Update of /cvsroot/fink/dists/10.4/unstable/main/finkinfo/libs/perlmods
In directory sc8-pr-cvs17:/tmp/cvs-serv7302
Modified Files:
bioperl-pm.info bioperl-pm.patch
Log Message:
new upstream version
Index: bioperl-pm.info
===================================================================
RCS file:
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/libs/perlmods/bioperl-pm.info,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- bioperl-pm.info 2 Nov 2007 01:31:33 -0000 1.5
+++ bioperl-pm.info 4 Nov 2007 02:14:37 -0000 1.6
@@ -1,64 +1,63 @@
Info2: <<
Package: bioperl-pm%type_pkg[perl]
-Version: 1.5.1
-Revision: 2
+Version: 1.5.2
+Revision: 1
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)
Depends: <<
- io-string-pm,
- io-stringy-pm,
- xml-writer-pm,
- xml-parser-pm%type_pkg[perl],
- html-parser-pm%type_pkg[perl],
- gd-pm%type_pkg[perl],
+ clone-pm%type_pkg[perl],
+ gd-pm%type_pkg[perl] (>= 1.3),
gd-svg-pm%type_pkg[perl],
graph-pm,
+ html-parser-pm%type_pkg[perl] (>= 3.0),
+ io-string-pm,
+ io-stringy-pm,
libxml-pm%type_pkg[perl],
- xml-twig-pm%type_pkg[perl],
- text-shellwords-pm,
- xml-node-pm%type_pkg[perl],
+ set-scalar-pm,
soap-lite-pm%type_pkg[perl],
+ svg-pm,
+ test-harness-pm%type_pkg[perl] (>= 2.62),
+ text-shellwords-pm,
xml-dom-pm%type_pkg[perl],
+ xml-node-pm%type_pkg[perl],
+ xml-parser-pm%type_pkg[perl],
xml-sax-pm%type_pkg[perl],
- xml-sax-writer-pm%type_pkg[perl]
+ xml-sax-writer-pm%type_pkg[perl],
+ xml-twig-pm%type_pkg[perl],
+ xml-writer-pm
<<
-Source: http://www.bioperl.org/DIST/bioperl-%v.tar.bz2
+Source: http://www.bioperl.org/DIST/bioperl-%v_102.tar.bz2
Enhances: dbd-mysql-pm%type_pkg[perl]
Replaces: bioperl-pm560, bioperl-pm580, bioperl-pm581, bioperl-pm586
Type: perl (5.8.1 5.8.6 5.8.8)
UpdatePOD: True
NoPerlTests: True
Patch: %{ni}.patch
-Source-MD5: ba24f59a00c9919840a9b58f7fbd4d94
+Source-MD5: 71f22246979ee5d6e19d547319962eea
InstallScript: <<
- %{default_script}
-
+# %{default_script}
+ make install UNINST=1 prefix=%i
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
- mv %i/lib/perl5/%type_raw[perl]/bptutorial.pl %i/share/%n
- mv %i/bin/*.pl %i/share/%n/examples/
+# mv %i/lib/perl5/%type_raw[perl]/bptutorial.pl %i/share/%n
+# mv %i/bin/*.pl %i/share/%n/examples/
<<
-DocFiles: Changes INSTALL README LICENSE PLATFORMS FAQ BUGS AUTHORS
-Description: Perl module for biology
+DocFiles: Changes INSTALL README LICENSE PLATFORMS BUGS AUTHORS DEPENDENCIES
+Description: Perl module for molecular biology
DescDetail: <<
-Bioperl is a collection of perl modules that facilitate the development of
-perl scripts for bioinformatics applications. As such, it does not include
-ready to use programs in the sense that many commercial packages and free
-web-based interfaces (eg Entrez, SRS) do. On the other hand, bioperl does
-provide reusable perl modules that facilitate writing perl scripts for
-sequence manipulation, accessing of databases using a range of data formats
-and execution and parsing of the results of various molecular biology
-programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER.
-Consequently, bioperl enables developing scripts that can analyze large
-quantities of sequence data in ways that are typically difficult or impossible
-with web based systems.
+Bioperl is a package of public domain Perl tools for computational
+ molecular biology.
+
+ Our website, http://bioperl.org, provides an online resource of
+ modules, scripts, and web links for developers of Perl-based software
+ for life science research.
