[med-svn] r9025 - trunk/packages/R/r-other-mott-happy/trunk/debian
Andreas Tille
tille at alioth.debian.org
Sat Dec 17 17:42:02 UTC 2011
Author: tille
Date: 2011-12-17 17:42:02 +0000 (Sat, 17 Dec 2011)
New Revision: 9025
Added:
trunk/packages/R/r-other-mott-happy/trunk/debian/README.Debian
trunk/packages/R/r-other-mott-happy/trunk/debian/lintian-overrides
trunk/packages/R/r-other-mott-happy/trunk/debian/r-cran_without_simple-patchsys.mk
Modified:
trunk/packages/R/r-other-mott-happy/trunk/debian/changelog
trunk/packages/R/r-other-mott-happy/trunk/debian/control
trunk/packages/R/r-other-mott-happy/trunk/debian/rules
Log:
Nasty hack around #652456 but tried this as a reference for enhancing r-cran-dev; shortened (too) long description; upload to unstable
Added: trunk/packages/R/r-other-mott-happy/trunk/debian/README.Debian
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/README.Debian 2011-12-17 17:42:02 UTC (rev 9025)
@@ -0,0 +1,52 @@
+GNU R package for fine-mapping complex diseases
+
+ Most phenotypes of medical importance can be measured quantitatively,
+ and in many cases the genetic contribution is substantial, accounting
+ for 40% or more of the phenotypic variance. Considerable efforts have
+ been made to isolate the genes responsible for quantitative genetic
+ variation in human populations, but with little success, mostly
+ because genetic loci contributing to quantitative traits
+ (quantitative trait loci, QTL) have only a small effect on the
+ phenotype. Association studies have been proposed as the most
+ appropriate method for finding the genes that influence complex
+ traits. However, family-based studies may not provide the resolution
+ needed for positional cloning, unless they are very large, while
+ environmental or genetic differences between cases and controls may
+ confound population-based association studies.
+ .
+ These difficulties have led to the study of animal models of human
+ traits. Studies using experimental crosses between inbred animal
+ strains have been successful in mapping QTLs with effects on a number
+ of different phenotypes, including behaviour, but attempts to
+ fine-map QTLs in animals have often foundered on the discovery that a
+ single QTL of large effect was in fact due to multiple loci of small
+ effect positioned within the same chromosomal region. A further
+ potential difficulty with detecting QTLs between inbred crosses is
+ the significant reduction in genetic heterogeneity compared to the
+ total genetic variation present in animal populations: a QTL
+ segregating in the wild need not be present in the experimental
+ cross.
+ .
+ The idea behind this package is that when multiple strains of
+ animals that differ in their susceptibility to multiple diseases
+ are bread over multiple generations, then one can analyse the
+ contribution that a particular genetic locus has to each of those
+ diseases. While in the past this approach has been performed
+ for one disease at a time, this tool extends the statistics
+ for allowing multiple crosses and thus save animal lifes. A larger
+ stock of animals with more generations to keep them will further
+ help producing larger numbers of observable cross-over events
+ and thus help increasing the resolution of the mapping.
+ .
+ Happy is an R interface into the HAPPY C package for fine-mapping
+ Quantitative Trait Loci (QTL) in Heterogenous Stocks (HS). An HS is
+ an advanced intercross between (usually eight) founder inbred strains
+ of mice. HS are suitable for fine-mapping QTL. It uses a multipoint
+ analysis which offers significant improvements in statistical power to
+ detect QTLs over that achieved by single-marker association.
+ .
+ The happy package is
+ an extension of the original C program happy; it uses the C code to
+ compute the probability of descent from each of the founders, at each
+ locus position, but the happy packager allows a much richer range of
+ models to be fit to the data.
Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/changelog
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/changelog 2011-12-17 12:38:12 UTC (rev 9024)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/changelog 2011-12-17 17:42:02 UTC (rev 9025)
@@ -1,9 +1,9 @@
-r-other-mott-happy (2.1-6) UNRELEASED; urgency=low
+r-other-mott-happy (2.1-6) unstable; urgency=low
[ Steffen Möller ]
* debian/control:
- Build-Depends: r-cran-multicore
- - Recommends: r-cran-vr, r-cran-multicore
+ - Removed Recommends: r-cran-vr, r-cran-multicore
* Source Format 3.0 (quilt)
* debian/README.source (no need to tell what pacth is applied or not)
@@ -11,7 +11,17 @@
* debian/control:
- Standards-Version: 3.9.2 (no changes needed)
- Fixed Vcs fields
- - Versioned Build-Depends r-base-dev (>= 2.10)
+ - Versioned Build-Depends r-base-dev (>= 2.12)
+ - Use Depends: ${R:Depends} as in all other R packages of Debian Med
+ - Moved large parts of the long description to README.Debian
+ Closes: #622295
+ * debian/rules:
+ - Usual rules script of Debian Med team for R packages
+ - Work around bug #652456 and call private copy of r-cran.mk
+ to enable using source format 3.0
+ * debian/r-cran_without_simple-patchsys.mk
+ --> This should be removed once #652456 is solved and a versioned
+ Build-Depends should be used
-- Andreas Tille <tille at debian.org> Sat, 17 Dec 2011 13:05:47 +0100
Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/control
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/control 2011-12-17 12:38:12 UTC (rev 9024)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/control 2011-12-17 17:42:02 UTC (rev 9025)
@@ -4,7 +4,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), cdbs, r-base-dev (>= 2.10), r-cran-g.data, r-cran-multicore, r-cran-mass
+Build-Depends: debhelper (>= 8), cdbs, r-base-dev (>= 2.12), r-cran-g.data, r-cran-multicore, r-cran-mass
Standards-Version: 3.9.2
Homepage: http://www.well.ox.ac.uk/happy/happyR.shtml
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-other-mott-happy/trunk/
@@ -12,46 +12,8 @@
Package: r-other-mott-happy
Architecture: any
-Depends: ${shlibs:Depends}, r-base-core (>= 2.10.0), r-cran-g.data, r-cran-multicore, r-cran-mass
+Depends: ${shlibs:Depends}, ${R:Depends}
Description: GNU R package for fine-mapping complex diseases
- Most phenotypes of medical importance can be measured quantitatively,
- and in many cases the genetic contribution is substantial, accounting
- for 40% or more of the phenotypic variance. Considerable efforts have
- been made to isolate the genes responsible for quantitative genetic
- variation in human populations, but with little success, mostly
- because genetic loci contributing to quantitative traits
- (quantitative trait loci, QTL) have only a small effect on the
- phenotype. Association studies have been proposed as the most
- appropriate method for finding the genes that influence complex
- traits. However, family-based studies may not provide the resolution
- needed for positional cloning, unless they are very large, while
- environmental or genetic differences between cases and controls may
- confound population-based association studies.
- .
- These difficulties have led to the study of animal models of human
- traits. Studies using experimental crosses between inbred animal
- strains have been successful in mapping QTLs with effects on a number
- of different phenotypes, including behaviour, but attempts to
- fine-map QTLs in animals have often foundered on the discovery that a
- single QTL of large effect was in fact due to multiple loci of small
- effect positioned within the same chromosomal region. A further
- potential difficulty with detecting QTLs between inbred crosses is
- the significant reduction in genetic heterogeneity compared to the
- total genetic variation present in animal populations: a QTL
- segregating in the wild need not be present in the experimental
- cross.
- .
- The idea behind this package is that when multiple strains of
- animals that differ in their susceptibility to multiple diseases
- are bread over multiple generations, then one can analyse the
- contribution that a particular genetic locus has to each of those
- diseases. While in the past this approach has been performed
- for one disease at a time, this tool extends the statistics
- for allowing multiple crosses and thus save animal lifes. A larger
- stock of animals with more generations to keep them will further
- help producing larger numbers of observable cross-over events
- and thus help increasing the resolution of the mapping.
- .
Happy is an R interface into the HAPPY C package for fine-mapping
Quantitative Trait Loci (QTL) in Heterogenous Stocks (HS). An HS is
an advanced intercross between (usually eight) founder inbred strains
@@ -64,3 +26,6 @@
compute the probability of descent from each of the founders, at each
locus position, but the happy packager allows a much richer range of
models to be fit to the data.
+ .
+ Read /usr/share/doc/r-other-mott-happy/README.Debian for a more
+ detailed explanation.
Added: trunk/packages/R/r-other-mott-happy/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/lintian-overrides (rev 0)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/lintian-overrides 2011-12-17 17:42:02 UTC (rev 9025)
@@ -0,0 +1,2 @@
+# Usage of cdbs is hidden in r-cran.mk
+r-other-mott-happy source: unused-build-dependency-on-cdbs
Added: trunk/packages/R/r-other-mott-happy/trunk/debian/r-cran_without_simple-patchsys.mk
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/r-cran_without_simple-patchsys.mk (rev 0)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/r-cran_without_simple-patchsys.mk 2011-12-17 17:42:02 UTC (rev 9025)
@@ -0,0 +1,108 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+#
+# Generic debian/rules file for the Debian/GNU Linux r-cran-* packages
+#
+# Should be sufficient for Debianization of CRAN (http://cran.r-project.org)
+# packages. Note that you still need to provide the other files in debian/*,
+# in particular control, changelog and copyright.
+#
+# Copyright 2003-2008 by Dirk Eddelbuettel <edd at debian.org>
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/langcore.mk
+## include /usr/share/cdbs/1/rules/dpatch.mk
+# Check whether source format 3.0 (quilt) is used. If yes, do not include the conflicting simple-patchsys.mk
+formatfile := $(CURDIR)/debian/source/format
+format_3_quilt = $(shell if [ -f $(formatfile) ] ; then if grep -q '3.0[[:space:]]*(quilt)' $(formatfile) ; then echo 1 ; else echo 0 ; fi else echo 0 ; fi )
+ifeq ($(format_3_quilt),0)
+ include /usr/share/cdbs/1/rules/simple-patchsys.mk
+endif
+
+# awk command to extract word after Package or Bundle, not lowercased
+awkString := "'/^(Package|Bundle):/ {print $$2 }'"
+
+# apply it to the upstream meta-info file DESCRIPTION, also generate a lc version
+cranNameOrig := $(shell awk "$(awkString)" DESCRIPTION)
+cranName := $(shell echo "$(cranNameOrig)" | tr A-Z a-z)
+
+## if no debRreposname is known, set default to cran -- thanks, Steffen!
