Author: alexlan
Update of /cvs/extras/rpms/perl-bioperl/devel
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv28895
Modified Files:
perl-bioperl.spec sources
Added Files:
.cvsignore bioperl-1.5.9-paths.patch
Log Message:
- Update to latest upstream, 1.5.9, which is release candidate 1 for 1.6.0
- Add BuildRequires for perl(Array::Compare) and perl(GraphViz).
- Fix patch to apply to new release.
- Remove Bio::PhyloNetwork from installation, currently has unfilled
deps and not ready for primetime according to upstream.
Index: .cvsignore
===================================================================
RCS file: .cvsignore
diff -N .cvsignore
--- /dev/null 1 Jan 1970 00:00:00 -0000
+++ .cvsignore 28 Dec 2008 04:23:11 -0000 1.4
@@ -0,0 +1 @@
+BioPerl-1.5.9_1.tar.bz2
bioperl-1.5.9-paths.patch:
--- NEW FILE bioperl-1.5.9-paths.patch ---
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,
'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-1.5.2_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
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';
}
$USAGE =
qq{align_on_codons.pl < file.fa
diff -u -r bioperl-1.5.2_102/examples/db/dbfetch bioperl-1.5.2_102.mod/examples/db/dbfetch
--- bioperl-1.5.2_102/examples/db/dbfetch 2007-02-14 04:37:48.000000000 -0700
+++ bioperl-1.5.2_102.mod/examples/db/dbfetch 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -- # -*-Perl-*-
+#!/usr/bin/perl -- # -*-Perl-*-
=head1 NAME
diff -u -r bioperl-1.5.2_102/examples/db/getGenBank.pl bioperl-1.5.2_102.mod/examples/db/getGenBank.pl
--- bioperl-1.5.2_102/examples/db/getGenBank.pl 2007-02-14 04:37:47.000000000 -0700
+++ bioperl-1.5.2_102.mod/examples/db/getGenBank.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
#
# How to retrieve GenBank entries over the Web
#
diff -u -r bioperl-1.5.2_102/examples/db/get_seqs.pl bioperl-1.5.2_102.mod/examples/db/get_seqs.pl
--- bioperl-1.5.2_102/examples/db/get_seqs.pl 2007-02-14 04:37:48.000000000 -0700
+++ bioperl-1.5.2_102.mod/examples/db/get_seqs.pl 2008-09-25 02:03:26.000000000 -0700
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl -w
+#!/usr/bin/perl -w
use strict;
use vars qw($USAGE);
use Carp;
diff -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 -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 -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 -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 -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 -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
--- bioperl-1.5.9._1/MANIFEST.orig 2008-12-27 20:29:43.000000000 -0700
+++ bioperl-1.5.9._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: perl-bioperl.spec
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/devel/perl-bioperl.spec,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- perl-bioperl.spec 25 Sep 2008 09:17:06 -0000 1.14
+++ perl-bioperl.spec 28 Dec 2008 04:23:11 -0000 1.15
@@ -1,13 +1,13 @@
Name: perl-bioperl
-Version: 1.5.2_102
-Release: 13%{?dist}
+Version: 1.5.9
+Release: 0.1.1%{?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-1.5.2_102-paths.patch
+Source0: http://bioperl.org/DIST/BioPerl-%{version}_1.tar.bz2
+Patch0: bioperl-1.5.9-paths.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
BuildArch: noarch
@@ -45,6 +45,11 @@
BuildRequires: perl(XML::Writer) > 0.4
BuildRequires: perl(Module::Build)
BuildRequires: perl(Test::More)
+BuildRequires: perl(Array::Compare)
+BuildRequires: perl(GraphViz)
+# disable the following BRs until they are packaged for Fedora
+#BuildRequires: perl(Math::Random)
+#BuildRequires: perl(Algorithm::Munkres)
Requires: perl(:MODULE_COMPAT_%(eval "`%{__perl} -V:version`"; echo $version))
%description
@@ -53,9 +58,13 @@
many modules depend on each other to achieve a task.
%prep
-%setup -q -n bioperl-%{version}
+%setup -q -n bioperl-%{version}._1
%patch0 -p1
+# temporarily remove PhyloNetwork before compiling
+rm -r Bio/PhyloNetwork*
+rm -r t/Tree/PhyloNetwork
+
# Temporary hack for bootstrapping
# Filter unwanted Requires:
# cat << \EOF > %{_builddir}/bioperl-%{version}/%{name}-req
@@ -110,13 +119,20 @@
%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 ChangeLog DEPRECATED INSTALL LICENSE PLATFORMS README
%{_bindir}/*
%{perl_vendorlib}/*
%{_mandir}/man1/*.1*
%{_mandir}/man3/*.3*
%changelog
+* Fri Dec 26 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.5.9-0.1.1
+- Update to latest upstream, 1.5.9, which is release candidate 1 for 1.6.0
+- Add BuildRequires for perl(Array::Compare) and perl(GraphViz).
+- Fix patch to apply to new release.
+- Remove Bio::PhyloNetwork from installation, currently has unfilled
+ deps and not ready for primetime according to upstream.
+
* Thu Sep 25 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.5.2_102-13
- Fix patch fuzz
Index: sources
===================================================================
RCS file: /cvs/extras/rpms/perl-bioperl/devel/sources,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- sources 5 Apr 2007 11:02:34 -0000 1.4
+++ sources 28 Dec 2008 04:23:11 -0000 1.5
@@ -1 +1 @@
-71f22246979ee5d6e19d547319962eea bioperl-1.5.2_102.tar.bz2
+f7c85ef9cf175055eb56a097ae9d49b4 BioPerl-1.5.9_1.tar.bz2
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