rpms/perl-bioperl/devel .cvsignore, 1.3, 1.4 bioperl-1.5.9-paths.patch, NONE, 1.1 perl-bioperl.spec, 1.14, 1.15 sources, 1.4, 1.5

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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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