<<
DescPackaging: <<
Previous maintainer: Christopher Dithi <[EMAIL PROTECTED]>
Index: bioperl-pm.patch
===================================================================
RCS file:
/cvsroot/fink/dists/10.4/unstable/main/finkinfo/libs/perlmods/bioperl-pm.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -d -r1.1 -r1.2
--- bioperl-pm.patch 20 Jan 2006 20:21:21 -0000 1.1
+++ bioperl-pm.patch 4 Nov 2007 02:14:37 -0000 1.2
@@ -1,47 +1,109 @@
-diff -Naur bioperl-1.5.1/Makefile.PL bioperl-1.5.1-patched/Makefile.PL
---- bioperl-1.5.1/Makefile.PL 2005-10-09 11:16:18.000000000 -0400
-+++ bioperl-1.5.1-patched/Makefile.PL 2005-11-03 21:17:42.000000000 -0500
-@@ -17,7 +17,7 @@
- 'HTTP::Request::Common' => '0.0/Part of the LWP
package/GenBank+GenPept sequence retrieval, remote http Blast
jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast',
- 'LWP::UserAgent' => '0.0/Part of the LWP
package/GenBank+GenPept sequence retrieval, remote http Blast
jobs/Bio::DB::*,Bio::Tools::Run::RemoteBlast',
- 'HTML::Entities' => '0.0/To parse POST request URL
formas/Remote Analysis POST submissions/Bio::Tools::Run::Analysis::*',
-- 'Ace' => '0.0/Aceperl/access of ACeDB
database/Bio::DB::Ace',
-+# 'Ace' => '0.0/Aceperl/access of ACeDB
database/Bio::DB::Ace',
- 'IO::Scalar' => '0.0/IO handle to read or write to a
scalar/remote http Blast jobs/Bio::Tools::Blast::Run::Webblast',
- 'IO::String' => '0.0/IO handle to read or write to a
string/GenBank+GenPept sequence retrieval, Variation
code/Bio::DB::*,Bio::Variation::*,Bio::Tools::Blast::Run::Webblast,
Bio::Index::Blast',
- 'XML::Parser' => '0.0/Parsing of XML
documents/Bio::Variation code, GAME parser/Bio::SeqIO::game,Bio::Variation::*',
-@@ -27,7 +27,7 @@
- 'File::Temp' => '0.0/Temporary File
creation/Bio::Root::IO uses if present/Bio::DB::WebDBSeqI,
Bio::Seq::LargePrimarySeq',
- 'SOAP::Lite' => '0.0/SOAP protocol/XEMBL Services
(also Bibliographic queries in Biblio::) /Bio::DB::XEMBLService',
- 'HTML::Parser' => '0.0/HTML parsing/HTML parsing of
GDB page/Bio::DB::GDB',
-- 'DBD::mysql' => '0.0/Mysql driver/loading and
querying of Mysql-based GFF feature databases/Bio::DB::GFF',
-+# 'DBD::mysql' => '0.0/Mysql driver/loading and
querying of Mysql-based GFF feature databases/Bio::DB::GFF',
- 'GD' => '1.3/Graphical Drawing
Toolkit/rendering Sequences and Features/Bio::Graphics',
- 'Text::Shellwords' => '0.0/Execute shell commands/test
scripts/Bio::Graphics',
- 'SVG' => '2.26/Generate optional SVG
output/Bio::Graphics/Bio::Graphics::Pictogram',
-@@ -94,8 +94,9 @@
+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 @@
+ 'Test::More' => 0,
+ 'Module::Build' => 0.2805,
+ 'Test::Harness' => 2.62,
+- '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
+@@ -71,22 +71,22 @@
+ get_options => {
+ network => { } # not actually used by anything
yet, but in the future say perl Build.PL --network
+ },
+- 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",
+@@ -94,7 +94,7 @@
+ # options =>
['network'], # ModuleBuildBioperl unique requirement that --network was supplied
+ # test =>
\&ModuleBuildBioperl::test_internet
+ # }
+- },
++# },
+ dynamic_config => 1
+
+ #pm_files => {} # modules in Bio are treated as if they were in
lib and auto-installed
+@@ -118,7 +118,7 @@
- sub prompt_for_biodbgff {
- if( eval { require DBI } && grep {/mysql/} DBI->available_drivers) {
-- print "\n** Bio::DB::GFF Tests section** \n";
-- my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a
mysql, postgres or oracle database) y/n",'n');
-+# print "\n** Bio::DB::GFF Tests section** \n";
-+# my $proceed = prompt("Do you want to run the BioDBGFF tests (requires a
mysql, postgres or oracle database) y/n",'n');
-+ my $proceed = 'n';
- if( $proceed =~ /^[yY]/) {
- my $cfg = {dbd_driver => 'mysql'};
- GFFQueryDb($cfg,{'prompt'=>1,'verbose'=>1});
-@@ -127,9 +128,10 @@
- }
+ # Ask questions
+ $build->choose_scripts;
+-prompt_for_biodbgff() if $build->feature('BioDBGFF');
++#prompt_for_biodbgff() if $build->feature('BioDBGFF');
- sub get_scripts_to_install {
-- print "\n*** Script Install Section ****\n";
-- print "\nBioperl comes with a number of useful scripts which you may wish
to install.\n";
-- my $prompt_mode = prompt("Install [a]ll Bioperl scripts, [n]one, or choose
groups [i]nteractively?",'a');
-+# print "\n*** Script Install Section ****\n";
-+# print "\nBioperl comes with a number of useful scripts which you may wish
to install.\n";
-+# my $prompt_mode = prompt("Install [a]ll Bioperl scripts, [n]one, or choose
groups [i]nteractively?",'a');
-+ my $prompt_mode = 'a';
- return if $prompt_mode =~ /^[nN]/;
- my @scripts;
- my $script_dir = './scripts';
+ # Request that some scripts run post-installation
+ $build->add_post_install_script('maintenance/symlink_script.pl'); # takes a
unix file path regardless of local OS
+diff -Naur bioperl-1.5.2_102/ModuleBuildBioperl.pm
bioperl-1.5.2_102-patched/ModuleBuildBioperl.pm
+--- bioperl-1.5.2_102/ModuleBuildBioperl.pm 2007-02-14 06:37:47.000000000
-0500
++++ bioperl-1.5.2_102-patched/ModuleBuildBioperl.pm 2007-11-03
14:54:41.000000000 -0400
+@@ -91,10 +91,11 @@
+ }
+ }
+ closedir($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 $prompt = 'n';
++
+ if ($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");
+ $self->notes(chosen_scripts => 'none');
+ }
+
+@@ -402,6 +403,7 @@
+ # install optional modules listed in 'recommends' arg to new that weren't
+ # already installed. Should only be called by prereq_failures
+ sub install_optional {
++ return 'ok';
+ my ($self, $desired, $version, $msg) = @_;
+
+ unless (defined $self->{ask_optional}) {
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