debian/0000755000000000000000000000000012232223723007164 5ustar debian/control0000644000000000000000000000231412232220052010557 0ustar Source: libbio-mage-utils-perl Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/libbio-mage-utils-perl/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/libbio-mage-utils-perl/trunk/ Homepage: http://mged.sourceforge.net/ Package: libbio-mage-utils-perl Architecture: all Section: perl Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}, libtie-ixhash-perl Suggests: libbio-mage-perl Description: Extra modules for classes in the MAGE package: MAGE MAGE-TAB (MicroArray Gene Expression Tabular) format is a standard from the Microarray Gene Expression Data Society (MGED). This package contains Perl modules in the Bio::MAGE hierarchy to manipulate MIAME-compliant (Minimum Information About a Microarray Experiment) records of microarray ("DNA chips") experiments. . Bio-MAGE-Utils contains extra modules for handling MAGE XML and MGED ontology, as well as SQL utilities. debian/rules0000755000000000000000000000003712232214470010243 0ustar #!/usr/bin/make -f %: dh $@ debian/watch0000644000000000000000000000007212214301263010210 0ustar version=3 http://sf.net/mged/Bio-MAGE-Utils-(.*)\.tar\.gz debian/copyright0000644000000000000000000000505012232223621011114 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Bio-MAGE-Utils Upstream-Contact: The MAGE-Perl Hackers Jason E. Stewart Source: http://downloads.sourceforge.net/mged/Bio-MAGE-Utils-20030502.0.tar.gz Files: * Copyright: © 2001-2002 The MicroArray Gene Expression Database Society (MGED) © 2001-2002 Rosetta Inpharmatics License: MIT Comment: Upstream author Jason Stewart confirmed me that the files with no license statements have the same license as Bio::MAGE, MIT/X11. -- Charles Plessy Files: MAGE/XML/Handler/ObjectHandler/SQL.pm MAGE/XML/Handler/ObjectHandlerI.pm Copyright: © 2003 Allen Day License: Perl You may distribute this module under the same terms as perl itself . License: Perl . This program is free software; you can redistribute it and/or modify it under the terms of either: . a) the GNU General Public License as published by the Free Software Foundation; either version 1, or (at your option) any later version, or . b) the "Artistic License" which comes with Perl. . On Debian GNU/Linux systems, the complete text of the latest version of the GNU General Public License can be found in ‘/usr/share/common-licenses/GPL’ and the Artistic Licence in ‘/usr/share/common-licenses/Artistic’. Files: debian/* Copyright: © 2008–2010 Charles Plessy © 2013 Andreas Tille License: MIT License: MIT Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. debian/source/0000755000000000000000000000000012214301046010457 5ustar debian/source/format0000644000000000000000000000001412214301046011665 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000040612214301263011221 0ustar libbio-mage-utils-perl for Debian --------------------------------- Modules are moved from Bio::MAGE::Utils to Bio::MAGE in order to make them functional on a default Debian installation. -- Charles Plessy Wed, 26 May 2010 20:54:49 +0900 debian/changelog0000644000000000000000000000120012232223723011027 0ustar libbio-mage-utils-perl (20030502.0-2) unstable; urgency=low * debian/source/format: 3.0 (quilt) * debian/control: - added myself to Uploaders - cme fix dpkg-control - canonical Vcs fields - debhelper 9 - drop quilt, cdbs from Build-Depends * debian/README.source: deleted because not up to date / not needed * debian/rules: cdbs -> dh * debian/copyright: DEP5 -- Andreas Tille Thu, 24 Oct 2013 15:21:43 +0200 libbio-mage-utils-perl (20030502.0-1) unstable; urgency=low * Initial release (Closes: #476202) -- Charles Plessy Wed, 26 May 2010 20:40:26 +0900 debian/patches/0000755000000000000000000000000012232217661010617 5ustar debian/patches/series0000644000000000000000000000002512232217057012030 0ustar move-MAGE-root.patch debian/patches/move-MAGE-root.patch0000644000000000000000000000123112232217661014273 0ustar Description: Move from Bio::MAGE::Utils to Bio::MAGE. This patch is necessary for the installation process to complete and for third-party applications to function. Author: Charles Plessy Forwarded: mged-mage-perl@lists.sourceforge.net --- a/Makefile.PL +++ b/Makefile.PL @@ -2,7 +2,7 @@ use ExtUtils::MakeMaker; # See lib/ExtUtils/MakeMaker.pm for details of how to influence # the contents of the Makefile that is written. WriteMakefile( - 'NAME' => 'Bio::MAGE::Utils', + 'NAME' => 'Bio::MAGE', 'VERSION' => '20030502.0', 'PREREQ_PM' => {Tie::IxHash=>1.21}, ($] >= 5.005 ? debian/compat0000644000000000000000000000000212232217474010370 0ustar 9