biology/p5-bioperl 1.007008

biology/p5-BioPerl: Update to 1.007008

- Update WWW
- Sort *_DEPENDS

Changes:	https://metacpan.org/dist/BioPerl/changes

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.

Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113

- Fix LICENSE_FILE
- Update pkg-descr
- Update WWW
- Bump PORTREVISION of dependent ports for dependency change

Changes:	https://metacpan.org/changes/distribution/IO-Stringy

Update to 1.007007 (1.7.7)

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

Update to 1.007006 (1.7.6)

- Remove PGTEST and SQLITETEST options: DBD::Pg and DBD::SQLite have been removed from BioPerl by upstream for the move of modules and programs into separate distributions

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

Update to 1.007005 (1.7.5)

- Fix DISTNAME
- Bump PORTREVISION for package change

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

Update WWW

Update to 1.007005 (1.7.5)

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

Update to 1.007004 (1.7.4)

- Add LICENSE_FILE
- Use USES=shebangfix
- Use COPYTREE_SHARE instead of CP -R
- Take maintainership

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

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)

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

Sponsored by:	Absolight

- Update to 1.007002 Changes: http://search.cpan.org/src/CJFIELDS/BioPerl-1.007002/Changes

Remove outdated PERL_LEVEL check

- Fix shebangs

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 - Update *_DEPENDS - Use TEST_DEPENDS: Test::Most and URI::Escape are test-only dependencies - Use PORTDATA, PORTDOCS and PORTEXAMPLES

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

- Move biology/p5-bioperl to biology/p5-BioPerl - Sort *_DEPENDS - Bump PORTREVISION for dependent ports

- Remove unnecessary USES=shebangfix - Convert to new options target helper

- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket

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

With hat:	portmgr
Sponsored by:	Absolight

Make it so that the default Perl is always called perl5.

- Move Perl's man1 files along with its man3 files.
- Move where Perl installs its modules man1 pages.
- Convert the ports installing man1 pages.
- Make different Perl versions installable at the same time.
  Though you should note that only the default version can be used to
  install Perl modules, and the non default Perl versions cannot use the
  modules installed via ports if they contain .so as they are installed
  in a version specific directory.

Reviewed by:	bapt (the Mk bits)
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D3542

- Fix shebangs - Add NO_ARCH - Add missing EXAMPLES option

Approved by:	portmgr blanket
MFH:		2015Q2

Reassign biology/ perl modules to perl@.

While here:

Regenerate p5-AcePerl's patches using makepatch.
Make p5-Bio-ASN1-EntrezGene depend on p5-bioperl, instead of the
other way around. Bump PORTREVISION on those two ports.

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

biology/p5-bioperl: fix pkg-descr sidenote link

- Update to 1.6.924 [1] - Reset maintainer to perl@

PR:		192088 [1]
Submitted by:	Kurt Jaeger<pi@FreeBSD.org> [1]

- Update to 1.6.923 - Add STAGE support

PR:		190342
Submitted by:	Muhammad Moinur Rahman <5u623l20@gmail.com>

Mark as broken unstaged perl ports

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 new perl framework - Trim Makefile header

Approved by:	wen@ (maintainer)

- Avoid of using SITE_PERL - Remove depend on DB_File.pm since it part of perl distribution

PR:		ports/178877
Submitted by:	az
Approved by:	matainer (timeout)

- Take maintainership

- Reassign to the heap at maintainer's request

- 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

- remove maintainer tags from pkg-descr

Approved by:	portmgr
Approved by:	bapt (mentor)

- Get Rid MD5 support

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

- update to jpeg-8

- Remove unneeded dependencies which is in perl-5.8.9 dist   (part 19; last!).

Approved by:	portmgr (itetcu)

- Update to 1.6.1

Approved by:	maintainer (via Email)