From owner-freebsd-ports Fri Oct 13 5:20:17 2000 Delivered-To: freebsd-ports@freebsd.org Received: from freefall.freebsd.org (freefall.FreeBSD.org [216.136.204.21]) by hub.freebsd.org (Postfix) with ESMTP id 9E14C37B66D for ; Fri, 13 Oct 2000 05:20:01 -0700 (PDT) Received: (from gnats@localhost) by freefall.freebsd.org (8.9.3/8.9.2) id FAA13588; Fri, 13 Oct 2000 05:20:01 -0700 (PDT) (envelope-from gnats@FreeBSD.org) Received: from fling.sanbi.ac.za (fling.sanbi.ac.za [196.38.142.119]) by hub.freebsd.org (Postfix) with ESMTP id 7D48E37B66E for ; Fri, 13 Oct 2000 05:11:51 -0700 (PDT) Received: from johann by fling.sanbi.ac.za with local (Exim 3.13 #4) id 13k3ga-00038M-00 for FreeBSD-gnats-submit@freebsd.org; Fri, 13 Oct 2000 14:11:40 +0200 Message-Id: Date: Fri, 13 Oct 2000 14:11:40 +0200 From: johann@egenetics.com To: FreeBSD-gnats-submit@freebsd.org X-Send-Pr-Version: 3.2 Subject: ports/21954: Port update: biology/p5-bioperl (maintainer) Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk X-Loop: FreeBSD.org >Number: 21954 >Category: ports >Synopsis: Port update: biology/p5-bioperl (maintainer) >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Fri Oct 13 05:20:01 PDT 2000 >Closed-Date: >Last-Modified: >Originator: Johann Visagie >Release: FreeBSD 3.5-STABLE i386 >Organization: Electric Genetics >Environment: >Description: - Update port biology/p5-bioperl from 0.6.1 to 0.6.2 (significant bugfix release) - Update Makefile to make use of PERL_CONFIGURE - Alphabetise $PLIST, as well as MAN3 in Makefile - General cleaning up of Makefile - Tested on 3.5-STABLE and 5.0-CURRENT >How-To-Repeat: >Fix: diff -ruN p5-bioperl.bak/Makefile p5-bioperl/Makefile --- p5-bioperl.bak/Makefile Fri Oct 13 13:57:18 2000 +++ p5-bioperl/Makefile Fri Oct 13 13:52:43 2000 @@ -6,7 +6,7 @@ # PORTNAME= bioperl -PORTVERSION= 0.6.1 +PORTVERSION= 0.6.2 CATEGORIES= biology perl5 MASTER_SITES= ftp://bio.perl.org/pub/DIST/ \ http://bio.perl.org/Core/Latest/ \ @@ -17,108 +17,67 @@ MAINTAINER= johann@egenetics.com -BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \ - ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \ - ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl - -USE_PERL5= YES - -EXT_WRKSRC= ${WRKDIR}/bioperl-ext-06 - -MAN3= Bio::Tools::CodonTable.3 \ - Bio::PrimarySeq.3 \ - Bio::Tools::SeqStats.3 \ - Bio::SimpleAlign.3 \ - Bio::Search::Processor::Fasta.3 \ - Bio::Root::Xref.3 \ - Bio::Annotation::DBLink.3 \ - Bio::SeqIO::swiss.3 \ - Bio::Annotation::Comment.3 \ - Bio::Tools::Sim4::Results.3 \ - Bio::Annotation::Reference.3 \ - Bio::SeqIO::pir.3 \ - Bio::Search::Hit::Fasta.3 \ - Bio::Tools::SeqAnal.3 \ - Bio::Annotation.3 \ - Bio::Tools::Blast::HTML.3 \ - Bio::Tools::HMMER::Results.3 \ - Bio::SeqIO::scf.3 \ - Bio::SeqIO::genbank.3 \ - Bio::Root::RootI.3 \ - Bio::Tools::SeqWords.3 \ - Bio::Root::Global.3 \ - Bio::Tools::pSW.3 \ - Bio::SeqIO::raw.3 \ - Bio::Tools::Blast::HSP.3 \ - bioperl.3 \ - Bio::RangeI.3 \ - Bio::Search::Processor.3 \ - Bio::Root::Object.3 \ - Bio::Tools::WWW.3 \ - Bio::PrimarySeqI.3 \ - Bio::Index::Abstract.3 \ - Bio::DB::Ace.3 \ - Bio::SeqFeature::Generic.3 \ - Bio::DB::SeqI.3 \ - Bio::Root::Vector.3 \ - Bio::Seq.3 \ - Bio::Range.3 \ - Bio::UnivAln.3 \ - Bio::Tools::Blast::Run::Webblast.3 \ - Bio::SeqIO::gcg.3 \ - biodesign.3 \ - Bio::Tools::RestrictionEnzyme.3 \ - Bio::DB::RandomAccessI.3 \ - biostart.3 \ - Bio::Tools::Sim4::Exon.3 \ - Bio::Search::Hit::HitI.3 \ - bioback.3 \ - Bio::Tools::HMMER::Domain.3 \ - Bio::SeqIO::FTHelper.3 \ - Bio::Root::IOManager.3 \ - Bio::LocatableSeq.3 \ - Bio::Index::AbstractSeq.3 \ - Bio::Tools::Fasta.3 \ - Bio::Tools::Blast::Sbjct.3 \ - Bio::Tools::IUPAC.3 \ - Bio::SeqIO.3 \ - Bio::SeqIO::MultiFile.3 \ - Bio::Tools::AlignFactory.3 \ - Bio::SeqIO::fasta.3 \ - Bio::SeqFeature::FeaturePair.3 \ - Bio::DB::GenBank.3 \ - Bio::SeqI.3 \ - Bio::Tools::Blast.3 \ - Bio::Tools::HMMER::Set.3 \ - Bio::SeqFeatureI.3 \ - Bio::SearchDist.3 \ - Bio::Tools::Sigcleave.3 \ - Bio::Search::Result::ResultI.3 \ - Bio::Root::Utilities.3 \ - Bio::Root::Err.3 \ - Bio::Search::Result::Fasta.3 \ - Bio::Tools::SeqPattern.3 \ +BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \ + ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \ + ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \ + ${LOCALBASE}/lib/perl5/site_perl/${PERL_VER}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy + +PERL_CONFIGURE= YES + +MAN3= Bio::Annotation.3 Bio::Annotation::Comment.3 \ + Bio::Annotation::DBLink.3 Bio::Annotation::Reference.3 \ + Bio::DB::Ace.3 Bio::DB::GenBank.3 Bio::DB::GenPept.3 \ + Bio::DB::RandomAccessI.3 Bio::DB::SeqI.3 \ + Bio::Index::Abstract.3 Bio::Index::AbstractSeq.3 \ + Bio::Index::EMBL.3 Bio::Index::Fasta.3 \ + Bio::Index::SwissPfam.3 Bio::LocatableSeq.3 \ + Bio::PrimarySeq.3 Bio::PrimarySeqI.3 Bio::Range.3 \ + Bio::RangeI.3 Bio::Root::Err.3 Bio::Root::Global.3 \ + Bio::Root::IOManager.3 Bio::Root::Object.3 \ + Bio::Root::RootI.3 Bio::Root::Utilities.3 \ + Bio::Root::Vector.3 Bio::Root::Xref.3 \ + Bio::Search::Hit::Fasta.3 Bio::Search::Hit::HitI.3 \ + Bio::Search::Processor.3 Bio::Search::Processor::Fasta.3 \ Bio::Search::Processor::ProcessorI.3 \ - Bio::Index::EMBL.3 \ - Bio::Species.3 \ + Bio::Search::Result::Fasta.3 \ + Bio::Search::Result::ResultI.3 Bio::SearchDist.3 \ + Bio::Seq.3 Bio::SeqFeature::FeaturePair.3 \ + Bio::SeqFeature::Generic.3 Bio::SeqFeatureI.3 Bio::SeqI.3 \ + Bio::SeqIO.3 