Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/libs/perlmods
In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv759
Modified Files:
bioperl-pm.info bioperl-pm.patch
Log Message:
fixed conflict with Module::Build
Index: bioperl-pm.info
===================================================================
RCS file:
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/libs/perlmods/bioperl-pm.info,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -d -r1.8 -r1.9
--- bioperl-pm.info 8 Nov 2007 02:10:40 -0000 1.8
+++ bioperl-pm.info 1 Dec 2007 18:57:44 -0000 1.9
@@ -2,10 +2,10 @@
Package: bioperl-pm%type_pkg[perl]
Version: 1.5.2
-Revision: 3
+Revision: 4
Architecture: (%type_pkg[perl] = 581) powerpc, (%type_pkg[perl] = 584) powerpc
Distribution: (%type_pkg[perl] = 581) 10.3, (%type_pkg[perl] = 581) 10.4,
(%type_pkg[perl] = 584) 10.3, (%type_pkg[perl] = 584) 10.4
-BuildDepends: perl%type_pkg[perl]-core, fink (>= 0.20.1-1)
+BuildDepends: perl%type_pkg[perl]-core, fink (>= 0.20.1-1),
module-build-pm%type_pkg[perl] (>= 0.2808)
Depends: <<
clone-pm%type_pkg[perl] (>= 0.27),
gd-pm%type_pkg[perl],
@@ -41,17 +41,34 @@
UpdatePOD: True
NoPerlTests: True
Patch: %{ni}.patch
+
+CompileScript: <<
+#!/bin/sh -ex
+ exec 2>&1
+ perlversion=%type_raw[perl]
+ eval "`perl$perlversion -V:archname`"
+ perl$perlversion Build.PL \
+ --install_path arch=%i/lib/perl5/$perlversion/$archname \
+ --install_path bin=%i/bin \
+ --install_path bindoc=%i/lib/perl5/$perlversion/man/man1 \
+ --install_path lib=%i/lib/perl5/$perlversion \
+ --install_path libdoc=%i/lib/perl5/$perlversion/man/man3 \
+ --install_path script=%i/bin
+ ./Build
+# ./Build test
+<<
+
InstallScript: <<
- %{default_script}
+ ./Build install
+ find %d -name .packlist -exec rm -rf {} \;
- mkdir -p %i/share/%n
- cp -r models examples doc %i/share/%n
- mkdir -p %i/share/%n/t
- cp -r t/data %i/share/%n/t
+ mkdir -p %i/share/%n
+ mkdir -p %i/share/%n/t
- mkdir -p %i/lib/perl5/%type_raw[perl]
- mv %i/man %i/lib/perl5/%type_raw[perl]
- mv %i/lib/perl5/site_perl/Bio %i/lib/perl5/%type_raw[perl]
+ cp -r models examples scripts doc %i/share/%n
+ cp -r t/data %i/share/%n/t
+
+ mv %i/bin/*.pl %i/share/%n/scripts/
<<
DocFiles: Changes INSTALL README LICENSE PLATFORMS BUGS AUTHORS DEPENDENCIES
@@ -63,17 +80,17 @@
software for life science research.
<<
DescPackaging: <<
-Modules are installed in %p/lib/perl5/%type_raw[perl], not in
%p/lib/perl5/site_perl
+Tests are disabled, because they need network access
+Switched to use Module::Build in version 1.5.2-4
Previous maintainer: Christopher Dithi <[EMAIL PROTECTED]>
<<
DescUsage: <<
Additional functionality for bioperl (eg for maintaining a local database)
can be obtained by installing the required perl modules before installing
-bioperl-pm. See %p/share/doc/bioperl-pm/DEPENDENCIES.
+bioperl-pm. See %p/share/doc/%n/DEPENDENCIES.
Note that not all optional perl modules are available through fink.
