10:09 p.m.
Author: alexlan
Update of /cvs/extras/rpms/perl-bioperl/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv20247
Modified Files:
.cvsignore perl-bioperl.spec sources
Added Files:
bioperl-1.6.1-paths.patch
Log Message:
- 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
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/devel/.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 04:09:41 -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/devel/perl-bioperl.spec,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -p -r1.22 -r1.23
--- perl-bioperl.spec 26 Jul 2009 17:44:46 -0000 1.22
+++ perl-bioperl.spec 12 Nov 2009 04:09:42 -0000 1.23
@@ -1,13 +1,13 @@
Name: perl-bioperl
-Version: 1.6.0
-Release: 3%{?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 +124,19 @@ 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(a)lists.fedoraproject.org> -
1.6.0-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
Index: sources
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/devel/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 04:09:42 -0000 1.10
@@ -1 +1 @@
-b5bc873aa990892651c3092d7e504397 BioPerl-1.6.0.tar.bz2
+d629dbdb3efca353f8f52108f41c09e0 BioPerl-1.6.1.tar.bz2