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)