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Port details
p5-Bio-ASN1-EntrezGene Regular expression-based Perl Parser for NCBI Entrez Gene
1.73_2,1 biology on this many watch lists=1 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 1.73_2,1Version of this port present on the latest quarterly branch.
Maintainer: sunpoet@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2005-10-15 20:11:03
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
People watching this port, also watch:: p5-Syntax-Highlight-Perl-Improved, py39-biopython, p5-XML-DOM-XPath
Also Listed In: perl5
License: ART10 GPLv1+
WWW:
https://metacpan.org/release/Bio-ASN1-EntrezGene
Description:
Bio::ASN1::EntrezGene is a regular expression-based Perl Parser for NCBI Entrez Gene genome databases [1]. It parses an ASN.1-formatted Entrez Gene record and returns a data structure that contains all data items from the gene record. [1] http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene The parser will report error & line number if input data does not conform to the NCBI Entrez Gene genome annotation file format.
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 (17 items)
Collapse this list.
  1. /usr/local/share/licenses/p5-Bio-ASN1-EntrezGene-1.73_2,1/catalog.mk
  2. /usr/local/share/licenses/p5-Bio-ASN1-EntrezGene-1.73_2,1/LICENSE
  3. /usr/local/share/licenses/p5-Bio-ASN1-EntrezGene-1.73_2,1/ART10
  4. /usr/local/share/licenses/p5-Bio-ASN1-EntrezGene-1.73_2,1/GPLv1+
  5. lib/perl5/site_perl/Bio/ASN1/EntrezGene.pm
  6. lib/perl5/site_perl/Bio/ASN1/EntrezGene/Indexer.pm
  7. lib/perl5/site_perl/Bio/ASN1/Sequence.pm
  8. lib/perl5/site_perl/Bio/ASN1/Sequence/Indexer.pm
  9. lib/perl5/site_perl/Bio/SeqIO/entrezgene.pm
  10. lib/perl5/site_perl/man/man3/Bio::ASN1::EntrezGene.3.gz
  11. lib/perl5/site_perl/man/man3/Bio::ASN1::EntrezGene::Indexer.3.gz
  12. lib/perl5/site_perl/man/man3/Bio::ASN1::Sequence.3.gz
  13. lib/perl5/site_perl/man/man3/Bio::ASN1::Sequence::Indexer.3.gz
  14. lib/perl5/site_perl/man/man3/Bio::SeqIO::entrezgene.3.gz
  15. @owner
  16. @group
  17. @mode
Collapse this list.
Dependency lines:
  • p5-Bio-ASN1-EntrezGene>0:biology/p5-Bio-ASN1-EntrezGene
To install the port:
cd /usr/ports/biology/p5-Bio-ASN1-EntrezGene/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/p5-Bio-ASN1-EntrezGene
  • pkg install p5-Bio-ASN1-EntrezGene
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: p5-Bio-ASN1-EntrezGene
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1539026438 SHA256 (Bio-ASN1-EntrezGene-1.73.tar.gz) = f9e778db705ce5c35ad2798e38a8490b644edfdc14253aa1b74a1f5e79fc6a4b SIZE (Bio-ASN1-EntrezGene-1.73.tar.gz) = 157307

Packages (timestamps in pop-ups are UTC):
p5-Bio-ASN1-EntrezGene
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.73_2,11.73_2,11.73_2,11.73_2,11.73_2,1-1.73_2,1-
FreeBSD:13:quarterly1.73_2,11.73_2,11.73_2,11.73_2,11.73_2,11.73_2,11.73_2,11.73_2,1
FreeBSD:14:latest1.73_2,11.73_2,11.73_2,11.73_2,11.73_2,11.73_2,1-1.73_2,1
FreeBSD:14:quarterly1.73_2,11.73_2,1-1.73_2,11.73_2,11.73_2,11.73_2,11.73_2,1
FreeBSD:15:latest1.73_2,11.73_2,1n/a1.73_2,1n/a1.73_2,11.73_2,11.73_2,1
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. p5-Bio-Cluster>=0 : biology/p5-Bio-Cluster
  2. p5-BioPerl>=0 : biology/p5-BioPerl
  3. perl5>=5.32.r0<5.33 : lang/perl5.32
  4. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. p5-Bio-Cluster>=0 : biology/p5-Bio-Cluster
  2. p5-BioPerl>=0 : biology/p5-BioPerl
  3. perl5>=5.32.r0<5.33 : lang/perl5.32
This port is required by:
for Build
  1. biology/p5-Bio-DB-NCBIHelper
for Run
  1. biology/p5-Bio-DB-NCBIHelper

