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4476 commits

Author SHA1 Message Date
Yuri Victorovich
a3fee0ff6d science/nest: Update 2.14.0-2100 -> 2.16.0 
Reported by:	portscout
 2019-05-12 08:24:10 +00:00
Mathieu Arnold
5944e9ef33 Cleanup cython dependency. 2019-05-11 21:10:31 +00:00
Yuri Victorovich
81a5212217 science/nest: PYTHON_USE=python=cython instead of PYTHON_BUILD_DEPENDS 
Reported by:	mat
 2019-05-11 21:01:54 +00:00
Yuri Victorovich
85cb72892b science/coot: Fix build with GCC-based architectures 
PR:		237842
Submitted by:	pkubaj
 2019-05-11 20:40:33 +00:00
Piotr Kubaj
1f4241358e science/clipper: add USES=compiler:c++11-lang 
This is needed to build science/coot.

Approved by:	mentors (implicit approval)
 2019-05-11 20:30:19 +00:00
Yuri Victorovich
5e8b580aa9 New port: science/nest: Simulator for spiking neural network models 2019-05-11 20:29:56 +00:00
Yuri Victorovich
e721b925ab science/avogadrolibs: Update 1.92.0 -> 1.92.1 2019-05-11 18:10:31 +00:00
Antoine Brodin
ef73356c19 Those ports link against llvm's libomp.so 2019-05-11 09:36:21 +00:00
Yuri Victorovich
20a2b516de science/opsin: Update 3.0.20190208 -> 3.0.20190223 2019-05-11 06:00:09 +00:00
Yuri Victorovich
25a7016bf4 science/nwchem: Update 6.8.1.20190412 -> 6.8.1.20190509 2019-05-11 03:41:13 +00:00
Yuri Victorovich
3b5fce1f01 science/agrum: Update 0.14.3 -> 0.15.0 
Reported by:	portscout
 2019-05-10 06:15:21 +00:00
Yuri Victorovich
e0083390a0 science/py-gpaw: Update 1.5.1 -> 1.5.2 
Reported by:	portscout
 2019-05-09 20:12:51 +00:00
Piotr Kubaj
3edb29c651 science/luscus: fix build with GCC-based architectures 
Add USES=compiler:c++11-lang to fix linking:
/usr/local/lib/libgraphite2.so.3: undefined reference to `__cxa_throw_bad_array_new_length@CXXABI_1.3.8'

Approved by:	mentors (implicit approval)
 2019-05-09 19:59:20 +00:00
Tobias C. Berner
d27fcc13c5 Update KDE Applications to 19.04.1 
Changelog:
	https://kde.org/announcements/fulllog_applications-aether.php?version=19.04.1
 2019-05-09 18:18:04 +00:00
Jan Beich
3b1a1bcee4 devel/openmp: phase out 
- Expire after the last version without /usr/lib/libomp.so
- Drop SOVERSION for seamless transition (i.e., avoid conditionals)

PR:		236907
Approved by:	bapt (maintainer)
Differential Revision:	https://reviews.freebsd.org/D19767
 2019-05-08 16:05:53 +00:00
Yuri Victorovich
bab17abceb science/py-phonopy: Update 2.0.0 -> 2.1.3 2019-05-08 06:35:50 +00:00
Yuri Victorovich
2084646704 science/py-phonopy: 1.13.2.107 -> 2.0.0 2019-05-08 06:11:16 +00:00
Yuri Victorovich
68197f1a2f science/py-pymatgen: Update 2019.1.24 -> 2019.2.28 2019-05-08 05:49:01 +00:00
Yuri Victorovich
60e2c08fee science/chrono: Update 2.0.0-9070 -> 4.0.0-89 2019-05-05 01:42:48 +00:00
Tobias Kortkamp
9b8c35db19 science/ALPSCore: Fix OPENMPI2 spelling after r500723 2019-05-04 11:02:15 +00:00
Yuri Victorovich
f6ccdc8eb7 science/harminv: Add -fPIC 
PR:		234105
Submitted by:	devel@stasyan.com (maintainer)
 2019-05-04 02:08:19 +00:00
Mark Linimon
922dee671e These ports now build on aarch64. 
Where necessary, pet portlint.

Approved by:	portmgr
Obtained from:	aarch64 TRYBROKEN run
 2019-05-03 21:06:51 +00:00
Mathieu Arnold
b139bbf73f Fix the a ports that were broken but did not know it. 
Differential Revision:	https://reviews.freebsd.org/D20140
 2019-05-03 13:58:33 +00:00
Adam Weinberger
a388e76374 compiler.mk is unhappy if CC/CXX is defined before bsd.port.pre.mk 
Reported by:	Peter Jeremy
Submitted by:	mat
 2019-05-03 12:30:40 +00:00
Yuri Victorovich
5ee82ae77a science/apbs: Fix license 2019-05-03 06:15:44 +00:00
Yuri Victorovich
1535bb293d New port: science/apbs: Electrostatic and solvation properties for complex molecules 2019-05-03 06:14:57 +00:00
Yuri Victorovich
b3f8e63dfc science/metaphysicl: Update 0.3.3 -> 0.5.0 
Reported by:	portscout
 2019-05-03 03:46:01 +00:00
Yuri Victorovich
d8b1947608 science/jmol: Update 14.29.40 -> 14.29.42 
Reported by:	portscout
 2019-05-02 07:59:18 +00:00
Yuri Victorovich
7346f80c67 New port: science/pagmo2: Platform to perform parallel computations of optimization tasks 2019-05-01 07:16:57 +00:00
Yuri Victorovich
35ebe83873 science/lammps: Update patch_29Mar2019 -> patch_30Apr2019 
Reported by:	github release notification
 2019-05-01 05:40:18 +00:00
Sunpoet Po-Chuan Hsieh
b136119d69 Update to 4.7.0 
- Update LICENSE

