Index: head/biology/p5-Bio-MAGETAB/Makefile =================================================================== --- head/biology/p5-Bio-MAGETAB/Makefile (revision 499677) +++ head/biology/p5-Bio-MAGETAB/Makefile (revision 499678) @@ -1,36 +1,36 @@ # Created by: Wen Heping # $FreeBSD$ PORTNAME= Bio-MAGETAB PORTVERSION= 1.31 PORTREVISION= 1 CATEGORIES= biology perl5 MASTER_SITES= CPAN PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Data model and utility API for the MAGE-TAB format LICENSE= GPLv2 BUILD_DEPENDS= ${RUN_DEPENDS} -RUN_DEPENDS= p5-Date-Manip>=5.44:devel/p5-Date-Manip \ +xRUN_DEPENDS= p5-Date-Manip>=5.44:devel/p5-Date-Manip \ p5-DateTime>=0.43.02:devel/p5-DateTime \ p5-DateTime-Format-DateManip>=0.04:devel/p5-DateTime-Format-DateManip \ p5-Email-Valid>=0.179:mail/p5-Email-Valid \ p5-Moose>=0.43:devel/p5-Moose \ p5-MooseX-FollowPBP>=0.04:devel/p5-MooseX-FollowPBP \ p5-MooseX-Types>=0.10:devel/p5-MooseX-Types \ p5-Params-Coerce>=0.14:devel/p5-Params-Coerce \ p5-Parse-RecDescent>=1.965001:devel/p5-Parse-RecDescent \ p5-Text-CSV_XS>=0.32:textproc/p5-Text-CSV_XS \ p5-URI>=1.35:net/p5-URI TEST_DEPENDS= p5-Test-Exception>=0.26:devel/p5-Test-Exception USES= perl5 USE_PERL5= configure post-patch: @${REINPLACE_CMD} -e '/^auto_install;/d' ${WRKSRC}/Makefile.PL .include Index: head/biology/p5-Bio-MAGETAB/pkg-plist =================================================================== --- head/biology/p5-Bio-MAGETAB/pkg-plist (revision 499677) +++ head/biology/p5-Bio-MAGETAB/pkg-plist (revision 499678) @@ -1,118 +1,118 @@ bin/deploy_magetab_db.pl bin/fix_ae_magetab.pl bin/read_magetab.pl bin/unload_magetab_namespace.pl -%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/DataMatrix.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/TagValueFile.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/Tabfile.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/ADF.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/IDF.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/SDRF.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/ADF.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/GraphViz.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/IDF.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/SDRF.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/Tabfile.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Writer.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Reader.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Builder.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/DBLoader.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/RewriteAE.pm -%%SITE_PERL%%/Bio/MAGETAB/Util/Persistence.pm +%%SITE_PERL%%/Bio/MAGETAB.pm %%SITE_PERL%%/Bio/MAGETAB/ArrayDesign.pm %%SITE_PERL%%/Bio/MAGETAB/Assay.pm %%SITE_PERL%%/Bio/MAGETAB/BaseClass.pm %%SITE_PERL%%/Bio/MAGETAB/Comment.pm %%SITE_PERL%%/Bio/MAGETAB/CompositeElement.pm %%SITE_PERL%%/Bio/MAGETAB/Contact.pm %%SITE_PERL%%/Bio/MAGETAB/ControlledTerm.pm +%%SITE_PERL%%/Bio/MAGETAB/Data.pm %%SITE_PERL%%/Bio/MAGETAB/DataAcquisition.pm %%SITE_PERL%%/Bio/MAGETAB/DataFile.pm %%SITE_PERL%%/Bio/MAGETAB/DataMatrix.pm %%SITE_PERL%%/Bio/MAGETAB/DatabaseEntry.pm -%%SITE_PERL%%/Bio/MAGETAB/Data.pm %%SITE_PERL%%/Bio/MAGETAB/DesignElement.pm %%SITE_PERL%%/Bio/MAGETAB/Edge.pm %%SITE_PERL%%/Bio/MAGETAB/Event.pm %%SITE_PERL%%/Bio/MAGETAB/Extract.pm -%%SITE_PERL%%/Bio/MAGETAB/FactorValue.pm %%SITE_PERL%%/Bio/MAGETAB/Factor.pm +%%SITE_PERL%%/Bio/MAGETAB/FactorValue.pm %%SITE_PERL%%/Bio/MAGETAB/Feature.pm %%SITE_PERL%%/Bio/MAGETAB/Investigation.pm %%SITE_PERL%%/Bio/MAGETAB/LabeledExtract.pm %%SITE_PERL%%/Bio/MAGETAB/Material.pm %%SITE_PERL%%/Bio/MAGETAB/MatrixColumn.pm %%SITE_PERL%%/Bio/MAGETAB/MatrixRow.pm %%SITE_PERL%%/Bio/MAGETAB/Measurement.pm %%SITE_PERL%%/Bio/MAGETAB/Node.pm %%SITE_PERL%%/Bio/MAGETAB/Normalization.pm %%SITE_PERL%%/Bio/MAGETAB/ParameterValue.pm +%%SITE_PERL%%/Bio/MAGETAB/Protocol.pm %%SITE_PERL%%/Bio/MAGETAB/ProtocolApplication.pm %%SITE_PERL%%/Bio/MAGETAB/ProtocolParameter.pm -%%SITE_PERL%%/Bio/MAGETAB/Protocol.pm %%SITE_PERL%%/Bio/MAGETAB/Publication.pm %%SITE_PERL%%/Bio/MAGETAB/Reporter.pm -%%SITE_PERL%%/Bio/MAGETAB/SDRFRow.pm %%SITE_PERL%%/Bio/MAGETAB/SDRF.pm +%%SITE_PERL%%/Bio/MAGETAB/SDRFRow.pm %%SITE_PERL%%/Bio/MAGETAB/Sample.pm %%SITE_PERL%%/Bio/MAGETAB/Source.pm %%SITE_PERL%%/Bio/MAGETAB/TermSource.pm %%SITE_PERL%%/Bio/MAGETAB/Types.pm -%%SITE_PERL%%/Bio/MAGETAB.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Builder.