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
This commit is contained in:
Git OBS Bridge
3
BioPerl-1.007002.tar.gz
Normal file
3
BioPerl-1.007002.tar.gz
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1
|
||||
size 12362741
|
||||
@@ -1,3 +0,0 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:ad20a3e2bd93342007aabd5aba68712eddc359ab3d80d08449b87f50aa5acd34
|
||||
size 8167267
|
||||
28
cpanspec.yml
Normal file
28
cpanspec.yml
Normal file
@@ -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
|
||||
@@ -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
|
||||
|
||||
|
||||
@@ -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
|
||||
|
||||
Reference in New Issue
Block a user