96b science/abinit: Fix libomp.so in LDFLAGS (this also might fix the breakage on 13) 
Reported by:	fallout
 2019-05-19 03:01:48 +00:00
Yuri Victorovich
d95813f563 science/dftbplus: Fix libomp.so in LDFLAGS (this also might fix the breakage on 13) 2019-05-19 02:47:01 +00:00
Yuri Victorovich
771d3b45a5 science/py-phono3py: Unbreak on 13: /usr/lib/libomp.so conflicting with the 'openmp' package has been added to 13-CURRENT 
Reported by:	fallout
 2019-05-19 02:40:34 +00:00
Yuri Victorovich
0a3ad2a5f4 science/gabedit: Unbreak on 13: /usr/lib/libomp.so conflicting with the 'openmp' package has been added to 13-CURRENT 
Reported by:	fallout
 2019-05-19 02:38:14 +00:00
Yuri Victorovich
34c0e7d61e science/py-GPy: Unbreak on 13: /usr/lib/libomp.so conflicting with the 'openmp' package has been added to 13-CURRENT 
Reported by:	fallout
 2019-05-19 02:35:46 +00:00
Yuri Victorovich
1837418d06 science/openmx: Unbreak on 13: /usr/lib/libomp.so conflicting with the 'openmp' package has been added to 13-CURRENT 
LIB_DEPENDS=libomp.so:devel/openmp now causes this problem in multiple ports.

Reported by:	fallout
 2019-05-19 02:24:59 +00:00
Yuri Victorovich
c17f9e6a78 science/esys-particle: Broken on 13-CURRENT 
Reported by:	fallout
 2019-05-18 22:58:19 +00:00
Yuri Victorovich
7d0e3eaf2a science/chrono: Broken on i386 
Reported by:	fallout
 2019-05-18 22:28:29 +00:00
Yuri Victorovich
d7cca70b67 science/nest: Broken on i386 
Reported by:	fallout
 2019-05-18 22:12:49 +00:00
Yuri Victorovich
72a5a25bc9 science/py-paramz: Update 0.9.4 -> 0.9.5 
Reported by:	portscout
 2019-05-18 15:56:47 +00:00
Yuri Victorovich
b399938765 New port: science/libvdwxc: Van der Waals density functional (DFT) library 2019-05-18 05:40:31 +00:00
Yuri Victorovich
e9a104fd10 New port: science/simgrid: Simulator of the behavior of large-scale distributed systems 2019-05-16 16:00:15 +00:00
Yuri Victorovich
2c32727d61 science/lammps: Update patch_30Apr2019 -> patch_15May2019 
Reported by:	github notification
 2019-05-15 04:29:09 +00:00