diff -Nru bioperl-1.6.901/debian/changelog bioperl-1.6.901/debian/changelog --- bioperl-1.6.901/debian/changelog 2011-12-14 08:11:45.000000000 +0000 +++ bioperl-1.6.901/debian/changelog 2012-03-02 12:01:49.000000000 +0000 @@ -1,3 +1,16 @@ +bioperl (1.6.901-3) unstable; urgency=low + + * Team upload. + [ Olivier Sallou ] + + add patch fix_berkeleydb3_temp_file_creation (Closes: #661793). + Fixed upstream for next release. + * debian/control: update Standards version + * debian/copyright: update Format to latest officiel URL v1.0 + * debian/patches/fix_examples_perl_location: fix wrong perl location + * debian/rules: fix file access rights in dh_install + + -- Olivier Sallou Fri, 02 Mar 2012 11:10:36 +0100 + bioperl (1.6.901-2) unstable; urgency=low [ Luca Capello ] diff -Nru bioperl-1.6.901/debian/changelog_ bioperl-1.6.901/debian/changelog_ --- bioperl-1.6.901/debian/changelog_ 2011-12-14 08:04:29.000000000 +0000 +++ bioperl-1.6.901/debian/changelog_ 1970-01-01 00:00:00.000000000 +0000 @@ -1,276 +0,0 @@ -bioperl (1.6.901-2) unstable; urgency=low - - * debian/source/format: 3.0 (quilt) - * - - -- Andreas Tille Wed, 14 Dec 2011 09:04:08 +0100 - -bioperl (1.6.901-1) unstable; urgency=low - - * New upstream release. - * Point debian/watch to search.cpan.org. - * Build using dh and overrides: - - Use Debhelper 8 (debian/rules, debian/control). - - Simplified debian/rules. - * Split into libbio-perl-perl, as discussed with the Debian Perl team. - (debian/control, debian/bioperl.install, debian libbio-perl-perl.install) - * debian/control: - - Incremented Standards-Version to reflect conformance with Policy 3.9.2. - No other changes needed. - - Vcs-Browser URL made redirectable to viewvc. - - Removed useless ‘svn’ in the Vcs-Svn URL. - - -- Charles Plessy Fri, 17 Jun 2011 13:51:18 +0900 - -bioperl (1.6.1-2) unstable; urgency=low - - * Removed bibliographic information from the long description - (debian/control). - * Incremented Standards-Version to reflect conformance with Policy 3.8.4 - (debian/control, no changes needed). - * Build-depends on libxml-sax-expatxs-perl to avoid downloading DTDs during - the tests and therefore fail when network is not available - (debian/control, Closes: #562442). - * Depend on the ${misc:Depends} substvar (debian/control). - - -- Charles Plessy Fri, 26 Feb 2010 23:52:23 +0900 - -bioperl (1.6.1-1) unstable; urgency=low - - * New upstream release with new features and many corrections in the - test suite (Closes: #533976). - * debian/rules: trigger network tests with DEB_MAINTAINER_MODE. - * debian/control: - - Build-depend on perl-modules >= 5.10.1 to have ExtUtils::Manifest 1.52 or - higher, and on libtest-pod-perl. - - Added liblist-moreutils-perl, libspreadsheet-writeexcel-perl, - libsvg-perl, and libxml-simple-perl, libdbd-pg-perl, libdbd-mysql-perl, - libdbd-sqlite3-perl to build and package dependencies (needed by some - components of Bioperl, and therefore for the tests). - - -- Charles Plessy Wed, 30 Sep 2009 18:56:42 +0900 - -bioperl (1.6.0-3) unstable; urgency=low - - [ David Paleino ] - * Removed myself from Uploaders - - [ Charles Plessy ] - * debian/control: - - Added libdata-stag-perl in bioperl’s Depends field, since it is - required in Build.PL. - - Added libxml-simple-perl in bioperl’s Recommends and Build-Depends - fields, since they are listed in DEPENDENCIES. - - Incremented Standards-Version