3 files changed, 0 insertions, 260 deletions

diff --git a/biology/p5-bioperl-devel/files/Makefile.man b/biology/p5-bioperl-devel/files/Makefile.man
deleted file mode 100644
index 4d3b300f0cb9..000000000000
--- a/biology/p5-bioperl-devel/files/Makefile.man
+++ /dev/null
@@ -1,235 +0,0 @@
-# $FreeBSD$
-
-MAN3=		Bio::AlignIO.3 \
-		Bio::AlignIO::bl2seq.3 \
-		Bio::AlignIO::clustalw.3 \
-		Bio::AlignIO::fasta.3 \
-		Bio::AlignIO::mase.3 \
-		Bio::AlignIO::meme.3 \
-		Bio::AlignIO::msf.3 \
-		Bio::AlignIO::nexus.3 \
-		Bio::AlignIO::pfam.3 \
-		Bio::AlignIO::phylip.3 \
-		Bio::AlignIO::prodom.3 \
-		Bio::AlignIO::selex.3 \
-		Bio::AlignIO::stockholm.3 \
-		Bio::Annotation.3 \
-		Bio::Annotation::Comment.3 \
-		Bio::Annotation::DBLink.3 \
-		Bio::Annotation::Reference.3 \
-		Bio::DB::Ace.3 \
-		Bio::DB::EMBL.3 \
-		Bio::DB::Fasta.3 \
-		Bio::DB::GDB.3 \
-		Bio::DB::GFF.3 \
-		Bio::DB::GFF::Adaptor::dbi.3 \
-		Bio::DB::GFF::Aggregator.3 \
-		Bio::DB::GFF::Aggregator::alignment.3 \
-		Bio::DB::GFF::Aggregator::clone.3 \
-		Bio::DB::GFF::Aggregator::none.3 \
-		Bio::DB::GFF::Aggregator::transcript.3 \
-		Bio::DB::GFF::Featname.3 \
-		Bio::DB::GFF::Feature.3 \
-		Bio::DB::GFF::Homol.3 \
-		Bio::DB::GFF::RelSegment.3 \
-		Bio::DB::GFF::Segment.3 \
-		Bio::DB::GFF::Typename.3 \
-		Bio::DB::GenBank.3 \
-		Bio::DB::GenPept.3 \
-		Bio::DB::NCBIHelper.3 \
-		Bio::DB::RandomAccessI.3 \
-		Bio::DB::SeqI.3 \
-		Bio::DB::SwissProt.3 \
-		Bio::DB::Universal.3 \
-		Bio::DB::UpdateableSeqI.3 \
-		Bio::DB::WebDBSeqI.3 \
-		Bio::DBLinkContainerI.3 \
-		Bio::Factory::ApplicationFactoryI.3 \
-		Bio::Factory::DriverFactory.3 \
-		Bio::Factory::EMBOSS.3 \
-		Bio::Factory::SeqAnalysisParserFactory.3 \
-		Bio::Factory::SeqAnalysisParserFactoryI.3 \
-		Bio::Index::Abstract.3 \
-		Bio::Index::AbstractSeq.3 \
-		Bio::Index::EMBL.3 \
-		Bio::Index::Fasta.3 \
-		Bio::Index::GenBank.3 \
-		Bio::Index::SwissPfam.3 \
-		Bio::Index::Swissprot.3 \
-		Bio::LiveSeq::AARange.3 \
-		Bio::LiveSeq::Chain.3 \
-		Bio::LiveSeq::ChainI.3 \
-		Bio::LiveSeq::DNA.3 \
-		Bio::LiveSeq::Exon.3 \
-		Bio::LiveSeq::Gene.3 \
-		Bio::LiveSeq::IO::BioPerl.3 \
-		Bio::LiveSeq::IO::Loader.3 \
-		Bio::LiveSeq::IO::SRS.3 \
-		Bio::LiveSeq::Intron.3 \
-		Bio::LiveSeq::Mutation.3 \
-		Bio::LiveSeq::Mutator.3 \
-		Bio::LiveSeq::Prim_Transcript.3 \
-		Bio::LiveSeq::Range.3 \
-		Bio::LiveSeq::Repeat_Region.3 \
-		Bio::LiveSeq::Repeat_Unit.3 \
-		Bio::LiveSeq::SeqI.3 \
-		Bio::LiveSeq::Transcript.3 \
-		Bio::LiveSeq::Translation.3 \
-		Bio::LocatableSeq.3 \
-		Bio::Location::AvWithinCoordPolicy.3 \
-		Bio::Location::CoordinatePolicyI.3 \
-		Bio::Location::Fuzzy.3 \
-		Bio::Location::FuzzyLocationI.3 \
-		Bio::Location::NarrowestCoordPolicy.3 \
-		Bio::Location::Simple.3 \
-		Bio::Location::Split.3 \
-		Bio::Location::SplitLocationI.3 \
-		Bio::Location::WidestCoordPolicy.3 \