-All examples, docs, etc can be found in %p/share/bioperl-pm%type_pkg[perl]/
-The modules are installed in %p/lib/perl5/%type_raw[perl]/
+All examples, docs, etc can be found in %p/share/%n/
<<
License: Artistic
Maintainer: Koen van der Drift <[EMAIL PROTECTED]>
Index: bioperl-pm.patch
===================================================================
RCS file:
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/libs/perlmods/bioperl-pm.patch,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- bioperl-pm.patch 4 Nov 2007 02:14:37 -0000 1.2
+++ bioperl-pm.patch 1 Dec 2007 18:57:44 -0000 1.3
@@ -1,19 +1,18 @@
diff -Naur bioperl-1.5.2_102/Build.PL bioperl-1.5.2_102-patched/Build.PL
--- bioperl-1.5.2_102/Build.PL 2007-02-14 06:37:47.000000000 -0500
-+++ bioperl-1.5.2_102-patched/Build.PL 2007-11-03 14:41:55.000000000 -0400
-@@ -32,10 +32,10 @@
++++ bioperl-1.5.2_102-patched/Build.PL 2007-12-01 08:24:40.000000000 -0500
+@@ -30,9 +30,9 @@
+ },
+ build_requires => {
'Test::More' => 0,
- 'Module::Build' => 0.2805,
+- 'Module::Build' => 0.2805,
++ 'Module::Build' => 0.26,
'Test::Harness' => 2.62,
- 'CPAN' => 1.81
-+ # 'CPAN' => 1.81
++ # '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',
-+ # 'Ace' => '0/access of
ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
- # this won't actually install due to circular
dep, but we have no way of doing a post-install
- 'Bio::ASN1::EntrezGene' => '0/parsing
entrezgene/Bio::SeqIO::entrezgene',
- # we actually need 1.01 of Class::AutoClass, but
unfortunately it is versioned as 1.0
+ 'Ace' => '0/access of ACeDB
database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace',
@@ -71,22 +71,22 @@
get_options => {
network => { } # not actually used by anything
yet, but in the future say perl Build.PL --network
@@ -34,22 +33,22 @@
- feature_requires => {
'DBI' => 0, 'DBD::mysql' => 0 },
- test =>
\&test_db
- },
-+ # auto_features => {
-+ # BioDBSeqFeature_BDB => {
-+ # description =>
"BDB tests for Bio::DB::SeqFeature::Store",
-+ # feature_requires =>
{ 'DB_File' => 0 } # feature_requires is like requires, execpt that it doesn't
trigger installation
-+ # },
-+ # BioDBGFF => {
-+ # description =>
"BioDBGFF database tests (will need to answer questions before really
enabling)",
-+ # feature_requires =>
{ 'DBI' => 0 },
-+ # excludes_os =>
['mswin'],
-+ # test =>
\&test_biodbgff # ModuleBuildBioperl unique requirement that after everything
else succeeds, supplied code ref must also return undef
-+ # },
-+ # BioDBSeqFeature_mysql => {
-+ # description =>
"MySQL tests for Bio::DB::SeqFeature::Store",
-+ # feature_requires =>
{ 'DBI' => 0, 'DBD::mysql' => 0 },
-+ # test =>
\&test_db
-+ # },
++# auto_features => {
++# BioDBSeqFeature_BDB => {
++# description =>
"BDB tests for Bio::DB::SeqFeature::Store",
++# feature_requires =>
{ 'DB_File' => 0 } # feature_requires is like requires, execpt that it doesn't
trigger installation
++# },
++# BioDBGFF => {
++# description =>
"BioDBGFF database tests (will need to answer questions before really
enabling)",
++# feature_requires =>
{ 'DBI' => 0 },
++# excludes_os =>
['mswin'],
++# test =>
\&test_biodbgff # ModuleBuildBioperl unique requirement that after everything
else succeeds, supplied code ref must also return undef
++# },
++# BioDBSeqFeature_mysql => {
++# description =>
"MySQL tests for Bio::DB::SeqFeature::Store",
++# feature_requires =>
{ 'DBI' => 0, 'DBD::mysql' => 0 },
++# test =>
\&test_db
++# },
# The following code works, but since no tests in the test suite actually
make use of this functionality, don't use it yet
# Network => {
# description =>
"Enable tests that need an internet connection",
@@ -71,39 +70,105 @@
# Request that some scripts run post-installation
$build->add_post_install_script('maintenance/symlink_script.pl'); # takes a
unix file path regardless of local OS
+diff -Naur bioperl-1.5.2_102/Makefile.PL bioperl-1.5.2_102-patched/Makefile.PL
+--- bioperl-1.5.2_102/Makefile.PL 2007-02-14 06:37:47.000000000 -0500
++++ bioperl-1.5.2_102-patched/Makefile.PL 2007-12-01 07:57:56.000000000
-0500
+@@ -1,29 +1,29 @@
+ # Note: this file was auto-generated by Module::Build::Compat version 0.03
+
+- unless (eval "use Module::Build::Compat 0.02; 1" ) {
+- print "This module requires Module::Build to install itself.\n";
+-
+- require ExtUtils::MakeMaker;
+- my $yn = ExtUtils::MakeMaker::prompt
+- (' Install Module::Build now from CPAN?', 'y');
+-
+- unless ($yn =~ /^y/i) {
+- die " *** Cannot install without Module::Build. Exiting ...\n";
+- }
+-
+- require Cwd;
+- require File::Spec;
+- require CPAN;
+-
+- # Save this 'cause CPAN will chdir all over the place.
