biology/p5-bioperl-run 1.007003

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.

Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago

Update to 1.007003

- Take maintainership

Changes:	https://metacpan.org/changes/distribution/BioPerl-Run

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 to 1.007002

Changes:	http://search.cpan.org/dist/BioPerl-Run/Changes

Fix license information for portgs that use "the same license as Perl".

Sponsored by:	Absolight

Bump PORTREVISION for ports affected by the fix the last commit.

Done with:	Tools/scripts/bump-revision.sh
Sponsored by:	Absolight

- Update to 1.007001

Changes:	http://search.cpan.org/dist/BioPerl-Run/Changes

- Update to 1.007000 - Change MASTER_SITES back to CPAN - Update LICENSE - Add LICENSE_FILE - Use PORTDOCS - Convert to options target helper - Use INSTALL_SCRIPT - Pet portlint: fix diff header of patch file

Changes:	http://search.cpan.org/dist/BioPerl-Run/Changes

- Move biology/p5-bioperl-run to biology/p5-BioPerl-Run - Sort *_DEPENDS - Add NO_ARCH - Bump PORTREVISION for biology/p5-bioperl renaming

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

With hat:	portmgr
Sponsored by:	Absolight

For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME to include GH_PROJECT/GH_ACCOUNT/GH_TAGNAME. This prevents the distfile having the same name despite changing one of these values and causing a bad checksum.

Differential Revision:	https://reviews.freebsd.org/D2103
Reviewed by:	mat
With hat:	bdrewery

Convert to new USE_GITHUB.

While there, cleanup.

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.

- Simplify Makefile - Use tab instead of space - Sort PLIST - Pass maintainership to perl@

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

biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagify

Reset maintainership for ports not staged with no pending PR

With hat:	portmgr

Mark BROKEN: Fails to configure

===>  Configuring for p5-bioperl-run-1.6.1_4
Invalid prerequisite condition '0/processing XML data/Bio::Tools::Run::EMBOSSacd' for XML::Twig at /usr/local/lib/perl5/site_perl/5.16/Module/Build/Base.pm line 1702.
*** [do-configure] Error code 25

Reported by:	pkg-fallout
With hat:	portmgr

Remove trailing whitespaces from category biology

According to the Porter's Handbook (5.12.2.3.) default options must be added to OPTIONS_DEFINE. This policy has been implemented only recently that's why we have many ports violating this policy.

This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.

Approved by:    portmgr (bapt)

Convert biology to MDOCS and MEXAMPLES

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

- convert to the new perl5 framework

Approved by:	portmgr (bapt@, blanket)

- Remove SITE_PERL from *_DEPENDS

Approved by: portmgr@ (bapt@)

- update png to 1.5.10

At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450 ports use BUILD_DEPENDS:= ${RUN_DEPENDS}. This patch fixes ports that are currently broken. This is a temporary measure until we organically stop using := or someone(s) spend a lot of time changing all the ports over.

Explicit duplication > := > = and this just moves ports one step to the left

Approved by:	portmgr

- Get Rid MD5 support

- update to 1.4.1 Reviewed by:	exp8 run on pointyhat Supported by:	miwi

- update to jpeg-8

- Relax check on bioperl version; people keep forgetting to update this check   when updating bioperl port

Reported by:	pointyhat

- bump all port that indirectly depends on libjpeg and have not yet been bumped or updated Requested by:	edwin

- Update to 1.6.1

PR:		132122
Submitted by:	Wen Heping <wenheping@gmail.com>
Approved by:	maintainer

- Unbreak after p5-bioperl changed portrevision

- Take advantage of CPAN macro from bsd.sites.mk, change ${MASTER_SITE_PERL_CPAN} to CPAN.

PR:		ports/122674
Submitted by:	Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:	araujo (myself)
Approved by:	portmgr (pav)

Welcome bsd.perl.mk.  Add support for constructs such as USE_PERL5=5.8.0+. Drop support for antique perl.

Work done by:	gabor
Sponsored by:	Google Summer of Code 2007
Hat:		portmgr

- Welcome X.org 7.2 \o/. - Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}. - Bump PORTREVISION for ports intalling files in ${X11BASE}.

Bioperl-run contain modules that provides a PERL interface to various bioinformatics applications. This allows various applications to be used with common Bioperl objects.

WWW: http://bioperl.org/

PR:		ports/93674
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>