to reflect conformance with Policy 3.8.3 - (no changes needed). - * Collected some informations in debian/upstream-metadata.yaml. - - -- Charles Plessy Fri, 18 Sep 2009 20:23:51 +0900 - -bioperl (1.6.0-2) unstable; urgency=low - - * Removed patch system (not used): - - removed instructions in debian/rules; - - removed quilt from Build-Depends in debian/control. - * Re-enabled tests: - - uncommented test command in debian/rules; - - uncommented previously missing build-dependencies in debian/control. - - Re-enabled tests and uncommented build-dependencies accordingly. - * Removed libmodule-build-perl and libtest-harness-perl from - Build-Depends-Indep (provided by perl-modules). - * Better cleaning of empty directories using find -type d -empty -delete - instead of rmdir in debian/rules (LP: #324001). - - -- Charles Plessy Tue, 10 Mar 2009 07:19:11 +0100 - -bioperl (1.6.0-1) experimental; urgency=low - - [ Charles Plessy ] - * debian/control - - Updated dependencies according to the new upstream release. - - Added the CPAN dependencies of BioPerl to Build-Depends-Indep in order to - run the tests at build time. - - Added bioperl-run to the recommended packages. - - Updated my email address. - - Uses Debhelper 7 (debian/compat modified accordingly). - * debian/patches: removed as not needed (no downloads by default). - * debian/rules: - - Uses Build.PL instead of Makefile.PL. - - Tests disabled for the experimental upload: not all dependencies are - available yet. - * debian/README.{Debian,source}: removed as not needed anymore - * debian/watch: BioPerl is now mixed case. - - [ David Paleino ] - * New upstream stable release: - - fixes Bio::AlignIO::next_aln bug (Closes: #266921). - - New modules, deprecated modules,… please consult Upstream documents in - /usr/share/doc/bioperl. - * debian/control: - - fields values rewrapped to easily spot diffs in commit mails - - dropped B-D-I versioning on perl, since Etch already has a greater - version - - Standards-Version bumped to 3.8.0 (no changes needed). - - -- Charles Plessy Mon, 26 Jan 2009 12:58:28 +0900 - -bioperl (1.5.2.102-3) unstable; urgency=low - - * debian/control: - - Removed MIA Matt Hope (dopey) from the Uploaders field. - Thank you for your work, Matt. I hope you are doing well. - - Downgraded some recommended package to the 'Suggests' priority, - according to the following discussion on Upstream's mail list. - http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html - (Closes: #448890) - * debian/copyright converted to machine-readable format. - - -- Charles Plessy Tue, 18 Mar 2008 14:44:57 +0900 - -bioperl (1.5.2.102-2) unstable; urgency=low - - [ Steffen Moeller ] - * Added reference to libsvg-graph-perl (Closes: #342475). - - [ Nelson A. de Oliveira ] - * debian/control: - - Removed the XS- prefix from Vcs-Browser and Vcs-Svn - - Moved debhelper and quilt from Build-Depends-Indep to Build-Depends - * Updated debian/copyright - - [ David Paleino ] - * debian/control: - - updated Recommends (libpostscript-textblock-perl won't exist - - the package will be named libpostscript-perl) - - fields wrapped at around 80 columns - - added myself to Uploaders - - added libio-string-perl to Build-Depends-Indep (Closes: #453923) - - fixed Vcs-* fields - - removed XS- from DM-Upload-Allowed - * debian/changelog: - - fixing incorrect first line (leading tab) - * debian/rules updated - * debian/dirs removed (passing arguments to dh_installdirs directly) - - -- David Paleino Wed, 06 Feb 2008 12:01:15 +0100 - -bioperl (1.5.2.102-1) unstable; urgency=low - - * Developer release. - * Upgraded source package to debhelper 5 and standards-version 3.7.2. - * Added libmodule-build-perl and libtest-harness-perl to - build-depends-indep. - * Disabled automatic CPAN download. - * Using quilt instead of .diff.gz to manage modifications. - * Updated Recommends list for the binary package. - * Moved the "production-quality" scripts to /usr/bin/. - * New maintainer: Debian-Med packaging team mailing list. - * New uploaders: Charles Plessy and Steffen Moeller. - * Updated Depends, Recommends and Suggests. - * Imported in Debian-Med's SVN repository on Alioth. - * Executing the regression tests during package building. - * Moved the Homepage: field out from the package's description. - * Updated watch file. - - -- Charles Plessy Fri, 21 Sep 2007 22:52:22 +0900 - -bioperl (1.4-1) unstable; urgency=low - - * New upstream release - * Examples and working code are installed by default to usr/bin, - this has been moved to usr/share/doc/bioperl/bin - - -- Matt Hope Sun, 18 Apr 2004 14:24:11 +1000 - -bioperl (1.2.1-2) unstable; urgency=low - - * Updated dependencies to libgd-gd2-perl - (Closes: Bug#192210) - * Same maintainer, different email address - - -- Matt Hope Mon, 30 Jun 2003 23:40:59 +1000 - -bioperl (1.2.1-1) unstable; urgency=low - - * New upstream release - * Added more Depends/Recommends. - * Added Depend: libio-string-perl - (Closes: Bug#188395) - - -- Matt Hope Sat, 3 May 2003 01:21:54 +1000 - -bioperl (1.2-1) unstable; urgency=low - - * New upstream release - - -- Matt Hope Fri, 25 Apr 2003 12:30:10 +1000 - -bioperl (1.0.2-1) unstable; urgency=low - - * *Another* new upstream release. - - -- Matt Hope Wed, 17 Jul 2002 09:58:09 +1000 - -bioperl (1.0.1-1) unstable; urgency=low - - * New upstream release - - -- Matt Hope Sat, 29 Jun 2002 22:35:08 +1000 - -bioperl (1.0-1) unstable; urgency=low - - * New upstream release - - -- Matt Hope Wed, 20 Mar 2002 01:16:30 +1100 - -bioperl (0.7.2-1) unstable; urgency=low - - * New upstream release. - * Adopted by new maintainer; closes: #100208 - * Fixed lintian errors. - - -- Matt Hope Thu, 22 Nov 2001 19:31:26 +1100 - -bioperl (0.7.1-1) unstable; urgency=low - - * Maintainer set to Debian QA Group . - * New upstream release. - - -- Adrian Bunk Fri, 24 Aug 2001 20:47:57 +0200 - -bioperl (0.7.0-1) unstable; urgency=low - - * New upstream release; closes: #44245 - - -- Dr. Guenter Bechly Sat, 5 May 2001 18:35:44 +0200 - -bioperl (0.05.1-3) unstable; urgency=low - - * Fixed compliance with perl policy; closes: #95880, #95418 - - -- Dr. Guenter Bechly Tue, 1 May 2001 08:13:09 +0200 - -bioperl (0.05.1-2) unstable; urgency=low - - * Adopted by new maintainer; closes: #92806 - * Updated to latest standards version and added Build-Depends (changed - control, copyright, dirs, docs, and rules); - closes: #70154, #91121, #91397 - * Fixed some lintian errors in rules. - * Moved package to section non-free/science, because it is a tool that - is exclusively useful for molecular biologists. - - -- Dr. Guenter Bechly Fri, 20 Apr 2001 19:48:05 +0200 - -bioperl (0.05.1-1) unstable; urgency=low - - * Complies with the new Perl policy. Closes #40564 - * New upstream release - - -- Stephane Bortzmeyer