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Port details
p5-Bio-GFF3 Fast low-level functions for parsing and formatting GFF3
2.0_2 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.0_2Version of this port present on the latest quarterly branch.
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2011-04-22 08:51:49
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: perl5
License: ART10 GPLv1+
WWW:
https://metacpan.org/release/Bio-GFF3
Description:
Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files. All they do is convert back and forth between low-level Perl data structures and GFF3 text.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (19 items)
Collapse this list.
  1. /usr/local/share/licenses/p5-Bio-GFF3-2.0_2/catalog.mk
  2. /usr/local/share/licenses/p5-Bio-GFF3-2.0_2/LICENSE
  3. /usr/local/share/licenses/p5-Bio-GFF3-2.0_2/ART10
  4. /usr/local/share/licenses/p5-Bio-GFF3-2.0_2/GPLv1+
  5. bin/gff3_from_fasta
  6. lib/perl5/site_perl/Bio/GFF3/LowLevel.pm
  7. lib/perl5/site_perl/Bio/GFF3/LowLevel/Parser.pm
  8. lib/perl5/site_perl/Bio/GFF3/LowLevel/Parser/1_0_backcompat.pm
  9. lib/perl5/site_perl/Bio/GFF3/Transform/FromFasta.pm
  10. lib/perl5/site_perl/Bio/GFF3/Transform/SyncDirectives.pm
  11. lib/perl5/site_perl/man/man3/Bio::GFF3::LowLevel.3.gz
  12. lib/perl5/site_perl/man/man3/Bio::GFF3::LowLevel::Parser.3.gz
  13. lib/perl5/site_perl/man/man3/Bio::GFF3::LowLevel::Parser::1_0_backcompat.3.gz
  14. lib/perl5/site_perl/man/man3/Bio::GFF3::Transform::FromFasta.3.gz
  15. lib/perl5/site_perl/man/man3/Bio::GFF3::Transform::SyncDirectives.3.gz
  16. lib/perl5/site_perl/man/man1/gff3_from_fasta.1.gz
  17. @owner
  18. @group
  19. @mode
Collapse this list.
Dependency lines:
  • p5-Bio-GFF3>0:biology/p5-Bio-GFF3
To install the port:
cd /usr/ports/biology/p5-Bio-GFF3/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/p5-Bio-GFF3
  • pkg install p5-Bio-GFF3
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: p5-Bio-GFF3
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (Bio-GFF3-2.0.tar.gz) = cbfef8376d3d9026483360150e3745a27dad78e995348d0c08ef5b2e4374170c SIZE (Bio-GFF3-2.0.tar.gz) = 74951

Packages (timestamps in pop-ups are UTC):
p5-Bio-GFF3
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.0_22.0_22.0_22.0_22.0_2-2.0_2-
FreeBSD:13:quarterly2.0_22.0_22.0_22.0_22.0_22.0_22.0_22.0_2
FreeBSD:14:latest2.0_22.0_22.0_22.0_22.0_22.0_2-2.0_2
FreeBSD:14:quarterly2.0_22.0_2-2.0_22.0_22.0_22.0_22.0_2
FreeBSD:15:latest2.0_22.0_2n/a2.0_2n/a2.0_22.0_22.0_2
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. p5-File-ReadBackwards>=0 : devel/p5-File-ReadBackwards
  2. p5-List-MoreUtils>=0 : lang/p5-List-MoreUtils
  3. p5-URI>=0 : net/p5-URI
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
  5. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. p5-File-ReadBackwards>=0 : devel/p5-File-ReadBackwards
  2. p5-List-MoreUtils>=0 : lang/p5-List-MoreUtils
  3. p5-URI>=0 : net/p5-URI
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_p5-Bio-GFF3
USES:
perl5
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (12 items)
Collapse this list.
  1. ftp://ftp.auckland.ac.nz/pub/perl/CPAN/modules/by-module/Bio/
  2. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/
  3. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/Bio/
  4. ftp://ftp.funet.fi/pub/languages/perl/CPAN/modules/by-module/Bio/
  5. ftp://ftp.kddlabs.co.jp/lang/perl/CPAN/modules/by-module/Bio/
  6. ftp://ftp.mirrorservice.org/sites/cpan.perl.org/CPAN/modules/by-module/Bio/
  7. http://backpan.perl.org/modules/by-module/Bio/
  8. http://ftp.jaist.ac.jp/pub/CPAN/modules/by-module/Bio/
  9. http://ftp.twaren.net/Unix/Lang/CPAN/modules/by-module/Bio/
  10. https://cpan.metacpan.org/modules/by-module/
  11. https://cpan.metacpan.org/modules/by-module/Bio/
  12. https://www.cpan.org/modules/by-module/Bio/
Collapse this list.

