science/afni: update to 20.1.03

Reported by:	portscout

science/afni: update to 20.1.02

Reported by:	portscout

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

science/afni: Remove dependency on libXp

Remove dependency on libXp from science/afni, it is not needed, and libXp is
being deprecated.
Remove deprecation from science/afni

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 science/netcdf-fortran shlib change

Convert to UCL & cleanup pkg-message (categories s)

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 19.1.20

Upstreamed FreeBSD patches, other minor fixes and enhancements

Reported by:    portscout, Rick Reynolds (NIH)

science/afni: Upgrade to 19.1.18

Minor bugfixes/enhancements

science/afni: Upgrade to 19.1.14

Minor bug fixes and enhancements, some FreeBSD patches upstreamed

science/afni: Upgrade to 19.1.10

Rapid response from upstream on reported issue.  Additional patches to be
upstreamed in next release.

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

Add DOCS options to ports that should have one.

Also various fixes related to said option.

PR:		230864
Submitted by:	mat
exp-runs by:	antoine

Update math/gsl to 2.5

PR:		229067

Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).

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

Mark more recently failing ports broken on aarch64.

While here, pet portlint and reformat some other BROKEN statements.

Approved by:	portmgr (tier-2 blanket)

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 2.4

Exp-Run by:	antoine
PR:		220408

Revision bump of all ports with USE_GL after consolidation of mesa-libs

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D10845

Fix shebangs

Reviewed by:		mat
Approved by:		mat (mentor)
Differential Revision:	https://reviews.freebsd.org/D10527

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

- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket

- Fix trailing whitespace in Makefiles

Approved by:	portmgr blanket

Remove ${PORTSDIR}/ from dependencies, categories r, s, t, and u.

With hat:	portmgr
Sponsored by:	Absolight

Update to 2015.11.13.

Upgrade to a more recent snapshot, and stop requiring GCC.

PR:		206930
Submitted by:	Jason Bacon <bacon4000@gmail.com> (maintainer)

- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493

- Pet portlint
- Switch to options helpers

Approved by:	portmgr blanket

Convert to USES=jpeg

Fix some _DEPENDS

Cleanup plist

Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.

Part II, Bump PORTREVISIONs.

PR:		192025
Tested by:	antoine (-exp runs)
Approved by:	portmgr (implicit)

math/gsl:
- Add USES=libtool and bump dependent ports
- Add USES=pathfix and INSTALL_TARGET=install-strip

Approved by:	portmgr (implicit, bump unstage port)

- 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]

Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS.

Convert GMAKE to MAKE_CMD
Please note that lots of invocation of MAKE_CMD here are wrong as they do not
properly respect MAKE_ENV and friends

With hat:	portmgr

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)

Deprecate ports BROKEN for more than 6 months

With hat:	portmgr

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 math/R to 3.0.2 patched r64207 and math/R-cran-SuppDists to 1.1-9.1;
adjust dependent ports

Reviewed by:	pfg, thierry, tota

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

Add NO_STAGE all over the place in preparation for the staging support (cat:
science)

Update math/gsl to 1.16 and adjust some dependent ports

Convert from USE_MOTIF to USES=motif
While here:
- Trim headers
- Convert USE_GMAKE to USES=gmake
- Remove indefinite article from comment

Update math/R to 3.0.1-patched, and adjust dependent ports;
synchronize math/rpy with upstream repository

Reviewed by:	wen
Approved by:	wen, tota

- Convert USE_ICONV=yes to USES=iconv
- Change USE_GNOME=pkgconfig|gnomehack to USES=pathfix|pkgconfig and
  USE_GETTEXT=yes to USES=gettext while here

update math/R to 2.15.3, and adjust dependent ports

update the R base ports to 2.15.2 and adjust dependent ports

Reviewed by:	thierry, tota, wen

s/X11BASE/LOCALBASE/, or equivalent.

The X11BASE variable is long gone, however these ports were not updated.

- update png to 1.5.10

- Update to build 2012-04-17 [1]
- Projest has new homepage [1]
- Mark MAKE_JOBS_UNSAFE

PR:             ports/167651 [1]
Submitted by:   Jason Bacon <jwbacon@tds.net> (maintainer) [1]

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

 - remove MD5

Bump PORTREVISION after open-mofit update

Bounce PORTREVISION for gettext-related ports.  Have fun, ya'll.

- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi

- update to jpeg-8

Update maintainer's email address.  Had already been done for his
other ports.

Fix science/afni after X.org 7.4 import (needs Xi).

Reported by:    pointyhat (via pav)

- Remove duplicates from MAKE_ENV after inclusion of CC and CXX in default
MAKE_ENV

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)

- Update to 2008.01.02.1043

PR:             ports/119961
Submitted by:   Jason Bacon <bacon smithers.neuro.mcw.edu> (maintainer)

- Update to 2007.06.15.1339
- Unbreak

PR:             113887
Submitted by:   Jason Bacon <bacon@smithers.neuro.mcw.edu> (maintainer)

BROKEN: Does not compile

- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.

- Update to 2007.04.18.1830
- Respect X11BASE

PR:             111890
Submitted by:   Jason Bacon <bacon@smithers.neuro.mcw.edu> (maintainer)

Respect X11BASE

PR:     ports/106101
Submitted by:   self
Approved by:    Jason Bacon <bacon@smithers.neuro.mcw.edu> (maintainer)
Reported by:    pointyhat

- Fix plugins
- Update to 2006.06.30.1332

PR:             ports/103318
Submitted by:   Jason Bacon <bacon@smithers.neuro.mcw.edu> (maintainer)

Remove backquote from BROKEN string to avoid upsetting portsmon code.

Hat:            portmgr

Update to 2006.03.21.1314

PR:             97404
Submitted by:   Jason Bacon <bacon@smithers.neuro.mcw.edu>

Update to 2005.12.30.0934.2

PR:             94302
Submitted by:   maintainer

Change `NOT_FOR_ARCHS' with `if ARCH then BROKEN'

Noticed by:     danfe
Approved by:    garga (mentor)

Mark NOT_FOR_ARCHS=sparc64, maintainer did not fix the build for 7 days
after kris' mail

Approved by:    garga (mentor)

Changes to the port:
Author fixed the problem with filename versioning by placing filenames
without version in their name in a subdirectory on the web server.

Changes to the software itself:
-DPIC -fPIC used only for amd64 and ia64, suggested by kris

Approved by:    garga (mentor)

Update Makefile.FreeBSD_PORT's checksum.

-DPIC -fPIC were added to CFLAGS in Makefile.FreeBSD_PORT to make it
compile on amd64.

Approved by:    garga (mentor)

Add new port science/afni

AFNI (Advanced Functional Neuro Imaging) is a tool for analyzing
3 dimensional images, especially functional MRI images used in
brain mapping research.

WWW: http://afni.nimh.nih.gov/

PR:             ports/90752
Submitted by:   Jason Bacon <bacon@smithers.neuro.mcw.edu>
Reviewed by:    garga (mentor)
Approved by:    garga (mentor)