debian/0000755000000000000000000000000012211353146007164 5ustar debian/rules0000755000000000000000000000063512207045557010261 0ustar #!/usr/bin/make -f PACKAGE = $(shell dh_listpackages) TMP = $(CURDIR)/debian/$(PACKAGE) TEST_FILES=$(filter-out t/remote.t,$(shell echo t/*.t)) %: dh $@ --buildsystem=perl_build override_dh_auto_test: dh_auto_test -- --test_files "$(TEST_FILES)" override_dh_auto_install: dh_auto_install # remove empty manpage without whatis entry $(RM) -v $(TMP)/usr/share/man/man3/Bio::PrimerDesigner::Config.3pm debian/patches/0000755000000000000000000000000012211352762010616 5ustar debian/patches/series0000644000000000000000000000010212211352247012022 0ustar build.pl-getopt-long.patch no-hash-manipulation-inside-each.patch debian/patches/no-hash-manipulation-inside-each.patch0000644000000000000000000000177312211352354020046 0ustar Description: avoid changing hash keys in an "each %hash" loop This leads to undefined behaviour Instead, mark what needs to be added/deleted and do it outside of the loop. Bug-Debian: http://bugs.debian.org/711426 Bug: https://rt.cpan.org/Public/Bug/Display.html?id=85968 Author: Damyan Ivanov Forwarded: yes --- a/lib/Bio/PrimerDesigner/primer3.pm +++ b/lib/Bio/PrimerDesigner/primer3.pm @@ -106,12 +106,16 @@ that can be used to call result methods. # my %aliases = $self->list_aliases; my %lookup = reverse %aliases; + my @delete; + my %add; while ( my ( $k, $v ) = each %$args ) { next if exists $aliases{ $k }; my $alias = $lookup{ $k } or return $self->error("No alias for '$k'"); - delete $args->{ $k }; - $args->{ $alias } = $v; + push @delete, $k; + $add{ $alias } = $v; } + delete $args->{$_} for @delete; + $args->{$_} = $add{$_} for keys %add; # # Check that everything required is present. debian/patches/build.pl-getopt-long.patch0000644000000000000000000000457412207045557015625 0ustar Description: Use of Getopt::Long was breaking the Build.PL interface for passing Module::Build long options (for example --installdirs). Refactor Build.PL to use the built-in args() method. Origin: vendor Bug-Debian: http://bugs.debian.org/718056 Forwarded: not-yet Author: gregor herrmann Last-Update: 2013-07-29 --- a/Build.PL +++ b/Build.PL @@ -4,7 +4,6 @@ use warnings; use Cwd; use Data::Dumper; -use Getopt::Long; use Pod::Usage; use File::Spec::Functions 'catfile'; @@ -14,36 +13,6 @@ exit(0); } -my $help = ''; -my $url = ''; -GetOptions( - 'h|help' => \$help, - 'url:s' => \$url, -); - -if ( $help ) { - pod2usage({ -exitval => 0 }); -} - -# -# Write any local config info to the Config file -# -if ( $url && $url !~ m{^http://} ) { - $url = 'http://' . $url; -} - -my $cwd = cwd; -my $tmpl_file = catfile( $cwd, 'templates', 'Config.pm' ); -open my $in_fh, '<', $tmpl_file or die "Can't read $tmpl_file: $!\n"; -my $tmpl = join('', <$in_fh>); -my $config = sprintf( $tmpl, " local_url => '$url'," ); -close $in_fh; - -my $config_pm = catfile( cwd(), 'lib', 'Bio', 'PrimerDesigner', 'Config.pm' ); -open my $out_fh, '>', $config_pm or die "Can't write '$config': $!\n"; -print $out_fh $config; -close $out_fh; - # # Here we make the Build script # @@ -70,6 +39,34 @@ }, ); +my %args = $builder->args; + +my $help = exists $args{help}; +my $url = $args{url}; + +if ( $help ) { + pod2usage({ -exitval => 0 }); +} + +# +# Write any local config info to the Config file +# +if ( $url && $url !~ m{^http://} ) { + $url = 'http://' . $url; +} + +my $cwd = cwd; +my $tmpl_file = catfile( $cwd, 'templates', 'Config.pm' ); +open my $in_fh, '<', $tmpl_file or die "Can't read $tmpl_file: $!\n"; +my $tmpl = join('', <$in_fh>); +my $config = sprintf( $tmpl, " local_url => '$url'," ); +close $in_fh; + +my $config_pm = catfile( cwd(), 'lib', 'Bio', 'PrimerDesigner', 'Config.pm' ); +open my $out_fh, '>', $config_pm or die "Can't write '$config': $!\n"; +print $out_fh $config; +close $out_fh; + my $tarball = $builder->dist_dir . '.tar.gz'; $builder->add_to_cleanup( $tarball, 'lib/Bio/PrimerDesigner/Config.pm' ); @@ -94,7 +91,7 @@ Options: - -h|--help Show usage + --help Show usage --url The URL to use for remote program access, e.g., http://my.org/cgi-bin/primer_designer.cgi debian/copyright0000644000000000000000000000315412211351171011116 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Bio-PrimerDesigner Upstream-Contact: Sheldon McKay , Ken Youens-Clark Source: https://metacpan.org/release/Bio-PrimerDesigner/ Files: * Copyright: 2003–2009 Sheldon McKay 2003–2009 Ken Youens-Clark License: GPL-3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in ‘/usr/share/common-licenses/GPL-3’. Files: debian/* Copyright: © 2009 Charles Plessy License: Poetic This work ‘as-is’ we provide. No warranty, express or implied. We’ve done our best, to debug and test. Liability for damages denied. . Permission is granted hereby, to copy, share, and modify. Use as is fit, free or for profit. On this notice these rights rely. Comment: The text of this license is © 2005 Alexander E Genaud, see ‘http://genaud.net/2005/10/poetic-license/’. debian/watch0000644000000000000000000000020212207045557010220 0ustar version=3 https://metacpan.org/release/Bio-PrimerDesigner/ .