Date: Thu, 20 Aug 2009 00:34:40 GMT From: Wen Heping <wenheping@gmail.comw> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/137983: [NEW PORT]biology/p5-Bio-NEXUS:An object-oriented Perl API for the NEXUS file format Message-ID: <200908200034.n7K0YeNI024911@www.freebsd.org> Resent-Message-ID: <200908200040.n7K0e1Ho017217@freefall.freebsd.org>
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>Number: 137983 >Category: ports >Synopsis: [NEW PORT]biology/p5-Bio-NEXUS:An object-oriented Perl API for the NEXUS file format >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Thu Aug 20 00:40:01 UTC 2009 >Closed-Date: >Last-Modified: >Originator: Wen Heping >Release: FreeBSD 8.0-Current >Organization: ChangAn Middle School >Environment: FreeBSD fb8.wenjing.com 8.0-CURRENT FreeBSD 8.0-CURRENT #0: Sun Mar 22 22:12:06 CST 2009 root@fb8.wenjing.com:/usr/obj/usr/src/sys/GENERIC i386 >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). WWW: http://search.cpan.org/dist/Bio-NEXUS/ >How-To-Repeat: >Fix: Patch attached with submission follows: # This is a shell archive. Save it in a file, remove anything before # this line, and then unpack it by entering "sh file". Note, it may # create directories; files and directories will be owned by you and # have default permissions. # # This archive contains: # # p5-Bio-NEXUS # p5-Bio-NEXUS/Makefile # p5-Bio-NEXUS/distinfo # p5-Bio-NEXUS/pkg-descr # p5-Bio-NEXUS/pkg-plist # echo c - p5-Bio-NEXUS mkdir -p p5-Bio-NEXUS > /dev/null 2>&1 echo x - p5-Bio-NEXUS/Makefile sed 's/^X//' >p5-Bio-NEXUS/Makefile << '0fe000fba07281d505e3c57ae6f1b769' X# New ports collection makefile for: Bio-NEXUS X# Date created: 20 Sug, 2009 X# Whom: Wen Heping <wenheping@gmail.com> X# X# $FreeBSD$ X# X XPORTNAME= Bio-NEXUS XPORTVERSION= 0.72 XCATEGORIES= biology perl5 XMASTER_SITES= CPAN XPKGNAMEPREFIX= p5- X XMAINTAINER= wenheping@gmail.com XCOMMENT= An object-oriented Perl API for the NEXUS file format X XBUILD_DEPENDS= p5-Clone-PP>=1.02:${PORTSDIR}/devel/p5-Clone-PP \ X p5-Test-Deep>=0.106:${PORTSDIR}/devel/p5-Test-Deep XRUN_DEPENDS= ${BUILD_DEPENDS} X XPERL_CONFIGURE= yes X XMAN1= nextool.pl.1 nex2text_tree.pl.1 nexplot.pl.1 XMAN3= Bio::NEXUS::DataBlock.3 Bio::NEXUS::CodonsBlock.3 \ X Bio::NEXUS::NotesBlock.3 Bio::NEXUS::NHXCmd.3 \ X Bio::NEXUS::HistoryBlock.3 Bio::NEXUS::TaxUnit.3 \ X Bio::NEXUS::CharactersBlock.3 Bio::NEXUS::SpanBlock.3 \ X Bio::NEXUS::UnalignedBlock.3 Bio::NEXUS::TaxUnitSet.3 \ X Bio::NEXUS::DistancesBlock.3 Bio::NEXUS::UnknownBlock.3 \ X Bio::NEXUS::Node.3 Bio::NEXUS::Matrix.3 \ X Bio::NEXUS::Tree.3 Bio::NEXUS::WeightSet.3 \ X Bio::NEXUS::TreesBlock.3 Bio::NEXUS::Util::Exceptions.3 \ X Bio::NEXUS::SetsBlock.3 Bio::NEXUS::TaxaBlock.3 \ X Bio::NEXUS::Util::Logger.3 Bio::NEXUS::AssumptionsBlock.3 \ X Bio::NEXUS::Block.3 Bio::NEXUS::Functions.3 \ X Bio::NEXUS.3 X X.include <bsd.port.mk> 