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

.gitattributes

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+## Default LFS
+*.7z filter=lfs diff=lfs merge=lfs -text
+*.bsp filter=lfs diff=lfs merge=lfs -text
+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.gem filter=lfs diff=lfs merge=lfs -text
+*.gz filter=lfs diff=lfs merge=lfs -text
+*.jar filter=lfs diff=lfs merge=lfs -text
+*.lz filter=lfs diff=lfs merge=lfs -text
+*.lzma filter=lfs diff=lfs merge=lfs -text
+*.obscpio filter=lfs diff=lfs merge=lfs -text
+*.oxt filter=lfs diff=lfs merge=lfs -text
+*.pdf filter=lfs diff=lfs merge=lfs -text
+*.png filter=lfs diff=lfs merge=lfs -text
+*.rpm filter=lfs diff=lfs merge=lfs -text
+*.tbz filter=lfs diff=lfs merge=lfs -text
+*.tbz2 filter=lfs diff=lfs merge=lfs -text
+*.tgz filter=lfs diff=lfs merge=lfs -text
+*.ttf filter=lfs diff=lfs merge=lfs -text
+*.txz filter=lfs diff=lfs merge=lfs -text
+*.whl filter=lfs diff=lfs merge=lfs -text
+*.xz filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text
+*.zst filter=lfs diff=lfs merge=lfs -text

.gitignore

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+.osc

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
+--- 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

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+version https://git-lfs.github.com/spec/v1
+oid sha256:f27d533054c97fb5f21caebb3c27a585095ee0a9005e8df19682bb6e580e3942
+size 6919840

perl-BioPerl.changes

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+-------------------------------------------------------------------
+Mon Aug 16 15:02:25 UTC 2010 - chris@computersalat.de
+
+- enabled some more optional tests
+  o Algorithm::Munkres, Convert::Binary::C, GraphViz,
+    PostScript::TextBlock, Spreadsheet::ParseExcel
+
+-------------------------------------------------------------------
+Wed Aug  4 16:11:26 UTC 2010 - chris@computersalat.de
+
+- add Build patch
+  o do not try to connect CPAN ;)
+- added recommended pkgs
+  o + BuildRequires (recommended) --with test
+
+-------------------------------------------------------------------
+Mon Aug  2 21:13:45 UTC 2010 - chris@computersalat.de
+
+- initial package 1.6.1
+  * created by cpanspec 1.78
+

