debian/0000755000000000000000000000000012177410435007172 5ustar debian/watch0000644000000000000000000000037412007654171010226 0ustar version=3 # This tracks the current stable version of bioconductor opts=dversionmangle=s|~dfsg||,downloadurlmangle=s/\.\./packages\/release\/bioc/ \ http://www.bioconductor.org/packages/release/bioc/html/limma.html \ ../src/contrib/limma_(.*).tar.gz debian/README.source0000644000000000000000000000022712007654171011351 0ustar The original upstream sources are repacked using the filter option of git-import-orig, see debian/gbp.conf, debian/copyright and debian/README.Debian. debian/control0000644000000000000000000000216112177410210010564 0ustar Source: r-bioc-limma Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/r-bioc-limma.git Vcs-Git: git://anonscm.debian.org/debian-med/r-bioc-limma.git Homepage: http://bioinf.wehi.edu.au/limma/ XS-Testsuite: autopkgtest Package: r-bioc-limma Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${R:Depends} Description: linear models for microarray data A Bioconductor package for the analysis of gene expression microarray data, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The package includes pre-processing capabilities for two-colour spotted arrays. The differential expression methods apply to all array platforms and treat Affymetrix, single channel and two channel experiments in a unified way. debian/README.test0000644000000000000000000000066512007655131011033 0ustar Notes on how this package is tested. ──────────────────────────────────── After building on the maintainer's computer, this package was tested with autopkgtest (see http://dep.debian.net/deps/dep8/), using the following commands. sudo adt-run --no-built-binaries foo.dsc --- adt-virt-null -- Charles Plessy Mon, 06 Aug 2012 14:46:57 +0900 debian/changelog0000644000000000000000000000532012177410370011042 0ustar r-bioc-limma (3.16.7~dfsg-1) unstable; urgency=low be4e6a5 Imported Upstream version 3.16.7~dfsg 5d10f8d Normalised VCS URLs. 3ed3572 Signal the presence of autopkgtest suite with a XS-Testsuite field. -- Charles Plessy Sun, 04 Aug 2013 17:28:41 +0900 r-bioc-limma (3.16.3~dfsg-1) unstable; urgency=low [ Charles Plessy ] ff8c6db Imported Upstream version 3.12.1~dfsg b4f097e Effective license is GPL-2, without the '+', as R is GPL-2. [ Andreas Tille ] * Imported new upstream version 3.16.3~dfsg * debian/control - added myself to Uploaders - Removed DM-Upload-Allowed - Standards-Version: 3.9.4 (no changes needed) - Debhelper 9 - Fake normalisation as it is done by `cme fix dpkg-control` (the command did actually no change - the control file was brought into shape manually) - Removed versioned dependency of r-base-dev * debian/copyright: - s/Removed/Files-Excluded/ to comply with the suggested format that might be processed by uscan as alternative method to filter-pristine-tar - checked new upstream version and bumped version number - Add years to Copyright fields * debian/rules: Remove executable flag from doc files * debian/source/format: Add explicit source format specification -- Andreas Tille Thu, 16 May 2013 15:16:13 +0200 r-bioc-limma (3.12.0~dfsg-1) unstable; urgency=low [ Charles Plessy ] 2d3420e Imported Upstream version 3.12.0~dfsg 4bbb8e4 Document LIMMA's copyright as a whole. [ Andreas Tille ] 8a61a4c Obtain references from inst/CITATION -- Charles Plessy Thu, 12 Apr 2012 11:40:40 +0900 r-bioc-limma (3.10.3-1) unstable; urgency=low 0ddb00d New Upstream version. [ Carlos Borroto ] afe6f31 Fix for watch file. [ Charles Plessy ] 7ef2264 Removing inst/doc/usersguide.pdf, as its source is missing. 4713d97 Obtain ${R:Depends} through r-base-dev. 756a1da Conforms to Policy 3.9.3. 68495e3 Renamed debian/upstream-metadata.yaml to debian/upstream. 