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.
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.
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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>
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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.
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)
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.
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
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- 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