Changes:	https://github.com/Unidata/netcdf-c/releases
 2019-04-30 19:07:06 +00:00
Yuri Victorovich
7639c5a9a6 science/libint: Update 1-2-1 -> 1-2-1-15 2019-04-28 18:12:59 +00:00
Yuri Victorovich
24deb98c5e science/gromacs: Broken on i386 
Reported by:	fallout
 2019-04-28 08:30:15 +00:00
Yuri Victorovich
8183bc2389 science/jmol: Update to 14.29.38 -> 14.29.40 
Reported by:	portscout
 2019-04-28 07:01:08 +00:00
Piotr Kubaj
889392b50e science/ALPSCore: fix build with GCC-based architectures 
CMake Error at common/cmake/ALPSCommonModuleDefinitions.cmake:194 (target_compile_features):
  target_compile_features The compiler feature "cxx_std_11" is not known to
  CXX compiler

  "GNU"

  version 4.2.1.

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D20049
 2019-04-27 09:30:30 +00:00
Piotr Kubaj
bf6aa4f49e science/massxpert: fix build with GCC-based architectures 
Replace USE_GCC=any with USE_GCC=yes to fix build on GCC architectures.

Build failure log:
CMake Error in lib/CMakeLists.txt:

  The compiler feature "cxx_decltype" is not known to CXX compiler

  "GNU"

   version 4.2.1.

Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D20067
 2019-04-27 08:46:32 +00:00
Antoine Brodin
029aacfc97 Clean up plist 2019-04-25 13:51:20 +00:00
Yuri Victorovich
709668b071 science/chrono: fix build with GCC-based architectures 
PR:		236847
Submitted by:	pkubaj
 2019-04-24 22:11:06 +00:00
Thierry Thomas
77c8d5230f Fix on head by setting LLD_UNSAFE: 
ld: error: /usr/lib/libpmc.so: undefined reference to std::__1::__basic_string_common<true>::__throw_length_error() const
ld: error: /usr/lib/libpmc.so: undefined reference to std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >::append(char const*, unsigned long)
cc: error: linker command failed with exit code 1 (use -v to see invocation)

Since I'm here, add USES=gl.
 2019-04-24 19:35:06 +00:00
Yuri Victorovich
a5d01b17a3 science/sparta: fix build with GCC-based architectures 
PR:		237537
Submitted by:	pkubaj
 2019-04-24 18:27:08 +00:00
Yuri Victorovich
c20f216053 science/sparta: Update 15Feb2019 -> 16Apr2019 
Reported by:	github notification
 2019-04-24 16:28:36 +00:00
Gerald Pfeifer
879e75a659 Related to revision 499061 bump ports with USES=fortran to have them 
benefit from the improved situation where libgcc_s is only used when
absolutely necessary.

Suggested by:	tijl
 2019-04-22 13:16:33 +00:00
Yuri Victorovich
05bb8a1568 science/jmol: Update 14.29.37 -> 14.29.38 
Reported by:	portscout
 2019-04-22 06:56:12 +00:00
Stephen Montgomery-Smith
51df889f24 - Update to 3.1.0. 2019-04-22 01:12:30 +00:00
Max Brazhnikov
bd781394ba science/kst2: 
- Update to 2019.03.25 snapshot
- Download tarball from the official KDE repo on Github
- Remove kde from CATEGORIES: kst is pure Qt app
- Add option for HDF5 data files support
- Enable all options by default
 2019-04-21 20:53:50 +00:00
Yuri Victorovich
687977db77 science/qbox: Update 1_66_3 -> 1_67_1 
Reported by:	portscout
 2019-04-20 15:49:52 +00:00
Yuri Victorovich
161c93b9f6 science/gromacs: Update 2019.1 -> 2019.2 
Reported by:	portscout
 2019-04-20 15:47:27 +00:00
Yuri Victorovich
897def7f25 science/jmol: Update 14.29.36 -> 14.29.37 
Reported by:	portscout
 2019-04-20 15:41:33 +00:00
Sunpoet Po-Chuan Hsieh
f7b0b5b608 Update to 0.112 
Changes:	https://metacpan.org/changes/distribution/Geo-WebService-Elevation-USGS
 2019-04-19 23:27:17 +00:00
Sunpoet Po-Chuan Hsieh
8f9664371e Update to 4.1 
- Update pkg-descr
- Update WWW
- Take maintainership

Changes:	https://pyteomics.readthedocs.io/en/latest/changelog.html
 2019-04-18 18:00:52 +00:00