biology/fasta336.3.8_1

MAN?PREFIX: eleminate its usage  and move man to share/man

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

Deorbit RESTRICTED && NO_CDROM, part one.

For ports that already use the licenses framwork, merge the content of
RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs.

Approved by:	rene
Differential Revision:	https://reviews.freebsd.org/D30010

Remove # $FreeBSD$ from Makefiles.

Convert to UCL & cleanup pkg-message (categories a-c)

- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket

- Update to 36.3.8 - Pass maintainership to submitter

PR:		203817
Submitted by:	Wendell Borges <wendell@bsd.com.br>

- Update to 36.3.7a

Cleanup plist

biology/fasta3: Checked new distfile and regenerated distinfo to unbreak

Fasta3 distfile was significantly changed.  This should have been released
as a new version (e.g. 36.3.6e), so it's not clear why the distfile was
rerolled.  There are significant changes to makefiles, conf files and even
a few .c and .h files.  They all look like legitimate updates to me
though.

Set DIST_SUBDIR since this port is now known for rerolling, then
regenerate distinfo.  Also add Fasta license and bump revision.

Mark as broken: Invalid checksum, seems like the software was rerolled

Update to version 36.3.6d

PR:		ports/181883
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>

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

- Use single space after WWW:

- Update to 36.3.6 - Drop maintainership

- Take maintainership

- Reassign to the heap at maintainer's request

- remove maintainer tags from pkg-descr

Approved by:	portmgr
Approved by:	bapt (mentor)

- Update to 36.3.2 to fix distfile fetching on pointyhat

PR:		ports/154267
Submitted by:	Fernan Aguero <fernan AT iib.unsam.edu.ar> (maintainer)
Feature safe:	yes

Update to 35.4.9

PR:		ports/137991
Submitted by:	Fernan Aguero (maintainer)

- Update to 35.4.7 [1] - Obey PREFIX [2]

Submitted by:	maintainer [1] [2]
Reported by:	QATty [2]

- Add forgotten patch

- Update to 35.4.4

PR:		132007
Submitted by:	Fernan Aguero <fernan at iib dot unsam dot edu dot ar> (maintainer)

- Update to 35.3.6

PR:		ports/122607
Submitted by:	maintainer (Fernan Aguero)

- Update to 35.3.5 - Switch to .tar.gz distfile so that we don't define our do-extract - While I'm here, using substitution for version numbers in pkg-plist   for easier upgrade

PR:		ports/121690
Submitted by:	Wen heping <wenheping at gmail.com>
Approved by:	maintainer timeout (2 weeks)

- Update to 34.26.2

PR:             110079
Submitted by:   Fernan Aguero<fernan@iib.unsam.edu.ar> (maintainer)

- Update to 34.t26.b3

PR:		ports/104508
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- Update to 34.t25.d9

PR:		ports/98761
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

- Update to 34.t25.d8 [1] - While I'm here, pet portlint [2]

PR:		98398 [1]
Submitted by:	miwi [1], self [2]
Approved by:	maintainer [1]

- update to 34.t25.d7 - add MASTER_SITE_LOCAL as a second master site

PR:		ports/97310
Submitted by:	maintainer

BROKEN: Unfetchable

- Update to 34.t25.d6

PR:		ports/96063
Submitted by:	maintainer

- Update to 34.t25.d5

PR:		ports/94741
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

Update to 34.t25.d4.

PR:		ports/93052
Submitted by:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

SHA256ify

Approved by:    krion@

Chase mastersite and fix checksum to unbreak.  (Changes are inclusion of a logfile, one Linux-only change, and one change in a test script).  Assign submitter as new maintainer as current one has not responded to PRs for some time.

PR:		ports/68199
Submitted by:	Fernan Aguero <fernan at iib dot unsam dot edu dot ar>

Set an expiry date of 2004-08-20 for these BROKEN/IGNORE/FORBIDDEN ports.  They will be removed on or after that date if they are still broken and no fix has been submitted to GNATS.

SIZEify (maintainer timeout)

BROKEN: Checksum mismatch

unPERLify by using REINPLACE_CMD and SED where appropriate.

PR:		47654
Submitted by:	Simon 'portlint' Schubert <corecode@corecode.ath.cx>

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

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

Clear moonlight beckons. Requiem mors pacem pkg-comment, And be calm ports tree.

E Nomini Patri, E Fili, E Spiritu Sancti.

Prefer <limits.h> over <values.h> as the latter has been removed from -current.

Noticed by:	bento

Replace erroneous usage of INSTALL_MAN with INSTALL_DATA.

PR:		28666
Submitted by:	Patrick Li <pat@databits.net>

Updating my email address in my remaining ports.

Prompted by:	vanilla

Updata biology/fasta3 to version 33.t08.d4

PR:		27176
Submitted by:	Johann Visagie <johann@egenetics.com> MAINTAINER

Update to 33.t08.d3.

Submitted by:	maintainer

- A small bugfix lead to a rerelease without a version number change. - Bumped PORTREVISION.

Submitted by:	Johann Visagie <johann@egenetics.com>
PR:		25725