rpms/perl-bioperl/F-11 bioperl-1.6.1-paths.patch, NONE, 1.1 .cvsignore, 1.8, 1.9 perl-bioperl.spec, 1.21, 1.22 sources, 1.9, 1.10

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Author: alexlan

Update of /cvs/extras/rpms/perl-bioperl/F-11
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv26675

Modified Files:
	.cvsignore perl-bioperl.spec sources 
Added Files:
	bioperl-1.6.1-paths.patch 
Log Message:
Sync with F_11 branch: Update to latest upstream 1.6.1


bioperl-1.6.1-paths.patch:
 BioPerl-1.6.1.mod/Bio/Variation/IO.pm                    |    2 +-
 BioPerl-1.6.1.mod/Bio/Variation/IO.pm.orig               |only
 BioPerl-1.6.1.mod/Build.PL                               |    6 +++---
 BioPerl-1.6.1.mod/examples/align/align_on_codons.pl      |    4 ++--
 BioPerl-1.6.1.mod/examples/db/dbfetch                    |    2 +-
 BioPerl-1.6.1.mod/examples/db/getGenBank.pl              |    2 +-
 BioPerl-1.6.1.mod/examples/db/get_seqs.pl                |    2 +-
 BioPerl-1.6.1.mod/examples/generate_random_seq.pl        |    2 +-
 BioPerl-1.6.1.mod/examples/searchio/psiblast_features.pl |    2 +-
 BioPerl-1.6.1.mod/examples/structure/structure-io.pl     |    2 +-
 BioPerl-1.6.1.mod/examples/tk/hitdisplay.pl              |    2 +-
 BioPerl-1.6.1.mod/examples/tools/gb_to_gff.pl            |    2 +-
 BioPerl-1.6.1.mod/examples/tools/gff2ps.pl               |    2 +-
 BioPerl-1.6.1/MANIFEST                                   |   15 ---------------
 14 files changed, 15 insertions(+), 30 deletions(-)

--- NEW FILE bioperl-1.6.1-paths.patch ---
diff -u -r BioPerl-1.6.1/Bio/Variation/IO.pm BioPerl-1.6.1.mod/Bio/Variation/IO.pm
--- BioPerl-1.6.1/Bio/Variation/IO.pm	2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.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-1.6.1.mod/Bio/Variation: IO.pm.orig
diff -u -r BioPerl-1.6.1/Build.PL BioPerl-1.6.1.mod/Build.PL
--- BioPerl-1.6.1/Build.PL	2009-09-29 12:33:45.000000000 -0400
+++ BioPerl-1.6.1.mod/Build.PL	2009-11-11 22:23:17.000000000 -0500
@@ -31,13 +31,13 @@
                             'DB_File'                   => 0,
                             'Data::Stag'                => 0.11, # Bio::SeqIO::swiss, we can change to 'recommend' if needed
                             'Scalar::Util'              => 0,    # not in Perl 5.6.1, arrived in core in 5.7.3
-                            'ExtUtils::Manifest'        => '1.52', # allows spaces in file names
+#                            'ExtUtils::Manifest'        => '1.52', # allows spaces in file names
                            },
     build_requires      => {
                             'Test::More'                => 0,
                             'Module::Build'             => 0.2805,
-                            'Test::Harness'             => 2.62,
-                            'CPAN'                      => 1.81
+#                            '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',
diff -u -r BioPerl-1.6.1/examples/align/align_on_codons.pl BioPerl-1.6.1.mod/examples/align/align_on_codons.pl
--- BioPerl-1.6.1/examples/align/align_on_codons.pl	2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.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
     if( ! defined $ENV{'CLUSTALDIR'} ) { 
-	$ENV{'CLUSTALDIR'} = '/usr/local/bin';
+	$ENV{'CLUSTALDIR'} = '/usr/bin';
     } 
     if( ! defined $ENV{'TCOFFEEDIR'} ) { 
-	$ENV{'TCOFFEEDIR'} = '/usr/local/bin';
+	$ENV{'TCOFFEEDIR'} = '/usr/bin';
     }
     $USAGE = 
 qq{align_on_codons.pl < file.fa
diff -u -r BioPerl-1.6.1/examples/db/dbfetch BioPerl-1.6.1.mod/examples/db/dbfetch
--- BioPerl-1.6.1/examples/db/dbfetch	2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.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 -u -r BioPerl-1.6.1/examples/db/getGenBank.pl BioPerl-1.6.1.mod/examples/db/getGenBank.pl
--- BioPerl-1.6.1/examples/db/getGenBank.pl	2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.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 -u -r BioPerl-1.6.1/examples/db/get_seqs.pl BioPerl-1.6.1.mod/examples/db/get_seqs.pl
--- BioPerl-1.6.1/examples/db/get_seqs.pl	2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.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($USAGE);
 use Carp;
diff -u -r BioPerl-1.6.1/examples/generate_random_seq.pl BioPerl-1.6.1.mod/examples/generate_random_seq.pl
--- BioPerl-1.6.1/examples/generate_random_seq.pl	2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.mod/examples/generate_random_seq.pl	2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/bin/perl -w
+#!/usr/bin/perl -w
 use strict;
 use vars qw($USAGE);
 
