Accepting request 45939 from home:computersalat:devel:perl
Copy from home:computersalat:devel:perl/perl-BioPerl via accept of submit request 45939 revision 3. Request was accepted with message: self accept OBS-URL: https://build.opensuse.org/request/show/45939 OBS-URL: https://build.opensuse.org/package/show/devel:languages:perl/perl-BioPerl?expand=0&rev=1
This commit is contained in:
Christian Wittmer
Git OBS Bridge
23
.gitattributes
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23
.gitattributes
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## Default LFS
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*.7z filter=lfs diff=lfs merge=lfs -text
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*.bsp filter=lfs diff=lfs merge=lfs -text
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*.bz2 filter=lfs diff=lfs merge=lfs -text
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*.gem filter=lfs diff=lfs merge=lfs -text
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*.gz filter=lfs diff=lfs merge=lfs -text
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*.jar filter=lfs diff=lfs merge=lfs -text
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*.lz filter=lfs diff=lfs merge=lfs -text
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*.lzma filter=lfs diff=lfs merge=lfs -text
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*.obscpio filter=lfs diff=lfs merge=lfs -text
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*.oxt filter=lfs diff=lfs merge=lfs -text
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*.pdf filter=lfs diff=lfs merge=lfs -text
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*.png filter=lfs diff=lfs merge=lfs -text
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*.rpm filter=lfs diff=lfs merge=lfs -text
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*.tbz filter=lfs diff=lfs merge=lfs -text
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*.tbz2 filter=lfs diff=lfs merge=lfs -text
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*.tgz filter=lfs diff=lfs merge=lfs -text
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*.ttf filter=lfs diff=lfs merge=lfs -text
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*.txz filter=lfs diff=lfs merge=lfs -text
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*.whl filter=lfs diff=lfs merge=lfs -text
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*.xz filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.zst filter=lfs diff=lfs merge=lfs -text
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1
.gitignore
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1
.gitignore
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.osc
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12
BioPerl-1.6.1-Build.patch
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12
BioPerl-1.6.1-Build.patch
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diff -ruN BioPerl-1.6.1-orig/Bio/Root/Build.pm BioPerl-1.6.1/Bio/Root/Build.pm
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--- BioPerl-1.6.1-orig/Bio/Root/Build.pm 2009-09-29 18:33:53.000000000 +0200
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+++ BioPerl-1.6.1/Bio/Root/Build.pm 2010-08-04 15:56:14.000000000 +0200
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@@ -425,7 +425,7 @@
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else {
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my $question = $required ? "$desired is absolutely required prior to installation: shall I install it now using a CPAN shell?" :
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"To install $desired I'll need to open a CPAN shell right now; is that OK?";
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- my $do_install = $self->y_n($question.' y/n', 'y');
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+ my $do_install = $self->y_n($question.' y/n', 'n');
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if ($do_install) {
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# Here we use CPAN to actually install the desired module, the benefit
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3
BioPerl-1.6.1.tar.bz2
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3
BioPerl-1.6.1.tar.bz2
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version https://git-lfs.github.com/spec/v1
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oid sha256:f27d533054c97fb5f21caebb3c27a585095ee0a9005e8df19682bb6e580e3942
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size 6919840
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21
perl-BioPerl.changes
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21
perl-BioPerl.changes
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-------------------------------------------------------------------
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Mon Aug 16 15:02:25 UTC 2010 - chris@computersalat.de
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- enabled some more optional tests
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o Algorithm::Munkres, Convert::Binary::C, GraphViz,
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PostScript::TextBlock, Spreadsheet::ParseExcel
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-------------------------------------------------------------------
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Wed Aug 4 16:11:26 UTC 2010 - chris@computersalat.de
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- add Build patch
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o do not try to connect CPAN ;)
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- added recommended pkgs
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o + BuildRequires (recommended) --with test
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-------------------------------------------------------------------
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Mon Aug 2 21:13:45 UTC 2010 - chris@computersalat.de
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- initial package 1.6.1
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* created by cpanspec 1.78
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197
perl-BioPerl.spec
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197
perl-BioPerl.spec
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#
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# spec file for package perl-BioPerl (Version 1.6.1)
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#
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# Copyright (c) 2010 SUSE LINUX Products GmbH, Nuernberg, Germany.
