biology/babel1.6_4

biology/babel: Update WWW

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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 redundant '-*' from CONFLICTS definitions

The conflict checks compare the patterns first against the package
names without version (as reported by "pkg query "%n"), then - if
there was no match - agsinst the full package names including the
version (as reported by "pkg query "%n-%v").

Approved by: portmgr (blanket)

all: Remove all other $FreeBSD keywords.

Remove # $FreeBSD$ from Makefiles.

Unbreak the build on PowerPC (at least) by always using va_copy() macro for copying variable argument lists, not just on AMD64.

Remove $FreeBSD$ from patches files in categories a-j.

With hat:	portmgr
Sponsored by:	Absolight

Rename biology/ patch-xy patches to reflect the files they modify.

Support stage Reduce over inclusions of bsd.port.mk Use BROKEN_${ARCH}

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

. NOPORTDOCS -> PORT_OPTIONS:MDOCS; . use PLIST_FILES, PORTDATA and PORTDOCS; . use standard DATADIR and DOCSDIR (rather PREFIX/foo/bar); . remove pkg-plist.

- Mark conflict with science/openbabel - Trim Makefile header

Fix build with clang

- Get Rid MD5 support

Mark various ports as broken or ignore on powerpc.

While here, remove remnants of alpha.

- Add SHA256

- Remove obsolete MASTER_SITES

PR:		ports/67690
Submitted by:	Roman Neuhauser <neuhauser@chello.cz>

- Fix build on AMD64 - Use DOCSDIR

Add SIZE.

Cosmetic fix: use %%DOCSDIR%% macro. No functionally changes.

Submitted by:	Oleg Karachevtsev <ok@etrust.ru>
A part of PR:	57992

De-pkg-comment.

update biology/babel to properly output mm3 files.

PR:		ports/42425
Submitted by:	Glenn Johnson <glennpj@charter.net>

o Rollback PORTCOMMENT modifications while this feature's implementation   is better studied o Turn PORTCOMMENT variable in Makefile back into pkg-comment files

Approved by:	kris (portmgr hat),
		portmgr, re (silence)

Use PORTCOMMENT in the Makefile, and whack the pkg-comment.

Approved by:	pat

* Replace pkg-message about setting BABEL_DIR with a wrapper script   that does. * Remove misleading full path name from usage message. * Improve fgets() usage. * Add converters category. * Improve pkg-comment and pkg-descr.

- Update MASTER_SITES and WWW: line - Support CC/CFLAGS properly - Support install macros - Add PORTDOCS to pkg-plist

PR: 26228
Submitted by: Ports Fury

pass maintainership to ports@.

PR:		25685
Submitted by:	maintainer

Massive style enforcement - use ^I instead of spaces for variables identation.

update with the new PORTNAME/PORTVERSION variables

fix some pkg/MESSAGE stuff

Change Id->FreeBSD.

As threatened, enforce the "Capital, no period" rule.  Ellipses are permitted.  Note that, given current numeric motif of PW, this is done in four equally-sized commits of 393 files each.

Install into ${PREFIX}, not /usr/local.

PR:	12214
Submitted by:	n_hibma

Weasal and Wabbits and BIG FOOT.

Move pkg/INSTALL to pkg/MESSAGE, add another patch from maintainer. PR:		ports/5361 Reviewed by:	asami Submitted by:	maintainer

This is a port of a molecular file format converter, babel. Babel is developed by Dolata Group, Department of Chemistry, University of Arizona and Ohio State University. PR:		ports/5215 Submitted by:	Frank Chen Hsiung Chan <frankch@waru.life.nthu.edu.tw>