Attachment 90932 Details for Bug 128193 – file.diff

[patch] file.diff

file.diff (text/plain), 13.06 KB, created by Mauricio Herrera Cuadra on 2008-10-18 06:20:01 UTC

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Creator: Mauricio Herrera Cuadra

Created: 2008-10-18 06:20:01 UTC

Size: 13.06 KB

patch

obsolete

>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

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Attachments on bug 128193: 90932