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#
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# All modifications and additions to the file contributed by third parties
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# remain the property of their copyright owners, unless otherwise agreed
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# upon. The license for this file, and modifications and additions to the
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# file, is the same license as for the pristine package itself (unless the
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# license for the pristine package is not an Open Source License, in which
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# case the license is the MIT License). An "Open Source License" is a
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# license that conforms to the Open Source Definition (Version 1.9)
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# published by the Open Source Initiative.
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# Please submit bugfixes or comments via http://bugs.opensuse.org/
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#
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# norootforbuild
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%bcond_with test
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Name: perl-BioPerl
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%define cpan_name BioPerl
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Summary: Perl Modules for Biology
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Version: 1.6.1
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Release: 1
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License: GPL+ or Artistic
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Group: Development/Libraries/Perl
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Url: http://search.cpan.org/dist/BioPerl/
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#Source: http://www.cpan.org/modules/by-module/BioPerl/BioPerl-%{version}.tar.gz
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Source: %{cpan_name}-%{version}.tar.bz2
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Patch0: %{cpan_name}-1.6.1-Build.patch
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BuildArch: noarch
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BuildRoot: %{_tmppath}/%{name}-%{version}-build
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BuildRequires: perl
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BuildRequires: perl(Module::Build)
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%if 0%{?suse_version} < 1120
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BuildRequires: perl-macros
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%endif
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BuildRequires: perl(Test::More)
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BuildRequires: perl(Test::Harness) >= 2.62
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BuildRequires: perl(Data::Stag) >= 0.11
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BuildRequires: perl(ExtUtils::Manifest) >= 1.52
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BuildRequires: perl(IO::String)
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BuildRequires: perl(Scalar::Util)
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# FIXME: not mentioned in Build.PL
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BuildRequires: perl(URI::Escape)
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# recommended packages
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%if %{with test}
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BuildRequires: perl(Ace)
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BuildRequires: perl(Algorithm::Munkres)
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BuildRequires: perl(Array::Compare)
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# this won't actually install due to circular dep, but we have no way of doing a post-install
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# the [circular dependency!] specifies it is only installed on explicit request for this specific module,
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# not when simply choosing to install 'all' modules
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#BuildRequires: perl(Bio::ASN1::EntrezGene)
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# we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
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BuildRequires: perl(Clone)
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BuildRequires: perl(Convert::Binary::C)
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BuildRequires: perl(Graph)
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BuildRequires: perl(GraphViz)
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BuildRequires: perl(HTML::Entities)
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BuildRequires: perl(HTML::HeadParser) >= 3
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BuildRequires: perl(HTTP::Request::Common)
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BuildRequires: perl(LWP::UserAgent)
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BuildRequires: perl(List::MoreUtils)
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BuildRequires: perl(Math::Random)
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BuildRequires: perl(PostScript::TextBlock)
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BuildRequires: perl(SOAP::Lite)
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BuildRequires: perl(Set::Scalar)
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BuildRequires: perl(Spreadsheet::ParseExcel)
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BuildRequires: perl(Spreadsheet::WriteExcel)
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BuildRequires: perl(Storable) >= 2.05
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BuildRequires: perl(SVG) >= 2.26
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BuildRequires: perl(SVG::Graph) >= 0.01
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BuildRequires: perl(Text::ParseWords)
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BuildRequires: perl(XML::DOM::XPath) >= 0.13
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BuildRequires: perl(XML::Parser)
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BuildRequires: perl(XML::Parser::PerlSAX)
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BuildRequires: perl(XML::SAX) >= 0.15
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BuildRequires: perl(XML::SAX::Writer)
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BuildRequires: perl(XML::Simple)
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BuildRequires: perl(XML::Twig)
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BuildRequires: perl(XML::Writer) >= 0.4
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%endif
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#
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Requires: perl = %{perl_version}
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Requires: perl(Data::Stag) >= 0.11
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Requires: perl(ExtUtils::Manifest) >= 1.52
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Requires: perl(IO::String)
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Requires: perl(Scalar::Util)
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# FIXME: not mentioned in Build.PL
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Requires: perl(URI::Escape)
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# FIXME: add reccomends :)
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Recommends: perl(Ace)
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Recommends: perl(Algorithm::Munkres)
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Recommends: perl(Array::Compare)
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# this won't actually install due to circular dep, but we have no way of doing a post-install
