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

BioPerl-1.007002.tar.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1
+size 12362741

BioPerl-1.6.901.tar.bz2

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

cpanspec.yml

@@ -0,0 +1,28 @@
+---
+#description_paragraphs: 3
+#description: |-
+#  override description from CPAN
+#summary: override summary from CPAN
+#no_testing: broken upstream
+#sources:
+#  - source1
+#  - source2
+#patches:
+#  foo.patch: -p1
+#  bar.patch:
+#preamble: |-
+# BuildRequires:  gcc-c++
+#post_prep: |-
+# hunspell=`pkg-config --libs hunspell | sed -e 's,-l,,; s,  *,,g'`
+# sed -i -e "s,hunspell-X,$hunspell," t/00-prereq.t Makefile.PL 
+#post_build: |-
+# rm unused.files
+#post_install: |-
+# sed on %{name}.files
+#license: SUSE-NonFree
+#skip_noarch: 1
+#custom_build: |-
+#./Build build flags=%{?_smp_mflags} --myflag
+#custom_test: |-
+#startserver && make test
+#ignore_requires: Bizarre::Module

perl-BioPerl.changes

@@ -1,3 +1,9 @@
+-------------------------------------------------------------------
+Wed Feb  7 16:10:23 UTC 2018 - coolo@suse.com
+
+- updated to 1.007002
+   see /usr/share/doc/packages/perl-BioPerl/Changes
+
 -------------------------------------------------------------------
 Thu Jul 26 13:25:33 UTC 2012 - chris@computersalat.de
 

perl-BioPerl.spec

@@ -1,7 +1,7 @@
 #
 # spec file for package perl-BioPerl
 #
-# Copyright (c) 2012 SUSE LINUX Products GmbH, Nuernberg, Germany.
+# Copyright (c) 2018 SUSE LINUX GmbH, Nuernberg, Germany.
 #
 # All modifications and additions to the file contributed by third parties
 # remain the property of their copyright owners, unless otherwise agreed
@@ -16,116 +16,58 @@
 #
 
 
-%bcond_with test
-
 Name:           perl-BioPerl
+Version:        1.007002
+Release:        0
 %define cpan_name BioPerl
 Summary:        Perl Modules for Biology
-License:        GPL-3.0 or Artistic-1.0
+License:        Artistic-1.0 or GPL-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
+Source0:        https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/%{cpan_name}-%{version}.tar.gz
-Source:         %{cpan_name}-%{version}.tar.bz2
+Source1:        cpanspec.yml
-Patch0:         deps.patch
 BuildArch:      noarch
 BuildRoot:      %{_tmppath}/%{name}-%{version}-build
-%{perl_requires}
 BuildRequires:  perl
 BuildRequires:  perl-macros
-BuildRequires:  perl(Module::Build)
+BuildRequires:  perl(CPAN) >= 1.81
-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)
+BuildRequires:  perl(Module::Build) >= 0.420000
-# FIXME: not mentioned in Build.PL
+BuildRequires:  perl(Test::Harness) >= 2.62
-## 
+BuildRequires:  perl(Test::Most)
 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(Error)
-BuildRequires:  perl(GD)
-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(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)
-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
-BuildRequires:  perl(YAML)
-%endif
-#
 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
+Recommends:     perl(Bio::Phylo)
-# the [circular dependency!] specifies it is only installed on explicit request for this specific module,
+Recommends:     perl(CGI)
-# 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(Error)
 Recommends:     perl(GD)
-Recommends:     perl(Graph)
+Recommends:     perl(Graph) >= 0.5
 Recommends:     perl(GraphViz)
 Recommends:     perl(HTML::Entities)
 Recommends:     perl(HTML::HeadParser) >= 3
+Recommends:     perl(HTML::TableExtract)
 Recommends:     perl(HTTP::Request::Common)
-Recommends:     perl(LWP::UserAgent)
+Recommends:     perl(Inline::C) >= 0.67
+Recommends:     perl(IO::Scalar)
 Recommends:     perl(List::MoreUtils)
-Recommends:     perl(Math::Random)
+Recommends:     perl(LWP::UserAgent)
 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
 Recommends:     perl(SVG) >= 2.26
 Recommends:     perl(SVG::Graph) >= 0.01
-Recommends:     perl(Text::ParseWords)
+Recommends:     perl(XML::DOM)
-Recommends:     perl(XML::DOM::XPath) >= 0.13
+Recommends:     perl(XML::DOM::XPath)
+Recommends:     perl(XML::LibXML)
 Recommends:     perl(XML::Parser)
 Recommends:     perl(XML::Parser::PerlSAX)
 Recommends:     perl(XML::SAX) >= 0.15
@@ -134,6 +76,7 @@ Recommends:     perl(XML::Simple)
 Recommends:     perl(XML::Twig)
 Recommends:     perl(XML::Writer) >= 0.4
 Recommends:     perl(YAML)
+%{perl_requires}
 
 %description
 BioPerl is the product of a community effort to produce Perl code which is
@@ -145,48 +88,39 @@ 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.
 
+BioPerl development focuses on Perl classes, or code that is used to create
+objects representing biological entities. There are scripts provided in the
+scripts/ and examples/ directories but scripts are not the main focus of
+the BioPerl developers. Of course, as the objects do most of the hard work
+for you, all you have to do is combine a number of objects together
+sensibly to make useful scripts.
+
+The intent of the BioPerl development effort is to make reusable tools that
+aid people in creating their own sites or job-specific applications.
+
+The BioPerl website at http://bioperl.org also attempts to maintain links
+and archives of standalone bio-related Perl tools that are not affiliated
+or related to the core BioPerl effort. Check the site for useful code ideas
+and contribute your own if possible.
+
 %prep
 %setup -q -n %{cpan_name}-%{version}
-%patch0
+find . -type f ! -name \*.pl -print0 | xargs -0 chmod 644
-## 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
+./Build build flags=%{?_smp_mflags}
 
 %check
 ./Build test
 
 %install
-./Build install destdir=$RPM_BUILD_ROOT create_packlist=0
+./Build install destdir=%{buildroot} create_packlist=0
 %perl_gen_filelist
 
-%clean
-%{__rm} -rf $RPM_BUILD_ROOT
-
 %files -f %{name}.files
-%defattr(-,root,root,-)
+%defattr(-,root,root,755)
-%doc AUTHORS BUGS Changes DEPENDENCIES DEPRECATED doc examples ide LICENSE maintenance models README scripts
+%doc AUTHORS Bio BUGS Changes deobfuscator DEPENDENCIES DEPRECATED examples ide maintenance models README.md scripts travis_scripts
+%license LICENSE
 
 %changelog