Configuration Options:
No options to configure
Options name:
biology_p5-Bio-ASN1-EntrezGene
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: 32

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)
1.73_2,1
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)
1.73_2,1
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)
1.73_2,1
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.
1.73_2,1
08 Jan 2020 18:36:30
Revision:522439Original commit files touched by this commit
sunpoet search for other commits by this committer
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.
1.73_1,1
08 Dec 2019 16:57:14
Revision:519354Original commit files touched by this commit
sunpoet search for other commits by this committer
Install Bio::SeqIO::entrezgene

- Bump PORTREVISION for package change
- Take maintainership

Bio::SeqIO::entrezgene has been removed from BioPerl since 1.7.3.
1.73,1
10 Oct 2018 10:23:11
Revision:481714Original commit files touched by this commit
sunpoet search for other commits by this committer
Update to 1.73

Changes:	https://metacpan.org/changes/distribution/Bio-ASN1-EntrezGene
1.72_1,1
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)
1.72_1,1
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
1.72_1,1
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
1.72_1,1
18 Dec 2016 15:25:14
Revision:428869Original commit files touched by this commit
sunpoet search for other commits by this committer
- Add LICENSE
- Add NO_ARCH
- Bump PORTREVISION for biology/p5-bioperl renaming
1.72,1
11 Sep 2016 05:26:01
Revision:421793Original commit files touched by this commit
wen search for other commits by this committer
- Update to 1.72
Changes: http://search.cpan.org/~cjfields/Bio-ASN1-EntrezGene-1.72/
1.70_1,1
19 May 2016 10:21:25
Revision:415498Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
1.70_1,1
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
1.70_1,1
24 Jun 2015 15:16:24
Revision:390487Original commit files touched by this commit
adamw search for other commits by this committer
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).
1.70_1,1
08 May 2015 18:12:37
Revision:385811Original commit files touched by this commit
adamw search for other commits by this committer
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.
1.70,1
11 Apr 2015 15:19:04
Revision:383807Original commit files touched by this commit
marino search for other commits by this committer
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
1.70
11 Apr 2015 15:00:13
Revision:383805Original commit files touched by this commit
marino search for other commits by this committer
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.
1.091_1
05 Apr 2015 17:55:36
Revision:383309Original commit files touched by this commit
bapt search for other commits by this committer
Mark as broken unfetchable ports
1.091_1
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)
1.091
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
1.091
29 Jul 2014 19:11:53
Revision:363374Original commit files touched by this commit
adamw search for other commits by this committer
Convert a bunch of EXTRACT_SUFX=... into USES=tar:...

Approved by:	portmgr (not really, but touches unstaged ports)
1.091
06 Jan 2014 09:57:19
Revision:338853Original commit files touched by this commit
az search for other commits by this committer
- add stage support

Approved by:	portmgr (blanket infrastructure)
1.091
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)
1.091
07 Sep 2013 07:44:27
Revision:326575Original commit files touched by this commit
az search for other commits by this committer
- convert to the new perl5 framework

Approved by:	portmgr (bapt@, blanket)
1.091
22 Oct 2011 23:50:23
Original commit files touched by this commit
eadler search for other commits by this committer
- remove maintainer tags from pkg-descr

Approved by:    portmgr
Approved by:    bapt (mentor)
1.091
19 Mar 2011 12:38:54
Original commit files touched by this commit
miwi search for other commits by this committer
- Get Rid MD5 support
1.091
17 Apr 2008 14:30:31
Original commit files touched by this commit
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)
1.091
08 Sep 2007 00:53:15
Original commit files touched by this commit
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
1.091
22 Jan 2006 08:20:34
Original commit files touched by this commit
edwin search for other commits by this committer
SHA256ify

Approved by:    krion@
1.091
22 Jan 2006 01:25:24
Original commit files touched by this commit
edwin search for other commits by this committer
Replace ugly "@unexec rmdir %D... 2>/dev/null || true" with @dirrmtry

Approved by:    krion@
PR:             ports/88711 (related)
1.091
15 Oct 2005 20:09:50
Original commit files touched by this commit
ehaupt search for other commits by this committer
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)

Number of commits found: 32