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# the [circular dependency!] specifies it is only installed on explicit request for this specific module,
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# not when simply choosing to install 'all' modules
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Recommends: perl(Bio::ASN1::EntrezGene)
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# we actually need 1.01 of Class::AutoClass, but unfortunately it is versioned as 1.0
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Recommends: perl(Clone)
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Recommends: perl(Convert::Binary::C)
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Recommends: perl(Graph)
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Recommends: perl(GraphViz)
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Recommends: perl(HTML::Entities)
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Recommends: perl(HTML::HeadParser) >= 3
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Recommends: perl(HTTP::Request::Common)
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Recommends: perl(LWP::UserAgent)
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Recommends: perl(List::MoreUtils)
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Recommends: perl(Math::Random)
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Recommends: perl(PostScript::TextBlock)
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Recommends: perl(SOAP::Lite)
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Recommends: perl(Set::Scalar)
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Recommends: perl(Spreadsheet::ParseExcel)
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Recommends: perl(Spreadsheet::WriteExcel)
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Recommends: perl(Storable) >= 2.05
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Recommends: perl(SVG) >= 2.26
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Recommends: perl(SVG::Graph) >= 0.01
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Recommends: perl(Text::ParseWords)
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Recommends: perl(XML::DOM::XPath) >= 0.13
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Recommends: perl(XML::Parser)
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Recommends: perl(XML::Parser::PerlSAX)
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Recommends: perl(XML::SAX) >= 0.15
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Recommends: perl(XML::SAX::Writer)
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Recommends: perl(XML::Simple)
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Recommends: perl(XML::Twig)
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Recommends: perl(XML::Writer) >= 0.4
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%description
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BioPerl is the product of a community effort to produce Perl code which is
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useful in biology. Examples include Sequence objects, Alignment objects and
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database searching objects. These objects not only do what they are
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advertised to do in the documentation, but they also interact - Alignment
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objects are made from the Sequence objects, Sequence objects have access to
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Annotation and SeqFeature objects and databases, Blast objects can be
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converted to Alignment objects, and so on. This means that the objects
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provide a coordinated and extensible framework to do computational biology.
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Authors:
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--------
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Georg Fuellen
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Richard Resnick
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Steven E. Brenner
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Chris Dagdigian
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Steve Chervitz
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Ewan Birney
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James Gilbert
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Elia Stupka
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and others.
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%prep
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%setup -q -n %{cpan_name}-%{version}
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%patch0 -p1
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## some rpmlint stuff :(
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# script-without-shebang
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find ./Bio -name "*.pm" -exec %{__chmod} 0644 {} \;
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# wrong-script-end-of-line-encoding
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%{__perl} -p -i -e 's|\r\n|\n|' Bio/Search/Tiling/MapTileUtils.pm
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%{__perl} -p -i -e 's|\r\n|\n|' Bio/Search/Tiling/MapTileUtils.pm
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%{__perl} -p -i -e 's|\r\n|\n|' ide/bioperl-mode/etc/images/bpmode-tool.xpm
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%{__perl} -p -i -e 's|\r\n|\n|' ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
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%{__perl} -p -i -e 's|\r\n|\n|' maintenance/module_usage.pl
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# zero-length
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%{__rm} ide/bioperl-mode/dist/SKIP
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# executable-docs
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%{__chmod} a-x examples/root/README
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%{__chmod} a-x ide/bioperl-mode/README
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%{__chmod} a-x scripts/README
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# spurious-executable-perm
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for dir in doc ide maintenance; do
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find -type f -exec %{__chmod} 0644 {} \;
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done
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# wrong-script-interpreter
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find ./ -type f -exec %{__sed} -i -e "s@/usr/local/bin/perl@%{__perl}@" {} \;
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find ./ -type f -exec %{__sed} -i -e "s@^#\!perl@#\!%{__perl}@" {} \;
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%build
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%{__perl} Build.PL installdirs=vendor
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./Build
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%check
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./Build test
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%install
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./Build install destdir=$RPM_BUILD_ROOT create_packlist=0
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%perl_gen_filelist
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%clean
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%{__rm} -rf $RPM_BUILD_ROOT
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%files -f %{name}.files
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%defattr(-,root,root,-)
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%doc AUTHORS BUGS Changes DEPENDENCIES DEPRECATED doc examples ide LICENSE maintenance models README scripts
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%changelog
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