From owner-freebsd-ports-bugs@FreeBSD.ORG Sat Oct 18 05:20:02 2008 Return-Path: Delivered-To: freebsd-ports-bugs@hub.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id 6C03C1065698 for ; Sat, 18 Oct 2008 05:20:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (freefall.freebsd.org [IPv6:2001:4f8:fff6::28]) by mx1.freebsd.org (Postfix) with ESMTP id 467748FC17 for ; Sat, 18 Oct 2008 05:20:02 +0000 (UTC) (envelope-from gnats@FreeBSD.org) Received: from freefall.freebsd.org (gnats@localhost [127.0.0.1]) by freefall.freebsd.org (8.14.3/8.14.3) with ESMTP id m9I5K2G2091136 for ; Sat, 18 Oct 2008 05:20:02 GMT (envelope-from gnats@freefall.freebsd.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.14.3/8.14.3/Submit) id m9I5K2o2091135; Sat, 18 Oct 2008 05:20:02 GMT (envelope-from gnats) Resent-Date: Sat, 18 Oct 2008 05:20:02 GMT Resent-Message-Id: <200810180520.m9I5K2o2091135@freefall.freebsd.org> Resent-From: FreeBSD-gnats-submit@FreeBSD.org (GNATS Filer) Resent-To: freebsd-ports-bugs@FreeBSD.org Resent-Reply-To: FreeBSD-gnats-submit@FreeBSD.org, Mauricio Herrera Cuadra Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:4f8:fff6::34]) by hub.freebsd.org (Postfix) with ESMTP id F0857106568B for ; Sat, 18 Oct 2008 05:14:51 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (www.freebsd.org [IPv6:2001:4f8:fff6::21]) by mx1.freebsd.org (Postfix) with ESMTP id DDA7E8FC0A for ; Sat, 18 Oct 2008 05:14:51 +0000 (UTC) (envelope-from nobody@FreeBSD.org) Received: from www.freebsd.org (localhost [127.0.0.1]) by www.freebsd.org (8.14.3/8.14.3) with ESMTP id m9I5EpQp069359 for ; Sat, 18 Oct 2008 05:14:51 GMT (envelope-from nobody@www.freebsd.org) Received: (from nobody@localhost) by www.freebsd.org (8.14.3/8.14.3/Submit) id m9I5EpN1069357; Sat, 18 Oct 2008 05:14:51 GMT (envelope-from nobody) Message-Id: <200810180514.m9I5EpN1069357@www.freebsd.org> Date: Sat, 18 Oct 2008 05:14:51 GMT From: Mauricio Herrera Cuadra To: freebsd-gnats-submit@FreeBSD.org X-Send-Pr-Version: www-3.1 Cc: Subject: ports/128193: Fix port: biology/p5-bioperl-devel X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.5 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 18 Oct 2008 05:20:02 -0000 >Number: 128193 >Category: ports >Synopsis: Fix port: biology/p5-bioperl-devel >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Sat Oct 18 05:20:01 UTC 2008 >Closed-Date: >Last-Modified: >Originator: Mauricio Herrera Cuadra >Release: FreeBSD 7.1-PRERELEASE i386 >Organization: Intelligenomes >Environment: FreeBSD freebsd-vm.ultratrail.intelligenomes.com 7.1-PRERELEASE FreeBSD 7.1-PRERELEASE #0: Wed Oct 8 14:36:05 CDT 2008 root@freebsd-vm.ultratrail.intelligenomes.com:/usr/obj/usr/src/sys/freebsd-vm i386 >Description: This patch fixes the biology/p5-bioperl-devel port, which is currently broken. >How-To-Repeat: >Fix: Patch attached with submission follows: diff -ruN p5-bioperl-devel.old/Makefile p5-bioperl-devel/Makefile --- p5-bioperl-devel.old/Makefile 2008-10-17 23:11:55.000000000 -0500 +++ p5-bioperl-devel/Makefile 2008-10-17 23:19:58.000000000 -0500 @@ -2,7 +2,7 @@ # Date created: 21 November 2005 # Whom: Mauricio Herrera Cuadra # -# $FreeBSD: ports/biology/p5-bioperl-devel/Makefile,v 1.13 2008/07/07 22:57:49 pav Exp $ +# $FreeBSD: ports/biology/p5-bioperl-devel/Makefile,v 1.11 2007/09/08 00:53:11 linimon Exp $ # PORTNAME= bioperl @@ -33,6 +33,7 @@ ${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \ ${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \ ${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \ + ${SITE_PERL}/Test/Harness.pm:${PORTSDIR}/devel/p5-Test-Harness \ ${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords \ ${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \ ${SITE_PERL}/XML/DOM/XPath.pm:${PORTSDIR}/textproc/p5-XML-DOM-XPath \ @@ -53,18 +54,12 @@ ${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser RUN_DEPENDS= ${BUILD_DEPENDS} -BROKEN= missing dependencies - CONFLICTS= p5-bioperl-1.