--- r-cran-qvalue-1.20.0.orig/debian/README.Debian +++ r-cran-qvalue-1.20.0/debian/README.Debian @@ -0,0 +1,7 @@ +Notes on how this package is tested. +──────────────────────────────────── + +After building on the maintainer's computer, this package was locally installed +and the library loaded into R in order to confirm its integrity. + + -- Charles Plessy Sun, 29 Nov 2009 13:35:17 +0900 --- r-cran-qvalue-1.20.0.orig/debian/control +++ r-cran-qvalue-1.20.0/debian/control @@ -0,0 +1,24 @@ +Source: r-cran-qvalue +Section: gnu-r +Priority: optional +Maintainer: Debian Med Packaging Team +Uploaders: Steffen Moeller , Charles Plessy +Build-Depends: debhelper (>= 7), cdbs, r-base-dev +Standards-Version: 3.8.3 +Homepage: http://cran.r-project.org/web/packages/qvalue +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-qvalue/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/R/r-cran-qvalue/trunk/ + +Package: r-cran-qvalue +Architecture: all +Depends: ${R:Depends}, ${misc:Depends} +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. --- r-cran-qvalue-1.20.0.orig/debian/changelog +++ r-cran-qvalue-1.20.0/debian/changelog @@ -0,0 +1,49 @@ +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 --- r-cran-qvalue-1.20.0.orig/debian/rules +++ r-cran-qvalue-1.20.0/debian/rules @@ -0,0 +1,13 @@ +#!/usr/bin/make -f +# -*- makefile -*- +# debian/rules file for the Debian/GNU Linux r-cran-qtl package +# Copyright 2003-2006 by Dirk Eddelbuettel + +include /usr/share/R/debian/r-cran.mk + +# Require a number equal or superior than the R version the package was built with. +install/r-cran-qvalue:: + echo "R:Depends=r-base-core (>= $(shell R --version | head -n1 | perl -ne 'print / +([0-9]\.[0-9]+\.[0-9])/'))" >> debian/r-$(debRreposname)-$(cranName).substvars + +clean:: + find . -name "*.pdf" -o -name "*.tex" -o -name "*-eps" -o -name "*.log" -o -name "*.ps" -o -name "*.txt" | xargs -r chmod -x --- r-cran-qvalue-1.20.0.orig/debian/copyright +++ r-cran-qvalue-1.20.0/debian/copyright @@ -0,0 +1,29 @@ +Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’. + +Name: qvalue +Contact: John D. Storey +Source: http://cran.r-project.org/src/contrib/qvalue_1.20.0.tar.gz + +Copyright: Alan Dabney and John D. Storey +License: LGPL-3+ + + 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-3’, and the GNU GPL license +version 3 is included in the file ‘/usr/share/common-licenses/GPL-3’. + +This package was created by Steffen Moeller , +based on work for the r-cran-rodbc package of Dirk +Eddelbuettel . --- r-cran-qvalue-1.20.0.orig/debian/upstream-metadata.yaml +++ r-cran-qvalue-1.20.0/debian/upstream-metadata.yaml @@ -0,0 +1,20 @@ +Bioconductor: http://www.bioconductor.org/packages/bioc/html/qvalue.html +Contact: John D. Storey +CRAN: http://cran.r-project.org/web/packages/qvalue/ +DOI: 10.1073/pnas.1530509100 +Homepage: http://cran.r-project.org/web/packages/qvalue/ +Name: qvalue +PMID: 12883005 +Reference: | + @article{John D.Storey08052003, + author = {Storey, John D. and Tibshirani, Robert}, + 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}, + year = {2003}, + URL = {http://www.pnas.org/content/100/16/9440.abstract}, + eprint = {http://www.pnas.org/content/100/16/9440.full.pdf+html} + } --- r-cran-qvalue-1.20.0.orig/debian/watch +++ r-cran-qvalue-1.20.0/debian/watch @@ -0,0 +1,3 @@ +version=3 +http://cran.r-project.org/src/contrib/qvalue_([-0-9\.]*)\.tar\.gz + --- r-cran-qvalue-1.20.0.orig/debian/compat +++ r-cran-qvalue-1.20.0/debian/compat @@ -0,0 +1 @@ +7