0fe000fba07281d505e3c57ae6f1b769 echo x - p5-Bio-NEXUS/distinfo sed 's/^X//' >p5-Bio-NEXUS/distinfo << '6208db6bcdd56891147b337c53cca39a' XMD5 (Bio-NEXUS-0.72.tar.gz) = 2dc7506f6d9fa9bea615f0855b8ff2dd XSHA256 (Bio-NEXUS-0.72.tar.gz) = 645203f64b61df3d403108dd4b9057c492e67dfa46ecd1c280980b3e58a1fb40 XSIZE (Bio-NEXUS-0.72.tar.gz) = 946520 6208db6bcdd56891147b337c53cca39a echo x - p5-Bio-NEXUS/pkg-descr sed 's/^X//' >p5-Bio-NEXUS/pkg-descr << '83ede60d9d092a913a55611b060233fd' XBio::NEXUS package provides an object-oriented, Perl-based Xapplications programming interface (API) to the NEXUS file Xformat of Maddison, et al., 1997 (Syst. Biol. 46:590-621). XNEXUS is a powerful and extensible format designed for use Xin evolutionary analysis, including the analysis of molecular Xsequence data as well as classical morphological and life-history Xdata. NEXUS is the input or output format for software such as XPAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and Xso on. This package also contains the demonstration applications Xnexplot.pl (plot character data with a tree) and nextool.pl X(allowing programmatic editing, e.g., selecting particular Xclades or subsets of data). X XWWW: http://search.cpan.org/dist/Bio-NEXUS/ 83ede60d9d092a913a55611b060233fd echo x - p5-Bio-NEXUS/pkg-plist sed 's/^X//' >p5-Bio-NEXUS/pkg-plist << '177f6c0a732b5019548100eba750e60e' Xbin/nex2text_tree.pl Xbin/nexplot.pl Xbin/nextool.pl X%%SITE_PERL%%/Bio/NEXUS.pm X%%SITE_PERL%%/Bio/NEXUS/DataBlock.pm X%%SITE_PERL%%/Bio/NEXUS/._Functions.pm X%%SITE_PERL%%/Bio/NEXUS/CodonsBlock.pm X%%SITE_PERL%%/Bio/NEXUS/NotesBlock.pm X%%SITE_PERL%%/Bio/NEXUS/NHXCmd.pm X%%SITE_PERL%%/Bio/NEXUS/HistoryBlock.pm X%%SITE_PERL%%/Bio/NEXUS/TaxUnit.pm X%%SITE_PERL%%/Bio/NEXUS/CharactersBlock.pm X%%SITE_PERL%%/Bio/NEXUS/SpanBlock.pm X%%SITE_PERL%%/Bio/NEXUS/UnalignedBlock.pm X%%SITE_PERL%%/Bio/NEXUS/TaxUnitSet.pm X%%SITE_PERL%%/Bio/NEXUS/DistancesBlock.pm X%%SITE_PERL%%/Bio/NEXUS/UnknownBlock.pm X%%SITE_PERL%%/Bio/NEXUS/Node.pm X%%SITE_PERL%%/Bio/NEXUS/Matrix.pm X%%SITE_PERL%%/Bio/NEXUS/Tree.pm X%%SITE_PERL%%/Bio/NEXUS/WeightSet.pm X%%SITE_PERL%%/Bio/NEXUS/SetsBlock.pm X%%SITE_PERL%%/Bio/NEXUS/TaxaBlock.pm X%%SITE_PERL%%/Bio/NEXUS/TreesBlock.pm X%%SITE_PERL%%/Bio/NEXUS/AssumptionsBlock.pm X%%SITE_PERL%%/Bio/NEXUS/Block.pm X%%SITE_PERL%%/Bio/NEXUS/Functions.pm X%%SITE_PERL%%/Bio/NEXUS/Util/Exceptions.pm X%%SITE_PERL%%/Bio/NEXUS/Util/Logger.pm X%%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/NEXUS/.packlist X@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio/NEXUS X@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio X@dirrmtry %%SITE_PERL%%/Bio/NEXUS/Util X@dirrmtry %%SITE_PERL%%/Bio/NEXUS X@dirrmtry %%SITE_PERL%%/Bio 177f6c0a732b5019548100eba750e60e exit >Release-Note: >Audit-Trail: >Unformatted:
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