biology/mafft7.267_1

biology/mafft: Moved man to share/man

Approved by:    portmgr (blanket)

*/*: Sunset 12.4-RELEASE/12-STABLE from ports tree

- Remove all references to defunct ARCH arm
- Remove all references to defunct ARCH sparc64
- Remove x11-drivers/xf86-video-sunffb which requires defunct sparc64
  ARCH
- Remove sysutils/afbinit requires defunct sparc64 ARCH
- Remove all references to bktr driver
- Remove all references to defunct FreeBSD_12
- Remove all references to OSVERSION/OSREL corresponding to 12
- Remove conditionals in Mk/Uses/cabal.mk
- Remove sparc reference from Mk/Uses/qt-dist.mk
- Remove BROKEN_sparc64/NOT_FOR_ARCH=sparc64
- Remove BROKEN_FreeBSD_12* from:
- Remove OpenSSL patches from:
- Remove conditional flags for OSVERSION >= 1300000 to fixed flags.
  Also move conditional flags for non sparc64/arm ARCH to fixed flags.

Reviewed by:	brooks, jbeich, rene, salvadore
Differential Revision: https://reviews.freebsd.org/D42068

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

biology/mafft: Update to 7.267

PR:		259315
Reported by:	gspurki@gmail.com
Approved by:	maintainer

Remove # $FreeBSD$ from Makefiles.

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

Approved by:	portmgr blanket

- Update to 7.266

PR:		205558
Submitted by:	cartwright@asu.edu(maintainer)

Use BROKEN helpers

biology/mafft: update 7.149 -> 7.221

PR:		200603
Submitted by:	Reed A. Cartwright <cartwright@asu.edu> (maintainer)

6 ports categories: Remove $PTHREAD_LIBS

Categories: cad, devel, java, x11-fm, biology, deskutils

approved by:	PTHREAD blanket

Cleanup plist

Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)

Add DOCS and EXAMPLE options to biology/mafft

PR:		ports/190161
Submitted by:	"Reed A. Cartwright" <cartwright@asu.edu> (maintainer)
Approved by:	swills (maintainer)

- Update to 7.149 - Clarify LICENSE - Stagify

PR:		189746
Submitted by:	"Reed A. Cartwright" <cartwright@asu.edu> (maintainer)

- Convert USE_GMAKE to USES

Convert biology to MDOCS and MEXAMPLES

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

Mark as broken on sparc64: depends on thread-local storage, which is not available on sparc64.

Hat:		portmgr

- Submitter is now maintainer

PR:		ports/169920
Approved by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- Update to version 6.903

PR:		ports/169920
Submitted by:	"Reed A. Cartwright" <cartwright@asu.edu>
Approved by:	maintainer (timeout, 21 days)

- Get Rid MD5 support

- Change depobj for fasta3 to something that does not change on fasta updates

Reported by:	pointyhat
Feature safe:	yes

- Update download locations, update WWW

Reported by:    -fetch-original pointyhat run

- Chase fasta3 update

Reported by:	pointyhat

- Update to 5.743 - Add a MASTER_SITE backup since oficial one just have last version and make   it fetchable again

Submitted by:	maintainer by email
Reported by:	krismail

Add mafft 5.734, multiple sequence alignments based on fast Fourier transform.

PR:		ports/93059
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar>