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Port details
p5-Bio-NEXUS Object-oriented Perl API for the NEXUS file format
0.78_1 biology on this many watch lists=0 search for ports that depend on this port
Maintained by: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 22 Aug 2009 20:40:26
Also Listed In: perl5
License: not specified in port
Bio::NEXUS package provides an object-oriented, Perl-based
applications programming interface (API) to the NEXUS file
format of Maddison, et al., 1997 (Syst. Biol. 46:590-621).
NEXUS is a powerful and extensible format designed for use
in evolutionary analysis, including the analysis of molecular
sequence data as well as classical morphological and life-history
data. NEXUS is the input or output format for software such as
PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and
so on.  This package also contains the demonstration applications
nexplot.pl (plot character data with a tree) and nextool.pl
(allowing programmatic editing, e.g., selecting particular
clades or subsets of data). 

WWW: http://search.cpan.org/dist/Bio-NEXUS/
SVNWeb : Main Web Site : Distfiles Availability : PortsMon

NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Required To Build:
  1. devel/p5-Clone-PP
  2. lang/perl5.18
Required To Run:
  1. devel/p5-Clone-PP
  2. lang/perl5.18
There are no ports dependent upon this port

To install the port: cd /usr/ports/biology/p5-Bio-NEXUS/ && make install clean
To add the package: pkg install biology/p5-Bio-NEXUS


Configuration Options
     No options to configure

Master Sites:
  1. ftp://ftp.auckland.ac.nz/pub/perl/CPAN/modules/by-module/Bio/
  2. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/Bio/
  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. ftp://ftp.sunet.se/pub/lang/perl/CPAN/modules/by-module/Bio/
  8. http://backpan.perl.org/modules/by-module/Bio/
  9. http://cpan.metacpan.org/modules/by-module/Bio/
  10. http://distcache.FreeBSD.org/ports-distfiles/
  11. http://ftp.jaist.ac.jp/pub/CPAN/modules/by-module/Bio/
  12. http://ftp.twaren.net/Unix/Lang/CPAN/modules/by-module/Bio/
  13. http://www.cpan.dk/modules/by-module/Bio/
  14. http://www.cpan.dk/modules/by-module/Bio/
  15. http://www.cpan.org/modules/by-module/Bio/

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
26 Nov 2014 13:08:38
Original commit files touched by this commit  0.78_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  0.78
Revision:371237
bapt search for other commits by this committer
Cleanup plist
31 Jan 2014 12:47:07
Original commit files touched by this commit  0.78
Revision:341989
miwi search for other commits by this committer
- Stage support
20 Sep 2013 15:55:44
Original commit files touched by this commit  0.78
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)
02 Aug 2013 18:52:11
Original commit files touched by this commit  0.78
Revision:324174
mat search for other commits by this committer
- Convert to new perl framework
- Trim Makefile header
- Remove MAKE_JOBS_SAFE=yes, it's the default.
29 Mar 2013 00:44:54
Original commit files touched by this commit  0.78
Revision:315509
eadler search for other commits by this committer
For perl@ owned ports:

- Fix COMMENT
- Trim header
11 Feb 2012 02:04:41
Original commit files touched by this commit  0.78
sunpoet search for other commits by this committer
- Update to 0.78
- Sort TEST_DEPENDS, MAN1, MAN3 and PLIST

Changes:        http://search.cpan.org/dist/Bio-NEXUS/doc/changes.txt
09 Feb 2012 01:23:59
Original commit files touched by this commit  0.77
wen search for other commits by this committer
- Update to 0.77
21 Jan 2012 17:40:15
Original commit files touched by this commit  0.76
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
25 Dec 2010 16:55:41
Original commit files touched by this commit  0.76
sunpoet search for other commits by this committer
- Use canonical format for FreeBSD.org MAINTAINER addresses
- Remove obsolete MD5 checksum while I'm here

PR:             ports/152844
Submitted by:   sunpoet (myself)
Approved by:    miwi (with portmgr hat)
25 Sep 2010 08:14:02
Original commit files touched by this commit  0.76
wen search for other commits by this committer
- Update to 0.76
07 Sep 2010 07:15:24
Original commit files touched by this commit  0.75
wen search for other commits by this committer
- Update to 0.75
- Reset maintainer to perl@
22 Aug 2009 20:39:51
Original commit files touched by this commit  0.72
miwi search for other commits by this committer
Bio::NEXUS package provides an object-oriented, Perl-based
applications programming interface (API) to the NEXUS file
format of Maddison, et al., 1997 (Syst. Biol. 46:590-621).
NEXUS is a powerful and extensible format designed for use
in evolutionary analysis, including the analysis of molecular
sequence data as well as classical morphological and life-history
data. NEXUS is the input or output format for software such as
PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and
so on.  This package also contains the demonstration applications
nexplot.pl (plot character data with a tree) and nextool.pl
(allowing programmatic editing, e.g., selecting particular
clades or subsets of data).

WWW: http://search.cpan.org/dist/Bio-NEXUS/

PR:             ports/137983
Submitted by:   Wen Heping <wenheping at gmail.com>

Number of commits found: 13

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