[02468]* LATEST_LINK= p5-bioperl-devel PERL_MODBUILD= YES -NOPORTDOCS= yes -NOPORTEXAMPLES= yes -NOPORTDATA= yes - MAN1= bp_aacomp.pl.1 \ bp_biblio.pl.1 \ bp_biofetch_genbank_proxy.pl.1 \ @@ -993,10 +988,8 @@ post-install: ${MKDIR} ${DATADIR} ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR} -.if !defined(NOPORTEXAMPLES) ${MKDIR} ${EXAMPLESDIR} ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR} -.endif .if !defined(NOPORTDOCS) ${MKDIR} ${DOCSDIR} .for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE PLATFORMS README @@ -1006,4 +999,3 @@ .endif .include - diff -ruN p5-bioperl-devel.old/files/patch-Build.PL p5-bioperl-devel/files/patch-Build.PL --- p5-bioperl-devel.old/files/patch-Build.PL 1969-12-31 18:00:00.000000000 -0600 +++ p5-bioperl-devel/files/patch-Build.PL 2008-10-17 23:13:16.000000000 -0500 @@ -0,0 +1,19 @@ +--- Build.PL.orig Wed Feb 14 05:37:47 2007 ++++ Build.PL Sun Jun 15 02:24:07 2008 +@@ -32,7 +32,6 @@ + 'Test::More' => 0, + 'Module::Build' => 0.2805, + 'Test::Harness' => 2.62, +- 'CPAN' => 1.81 + }, + recommends => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml + 'Ace' => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace', +@@ -174,7 +173,7 @@ + } + + sub prompt_for_biodbgff { +- my $proceed = $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n'); ++ my $proceed = undef; # $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n'); + + if ($proceed) { + my @driver_choices; diff -ruN p5-bioperl-devel.old/files/patch-ModuleBuildBioperl.pm p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm --- p5-bioperl-devel.old/files/patch-ModuleBuildBioperl.pm 1969-12-31 18:00:00.000000000 -0600 +++ p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm 2008-10-17 23:17:08.000000000 -0500 @@ -0,0 +1,20 @@ +--- ModuleBuildBioperl.pm.orig 2007-02-14 05:37:47.000000000 -0600 ++++ ModuleBuildBioperl.pm 2008-10-17 23:16:52.000000000 -0500 +@@ -93,7 +93,7 @@ + closedir($scripts_dir); + my $question = $int_ok ? "Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll Bioperl scripts or [n]one?"; + +- my $prompt = $self->prompt($question, 'a'); ++ my $prompt = 'a'; # $self->prompt($question, 'a'); + + if ($prompt =~ /^[aA]/) { + $self->log_info(" - will install all scripts\n"); +@@ -328,7 +328,7 @@ + + $status->{message} .= "\n (wanted for $why, used by $by_what)"; + +- my $installed = $self->install_optional($modname, $preferred_version, $status->{message}); ++ my $installed = 'skip'; # $self->install_optional($modname, $preferred_version, $status->{message}); + next if $installed eq 'ok'; + $status->{message} = $installed unless $installed eq 'skip'; + } diff -ruN p5-bioperl-devel.old/pkg-plist p5-bioperl-devel/pkg-plist --- p5-bioperl-devel.old/pkg-plist 2008-10-17 23:11:55.000000000 -0500 +++ p5-bioperl-devel/pkg-plist 2008-10-17 23:13:16.000000000 -0500 @@ -941,77 +941,77 @@ %%PORTDOCS%%%%DOCSDIR%%/doc/Deobfuscator/MANIFEST %%PORTDOCS%%%%DOCSDIR%%/doc/README %%PORTDOCS%%%%DOCSDIR%%/doc/makedoc.PL -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestObject.pm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestInterface.pm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions2.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions4.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/README -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions1.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions3.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_genscan.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gff2ps.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/extract_genes.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/seq_pattern.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gb_to_gff.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/psw.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/standaloneblast.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_primer3.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/parse_codeml.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/gsequence.