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

Number of commits found: 50

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 
Tuesday, 26 Dec 2017
23:20 sunpoet search for other commits by this committer
Update to 2.0.1

Changes:	https://github.com/rvosa/bio-phylo/releases
Original commitRevision:457333 
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_FILE
- Add NO_ARCH
- Bump PORTREVISION for biology/p5-bioperl renaming
Original commitRevision:428871 
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 
Sunday, 7 Dec 2014
04:41 wen search for other commits by this committer
- Update to 0.58
Original commitRevision:374171 
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 
Saturday, 20 Jul 2013
10:04 wen search for other commits by this committer
- Update to 0.56
Original commitRevision:323340 
Saturday, 16 Feb 2013
14:58 culot search for other commits by this committer
- Update to 0.52 [1]
- Capitalize names (Perl) in COMMENT

PR:		ports/176003 [1]
Submitted by:	Gea-Suan Lin <gslin@gslin.org>
Original commitRevision:312356 
Tuesday, 12 Jun 2012
18:55 sunpoet search for other commits by this committer
- Update to 0.50
- Add TEST_DEPENDS
- Sort PLIST
Original commit
Sunday, 3 Jun 2012
15:12 sunpoet search for other commits by this committer
- Update to 0.49
Original commit
Friday, 1 Jun 2012
05:26 dinoex search for other commits by this committer
- update png to 1.5.10
Original commit
Thursday, 3 May 2012
09:48 sunpoet search for other commits by this committer
- Update to 0.48
- Add BUILD_DEPENDS
Original commit
Wednesday, 11 Apr 2012
01:34 wen search for other commits by this committer
- Update to 0.47
Original commit
Monday, 5 Mar 2012
08:22 wen search for other commits by this committer
- Update to 0.46
Original commit
Saturday, 29 Oct 2011
06:20 sunpoet search for other commits by this committer
- Update to 0.45
Original commit
Monday, 17 Oct 2011
01:38 sunpoet search for other commits by this committer
- Update to 0.43
Original commit
Tuesday, 9 Aug 2011
18:26 culot search for other commits by this committer
- Update to 0.40
- Add LICENSE (Artistic 1 & GPLv1)
Original commit
Monday, 1 Aug 2011
03:11 sunpoet search for other commits by this committer
- Update to 0.39
Original commit
Saturday, 16 Jul 2011
06:08 sunpoet search for other commits by this committer
- Update to 0.38
- Sort MAN3 and PLIST
Original commit
Friday, 1 Apr 2011
08:34 wen search for other commits by this committer
- Update to 0.36
Original commit
Monday, 28 Feb 2011
01:30 wen search for other commits by this committer
- Update to 0.35
Original commit
Thursday, 23 Dec 2010
06:33 wen search for other commits by this committer
- Update to 0.34
Original commit
Thursday, 16 Dec 2010
08:19 wen search for other commits by this committer
- Update to 0.33
Original commit
Sunday, 12 Dec 2010
21:29 pgollucci search for other commits by this committer
- Update to 0.32

With Hat:       perl@
Changes:        http://search.cpan.org/dist/Bio-Phylo/Changes
Original commit
Monday, 22 Nov 2010
08:50 wen search for other commits by this committer
- Update to 0.31
Original commit
Wednesday, 17 Nov 2010
06:24 wen search for other commits by this committer
- Update to 0.30

PR:             ports/152205
Submitted by:   Gea-Suan Lin <gslin@gslin.org>
Original commit
Tuesday, 9 Nov 2010
14:15 jadawin search for other commits by this committer
- Update to 0.28
Original commit
Monday, 25 Oct 2010
10:59 wen search for other commits by this committer
- Update to 0.26
- Reset maintainer to perl@
Original commit
Friday, 22 Oct 2010
09:29 wen search for other commits by this committer
- Update to 0.22
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
Tuesday, 9 Mar 2010
07:34 wen search for other commits by this committer
- Update to 0.21
Original commit
Wednesday, 3 Mar 2010
13:44 wen search for other commits by this committer
- Update to 0.18
- Adopt

Feature safe:   yes
Original commit
Friday, 5 Feb 2010
11:46 dinoex search for other commits by this committer
- update to jpeg-8
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
Tuesday, 29 Apr 2008
05:27 linimon search for other commits by this committer
Reset aaron's port maintainerships due to many maintainer-timeouts.
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
Saturday, 8 Sep 2007
00:53 linimon search for other commits by this committer
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
Original commit
Tuesday, 19 Jun 2007
20:15 aaron search for other commits by this committer
Bump to v0.16.

PR:             111719
Submitted by:   araujo@bsdmail.org
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, 27 Dec 2006
18:58 aaron search for other commits by this committer
Update to v0.15
Original commit
Thursday, 7 Dec 2006
15:43 laszlof search for other commits by this committer
- Update to 0.14

Submitted by:   Jin-Shan Tseng <tjs@cdpa.nsysu.edu.tw>
Approved by:    maintainer timeout (3 months)
Original commit
Friday, 19 May 2006
23:18 aaron search for other commits by this committer
- Updated from 0.07 to 0.12

Approved by:    tobez (implicit)

0.08 20/Feb/2006 15:14
                       Improved referential integrity between nodes,
                                taxa, and data.
                       Implemented Fastnexus parser
                       Node object silently implements Bio::Tree::NodeI
                                interface if BioPerl is installed
                       Tree object silently implements Bio::Tree::TreeI
                                interface if BioPerl is installed
                       Added convertor methods for XML and CIPRES
                       Implemented more Matrix methods
                       Implemented symbol tables in Bio::Phylo::Util::CONSTANT
                       Implemented visit method for listable objects
                       Implemented caching infrastructure for calculations
                       Changed object-model to inside-out arrays
                       Added Biodiversity measures code by Aki Mimoto
                       Moved constants and exceptions to Bio::Phylo::Util::*
                       Fixed memory leak due to circular references
Original commit
Saturday, 13 May 2006
16:48 aaron search for other commits by this committer
Adding port biology/p5-Bio-Phylo, Phylogenetic analysis using perl.

Approved by:    tobez (implicit)
Original commit

Number of commits found: 50