Wed, 7 Jul 1999 14:49:16 +0200 - -bioperl (0.05-1) unstable; urgency=low - - * Initial Release. - - -- Stephane Bortzmeyer Wed, 19 May 1999 11:35:30 +0200 diff -Nru bioperl-1.6.901/debian/control bioperl-1.6.901/debian/control --- bioperl-1.6.901/debian/control 2011-12-14 08:11:39.000000000 +0000 +++ bioperl-1.6.901/debian/control 2012-03-02 11:33:26.000000000 +0000 @@ -47,7 +47,7 @@ libwww-perl, # Needed to avoid downloading DTDs during the tests and therefore fail when network is not available: libxml-sax-expatxs-perl -Standards-Version: 3.9.2 +Standards-Version: 3.9.3 Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/bioperl/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bioperl/trunk/ Homepage: http://www.bioperl.org/ diff -Nru bioperl-1.6.901/debian/copyright bioperl-1.6.901/debian/copyright --- bioperl-1.6.901/debian/copyright 2011-12-14 07:53:07.000000000 +0000 +++ bioperl-1.6.901/debian/copyright 2012-03-02 11:31:26.000000000 +0000 @@ -1,4 +1,4 @@ -Format: http://dep.debian.net/deps/dep5/ +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.901.tar.gz Files: * diff -Nru bioperl-1.6.901/debian/patches/fix_berkeleydb3_temp_file_creation bioperl-1.6.901/debian/patches/fix_berkeleydb3_temp_file_creation --- bioperl-1.6.901/debian/patches/fix_berkeleydb3_temp_file_creation 1970-01-01 00:00:00.000000000 +0000 +++ bioperl-1.6.901/debian/patches/fix_berkeleydb3_temp_file_creation 2012-03-02 10:22:48.000000000 +0000 @@ -0,0 +1,17 @@ +Subject: wrong order in file creation +Description: tie operation has flags and mode in the wrong order. + Fixed upstream with commit 2b0daf196e0f2acf373c2bc8f0bf2449c36edf40. + Patch should be removed with next upstream release. +Author: Olivier Sallou new; + $numeric_cmp->{compare} = sub { $_[0] <=> $_[1] }; + $numeric_cmp->{flags} = R_DUP; +- my $s = tie %sort,'DB_File',$name,0666,O_CREAT|O_RDWR,$numeric_cmp ++ my $s = tie %sort,'DB_File',$name,O_CREAT|O_RDWR,0666,$numeric_cmp + or $self->throw("Couldn't create temporary file for sorting: $!"); + + my $index = $self->index_db('locations'); diff -Nru bioperl-1.6.901/debian/patches/fix_examples_perl_location bioperl-1.6.901/debian/patches/fix_examples_perl_location --- bioperl-1.6.901/debian/patches/fix_examples_perl_location 1970-01-01 00:00:00.000000000 +0000 +++ bioperl-1.6.901/debian/patches/fix_examples_perl_location 2012-03-02 11:59:31.000000000 +0000 @@ -0,0 +1,60 @@ +Subject: fix perl location +Description: wrong shebang perl location +Author: Olivier Sallou +Last-Updated: 02/03/2012 +--- a/examples/db/getGenBank.pl ++++ b/examples/db/getGenBank.pl +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # How to retrieve GenBank entries over the Web + # +--- a/examples/db/get_seqs.pl ++++ b/examples/db/get_seqs.pl +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + use strict; + use vars qw($USAGE); + use Carp; +--- a/examples/generate_random_seq.pl ++++ b/examples/generate_random_seq.pl +@@ -1,4 +1,4 @@ +-#!/bin/perl ++#!/usr/bin/perl + use strict; + use vars qw($USAGE); + +--- a/examples/searchio/psiblast_features.pl ++++ b/examples/searchio/psiblast_features.pl +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + + # Example usage of a SearchIO::psiblast parser of traditional format Blast + # and PSI-Blast reports. +--- a/examples/structure/structure-io.pl ++++ b/examples/structure/structure-io.pl +@@ -1,4 +1,4 @@ +-#!/bin/perl ++#!