debian/0000755000000000000000000000000012144676147007202 5ustar debian/control0000644000000000000000000000424012144676116010601 0ustar Source: qtl Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-cran-qtl/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/R/r-cran-qtl/trunk/ Homepage: http://www.rqtl.org Package: r-cran-qtl Architecture: any Depends: ${shlibs:Depends}, ${R:Depends} Recommends: r-cran-rlecuyer Suggests: r-cran-snow Description: GNU R package for genetic marker linkage analysis R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTLs) in experimental crosses. It is implemented as an add-on-package for the freely available and widely used statistical language/software R (see http://www.r-project.org). . The development of this software as an add-on to R allows one to take advantage of the basic mathematical and statistical functions, and powerful graphics capabilities, that are provided with R. Further, the user will benefit by the seamless integration of the QTL mapping software into a general statistical analysis program. The goal is to make complex QTL mapping methods widely accessible and allow users to focus on modeling rather than computing. . A key component of computational methods for QTL mapping is the hidden Markov model (HMM) technology for dealing with missing genotype data. The main HMM algorithms were implemented, with allowance for the presence of genotyping errors, for backcrosses, intercrosses, and phase-known four-way crosses. . The current version of R/qtl includes facilities for estimating genetic maps, identifying genotyping errors, and performing single-QTL genome scans and two-QTL, two-dimensional genome scans, by interval mapping (with the EM algorithm), Haley-Knott regression, and multiple imputation. All of this may be done in the presence of covariates (such as sex, age or treatment). One may also fit higher-order QTL models by multiple imputation. debian/rules0000755000000000000000000000007211733177757010267 0ustar #!/usr/bin/make -f include /usr/share/R/debian/r-cran.mk debian/watch0000644000000000000000000000011011402163052010201 0ustar version=3 http://cran.r-project.org/src/contrib/qtl_([-0-9\.]*).tar.gz debian/upstream0000644000000000000000000000063011752660136010757 0ustar Reference: Title: "R/qtl: QTL mapping in experimental crosses" Author: Karl W. Broman and Hao Wu and Saunak Sen and Gary A. Churchill Year: 2003 Journal: Bioinformatics Volume: 19 Pages: 889-890 PMID: 12724300 DOI: 10.1093/bioinformatics/btg112 URL: http://bioinformatics.oxfordjournals.org/content/19/7/889 eprint: http://bioinformatics.oxfordjournals.org/content/19/7/889.full.pdf+html debian/copyright0000644000000000000000000000244011733202737011126 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Qtl Upstream-Contact: Karl W. Broman , Hao Wu Source: http://cran.r-project.org/src/contrib/ Files: * Copyright: 2001-2012 Karl W. Broman Hao Wu , Gary Churchill and Śaunak Sen License: GPL3+ Files: debian/* Copyright: 2003-2012 Steffen Moeller , 2009-2012 Andreas Tille License: GPL3+ License: GPL3+ 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 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 General Public License along with this program. If not, see . . On a Debian system, the GNU GPL license is distributed in the file ‘/usr/share/common-licenses/GPL’. debian/source/0000755000000000000000000000000012144674746010505 5ustar debian/source/format0000644000000000000000000000001411301174376011677 0ustar 3.0 (quilt) debian/README.test0000644000000000000000000000055111733200372011023 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(qtl)’ in order to confirm its integrity. -- Steffen Moeller Wed, 10 Oct 2007 13:43:39 +0200 debian/changelog0000644000000000000000000002320512144676147011056 0ustar qtl (1.27-10-1) unstable; urgency=low * New upstream version * debian/control: - debhelper 9 (also debian/compat) - normalised using `cme fix dpkg-control` - better wording in long description - drop versioned Build-Depends from r-base-dev because the version in latest stable is sufficient -- Andreas Tille