biology/p5-Bio-Das1.17_4

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 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

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

Sponsored by:	Absolight

- Add LICENSE - Add NO_ARCH - Sort *_DEPENDS - Bump PORTREVISION for biology/p5-bioperl renaming

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

With hat:	portmgr
Sponsored by:	Absolight

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

- support stage

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.

Cleanup supporting perl version 5.8 and 5.10, lang/perl5.8 and lang/5.10 will be removed from ports tree soon.

- Convert all remaining instances of BUILD_DEPENDS=${RUN_DEPENDS} or   RUN_DEPENDS=${BUILD_DEPENDS} to use := which portlint has warned   about for a while.

PR:		ports/168208
Approved by:	portmgr (miwi)

- update png to 1.5.10

- Revert ports/165605 as requested by portmgr@

Note: devel/p5-B-Size and devel/p5-Devel-Arena
where intentionally not restored.

PR:             ports/165605
Approved by:    portmgr (bapt)
Feature safe:   yes (I sure hope so)

- Remove ports that only work with < perl 5.12 (devel/p5-B-Size, devel/p5-Devel-Arena) - Remove conditionals for PERL_LEVEL < 501200 - Remove regression-test targets b/c this will be centralized in Mk/bsd.perl.mk - Other minor cleanups   RUN_DEPENDS = ${BUILD_DEPENDS} -> RUN_DEPENDS:= ${BUILD_DEPENDS}

PR:             ports/165605
Submitted by:   pgollucci (myself)
Approved by:    portmgr (linimon)
Exp Run by:     linimon
Tested by:      make index

- remove maintainer tags from pkg-descr

Approved by:	portmgr
Approved by:	bapt (mentor)

- Get Rid MD5 support

Change dependency on old p5-Compress-Zlib, p5-IO-Compress-Base, p5-IO-Compress-Zlib and p5-IO-Compress-Bzip2 modules to p5-IO-Compress. Explicitly depend on p5-IO-Compress only if PERL_LEVEL < 500903 Bump PORTREVISION

- Update to 1.17

Feature safe:	yes

- Update to 1.16

Feature safe:	yes

- Update to 1.15

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

- update to jpeg-8

- Update to 1.14

- Update to 1.12

PR:		138230
Submitted by:	Wen Heping <wenheping@gmail.com>

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

- lang/perl5.6 is dead, remove PERL_LEVEL/PERL_VERSION < 500801 checks

PR:             ports/135398
Tested by:      2 -exp runs by pav
Approved by:    portmgr (pav)

- Update to 1.11

- update to 1.10

- Update to 1.09

Update to 1.08

- Include some ports in perl5 category.

PR:		ports/123530
Submitted by:	Philip M. Gollucci <pgollucci@p6m7g8.com>
Reworked by:	araujo (myself)
Approved by:	flz (portmgr)

- 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)

- Update to 1.07

- Update to 1.06 - Remove 4.X cruft

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

Reset razi@genet.sickkids.on.ca due to maintainer-timeouts and no response to email.

Hat:		portmgr

- Update to 1.03

PR:		ports/106300
Submitted by:	chinsan
Approved by:	maintainer timeout (15 days)

Correct path to Compress::Zlib.pm after recent p5-Compress-Zlib update.

SHA256ify

Approved by:    krion@

- Remove symlinks that belong to mtree

Approved by:	maintainers

Add the right MASTER_SITE_SUBDIR, so that this port is fetchable from  20 sites instead of just 1.

Add p5-Bio-Das 1.02, client-side library for Distributed Genome Annotation System.

PR:		ports/76379
Submitted by:	Razi Khaja <razi@genet.sickkids.on.ca>