debian/0000755000000000000000000000000012263212152007162 5ustar debian/gbp.conf0000644000000000000000000000055712263212152010610 0ustar # This package is managed with git-buildpackage and git-buildpackage. [DEFAULT] # use pristine-tar: pristine-tar = True [git-import-orig] # import filter: filter = ['inst/doc/edgeRUsersGuide.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 entry: id-length = 7 debian/control0000644000000000000000000000223512263212152010567 0ustar Source: r-bioc-edger Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Section: gnu-r XS-Testsuite: autopkgtest Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-bioc-limma Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/r-bioc-edger.git Vcs-Git: git://anonscm.debian.org/debian-med/r-bioc-edger.git Homepage: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html Package: r-bioc-edger Architecture: any Depends: ${R:Depends}, r-bioc-limma, ${misc:Depends}, ${shlibs:Depends}, r-cran-statmod Suggests: r-cran-mass Description: Empirical analysis of digital gene expression data in R Bioconductor package for differential expression analysis of whole transcriptome sequencing (RNA-seq) and digital gene expression profiles with biological replication. It uses empirical Bayes estimation and exact tests based on the negative binomial distribution. It is also useful for differential signal analysis with other types of genome-scale count data. debian/README.source0000644000000000000000000000022712263212152011342 0ustar The original upstream sources are repacked using the filter option of git-import-orig, see debian/gbp.conf, debian/copyright and debian/README.Debian. debian/rules0000755000000000000000000000033412263212152010242 0ustar #!/usr/bin/make -f export DH_VERBOSE=1 debRreposname = bioc DEB_DH_BUILDDEB_ARGS = -- -Z xz include /usr/share/R/debian/r-cran.mk install/$(package):: chmod 644 debian/$(package)/usr/lib/R/site-library/edgeR/doc/* debian/watch0000644000000000000000000000034712263212152010217 0ustar version=3 # This tracks the current stable version of edgeR opts="dversionmangle=s|~dfsg||,downloadurlmangle=s|\.\.|packages/release/bioc|" \ http://www.bioconductor.org/packages/release/bioc/html/edgeR.html .*/edgeR_(.*).tar.gz debian/upstream0000644000000000000000000000267612263212152010760 0ustar Archive: Bioconductor Bioconductor: edgeR Contact: Mark Robinson , Davis McCarthy , Gordon Smyth Download: http://bioconductor.org/packages/release/bioc/src/contrib/ Homepage: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html Name: edgeR Reference: - author: Mark D. Robinson and Davis J. McCarthy and Gordon K. Smyth title: "edgeR: a Bioconductor package for differential expression analysis of digital gene expression data" journal: Bioinformatics volume: 26, pages: 139-140 year: 2010 DOI: 10.1093/bioinformatics/btp616 PMID: 19910308 URL: http://bioinformatics.oxfordjournals.org/content/26/1/139 eprint: http://bioinformatics.oxfordjournals.org/content/26/1/139.full.pdf+html - author: Mark D. Robinson and Gordon K. Smyth title: Moderated statistical tests for assessing differences in tag abundance journal: Bioinformatics volume: 23 number: 21 pages: 2881-2887 doi: 10.1093/bioinformatics/btm453 PMID: 17881408 year: 2007 URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2881 eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2881.pdf Watch: | version=3 # This tracks the current stable version of edgeR opts="dversionmangle=s|~dfsg||,downloadurlmangle=s|\.\.|packages/release/bioc|" \ http://www.bioconductor.org/packages/release/bioc/html/edgeR.html .*/edgeR_(.*).tar.gz debian/copyright0000644000000000000000000000254112263212152011117 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://www.bioconductor.org/packages/release/bioc/src/contrib/edgeR_3.4.0.tar.gz Comment: inst/doc/edgeRUsersGuide.pdf is not accompanied by its source. License: GPL-2 edgeR is GPL-2+, but depend on LIMMA (LGPL-2+) and R (GPL-2), so its effective license is GPL-2. Files-Excluded: inst/doc/edgeRUsersGuide.pdf Files: * Copyright: 2007-2013 Mark Robinson , Davis McCarthy , Gordon Smyth License: GPL-2+ 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 2 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, 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 General Public version 2 is available in ‘/usr/share/common-licenses/GPL-2’. debian/source/0000755000000000000000000000000012263212152010462 5ustar debian/source/format0000644000000000000000000000001412263212152011670 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000042212263212152011221 0ustar The file inst/doc/edgeRUsersGuide.