diff --git a/BioPerl-1.007002.tar.gz b/BioPerl-1.007002.tar.gz new file mode 100644 index 0000000..0d04afd --- /dev/null +++ b/BioPerl-1.007002.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1 +size 12362741 diff --git a/BioPerl-1.6.901.tar.bz2 b/BioPerl-1.6.901.tar.bz2 deleted file mode 100644 index 9a182ba..0000000 --- a/BioPerl-1.6.901.tar.bz2 +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:ad20a3e2bd93342007aabd5aba68712eddc359ab3d80d08449b87f50aa5acd34 -size 8167267 diff --git a/cpanspec.yml b/cpanspec.yml new file mode 100644 index 0000000..76ad4a4 --- /dev/null +++ b/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 diff --git a/perl-BioPerl.changes b/perl-BioPerl.changes index 164cf26..74cf318 100644 --- a/perl-BioPerl.changes +++ b/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 diff --git a/perl-BioPerl.spec b/perl-BioPerl.spec index 1462b70..f810f28 100644 --- a/perl-BioPerl.spec +++ b/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 -Source: %{cpan_name}-%{version}.tar.bz2 -Patch0: deps.patch +Source0: https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/%{cpan_name}-%{version}.tar.gz +Source1: cpanspec.yml BuildArch: noarch BuildRoot: %{_tmppath}/%{name}-%{version}-build -%{perl_requires} BuildRequires: perl BuildRequires: perl-macros -BuildRequires: perl(Module::Build) -BuildRequires: perl(Test::Harness) >= 2.62 -BuildRequires: perl(Test::More) -# +BuildRequires: perl(CPAN) >= 1.81 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(Module::Build) >= 0.420000 +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 -# 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(Bio::Phylo) +Recommends: perl(CGI) 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::XPath) >= 0.13 +Recommends: perl(XML::DOM) +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 -## 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}@" {} \; +find . -type f ! -name \*.pl -print0 | xargs -0 chmod 644 %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,-) -%doc AUTHORS BUGS Changes DEPENDENCIES DEPRECATED doc examples ide LICENSE maintenance models README scripts +%defattr(-,root,root,755) +%doc AUTHORS Bio BUGS Changes deobfuscator DEPENDENCIES DEPRECATED examples ide maintenance models README.md scripts travis_scripts +%license LICENSE %changelog