Accepting request 129021 from home:computersalat:devel:perl

update to 1.6.901

OBS-URL: https://build.opensuse.org/request/show/129021
OBS-URL: https://build.opensuse.org/package/show/devel:languages:perl/perl-BioPerl?expand=0&rev=4

BioPerl-1.6.1-Build.patch

@@ -1,12 +0,0 @@
-diff -ruN BioPerl-1.6.1-orig/Bio/Root/Build.pm BioPerl-1.6.1/Bio/Root/Build.pm
---- BioPerl-1.6.1-orig/Bio/Root/Build.pm	2009-09-29 18:33:53.000000000 +0200
-+++ BioPerl-1.6.1/Bio/Root/Build.pm	2010-08-04 15:56:14.000000000 +0200
-@@ -425,7 +425,7 @@
-     else {
-         my $question = $required ?  "$desired is absolutely required prior to installation: shall I install it now using a CPAN shell?" :
-                                     "To install $desired I'll need to open a CPAN shell right now; is that OK?";
--        my $do_install = $self->y_n($question.' y/n', 'y');
-+        my $do_install = $self->y_n($question.' y/n', 'n');
-         
-         if ($do_install) {
-             # Here we use CPAN to actually install the desired module, the benefit

BioPerl-1.6.1.tar.bz2

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:f27d533054c97fb5f21caebb3c27a585095ee0a9005e8df19682bb6e580e3942
-size 6919840

BioPerl-1.6.901.tar.bz2

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ad20a3e2bd93342007aabd5aba68712eddc359ab3d80d08449b87f50aa5acd34
+size 8167267

deps.patch

@@ -0,0 +1,30 @@
+Index: Build.PL
+===================================================================
+--- Build.PL.orig
++++ Build.PL
+@@ -138,11 +138,6 @@ my %recommends = (
+     'Text::ParseWords'          => [0,
+         'Test scripts/Bio::DB::SeqFeature::Store::FeatureFileLoader'],
+     
+-    'URI::Escape'               => [0,
+-        'Dealing with web resources/Bio::FeatureIO::gff,Bio::FeatureIO::interpro,'.
+-        'Bio::DB::Biblio::eutils,Bio::DB::EUtilParameters,'.
+-        'Bio::DB::Query::GenBank,Bio::DB::NCBIHelper,Bio::SeqFeature::Annotated'],
+-    
+     'XML::DOM::XPath'           => [0.13,
+         'parsing interpro features/Bio::FeatureIO::interpro'],
+     
+@@ -195,10 +190,11 @@ my $build = Bio::Root::Build->new(
+                            },
+     
+     build_requires      => {
+-                            'Test::More'                => 0,
++                            'CPAN'                      => 1.81,
+                             'Module::Build'             => 0.2805,
+                             'Test::Harness'             => 2.62,
+-                            'CPAN'                      => 1.81
++                            'Test::More'                => 0,
++                            'URI::Escape'               => 0
+                            },
+     
+     recommends          => {