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/DBLoader.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Persistence.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Reader.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/ADF.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/DataMatrix.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/IDF.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/SDRF.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/Tabfile.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Reader/TagValueFile.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/RewriteAE.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Writer.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/ADF.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/GraphViz.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/IDF.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/SDRF.pm +%%SITE_PERL%%/Bio/MAGETAB/Util/Writer/Tabfile.pm %%PERL5_MAN3%%/Bio::MAGETAB.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::ArrayDesign.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Assay.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::BaseClass.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Comment.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::CompositeElement.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Contact.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::ControlledTerm.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Data.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::DataAcquisition.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::DataFile.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::DataMatrix.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::DatabaseEntry.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::DesignElement.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Edge.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Event.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Extract.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Factor.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::FactorValue.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Feature.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Investigation.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::LabeledExtract.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Material.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::MatrixColumn.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::MatrixRow.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Measurement.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Node.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Normalization.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::ParameterValue.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Protocol.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::ProtocolApplication.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::ProtocolParameter.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Publication.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Reporter.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::SDRF.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::SDRFRow.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Sample.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Source.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::TermSource.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Types.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Builder.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::DBLoader.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Persistence.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Reader.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Reader::ADF.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Reader::DataMatrix.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Reader::IDF.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Reader::SDRF.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Reader::Tabfile.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Reader::TagValueFile.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::RewriteAE.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::ADF.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::GraphViz.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::IDF.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::SDRF.3.gz %%PERL5_MAN3%%/Bio::MAGETAB::Util::Writer::Tabfile.3.gz