biology/p5-Bio-ASN1-EntrezGene 1.73_2,1

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.

Update *_DEPENDS

- Bump PORTREVISION for dependency change

The circular dependency among p5-Bio-Cluster, p5-Bio-DB-NCBIHelper, p5-Bio-Variation and this port has been resolved in p5-Bio-Variation 1.7.5 update.

Install Bio::SeqIO::entrezgene

- Bump PORTREVISION for package change
- Take maintainership

Bio::SeqIO::entrezgene has been removed from BioPerl since 1.7.3.

Update to 1.73

Changes:	https://metacpan.org/changes/distribution/Bio-ASN1-EntrezGene

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 - Bump PORTREVISION for biology/p5-bioperl renaming

- Update to 1.72 Changes: http://search.cpan.org/~cjfields/Bio-ASN1-EntrezGene-1.72/

- 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

Start removing MASTER_SITE_SUBDIR=CPAN:username where possible. The downside to having this set is that portscout cannot find new releases when the username changes (which happens often in large projects with multiple maintainers).

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.

biology/p5-Bio-ASN1-EntrezGene: bump PORTEPOCH

Apparently in some world I don't live in 1.091 > 1.70
pkg needs this port's epoch to be bumped

reported by: 	wen

biology/p5-Bio-ASN1-EntrezGene: Upgrade 1.09 => 1.70 to unbreak

While here, reset the port.  The last time the maintainer was seen was
in 2005, when the port was created.  Also, rewrap the package description
such that it keeps within 75 characters; also move the url so it won't
wrap across lines.

Mark as broken unfetchable ports

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

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

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

- add stage support

Approved by:	portmgr (blanket infrastructure)

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 maintainer tags from pkg-descr

Approved by:	portmgr
Approved by:	bapt (mentor)

- Get Rid MD5 support

- 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

SHA256ify

Approved by:    krion@

Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry

Approved by:    krion@
PR:             ports/88711 (related)

Add p5-Bio-ASN1-EntrezGene, a Regular expression-based Perl Parser for NCBI Entrez Gene.

PR:		87423
Submitted by:	Mauricio Herrera Cuadra <mauricio@arareko.net>
Approved by:	novel (mentor) (implicit)