*/Bio-PrimerDesigner-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ debian/source/0000755000000000000000000000000012207045557010475 5ustar debian/source/format0000644000000000000000000000001412207045557011703 0ustar 3.0 (quilt) debian/control0000644000000000000000000000272212207045557010603 0ustar Source: libbio-primerdesigner-perl Maintainer: Debian Perl Group Uploaders: gregor herrmann , Charles Plessy , Jonathan Yu , Ryan Niebur Section: perl Priority: optional Build-Depends: debhelper (>= 8) Build-Depends-Indep: perl, libwww-perl, libclass-base-perl, libreadonly-perl, libtest-pod-perl, libtest-pod-coverage-perl, primer3, ncbi-epcr Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=pkg-perl/packages/libbio-primerdesigner-perl.git Vcs-Git: git://anonscm.debian.org/pkg-perl/packages/libbio-primerdesigner-perl.git Homepage: https://metacpan.org/release/Bio-PrimerDesigner/ Package: libbio-primerdesigner-perl Architecture: all Depends: ${perl:Depends}, ${misc:Depends}, libwww-perl, libclass-base-perl, libreadonly-perl, primer3, ncbi-epcr Description: Perl module to design PCR primers using primer3 and epcr Bio::PrimerDesigner provides a low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. In addition to accessing local installations of primer3 or e-PCR, it also offers the ability to accessing the primer3 binary via a remote server. debian/compat0000644000000000000000000000000212207045557010373 0ustar 8 debian/changelog0000644000000000000000000000642712211353146011047 0ustar libbio-primerdesigner-perl (0.07-3) unstable; urgency=low * Team upload * add patch fixing hash manipulation inside each. Fixes test failures with perl 5.18 (Closes: #711426) -- Damyan Ivanov Tue, 03 Sep 2013 15:30:18 +0300 libbio-primerdesigner-perl (0.07-2) unstable; urgency=low [ Ryan Niebur ] * Email change: Jonathan Yu -> jawnsy@cpan.org * Email change: Ryan Niebur -> ryan@debian.org [ gregor herrmann ] * debian/control: Changed: (build-)depend on perl instead of perl- modules. * Re-wrap long description. * Don't install empty Bio::PrimerDesigner::Config.3pm manpage; thanks lintian. * Remove alternative (build) dependencies that are already satisfied in oldstable. [ Ansgar Burchardt ] * debian/control: Convert Vcs-* fields to Git. [ gregor herrmann ] * debian/control: update {versioned,alternative} (build) dependencies. [ Salvatore Bonaccorso ] * Change search.cpan.org based URIs to metacpan.org based URIs [ gregor herrmann ] * Switch to "3.0 (quilt)" source format. * Add a patch to use Module::Build's args() instead of Getopt::Long. (Closes: #718120) * debian/copyright: switch formatting to Copyright-Format 1.0. * Update debian/rules and remove debian/clean. * Bump debhelper compatibility level to 8. * Declare compliance with Debian Policy 3.9.4. -- gregor herrmann Wed, 07 Aug 2013 17:59:09 +0200 libbio-primerdesigner-perl (0.07-1) unstable; urgency=low * New upstream release (no changes on Linux systems). [ Jonathan Yu ] * Standards-Version 3.8.2 * Added myself to Uploaders. * Do real clean to clean things up (get rid of the generated Makefile) [ Nathan Handler ] * debian/watch: Update to ignore development releases. [ Charles Plessy ] * Refreshed and prettified debian/copyright. * Restored the skipping of the remote.t test in debian/rules after it was factorised using Debhelper’s ”dh” command. [ Ryan Niebur ] * Use --buildsystem=perl_build in debian/rules. * Test if Build is present before calling dh_auto_clean in debian/rules. (Temporary workaround for debhelper bug #539848.) * Add myself to Uploaders -- Charles Plessy Tue, 04 Aug 2009 12:55:56 +0900 libbio-primerdesigner-perl (0.06-1) unstable; urgency=low [ Charles Plessy ] * debian/copyright: show the way to GPLv3, not GPLv2. [ gregor herrmann ] * debian/rules: skip test t/remote.t which tries to connect to somewhere and causes a FBTFS; thanks to Daniel Schepler for the bug report (closes: #526566) * New upstream release. * debian/copyright: update years of upstream copyright. * Set Standards-Version to 3.8.1 (no changes). * Add /me to Uploaders. * debian/control: make the short description a noun phrase. -- gregor herrmann Sat, 02 May 2009 01:38:10 +0200 libbio-primerdesigner-perl (0.05-1) unstable; urgency=low * New upstream release clarifying license. * debian/control: - Build-depend on libtest-pod-perl for automatic tests at build time. -- Charles Plessy Sun, 08 Mar 2009 14:01:27 +0900 libbio-primerdesigner-perl (0.04-1) unstable; urgency=low * Initial Release (Closes: #512718). -- Charles Plessy Thu, 22 Jan 2009 23:50:23 +0900