diff -u -r BioPerl-1.6.1/examples/searchio/psiblast_features.pl BioPerl-1.6.1.mod/examples/searchio/psiblast_features.pl
--- BioPerl-1.6.1/examples/searchio/psiblast_features.pl	2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.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 -u -r BioPerl-1.6.1/examples/structure/structure-io.pl BioPerl-1.6.1.mod/examples/structure/structure-io.pl
--- BioPerl-1.6.1/examples/structure/structure-io.pl	2007-02-14 04:37:48.000000000 -0700
+++ BioPerl-1.6.1.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 -u -r BioPerl-1.6.1/examples/tk/hitdisplay.pl BioPerl-1.6.1.mod/examples/tk/hitdisplay.pl
--- BioPerl-1.6.1/examples/tk/hitdisplay.pl	2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.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 -u -r BioPerl-1.6.1/examples/tools/gb_to_gff.pl BioPerl-1.6.1.mod/examples/tools/gb_to_gff.pl
--- BioPerl-1.6.1/examples/tools/gb_to_gff.pl	2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.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 -u -r BioPerl-1.6.1/examples/tools/gff2ps.pl BioPerl-1.6.1.mod/examples/tools/gff2ps.pl
--- BioPerl-1.6.1/examples/tools/gff2ps.pl	2007-02-14 04:37:47.000000000 -0700
+++ BioPerl-1.6.1.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
--- BioPerl-1.6.1/MANIFEST.orig	2008-12-27 20:29:43.000000000 -0700
+++ BioPerl-1.6.1/MANIFEST	2008-12-27 20:31:23.000000000 -0700
@@ -424,15 +424,6 @@
 Bio/Phenotype/OMIM/OMIMparser.pm
 Bio/Phenotype/Phenotype.pm
 Bio/Phenotype/PhenotypeI.pm
-Bio/PhyloNetwork.pm
-Bio/PhyloNetwork/Factory.pm
-Bio/PhyloNetwork/FactoryX.pm
-Bio/PhyloNetwork/GraphViz.pm
-Bio/PhyloNetwork/muVector.pm
-Bio/PhyloNetwork/RandomFactory.pm
-Bio/PhyloNetwork/TreeFactory.pm
-Bio/PhyloNetwork/TreeFactoryMulti.pm
-Bio/PhyloNetwork/TreeFactoryX.pm
 Bio/PopGen/Genotype.pm
 Bio/PopGen/GenotypeI.pm
 Bio/PopGen/HtSNP.pm
@@ -1994,12 +1985,6 @@
 t/Tools/tRNAscanSE.t
 t/Tree/Compatible.t
 t/Tree/Node.t
-t/Tree/PhyloNetwork/Factory.t
-t/Tree/PhyloNetwork/GraphViz.t
-t/Tree/PhyloNetwork/MuVector.t
-t/Tree/PhyloNetwork/PhyloNetwork.t
-t/Tree/PhyloNetwork/RandomFactory.t
-t/Tree/PhyloNetwork/TreeFactory.t
 t/Tree/RandomTreeFactory.t
 t/Tree/Tree.t
 t/Tree/TreeIO.t


Index: .cvsignore
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/F-11/.cvsignore,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -p -r1.8 -r1.9
--- .cvsignore	26 Jan 2009 07:28:04 -0000	1.8
+++ .cvsignore	12 Nov 2009 06:33:39 -0000	1.9
@@ -1 +1 @@
-BioPerl-1.6.0.tar.bz2
+BioPerl-1.6.1.tar.bz2


Index: perl-bioperl.spec
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/F-11/perl-bioperl.spec,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -p -r1.21 -r1.22
--- perl-bioperl.spec	27 Feb 2009 05:03:51 -0000	1.21
+++ perl-bioperl.spec	12 Nov 2009 06:33:39 -0000	1.22
@@ -1,13 +1,13 @@
 Name:           perl-bioperl
-Version:        1.6.0
-Release:        2%{?dist}
+Version:        1.6.1
+Release:        1%{?dist}
 Summary:        Perl tools for computational molecular biology
 
 Group:          Development/Libraries
 License:        GPL+ or Artistic
 URL:            http://www.bioperl.org/
 Source0:        http://bioperl.org/DIST/BioPerl-%{version}.tar.bz2
-Patch0:         bioperl-1.5.9-paths.patch
+Patch0:         bioperl-1.6.1-paths.patch
 BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 
 BuildArch:      noarch
@@ -18,6 +18,7 @@ BuildRequires:  perl(Convert::Binary::C)
 BuildRequires:  perl(Data::Stag::XMLWriter)
 BuildRequires:  perl(DBD::mysql)
 BuildRequires:  perl(DBD::Pg)
+BuildRequires:  perl(DBD::SQLite)
 BuildRequires:  perl(GD) >= 1.3
 BuildRequires:  perl(GD::SVG)
 BuildRequires:  perl(Graph)
@@ -41,6 +42,7 @@ BuildRequires:  perl(XML::Parser)
 BuildRequires:  perl(XML::Parser::PerlSAX)
 BuildRequires:  perl(XML::SAX) >= 0.14
 BuildRequires:  perl(XML::SAX::Writer)
+BuildRequires:  perl(XML::Simple)
 BuildRequires:  perl(XML::Twig)
 BuildRequires:  perl(XML::Writer) > 0.4
 BuildRequires:  perl(Module::Build)
@@ -122,13 +124,22 @@ rm -rf $RPM_BUILD_ROOT
 %defattr(-,root,root,-)
 ## don't distribute "doc" subdirectory,  doesn't contain docs
 %doc examples models 
-%doc AUTHORS BUGS Changes DEPRECATED INSTALL LICENSE PLATFORMS README
+%doc AUTHORS BUGS Changes DEPRECATED INSTALL LICENSE README
 %{_bindir}/*
 %{perl_vendorlib}/*
 %{_mandir}/man1/*.1*
 %{_mandir}/man3/*.3*    
 
 %changelog
+* Wed Nov  4 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.6.1-1
+- Update to latest upstream 1.6.1
+- Add BR: perl(XML::Simple), perl(DBD:SQLite) for new modules
+- Disable ExtUtils::Manifest build requirement, don't require a MANIFEST
+- Fix doc distributed
+
+* Sun Jul 26 2009 Fedora Release Engineering <rel-eng@xxxxxxxxxxxxxxxxxxxxxxx> - 1.6.0-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
+
 * Thu Feb 26 2009 Fedora Release Engineering <rel-eng@xxxxxxxxxxxxxxxxxxxxxxx> - 1.6.0-2
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild
 


Index: sources
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/F-11/sources,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -p -r1.9 -r1.10
--- sources	26 Jan 2009 07:28:04 -0000	1.9
+++ sources	12 Nov 2009 06:33:39 -0000	1.10
@@ -1 +1 @@
-b5bc873aa990892651c3092d7e504397  BioPerl-1.6.0.tar.bz2
+d629dbdb3efca353f8f52108f41c09e0  BioPerl-1.6.1.tar.bz2

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