Number of commits found: 31

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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)
2.0_2
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (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.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.0_2
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
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>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.0_2
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
2.0_2
06 Oct 2018 13:06:45
Revision:481365Original commit files touched by this commit
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)
2.0_2
27 May 2018 20:15:20
Revision:470993Original commit files touched by this commit
sunpoet search for other commits by this committer
Update WWW

search.cpan.org is shutting down.
It will redirect to metacpan.org after June 25, 2018.

With hat:	perl
2.0_2
15 Sep 2017 08:58:50
Revision:449893Original commit files touched by this commit
mat search for other commits by this committer
Fix license information for portgs that use "the same license as Perl".

Sponsored by:	Absolight
2.0_2
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
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
2.0_2
14 Sep 2015 12:19:50
Revision:396892Original commit files touched by this commit
mat search for other commits by this committer
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
2.0_2
26 Nov 2014 13:08:38
Revision:373448Original commit files touched by this commit
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
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.0_1
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
2.0_1
26 Mar 2014 14:23:09
Revision:349256Original commit files touched by this commit
sunpoet search for other commits by this committer
- Fix PLIST
- Bump PORTREVISION for package change

Reported by:	swills
2.0
25 Mar 2014 19:34:04
Revision:349176Original commit files touched by this commit
sunpoet search for other commits by this committer
- Update to 2.0

Changes:	http://search.cpan.org/dist/Bio-GFF3/Changes
1.9
23 Jan 2014 03:28:37
Revision:340794Original commit files touched by this commit
sunpoet search for other commits by this committer
- Update to 1.9
- Sort PLIST

Changes:	http://search.cpan.org/dist/Bio-GFF3/Changes
1.8
02 Nov 2013 19:55:32
Revision:332533Original commit files touched by this commit
sunpoet search for other commits by this committer
- Update to 1.8

Changes:	http://search.cpan.org/dist/Bio-GFF3/Changes
1.7
03 Oct 2013 16:19:59
Revision:329204Original commit files touched by this commit
sunpoet search for other commits by this committer
- Update to 1.7
- Support STAGEDIR

Changes:	http://search.cpan.org/dist/Bio-GFF3/Changes
1.6
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
1.6
06 Aug 2013 13:03:54
Revision:324315Original commit files touched by this commit
sunpoet search for other commits by this committer
- Pet portlint: remove blank line among *_DEPENDS
1.6
01 Aug 2013 13:15:49
Revision:324103Original commit files touched by this commit
jadawin search for other commits by this committer
- Update to 1.6
- Convert to new perl5 framework
- Changelog: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-1.6/Changes
1.5
16 Dec 2012 04:22:15
Revision:308979Original commit files touched by this commit
wen search for other commits by this committer
- Update to 1.5
Changes: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-1.5/Changes
1.4
30 Oct 2012 01:59:37
Revision:306654Original commit files touched by this commit
wen search for other commits by this committer
- Update to 1.4
Changes: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-1.4/Changes
- Trim Makefile headers

Feature safe:	yes
1.3
25 Jul 2012 06:32:08
Original commit files touched by this commit
cs search for other commits by this committer
Fix typos in COMMENT
1.3
26 Apr 2012 10:37:09
Original commit files touched by this commit
culot search for other commits by this committer
- Update to 1.3

Changes:        http://search.cpan.org/dist/Bio-GFF3/Changes
1.2
16 Apr 2012 13:06:04
Original commit files touched by this commit
culot search for other commits by this committer
- Update to 1.2
- Add LICENSE (Artistic 1 & GPL 1)
- Add TEST_DEPENDS

Changes:        http://search.cpan.org/dist/Bio-GFF3/Changes
1.0
22 Mar 2012 11:08:28
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 1.0
- Reset maintainer to perl@

Feature safe:   yes
0.7
10 Oct 2011 02:33:51
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.7
ChangeLog: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-0.7/Changes
0.6
22 Sep 2011 07:34:49
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.6
ChangeLog: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-0.6/Changes
0.5
18 Aug 2011 01:30:02
Original commit files touched by this commit
swills search for other commits by this committer
- Add missing BUILD_DEPENDS

PR:             ports/159827
Submitted by:   swills (me)
Approved by:    wen (maintainer)
0.5
10 Jun 2011 08:12:40
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.5
ChangeLog: http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-0.5/Changes
0.4
09 May 2011 06:32:51
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.4
http://cpansearch.perl.org/src/RBUELS/Bio-GFF3-0.4/Changes
0.3
22 Apr 2011 08:51:25
Original commit files touched by this commit
wen search for other commits by this committer
Bio::GFF3 are low-level, fast functions for parsing GFF version 3 files.
All they do is convert back and forth between low-level Perl data
structures and GFF3 text.

WWW: http://search.cpan.org/dist/Bio-GFF3/

Number of commits found: 31