biology/p5-Bio-MAGETAB1.31_2

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.

Fix typo

- Bump PORTREVISION for dependency change

Notified by:	mat

Sort PLIST

Use real PORTVERSION of devel/p5-Parse-RecDescent

Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except for where it resulted in a change in output from build-depends-list or run-depends-list.

Approved by:	portmgr (adamw)

Update WWW

search.cpan.org is shutting down.
It will redirect to metacpan.org after June 25, 2018.

With hat:	perl

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

Some OCD cleanups on some of the perl@ ports.

- Remove dependencies in core
- Put testing depends in TEST_DEPENDS
- Remove unnecessary bsd.port.options.mk inclusions
- Remove checks for Perl versions that no longer exist in the ports tree
- Sort plists, some of which were so jumbled that I have to assume
  the plist was randomized before committing

A lot of the plist changes in this commit are moving PERL5_MAN3 after
SITE_PERL. It's repo churn now, but it makes updating the ports later
far easier.

Change the way Perl modules are installed, update the default Perl to 5.18.

Before, we had:

  site_perl :           lib/perl5/site_perl/5.18
  site_perl/perl_arch : lib/perl5/site_perl/5.18/mach
  perl_man3 :           lib/perl5/5.18/man/man3

Now we have:

  site_perl : lib/perl5/site_perl
  site_arch : lib/perl5/site_perl/mach/5.18
  perl_man3 : lib/perl5/site_perl/man/man3

Modules without any .so will be installed at the same place regardless of the
Perl version, minimizing the upgrade when the major Perl version is changed.
It uses a version dependent directory for modules with compiled bits.

As PERL_ARCH is no longer needed in plists, it has been removed from
PLIST_SUB.

The USE_PERL5=fixpacklist keyword is removed, the .packlist file is now
always removed, as is perllocal.pod.

The old site_perl and site_perl/arch directories have been kept in the
default Perl @INC for all Perl ports, and will be phased out as these old
Perl versions expire.

PR:		194969
Differential Revision:	https://reviews.freebsd.org/D1019
Exp-run by:	antoine
Reviewed by:	perl@
Approved by:	portmgr

Cleanup plist

- update to 1.31

- Update to 1.28

Sponsored by:	OBS

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

- Convert to new perl framework - Trim Makefile header - Remove MAKE_JOBS_SAFE=yes, it's the default.

For perl@ owned ports:

- Fix COMMENT
- Trim header

- Update to 1.27 - Changelog: http://cpansearch.perl.org/src/TFRAYNER/Bio-MAGETAB-1.27/Changes

- Update to 1.26 Changes: http://cpansearch.perl.org/src/TFRAYNER/Bio-MAGETAB-1.26/Changes

Feature safe:	yes

- Update to 1.23 - Add LICENSE - Remove WRKSRC

Changes:	http://search.cpan.org/dist/Bio-MAGETAB/Changes

- Update to 1.22

Changes:	http://search.cpan.org/dist/Bio-MAGETAB/Changes

- Update to 1.21

Changes:	http://search.cpan.org/dist/Bio-MAGETAB/Changes
Feature safe:	yes

- Add build depends to silence build warnings

- Update to 1.20 - Sort RUN_DEPENDS and MAN3

Changes:	http://search.cpan.org/dist/Bio-MAGETAB/Changes

- Get Rid MD5 support

- Update to 1.13

PR:		ports/150317
Submitted by:	Frederic Culot <frederic@culot.org>

Update to 1.12: - dependency on MooseX::FollowPBP added - dependency on Moose::Policy removed

PR:		ports/149612
Submitted by:	Frederic Culot <frederic@culot.org>

Update to 1.10.

Changes:	http://search.cpan.org/dist/Bio-MAGETAB/Changes

- Update to 1.00 - Set maintainer to perl@

- Update to 0.99 - Update my mail address to FreeBSD

Utilize %%SITE_PERL%% and %%PERL_ARCH%% in pkg-plists

PR:             ports/136771
Exp Run by:     pav
Approved by:    portmgr (pav)

p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This is a beta release. All functions have now been implemented and most have test suites; the exceptions include the modules involved in export of MAGE-TAB documents, which are still a little experimental in nature. The API is mostly finalised (and fully documented), but some details may yet change where necessary to improve usabil

WWW: http://search.cpan.org/dist/Bio-MAGETAB/

PR:		ports/136021
Submitted by:	Wen Heping <wenheping at gmail.com>