perl-BioPerl.changes

@@ -1,3 +1,64 @@
+-------------------------------------------------------------------
+Thu Jul 26 13:25:33 UTC 2012 - chris@computersalat.de
+
+- update to 1.6.901
+  - [Notes]
+    * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
+      modules using Ace will also be deprecated [lds, cjfields]
+    * Minor bug fix release
+    * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
+    * Address Build.PL issues when DBI is not present [hartzell]
+    * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
+    * Remove deprecated code for perl 5.14.0 compat [cjfields]
+    * Due to schema changes and lack of support for older versions, support
+      for NeXML 0.9 is only (very) partially implemented.
+      See: https://redmine.open-bio.org/issues/3207
+  - [Bug fixes]
+    * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
+      docs [genehack, cjfields]
+    * $VERSION for CPAN/cpanm-based installs was broken; force setting of
+      module version from dist_version (probably not the best way to do this,
+      but it seems to work) [rbuels, cjfields]
+- update to 1.6.900 April 14, 2011
+  - [Notes]
+    * This will probably be the last release to add significant features to
+      core modules; subsequent releases will be for bug fixes alone.
+      We are planning on a restructuring of core for summer 2011, potentially
+      as part of the Google Summer of Code.  This may become BioPerl 2.0.
+    * Version bump represents 'just prior to v 1.7'.  We may have point
+      releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
+      This code essentially is what is on the github master branch.
+  - [New features]
+    * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
+    * Bio::Tree refactor
+        - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
+        - removal of Scalar::Util::weaken code, which was causing odd headaches
+          with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
+    * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
+          many others]
+    * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
+          [Warren Kretzschmar]
+    * Bio::SeqIO::gbxml
+        - bug 2515 - new contribution [Ryan Golhar, jhannah]
+    * Bio::Assembly::IO
+        - support for reading Maq, Sam and Bowtie files [maj]
+        - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
+        - bug 2483: support for writing ACE files [Joshua Udall, fangly]
+        - bug 2599: support DBLINK annotation in GenBank files [cjfields]
+        - bug 2726: reading/writing granularity: whole scaffold or one contig
+          at a time [Joshua Udall, fangly]
+    * Bio::OntologyIO
+        - Added parsing of xrefs to OBO files, which are stored as secondary
+            dbxrefs of the cvterm [Naama Menda]
+        - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
+    * PAML code updated to work with PAML 4.4d [DaveMessina]
+  - [Bug fixes]
+    * [3198] - sort tabular BLAST hits by score [DaveMessina]
+    * a lot of BUG fixes, please see Changes file for more info
+- remove obsolete Build patch
+- remove Authors from description
+- add deps patch and send upstream
+
 -------------------------------------------------------------------
 Wed Dec  1 13:30:46 UTC 2010 - coolo@novell.com
 

perl-BioPerl.spec

@@ -1,7 +1,7 @@
 #
-# spec file for package perl-BioPerl (Version 1.6.1)
+# spec file for package perl-BioPerl
 #
-# Copyright (c) 2010 SUSE LINUX Products GmbH, Nuernberg, Germany.
+# Copyright (c) 2012 SUSE LINUX Products GmbH, Nuernberg, Germany.
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -15,34 +15,35 @@
 # Please submit bugfixes or comments via http://bugs.opensuse.org/
 #
 