/usr/bin/perl + # Getting Entry, Chain, Residue, and Atom objects given a PDB file + + use Bio::Structure::IO; +--- a/examples/tk/hitdisplay.pl ++++ b/examples/tk/hitdisplay.pl +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + # + # PROGRAM : hitdisplay.pl + # PURPOSE : Demonstrate Bio::Tk::HitDisplay +--- a/examples/tools/gb_to_gff.pl ++++ b/examples/tools/gb_to_gff.pl +@@ -1,4 +1,4 @@ +-#!/usr/local/bin/perl ++#!/usr/bin/perl + use strict; + + use Bio::Tools::GFF; diff -Nru bioperl-1.6.901/debian/patches/series bioperl-1.6.901/debian/patches/series --- bioperl-1.6.901/debian/patches/series 1970-01-01 00:00:00.000000000 +0000 +++ bioperl-1.6.901/debian/patches/series 2012-03-02 11:56:10.000000000 +0000 @@ -0,0 +1,2 @@ +fix_examples_perl_location +fix_berkeleydb3_temp_file_creation diff -Nru bioperl-1.6.901/debian/rules bioperl-1.6.901/debian/rules --- bioperl-1.6.901/debian/rules 2011-12-14 07:53:07.000000000 +0000 +++ bioperl-1.6.901/debian/rules 2012-03-02 12:15:12.000000000 +0000 @@ -19,6 +19,7 @@ # prename is the rename utility written in perl usually available as /usr/bin/rename in Debian. prename s/.pl$$// debian/bioperl/usr/bin/*pl prename s/.pl.1p$$/.1p/ debian/bioperl/usr/share/man/man1/*1p + chmod 644 debian/libbio-perl-perl/usr/share/perl5/Bio/DB/HIV/lanl-schema.xml override_dh_installchangelogs: dh_installchangelogs Changes diff -Nru bioperl-1.6.901/debian/upstream bioperl-1.6.901/debian/upstream --- bioperl-1.6.901/debian/upstream 1970-01-01 00:00:00.000000000 +0000 +++ bioperl-1.6.901/debian/upstream 2012-03-02 10:09:21.000000000 +0000 @@ -0,0 +1,20 @@ +Bug-Database: https://redmine.open-bio.org/projects/bioperl +Contact: Bioperl developers +Reference-DOI: 10.1101/gr.361602 +Homepage: http://www.bioperl.org/ +Name: BioPerl +Reference-PMID: 12368254 +Reference: + author: > + J.E. Stajich and D. Block and K. Boulez and S.E. Brenner + and S.A. Chervitz and C. Dagdigian and G. Fuellen and J.G. Gilbert + and I. Korf and H. Lapp and H. Lehvaslaiho and C. Matsalla and + C.J. Mungall and B.I. Osborne and M.R. Pocock and P. Schattner and + M. Senger and L.D. Stein and E. Stupka and M.D. Wilkinson and E. Birney + title: "The Bioperl toolkit: Perl modules for the life sciences." + journal: Genome Res. + year: 2002 + volume: 12 + number: 10 + pages: 1611-1618 +Repository: https://github.com/bioperl/bioperl-live diff -Nru bioperl-1.6.901/debian/upstream-metadata.yaml bioperl-1.6.901/debian/upstream-metadata.yaml --- bioperl-1.6.901/debian/upstream-metadata.yaml 2011-12-14 07:53:07.000000000 +0000 +++ bioperl-1.6.901/debian/upstream-metadata.yaml 1970-01-01 00:00:00.000000000 +0000 @@ -1,20 +0,0 @@ -Bug-Database: https://redmine.open-bio.org/projects/bioperl -Contact: Bioperl developers -DOI: 10.1101/gr.361602 -Homepage: http://www.bioperl.org/ -Name: BioPerl -PMID: 12368254 -Reference: - author: > - J.E. Stajich and D. Block and K. Boulez and S.E. Brenner - and S.A. Chervitz and C. Dagdigian and G. Fuellen and J.G. Gilbert - and I. Korf and H. Lapp and H. Lehvaslaiho and C. Matsalla and - C.J. Mungall and B.I. Osborne and M.R. Pocock and P. Schattner and - M. Senger and L.D. Stein and E. Stupka and M.D. Wilkinson and E. Birney - title: "The Bioperl toolkit: Perl modules for the life sciences." - journal: Genome Res. - year: 2002 - volume: 12 - number: 10 - pages: 1611-1618 -Repository: https://github.com/bioperl/bioperl-live