debian/0000755000000000000000000000000012141653370007170 5ustar debian/lintian-overrides0000644000000000000000000000012211715233512012542 0ustar r-cran-haplo.stats: extra-license-file usr/lib/R/site-library/haplo.stats/LICENSE debian/compat0000644000000000000000000000000212141652426010367 0ustar 9 debian/links0000644000000000000000000000016211723124224010226 0ustar usr/lib/R/site-library/haplo.stats/doc/manualHaploStats.pdf usr/share/doc/r-cran-haplo.stats/manualHaploStats.pdf debian/README.test0000644000000000000000000000044212141652751011030 0ustar Notes on how this package can be tested. ──────────────────────────────────────── This package can be tested by loading it into R with the command ‘library(haplo.stats)’ in order to confirm its integrity. debian/doc-base0000644000000000000000000000111211715317710010564 0ustar Document: r-cran-haplo.stats Title: Statistical Methods for Haplotypes When Linkage Phase is Ambiguous Author: Jason P. Sinnwell∗and Daniel J. Schaid Abstract: GNU R package for haplotype analysis Haplo Stats is a suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers), while also allowing for missing alleles. Section: Science/Biology Format: pdf Files: /usr/share/doc/r-cran-haplo.stats/manualHaploStats.pdf debian/copyright0000644000000000000000000000262712141652075011133 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: Haplo Stats Upstream-Contact: Jason P. Sinnwell Source: http://cran.r-project.org/src/contrib/haplo.stats_1.6.3.tar.gz Files: * Copyright: 2003-2012 Mayo Foundation for Medical Education and Research 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. . For other licensing arrangements, please contact Daniel J. Schaid. . On a Debian system, the GNU GPL license version 2 is distributed in the file ‘/usr/share/common-licenses/GPL-2’. Files: debian/* Copyright: 2008-2012 Steffen Moeller , Charles Plessy , Andreas Tille License: GPL-2+ Same as software itself. debian/changelog0000644000000000000000000000606712141653347011057 0ustar r-cran-haplo.stats (1.6.3-1) unstable; urgency=low * Team upload. * New upstream version. * Depend on R 2.15 according to DESCRIPTION. * Normalised VCS URLs following Lintian's standard. * Using Debhelper 9. * Normalised debian/control with config-model-edit. * Removed myself from Uploaders. * Renamed debian/README.Debian debian/README.test. * Conforms with Policy 3.9.4. -- Charles Plessy Mon, 06 May 2013 16:08:15 +0900 r-cran-haplo.stats (1.5.5-1) 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) which is supporting R:Depends substitution variable * debian/rules: Remove R:Depends substitution variable which isn now included in /usr/share/R/debian/r-cran.mk * debian/copyright: Fixed DEP5 issues using cme fix dpkg-copyright * debian/docs -> debian/links: Symlink to Manual rather than copying it * debian/doc_source: Removed because now part of upstream source -- Andreas Tille Tue, 28 Feb 2012 09:28:22 +0100 r-cran-haplo.stats (1.5.2-1) unstable; urgency=low [ Charles Plessy ] * debian/upstream-metadata.yaml -> debian/upstream [ Andreas Tille ] * New upstream version * debian/control: - Standards-Version: 3.9.2 - Fixed Vcs-Browser - Depends: ${R:Depends} * debhelper 8 (control+compat) * debian/source/format: 3.0 (quilt) * debian/rules: use usual R:depends variable substitution * debian/lintian-overrides: do not warn about duplicate license * debian/copyright: DEP5 * debian/doc_source/manualHaploStats.Rnw: Source for user manual provided by upstream Closes: #655439 * debian/docs: Install user manual * debian/doc-base: Doc-base control file * debian/README.Debian: Hint how to test the package -- Andreas Tille Fri, 10 Feb 2012 15:54:27 +0100 r-cran-haplo.stats (1.4.4-1) unstable; urgency=low * New upstream release (documentation update). * Updated Standards-Version to reflect conformance with Policy 3.8.3 (debian/control, no changes needed). * Added various informations in debian/upstream-metadata.yaml. -- Charles Plessy Wed, 21 Oct 2009 13:48:31 +0900 r-cran-haplo.stats (1.4.3-1) unstable; urgency=low * New upstream release. * 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). * Refreshed debian/copyright. -- Charles Plessy Wed, 08 Jul 2009 13:36:28 +0900 r-cran-haplo.stats (1.3.8-2) unstable; urgency=low * Following Dirk's request to remove him from the uploaders list. * debian/control: Better compliance with 3.8.0 policy. -- Steffen Moeller Thu, 15 Jan 2009 14:39:39 +0100 r-cran-haplo.stats (1.3.8-1) unstable; urgency=low * Initial release (closes: #492122). -- Steffen Moeller Wed, 23 Jul 2008 18:27:42 +0200 debian/source/0000755000000000000000000000000012141653370010470 5ustar debian/source/format0000644000000000000000000000001411715230173011674 0ustar 3.0 (quilt) debian/rules0000755000000000000000000000013412141652634010250 0ustar #!/usr/bin/make -f DEB_COMPRESS_EXCLUDE_ALL := .pdf include /usr/share/R/debian/r-cran.mk debian/watch0000644000000000000000000000012211041724064010211 0ustar version=3 http://cran.r-project.org/src/contrib/haplo.stats_([-0-9\.]*)\.tar\.gz debian/control0000644000000000000000000000223312141653334010573 0ustar Source: r-cran-haplo.stats Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Section: gnu-r Priority: optional Build-Depends: debhelper (>= 9), cdbs, r-base-dev (>= 2.15) Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/R/r-cran-haplo.stats/trunk Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/R/r-cran-haplo.stats/trunk/ Homepage: http://cran.r-project.org/web/packages/haplo.stats Package: r-cran-haplo.stats Architecture: any Depends: ${shlibs:Depends}, ${R:Depends} Description: GNU R package for haplotype analysis The package provides routines for the GNU R statistics environment for statistical Analysis of indirectly measured Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The main functions are: haplo.em, haplo.glm, haplo.score, haplo.power, and seqhap. debian/upstream0000644000000000000000000000020511711137235010747 0ustar Contact: Jason P. Sinnwell Homepage: http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm