science/afni26.3.04

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
 - 0^0, which returned (NaN,NaN) previously, now returns (1,+0).
 - Removed compatibility with K&R compilers, which was untestable due
   to lack of such compilers.
 - New functions
   . mpc_log10
   . mpc_mul_2si, mpc_div_2si
 - Speed-ups
   . mpc_fma
 - Bug fixes
   . mpc_div and mpc_norm now return a value indicating the effective
     rounding direction, as the other functions.
   . mpc_mul, mpc_sqr and mpc_norm now return correct results even if
     there are over- or underflows during the computation.
   . mpc_asin, mpc_proj, mpc_sqr: Wrong result when input variable has
     infinite part and equals output variable is corrected.
   . mpc_fr_sub: Wrong return value for imaginary part is corrected.

Convert to the new LIB_DEPENDS standard and remove hard-coded
.so versions from a couple of dependent ports.

Bump PORTREVISIONS of all dependent ports.

PR:		183141
Approved by:	portmgr (bdrewery)

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)