Update of /cvsroot/fink/dists/10.4/stable/main/finkinfo/libs/perlmods
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23579
Modified Files:
bioperl-pm.info bioperl-pm.patch
Log Message:
latest version to stable
Index: bioperl-pm.info
===================================================================
RCS file:
/cvsroot/fink/dists/10.4/stable/main/finkinfo/libs/perlmods/bioperl-pm.info,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -d -r1.2 -r1.3
--- bioperl-pm.info 17 Feb 2006 01:39:16 -0000 1.2
+++ bioperl-pm.info 14 Mar 2006 05:33:44 -0000 1.3
@@ -1,8 +1,8 @@
Info2: <<
Package: bioperl-pm%type_pkg[perl]
-Version: 1.4
-Revision: 5
+Version: 1.5.1
+Revision: 2
Architecture: (%type_pkg[perl] = 581) powerpc, (%type_pkg[perl] = 584) powerpc
BuildDepends: perl%type_pkg[perl]-core, fink (>= 0.20.1-1)
Depends: <<
@@ -12,13 +12,16 @@
xml-parser-pm%type_pkg[perl],
html-parser-pm%type_pkg[perl],
gd-pm%type_pkg[perl],
+ gd-svg-pm%type_pkg[perl],
graph-pm,
libxml-pm%type_pkg[perl],
xml-twig-pm%type_pkg[perl],
text-shellwords-pm,
xml-node-pm%type_pkg[perl],
soap-lite-pm%type_pkg[perl],
- xml-dom-pm%type_pkg[perl]
+ xml-dom-pm%type_pkg[perl],
+ xml-sax-pm%type_pkg[perl],
+ xml-sax-writer-pm%type_pkg[perl]
<<
Source: http://www.bioperl.org/DIST/bioperl-%v.tar.bz2
Enhances: dbd-mysql-pm%type_pkg[perl]
@@ -27,17 +30,19 @@
UpdatePOD: True
NoPerlTests: True
Patch: %{ni}.patch
-Source-MD5: c49922bb58699cf42765056da8944f6e
+Source-MD5: ba24f59a00c9919840a9b58f7fbd4d94
InstallScript: <<
- mkdir -p %i/share/%n
%{default_script}
+ 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/
+
<<
DocFiles: Changes INSTALL README LICENSE PLATFORMS FAQ BUGS AUTHORS
Description: Perl module for biology
@@ -63,7 +68,7 @@
bioperl-pm. See /sw/share/doc/bioperl-pm/INSTALL. Note that not all optional
perl modules are available through fink.
-All examples, docs, etc can be found in /sw/share/bioperl-pm/.
+All examples, docs, etc can be found in /sw/share/bioperl-pm%type_pkg[perl]/.
<<
License: Artistic
Maintainer: Koen van der Drift <[EMAIL PROTECTED]>
Index: bioperl-pm.patch
===================================================================
RCS file:
/cvsroot/fink/dists/10.4/stable/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 20:12:55 -0000 1.1
+++ bioperl-pm.patch 14 Mar 2006 05:33:44 -0000 1.2
@@ -1,6 +1,6 @@
-diff -Naur bioperl-1.4/Makefile.PL bioperl-1.4-patched/Makefile.PL
---- bioperl-1.4/Makefile.PL Mon Dec 15 06:21:47 2003
-+++ bioperl-1.4-patched/Makefile.PL Fri Jan 2 10:09:05 2004
+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',
@@ -16,22 +16,22 @@
'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',
+ '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',
-@@ -84,8 +84,9 @@
+ 'SVG' => '2.26/Generate optional SVG
output/Bio::Graphics/Bio::Graphics::Pictogram',
+@@ -94,8 +94,9 @@
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';
++# 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});
-@@ -108,9 +109,10 @@
+@@ -127,9 +128,10 @@
}
sub get_scripts_to_install {
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