Author: alexlan
Update of /cvs/extras/rpms/perl-bioperl/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv13363
Modified Files:
bioperl-1.5.2_102-paths.patch perl-bioperl.spec
Log Message:
* Thu Sep 25 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.5.2_102-13
- Fix patch fuzz
bioperl-1.5.2_102-paths.patch:
Index: bioperl-1.5.2_102-paths.patch
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/devel/bioperl-1.5.2_102-paths.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- bioperl-1.5.2_102-paths.patch 5 Apr 2007 11:02:34 -0000 1.1
+++ bioperl-1.5.2_102-paths.patch 25 Sep 2008 09:17:06 -0000 1.2
@@ -1,6 +1,19 @@
-diff -u bioperl-1.5.2_102.orig/Build.PL bioperl-1.5.2_102/Build.PL
---- bioperl-1.5.2_102.orig/Build.PL 2007-03-14 03:46:30.000000000 -0700
-+++ bioperl-1.5.2_102/Build.PL 2007-03-14 03:46:40.000000000 -0700
+diff -u -r bioperl-1.5.2_102/Bio/Variation/IO.pm bioperl-1.5.2_102.mod/Bio/Variation/IO.pm
+--- bioperl-1.5.2_102/Bio/Variation/IO.pm 2007-02-14 04:37:48.000000000 -0700
++++ bioperl-1.5.2_102.mod/Bio/Variation/IO.pm 2008-09-25 02:03:26.000000000 -0700
+@@ -86,7 +86,7 @@
+
+ This makes the simplest ever reformatter
+
+- #!/usr/local/bin/perl
++ #!/usr/bin/perl
+
+ $format1 = shift;
+ $format2 = shift;
+Only in bioperl-1.5.2_102.mod/Bio/Variation: IO.pm.orig
+diff -u -r bioperl-1.5.2_102/Build.PL bioperl-1.5.2_102.mod/Build.PL
+--- bioperl-1.5.2_102/Build.PL 2007-02-14 04:37:47.000000000 -0700
++++ bioperl-1.5.2_102.mod/Build.PL 2008-09-25 02:03:26.000000000 -0700
@@ -31,8 +31,8 @@
build_requires => {
'Test::More' => 0,
@@ -21,21 +34,9 @@
'XML::SAX::Writer' => '0/writing xml/Bio::SeqIO::tigrxml',
'XML::Twig' => '0/parsing xml/Bio::Variation::IO::xml,Bio::DB::Taxonomy::entrez,Bio::DB::Biblio::eutils,Bio::Graph::IO::psi_xml',
'XML::Writer' => '0.4/parsing and writing xml/Bio::SeqIO::agave,Bio::SeqIO::game::gameWriter,Bio::SeqIO::chadoxml,Bio::SeqIO::tinyseq,Bio::Variation::IO::xml,Bio::SearchIO::Writer::BSMLResultWriter'
-diff -ru bioperl-1.5.2_102.orig/Bio/Variation/IO.pm bioperl-1.5.2_102/Bio/Variation/IO.pm
---- bioperl-1.5.2_102.orig/Bio/Variation/IO.pm 2003-06-04 04:36:44.000000000 -0400
-+++ bioperl-1.5.2_102/Bio/Variation/IO.pm 2005-03-21 20:21:54.000000000 -0500
-@@ -83,7 +83,7 @@
-
- This makes the simplest ever reformatter
-
-- #!/usr/local/bin/perl
-+ #!/usr/bin/perl
-
- $format1 = shift;
- $format2 = shift || die "Usage: reformat format1 format2 < input > output";
-diff -ru bioperl-1.5.2_102.orig/examples/align/align_on_codons.pl bioperl-1.5.2_102/examples/align/align_on_codons.pl
---- bioperl-1.5.2_102.orig/examples/align/align_on_codons.pl 2003-07-07 14:20:58.000000000 -0400
-+++ bioperl-1.5.2_102/examples/align/align_on_codons.pl 2005-03-21 20:24:44.000000000 -0500
+diff -u -r bioperl-1.5.2_102/examples/align/align_on_codons.pl bioperl-1.5.2_102.mod/examples/align/align_on_codons.pl
+--- bioperl-1.5.2_102/examples/align/align_on_codons.pl 2007-02-14 04:37:47.000000000 -0700
++++ bioperl-1.5.2_102.mod/examples/align/align_on_codons.pl 2008-09-25 02:03:26.000000000 -0700
@@ -13,10 +13,10 @@
BEGIN {
$CODONSIZE = 3; # parametrize everything like a good little programmer
@@ -49,99 +50,99 @@
}
$USAGE =
