Date: Thu, 25 Jun 2009 07:12:22 GMT From: Wen Heping <wenheping@gmail.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/136021: [NEW PORT]biology/p5-Bio-MAGETAB:A data model and utility API for the MAGE-TAB format Message-ID: <200906250712.n5P7CMRO019989@www.freebsd.org> Resent-Message-ID: <200906250720.n5P7K1kl061851@freefall.freebsd.org>
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>Number: 136021 >Category: ports >Synopsis: [NEW PORT]biology/p5-Bio-MAGETAB:A data model and utility API for the MAGE-TAB format >Confidential: no >Severity: serious >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Thu Jun 25 07:20:01 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 #4: Fri Apr 10 16:36:28 HKT 2009 root@fb8.wenjing.com:/usr/obj/usr/src/sys/wen1 i386 >Description: p5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This is a beta release. All functions have now been implemented and most have test suites; the exceptions include the modules involved in export of MAGE-TAB documents, which are still a little experimental in nature. The API is mostly finalised (and fully documented), but some details may yet change where necessary to improve usability. WWW: http://search.cpan.org/dist/Bio-MAGETAB/ >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-MAGETAB # p5-Bio-MAGETAB/pkg-plist # p5-Bio-MAGETAB/pkg-descr # p5-Bio-MAGETAB/distinfo # p5-Bio-MAGETAB/Makefile # echo c - p5-Bio-MAGETAB mkdir -p p5-Bio-MAGETAB > /dev/null 2>&1 echo x - p5-Bio-MAGETAB/pkg-plist sed 's/^X//' >p5-Bio-MAGETAB/pkg-plist << 'b2d782d6bada6d1197c854636d13ebe8' Xbin/deploy_magetab_db.pl Xbin/fix_ae_magetab.pl Xbin/read_magetab.pl Xbin/unload_magetab_namespace.pl X%%SITE_PERL%%/mach/auto/Bio/MAGETAB/.packlist X%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/DataMatrix.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/TagValueFile.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/Tabfile.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/SDRF.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/IDF.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/ADF.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/ADF.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/Tabfile.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/IDF.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/SDRF.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/GraphViz.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Writer.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Reader.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Builder.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/DBLoader.