FreshPorts -- science/v_sim: Visualization of atomic structures

v_sim
ABI	latest	quarterly
FreeBSD:11:aarch64	3.7.2_8	3.7.2_12
FreeBSD:11:amd64	3.8.0	3.7.2_12
FreeBSD:11:armv6	-	-
FreeBSD:11:i386	3.8.0	3.7.2_12
FreeBSD:11:mips	-	-
FreeBSD:11:mips64	-	-
FreeBSD:12:aarch64	3.7.2_8	-
FreeBSD:12:amd64	3.8.0	3.7.2_12
FreeBSD:12:armv6	3.7.2_8	-
FreeBSD:12:armv7	3.7.2_8	-
FreeBSD:12:i386	3.8.0	3.7.2_12
FreeBSD:12:mips	-	-
FreeBSD:12:mips64	-	-
FreeBSD:12:powerpc64	-	3.7.2_12
FreeBSD:13:aarch64	-	-
FreeBSD:13:amd64	3.8.0	-
FreeBSD:13:armv6	-	-
FreeBSD:13:armv7	-	-
FreeBSD:13:i386	3.8.0	-
FreeBSD:13:mips	-	-
FreeBSD:13:mips64	-	-
FreeBSD:13:powerpc64	-	-

- Fix build without NLS (missing gettext-tools dependency) and without EXAMPLES (broken patching) - Convert patching to options helpers, silence, fix whitespace and make more future proof Approved by: portmgr blanket

Bump PORTREVISION for ports depending on the canonical version of GCC as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, everything INDEX-11 shows with a dependency on lang/gcc9 now. PR: 238330

Update science/netcdf to 4.6.3 - Bump PORTREVISION of dependent ports for shlib change Changes: https://github.com/Unidata/netcdf-c/releases https://github.com/Unidata/netcdf-c/blob/master/RELEASE_NOTES.md

Bump PORTREVISION for ports depending on the canonical version of GCC defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, as a double check, everything INDEX-11 showed depending on lang/gcc7. PR: 231590

Bump PORTREVISION for ports depending on the canonical version of GCC in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which has now moved from GCC 6 to GCC 7 by default. This includes ports - featuring USE_GCC=yes or USE_GCC=any, - featuring USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and those - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x, c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib. PR: 222542

Bump PORTREVISION for ports depending on the canonical version of GCC (via Mk/bsd.default-versions.mk and lang/gcc) which has moved from GCC 5.4 to GCC 6.4 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang, c++14-lang, c++0x, c11, or gcc-c++11-lib. PR: 219275

Bump PORTREVISIONs for ports depending on the canonical version of GCC and lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some circumstances such as versions of FreeBSD or platforms). This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using using Mk/bsd.octave.mk which in turn has USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang, c++11-lang, c++0x, c11, or gcc-c++11-lib. PR: 216707

Bump PORTREVISIONS for ports depending on the canonical version of GCC and lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some circumstances such as versions of FreeBSD or platforms), part II. The first part covered ports with USE_GCC=yes, USE_GCC=any, or one of gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang, c++11-lang, c++0x, c11 requested via USES=compiler. This adds ports with USES=fortran and ports using Mk/bsd.octave.mk which in turn has USES=fortran. PR: 214965 Reported by: thierry

Part 1 of adding USE_GNOME=intltool to ports that require it. The reason for this is that in the GNOME 3.16 update, USE_GNOME gtk20 and gtk30 don't pull intltool in anymore. PR: 201980 Exp-run by: antoine@

- Update to 4.3.2 (from science/netcdf4) - Bump PORTREVISION for science/netcdf shlib change and dependency change from science/netcdf4 to science/netcdf [1] Changes: http://www.unidata.ucar.edu/software/netcdf/docs/release_notes.html Approved by: portmgr (bapt) [1]

Update the default version of GCC used in the Ports Collection from GCC 4.6.4 to GCC 4.7.3. This entails updating the lang/gcc port as well as changing the default in Mk/bsd.default-versions.mk. Part II, Bump PORTREVISIONs. PR: 182136 Supported by: Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports) Tested by: bdrewery (two -exp runs)

Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes". In most cases USE_GCC=yes has been omitted though. Remove USE_FORTRAN handling from bsd.port.mk and bsd.gcc.mk. Minor cleanups in some ports like USE_GMAKE, NOPORTDOCS,... Exp-run: bdrewery Approved by: portmgr (bdrewery)

According to the Porter's Handbook (5.12.2.3.) default options must be added to OPTIONS_DEFINE. This policy has been implemented only recently that's why we have many ports violating this policy. This patch adds the default options specified in the Porter's Handbook to OPTIONS_DEFINE where they are being used. Ports maintained by gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded. Approved by: portmgr (bapt)

Update to libmpc version 1.0.1 which brings the following fixes: - Switched to automake 1.11.6, see CVE-2012-3386. - #14669: Fixed extraction of CC from gmp.h. - Fixed case of intermediate zero real or imaginary part in mpc_fma, found by hydra with GMP_CHECK_RANDOMIZE=1346362345. This is on top of the following changes from version 1.0 - Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no invariant sections) for the documentation. - 100% of all lines are covered by tests - Renamed functions . mpc_mul_2exp to mpc_mul_2ui . mpc_div_2exp to mpc_div_2ui

science/openbabel: - Update openbabel to 2.3.2 - Switch to CMake build system - Add PYTHON and CAIRO options - Don't rename babel binary, mark conflict with ancient biology/babel science/py-openbabel: - Merge py-openbabel to openbabel other: - chase openbabel update

- Add LDFLAGS to CONFIGURE_ENV and MAKE_ENV (as it was done with LDFLAGS) - Fix all ports that add {CPP,LD}FLAGS to *_ENV to modify flags instead PR: 157936 Submitted by: myself Exp-runs by: pav Approved by: pav

Bump portrevision due to upgrade of devel/gettext. The affected ports are the ones with gettext as a run-dependency according to ports/INDEX-7 (5007 of them) and the ones with USE_GETTEXT in Makefile (29 of them). PR: ports/124340 Submitted by: edwin@ Approved by: portmgr (pav)

- Remove unneeded dependency from gtk12/gtk20 [1] - Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG - Remove X11BASE support in favor of LOCALBASE or PREFIX - Use USE_LDCONFIG instead of INSTALLS_SHLIB - Remove unneeded USE_GCC 3.4+ Thanks to all Helpers: Dmitry Marakasov, Chess Griffin, beech@, dinoex, rafan, gahr, ehaupt, nox, itetcu, flz, pav PR: 116263 Tested on: pointyhat Approved by: portmgr (pav)

science/netcdf - Update to 3.6.2 graphics/gmt math/grace math/gri math/p5-NetCDF math/py-scientific math/ruby-netcdf science/gnudatalanguage science/minc science/minc2 science/v_sim science/vis5d+ - Bump PORTREVISION for the changing of science/netcdf's major library version number PR: 111347 Submitted by: Sunpoet Po-Chuan Hsieh <sunpoet AT sunpoet.net> (maintainer) Approved by: clsung (mentor)

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