perl-BioPerl.spec

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+#
+# spec file for package perl-BioPerl (Version 1.6.1)
+#
+# Copyright (c) 2010 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
+# upon. The license for this file, and modifications and additions to the
+# file, is the same license as for the pristine package itself (unless the
+# license for the pristine package is not an Open Source License, in which
+# case the license is the MIT License). An "Open Source License" is a
+# license that conforms to the Open Source Definition (Version 1.9)
+# published by the Open Source Initiative.
+
+# 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
+Group:          Development/Libraries/Perl
+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
+BuildArch:      noarch
+BuildRoot:      %{_tmppath}/%{name}-%{version}-build
+BuildRequires:  perl
+BuildRequires:  perl(Module::Build)
+%if 0%{?suse_version} < 1120
+BuildRequires:  perl-macros
+%endif
+BuildRequires:  perl(Test::More)
+BuildRequires:  perl(Test::Harness) >= 2.62
+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}
+BuildRequires:  perl(Ace)
+BuildRequires:  perl(Algorithm::Munkres)
+BuildRequires:  perl(Array::Compare)
+# this won't actually install due to circular dep, but we have no way of doing a post-install
+# the [circular dependency!] specifies it is only installed on explicit request for this specific module,
+# not when simply choosing to install 'all' modules
+#BuildRequires:  perl(Bio::ASN1::EntrezGene)
+# 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(Graph)
+BuildRequires:  perl(GraphViz)
+BuildRequires:  perl(HTML::Entities)
+BuildRequires:  perl(HTML::HeadParser) >= 3
+BuildRequires:  perl(HTTP::Request::Common)
+BuildRequires:  perl(LWP::UserAgent)
+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(Text::ParseWords)
+BuildRequires:  perl(XML::DOM::XPath) >= 0.13
+BuildRequires:  perl(XML::Parser)
+BuildRequires:  perl(XML::Parser::PerlSAX)
+BuildRequires:  perl(XML::SAX) >= 0.15
+BuildRequires:  perl(XML::SAX::Writer)
+BuildRequires:  perl(XML::Simple)
+BuildRequires:  perl(XML::Twig)
+BuildRequires:  perl(XML::Writer) >= 0.4
+%endif
+#
+Requires:       perl = %{perl_version}
+Requires:       perl(Data::Stag) >= 0.11
+Requires:       perl(ExtUtils::Manifest) >= 1.52
+Requires:       perl(IO::String)
+Requires:       perl(Scalar::Util)
+# FIXME: not mentioned in Build.PL
+Requires:       perl(URI::Escape)
+# FIXME: add reccomends :)
+Recommends:     perl(Ace)
+Recommends:     perl(Algorithm::Munkres)
+Recommends:     perl(Array::Compare)
+# this won't actually install due to circular dep, but we have no way of doing a post-install
+# the [circular dependency!] specifies it is only installed on explicit request for this specific module,
+# not when simply choosing to install 'all' modules
+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(Graph)
+Recommends:     perl(GraphViz)
+Recommends:     perl(HTML::Entities)
+Recommends:     perl(HTML::HeadParser) >= 3
+Recommends:     perl(HTTP::Request::Common)
+Recommends:     perl(LWP::UserAgent)
+Recommends:     perl(List::MoreUtils)
+Recommends:     perl(Math::Random)
+Recommends:     perl(PostScript::TextBlock)
+Recommends:     perl(SOAP::Lite)
+Recommends:     perl(Set::Scalar)
+Recommends:     perl(Spreadsheet::ParseExcel)
+Recommends:     perl(Spreadsheet::WriteExcel)
+Recommends:     perl(Storable) >= 2.05
+Recommends:     perl(SVG) >= 2.26
+Recommends:     perl(SVG::Graph) >= 0.01
+Recommends:     perl(Text::ParseWords)
+Recommends:     perl(XML::DOM::XPath) >= 0.13
+Recommends:     perl(XML::Parser)
+Recommends:     perl(XML::Parser::PerlSAX)
+Recommends:     perl(XML::SAX) >= 0.15
+Recommends:     perl(XML::SAX::Writer)
+Recommends:     perl(XML::Simple)
+Recommends:     perl(XML::Twig)
+Recommends:     perl(XML::Writer) >= 0.4
+
+%description
+BioPerl is the product of a community effort to produce Perl code which is
+useful in biology. Examples include Sequence objects, Alignment objects and
+database searching objects. These objects not only do what they are
+advertised to do in the documentation, but they also interact - Alignment
+objects are made from the Sequence objects, Sequence objects have access to
+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
+## some rpmlint stuff :(
+# script-without-shebang
+find ./Bio -name "*.pm" -exec %{__chmod} 0644 {} \;
+# wrong-script-end-of-line-encoding
+%{__perl} -p -i -e 's|\r\n|\n|' Bio/Search/Tiling/MapTileUtils.pm
+%{__perl} -p -i -e 's|\r\n|\n|' Bio/Search/Tiling/MapTileUtils.pm
+%{__perl} -p -i -e 's|\r\n|\n|' ide/bioperl-mode/etc/images/bpmode-tool.xpm
+%{__perl} -p -i -e 's|\r\n|\n|' ide/bioperl-mode/etc/images/bpmode-tool-dis.xpm
+%{__perl} -p -i -e 's|\r\n|\n|' maintenance/module_usage.pl
+# zero-length
+%{__rm} ide/bioperl-mode/dist/SKIP
+# executable-docs
+%{__chmod} a-x examples/root/README
+%{__chmod} a-x ide/bioperl-mode/README
+%{__chmod} a-x scripts/README 
+# spurious-executable-perm
+for dir in doc ide maintenance; do
+  find -type f -exec %{__chmod} 0644 {} \;
+done
+# wrong-script-interpreter
+find ./ -type f -exec %{__sed} -i -e "s@/usr/local/bin/perl@%{__perl}@" {} \;
+find ./ -type f -exec %{__sed} -i -e "s@^#\!perl@#\!%{__perl}@" {} \;
+
+%build
+%{__perl} Build.PL installdirs=vendor
+./Build
+
+%check
+./Build test
+
+%install
+./Build install destdir=$RPM_BUILD_ROOT create_packlist=0
+%perl_gen_filelist
+
+%clean
+%{__rm} -rf $RPM_BUILD_ROOT
+
+%files -f %{name}.files
+%defattr(-,root,root,-)
+%doc AUTHORS BUGS Changes DEPENDENCIES DEPRECATED doc examples ide LICENSE maintenance models README scripts
+
+%changelog