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non port: biology/p5-Bio-Das/Makefile

Number of commits found: 40

Wednesday, 7 Sep 2022
21:10 Stefan E├čer (se) search for other commits by this committer
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)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Wednesday, 20 Jul 2022
14:20 Tobias C. Berner (tcberner) search for other commits by this committer
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
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 37526bb
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Saturday, 6 Oct 2018
13:06 des search for other commits by this committer
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)
Original commitRevision:481365 
Friday, 15 Sep 2017
08:58 mat search for other commits by this committer
Fix license information for portgs that use "the same license as Perl".

Sponsored by:	Absolight
Original commitRevision:449893 
Sunday, 18 Dec 2016
15:25 sunpoet search for other commits by this committer
- Add LICENSE
- Add NO_ARCH
- Sort *_DEPENDS
- Bump PORTREVISION for biology/p5-bioperl renaming
Original commitRevision:428870 
Friday, 1 Apr 2016
13:29 mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Original commitRevision:412344 
Wednesday, 26 Nov 2014
13:08 mat search for other commits by this committer
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
Original commitRevision:373448 
Sunday, 5 Jan 2014
12:07 az search for other commits by this committer
- support stage
Original commitRevision:338751 
Friday, 20 Sep 2013
15:55 bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
Original commitRevision:327709 
Friday, 2 Aug 2013
18:52 mat search for other commits by this committer
- Convert to new perl framework
- Trim Makefile header
- Remove MAKE_JOBS_SAFE=yes, it's the default.
Original commitRevision:324174 
Monday, 17 Dec 2012
15:39 az search for other commits by this committer
Cleanup supporting perl version 5.8 and 5.10,
lang/perl5.8 and lang/5.10 will be removed from ports tree soon.
Original commitRevision:309105 
Sunday, 10 Jun 2012
18:42 swills search for other commits by this committer
- 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)
Original commit
Friday, 1 Jun 2012
05:26 dinoex search for other commits by this committer
- update png to 1.5.10
Original commit
Tuesday, 13 Mar 2012
16:15 pgollucci search for other commits by this committer
- 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)
Original commit
Thursday, 8 Mar 2012
18:45 pgollucci search for other commits by this committer
- 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
Original commit
Tuesday, 21 Sep 2010
07:56 mm search for other commits by this committer
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
Original commit
Wednesday, 30 Jun 2010
07:36 wen search for other commits by this committer
- Update to 1.17

Feature safe:   yes
Original commit
Thursday, 24 Jun 2010
00:24 wen search for other commits by this committer
- Update to 1.16

Feature safe:   yes
Original commit
Saturday, 12 Jun 2010
06:18 wen search for other commits by this committer
- Update to 1.15
Original commit
Sunday, 28 Mar 2010
06:47 dinoex search for other commits by this committer
- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi
Original commit
Friday, 5 Feb 2010
11:46 dinoex search for other commits by this committer
- update to jpeg-8
Original commit
Tuesday, 8 Sep 2009
12:08 jadawin search for other commits by this committer
- Update to 1.14
Original commit
Thursday, 27 Aug 2009
20:34 miwi search for other commits by this committer
- Update to 1.12

PR:             138230
Submitted by:   Wen Heping <wenheping@gmail.com>
Original commit
Friday, 31 Jul 2009
13:57 dinoex search for other commits by this committer
- bump all port that indirectly depends on libjpeg and have not yet been bumped
or updated
Requested by:   edwin
Original commit
Wednesday, 22 Jul 2009
16:27 pgollucci search for other commits by this committer
- 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)
Original commit
Monday, 8 Jun 2009
09:30 jadawin search for other commits by this committer
- Update to 1.11
Original commit
Thursday, 11 Dec 2008
05:19 leeym search for other commits by this committer
- update to 1.10
Original commit
Saturday, 31 May 2008
13:46 miwi search for other commits by this committer
- Update to 1.09
Original commit
Friday, 23 May 2008
12:22 mat search for other commits by this committer
Update to 1.08
Original commit
Monday, 19 May 2008
13:12 araujo search for other commits by this committer
- 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)
Original commit
Thursday, 17 Apr 2008
14:30 araujo search for other commits by this committer
- 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)
Original commit
Wednesday, 12 Mar 2008
12:24 miwi search for other commits by this committer
- Update to 1.07
Original commit
Friday, 7 Sep 2007
14:45 miwi search for other commits by this committer
- Update to 1.06
- Remove 4.X cruft
Original commit
Saturday, 19 May 2007
20:32 flz search for other commits by this committer
- Welcome X.org 7.2 \o/.
- Set X11BASE to ${LOCALBASE} for recent ${OSVERSION}.
- Bump PORTREVISION for ports intalling files in ${X11BASE}.
Original commit
Wednesday, 14 Mar 2007
08:18 linimon search for other commits by this committer
Reset razi@genet.sickkids.on.ca due to maintainer-timeouts and no response to
email.

Hat:            portmgr
Original commit
Tuesday, 19 Dec 2006
06:47 rafan search for other commits by this committer
- Update to 1.03

PR:             ports/106300
Submitted by:   chinsan
Approved by:    maintainer timeout (15 days)
Original commit
Sunday, 3 Dec 2006
12:45 demon search for other commits by this committer
Correct path to Compress::Zlib.pm after recent p5-Compress-Zlib update.
Original commit
Saturday, 26 Nov 2005
03:40 fenner search for other commits by this committer
Add the right MASTER_SITE_SUBDIR, so that this port is fetchable from
 20 sites instead of just 1.
Original commit
Thursday, 1 Sep 2005
13:09 garga search for other commits by this committer
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>
Original commit

Number of commits found: 40