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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 Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.78_1Version of this port present on the latest quarterly branch.
Maintainer: perl@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-08-22 20:40:26
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
Also Listed In: perl5
License: not specified in port
WWW:
https://metacpan.org/release/Bio-NEXUS
Description:
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).
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (65 items)
Collapse this list.
  1. bin/nex2text_tree.pl
  2. bin/nexplot.pl
  3. bin/nextool.pl
  4. lib/perl5/site_perl/Bio/NEXUS.pm
  5. lib/perl5/site_perl/Bio/NEXUS/AssumptionsBlock.pm
  6. lib/perl5/site_perl/Bio/NEXUS/Block.pm
  7. lib/perl5/site_perl/Bio/NEXUS/CharactersBlock.pm
  8. lib/perl5/site_perl/Bio/NEXUS/CodonsBlock.pm
  9. lib/perl5/site_perl/Bio/NEXUS/DataBlock.pm
  10. lib/perl5/site_perl/Bio/NEXUS/DistancesBlock.pm
  11. lib/perl5/site_perl/Bio/NEXUS/Functions.pm
  12. lib/perl5/site_perl/Bio/NEXUS/HistoryBlock.pm
  13. lib/perl5/site_perl/Bio/NEXUS/Matrix.pm
  14. lib/perl5/site_perl/Bio/NEXUS/NHXCmd.pm
  15. lib/perl5/site_perl/Bio/NEXUS/Node.pm
  16. lib/perl5/site_perl/Bio/NEXUS/NotesBlock.pm
  17. lib/perl5/site_perl/Bio/NEXUS/SetsBlock.pm
  18. lib/perl5/site_perl/Bio/NEXUS/SpanBlock.pm
  19. lib/perl5/site_perl/Bio/NEXUS/TaxUnit.pm
  20. lib/perl5/site_perl/Bio/NEXUS/TaxUnitSet.pm
  21. lib/perl5/site_perl/Bio/NEXUS/TaxaBlock.pm
  22. lib/perl5/site_perl/Bio/NEXUS/Tools/GraphicsParams.pm
  23. lib/perl5/site_perl/Bio/NEXUS/Tools/NexModifier.pm
  24. lib/perl5/site_perl/Bio/NEXUS/Tools/NexPlotter.pm
  25. lib/perl5/site_perl/Bio/NEXUS/Tree.pm
  26. lib/perl5/site_perl/Bio/NEXUS/TreesBlock.pm
  27. lib/perl5/site_perl/Bio/NEXUS/UnalignedBlock.pm
  28. lib/perl5/site_perl/Bio/NEXUS/UnknownBlock.pm
  29. lib/perl5/site_perl/Bio/NEXUS/Util/Exceptions.pm
  30. lib/perl5/site_perl/Bio/NEXUS/Util/Logger.pm
  31. lib/perl5/site_perl/Bio/NEXUS/WeightSet.pm
  32. lib/perl5/site_perl/man/man3/Bio::NEXUS.3.gz
  33. lib/perl5/site_perl/man/man3/Bio::NEXUS::AssumptionsBlock.3.gz
  34. lib/perl5/site_perl/man/man3/Bio::NEXUS::Block.3.gz
  35. lib/perl5/site_perl/man/man3/Bio::NEXUS::CharactersBlock.3.gz
  36. lib/perl5/site_perl/man/man3/Bio::NEXUS::CodonsBlock.3.gz
  37. lib/perl5/site_perl/man/man3/Bio::NEXUS::DataBlock.3.gz
  38. lib/perl5/site_perl/man/man3/Bio::NEXUS::DistancesBlock.3.gz
  39. lib/perl5/site_perl/man/man3/Bio::NEXUS::Functions.3.gz
  40. lib/perl5/site_perl/man/man3/Bio::NEXUS::HistoryBlock.3.gz
  41. lib/perl5/site_perl/man/man3/Bio::NEXUS::Matrix.3.gz
  42. lib/perl5/site_perl/man/man3/Bio::NEXUS::NHXCmd.3.gz
  43. lib/perl5/site_perl/man/man3/Bio::NEXUS::Node.3.gz
  44. lib/perl5/site_perl/man/man3/Bio::NEXUS::NotesBlock.3.gz
  45. lib/perl5/site_perl/man/man3/Bio::NEXUS::SetsBlock.3.gz
  46. lib/perl5/site_perl/man/man3/Bio::NEXUS::SpanBlock.3.gz
  47. lib/perl5/site_perl/man/man3/Bio::NEXUS::TaxUnit.3.gz
  48. lib/perl5/site_perl/man/man3/Bio::NEXUS::TaxUnitSet.3.gz
  49. lib/perl5/site_perl/man/man3/Bio::NEXUS::TaxaBlock.3.gz
  50. lib/perl5/site_perl/man/man3/Bio::NEXUS::Tools::GraphicsParams.3.gz
  51. lib/perl5/site_perl/man/man3/Bio::NEXUS::Tools::NexModifier.3.gz
  52. lib/perl5/site_perl/man/man3/Bio::NEXUS::Tools::NexPlotter.3.gz
  53. lib/perl5/site_perl/man/man3/Bio::NEXUS::Tree.3.gz
  54. lib/perl5/site_perl/man/man3/Bio::NEXUS::TreesBlock.3.gz
  55. lib/perl5/site_perl/man/man3/Bio::NEXUS::UnalignedBlock.3.gz
  56. lib/perl5/site_perl/man/man3/Bio::NEXUS::UnknownBlock.3.gz
  57. lib/perl5/site_perl/man/man3/Bio::NEXUS::Util::Exceptions.3.gz
  58. lib/perl5/site_perl/man/man3/Bio::NEXUS::Util::Logger.3.gz
  59. lib/perl5/site_perl/man/man3/Bio::NEXUS::WeightSet.3.gz
  60. lib/perl5/site_perl/man/man1/nex2text_tree.pl.1.gz
  61. lib/perl5/site_perl/man/man1/nexplot.pl.1.gz
  62. lib/perl5/site_perl/man/man1/nextool.pl.1.gz
  63. @owner
  64. @group
  65. @mode
Collapse this list.
Dependency lines:
  • p5-Bio-NEXUS>0:biology/p5-Bio-NEXUS
To install the port:
cd /usr/ports/biology/p5-Bio-NEXUS/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/p5-Bio-NEXUS
  • pkg install p5-Bio-NEXUS
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: p5-Bio-NEXUS
Flavors: there is no flavor information for this port.
distinfo:
SHA256 (Bio-NEXUS-0.78.tar.gz) = a99cda4e97fd40ee0bee05089a034e84280be9532b0300cd98ed16c303bc85dc SIZE (Bio-NEXUS-0.78.tar.gz) = 1033563