-		Bio::LocationI.3 \
-		Bio::PrimarySeq.3 \
-		Bio::PrimarySeqI.3 \
-		Bio::Range.3 \
-		Bio::RangeI.3 \
-		Bio::Root::Err.3 \
-		Bio::Root::Global.3 \
-		Bio::Root::IO.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::SearchDist.3 \
-		Bio::Seq.3 \
-		Bio::Seq::LargePrimarySeq.3 \
-		Bio::Seq::LargeSeq.3 \
-		Bio::Seq::RichSeq.3 \
-		Bio::Seq::RichSeqI.3 \
-		Bio::SeqAnalysisParserI.3 \
-		Bio::SeqFeature::Computation.3 \
-		Bio::SeqFeature::Exon.3 \
-		Bio::SeqFeature::FeaturePair.3 \
-		Bio::SeqFeature::Gene::Exon.3 \
-		Bio::SeqFeature::Gene::ExonI.3 \
-		Bio::SeqFeature::Gene::GeneStructure.3 \
-		Bio::SeqFeature::Gene::GeneStructureI.3 \
-		Bio::SeqFeature::Gene::Transcript.3 \
-		Bio::SeqFeature::Gene::TranscriptI.3 \
-		Bio::SeqFeature::Generic.3 \
-		Bio::SeqFeature::Intron.3 \
-		Bio::SeqFeature::PolyA.3 \
-		Bio::SeqFeature::Promoter.3 \
-		Bio::SeqFeature::Similarity.3 \
-		Bio::SeqFeature::SimilarityPair.3 \
-		Bio::SeqFeature::UTR3.3 \
-		Bio::SeqFeature::UTR5.3 \
-		Bio::SeqFeatureI.3  \
-		Bio::SeqI.3 \
-		Bio::SeqIO.3 \
-		Bio::SeqIO::FTHelper.3 \
-		Bio::SeqIO::MultiFile.3 \
-		Bio::SeqIO::ace.3 \
-		Bio::SeqIO::embl.3 \
-		Bio::SeqIO::fasta.3 \
-		Bio::SeqIO::game.3 \
-		Bio::SeqIO::game::featureHandler.3 \
-		Bio::SeqIO::game::idHandler.3 \
-		Bio::SeqIO::game::seqHandler.3 \
-		Bio::SeqIO::gcg.3 \
-		Bio::SeqIO::genbank.3 \
-		Bio::SeqIO::largefasta.3 \
-		Bio::SeqIO::pir.3 \
-		Bio::SeqIO::raw.3 \
-		Bio::SeqIO::scf.3 \
-		Bio::SeqIO::swiss.3 \
-		Bio::SeqUtils.3 \
-		Bio::SimpleAlign.3 \
-		Bio::Species.3 \
-		Bio::Tools::AlignFactory.3 \
-		Bio::Tools::AnalysisResult.3 \
-		Bio::Tools::BPbl2seq.3 \
-		Bio::Tools::BPlite.3 \
-		Bio::Tools::BPlite::Iteration.3 \
-		Bio::Tools::BPpsilite.3 \
-		Bio::Tools::Blast.3 \
-		Bio::Tools::Blast::HSP.3 \
-		Bio::Tools::Blast::HTML.3 \
-		Bio::Tools::Blast::Run::LocalBlast.3 \
-		Bio::Tools::Blast::Run::Webblast.3 \
-		Bio::Tools::Blast::Sbjct.3 \
-		Bio::Tools::CodonTable.3 \
-		Bio::Tools::EPCR.3 \
-		Bio::Tools::ESTScan.3 \
-		Bio::Tools::Fasta.3 \
-		Bio::Tools::GFF.3 \
-		Bio::Tools::Genemark.3 \
-		Bio::Tools::Genscan.3 \
-		Bio::Tools::Grail.3 \
-		Bio::Tools::HMMER::Domain.3 \
-		Bio::Tools::HMMER::Results.3 \
-		Bio::Tools::HMMER::Set.3 \
-		Bio::Tools::IUPAC.3 \
-		Bio::Tools::MZEF.3 \
-		Bio::Tools::OddCodes.3 \
-		Bio::Tools::Prediction::Exon.3 \
-		Bio::Tools::Prediction::Gene.3 \
-		Bio::Tools::RestrictionEnzyme.3 \
-		Bio::Tools::Run::Alignment::Clustalw.3 \
-		Bio::Tools::Run::Alignment::TCoffee.3 \
-		Bio::Tools::Run::EMBOSSApplication.3 \
-		Bio::Tools::Run::RemoteBlast.3 \
-		Bio::Tools::Run::StandAloneBlast.3 \
-		Bio::Tools::SeqAnal.3 \
-		Bio::Tools::SeqPattern.3 \
-		Bio::Tools::SeqStats.3 \
-		Bio::Tools::SeqWords.3 \
-		Bio::Tools::Sigcleave.3 \
-		Bio::Tools::Sim4::Exon.3 \
-		Bio::Tools::Sim4::Results.3 \