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/RewriteAE.pm X%%SITE_PERL%%/Bio/MAGETAB/Util/Persistence.pm X%%SITE_PERL%%/Bio/MAGETAB/Material.pm X%%SITE_PERL%%/Bio/MAGETAB/Types.pm X%%SITE_PERL%%/Bio/MAGETAB/ControlledTerm.pm X%%SITE_PERL%%/Bio/MAGETAB/Contact.pm X%%SITE_PERL%%/Bio/MAGETAB/DesignElement.pm X%%SITE_PERL%%/Bio/MAGETAB/Investigation.pm X%%SITE_PERL%%/Bio/MAGETAB/Comment.pm X%%SITE_PERL%%/Bio/MAGETAB/Publication.pm X%%SITE_PERL%%/Bio/MAGETAB/Sample.pm X%%SITE_PERL%%/Bio/MAGETAB/DataFile.pm X%%SITE_PERL%%/Bio/MAGETAB/ArrayDesign.pm X%%SITE_PERL%%/Bio/MAGETAB/Event.pm X%%SITE_PERL%%/Bio/MAGETAB/Edge.pm X%%SITE_PERL%%/Bio/MAGETAB/MatrixColumn.pm X%%SITE_PERL%%/Bio/MAGETAB/Normalization.pm X%%SITE_PERL%%/Bio/MAGETAB/ParameterValue.pm X%%SITE_PERL%%/Bio/MAGETAB/DataAcquisition.pm X%%SITE_PERL%%/Bio/MAGETAB/Assay.pm X%%SITE_PERL%%/Bio/MAGETAB/SDRFRow.pm X%%SITE_PERL%%/Bio/MAGETAB/SDRF.pm X%%SITE_PERL%%/Bio/MAGETAB/Data.pm X%%SITE_PERL%%/Bio/MAGETAB/MatrixRow.pm X%%SITE_PERL%%/Bio/MAGETAB/Extract.pm X%%SITE_PERL%%/Bio/MAGETAB/Measurement.pm X%%SITE_PERL%%/Bio/MAGETAB/TermSource.pm X%%SITE_PERL%%/Bio/MAGETAB/CompositeElement.pm X%%SITE_PERL%%/Bio/MAGETAB/BaseClass.pm X%%SITE_PERL%%/Bio/MAGETAB/Node.pm X%%SITE_PERL%%/Bio/MAGETAB/Protocol.pm X%%SITE_PERL%%/Bio/MAGETAB/Reporter.pm X%%SITE_PERL%%/Bio/MAGETAB/Factor.pm X%%SITE_PERL%%/Bio/MAGETAB/ProtocolApplication.pm X%%SITE_PERL%%/Bio/MAGETAB/LabeledExtract.pm X%%SITE_PERL%%/Bio/MAGETAB/Feature.pm X%%SITE_PERL%%/Bio/MAGETAB/DatabaseEntry.pm X%%SITE_PERL%%/Bio/MAGETAB/Source.pm X%%SITE_PERL%%/Bio/MAGETAB/ProtocolParameter.pm X%%SITE_PERL%%/Bio/MAGETAB/FactorValue.pm X%%SITE_PERL%%/Bio/MAGETAB/DataMatrix.pm X%%SITE_PERL%%/Bio/MAGETAB.pm X@dirrm %%SITE_PERL%%/mach/auto/Bio/MAGETAB X@dirrmtry %%SITE_PERL%%/mach/auto/Bio X@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util/Reader X@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util/Writer X@dirrm %%SITE_PERL%%/Bio/MAGETAB/Util X@dirrm %%SITE_PERL%%/Bio/MAGETAB X@dirrmtry %%SITE_PERL%%/Bio b2d782d6bada6d1197c854636d13ebe8 echo x - p5-Bio-MAGETAB/pkg-descr sed 's/^X//' >p5-Bio-MAGETAB/pkg-descr << 'c003dea7564135556c79263434369fed' Xp5-Bio-MAGETAB contains the core MAGE-TAB Utilities Perl modules. This Xis a beta release. All functions have now been implemented and most Xhave test suites; the exceptions include the modules involved in Xexport of MAGE-TAB documents, which are still a little experimental in Xnature. The API is mostly finalised (and fully documented), but some Xdetails may yet change where necessary to improve usability. X XWWW: http://search.cpan.org/dist/Bio-MAGETAB/ c003dea7564135556c79263434369fed echo x - p5-Bio-MAGETAB/distinfo sed 's/^X//' >p5-Bio-MAGETAB/distinfo << 'bb94b888cdb17aa849dae9aa20d11712' XMD5 (Bio-MAGETAB-0.98.tar.gz) = 91ddd45bdbe836a9be1f09a7049bb98a XSHA256 (Bio-MAGETAB-0.98.tar.gz) = 2a8bf1eb1883f9b9afa9c9caf2ebae74345fb3e0e1a1faf891f3790ebb223151 XSIZE (Bio-MAGETAB-0.98.tar.gz) = 240502 bb94b888cdb17aa849dae9aa20d11712 echo x - p5-Bio-MAGETAB/Makefile sed 's/^X//' >p5-Bio-MAGETAB/Makefile << '654f1ab6c42a753243f34928ee3d2cd8' X# New ports collection makefile for: p5-Bio-MAGETAB X# Date created: 23 June, 2009 X# Whom: Wen Heping <wenheping@gmail.com> X# X# $FreeBSD$ X# X XPORTNAME= Bio-MAGETAB XPORTVERSION= 0.98 XCATEGORIES= biology perl5 XMASTER_SITES= CPAN XPKGNAMEPREFIX= p5- X XMAINTAINER= wenheping@gmail.com