debian/0000755000000000000000000000000012261220074007162 5ustar debian/README.test0000644000000000000000000000044112261220074011017 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(cummeRbund)’ in order to confirm its integrity. debian/source/0000755000000000000000000000000012261220074010462 5ustar debian/source/format0000644000000000000000000000001412261220074011670 0ustar 3.0 (quilt) debian/docs0000644000000000000000000000002312261220074010030 0ustar debian/README.test debian/copyright0000644000000000000000000000125312261220074011116 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: cummeRbund Source: http://www.bioconductor.org/packages/2.10/bioc/src/contrib/cummeRbund_1.1.1.tar.gz Files: * Copyright: Loyal A. Goff Cole Trapnell License: Artistic-2.0 This program is free software; you can redistribute it and/or modify it under the terms of the "Artistic License". . On Debian GNU/Linux systems, the complete text of Artistic License can be found in `/usr/share/common-licenses/Artistic'. Files: debian/* Copyright: 2012 Carlos Borroto License: Artistic-2.0 Same as cummeRbund debian/upstream0000644000000000000000000000042612261220074010747 0ustar Archive: Bioconductor Homepage: http://compbio.mit.edu/cummeRbund/ Name: cummeRbund Reference: Author: L. Goff and C. Trapnell Title: "cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data" Year: 2012 Type: Misc debian/rules0000755000000000000000000000020112261220074010233 0ustar #!/usr/bin/make -f debRreposname = bioc include /usr/share/R/debian/r-cran.mk export DEB_BUILD_MAINT_OPTIONS = hardening=+all debian/gbp.conf0000644000000000000000000000027012261220074010600 0ustar # This package is managed with git-buildpackage. [DEFAULT] # use pristine-tar: pristine-tar = True [git-dch] # include 7 digits of the commit id in the changelog enty: id-length = 7 debian/watch0000644000000000000000000000040612261220074010213 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/cummeRbund.html \ ../src/contrib/cummeRbund_(.*).tar.gz debian/changelog0000644000000000000000000000265212261220074011041 0ustar r-bioc-cummerbund (2.4.1-1) unstable; urgency=low * New upstream version * debian/rules: Remove useless creation of ${R-Depends} * debian/control: Versioned Build-Depends: r-base-dev (>= 3.0) * debian/README.test: add hint how to test the package -- Andreas Tille Sat, 28 Dec 2013 17:17:25 +0100 r-bioc-cummerbund (1.2.0-2) unstable; urgency=low [ Charles Plessy ] f419ef1 Normalised VCS URLs following Lintian's standard. d5c4363 Removed obsolete DM-Upload-Allowed field. 6982298 Normalised Debian copyright file with 'cme fix dpkg-copyright'. 38bee3c Normalised debian/control with 'cme fix dpkg-copyright'. 9587f21 Use Debhelper 9. 9560362 Conforms with Policy 3.9.4. [ Andreas Tille ] * Upload to unstable after verifying that predepends are properly build -- Andreas Tille Sat, 18 May 2013 14:30:43 +0200 r-bioc-cummerbund (1.2.0-1) unstable; urgency=low * New upstream release * debian/watch: Track stable releases instead of development releases * debian/upstream: Reference as given in citation("cummeRbund") * debian/control: Standards-Version: 3.9.3 (no changes needed) * debian/rules: Enable hardening -- Andreas Tille Tue, 08 May 2012 08:52:06 +0200 r-bioc-cummerbund (1.1.3-1) unstable; urgency=low * Initial release (Closes: #657997) -- Carlos Borroto Tue, 24 Jan 2012 12:08:29 -0500 debian/compat0000644000000000000000000000000212261220074010360 0ustar 9 debian/control0000644000000000000000000000250512261220074010567 0ustar Source: r-bioc-cummerbund Maintainer: Debian Med Packaging Team Uploaders: Carlos Borroto , Andreas Tille Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev (>= 3.0), r-cran-rsqlite, r-cran-reshape2, r-cran-ggplot2, r-cran-fastcluster, r-bioc-biocgenerics, r-bioc-rtracklayer, r-bioc-gviz Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/r-bioc-cummerbund.git Vcs-Git: git://anonscm.debian.org/debian-med/r-bioc-cummerbund.git Homepage: http://compbio.mit.edu/cummeRbund/ Package: r-bioc-cummerbund Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, ${R:Depends}, r-cran-rsqlite, r-cran-reshape2, r-cran-ggplot2, r-cran-fastcluster, r-bioc-biocgenerics, r-bioc-rtracklayer, r-bioc-gviz Description: tool for analysis of Cufflinks RNA-Seq output Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.