debian/0000755000000000000000000000000012173157524007175 5ustar debian/control0000644000000000000000000000247512173157334010607 0ustar Source: r-cran-genabel Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Charles Plessy Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-cran-mass Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-genabel/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-genabel/trunk/ Homepage: http://www.genabel.org/ Package: r-cran-genabel Architecture: any Depends: ${shlibs:Depends}, ${R:Depends}, r-cran-mass Suggests: r-cran-genetics, r-cran-haplo.stats, r-bioc-qvalue Description: GNU R package for genome-wide SNP association analysis The package offers the R library GenABEL for the hunt of genetic contributions to a disease (or any other pheonypical trait) by so called genome-wide association analysis. Additional input commonly comes from DNA mircoarray experiments, performed on every individual, that determine differences (polymorphisms) in the population. GenABEL finds associations between quantitative or binary traits and single-nucleiotide polymorphisms (SNPs). debian/rules0000755000000000000000000000034512140275573010256 0ustar #!/usr/bin/make -f debRreposname=cran include /usr/share/R/debian/r-cran.mk install/$(package):: find debian/$(package)/usr/lib/R/site-library/GenABEL/ -type f -exec chmod 644 \{\} \; DEB_INSTALL_CHANGELOGS_ALL = CHANGES.LOG debian/watch0000644000000000000000000000025211545276551010231 0ustar version=3 #http://mga.bionet.nsc.ru/nlru/GenABEL/GenABEL_(.*)\.tar\.gz # The package has now arrived in CRAN http://cran.r-project.org/src/contrib/GenABEL_(.*)\.tar\.gz debian/upstream0000644000000000000000000000154211724071644010761 0ustar Archive: CRAN Bug-Database: https://r-forge.r-project.org/tracker/?atid=2058&group_id=505 Contact: GenABEL developers Name: GenABEL Homepage: http://www.genabel.org/ Reference: author: Aulchenko, Yurii S. and Ripke, Stephan and Isaacs, Aaron and van Duijn, Cornelia M. title: > GenABEL: an R library for genome-wide association analysis volume: 23 number: 10 pages: 1294-1296 year: 2007 doi: 10.1093/bioinformatics/btm108 URL: http://bioinformatics.oxfordjournals.org/content/23/10/1294.abstract eprint: http://bioinformatics.oxfordjournals.org/content/23/10/1294.full.pdf+html journal: Bioinformatics PMID: 17384015 Repostiory: svn://svn.r-forge.r-project.org/svnroot/genabel Repository-Browse: https://r-forge.r-project.org/scm/viewvc.php/?root=genabel Watch: | http://cran.r-project.org/src/contrib/GenABEL_(.*)\.tar\.gz debian/copyright0000644000000000000000000000233012140275573011125 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://cran.r-project.org/src/contrib/GenABEL_1.7-4.tar.gz Files: * Copyright: GenABEL is copyright 2006-2008 of Yurii Aulchenko, Maksim Struchalin, with contributions from Stephan Ripke, Terry Therneau and Toby Johnson and released under version 2 or later of the GNU General Public License (GPL). 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 a Debian GNU/Linux system, the GPL license version 2 is included in the file /usr/share/common-licenses/GPL-2. debian/source/0000755000000000000000000000000012173156464010477 5ustar debian/source/format0000644000000000000000000000001411545276551011707 0ustar 3.0 (quilt) debian/README.test0000644000000000000000000000054512103174573011033 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(GenABEL)’ in order to confirm its integrity. -- Andreas Tille Sat, 02 Feb 2013 12:32:39 +0100 debian/changelog0000644000000000000000000000631712173157524011056 0ustar r-cran-genabel (1.7-6-1) unstable; urgency=low * New upstream version * debian/control: Drop citation from long description because this information is provided in debian/upstream. -- Andreas Tille Mon, 22 Jul 2013 09:22:48 +0200 r-cran-genabel (1.7-4-1) unstable; urgency=low * New upstream version * Updated qvalue package name (moved from CRAN to Bioconductor). * Drop references to old name r-other-genabel. * Drop build-dependance on package only suggested. * Normalised VCS URLs following Lintian's standard. * Acquire R:Depends directly from r-base-dev. * Normalised control file with cme. -- Charles Plessy Wed, 01 May 2013 14:58:43 +0900 r-cran-genabel (1.7-3-1) unstable; urgency=low * New upstream version * Replace debian/README.Debian by debian/README.test * DEP5 copyright * Standards-Version: 3.9.4 (no changes needed) * debhelper 9 (control+compat) -- Andreas Tille Sat, 02 Feb 2013 12:32:39 +0100 r-cran-genabel (1.7-0-3) testing-proposed-updates; urgency=low * Upload to testing-proposed-updates -- Andreas Tille Sat, 02 Feb 2013 07:08:19 +0000 r-cran-genabel (1.7-0-2) unstable; urgency=low * Fixing the problem which prevents the package from loading while checking the version on CRAN Closes: #699260 -- Andreas Tille Wed, 30 Jan 2013 13:11:06 +0100 r-cran-genabel (1.7-0-1) unstable; urgency=low * New upstream release. * Depends and Suggests packages according to DESCRIPTION (debian/control). * Corrected VCS URLs (debian/control). * Conforms with Policy 3.9.2 (debian/control, no other changes needed). * Build-Depend on r-cran-mass instead of the whole r-recommended. -- Charles Plessy Fri, 13 Jan 2012 13:56:32 +0900 r-cran-genabel (1.6-5-1) unstable; urgency=low * New upstream release, buildable with R > 2.12 (closes: #620269). [ Andreas Tille ] * debian/control: - added myself to uploaders - changed section to gnu-r - Depend on ${R:Depends} * debian/rules: - fix permissions of files that should not be executable - Require a number equal or superior than the R version the package was built with, using a R:Depends substvar [ Charles Plessy ] * debian/control: - Added myself to uploaders. - Use debhelper 8 (debian/compat). - Build-depend on R > 2.10 according to DESCRIPTION. - Replaces r-other-genabel. - Added Vcs-Browser and Vcs-Svn fields. - Updated homepage. * Install CHANGES.LOG as upstream changelog (debian/rules). * Converted debian/copyright to DEP-5 format. -- Charles Plessy Fri, 01 Apr 2011 13:46:37 +0900 r-cran-genabel (1.6-4-1) unstable; urgency=low * New upstream release. * The package has now arrived in CRAN and is taken from there, which according to the R policy is also reflected by the name change. * Switch to source/format 3.0 (quilt) * Bumped policy-standard to 3.9.1. -- Steffen Moeller Sat, 05 Feb 2011 18:06:24 +0100 r-other-genabel (1.4-0-1) unstable; urgency=low * Initial release (Closes: #492044). -- Steffen Moeller Wed, 23 Jul 2008 15:43:37 +0200 debian/compat0000644000000000000000000000000212103200546010355 0ustar 9