-# norootforbuild
 
 %bcond_with test
 
 Name:           perl-BioPerl
 %define cpan_name BioPerl
 Summary:        Perl Modules for Biology
-Version:        1.6.1
+License:        GPL-3.0 or Artistic-1.0
-Release:        1
-License:        GPL+ or Artistic
 Group:          Development/Libraries/Perl
+Version:        1.6.901
+Release:        0
 Url:            http://search.cpan.org/dist/BioPerl/
 #Source:         http://www.cpan.org/modules/by-module/BioPerl/BioPerl-%{version}.tar.gz
 Source:         %{cpan_name}-%{version}.tar.bz2
-Patch0:         %{cpan_name}-1.6.1-Build.patch
+Patch0:         deps.patch
 BuildArch:      noarch
 BuildRoot:      %{_tmppath}/%{name}-%{version}-build
 %{perl_requires}
 BuildRequires:  perl
-BuildRequires:  perl(Module::Build)
 BuildRequires:  perl-macros
-BuildRequires:  perl(Test::More)
+BuildRequires:  perl(Module::Build)
 BuildRequires:  perl(Test::Harness) >= 2.62
+BuildRequires:  perl(Test::More)
+#
 BuildRequires:  perl(Data::Stag) >= 0.11
 BuildRequires:  perl(ExtUtils::Manifest) >= 1.52
 BuildRequires:  perl(IO::String)
 BuildRequires:  perl(Scalar::Util)
 # FIXME: not mentioned in Build.PL
+## 
 BuildRequires:  perl(URI::Escape)
 # recommended packages
 %if %{with test}
@@ -56,6 +57,8 @@ BuildRequires:  perl(Array::Compare)
 # we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
 BuildRequires:  perl(Clone)
 BuildRequires:  perl(Convert::Binary::C)
+BuildRequires:  perl(Error)
+BuildRequires:  perl(GD)
 BuildRequires:  perl(Graph)
 BuildRequires:  perl(GraphViz)
 BuildRequires:  perl(HTML::Entities)
@@ -66,12 +69,13 @@ BuildRequires:  perl(List::MoreUtils)
 BuildRequires:  perl(Math::Random)
 BuildRequires:  perl(PostScript::TextBlock)
 BuildRequires:  perl(SOAP::Lite)
-BuildRequires:  perl(Set::Scalar)
-BuildRequires:  perl(Spreadsheet::ParseExcel)
-BuildRequires:  perl(Spreadsheet::WriteExcel)
-BuildRequires:  perl(Storable) >= 2.05
 BuildRequires:  perl(SVG) >= 2.26
 BuildRequires:  perl(SVG::Graph) >= 0.01
+BuildRequires:  perl(Set::Scalar)
+BuildRequires:  perl(Sort::Naturally)
+BuildRequires:  perl(Spreadsheet::ParseExcel)
+#BuildRequires:  perl(Spreadsheet::WriteExcel)
+BuildRequires:  perl(Storable) >= 2.05
 BuildRequires:  perl(Text::ParseWords)
 BuildRequires:  perl(XML::DOM::XPath) >= 0.13
 BuildRequires:  perl(XML::Parser)
@@ -81,6 +85,7 @@ BuildRequires:  perl(XML::SAX::Writer)
 BuildRequires:  perl(XML::Simple)
 BuildRequires:  perl(XML::Twig)
 BuildRequires:  perl(XML::Writer) >= 0.4
+BuildRequires:  perl(YAML)
 %endif
 #
 Requires:       perl(Data::Stag) >= 0.11
@@ -100,6 +105,8 @@ Recommends:     perl(Bio::ASN1::EntrezGene)
 # we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
 Recommends:     perl(Clone)
 Recommends:     perl(Convert::Binary::C)
+Recommends:     perl(Error)
+Recommends:     perl(GD)
 Recommends:     perl(Graph)
 Recommends:     perl(GraphViz)
 Recommends:     perl(HTML::Entities)
@@ -111,6 +118,7 @@ Recommends:     perl(Math::Random)
 Recommends:     perl(PostScript::TextBlock)
 Recommends:     perl(SOAP::Lite)
 Recommends:     perl(Set::Scalar)
+Recommends:     perl(Sort::Naturally)
 Recommends:     perl(Spreadsheet::ParseExcel)
 Recommends:     perl(Spreadsheet::WriteExcel)
 Recommends:     perl(Storable) >= 2.05
@@ -125,6 +133,7 @@ Recommends:     perl(XML::SAX::Writer)
 Recommends:     perl(XML::Simple)
 Recommends:     perl(XML::Twig)
 Recommends:     perl(XML::Writer) >= 0.4
+Recommends:     perl(YAML)
 
 %description
 BioPerl is the product of a community effort to produce Perl code which is
@@ -136,21 +145,9 @@ Annotation and SeqFeature objects and databases, Blast objects can be
 converted to Alignment objects, and so on. This means that the objects
 provide a coordinated and extensible framework to do computational biology.
 
-Authors:
---------
-    Georg Fuellen
-    Richard Resnick
-    Steven E. Brenner
-    Chris Dagdigian
-    Steve Chervitz
-    Ewan Birney
-    James Gilbert
-    Elia Stupka
-     and others.
-
 %prep
 %setup -q -n %{cpan_name}-%{version}
-%patch0 -p1
+%patch0
 ## some rpmlint stuff :(
 # script-without-shebang
 find ./Bio -name "*.pm" -exec %{__chmod} 0644 {} \;