biology/tRNAscan-SE2.0.11

biology/tRNAscan-SE: Update to 2.0.11

ChangeLog:	http://lowelab.ucsc.edu/tRNAscan-SE/change_log.txt
PR:		266966

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/tRNAscan-SE: update to 2.0.5

This commit also changes maintainer's email.

PR:	243248
Submitted by:	mzaki@e-mail.ne.jp (maintainer)

biology/tRNAscan-SE: Update to 2.0.3

PR:		238253
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp>

biology/tRNAscan-SE: fix build with GCC-based architecturs

Add MAKE_JOBS_UNSAFE=yes to fix build.

Remove USES=compiler:c11, it's not necessary.

PR:		237848
Approved by:	mzaki@niid.go.jp (maintainer), linimon (mentor)
Differential Revision:	https://reviews.freebsd.org/D20439

biology/tRNAscan-SE: fix build with GCC-based architectures

Add USES=compiler:c11 to fix build.

Approved by:	mentors (implicit approval)

- Unbreak by adding missing pkg-plist

PR:		228758
Submitted by:	mzaki@niid.go.jp(maintainer)

Mark BROKEN: missing plist

Update to 2.0.0 and pass maintainership to committer.

PR:		228758
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp>

Deprecate ports broken for more than 6 months

Mark as broken ports with no public distfiles

Prevent collision with getline(3)

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

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

Support stage

biology/tRNAscan-SE: Fix hardcoded perl path

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

- Convert to new perl framework - Trim Makefile header

. NOPORTDOCS -> PORT_OPTIONS:MDOCS; . pet portlint: use {} instaed of () at variable; . use PLIST_FILES, PORTDATA and PORTDOCS at Makefile; . get rid of pkg-plist; . remove article from COMMENT; . trim Makefile headers.

- Get Rid MD5 support

- Update MASTER_SITES and WWW: line - Support CC/CFLAGS properly - Strip binary

PR:		123866
Submitted by:	Ports Fury

Update to 1.23

Reset chuynh@biolateral.com.au: address bounces.

Hat:		portmgr

SHA256ify

Approved by:    krion@

SIZEify (maintainer timeout)

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

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

De-pkg-comment.

Port needs perl to build. Seen on: bento

Add tRNAscan-SE 1.21, an improved tool for transfer RNA detection.

PR:		33853
Submitted by:	chuynh@biolateral.com.au