notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Ukraine
NOTE: the WWW: line in pkg-descr was relocated to a WWW= line in Makefile. Each port in FreshPorts has a homepage link. Look for it right after the Description: on each port's home page.

Do I know someone who can pick up a server from 7401 E. Ben White Blvd. Austin TX?

The emphasis is on know, or recommended by someone I know. This is the original FreshPorts server, way past useful: RAID, 8GB RAM, etc. The drives need to be wiped and everything recycled.
Port details
p5-bioperl-run Wrapper modules for common bioinformatics tools
1.6.901_1 biology Deleted 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 Version of this port present on the latest quarterly branch.
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2006-05-02 21:32:38
Last Update: 2016-12-18 15:25:44
SVN Revision: 428872
People watching this port, also watch:: cvsgraph, screen, python
Also Listed In: perl5
License: ART10 GPLv3
Description:
HomepagecgitGitHubGitLabSVNWeb
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • p5-bioperl-run>0:biology/p5-bioperl-run
No installation instructions:
This port has been deleted.
PKGNAME: p5-bioperl-run
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
p5-bioperl-run
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd64pkg-falloutpkg-fallout
FreeBSD:11:armv61.6.901_1pkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd64pkg-falloutpkg-fallout
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd64pkg-falloutpkg-fallout
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd64pkg-falloutpkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. p5-bioperl>=1.6.0 : biology/p5-bioperl
  2. p5-IPC-Run>=0 : devel/p5-IPC-Run
  3. p5-Algorithm-Diff>=0 : devel/p5-Algorithm-Diff
  4. p5-XML-Twig>=0 : textproc/p5-XML-Twig
  5. p5-File-Sort>=0 : misc/p5-File-Sort
  6. p5-Config-Any>=0 : devel/p5-Config-Any
  7. p5-Module-Build>=0.4206 : devel/p5-Module-Build
  8. perl5>=5.20<5.21 : lang/perl5.20
Runtime dependencies:
  1. p5-bioperl>=1.6.0 : biology/p5-bioperl
  2. p5-IPC-Run>=0 : devel/p5-IPC-Run
  3. p5-Algorithm-Diff>=0 : devel/p5-Algorithm-Diff
  4. p5-XML-Twig>=0 : textproc/p5-XML-Twig
  5. p5-File-Sort>=0 : misc/p5-File-Sort
  6. p5-Config-Any>=0 : devel/p5-Config-Any
  7. perl5>=5.20<5.21 : lang/perl5.20
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/bioperl/bioperl-run/tar.gz/96ccd93?dummy=/
Collapse this list.
Port Moves

Number of commits found: 30

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.6.901_1
18 Dec 2016 15:25:44
Revision:428872Original commit files touched by this commit
sunpoet search for other commits by this committer
- Move biology/p5-bioperl-run to biology/p5-BioPerl-Run
- Sort *_DEPENDS
- Add NO_ARCH
- Bump PORTREVISION for biology/p5-bioperl renaming
1.6.901_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
1.6.901_1
20 Mar 2015 20:07:51
Revision:381777Original commit files touched by this commit
bdrewery search for other commits by this committer
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
1.6.901_1
20 Mar 2015 09:43:21
Revision:381726Original commit files touched by this commit
mat search for other commits by this committer
Convert to new USE_GITHUB.

While there, cleanup.

Sponsored by:	Absolight
1.6.901_1
12 Mar 2015 23:00:03
Revision:381151Original commit files touched by this commit
adamw search for other commits by this committer
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.
1.6.901_1
18 Jan 2015 22:49:10
Revision:377369Original commit files touched by this commit
sunpoet search for other commits by this committer
- Simplify Makefile
- Use tab instead of space
- Sort PLIST
- Pass maintainership to perl@
1.6.901_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)
1.6.901
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
1.6.901
04 Aug 2014 08:54:10
Revision:363975Original commit files touched by this commit
pi search for other commits by this committer
biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagify
1.6.1_4
23 Jul 2014 16:44:28
Revision:362705Original commit files touched by this commit
bapt search for other commits by this committer
Reset maintainership for ports not staged with no pending PR

With hat:	portmgr
1.6.1_4
19 Jun 2014 21:31:16
Revision:358466Original commit files touched by this commit
antoine search for other commits by this committer
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
1.6.1_4
21 Feb 2014 13:35:26
Revision:345397Original commit files touched by this commit
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
1.6.1_4
10 Feb 2014 13:54:28
Revision:343634Original commit files touched by this commit
ehaupt search for other commits by this committer
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)
1.6.1_4
03 Jan 2014 15:46:52
Revision:338550Original commit files touched by this commit
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
1.6.1_4
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)
1.6.1_4
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)
1.6.1_4
30 Jun 2012 14:48:31
Original commit files touched by this commit
az search for other commits by this committer
- Remove SITE_PERL from *_DEPENDS

Approved by: portmgr@ (bapt@)
1.6.1_4
01 Jun 2012 05:26:28
Original commit files touched by this commit
dinoex search for other commits by this committer
- update png to 1.5.10
1.6.1_3
21 Jan 2012 17:40:15
Original commit files touched by this commit
eadler search for other commits by this committer
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
1.6.1_3
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
1.6.1_3
28 Mar 2010 06:47:48
Original commit files touched by this commit
dinoex search for other commits by this committer
- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi
1.6.1_2
05 Feb 2010 11:46:55
Original commit files touched by this commit
dinoex search for other commits by this committer
- update to jpeg-8
1.6.1_1
02 Aug 2009 20:00:09
Original commit files touched by this commit
pav search for other commits by this committer
- Relax check on bioperl version; people keep forgetting to update this check
  when updating bioperl port

Reported by:    pointyhat
1.6.1_1
31 Jul 2009 13:57:52
Original commit files touched by this commit
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
1.6.1
19 Mar 2009 20:54:05
Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 1.6.1

PR:             132122
Submitted by:   Wen Heping <wenheping@gmail.com>
Approved by:    maintainer
1.4_1
15 Jan 2009 22:47:02
Original commit files touched by this commit
pav search for other commits by this committer
- Unbreak after p5-bioperl changed portrevision
1.4_1
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)
1.4_1
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
1.4_1
19 May 2007 20:32:57
Original commit files touched by this commit
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}.
1.4
02 May 2006 21:30:08
Original commit files touched by this commit
garga search for other commits by this committer
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>

Number of commits found: 30