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Accepting request 129021 from home:computersalat:devel:perl

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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
This commit is contained in:
Christian Wittmer
2012-07-26 14:27:51 +00:00
committed by Git OBS Bridge
parent a69a704fdf
commit 5f59bd50c1
6 changed files with 117 additions and 41 deletions
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12
BioPerl-1.6.1-Build.patch
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@@ -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

3
BioPerl-1.6.1.tar.bz2
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@@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:f27d533054c97fb5f21caebb3c27a585095ee0a9005e8df19682bb6e580e3942
size 6919840

3
BioPerl-1.6.901.tar.bz2 Normal file
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@@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:ad20a3e2bd93342007aabd5aba68712eddc359ab3d80d08449b87f50aa5acd34
size 8167267

30
deps.patch Normal file
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@@ -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 => {

61
perl-BioPerl.changes
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@@ -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

49
perl-BioPerl.spec
View File

@@ -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
Release: 1
License: GPL+ or Artistic
License: GPL-3.0 or Artistic-1.0
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 {} \;