Bio::SeqIO::FTHelper.3 \ + Bio::SeqIO::MultiFile.3 Bio::SeqIO::embl.3 \ + Bio::SeqIO::fasta.3 Bio::SeqIO::gcg.3 \ + Bio::SeqIO::genbank.3 Bio::SeqIO::pir.3 Bio::SeqIO::raw.3 \ + Bio::SeqIO::scf.3 Bio::SeqIO::swiss.3 Bio::SimpleAlign.3 \ + Bio::Species.3 Bio::Tools::AlignFactory.3 \ + Bio::Tools::Blast.3 Bio::Tools::Blast::HSP.3 \ + Bio::Tools::Blast::HTML.3 \ Bio::Tools::Blast::Run::LocalBlast.3 \ - Bio::SeqIO::embl.3 \ - Bio::Index::SwissPfam.3 \ - Bio::DB::GenPept.3 \ - Bio::Index::Fasta.3 - + Bio::Tools::Blast::Run::Webblast.3 \ + Bio::Tools::Blast::Sbjct.3 Bio::Tools::CodonTable.3 \ + Bio::Tools::Fasta.3 Bio::Tools::HMMER::Domain.3 \ + Bio::Tools::HMMER::Results.3 Bio::Tools::HMMER::Set.3 \ + Bio::Tools::IUPAC.3 Bio::Tools::RestrictionEnzyme.3 \ + Bio::Tools::SeqAnal.3 Bio::Tools::SeqPattern.3 \ + Bio::Tools::SeqStats.3 Bio::Tools::SeqWords.3 \ + Bio::Tools::Sigcleave.3 Bio::Tools::WWW.3 \ + Bio::Tools::pSW.3 Bio::UnivAln.3 \ + bioback.3 biodesign.3 bioperl.3 biostart.3 MANPREFIX= ${PREFIX}/lib/perl5/${PERL_VERSION} -do-configure: - @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL) - @(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${SETENV} ${MAKE_ENV} ${PERL5} Makefile.PL) - -do-build: - @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}) - @(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}) - -do-install: - @(cd ${WRKSRC}; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}) - @(cd ${EXT_WRKSRC}/Bio/Ext/Align; ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}) +EXT_WRKSRC= ${WRKDIR}/bioperl-ext-06/Bio/Ext/Align + +post-configure: + @ (cd ${EXT_WRKSRC} && \ + ${SETENV} ${CONFIGURE_ENV} \ + ${PERL5} ${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}) + +post-build: + @ (cd ${EXT_WRKSRC} && \ + ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} ${ALL_TARGET}) + +post-install: + @ (cd ${EXT_WRKSRC} && \ + ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} \ + ${MAKEFILE} ${MAKE_ARGS} ${INSTALL_TARGET}) .include diff -ruN p5-bioperl.bak/distinfo p5-bioperl/distinfo --- p5-bioperl.bak/distinfo Fri Oct 13 13:57:18 2000 +++ p5-bioperl/distinfo Fri Oct 13 12:38:14 2000 @@ -1,2 +1,2 @@ -MD5 (bioperl-0.6.1.tar.gz) = e3506188027a94ea87443389a78c2fdc +MD5 (bioperl-0.6.2.tar.gz) = 26330f4f0c1e08a4f5cbcbe8b05b72f1 MD5 (bioperl-ext-0.6.tar.gz) = 5bf87e0cf94d3d41fabbfd209971d240 diff -ruN p5-bioperl.bak/pkg-plist p5-bioperl/pkg-plist --- p5-bioperl.bak/pkg-plist Fri Oct 13 13:57:18 2000 +++ p5-bioperl/pkg-plist Fri Oct 13 13:23:21 2000 @@ -1,109 +1,108 @@ -lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenBank.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SeqI.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs +lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so +lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/Ace.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenBank.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/GenPept.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/RandomAccessI.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/DB/SeqI.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Err.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Global.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Object.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Vector.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/RootI.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Utilities.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/IOManager.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/RangeI.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqI.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Vector.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Root/Xref.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/Fasta.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/HitI.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/Fasta.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/ProcessorI.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/Fasta.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/ResultI.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeatureI.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/genbank.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqI.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/FTHelper.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/raw.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/embl.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/scf.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/swiss.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/fasta.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/gcg.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/genbank.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/pir.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/MultiFile.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Results.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4/Exon.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/raw.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/scf.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO/swiss.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/AlignFactory.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Makefile.PL -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/postclient.pl -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/LocalBlast.