Date: Sat, 18 Oct 2008 05:14:51 GMT From: Mauricio Herrera Cuadra <mauricio@arareko.net> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/128193: Fix port: biology/p5-bioperl-devel Message-ID: <200810180514.m9I5EpN1069357@www.freebsd.org> Resent-Message-ID: <200810180520.m9I5K2o2091135@freefall.freebsd.org>
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>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 <mauricio@arareko.net>
#
-# $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 <bsd.port.post.mk>
-
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:
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