FreshPorts -- science/afni: Advanced Functional Neuro Imaging

afni
ABI	latest	quarterly
FreeBSD:11:aarch64	-	-
FreeBSD:11:amd64	21.0.04	20.3.04
FreeBSD:11:armv6	-	-
FreeBSD:11:i386	21.0.04	20.3.04
FreeBSD:11:mips	-	-
FreeBSD:11:mips64	-	-
FreeBSD:12:aarch64	-	-
FreeBSD:12:amd64	21.0.04	20.3.04
FreeBSD:12:armv6	-	-
FreeBSD:12:armv7	-	-
FreeBSD:12:i386	21.0.04	20.3.04
FreeBSD:12:mips	-	-
FreeBSD:12:mips64	-	-
FreeBSD:12:powerpc64	-	-
FreeBSD:13:aarch64	-	-
FreeBSD:13:amd64	21.0.03	-
FreeBSD:13:armv6	-	-
FreeBSD:13:armv7	-	-
FreeBSD:13:i386	21.0.04	-
FreeBSD:13:mips	-	-
FreeBSD:13:mips64	-	-
FreeBSD:13:powerpc64	-	-

science/afni: update to 20.2.16 Many utilities are not provided anymore. Most of them are marked in src/Makefile.INCLUDE under the comment "not distributed 25 Aug 2020" Others are not marked like that, but they are not shipped anyway, like 3dAnatNudge which has a comment that explains why: "This program (3dAnatNudge) is old, obsolete, and not maintained!" Reported by: portscout

math/R: Update to version 4.0.0 Upstream changes: https://stat.ethz.ch/pipermail/r-announce/2020/000653.html Also bump PORTREVISION of ports that depend on math/R. Submitted by: wen (in part) Reviewed by: jwb, Rainer Hurling <rhurlin@gwdg.de>, thierry Differential Revision: https://reviews.freebsd.org/D24572

science/afni: Upgrade to 20.1.02 Added some common R-cran run dependencies Removed obsolete reinplace patches Improved do-install to better fit filesystem hierarchy Releasing maintainership as I no longer work with any AFNI users Reported by: portscout

math/gsl: update to 2.6 - math/p5-Math-GSL does not seem to have any upstream activity to make it work with this version -> mark it broken - this also breaks the two consumers of this port - biology/gemma: has a conflict with cblas, and is makred broken. PR: 241363 Exp-run by: antoine

Deprecate x11/libXp, it is deprecated upstream Deprecate x11/libXp, since it is about to be deprecated upstream. Do *not* yet set a removal date for x11/libXp, this will be decided later, once most dependencies are fixed. Deprecate all ports depending on x11/libXp. * astro/xephem * audio/xmcd * audio/xmmix * biology/ncbi-toolkit * deskutils/xmdiary * ftp/llnlxdir * ftp/llnlxftp * graphics/SciPlot * misc/xtar * multimedia/mpeg2play * science/afni * textproc/mgdiff Sprinkle USES=xorg as needed. Discussed with: bapt

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

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

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

Multiple ports: Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org Remove Created by comments for same user Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14128

After r446199 libR.so has SONAME and was made visible for consumer ports. Register correct dependency by using LIB_DEPENDS instead of BUILD|RUN_DEPENDS dance. math/rkward-kde4: - Add 2 missing files to pkg-plist also PR: 219776 Submitted by: myself Approved by: maintainers timeouts

Update math/gsl to 2.3 This release introduces some new features and fixes several bugs: http://savannah.gnu.org/forum/forum.php?forum_id=8751 * update to 2.3 and take maintainership * update math/py-gsl to 2.2.0 for gsl2 support * update math/rubygem-rb-gsl to 2.1.0.2 for gsl2 support PR: 218952 Exp-run by: antoine Reviewed by: mat, rakuco Approved by: rakuco (mentor) Differential Revision: https://reviews.freebsd.org/D10522

science/afni: Use BUILD_DEPENDS/RUN_DEPENDS instead of LIB_DEPENDS for math/R, because R may be configured without libR. While here, fix some stage-qa warnings about indirect dependencies. Reviewed by: AMDmi3 Approved by: bacon4000@gmail.com (maintainer) swills (mentor) Differential Revision: https://reviews.freebsd.org/D8649

- Update to 4.4.0 - Bump PORTREVISION for science/netcdf-fortran shlib change [1] Changes: https://github.com/Unidata/netcdf-fortran/blob/master/RELEASE_NOTES.md Approved by: portmgr (implicit, unstaged port) [1]

science/afni: bring back into shape. - Stage support - Unexpire - Add license (GPLv2) - Use modern LIB_DEPENDS - Explicitly mention dependencies - Add CONFLICTS with im-*, nifticlib-* and open-usp-tukubai-* - Use perl5 and GCC - Tidy pkg-descr - Clean up pkg-plist - Bump PORTREVISION While here: - Use BROKEN_arch to avoid including bsd.port.pre.mk - Use PORT_OPTIONS:MDOCS instead of NOPORTDOCS - Remove obsolete post-install target PR: 186988 Submitted by: maintainer (jwbacon@tds.net)

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)

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

The vast majority of pkg-descr files had the following format when they had both lines: Author: ... WWW: .... So standardize on that, and move them to the end of the file when necessary. Also fix some more whitespace, and remove more "signature tags" of varying forms, like -- name, etc. s/AUTHOR/Author/ A few other various formatting issues

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)

Current status