Accepting request 573787 from devel:languages:perl:autoupdate
automatic update OBS-URL: https://build.opensuse.org/request/show/573787 OBS-URL: https://build.opensuse.org/package/show/devel:languages:perl/perl-BioPerl?expand=0&rev=5
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@@ -1,7 +1,7 @@
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#
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# spec file for package perl-BioPerl
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#
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# Copyright (c) 2012 SUSE LINUX Products GmbH, Nuernberg, Germany.
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# Copyright (c) 2018 SUSE LINUX 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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@@ -16,116 +16,58 @@
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#
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%bcond_with test
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Name: perl-BioPerl
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Version: 1.007002
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Release: 0
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%define cpan_name BioPerl
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Summary: Perl Modules for Biology
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License: GPL-3.0 or Artistic-1.0
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License: Artistic-1.0 or GPL-1.0+
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Group: Development/Libraries/Perl
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Version: 1.6.901
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Release: 0
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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: deps.patch
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Source0: https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/%{cpan_name}-%{version}.tar.gz
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Source1: cpanspec.yml
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BuildArch: noarch
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BuildRoot: %{_tmppath}/%{name}-%{version}-build
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%{perl_requires}
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BuildRequires: perl
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BuildRequires: perl-macros
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BuildRequires: perl(Module::Build)
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BuildRequires: perl(Test::Harness) >= 2.62
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BuildRequires: perl(Test::More)
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#
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BuildRequires: perl(CPAN) >= 1.81
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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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##
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BuildRequires: perl(Module::Build) >= 0.420000
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BuildRequires: perl(Test::Harness) >= 2.62
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BuildRequires: perl(Test::Most)
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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(Error)
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BuildRequires: perl(GD)
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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(SVG) >= 2.26
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BuildRequires: perl(SVG::Graph) >= 0.01
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BuildRequires: perl(Set::Scalar)
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BuildRequires: perl(Sort::Naturally)
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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(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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BuildRequires: perl(YAML)
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%endif
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#
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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(Bio::Phylo)
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Recommends: perl(CGI)
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Recommends: perl(Clone)
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Recommends: perl(Convert::Binary::C)
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Recommends: perl(Error)
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Recommends: perl(GD)
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Recommends: perl(Graph)
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Recommends: perl(Graph) >= 0.5
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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(HTML::TableExtract)
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Recommends: perl(HTTP::Request::Common)
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Recommends: perl(LWP::UserAgent)
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Recommends: perl(Inline::C) >= 0.67
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Recommends: perl(IO::Scalar)
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Recommends: perl(List::MoreUtils)
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Recommends: perl(Math::Random)
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Recommends: perl(LWP::UserAgent)
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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(Sort::Naturally)
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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::DOM)
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Recommends: perl(XML::DOM::XPath)
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Recommends: perl(XML::LibXML)
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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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@@ -134,6 +76,7 @@ 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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Recommends: perl(YAML)
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%{perl_requires}
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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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@@ -145,48 +88,39 @@ 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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BioPerl development focuses on Perl classes, or code that is used to create
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objects representing biological entities. There are scripts provided in the
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scripts/ and examples/ directories but scripts are not the main focus of
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the BioPerl developers. Of course, as the objects do most of the hard work
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for you, all you have to do is combine a number of objects together
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sensibly to make useful scripts.
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The intent of the BioPerl development effort is to make reusable tools that
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aid people in creating their own sites or job-specific applications.
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The BioPerl website at http://bioperl.org also attempts to maintain links
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and archives of standalone bio-related Perl tools that are not affiliated
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or related to the core BioPerl effort. Check the site for useful code ideas
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and contribute your own if possible.
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%prep
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%setup -q -n %{cpan_name}-%{version}
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%patch0
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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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find . -type f ! -name \*.pl -print0 | xargs -0 chmod 644
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%build
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%{__perl} Build.PL installdirs=vendor
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./Build
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./Build build flags=%{?_smp_mflags}
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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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./Build install destdir=%{buildroot} 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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%defattr(-,root,root,755)
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%doc AUTHORS Bio BUGS Changes deobfuscator DEPENDENCIES DEPRECATED examples ide maintenance models README.md scripts travis_scripts
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%license LICENSE
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%changelog
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