debian/0000755000000000000000000000000012140716070007164 5ustar debian/control0000644000000000000000000000265112140715724010600 0ustar Source: r-bioc-qvalue Section: gnu-r Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille DM-Upload-Allowed: yes Build-Depends: debhelper (>= 8), cdbs, r-base-dev (>= 3.0) Standards-Version: 3.9.4 Homepage: http://www.bioconductor.org/packages/release/bioc/html/qvalue.html Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-bioc-qvalue/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-bioc-qvalue/trunk/ Package: r-bioc-qvalue Architecture: all Depends: ${R:Depends}, ${misc:Depends} Replaces: r-cran-qvalue Provides: r-cran-qvalue Conflicts: r-cran-qvalue Description: GNU R package for Q-value estimation for FDR control This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. debian/compat0000644000000000000000000000000211602525210010356 0ustar 8 debian/README.test0000644000000000000000000000043511743747767011055 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(qvalue)’ in order to confirm its integrity. debian/watch0000644000000000000000000000035312025603126010215 0ustar version=3 opts=downloadurlmangle=s/\.\./packages\/release\/bioc/,dversionmangle=s/[~\+]dfsg[0-9]*// \ http://www.bioconductor.org/packages/release/bioc/html/qvalue.html \ .*/qvalue_([\d\.]+)\.tar\.gz \ debian debian/get-orig-source debian/copyright0000644000000000000000000000246412025603126011124 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: qvalue Upstream-Contact: John D. Storey Source: http://www.bioconductor.org/packages/release/bioc/html/qvalue.html Files-Excluded: manual.pdf Files: * Copyright: © 2006-2012 Alan Dabney and John D. Storey License: LGPL Files: debian/* Copyright: 2008-2009 Steffen Moeller 2009-2011 Charles Plessy 2010-2012 Andreas Tille License: LGPL License: LGPL This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 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 Lesser General Public License along with this program. If not, see . . On a Debian GNU/Linux system, the GNU Lesser GPL license version 3 is included in the file ‘/usr/share/common-licenses/LGPL’. debian/get-orig-source0000755000000000000000000000150711764145324012141 0ustar #!/bin/sh # Delete manual.pdf in upstream source because there is no source # and upstream did not responded when asking for it set -e NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` UNAME=`echo ${NAME} | sed 's/^r-bioc-//'` if ! echo $@ | grep -q upstream-version ; then VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` else VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${UNAME}.*?\1?"` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit fi fi mkdir -p ../tarballs cd ../tarballs tar xaf ../${UNAME}*.tar.gz find ${UNAME} -name manual.pdf -delete GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.gz "${UNAME}" rm -rf "$UNAME" debian/source/0000755000000000000000000000000012140716067010472 5ustar debian/source/format0000644000000000000000000000001411472465471011707 0ustar 3.0 (quilt) debian/upstream0000644000000000000000000000127711753056067010772 0ustar Bioconductor: http://www.bioconductor.org/packages/bioc/html/qvalue.html Contact: John D. Storey CRAN: http://cran.r-project.org/web/packages/qvalue/ Homepage: http://cran.r-project.org/web/packages/qvalue/ Name: qvalue Reference: article: John D.Storey08052003 author: John D Storey and Robert Tibshirani title: Statistical significance for genomewide studies journal: Proceedings of the National Academy of Sciences of the United States of America volume: 100 number: 16 pages: 9440-9445 doi: 10.1073/pnas.1530509100 PMID: 12883005 year: 2003 URL: http://www.pnas.org/content/100/16/9440.abstract eprint: http://www.pnas.org/content/100/16/9440.full.pdf+html debian/rules0000755000000000000000000000046011743744523010260 0ustar #!