notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)

Two new features

Two two features were added on 2020-05-30:
  1. Repology links - each port now has a link to repology.org. See issue 148 for details.
  2. Ports I maintain report - port maintainers can now subscribe to a daily report of commits to the ports they maintain. See Watch ports I maintain at Report Subscriptions. Details at issue 138
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. 1.6.901_1Version 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:
SVNWeb : Homepage

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.
The package name of this deleted port was:
PKGNAME: p5-bioperl-run
Flavors: there is no flavor information for this port.
distinfo:
Packages:
p5-bioperl-run
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd64--
FreeBSD:11:armv61.6.901_1-
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd64--
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
 

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

USES:

Master Sites:
  1. https://codeload.github.com/bioperl/bioperl-run/tar.gz/96ccd93?dummy=/
Port Moves

Number of commits found: 30

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
18 Dec 2016 15:25:44
Original commit files touched by this commit  1.6.901_1
Revision:428872
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
01 Apr 2016 13:29:17
Original commit files touched by this commit  1.6.901_1
Revision:412344
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
20 Mar 2015 20:07:51
Original commit files touched by this commit  1.6.901_1
Revision:381777
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
20 Mar 2015 09:43:21
Original commit files touched by this commit  1.6.901_1
Revision:381726
mat search for other commits by this committer
Convert to new USE_GITHUB.

While there, cleanup.

Sponsored by:	Absolight
12 Mar 2015 23:00:03
Original commit files touched by this commit  1.6.901_1
Revision:381151
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.
18 Jan 2015 22:49:10
Original commit files touched by this commit  1.6.901_1
Revision:377369
sunpoet search for other commits by this committer
- Simplify Makefile
- Use tab instead of space
- Sort PLIST
- Pass maintainership to perl@
26 Nov 2014 13:08:38
Original commit files touched by this commit  1.6.901_1
Revision:373448
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)
20 Oct 2014 07:10:48
Original commit files touched by this commit  1.6.901
Revision:371237
bapt search for other commits by this committer
Cleanup plist
04 Aug 2014 08:54:10
Original commit files touched by this commit  1.6.901
Revision:363975
pi search for other commits by this committer
biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagify
23 Jul 2014 16:44:28
Original commit files touched by this commit  1.6.1_4
Revision:362705
bapt search for other commits by this committer
Reset maintainership for ports not staged with no pending PR

With hat:	portmgr
19 Jun 2014 21:31:16
Original commit files touched by this commit  1.6.1_4
Revision:358466
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
21 Feb 2014 13:35:26
Original commit files touched by this commit  1.6.1_4
Revision:345397
ehaupt search for other commits by this committer
Remove trailing whitespaces from category biology
10 Feb 2014 13:54:28
Original commit files touched by this commit  1.6.1_4
Revision:343634
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)
03 Jan 2014 15:46:52
Original commit files touched by this commit  1.6.1_4
Revision:338550
adamw search for other commits by this committer
Convert biology to MDOCS and MEXAMPLES
20 Sep 2013 15:55:44
Original commit files touched by this commit  1.6.1_4
Revision:327709
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
07 Sep 2013 07:44:27
Original commit files touched by this commit  1.6.1_4
Revision:326575
az search for other commits by this committer
- convert to the new perl5 framework

Approved by:	portmgr (bapt@, blanket)
30 Jun 2012 14:48:31
Original commit files touched by this commit  1.6.1_4

az search for other commits by this committer
- Remove SITE_PERL from *_DEPENDS

Approved by: portmgr@ (bapt@)
01 Jun 2012 05:26:28
Original commit files touched by this commit  1.6.1_4

dinoex search for other commits by this committer
- update png to 1.5.10
21 Jan 2012 17:40:15
Original commit files touched by this commit  1.6.1_3

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
19 Mar 2011 12:38:54
Original commit files touched by this commit  1.6.1_3

miwi search for other commits by this committer
- Get Rid MD5 support
28 Mar 2010 06:47:48
Original commit files touched by this commit  1.6.1_3

dinoex search for other commits by this committer
- update to 1.4.1
Reviewed by:    exp8 run on pointyhat
Supported by:   miwi
05 Feb 2010 11:46:55
Original commit files touched by this commit  1.6.1_2

dinoex search for other commits by this committer
- update to jpeg-8
02 Aug 2009 20:00:09
Original commit files touched by this commit  1.6.1_1

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
31 Jul 2009 13:57:52
Original commit files touched by this commit  1.6.1_1

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
19 Mar 2009 20:54:05
Original commit files touched by this commit  1.6.1

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
15 Jan 2009 22:47:02
Original commit files touched by this commit  1.4_1

pav search for other commits by this committer
- Unbreak after p5-bioperl changed portrevision
17 Apr 2008 14:30:31
Original commit files touched by this commit  1.4_1

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)
08 Sep 2007 00:53:15
Original commit files touched by this commit  1.4_1

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
19 May 2007 20:32:57
Original commit files touched by this commit  1.4_1

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}.
02 May 2006 21:30:08
Original commit files touched by this commit  1.4

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

Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
The latest upgrade!
Privacy
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
rubygem-kramdownJul 08
gitlab-ceJul 07
mbedtlsJul 07
anydeskJul 04
dbusJul 03
py-matrix-synapseJul 03
coturnJul 02
gitlab-ceJul 02
powerdns-recursorJul 02
samba410Jul 02
samba411Jul 02
drupal7Jul 01
xrdpJun 30
mongodb36Jun 29
mongodb40Jun 29

25 vulnerabilities affecting 118 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last updated:
2020-07-08 20:51:12


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 39682
Broken 79
Deprecated 586
Ignore 310
Forbidden 5
Restricted 146
No CDROM 76
Vulnerable 19
Expired 4
Set to expire 556
Interactive 0
new 24 hours 3
new 48 hours6
new 7 days25
new fortnight57
new month143

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2020 Dan Langille. All rights reserved.