biology/clustalw2.1_3

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future.  I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required.  I am therefore releasing most of my scientific ports, along
with a few others, to ports@.  I will continue to maintain ports I am
actively using and those for which I am upstream.

biology/clustalw: Unbreak build for clang 16

Add -std=c++14

Reported by:    pkg-fallout

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.

biology/clustalw: Fix license, take maintainership

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15503

Remove useless WRKSRC definitions.

While there, correct DEV_WARNINGS when they occur.

Sponsored by:	Absolight

- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket

MASTER_SITES cleanup.

- Replace ${MASTER_SITE_FOO} with FOO.
- Merge MASTER_SITE_SUBDIR into MASTER_SITES when possible. (This means 99.9%
  of the time.)
- Remove occurrences of MASTER_SITE_LOCAL when no subdirectory was present and
  no hint of what it should be was present.
- Fix some logic.
- And generally, make things more simple and easy to understand.

While there, add magic values to the FESTIVAL, GENTOO, GIMP, GNUPG, QT and
SAMBA macros.

Also, replace some EXTRACT_SUFX occurences with USES=tar:*.

Checked by:	make fetch-urlall-list
With hat:	portmgr
Sponsored by:	Absolight

Multiple ports: reset maintainers 	Maintainers for these ports have been notified on 5 separate occasions 	over the course of several months about pending actions required.

We really appreciate the time and effort you put in to maintain
	these ports.

	If you are still interested in helping to maintain these ports just
	reply to me or file a PR and I will happily assign the port to you
	again.

Approved by:	portmgr (implicit)

- Fix build with clang/libc++. - Support staging.

PR:		184974
Submitted by:	tijl@

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

Remove USE_GNOME=gnometarget from ports. It has been a empty keyword since mid 2008.

PR:		ports/159624
Submitted by:	Ruslan Mahmatkhanov <cvs-src@yandex.ru>

- Fix fetch

Reported by:	QAT@

- Update to 2.1

- Fix fetch error

- Update to 2.0.12 - Update my mail address to FreeBSD

- Update to 2.0.6 - Pass maintainership to submitter

PR:		123193
Submitted by:	Wen heping <wenheping@gmail.com>

- Update to 2.0.5 - Add RESTRICTED due to non-commercial use licence.

PR:		ports/121794
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Approved by:	thierry and tabthorpe (mentors)

- Update to version 2.0.5 - Add RESTRICTED due to a non-commercial use licence.

PR:		ports/121794
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
Approved by:	thierry and tabthorpe (mentors)

- Restore clustalw symlink, other ports rely on it

Reported by:	pointyhat
Pointy hat to:	pav

- Update to 2.0.3

- Update to 2.0

PR:		ports/117713
Submitted by:	Motomichi Matsuzaki <mzaki@e-mail.ne.jp>

Reset dbader@eece.unm.edu due to maintainer-timeout.  While here, fix fetch.

SHA256ify

Approved by:    krion@

- Add an end-of-string to each line of the input   when parsing the input files

PR:		56043
Submitted by:	maintainer

Update to 1.83.

PR:		48264
Submitted by:	David A. Bader <dbader@eece.unm.edu>

- Add a new patch - Bump $PORTREVISION

PR:		36206
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)

- Fix certain mistakes in FreeBSD patches - Bump PORTREVISION - Poroblem originally reported by Fernan Aguero <fernan@iib.unsam.edu.ar> on   FreeBSD-bio list

PR:		36169
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)

${PREFIX}/share/${PORTNAME} --> ${DATADIR}

Update to version 1.82

PR:		28609
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)

- Support CC/CFLAGS/PREFIX properly - gets() -> fgets() - Add WWW: line into pkg/DESCR

Also bumped PORTREVISION to 1

PR:		21572
Submitted by:	tkato@prontomail.ne.jp <KATO@FreeBSD.ORG, Tsuguru@FreeBSD.ORG>
Reviewed by:	will
Approved by:	MAINTAINER (dbader@eece.unm.edu)

Adding clustalw version 1.81. A CLUSTAL W Multiple Sequence Alignment Program.

PR:		19746
Submitted by:	David A. Bader <dbader@cielo.eece.unm.edu>