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/CHANGES lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HSP.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Sbjct.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/README lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/HTML.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/README +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/LocalBlast.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Makefile.PL +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/Webblast.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run/postclient.pl +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Sbjct.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/CodonTable.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Fasta.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Results.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Set.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER/Domain.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sigcleave.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/IUPAC.pm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/RestrictionEnzyme.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SearchDist.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/HitI.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit/Fasta.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/Fasta.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor/ProcessorI.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/ResultI.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result/Fasta.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Seq.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeqI.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Range.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SimpleAlign.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/EMBL.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/AbstractSeq.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Fasta.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/Abstract.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Index/SwissPfam.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Species.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/PrimarySeq.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/LocatableSeq.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Comment.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/Reference.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation/DBLink.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/FeaturePair.pm -lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature/Generic.pm -lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqAnal.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqPattern.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqStats.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/SeqWords.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sigcleave.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/WWW.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/pSW.pm +lib/perl5/site_perl/%%PERL_VER%%/Bio/UnivAln.pm lib/perl5/site_perl/%%PERL_VER%%/bioback.pod lib/perl5/site_perl/%%PERL_VER%%/biodesign.pod +lib/perl5/site_perl/%%PERL_VER%%/bioperl.pod lib/perl5/site_perl/%%PERL_VER%%/biostart.pod -lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/.packlist -lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.bs -lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/Align.so -lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext/Align.pm -lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/.packlist -@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB -@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root -@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO -@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Sim4 +@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast/Run @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/Blast -@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools/HMMER @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Tools -@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit -@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor +@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqIO +@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Result +@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Processor +@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search/Hit @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Search +@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Root @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Index +@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/DB @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/Annotation -@dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio/SeqFeature @dirrm lib/perl5/site_perl/%%PERL_VER%%/Bio -@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align/ +@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext/Align @dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio/Ext @dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/auto/Bio +@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio/Ext +@dirrm lib/perl5/site_perl/%%PERL_VER%%/%%PERL_ARCH%%/Bio >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message