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/edgeR/inst/doc/edgeRUsersGuide.pdf debian/README.test0000644000000000000000000000036312263212152011022 0ustar Notes on how this package is tested. ──────────────────────────────────── sh debian/tests/upstream -- Andreas Tille Sat, 07 Dec 2013 10:13:45 +0100 debian/changelog0000644000000000000000000001035712263212152011042 0ustar r-bioc-edger (3.4.2+dfsg-2) unstable; urgency=medium [ Martin Pitt ] * debian/tests/control: Re-add @ test dependency which got dropped in the previous upload. * debian/tests/upstream: Run edger tests, not limma (copy&paste error). (Closes: #727695) [ Andreas Tille ] * Standards-Version: 3.9.5 -- Andreas Tille Wed, 08 Jan 2014 10:01:36 +0100 r-bioc-edger (3.4.2+dfsg-1) unstable; urgency=low [ Charles Plessy ] 1d47587 Removed myself from Uploaders. [ Andreas Tille ] * New upstream version * debian/control: - Add Depends: r-cran-statmod to enable running test successfully - Add r-cran-mass to Depends of autopkgtest Closes: #727695 - XS-Testsuite: autopkgtest * debian/README.test: Describe how to run testsuite -- Andreas Tille Sun, 08 Dec 2013 18:24:10 +0100 r-bioc-edger (3.2.4~dfsg-1) unstable; urgency=low 543a589 Imported Upstream version 3.2.4~dfsg 846128f Normalised VCS URLs. 735a2e9 Signal autopkgtest suite with XS-Testsuite field. a429231 Correct the autopkgtest as the test files are compressed. -- Charles Plessy Mon, 05 Aug 2013 19:26:22 +0900 r-bioc-edger (3.2.3~dfsg-1) unstable; urgency=low [ Charles Plessy ] 74f1a5f Imported Upstream version 2.6.10~dfsg d2d70ab Corrected VCS URLs. 44c9d4e Regression tests for autopkgtest. [ Andreas Tille ] * Imported new upstream version 3.2.3~dfsg * debian/control - Added myself as Uploader - Add ${shlibs:Depends} to ensure dependency from libc - Removed DM-Upload-Allowed - Standards-Version: 3.9.4 (no changes needed) - Debhelper 9 - normalised format - Removed unneeded Pre-Depends: dpkg (>= 1.15.6) - Removed versioned dependency of r-base-dev - Package is "Architecture: any" (rather than all) * debian/source/format: Add explicit source format specification * debian/copyright: - Update Source location - s/Removed/Files-Excluded/ to comply with the suggested format that might be processed by uscan as alternative method to filter-pristine-tar - Add years to Copyright field * debian/upstream: inst/CITATION asks for citing this more recent paper that is now on top of debian/upstream * debian/rules: remove executable flag from installed documentation -- Andreas Tille Fri, 17 May 2013 14:36:51 +0200 r-bioc-edger (2.6.1~dfsg-1) unstable; urgency=low 43f7a83 Imported Upstream version 2.6.1~dfsg -- Charles Plessy Tue, 01 May 2012 12:58:10 +0900 r-bioc-edger (2.6.0~dfsg-1) unstable; urgency=low 732665c Imported Upstream version 2.6.0~dfsg 3f0af26 Summarised the effective license of edgeR once it is loaded in R. -- Charles Plessy Thu, 12 Apr 2012 13:52:51 +0900 r-bioc-edger (2.4.6~dfsg-1) unstable; urgency=low 181300f New upstream version 2.4.6. -- Charles Plessy Sat, 17 Mar 2012 16:18:52 +0900 r-bioc-edger (2.4.3~dfsg-1) unstable; urgency=low 04cc8b8 New upstream 2.4.3. c494484 Renamed debian/upstream-metadata.yaml to debian/upstream. 27bae62 Corrected URLs, paths, and mangles in watch file. d6029fb Provide a more stable URL to the manual. 09acea4 Obtain ${R:Depends} directly throuhg r-base-dev. 5df05c4 Conforms to Policy 3.9.3. 2b01b4a Verbose Debhelper. -- Charles Plessy Mon, 05 Mar 2012 15:10:28 +0900 r-bioc-edger (2.4.0~dfsg-1) unstable; urgency=low 16d49d0 Bioconductor release 2.9. 0e79ff9 Removed User's Guide (no source) in agreement with the upstream authors, see “README.Debian”. -- Charles Plessy Fri, 18 Nov 2011 13:47:35 +0900 r-bioc-edger (2.2.6-1ubuntu1) precise; urgency=low * Pre-Depends: dpkg (>= 1.15.6) for xz compression support. Needed until after Ubuntu 12.04 LTS. -- Colin Watson Fri, 11 Nov 2011 14:25:32 +0000 r-bioc-edger (2.2.6-1) unstable; urgency=low c9512e2 New upstream release. 40876f8 Compress binary package with xz. -- Charles Plessy Wed, 19 Oct 2011 15:29:52 +0900 r-bioc-edger (2.2.5-1) unstable; urgency=low * Initial release (Closes: #628882) -- Charles Plessy Fri, 03 Jun 2011 15:22:29 +0900 debian/compat0000644000000000000000000000000212263212152010360 0ustar 9 debian/docs0000644000000000000000000000003112263212152010027 0ustar tests debian/README.test debian/tests/0000755000000000000000000000000012263212152010324 5ustar debian/tests/control0000644000000000000000000000005012263212152011722 0ustar Tests: upstream Depends: @, r-cran-mass debian/tests/upstream0000755000000000000000000000053012263212152012110 0ustar #!/bin/sh -e TEMPORARY_DIR=$(mktemp -d) cd $TEMPORARY_DIR cp /usr/share/doc/r-bioc-edger/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