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4545 Commits

Author SHA1 Message Date
Yuri Victorovich
c517ce256e science/h5z-zfp: Update 0.9.0 -> 1.0.1 
Reported by:	portscout
 2019-06-30 08:34:58 +00:00
Piotr Kubaj
f5f826f007 science/py-MDAnalysis: fix build 
Add USES=compiler:c++11-lang to fix:
cc1plus: error: unrecognized command line option "-std=c++11"

Approved by:	mentors (implicit approval)
 2019-06-29 10:28:48 +00:00
Tobias Kortkamp
3726f94254 Convert all Go ports to USES=go 
This allows for port testing with lang/go-devel via GO_PORT, setting
up the Go build environment in a single place, and is step one in
simplifying Go ports that often define too complicated do-build
targets themselves.

USES=go gains new arguments 'run' to add lang/go to RUN_DEPENDS and
'no_targets' for ports with composite builds that call 'go' themselves
and do not need the do-build/do-install targets of USES=go.

PR:		238849
Submitted by:	dg@syrec.org (also D20745)
Reviewed by:	mat, tobik
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20746
 2019-06-29 03:51:13 +00:00
Yuri Victorovich
6fd3cb6c9a science/nest: Update 2.16.0 -> 2.18.0 
Reported by:	portscout
 2019-06-28 09:10:18 +00:00
Mathieu Arnold
08bc95f4c0 Remove dupplicate port. 
Pointy hat:	yuri
 2019-06-28 06:57:09 +00:00
Yuri Victorovich
0d19872a61 science/py-phonopy: Update 2.1.3 -> 2.1.4 
Reported by:	portscout
 2019-06-28 05:04:05 +00:00
Yuri Victorovich
8bc4dee0ff science/atompaw: Update 4.1.0.5 -> 4.1.0.6 
Reported by:	portscout
 2019-06-28 04:52:35 +00:00
Yuri Victorovich
8e5eb0b6f8 New port: science/molden: Program for molecular and electronic structure visualization 2019-06-28 03:51:26 +00:00
Sunpoet Po-Chuan Hsieh
b98ac213c1 Cosmetic change 2019-06-27 20:03:54 +00:00
Sunpoet Po-Chuan Hsieh
1b91103fe7 Update graphics/libgeotiff to 1.5.1 
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/OSGeo/libgeotiff/blob/master/libgeotiff/NEWS
		https://lists.osgeo.org/pipermail/geotiff/2019-March/000861.html
		https://lists.osgeo.org/pipermail/geotiff/2019-March/000862.html
 2019-06-27 19:57:33 +00:00
Alexey Dokuchaev
3186e08e7c Update Guile to version 2.2.5, modern stable version, and fix dependent 
ports to build against it.  Most changes are rather minor and mechanical
except for the devel/gdb (obtained via their bugtracker [1], courtesy of
Doug Evans).  One port (science/meep) I had to mark BROKEN after fixing
it proved to be very tedious and actually unreliable.  It is very old,
there are newer versions available so it should be fixed by updating.

One port (devel/libruin) had revealed a bug in the new Guile code (an
auxiliary script, really) that had to be worked-round; reference to the
problematic upstream commit is provided in the patch.

PR:		229613
Exp-run by:	antoine

[1] https://sourceware.org/bugzilla/show_bug.cgi?id=21104#c8
 2019-06-27 09:02:56 +00:00
Wen Heping
3d23ba68ab - Update to 6.1.0 and fix some ports 
- Add missing DEPENDS
- Add TEST_TARGET
- Take maintainership

PR:		237932, 238795
Submitted by:	wenheping2000@hotmail.com,rhurlin@gwdg.de
Approved by:	maintainer(timeout, > 30 days), portmgr@(implicit, fix build)
Exp-run by:	antoine@
Thanks to:	antoine@, sunpoet@, rhurlin@gwdg.de
 2019-06-27 03:37:10 +00:00
Sunpoet Po-Chuan Hsieh
4f1d0ee1ec Update to 1.5.3 
Changes:	https://github.com/Try2Code/cdo-bindings/blob/master/README.md#changelog
		https://github.com/Try2Code/cdo-bindings/commits/master
 2019-06-25 20:52:05 +00:00
Tobias C. Berner
4196590fa5 KDE Applications: complete dependency lists 
This has been on the TODO list for forever...

PR:		238764
Reported by:	yuri
 2019-06-23 15:39:32 +00:00
Sunpoet Po-Chuan Hsieh
d12f07dc24 Update to 0.113 
Changes:	https://metacpan.org/changes/distribution/Geo-WebService-Elevation-USGS
 2019-06-22 21:50:07 +00:00
Yuri Victorovich
5204c782ce science/qbox: Update 1.67.2 -> 1.67.4 2019-06-20 22:06:56 +00:00
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