XCOMMENT= A data model and utility API for the MAGE-TAB format X XBUILD_DEPENDS= p5-Test-Exception>=0.26:${PORTSDIR}/devel/p5-Test-Exception \ X p5-DateTime-Format-DateManip>=0.04:${PORTSDIR}/devel/p5-DateTime-Format-DateManip \ X p5-Moose-Policy>=0.03:${PORTSDIR}/devel/p5-Moose-Policy \ X p5-MooseX-Types>=0.10:${PORTSDIR}/devel/p5-MooseX-Types \ X p5-Parse-RecDescent>=1.96:${PORTSDIR}/devel/p5-Parse-RecDescent \ X p5-Params-Coerce>=0.14:${PORTSDIR}/devel/p5-Params-Coerce \ X p5-URI>=1.35:${PORTSDIR}/net/p5-URI \ X p5-Test-Exception>=0.26:${PORTSDIR}/devel/p5-Test-Exception \ X p5-Date-Manip>=5.44:${PORTSDIR}/devel/p5-Date-Manip \ X p5-DateTime>=0.43:${PORTSDIR}/devel/p5-DateTime \ X p5-Text-CSV_XS>=0.32:${PORTSDIR}/textproc/p5-Text-CSV_XS \ X p5-Email-Valid>=0.179:${PORTSDIR}/mail/p5-Email-Valid \ X p5-Moose>=0.43:${PORTSDIR}/devel/p5-Moose XRUN_DEPENDS= ${BUILD_DEPENDS} X XPERL_CONFIGURE= YES X XMAN3= Bio::MAGETAB::Material.3 \ X Bio::MAGETAB::Types.3 \ X Bio::MAGETAB::ControlledTerm.3 \ X Bio::MAGETAB::Util::Reader::DataMatrix.3 \ X Bio::MAGETAB::DesignElement.3 \ X Bio::MAGETAB::Contact.3 \ X Bio::MAGETAB::Investigation.3 \ X Bio::MAGETAB::Comment.3 \ X Bio::MAGETAB::Sample.3 \ X Bio::MAGETAB::Publication.3 \ X Bio::MAGETAB::DataFile.3 \ X Bio::MAGETAB::Event.3 \ X Bio::MAGETAB::Edge.3 \ X Bio::MAGETAB::ArrayDesign.3 \ X Bio::MAGETAB.3 \ X Bio::MAGETAB::Util::Writer::ADF.3 \ X Bio::MAGETAB::MatrixColumn.3 \ X Bio::MAGETAB::Normalization.3 \ X Bio::MAGETAB::Util::Reader::TagValueFile.3 \ X Bio::MAGETAB::ParameterValue.3 \ X Bio::MAGETAB::Util::Reader::Tabfile.3 \ X Bio::MAGETAB::Util::Writer.3 \ X Bio::MAGETAB::Util::Writer::Tabfile.3 \ X Bio::MAGETAB::DataAcquisition.3 \ X Bio::MAGETAB::Util::Reader::SDRF.3 \ X Bio::MAGETAB::Assay.3 \ X Bio::MAGETAB::SDRFRow.3 \ X Bio::MAGETAB::Util::Writer::IDF.3 \ X Bio::MAGETAB::SDRF.3 \ X Bio::MAGETAB::MatrixRow.3 \ X Bio::MAGETAB::Data.3 \ X Bio::MAGETAB::Util::Reader.3 \ X Bio::MAGETAB::Extract.3 \ X Bio::MAGETAB::Util::Reader::IDF.3 \ X Bio::MAGETAB::TermSource.3 \ X Bio::MAGETAB::Measurement.3 \ X Bio::MAGETAB::Util::Builder.3 \ X Bio::MAGETAB::CompositeElement.3 \ X Bio::MAGETAB::Node.3 \ X Bio::MAGETAB::Util::DBLoader.3 \ X Bio::MAGETAB::BaseClass.3 \ X Bio::MAGETAB::Util::Writer::SDRF.3 \ X Bio::MAGETAB::Protocol.3 \ X Bio::MAGETAB::Reporter.3 \ X Bio::MAGETAB::Util::Reader::ADF.3 \ X Bio::MAGETAB::Factor.3 \ X Bio::MAGETAB::DatabaseEntry.3 \ X Bio::MAGETAB::Feature.3 \ X Bio::MAGETAB::LabeledExtract.3 \ X Bio::MAGETAB::ProtocolApplication.3 \ X Bio::MAGETAB::Util::RewriteAE.3 \ X Bio::MAGETAB::Source.3 \ X Bio::MAGETAB::Util::Persistence.3 \ X Bio::MAGETAB::Util::Writer::GraphViz.3 \ X Bio::MAGETAB::DataMatrix.3 \ X Bio::MAGETAB::FactorValue.3 \ X Bio::MAGETAB::ProtocolParameter.3 X Xpost-extract: X @${REINPLACE_CMD} -e 's?auto_install?#auto_install?g' \ X ${WRKSRC}/Makefile.PL X X.include <bsd.port.mk> 654f1ab6c42a753243f34928ee3d2cd8 exit >Release-Note: >Audit-Trail: >Unformatted:
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