Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.
WWW: https://github.com/bioperl/bioperl-run
===> The following configuration options are available for p5-bioperl-run-1.6.901_1:
DOCS=on: Build and/or install documentation
===> Use 'make config' to modify these settings
For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME to
include GH_PROJECT/GH_ACCOUNT/GH_TAGNAME. This prevents the distfile
having the same name despite changing one of these values and causing
a bad checksum.
Differential Revision: https://reviews.freebsd.org/D2103
Reviewed by: mat
With hat: bdrewery
Some OCD cleanups on some of the perl@ ports.
- Remove dependencies in core
- Put testing depends in TEST_DEPENDS
- Remove unnecessary bsd.port.options.mk inclusions
- Remove checks for Perl versions that no longer exist in the ports tree
- Sort plists, some of which were so jumbled that I have to assume
the plist was randomized before committing
A lot of the plist changes in this commit are moving PERL5_MAN3 after
SITE_PERL. It's repo churn now, but it makes updating the ports later
far easier.
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 )
Mark BROKEN: Fails to configure
===> Configuring for p5-bioperl-run-1.6.1_4
Invalid prerequisite condition '0/processing XML
data/Bio::Tools::Run::EMBOSSacd' for XML::Twig at
/usr/local/lib/perl5/site_perl/5.16/Module/Build/Base.pm line 1702.
*** [do-configure] Error code 25
Reported by: pkg-fallout
With hat: portmgr
According to the Porter's Handbook (5.12.2.3.) default options must be added to
OPTIONS_DEFINE. This policy has been implemented only recently that's why we
have many ports violating this policy.
This patch adds the default options specified in the Porter's Handbook to
OPTIONS_DEFINE where they are being used. Ports maintained by
gnome@FreeBSD.org, kde@FreeBSD.org and x11@FreeBSD.org have been excluded.
Approved by: portmgr (bapt)
At the moment 1385 ports use BUILD_DEPENDS= ${RUN_DEPENDS} and 450
ports use BUILD_DEPENDS:= ${RUN_DEPENDS}. This patch fixes ports that are
currently broken. This is a temporary measure until we organically stop using
:= or someone(s) spend a lot of time changing all the ports over.
Explicit duplication > := > = and this just moves ports one step to the left
Approved by: portmgr
- 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
Bioperl-run contain modules that provides a PERL interface to various
bioinformatics applications. This allows various applications to be used
with common Bioperl objects.
WWW: http://bioperl.org/
PR: ports/93674
Submitted by: Mauricio Herrera Cuadra <mauricio@arareko.net>
