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).

In particular that is 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.

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

With hat:	portmgr
Sponsored by:	Absolight

- Update to 5.0.6
- Pass maintainership to submitter
- Add distfile mirror

PR:		201921
Submitted by:	freebsd@skysmurf.nl

- Update to 5.0.5

PR:		200306
Submitted by:	tkato432@yahoo.com

Upgrade to 5.0.4.

PR:		197454
Submitted by:	Ports Fury.

Uses blaslapack.

- Update net/openmpi to 1.8.4

- Update to 5.0.2

PR:		193902
Submitted by:	tkato432@yahoo.com

science/gromacs: Fix build on DragonFly (fix from dports)

- Update net/openmpi from 1.8.2 to 1.8.3

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)

- Upgrade to 1.5;

- Bump PORTREVISION for consumers.

math/fftw3:
- Add USES=libtool and bump dependent ports
- Add INSTALL_TARGET=install-strip
- Remove PTHREAD_CFLAGS and PTHREAD_LIBS
- Use MAKE_CMD

Chase the upgrade of net/mpich2.

Approved by:	portmgr (non staged ports)

science/gromacs: Upgrade version 4.6.5 => 5.0

PR:		191826
Submitted by:	Ports Fury

- Convert net/openmpi to USES=libtool and bump dependent ports
- Add INSTALL_TARGET=install-strip
- Use BROKEN_sparc64

Approved by:	portmgr (implicit, bump unstaged port)

science/gromacs: Add DragonFly support (dports)

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)

- USES=fortran.
- Fix detection of dlopen(3) to support plugins from science/vmd.

- Update from 4.6.4 to 4.6.5 [1]
- Convert some "if's" in options helpers

PR:		ports/184903
Submitted by:	KATO Tsuguru <tkato432@yahoo.com> [1]

science/gromacs: Update to version 4.6.4

- Update to version 4.6.4
- Allow staging

PR:		ports/184224
Submitted by:	KATO Tsuguru <tkato432 yahoo.com>

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

- Remove MAKE_JOBS_SAFE variable

Approved by:	portmgr (bdrewery)

- Convert to new perl framework
- Trim Makefile header

- Update to 4.6.3

PR:		180503
Submitted by:	Ports Fury

- Update to 4.6.2

PR:		179208
Submitted by:	Ports Fury

Finish converting the whole ports tree to USES=pkgconfig

- Update to 4.6.1

PR:		177243
Submitted by:	ports fury

- convert USE_CMAKE to USES
- while here clean up some ports from CMAKE_VERBOSE, which is intended
  for users

Approved by:	portmgr (miwi)

- Update to 4.6

PR:		175589
Submitted by:	Ports Fury

- convert to optionsNG
- trim headers
- drop maintainership

- update fftw3* to 3.3 [1], and adjust dependent ports
- make use of optimizations by default, where possible
(quad flavor to follow shortly, and mpi at a later date)

Suggestions and patches from:   ache, C. Burns, wen

fix distinfo, the distfile was rerolled. Nothing major, mostly spelling fixes.

Reported by:    pav, erwin

- 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

- update to 4.5.5
- drop FreeBSD 6.x support

Update math/gsl to 1.15, and adjust PORTREVISION
and LIB_DEPENDS of dependent ports

- update to 4.5.4

PR:             ports/156214
Submitted by:   "Peter C. Lai" <cowbert@gmail.com>

- change MAINTAINER to my @FreeBSD.org address

Approved by: jadawin (mentor)

Sync to new bsd.autotools.mk

- Update to 4.5.3

PR:             ports/151888
Submitted by:   Florian Smeets <flo@smeets.im> (maintainer)

- Update maintainer email address flo@kasimir.com -> flo@smeets.im

PR:             ports/150855
Submitted by:   maintainer

- Bump PORTREVISION to chase the update of math/gsl

- Update to 4.0.7

PR:             141284
Submitted by:   Florian Smeets <flo@kasimir.com> (maintainer)

Chase math/gsl update,
bump PORTREVISION

- Chase relocation of net/mpich2

- Bump PORTREVISION if needed

- Fix some portlint errors.

-Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.

It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.

With help:      marcus and kwm
Pointyhat-exp:  a few times by pav
Tested by:      pgollucci, "Romain Tartière" <romain@blogreen.org>, and
                a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by:    marcus
Approved by:    portmgr

- Update to 4.0.5

PR:             135246
Submitted by:   Florian Smeets <flo@kasimir.com> (maintainer)

- Fix build on sparc64 by files/patch-include__gmx_cyclecounter.h
- Fix WITH_MPICH
- Use LOCALBASE for reference to bits installed by others
- Pass maintainership to the submitter
- Pet portlint(1): IGNORE

PR:             ports/133242
Submitted by:   Florian Smeets <flo at kasimir.com>
Approved by:    Stephen Montgomery-Smith <stephen at math.missouri.edu>
(maintainer)

- Chase fftw3 update

- Update maintainer mail address

PR:             ports/133397
Submitted by:   Stephen Montgomery-Smith <stephen@missouri.edu> (maintainer)
Approved by:    tabthorpe (co-mentor)

Mark as broken on sparc64: fails to compile.

- Update to 4.0.3

PR:             131655
Submitted by:   Joerg Pulz <Joerg.Pulz@frm2.tum.de>
Approved by:    maintainer

Update CONFIGURE_ARGS for how we pass CONFIGURE_TARGET to configure script.
Specifically, newer autoconf (> 2.13) has different semantic of the
configure target. In short, one should use --build=CONFIGURE_TARGET
instead of CONFIGURE_TARGET directly. Otherwise, you will get a warning
and the old semantic may be removed in later autoconf releases.

To workaround this issue, many ports hack the CONFIGURE_TARGET variable
so that it contains the ``--build='' prefix.

To solve this issue, under the fact that some ports still have
configure script generated by the old autoconf, we use runtime detection
in the do-configure target so that the proper argument can be used.

Changes to Mk/*:
 - Add runtime detection magic in bsd.port.mk

- 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)

- Remove USE_XLIB/USE_X_PREFIX/USE_XPM in favor of USE_XORG
- Bump PORTREVISION

Approved by:    portmgr (xorg cleanup)

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

Conversion to a single libtool environment.

Approved by:    portmgr (kris)

SHA256ify

Approved by: krion@

Mass-conversion to the USE_AUTOTOOLS New World Order.  The code present
in bsd.autotools.mk essentially makes this a no-op given that all the
old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in
exactly the same way as USE_AUTOTOOLS itself.

Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME
team -- all GNOME 2.12.x ports use it.

Preliminary documentation can be found at:
        http://people.FreeBSD.org/~ade/autotools.txt

which is in the process of being SGMLized before introduction into the
Porters Handbook.

Light blue touch-paper.  Run.

At Kris's request, back out the MACHINE_ARCH spelling correction until
after 5.4-RELEASE.

Assist getting more ports working on AMD64 by obeying the
Ports Collection documentation and use 'ARCH' rather than 'MACHINE_ARCH'.

- Fix pkg_plist and unbreak;
- Define USE_LIBTOOL_VER;
- Bump PORTREVISION.

PR:             ports/74828
Submitted by:   maintainer.

BROKEN: Broken pkg-plist

Fix build by adding
.ifndef WITH_FLOAT
CONFIGURE_ARGS+=        --disable-float

Submitted by:   Stephen Montgomery-Smith <stephen at math.missouri.edu>
Reported by:    kris via pointyhat and Bruno Afonso <brunomiguel at
dequim.ist.utl.pt>

New port science/gromacs
GROMACS is a versatile package to perform molecular dynamics,
i.e. simulate the Newtonian equations of motion for systems
with hundreds to millions of particles, and also the World's
fastest Molecular Dynamics under GPL.

PR:             71211
Submitted by:   Stephen Montgomery-Smith <stephen@math.missouri.edu>
Reviewed by:    Bruno Afonso <brunomiguel@dequim.ist.utl.pt>