13:23 Muhammad Moinur Rahman (bofh) 

biology/mafft: Moved man to share/man

Approved by:    portmgr (blanket)

    f5db692

00:37 Muhammad Moinur Rahman (bofh) 

*/*: 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

    bbab7f5

21:10 Stefan Eßer (se) 

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)

    b7f0544

14:20 Tobias C. Berner (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

    37526bb

05:11 Wen Heping (wen) 

biology/mafft: Update to 7.267

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

    98065e9

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

07:19 wen 

- Update to 7.266

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

 

14:30 bapt 

Use BROKEN helpers

 

17:04 robak 

biology/mafft: update 7.149 -> 7.221

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

 

16:01 marino 

6 ports categories: Remove $PTHREAD_LIBS

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

approved by:	PTHREAD blanket

 

19:11 adamw 

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

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

 

04:18 milki 

Add DOCS and EXAMPLE options to biology/mafft

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

 

19:35 amdmi3 

- Update to 7.149
- Clarify LICENSE
- Stagify

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

 

07:41 miwi 

- Convert USE_GMAKE to USES

 

15:46 adamw 

Convert biology to MDOCS and MEXAMPLES

 

15:55 bapt 

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

 

08:30 linimon 

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

Hat:		portmgr

 

13:54 scheidell 

- Submitter is now maintainer

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

12:26 scheidell 

- Update to version 6.903

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

17:26 pav 

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

Reported by:    pointyhat
Feature safe:   yes

03:31 pgollucci 

- Update download locations, update WWW

Reported by:    -fetch-original pointyhat run

22:24 pav 

- Chase fasta3 update

Reported by:    pointyhat

12:59 garga 

- 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

10:41 garga 

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

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