/usr/bin/make -f debRreposname=bioc include /usr/share/R/debian/r-cran.mk install/$(package):: chmod 644 debian/$(package)/usr/lib/R/site-library/$(cranName)/doc/* clean:: find . -name "*.pdf" -o -name "*.tex" -o -name "*-eps" -o -name "*.log" -o -name "*.ps" -o -name "*.txt" | xargs -r chmod -x debian/changelog0000644000000000000000000001045512140715773011054 0ustar r-bioc-qvalue (1.34.0+dfsg-1) unstable; urgency=low * New upstream version. * Bumped policy to 3.9.4 (no changes required) * Built for R version 3 -- Steffen Moeller Fri, 03 May 2013 11:55:42 +0200 r-bioc-qvalue (1.30.0+dfsg-1) UNRELEASED; urgency=low * debian/copyright: - Add Files-Excluded to document what was removed from original source * debian/watch: - deal with +dfsg suffix -- Andreas Tille Mon, 17 Sep 2012 13:10:46 +0200 r-bioc-qvalue (1.30.0-1) unstable; urgency=low * New upstream version which is now provided at BioConductor and thus we also do a name change in the packaging * debian/get-orig-source: Remove "binary without source" manual.pdf from upstream source * debian/control: - s/cran/bioc/ (package names, Vcs fields) - Replaces/Provides/Conflicts: r-cran-qvalue - Standards-Version: 3.9.3 (no changes needed) - Build-Depends: r-base-dev (>= 2.14.2~20120222) which is supporting R:Depends substitution variable * debian/rules: Remove R:Depends substitution variable which is now included in /usr/share/R/debian/r-cran.mk * debian/watch: Detect new version (thanks to Paul Wise for the tip) * debian/README.test: advise how to test the package * debian/copyright: - Fixed DEP5 issues using `cme fix dpkg-copyright` - s/LGPL-3+/LGPL/ as specified in DESCRIPTION * debian/README.Debian: Document removal of manual.pdf and where it can be found online -- Andreas Tille Thu, 07 Jun 2012 17:40:29 +0200 r-cran-qvalue (1.26.0-1) unstable; urgency=low * New upstream version. * debian/control: - Allow uploade by Debian Maintainers. - Use Debhelper 8 (debian/compat). - Incremented Standards-Version to reflect conformance with Policy 3.9.2. (no changes needed) - Corrected VCS URLs. * debian/copyright converted to machine-readable DEP 5 format. -- Charles Plessy Wed, 29 Jun 2011 13:14:28 +0900 r-cran-qvalue (1.24.0-1) unstable; urgency=low * New upstream version * Added myself to uploaders * debhelper version (>= 7.1) * Standards-Version: 3.9.1 (no changes needed) * debian/source/format: 3.0 (quilt) * debian/rules: - Fixed copy-n-pasto in header comments - Make sure installed docs will not have executable bit set * debian/copyright: Fixed copyright notice * debian/README.Debian: Give better advise for testing the package -- Andreas Tille Mon, 22 Nov 2010 13:23:45 +0100 r-cran-qvalue (1.20.0-1) unstable; urgency=low * New upstream release. * Require a number equal or superior than the R version the package was built with, using a R:Depends substvar (debian/control, debian/rules). * Use Debhelper's ${misc:Depends} and removed ${shlibs:Depends}, as the package is architecture-independent. * Added notes to explain how this package is tested (debian/README.Debian). -- Charles Plessy Sun, 29 Nov 2009 13:35:52 +0900 r-cran-qvalue (1.18.0-2) unstable; urgency=low * Rebuilt against R 2.10.0 because of its new documentation system. * debian/control: - Removed version in dependence to R packages (satisfied in Lenny). - Incremented Standards-Version to reflect conformance with Policy 3.8.3 (no changes needed). * Added various informations in debian/upstream-metadata.yaml. * debian/copyright adapted to the latest experimentation on the machine-readable format. -- Charles Plessy Thu, 22 Oct 2009 08:56:08 +0900 r-cran-qvalue (1.18.0-1) unstable; urgency=low * New upstream release: changes in documentation and bug corrected for TCL/Tk support. * debian/control: - Added myself to the Uploaders. - Changed section to ‘gnu-r’ and incremented Standards-Version to to reflect conformance with the Policy 3.8.2. - Use Debhelper 7 (debian/compat). - Added VCS URLs. -- Charles Plessy Fri, 26 Jun 2009 12:57:09 +0900 r-cran-qvalue (1.1-2) unstable; urgency=low * Fixed lintian warnings * Removed Dirk from Uploaders -- Steffen Moeller Wed, 14 Jan 2009 18:37:16 +0100 r-cran-qvalue (1.1-1) unstable; urgency=low * Initial release (closes: #49212). -- Steffen Moeller Wed, 23 Jul 2008 23:29:22 +0200 debian/README.Debian0000644000000000000000000000101511764145707011240 0ustar Bioconductor qvalue for Debian ────────────────────────────── Debian ftpmaster has requested to remove the "binary without source" manual.pdf. You can find it here online: http://www.bioconductor.org/packages/release/bioc/vignettes/qvalue/inst/doc/manual.pdf besides other PDF documentation at the qvalue homepage http://www.bioconductor.org/packages/release/bioc/html/qvalue.html -- Andreas Tille Thu, 07 Jun 2012 17:40:29 +0200