-		Bio::Tools::WWW.3 \
-		Bio::Tools::pSW.3 \
-		Bio::UnivAln.3 \
-		Bio::Variation::AAChange.3 \
-		Bio::Variation::AAReverseMutate.3 \
-		Bio::Variation::Allele.3 \
-		Bio::Variation::DNAMutation.3 \
-		Bio::Variation::IO.3 \
-		Bio::Variation::IO::flat.3 \
-		Bio::Variation::IO::xml.3 \
-		Bio::Variation::RNAChange.3 \
-		Bio::Variation::SeqDiff.3 \
-		Bio::Variation::VariantI.3 \
-		bioback.3 \
-		biodesign.3 \
-		bioperl.3 \
-		biostart.3 \
-		bptutorial.3
-.if defined(WITH_CORBA_CLIENT)
-MAN3+=		Bio::CorbaClient::PrimarySeq.3 \
-		Bio::CorbaClient::Seq.3 \
-		Bio::CorbaClient::SeqFeature.3 \
-		Bio::CorbaClient::Base.3 \
-		Bio::SeqIO::biocorba.3 \
-		Bio::DB::Biocorba.3 \
-		Bio::CorbaClient::Client.3 \
-		Bio::CorbaClient::ORB.3
-.endif
-.if defined(WITH_CORBA_SERVER)
-MAN3+=		Bio::CorbaServer::BioEnv.3 \
-		Bio::CorbaServer::AnonymousSeq.3 \
-		Bio::CorbaServer::PrimarySeq.3 \
-		Bio::CorbaServer::SeqFeature.3 \
-		Bio::CorbaServer::PrimarySeqDB.3 \
-		Bio::CorbaServer::PrimarySeqIterator.3 \
-		Bio::CorbaServer::PrimarySeqVector.3 \
-		Bio::CorbaServer::Seq.3 \
-		Bio::CorbaServer::SeqDB.3 \
-		Bio::CorbaServer::Base.3 \
-		Bio::CorbaServer::SeqFeatureIterator.3 \
-		Bio::CorbaServer::SeqFeatureVector.3 \
-		Bio::CorbaServer::Server.3
-.endif
-.if defined(WITH_GUI)
-MAN3+=		Bio::Tk::HitDisplay.3 \
-		Bio::Tk::SeqCanvas.3
-.endif
diff --git a/biology/p5-bioperl-devel/files/ext.msg b/biology/p5-bioperl-devel/files/ext.msg
deleted file mode 100644
index 1ba9af2f5f84..000000000000
--- a/biology/p5-bioperl-devel/files/ext.msg
+++ /dev/null
@@ -1,16 +0,0 @@
----------------------------------------------------------------------------
-This port includes support for a number of optional extensions to Bioperl.
-To build the port with these extensions, set the corresponding variables:
-
-To build with client-side CORBA support:	set WITH_CORBA_CLIENT
-To build with server-side CORBA support:	set WITH_CORBA_SERVER
-To build with (experimental) GUI support:	set WITH_GUI
-
-Additionally, the variable WITH_CORBA implies both WITH_CORBA_CLIENT and
-WITH_CORBA_SERVER.
-
-For example, to build and install the Bioperl port with all the currently
-available optional extensions:
-
-  make WITH_CORBA=yes WITH_GUI=yes install
----------------------------------------------------------------------------
diff --git a/biology/p5-bioperl-devel/files/patch-aa b/biology/p5-bioperl-devel/files/patch-aa
deleted file mode 100644
index 4aecbfe2a166..000000000000
--- a/biology/p5-bioperl-devel/files/patch-aa
+++ /dev/null
@@ -1,9 +0,0 @@
---- ../bioperl-ext-06/Bio/Ext/Align/libs/makefile.orig	Thu Sep 16 15:33:08 1999
-+++ ../bioperl-ext-06/Bio/Ext/Align/libs/makefile	Fri Jul 28 11:57:27 2000
-@@ -47,5 +47,5 @@
- # For NetBSD or Sun (solaris) installs, add -fPIC to the CFLAGS lines
- #
- 
--CFLAGS = -c -O
-+CFLAGS+= -c -O -fPIC
- CC     = cc