Wed, 15 May 2013 14:07:47 +0200 qtl (1.25-15-2) unstable; urgency=low * Rebuilt for R version 3 * Bumped policy to 3.9.4 -- Steffen Moeller Tue, 02 Apr 2013 00:48:41 +0200 qtl (1.25-15-1) unstable; urgency=low * New upstream version - suggesting rlecuyer R package - major fix for interpretation of numeric IDs in checkcovar -- Steffen Moeller Sat, 18 Aug 2012 21:42:30 +0200 qtl (1.23-16-2) UNRELEASED; urgency=low * debian/upstream: - Fixed yaml Syntax - Fixed authors syntax - Added URL -- Andreas Tille Mon, 26 Mar 2012 21:29:33 +0200 qtl (1.23-16-1) unstable; urgency=low * New upstream version * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Build-Depends: r-base-dev (>= 2.14.2~20120222) * debian/rules: - Remove R:Depends substitution variable which is now included in /usr/share/R/debian/r-cran.mk - Code is trivial enough to remove licensing comment * Split debian/README.Debian up into README.test and debian/upstream * debian/docs: Install README.test * debian/copyright: Rewritten to match DEP5 and verified using cme fix dpkg-copyright -- Andreas Tille Fri, 23 Mar 2012 23:54:28 +0100 qtl (1.22-21-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Mon, 09 Jan 2012 14:45:00 +0100 qtl (1.21-2-2) unstable; urgency=low * Rebuilded using latest R Closes: #646052 * Standards-Version: 3.9.2 (no changes needed) * Fixed Vcs fields -- Andreas Tille Fri, 21 Oct 2011 15:30:24 +0200 qtl (1.21-2-1) unstable; urgency=low * New upstream version -- Steffen Moeller Mon, 15 Aug 2011 10:59:08 +0200 qtl (1.20-15-1) unstable; urgency=low * New upstream version * Debhelper 8 (control+compat) -- Andreas Tille Mon, 14 Mar 2011 09:31:31 +0100 qtl (1.19-20-1) unstable; urgency=low * New upstream version -- Andreas Tille Wed, 26 Jan 2011 10:04:53 +0100 qtl (1.18-7-1) unstable; urgency=low * New upstream version * Standards-Version: 3.9.1 (no changes needed) -- Andreas Tille Wed, 24 Nov 2010 11:21:26 +0100 qtl (1.16-6-2) unstable; urgency=low * Added myself to Uploaders * Debhelper 7 * Moved from pkg-bioc to debian-med SVN repository * Updated README.Debian * Added upstream-metadata.yaml * debian/{control,rules}: Depends: ${R:Depends} * Source format 3.0 (quilt) * Fixed spelling of Debian Med (removed dash) -- Andreas Tille Fri, 04 Jun 2010 14:12:49 +0200 qtl (1.16-6-1) unstable; urgency=low * New upstream version - Integration of MQM mapping of mapqtl - Many smallish or larger improvements * Updated standards-version - Added debian/source/format indication -- Steffen Moeller Fri, 04 Jun 2010 13:05:47 +0200 qtl (1.14-2-1) unstable; urgency=low * dependency on R 2.7.10 * new upstream version with only minor changes -- Steffen Moeller Wed, 28 Oct 2009 23:09:18 +0000 qtl (1.13-7-1) unstable; urgency=low * new upstream version with various bug fixes * bumped standard compliance to 3.8.3 (no changes required) -- Steffen Moeller Mon, 28 Sep 2009 13:39:40 +0200 qtl (1.12-26-1) unstable; urgency=low * new upstream version - support for recombinant inbred lines (RIL) - simpler notation to reference pseudonmarkers * license change to GPL-3 * adapted section to gnu-r -- Steffen Moeller Thu, 09 Jul 2009 13:52:50 +0200 qtl (1.11-12-1) unstable; urgency=low * new upstream version -- Steffen Moeller Thu, 14 May 2009 13:47:06 +0200 qtl (1.10-28-1) unstable; urgency=low * new upstream version - resolves inconsistencies in copyright - various changes affecting stability or performance - more on http://www.rqtl.org/STATUS.txt * debian/copyright updated * removed PDFs from source tree -- Steffen Moeller Fri, 20 Feb 2009 18:50:00 +0100 qtl (1.09-43-2) unstable; urgency=low * Dirk requested to be removed from the uploaders list * Allowing Debian-Med community maintenance albeit package remaining under pkg-bioc control for now. * Added Vcs-Browser and Vcs-Svn fields. -- Steffen Moeller Mon, 29 Sep 2008 17:18:20 +0200 qtl (1.09-43-1) unstable; urgency=low * New upstream release. -- Steffen Moeller Wed, 30 Jul 2008 16:42:46 +0200 qtl (1.08-56-1) unstable; urgency=low * New upstream release. * Establishing compatibility to R release 2.7. -- Steffen Moeller Fri, 11 Apr 2008 11:48:30 +0200 qtl (1.07-12-2) unstable; urgency=low * [debian/control] - updated description - adhering to latest standards version * [debian/copyright] - updated Steffen's email adress * Recompilation will induce transition to gfortran -- Steffen Moeller Tue, 11 Mar 2008 10:41:54 +0100 qtl (1.07-12-1) unstable; urgency=low * New upstream version. * Major changes: - Upstream completely rewrote the effectscan function, so that it now uses multiple imputation results and deals with the X chromosome appropriately. - Upstream fixed an important bug in fitqtl, in which incorrect results could be obtained if covariates were placed before QTL terms in the formula. -- Steffen Moeller Wed, 10 Oct 2007 13:43:39 +0200 qtl (1.06-43-1) unstable; urgency=low * New upstream release * debian/control: (Build-)Depends: updated to r-base-dev (>= 2.4.0) -- Dirk Eddelbuettel Sun, 12 Aug 2007 15:30:27 -0500 qtl (1.05-2-1) unstable; urgency=low * New upstream release -- Dirk Eddelbuettel Thu, 9 Nov 2006 17:57:04 -0600 qtl (1.04-53-1) unstable; urgency=low * New upstream release -- Dirk Eddelbuettel Sun, 29 Oct 2006 11:17:51 -0600 qtl (1.04-52-1) unstable; urgency=low * New upstream release * debian/control: (Build-)Depends: updated to r-base-dev (>= 2.4.0) -- Dirk Eddelbuettel Sat, 28 Oct 2006 11:26:41 -0500 qtl (1.03-14-1) unstable; urgency=low * New upstream release -- Dirk Eddelbuettel Fri, 21 Jul 2006 18:16:41 -0500 qtl (1.02-26-1) unstable; urgency=low * New upstream release * New maintainer as Steffen's NM progress appears to have stalled * debian/rules: Simplified to cdbs-based one-liner sourcing r-cran.mk * debian/control: Hence Build-Depends: updated to r-base-dev (>= 2.3.0) * debian/control: Standards-Version: increased to 3.7.2 * debian/watch: Updated file to version: 3 -- Dirk Eddelbuettel Thu, 8 Jun 2006 21:13:27 -0500 qtl (1.01-9-1) unstable; urgency=low * New upstream version. [ Dirk Eddelbuettel ] * Rename upstream tarball correctly as .orig.tar.gz before building package to prevent accidental build as a Debian native package * debian/post{inst,rm}: No longer call R to update html help index -- Steffen Moeller Thu, 1 Dec 2005 15:20:00 +0100 qtl (0.99.24-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Sun, 15 May 2005 23:54:03 +0200 qtl (0.98.57-2.1) unstable; urgency=low * NMU * Coordinated with Maintainer as part of larger R 2.0.0 update effort * Rebuilt under R 2.0.0 * debian/control: Updated Build-Depends: and Depends: accordingly -- Dirk Eddelbuettel Sat, 9 Oct 2004 20:55:08 -0500 qtl (0.98.57-2) unstable; urgency=low * added postinst script * added postrm script too [ Dirk Eddelbuettel ] -- Steffen Moeller Tue, 19 Sep 2004 23:24:00 +0100 qtl (0.98.57-1) unstable; urgency=low * New upstream version. - Proper support of the X chromosome - many little improvements -- Steffen Moeller Tue, 19 Sep 2004 01:06:00 +0100 qtl (0.97.22-1) unstable; urgency=low * New upstream version. -- Steffen Moeller Tue, 14 Jan 2004 10:55:00 +0100 qtl (0.97.21-5) unstable; urgency=low * Retrieval of genetical map from EnsEMBL (http://www.ensembl.org) * Also implemented access to EnsEMBL via RMySQL, package r-cran-mysql available on mentors.debian.net -- Steffen Moeller Tue, 11 Nov 2003 13:14:00 +0100 qtl (0.97.21-4) unstable; urgency=low * Retrieval of physical map from EnsEMBL (http://www.ensembl.org) Requires RODBC. -- Steffen Moeller Tue, 11 Nov 2003 13:14:00 +0100 qtl (0.97.21-3) unstable; urgency=low * added demo, code copied from "A starting point" help to the qtl library -- Steffen Moeller Tue, 11 Nov 2003 13:14:00 +0100 qtl (0.97.21-2) unstable; urgency=low * dec and quote parameters passed to internally called R base function read.table for read.cross * second parameter (dir) interpreted as file if file unset -- Steffen Moeller Tue, 3 Nov 2003 22:05:03 +0100 qtl (0.97.21-1) unstable; urgency=low * Initial Debian Release (closes: #214601) -- Steffen Moeller Tue, 8 Oct 2003 09:02:03 +0100 debian/compat0000644000000000000000000000000212144675273010377 0ustar 9 debian/docs0000644000000000000000000000002311733175776010055 0ustar debian/README.test