qq{align_on_codons.pl < file.fa
-diff -ru bioperl-1.5.2_102.orig/examples/db/dbfetch bioperl-1.5.2_102/examples/db/dbfetch
---- bioperl-1.5.2_102.orig/examples/db/dbfetch 2003-07-15 12:12:16.000000000 -0400
-+++ bioperl-1.5.2_102/examples/db/dbfetch 2005-03-21 20:25:01.000000000 -0500
+diff -u -r bioperl-1.5.2_102/examples/db/dbfetch bioperl-1.5.2_102.mod/examples/db/dbfetch
+--- bioperl-1.5.2_102/examples/db/dbfetch 2007-02-14 04:37:48.000000000 -0700
++++ bioperl-1.5.2_102.mod/examples/db/dbfetch 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -- # -*-Perl-*-
+#!/usr/bin/perl -- # -*-Perl-*-
=head1 NAME
-diff -ru bioperl-1.5.2_102.orig/examples/db/getGenBank.pl bioperl-1.5.2_102/examples/db/getGenBank.pl
---- bioperl-1.5.2_102.orig/examples/db/getGenBank.pl 2003-07-07 14:20:59.000000000 -0400
-+++ bioperl-1.5.2_102/examples/db/getGenBank.pl 2005-03-21 20:24:57.000000000 -0500
+diff -u -r bioperl-1.5.2_102/examples/db/getGenBank.pl bioperl-1.5.2_102.mod/examples/db/getGenBank.pl
+--- bioperl-1.5.2_102/examples/db/getGenBank.pl 2007-02-14 04:37:47.000000000 -0700
++++ bioperl-1.5.2_102.mod/examples/db/getGenBank.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
#
# How to retrieve GenBank entries over the Web
#
-diff -ru bioperl-1.5.2_102.orig/examples/db/get_seqs.pl bioperl-1.5.2_102/examples/db/get_seqs.pl
---- bioperl-1.5.2_102.orig/examples/db/get_seqs.pl 2003-07-07 14:20:59.000000000 -0400
-+++ bioperl-1.5.2_102/examples/db/get_seqs.pl 2005-03-21 20:24:53.000000000 -0500
+diff -u -r bioperl-1.5.2_102/examples/db/get_seqs.pl bioperl-1.5.2_102.mod/examples/db/get_seqs.pl
+--- bioperl-1.5.2_102/examples/db/get_seqs.pl 2007-02-14 04:37:48.000000000 -0700
++++ bioperl-1.5.2_102.mod/examples/db/get_seqs.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use vars qw($USAGE);
use Carp;
-diff -ru bioperl-1.5.2_102.orig/examples/generate_random_seq.pl bioperl-1.5.2_102/examples/generate_random_seq.pl
---- bioperl-1.5.2_102.orig/examples/generate_random_seq.pl 2004-11-01 16:09:08.000000000 -0500
-+++ bioperl-1.5.2_102/examples/generate_random_seq.pl 2005-03-21 20:27:23.000000000 -0500
+diff -u -r bioperl-1.5.2_102/examples/generate_random_seq.pl bioperl-1.5.2_102.mod/examples/generate_random_seq.pl
+--- bioperl-1.5.2_102/examples/generate_random_seq.pl 2007-02-14 04:37:47.000000000 -0700
++++ bioperl-1.5.2_102.mod/examples/generate_random_seq.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use vars qw($USAGE);
-diff -ru bioperl-1.5.2_102.orig/examples/searchio/psiblast_features.pl bioperl-1.5.2_102/examples/searchio/psiblast_features.pl
---- bioperl-1.5.2_102.orig/examples/searchio/psiblast_features.pl 2004-02-21 05:50:34.000000000 -0500
-+++ bioperl-1.5.2_102/examples/searchio/psiblast_features.pl 2005-03-21 20:24:30.000000000 -0500
+diff -u -r bioperl-1.5.2_102/examples/searchio/psiblast_features.pl bioperl-1.5.2_102.mod/examples/searchio/psiblast_features.pl
+--- bioperl-1.5.2_102/examples/searchio/psiblast_features.pl 2007-02-14 04:37:48.000000000 -0700
++++ bioperl-1.5.2_102.mod/examples/searchio/psiblast_features.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# Example usage of a SearchIO::psiblast parser of traditional format Blast
# and PSI-Blast reports.
-diff -ru bioperl-1.5.2_102.orig/examples/structure/structure-io.pl bioperl-1.5.2_102/examples/structure/structure-io.pl
---- bioperl-1.5.2_102.orig/examples/structure/structure-io.pl 2004-11-01 16:09:33.000000000 -0500
-+++ bioperl-1.5.2_102/examples/structure/structure-io.pl 2005-03-21 20:27:17.000000000 -0500
+diff -u -r bioperl-1.5.2_102/examples/structure/structure-io.pl bioperl-1.5.2_102.mod/examples/structure/structure-io.pl
+--- bioperl-1.5.2_102/examples/structure/structure-io.pl 2007-02-14 04:37:48.000000000 -0700
++++ bioperl-1.5.2_102.mod/examples/structure/structure-io.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/usr/bin/perl -w
# Getting Entry, Chain, Residue, and Atom objects given a PDB file
use Bio::Structure::IO;
-diff -ru bioperl-1.5.2_102.orig/examples/tk/hitdisplay.pl bioperl-1.5.2_102/examples/tk/hitdisplay.pl
---- bioperl-1.5.2_102.orig/examples/tk/hitdisplay.pl 2003-07-07 14:20:59.000000000 -0400
-+++ bioperl-1.5.2_102/examples/tk/hitdisplay.pl 2005-03-21 20:24:26.000000000 -0500
+diff -u -r bioperl-1.5.2_102/examples/tk/hitdisplay.pl bioperl-1.5.2_102.mod/examples/tk/hitdisplay.pl
+--- bioperl-1.5.2_102/examples/tk/hitdisplay.pl 2007-02-14 04:37:47.000000000 -0700
++++ bioperl-1.5.2_102.mod/examples/tk/hitdisplay.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
#
# PROGRAM : hitdisplay.pl
# PURPOSE : Demonstrate Bio::Tk::HitDisplay
-diff -ru bioperl-1.5.2_102.orig/examples/tools/gb_to_gff.pl bioperl-1.5.2_102/examples/tools/gb_to_gff.pl
---- bioperl-1.5.2_102.orig/examples/tools/gb_to_gff.pl 2003-07-07 14:20:59.000000000 -0400
-+++ bioperl-1.5.2_102/examples/tools/gb_to_gff.pl 2005-03-21 20:24:21.000000000 -0500
+diff -u -r bioperl-1.5.2_102/examples/tools/gb_to_gff.pl bioperl-1.5.2_102.mod/examples/tools/gb_to_gff.pl
+--- bioperl-1.5.2_102/examples/tools/gb_to_gff.pl 2007-02-14 04:37:47.000000000 -0700
++++ bioperl-1.5.2_102.mod/examples/tools/gb_to_gff.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use Bio::Tools::GFF;
-diff -ru bioperl-1.5.2_102.orig/examples/tools/gff2ps.pl bioperl-1.5.2_102/examples/tools/gff2ps.pl
---- bioperl-1.5.2_102.orig/examples/tools/gff2ps.pl 2003-07-07 14:20:59.000000000 -0400
-+++ bioperl-1.5.2_102/examples/tools/gff2ps.pl 2005-03-21 20:24:17.000000000 -0500
+diff -u -r bioperl-1.5.2_102/examples/tools/gff2ps.pl bioperl-1.5.2_102.mod/examples/tools/gff2ps.pl
+--- bioperl-1.5.2_102/examples/tools/gff2ps.pl 2007-02-14 04:37:47.000000000 -0700
++++ bioperl-1.5.2_102.mod/examples/tools/gff2ps.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
=head1 NAME
-diff -ru bioperl-1.5.2_102.orig/t/Promoterwise.t bioperl-1.5.2_102/t/Promoterwise.t
---- bioperl-1.5.2_102.orig/t/Promoterwise.t 2003-03-10 13:21:03.000000000 -0500
-+++ bioperl-1.5.2_102/t/Promoterwise.t 2005-03-21 20:24:04.000000000 -0500
+diff -u -r bioperl-1.5.2_102/t/Promoterwise.t bioperl-1.5.2_102.mod/t/Promoterwise.t
+--- bioperl-1.5.2_102/t/Promoterwise.t 2007-02-14 04:37:47.000000000 -0700
++++ bioperl-1.5.2_102.mod/t/Promoterwise.t 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# -*-Perl-*-
## Bioperl Test Harness Script for Modules
-diff -ru bioperl-1.5.2_102.orig/t/testformats.pl bioperl-1.5.2_102/t/testformats.pl
---- bioperl-1.5.2_102.orig/t/testformats.pl 2001-06-29 17:17:02.000000000 -0400
-+++ bioperl-1.5.2_102/t/testformats.pl 2005-03-21 20:24:00.000000000 -0500
+diff -u -r bioperl-1.5.2_102/t/testformats.pl bioperl-1.5.2_102.mod/t/testformats.pl
+--- bioperl-1.5.2_102/t/testformats.pl 2007-02-14 04:37:47.000000000 -0700
++++ bioperl-1.5.2_102.mod/t/testformats.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
Index: perl-bioperl.spec
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/devel/perl-bioperl.spec,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- perl-bioperl.spec 5 Mar 2008 12:32:54 -0000 1.13
+++ perl-bioperl.spec 25 Sep 2008 09:17:06 -0000 1.14
@@ -1,6 +1,6 @@
Name: perl-bioperl
Version: 1.5.2_102
-Release: 12%{?dist}
+Release: 13%{?dist}
Summary: Perl tools for computational molecular biology
Group: Development/Libraries
@@ -117,6 +117,9 @@
%{_mandir}/man3/*.3*
%changelog
+* Thu Sep 25 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.5.2_102-13
+- Fix patch fuzz
+
* Wed Mar 5 2008 Tom "spot" Callaway <tcallawa@xxxxxxxxxx> 1.5.2_102-12
- bootstrapping done, building normally
--
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