+ifeq ($(debRreposname),)
+ debRreposname := cran
+endif
+
+## we can define additional flags for R's make, eg "CXXFLAGS=-g0" for
+## RQuantLib but the default is empty
+## makeFlags :=
+## if makeFlags are defined, then we'll use them in this variable
+## which would otherwise be empty
+ifneq ($(makeFlags),)
+ makeFlagsCall := MAKEFLAGS=$(makeFlags)
+endif
+
+## and use the results to build the Debian'ized package name
+package := r-$(debRreposname)-$(cranName)
+
+## awk command to extract word after Priority
+prioritystr := "'/^Priority:/ {print tolower($$2) }'"
+priority := $(shell awk "$(prioritystr)" DESCRIPTION)
+
+ifeq ($(priority),recommended)
+ debRdir := usr/lib/R/library
+else
+ debRdir := usr/lib/R/site-library
+endif
+
+## we use these results for the to-be-installed-in directory
+debRlib := $(CURDIR)/debian/$(package)/$(debRdir)
+
+## optional installation of a lintian silencer
+lintiandir := $(CURDIR)/debian/$(package)/usr/share/lintian/overrides
+
+common-install-indep:: R_any_arch
+common-install-arch:: R_any_arch
+
+R_any_arch:
+ ## create the target directory
+ dh_installdirs $(debRdir)
+ ##
+ ## call R to install the sources we're looking at
+ ## use this inside xvfb-run if this wrapper is installed
+ if test -f /usr/bin/xvfb-run; then \
+ $(makeFlagsCall) xvfb-run -a \
+ R CMD INSTALL -l $(debRlib) --clean \
+ $(extraInstallFlags) . ; \
+ else \
+ $(makeFlagsCall) R CMD INSTALL -l $(debRlib) \
+ --clean $(extraInstallFlags) . ;\
+ fi
+ ## remove extra files which are present in some packages
+ rm -vf $(debRlib)/R.css \
+ $(debRlib)/$(cranNameOrig)/COPYING \
+ $(debRlib)/$(cranNameOrig)/LICENSE.txt
+ ## if we have an overrides file for lintian, install it
+ if test -f debian/overrides; then \
+ install -d $(lintiandir) ; \
+ install -m 0644 debian/overrides \
+ $(lintiandir)/$(package); \
+ fi
+
+## clean target from patch by Steffen Moeller on 16 May 2009
+clean::
+ ## the re-invocation of a build process should not
+ ## leave a footprint in Debian's diff.gz.
+ if test -d src; then \
+ find src -regex ".*\..*o" | \
+ xargs --no-run-if-empty -r rm; \
+ fi
+ rm -f config.log config.status
+ ## the configure file is provided by upstream but
+ ## could be recreated by a call to 'autoconf'.
+ #if [ -r configure.in ]; then \
+ # rm -f configure \
+ #fi
+ ##
+ # if [ -r src/Makevars.in ]; then \
+ # rm -f src/Makevars; \
+ # fi
+
Property changes on: trunk/packages/R/r-other-mott-happy/trunk/debian/r-cran_without_simple-patchsys.mk
___________________________________________________________________
Added: svn:executable
+ *
Modified: trunk/packages/R/r-other-mott-happy/trunk/debian/rules
===================================================================
--- trunk/packages/R/r-other-mott-happy/trunk/debian/rules 2011-12-17 12:38:12 UTC (rev 9024)
+++ trunk/packages/R/r-other-mott-happy/trunk/debian/rules 2011-12-17 17:42:02 UTC (rev 9025)
@@ -1,5 +1,14 @@
#!/usr/bin/make -f
# -*- makefile -*-
-debRreposname=other-mott
-include /usr/share/cdbs/1/rules/patchsys-quilt.mk
-include /usr/share/R/debian/r-cran.mk
+# debian/rules file for the Debian/GNU Linux r-other-mott-happy package
+# Copyright 2008 by Andreas Tille <tille at debian.org>
+
+debRreposname := other-mott
+
+## FIXME: Dirty workaround for bug #652456
+# include /usr/share/R/debian/r-cran.mk
+include debian/r-cran_without_simple-patchsys.mk
+
+# Require a number equal or superior than the R version the package was built with.
+install/$(package)::
+ echo "R:Depends=r-base-core (>= $(shell R --version | head -n1 | perl -ne 'print / +([0-9]\.[0-9]+\.[0-9])/')~)" >> debian/$(package).substvars
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