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PR:		ports/128193
Submitted by:	Mauricio Herrera Cuadra <mauricio at arareko.net> (maintainer)
This commit is contained in:
Rong-En Fan 2008-10-21 15:24:46 +00:00
parent f246a0ef5b
commit 1153c04ff7
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=221872
3 changed files with 42 additions and 7 deletions
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10
biology/p5-bioperl-devel/Makefile
View File

@ -33,6 +33,7 @@ BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/${PERL_VER}/Text/Wrap.pm:${PORTSDIR}/lang/
${SITE_PERL}/Spreadsheet/ParseExcel.pm:${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 @@ BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/${PERL_VER}/Text/Wrap.pm:${PORTSDIR}/lang/
${SITE_PERL}/${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 \
@ -106,6 +101,7 @@ MAN1= bp_aacomp.pl.1 \
bp_nrdb.pl.1 \
bp_oligo_count.pl.1 \
bp_pairwise_kaks.pl.1 \
bp_parse_hmmsearch.pl.1 \
bp_process_gadfly.pl.1 \
bp_process_sgd.pl.1 \
bp_process_wormbase.pl.1 \
@ -123,6 +119,7 @@ MAN1= bp_aacomp.pl.1 \
bp_split_seq.pl.1 \
bp_sreformat.pl.1 \
bp_taxid4species.pl.1 \
bp_taxonomy2tree.pl.1 \
bp_translate_seq.pl.1 \
bp_tree2pag.pl.1 \
bp_unflatten_seq.pl.1
@ -1006,4 +1003,3 @@ post-install:
.endif
.include <bsd.port.post.mk>

19
biology/p5-bioperl-devel/files/patch-Build.PL Normal file
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@ -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;

20
biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm Normal file
View File

@ -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';
}