2db0d3d Verbose Debhelper. -- Charles Plessy Wed, 07 Mar 2012 13:13:47 +0900 r-bioc-limma (3.10.0-1) unstable; urgency=low eebb062 New upstream release (Bioconductor 2.9). c1a8767 Include 7 digits of the commit ID in the changelog entry. -- Charles Plessy Fri, 04 Nov 2011 13:35:49 +0900 r-bioc-limma (3.8.3-1) unstable; urgency=low 7b5440e New upstream release. e891bb6 Corrected VCS-Git url. -- Charles Plessy Sun, 14 Aug 2011 20:30:21 +0900 r-bioc-limma (3.8.2-1) unstable; urgency=low * Initial release (closes: #628548). -- Charles Plessy Thu, 02 Jun 2011 13:07:58 +0900 debian/docs0000644000000000000000000000003112007655344010041 0ustar tests debian/README.test debian/copyright0000644000000000000000000000310112177407175011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://www.bioconductor.org/packages/release/bioc/src/contrib/limma_3.16.7.tar.gz inst/doc/usersguide.pdf is not accompanied by its source, and therefore removed in the “dfsg” version. Comment: licensing discussed on https://stat.ethz.ch/pipermail/bioc-devel/2011-May/002620.html License: GPL-2 LIMMA is LGPL-2+ code, and depends on R (GPL-2) and the GNU C library (LGPL-2.1+). Taken as a whole, its license is effectively GPL-2, plus perhaps some additional BSD-like requirements depending on what it uses from the GNU C library. Files-Excluded: inst/doc/usersguide.pdf Files: * Copyright: 2005-2013 Gordon Smyth License: LGPL-2+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This library 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 Library General Public License for more details. . You should have received a copy of the GNU Library General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Comment: On Debian systems, a copy of the GNU Library General Public version 2 is available in ‘/usr/share/common-licenses/LGPL-2’. debian/upstream0000644000000000000000000000077512007654171010765 0ustar Archive: Bioconductor Homepage: http://bioinf.wehi.edu.au/limma/ Name: limma Reference: Title: "Limma: linear models for microarray data" Author: Gordon K. Smyth In: Bioinformatics and Computational Biology Solutions using R and Bioconductor Editor: R. Gentleman and V. Carey and S. Dudoit and R. Irizarry, W. Huber Publisher: Springer Address: New York Year: 2005 Pages: 397--420 URL: http://bioinf.wehi.edu.au/limma/ eprint: http://www.statsci.org/smyth/pubs/limma-biocbook-reprint.pdf debian/tests/0000755000000000000000000000000012007660760010334 5ustar debian/tests/control0000644000000000000000000000002012007651065011725 0ustar Tests: upstream debian/tests/upstream0000755000000000000000000000053012007660760012120 0ustar #!/bin/sh -e TEMPORARY_DIR=$(mktemp -d) cd $TEMPORARY_DIR cp /usr/share/doc/r-bioc-limma/tests/* . for test in *R.gz do zcat ${test} > `basename ${test} .gz` R CMD BATCH `basename ${test} .gz` R CMD Rdiff `basename ${test} .gz`out.save* `basename ${test} .gz`out rm `basename ${test} .gz`out .RData done cd - rm -rf $TEMPORARY_DIR debian/gbp.conf0000644000000000000000000000052412007654171010611 0ustar # This package is managed with git-buildpackage. [DEFAULT] # use pristine-tar: pristine-tar = True [git-import-orig] # import filter: filter = ['inst/doc/usersguide.pdf'] # filter out files from tarball passed to pristine tar: filter-pristine-tar = True [git-dch] # include 7 digits of the commit id in the changelog enty: id-length = 7 debian/README.Debian0000644000000000000000000000041012007654171011225 0ustar The file inst/doc/usersguide.pdf has been removed from the original upstream package, as it was not accompanied by its source. It can be downloaded at the following URL. http://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf debian/rules0000755000000000000000000000047712177405476010273 0ustar #!/usr/bin/make -f export DH_VERBOSE=1 debRreposname = bioc include /usr/share/R/debian/r-cran.mk DEB_INSTALL_CHANGELOGS_ALL = inst/doc/changelog.txt install/$(package):: chmod 644 debian/$(package)/usr/lib/R/site-library/$(cranName)/CITATION chmod 644 debian/$(package)/usr/lib/R/site-library/$(cranName)/doc/* debian/source/0000755000000000000000000000000012177405476010503 5ustar debian/source/format0000644000000000000000000000001412177405476011711 0ustar 3.0 (quilt) debian/compat0000644000000000000000000000000212177405476010401 0ustar 9