Packages (timestamps in pop-ups are UTC):
p5-Bio-NEXUS
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.78_10.78_10.78_10.78_10.78_1-0.78_1-
FreeBSD:13:quarterly0.78_10.78_10.78_10.78_10.78_10.78_10.78_10.78_1
FreeBSD:14:latest0.78_10.78_10.78_10.78_10.78_10.78_1-0.78_1
FreeBSD:14:quarterly0.78_10.78_1-0.78_10.78_10.78_10.78_10.78_1
FreeBSD:15:latest0.78_10.78_1n/a0.78_1n/a0.78_10.78_10.78_1
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. p5-Clone-PP>=1.02 : devel/p5-Clone-PP
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
  3. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. p5-Clone-PP>=1.02 : devel/p5-Clone-PP
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
There are no ports dependent upon this port

Configuration Options:
No options to configure
Options name:
biology_p5-Bio-NEXUS
USES:
perl5
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (12 items)
Collapse this list.
  1. ftp://ftp.auckland.ac.nz/pub/perl/CPAN/modules/by-module/Bio/
  2. ftp://ftp.cpan.org/pub/CPAN/modules/by-module/
  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. http://backpan.perl.org/modules/by-module/Bio/
  8. http://ftp.jaist.ac.jp/pub/CPAN/modules/by-module/Bio/
  9. http://ftp.twaren.net/Unix/Lang/CPAN/modules/by-module/Bio/
  10. https://cpan.metacpan.org/modules/by-module/
  11. https://cpan.metacpan.org/modules/by-module/Bio/
  12. https://www.cpan.org/modules/by-module/Bio/
Collapse this list.

Number of commits found: 23

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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)
0.78_1
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.78_1
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
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>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.78_1
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
0.78_1
06 Oct 2018 13:06:45
Revision:481365Original commit files touched by this commit
des search for other commits by this committer
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)
0.78_1
27 May 2018 20:15:20
Revision:470993Original commit files touched by this commit
sunpoet search for other commits by this committer
Update WWW

search.cpan.org is shutting down.
It will redirect to metacpan.org after June 25, 2018.

With hat:	perl
0.78_1
19 May 2016 10:21:25
Revision:415498Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
0.78_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
0.78_1
14 Sep 2015 12:19:50
Revision:396892Original commit files touched by this commit
mat search for other commits by this committer
Make it so that the default Perl is always called perl5.

- Move Perl's man1 files along with its man3 files.
- Move where Perl installs its modules man1 pages.
- Convert the ports installing man1 pages.
- Make different Perl versions installable at the same time.
  Though you should note that only the default version can be used to
  install Perl modules, and the non default Perl versions cannot use the
  modules installed via ports if they contain .so as they are installed
  in a version specific directory.

Reviewed by:	bapt (the Mk bits)
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D3542
0.78_1
31 May 2015 13:37:21
Revision:388088Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Add NO_ARCH

Approved by:	portmgr blanket
0.78_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)
0.78
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
0.78
31 Jan 2014 12:47:07
Revision:341989Original commit files touched by this commit
miwi search for other commits by this committer
- Stage support
0.78
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)
0.78
02 Aug 2013 18:52:11
Revision:324174Original commit files touched by this commit
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.
0.78
29 Mar 2013 00:44:54
Revision:315509Original commit files touched by this commit
eadler search for other commits by this committer
For perl@ owned ports:

- Fix COMMENT
- Trim header
0.78
11 Feb 2012 02:04:41
Original commit files touched by this commit
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
0.77
09 Feb 2012 01:23:59
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.77
0.76
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
0.76
25 Dec 2010 16:55:41
Original commit files touched by this commit
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)
0.76
25 Sep 2010 08:14:02
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.76
0.75
07 Sep 2010 07:15:24
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.75
- Reset maintainer to perl@
0.72
22 Aug 2009 20:39:51
Original commit files touched by this commit
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: 23