+- my $cwd = Cwd::cwd();
+-
+- CPAN::Shell->install('Module::Build::Compat');
+- CPAN::Shell->expand("Module", "Module::Build::Compat")->uptodate
+- or die "Couldn't install Module::Build, giving up.\n";
+-
+- chdir $cwd or die "Cannot chdir() back to $cwd: $!";
+- }
++# unless (eval "use Module::Build::Compat 0.02; 1" ) {
++# print "This module requires Module::Build to install itself.\n";
++#
++# require ExtUtils::MakeMaker;
++# my $yn = ExtUtils::MakeMaker::prompt
++# (' Install Module::Build now from CPAN?', 'y');
++#
++# unless ($yn =~ /^y/i) {
++# die " *** Cannot install without Module::Build. Exiting ...\n";
++# }
++#
++# require Cwd;
++# require File::Spec;
++# require CPAN;
++#
++# # Save this 'cause CPAN will chdir all over the place.
++# my $cwd = Cwd::cwd();
++#
++# CPAN::Shell->install('Module::Build::Compat');
++# CPAN::Shell->expand("Module", "Module::Build::Compat")->uptodate
++# or die "Couldn't install Module::Build, giving up.\n";
++#
++# chdir $cwd or die "Cannot chdir() back to $cwd: $!";
++# }
+ eval "use Module::Build::Compat 0.02; 1" or die $@;
+ use lib '.';
+ Module::Build::Compat->run_build_pl(args => [EMAIL PROTECTED]);
diff -Naur bioperl-1.5.2_102/ModuleBuildBioperl.pm
bioperl-1.5.2_102-patched/ModuleBuildBioperl.pm
--- bioperl-1.5.2_102/ModuleBuildBioperl.pm 2007-02-14 06:37:47.000000000
-0500
-+++ bioperl-1.5.2_102-patched/ModuleBuildBioperl.pm 2007-11-03
14:54:41.000000000 -0400
-@@ -91,10 +91,11 @@
++++ bioperl-1.5.2_102-patched/ModuleBuildBioperl.pm 2007-12-01
08:28:37.000000000 -0500
+@@ -15,8 +15,8 @@
+
+ BEGIN {
+ # we really need Module::Build to be installed
+- unless (eval "use Module::Build 0.2805; 1") {
+- print "This package requires Module::Build v0.2805 or greater to
install itself.\n";
++ unless (eval "use Module::Build 0.26; 1") {
++ print "This package requires Module::Build v0.26 or greater to
install itself.\n";
+
+ require ExtUtils::MakeMaker;
+ my $yn = ExtUtils::MakeMaker::prompt(' Install Module::Build now
from CPAN?', 'y');
+@@ -91,9 +91,10 @@
}
}
closedir($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 $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 = $self->prompt($question, 'a');
-+
-+ my $prompt = 'n';
-+
++ my $prompt = 'a';
+
if ($prompt =~ /^[aA]/) {
$self->log_info(" - will install all scripts\n");
- $self->notes(chosen_scripts => 'all');
@@ -129,7 +130,7 @@
$self->notes(chosen_scripts => $chosen_scripts);
}
else {
- $self->log_info(" - won't install any scripts\n");
-+# $self->log_info(" - won't install any scripts\n");
++ # $self->log_info(" - won't install any scripts\n");
$self->notes(chosen_scripts => 'none');
}
-@@ -402,6 +403,7 @@
+@@ -402,6 +403,8 @@
# install optional modules listed in 'recommends' arg to new that weren't
# already installed. Should only be called by prereq_failures
sub install_optional {
-+ return 'ok';
++ return 'ok';
++
my ($self, $desired, $version, $msg) = @_;
unless (defined $self->{ask_optional}) {
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