biology/protomol2.0.3_16

graphics/tiff: Update to 4.6.0

PR:		278577
Exp-run by:	antoine

*/*: Update WWW to use HTTPS for sourceforge.net projects

Homepage link is permanent redirected to its HTTPS counterpart

*/*: Bump jpeg-turbo users treewide

New major version 3.0.0

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)

biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr

Remove # $FreeBSD$ from Makefiles.

Add USES=xorg USES=gl, ports categories b

Add USES=xorg, USES=gl and in a few cases USES=gnome to ports in categories
starting with 'b'.

biology/protomol: Fix doubled USES overwriting the old value

- Make sure shebangfix is actually used

biology/protomol: Fix build with Clang 6

Report.cpp:208:12: error: invalid operands to binary expression ('std::ostream' (aka 'basic_ostream<char>') and 'const std::__1::ostream' (aka 'const basic_ostream<char>'))
        *myStream << a;
        ~~~~~~~~~ ^  ~
/usr/include/c++/v1/ostream:218:20: note: candidate function not viable: no known conversion from 'const std::__1::ostream' (aka 'const basic_ostream<char>') to 'const void *' for 1st argument; take the address of the argument with &
    basic_ostream& operator<<(const void* __p);
                   ^
... and so on ...

http://beefy11.nyi.freebsd.org/data/head-i386-default/p477696_s338122/logs/errors/protomol-2.0.3_13.log

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

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

biology/protomol: Support build with C++11 (taken from dports)

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

Convert ports to use the options helpers in categories [abc]*, and minor fixes.

Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D3412?

- Add LICENSE - Fix shebangs

Approved by:	porgmgr (bapt)

Convert to COPYTREE_SHARE Use options helpers

Convert to USES=jpeg

Cleanup DIST* variables.

When appropriate:
- Try to use DISTVERSION{SUF,PRE}FIX
- Replace PORTNAME-PORTVERSION by DISTNAME
- Convert MASTER_SITES to use macros
- Other light cleanup

With hat:	portmgr
Sponsored by:	Absolight

Bump portrevision after png update

Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgrade

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)

- Stagify - Fix build

Reset maintainership for ports not staged with no pending PR

With hat:	portmgr

The FreeBSD x11@ and graphics team proudly presents a zeising, kwm production, with help from dumbbell, bdrewery:

NEW XORG ON FREEBSD 9-STABLE AND 10-STABLE

This update switches over to use the new xorg stack by default on FreeBSD 9
and 10 stable, on osversions where vt(9) is available.
It is still possible to use the old stack by specifying WITHOUT_NEW_XORG in
/etc/make.conf .
FreeBSD 8-STABLE and released versions of FreeBSD still use
the old version.
A package repository with binary packages for new xorg will
be available soon.

This patch also contains updates of libxcb and related ports, pixman, as well
as some drivers and utilities.

Bump portrevisions for xf86-* ports, as well as virtualbox-ose-additions due
to xserver version change.

Apart from these updates, the way shared libraries are handled has been
changed for all xorg ports, as well as libxml2 and freetype, which means
ltverhack is gone and as a consequence shared libraries have been bumped.
The plan is that this change will make library bumps less likely in the
future.
All affected ports have had their portrevisions bumped as a consequence of
this.

Fix some issues where WITH_NEW_XORG weren't detected properly on CURRENT.

Update instructions, hardware support, and more notes can be found on
https://wiki.freebsd.org/Graphics

Thanks to:	all testers, bdrewery and the FreeBSD x11@ team
exp-run by:	bdrewery [1]
PR:		ports/187602 [1]
Approved by:	portmgr (bdrewery), core (jhb)

Reduce over inclusion of bsd.port.mk

In preparation for making libtool generate libraries with a sane name, fix all LIB_DEPENDS in biology

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

- adoption of optionsNG - trim historical header - fix mixture of DOCS/EXAMPLES -> EXAMPLES - add shared description for GLUT to bodm

Approved by:	portmgr (miwi)

Switch from libglut to freeglut and retire libglut. Libglut hasn't been developed in years and has been dropped from the MESA 8.0 distribution. Freeglut is a rewrite of glut and is actively developed and is used by many linux distributions instead of libglut.

Bump all ports that directly depend on libglut because of the shlib version
change.

There are some extra items in this patch.

*) Because freeglut doesn't have the same dependancies as libglut, some ports
	need extra dependencies added to USE_XORG to make them build.
*) Mark graphics/f90gl broken, f90gl depends on a header that is only shipped
	with libglut.
*) Remove option for libglut/freeglut selection in games/cake, only freeglut
	remains now.
*) While here fix a png related build issue games/vegastrike.

Thanks to miwi for running the exp-run.

Approved by:	portmgr (miwi)

Collaboration with:	zeising@
Obtained from:	xorg-dev staging area.

- update png to 1.5.10

- 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

- Get Rid MD5 support

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

- update to jpeg-8

- Switch SourceForge ports to the new File Release System: categories starting with B,C

- update to jpeg7 Tested by:	pav on pointyhat

- Update X.org ports to 7.4+ (few ports are more recent than the katamari). - Bump PORTREVISION for all ports depending on libglut since the shlib version number went from 4 to 3. - Bump PORTREVISION for all ports depending on libXaw as libXaw.so.8 isn't installed anymore. - Couple of ports fixes (mostly missing xorg components added to USE_XORG).

- Remove USE_GCC where it can be satisfied with base compiler on following   FreeBSD versions: 5.3 and up, 6.x, 7.x, 8-CURRENT

- 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)

- Fix build with GCC 4.2

Approved by:	miwi (mentor)

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

Approved by:	portmgr (xorg cleanup)

Mark as broken with gcc4.2.

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

Add protomol 2.0.3, OO, component based, framework for molecular dynamics (MD) simulations.

PR:		95123
Submitted by:	Sangwoo Shim <sangwoos@gmail.com>