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/hitdisplay.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tree/paup2phylip.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/structure/structure-io.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/rnai_finder.cgi -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/TAG -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/custom_writer.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/resultwriter.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/blast_example.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff3.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hspwriter.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_features.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/htmlwriter.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hitwriter.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/rawwriter.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/gb2features.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/dbfetch -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/use_registry.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/est_tissue_query.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/rfetch.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/getGenBank.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/db/get_seqs.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/clustalw.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/aligntutorial.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/simplealign.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/align/align_on_codons.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biblio/biblio-eutils-example.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biblio/biblio_soap.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biblio/biblio-soap-example.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/feature_data.gff -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/feature_data.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/render_sequence.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/dynamic_glyphs.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/all_glyphs.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/biographics/lots_of_glyphs.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cluster/dbsnp.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/liveseq/change_gene.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/prosite2perl.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/contributed/rebase2list.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/make_primers.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/longorf.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bioperl.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/generate_random_seq.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rev_and_trans.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/revcom_dir.pl -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/subsequence.cgi +%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeq.pm +%%EXAMPLESDIR%%/root/lib/Bio/SeqI.pm +%%EXAMPLESDIR%%/root/lib/Bio/Seq.pm +%%EXAMPLESDIR%%/root/lib/Bio/PrimarySeqI.pm +%%EXAMPLESDIR%%/root/lib/TestObject.pm +%%EXAMPLESDIR%%/root/lib/TestInterface.pm +%%EXAMPLESDIR%%/root/exceptions2.pl +%%EXAMPLESDIR%%/root/exceptions4.pl +%%EXAMPLESDIR%%/root/README +%%EXAMPLESDIR%%/root/exceptions1.pl +%%EXAMPLESDIR%%/root/exceptions3.pl +%%EXAMPLESDIR%%/tools/run_genscan.pl +%%EXAMPLESDIR%%/tools/gff2ps.pl +%%EXAMPLESDIR%%/tools/extract_genes.pl +%%EXAMPLESDIR%%/tools/seq_pattern.pl +%%EXAMPLESDIR%%/tools/gb_to_gff.pl +%%EXAMPLESDIR%%/tools/psw.pl +%%EXAMPLESDIR%%/tools/standaloneblast.pl +%%EXAMPLESDIR%%/tools/run_primer3.pl +%%EXAMPLESDIR%%/tools/parse_codeml.pl +%%EXAMPLESDIR%%/tk/gsequence.pl +%%EXAMPLESDIR%%/tk/hitdisplay.pl +%%EXAMPLESDIR%%/tree/paup2phylip.pl +%%EXAMPLESDIR%%/structure/structure-io.pl +%%EXAMPLESDIR%%/sirna/rnai_finder.cgi +%%EXAMPLESDIR%%/sirna/TAG +%%EXAMPLESDIR%%/searchio/custom_writer.pl +%%EXAMPLESDIR%%/searchio/resultwriter.pl +%%EXAMPLESDIR%%/searchio/blast_example.pl +%%EXAMPLESDIR%%/searchio/waba2gff3.pl +%%EXAMPLESDIR%%/searchio/hspwriter.pl +%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl +%%EXAMPLESDIR%%/searchio/waba2gff.pl +%%EXAMPLESDIR%%/searchio/psiblast_features.pl +%%EXAMPLESDIR%%/searchio/htmlwriter.pl +%%EXAMPLESDIR%%/searchio/hitwriter.pl +%%EXAMPLESDIR%%/searchio/rawwriter.pl +%%EXAMPLESDIR%%/db/gb2features.pl +%%EXAMPLESDIR%%/db/dbfetch +%%EXAMPLESDIR%%/db/use_registry.pl +%%EXAMPLESDIR%%/db/est_tissue_query.pl +%%EXAMPLESDIR%%/db/rfetch.pl +%%EXAMPLESDIR%%/db/getGenBank.pl +%%EXAMPLESDIR%%/db/get_seqs.pl +%%EXAMPLESDIR%%/align/clustalw.pl +%%EXAMPLESDIR%%/align/aligntutorial.pl +%%EXAMPLESDIR%%/align/simplealign.pl +%%EXAMPLESDIR%%/align/align_on_codons.pl +%%EXAMPLESDIR%%/biblio/biblio-eutils-example.pl +%%EXAMPLESDIR%%/biblio/biblio_soap.pl +%%EXAMPLESDIR%%/biblio/biblio-soap-example.pl +%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl +%%EXAMPLESDIR%%/biographics/feature_data.gff +%%EXAMPLESDIR%%/biographics/feature_data.txt +%%EXAMPLESDIR%%/biographics/render_sequence.pl +%%EXAMPLESDIR%%/biographics/dynamic_glyphs.pl +%%EXAMPLESDIR%%/biographics/all_glyphs.pl +%%EXAMPLESDIR%%/biographics/lots_of_glyphs.pl +%%EXAMPLESDIR%%/cluster/dbsnp.pl +%%EXAMPLESDIR%%/liveseq/change_gene.pl +%%EXAMPLESDIR%%/contributed/prosite2perl.pl +%%EXAMPLESDIR%%/contributed/nmrpdb_parse.pl +%%EXAMPLESDIR%%/contributed/rebase2list.pl +%%EXAMPLESDIR%%/Bio-DB-GFF/load_ucsc.pl +%%EXAMPLESDIR%%/make_primers.pl +%%EXAMPLESDIR%%/longorf.pl +%%EXAMPLESDIR%%/bioperl.pl +%%EXAMPLESDIR%%/generate_random_seq.pl +%%EXAMPLESDIR%%/rev_and_trans.pl +%%EXAMPLESDIR%%/revcom_dir.pl +%%EXAMPLESDIR%%/subsequence.cgi %%DATADIR%%/models/map_proposal.txt %%DATADIR%%/models/bio_liveseq_variation.dia %%DATADIR%%/models/maps_and_markers.dia @@ -1233,25 +1233,25 @@ %%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator %%PORTDOCS%%@dirrm %%DOCSDIR%%/doc %%PORTDOCS%%@dirrm %%DOCSDIR%% -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root/lib/Bio -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root/lib -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tools -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tk -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tree -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/structure -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sirna -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/searchio -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/db -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/align -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/biblio -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/popgen -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/biographics -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/cluster -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/liveseq -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/contributed -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF -%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% +@dirrm %%EXAMPLESDIR%%/root/lib/Bio +@dirrm %%EXAMPLESDIR%%/root/lib +@dirrm %%EXAMPLESDIR%%/root +@dirrm %%EXAMPLESDIR%%/tools +@dirrm %%EXAMPLESDIR%%/tk +@dirrm %%EXAMPLESDIR%%/tree +@dirrm %%EXAMPLESDIR%%/structure +@dirrm %%EXAMPLESDIR%%/sirna +@dirrm %%EXAMPLESDIR%%/searchio +@dirrm %%EXAMPLESDIR%%/db +@dirrm %%EXAMPLESDIR%%/align +@dirrm %%EXAMPLESDIR%%/biblio +@dirrm %%EXAMPLESDIR%%/popgen +@dirrm %%EXAMPLESDIR%%/biographics +@dirrm %%EXAMPLESDIR%%/cluster +@dirrm %%EXAMPLESDIR%%/liveseq +@dirrm %%EXAMPLESDIR%%/contributed +@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF +@dirrm %%EXAMPLESDIR%% @dirrm %%DATADIR%%/models @dirrm %%DATADIR%%/scripts/taxa @dirrm %%DATADIR%%/scripts/seq >Release-Note: >Audit-Trail: >Unformatted: