[med-svn] [r-bioc-deseq2] 05/05: update to latest release, add autopkgtest
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Jun 28 16:22:42 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository r-bioc-deseq2.
commit 32d189c2aa367670df6e0cb399e1a641d6d8cf61
Author: Michael R. Crusoe <crusoe at ucdavis.edu>
Date: Mon Jun 27 13:43:12 2016 -0700
update to latest release, add autopkgtest
---
debian/README.test | 8 ++
debian/changelog | 6 +-
debian/control | 28 ++++-
debian/copyright | 27 ++++-
debian/docs | 3 +
debian/patches/remove-locfit | 273 +++++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 1 +
debian/tests/control | 3 +
debian/tests/run-unit-test | 16 +++
10 files changed, 352 insertions(+), 14 deletions(-)
diff --git a/debian/README.test b/debian/README.test
new file mode 100644
index 0000000..55a9142
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+To run the unit tests provided by the package you can do
+
+ sh run-unit-test
+
+in this directory.
diff --git a/debian/changelog b/debian/changelog
index f8a216f..b05f4b3 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-r-bioc-deseq2 (1.10.1-1) UNRELEASED; urgency=medium
+r-bioc-deseq2 (1.12.3-1) UNRELEASED; urgency=medium
- * Initial release (Closes: #778586)
+ * Initial release (Closes: #828850)
- -- Michael R. Crusoe <crusoe at ucdavis.edu> Mon, 16 Feb 2015 19:26:42 -0500
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Mon, 27 Jun 2016 13:42:38 -0700
diff --git a/debian/control b/debian/control
index f7752ac..b135ba4 100644
--- a/debian/control
+++ b/debian/control
@@ -1,6 +1,6 @@
Source: r-bioc-deseq2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
+Uploaders: Michael R. Crusoe <michael.crusoe at gmail.com>
Section: gnu-r
Priority: optional
Build-Depends: debhelper (>= 9),
@@ -11,17 +11,33 @@ Build-Depends: debhelper (>= 9),
r-cran-hmisc,
r-cran-rcpparmadillo,
r-cran-foreign,
- r-cran-nnet
-Standards-Version: 3.9.6
+ r-cran-nnet,
+ r-bioc-genomicranges,
+ r-bioc-summarizedexperiment,
+ r-bioc-biocparallel,
+ r-bioc-geneplotter,
+ r-cran-knitr
+Standards-Version: 3.9.8
Homepage: https://bioconductor.org/packages/DESeq2/
-Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/r-bioc-deseq2.git
-Vcs-Git: git://anonscm.debian.org/debian-med/r-bioc-deseq2.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/r-bioc-deseq2.git
+Vcs-Git: https://anonscm.debian.org/debian-med/r-bioc-deseq2.git
Package: r-bioc-deseq2
Architecture: any
Depends: ${R:Depends},
${misc:Depends},
- ${shlibs:Depends}
+ ${shlibs:Depends},
+ r-bioc-genefilter,
+ r-cran-ggplot2,
+ r-cran-hmisc,
+ r-cran-rcpparmadillo,
+ r-cran-foreign,
+ r-cran-nnet,
+ r-bioc-genomicranges,
+ r-bioc-summarizedexperiment,
+ r-bioc-biocparallel,
+ r-bioc-geneplotter,
+ r-cran-testthat
Description: R package for RNA-Seq Differential Expression Analysis
Differential gene expression analysis based on the negative binomial
distribution. Estimate variance-mean dependence in count data from
diff --git a/debian/copyright b/debian/copyright
index 55f684a..6f6a6fd 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,13 +1,30 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: DESeq2
Source: https://bioconductor.org/packages/DESeq2/
Files: *
Copyright: © 2014 Michael Love, Simon Anders, Wolfgang Huber
-License: LGPL-3.0+
+License: LGPL-3+
Files: debian/*
-Copyright: © 2016 Regents of the University of California
-License: LGPL-3.0+
-
+Copyright: © 2016 Michael R. Crusoe <michael.crusoe at gmail.com>
+License: LGPL-3+
+License: LGPL-3+
+ This package 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 package 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
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this package; if not, write to the Free
+ Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
+ 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU Lesser General Public
+ License version 3 can be found in `/usr/share/common-licenses/LGPL-3'.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..960011c
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,3 @@
+tests
+debian/README.test
+debian/tests/run-unit-test
diff --git a/debian/patches/remove-locfit b/debian/patches/remove-locfit
new file mode 100644
index 0000000..5c53a4f
--- /dev/null
+++ b/debian/patches/remove-locfit
@@ -0,0 +1,273 @@
+Author: Michael R. Crusoe <michael.crusoe at gmail.com>
+Description: r-cran-locfit is non-free and not yet packaged for Debian
+--- r-bioc-deseq2.orig/R/core.R
++++ r-bioc-deseq2/R/core.R
+@@ -153,7 +153,7 @@
+ #' Wald significance tests (defined by \code{\link{nbinomWaldTest}}),
+ #' or the likelihood ratio test on the difference in deviance between a
+ #' full and reduced model formula (defined by \code{\link{nbinomLRT}})
+-#' @param fitType either "parametric", "local", or "mean"
++#' @param fitType either "parametric", or "mean"
+ #' for the type of fitting of dispersions to the mean intensity.
+ #' See \code{\link{estimateDispersions}} for description.
+ #' @param betaPrior whether or not to put a zero-mean normal prior on
+@@ -202,7 +202,6 @@
+ #' Michael I Love, Wolfgang Huber, Simon Anders: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology 2014, 15:550. \url{http://dx.doi.org/10.1186/s13059-014-0550-8}
+ #' @import BiocGenerics BiocParallel S4Vectors IRanges GenomicRanges SummarizedExperiment Biobase Rcpp methods
+ #'
+-#' @importFrom locfit locfit
+ #' @importFrom genefilter rowVars filtered_p
+ #' @importFrom Hmisc wtd.quantile
+ #'
+@@ -234,14 +233,14 @@
+ #'
+ #' @export
+ DESeq <- function(object, test=c("Wald","LRT"),
+- fitType=c("parametric","local","mean"), betaPrior,
++ fitType=c("parametric","mean"), betaPrior,
+ full=design(object), reduced, quiet=FALSE,
+ minReplicatesForReplace=7, modelMatrixType,
+ parallel=FALSE, BPPARAM=bpparam()) {
+ # check arguments
+ stopifnot(is(object, "DESeqDataSet"))
+ test <- match.arg(test, choices=c("Wald","LRT"))
+- fitType <- match.arg(fitType, choices=c("parametric","local","mean"))
++ fitType <- match.arg(fitType, choices=c("parametric","mean"))
+ stopifnot(is.logical(quiet))
+ stopifnot(is.numeric(minReplicatesForReplace))
+ stopifnot(is.logical(parallel))
+@@ -495,7 +494,7 @@
+ #' examples below.
+ #'
+ #' @param object a DESeqDataSet
+-#' @param fitType either "parametric", "local", or "mean"
++#' @param fitType either "parametric", or "mean"
+ #' for the type of fitting of dispersions to the mean intensity.
+ #' See \code{\link{estimateDispersions}} for description.
+ #' @param outlierSD the number of standard deviations of log
+@@ -677,7 +676,7 @@
+
+ #' @rdname estimateDispersionsGeneEst
+ #' @export
+-estimateDispersionsFit <- function(object,fitType=c("parametric","local","mean"),
++estimateDispersionsFit <- function(object,fitType=c("parametric","mean"),
+ minDisp=1e-8, quiet=FALSE) {
+
+ if (is.null(mcols(object)$allZero)) {
+@@ -694,7 +693,7 @@
+ ...then continue with testing using nbinomWaldTest or nbinomLRT")
+ }
+
+- fitType <- match.arg(fitType, choices=c("parametric","local","mean"))
++ fitType <- match.arg(fitType, choices=c("parametric","mean"))
+ stopifnot(length(fitType)==1)
+ stopifnot(length(minDisp)==1)
+ if (fitType == "parametric") {
+@@ -708,18 +707,18 @@
+ fitType <- "local"
+ }
+ }
+- if (fitType == "local") {
+- dispFunction <- localDispersionFit(means = mcols(objectNZ)$baseMean[useForFit],
+- disps = mcols(objectNZ)$dispGeneEst[useForFit],
+- minDisp = minDisp)
+- }
++ #if (fitType == "local") {
++ # dispFunction <- localDispersionFit(means = mcols(objectNZ)$baseMean[useForFit],
++ # disps = mcols(objectNZ)$dispGeneEst[useForFit],
++ # minDisp = minDisp)
++ #}
+ if (fitType == "mean") {
+ useForMean <- mcols(objectNZ)$dispGeneEst > 10*minDisp
+ meanDisp <- mean(mcols(objectNZ)$dispGeneEst[useForMean],na.rm=TRUE,trim=0.001)
+ dispFunction <- function(means) meanDisp
+ attr( dispFunction, "mean" ) <- meanDisp
+ }
+- if (!(fitType %in% c("parametric","local","mean"))) {
++ if (!(fitType %in% c("parametric","mean"))) {
+ stop("unknown fitType")
+ }
+
+@@ -1828,16 +1827,17 @@
+
+ # Local fit of dispersion to the mean intensity
+ # fitting is done on log dispersion, log mean scale
+-localDispersionFit <- function( means, disps, minDisp ) {
+- if (all(disps < minDisp*10)) {
+- return(rep(minDisp,length(disps)))
+- }
+- d <- data.frame(logDisps = log(disps), logMeans = log(means))
+- fit <- locfit(logDisps ~ logMeans, data=d[disps >= minDisp*10,,drop=FALSE],
+- weights = means[disps >= minDisp*10])
+- dispFunction <- function(means) exp(predict(fit, data.frame(logMeans=log(means))))
+- return(dispFunction)
+-}
++# locfit is non-free and not packaged at this time for Debian
++#localDispersionFit <- function( means, disps, minDisp ) {
++# if (all(disps < minDisp*10)) {
++# return(rep(minDisp,length(disps)))
++# }
++# d <- data.frame(logDisps = log(disps), logMeans = log(means))
++# fit <- locfit(logDisps ~ logMeans, data=d[disps >= minDisp*10,,drop=FALSE],
++# weights = means[disps >= minDisp*10])
++# dispFunction <- function(means) exp(predict(fit, data.frame(logMeans=log(means))))
++# return(dispFunction)
++#}
+
+
+ # convenience function for testing the log likelihood
+--- r-bioc-deseq2.orig/R/methods.R
++++ r-bioc-deseq2/R/methods.R
+@@ -493,7 +493,7 @@
+ setMethod("estimateSizeFactors", signature(object="DESeqDataSet"),
+ estimateSizeFactors.DESeqDataSet)
+
+-estimateDispersions.DESeqDataSet <- function(object, fitType=c("parametric","local","mean"),
++estimateDispersions.DESeqDataSet <- function(object, fitType=c("parametric","mean"),
+ maxit=100, quiet=FALSE, modelMatrix=NULL) {
+ # Temporary hack for backward compatibility with "old" DESeqDataSet
+ # objects. Remove once all serialized DESeqDataSet objects around have
+@@ -522,7 +522,7 @@
+ mcols(object) <- mcols(object)[,!(mcols(mcols(object))$type %in% c("intermediate","results")),drop=FALSE]
+ }
+ stopifnot(length(maxit)==1)
+- fitType <- match.arg(fitType, choices=c("parametric","local","mean"))
++ fitType <- match.arg(fitType, choices=c("parametric","mean"))
+
+ noReps <- checkForExperimentalReplicates(object, modelMatrix)
+ if (noReps) {
+@@ -615,7 +615,7 @@
+ #' @rdname estimateDispersions
+ #' @aliases estimateDispersions estimateDispersions,DESeqDataSet-method
+ #' @param object a DESeqDataSet
+-#' @param fitType either "parametric", "local", or "mean"
++#' @param fitType either "parametric", or "mean"
+ #' for the type of fitting of dispersions to the mean intensity.
+ #' \itemize{
+ #' \item parametric - fit a dispersion-mean relation of the form:
+@@ -623,10 +623,6 @@
+ #' via a robust gamma-family GLM. The coefficients \code{asymptDisp} and \code{extraPois}
+ #' are given in the attribute \code{coefficients} of the \code{\link{dispersionFunction}}
+ #' of the object.
+-#' \item local - use the locfit package to fit a local regression
+-#' of log dispersions over log base mean (normal scale means and dispersions
+-#' are input and output for \code{\link{dispersionFunction}}). The points
+-#' are weighted by normalized mean count in the local regression.
+ #' \item mean - use the mean of gene-wise dispersion estimates.
+ #' }
+ #' @param maxit control parameter: maximum number of iterations to allow for convergence
+--- r-bioc-deseq2.orig/R/vst.R
++++ r-bioc-deseq2/R/vst.R
+@@ -53,12 +53,6 @@
+ #' count data. The expression can be found in the file \file{vst.pdf}
+ #' which is distributed with the vignette.
+ #'
+-#' \code{fitType="local"},
+-#' the reciprocal of the square root of the variance of the normalized counts, as derived
+-#' from the dispersion fit, is then numerically
+-#' integrated, and the integral (approximated by a spline function) is evaluated for each
+-#' count value in the column, yielding a transformed value.
+-#'
+ #' \code{fitType="mean"}, a VST is applied for Negative Binomial distributed counts, 'k',
+ #' with a fixed dispersion, 'a': ( 2 asinh(sqrt(a k)) - log(a) - log(4) )/log(2).
+ #'
+@@ -202,7 +196,7 @@
+ vst <- function(q) ( 2 * asinh(sqrt(alpha * q)) - log(alpha) - log(4) ) / log(2)
+ return(vst(ncounts))
+ } else {
+- stop( "fitType is not parametric, local or mean" )
++ stop( "fitType is not parametric, or mean" )
+ }
+ }
+
+--- r-bioc-deseq2.orig/inst/doc/DESeq2.Rnw
++++ r-bioc-deseq2/inst/doc/DESeq2.Rnw
+@@ -936,9 +936,7 @@
+ closed-form expression for the variance stabilizing transformation is
+ used by \Rfunction{varianceStabilizingTransformation}, which is
+ derived in the file \texttt{vst.pdf}, that is distributed in the
+-package alongside this vignette. If a local fit is used (option
+-\Robject{fitType="locfit"} to \Rfunction{estimateDispersions}) a
+-numerical integration is used instead.
++package alongside this vignette.
+
+ The resulting variance stabilizing transformation is shown in Figure
+ \ref{figure/vsd1-1}. The code that produces the figure is hidden from
+--- r-bioc-deseq2.orig/tests/testthat/test_disp_fit.R
++++ r-bioc-deseq2/tests/testthat/test_disp_fit.R
+@@ -78,7 +78,7 @@
+ # test fit alternative
+ dds <- makeExampleDESeqDataSet()
+ dds <- estimateSizeFactors(dds)
+-ddsLocal <- estimateDispersions(dds, fitType="local")
++#ddsLocal <- estimateDispersions(dds, fitType="local")
+ ddsMean <- estimateDispersions(dds, fitType="mean")
+ ddsMed <- estimateDispersionsGeneEst(dds)
+ useForMedian <- mcols(ddsMed)$dispGeneEst > 1e-7
+--- r-bioc-deseq2.orig/tests/testthat/test_vst.R
++++ r-bioc-deseq2/tests/testthat/test_vst.R
+@@ -4,7 +4,7 @@
+ dds <- estimateDispersionsGeneEst(dds)
+ dds <- estimateDispersionsFit(dds, fitType="parametric")
+ vsd <- varianceStabilizingTransformation(dds, blind=FALSE)
+-dds <- estimateDispersionsFit(dds, fitType="local")
++#dds <- estimateDispersionsFit(dds, fitType="local")
+ vsd <- varianceStabilizingTransformation(dds, blind=FALSE)
+ dds <- estimateDispersionsFit(dds, fitType="mean")
+ vsd <- varianceStabilizingTransformation(dds, blind=FALSE)
+@@ -28,4 +28,4 @@
+ dds <- makeExampleDESeqDataSet(n=100, m=10, betaSD=1.5)
+ nf <- matrix(exp(rnorm(1000,0,.2)),ncol=10)
+ normalizationFactors(dds) <- nf
+-vsd <- varianceStabilizingTransformation(dds, fitType="local")
++#vsd <- varianceStabilizingTransformation(dds, fitType="local")
+--- r-bioc-deseq2.orig/vignettes/DESeq2.Rnw
++++ r-bioc-deseq2/vignettes/DESeq2.Rnw
+@@ -936,9 +936,7 @@
+ closed-form expression for the variance stabilizing transformation is
+ used by \Rfunction{varianceStabilizingTransformation}, which is
+ derived in the file \texttt{vst.pdf}, that is distributed in the
+-package alongside this vignette. If a local fit is used (option
+-\Robject{fitType="locfit"} to \Rfunction{estimateDispersions}) a
+-numerical integration is used instead.
++package alongside this vignette.
+
+ The resulting variance stabilizing transformation is shown in Figure
+ \ref{figure/vsd1-1}. The code that produces the figure is hidden from
+@@ -1458,15 +1456,6 @@
+ estimates used in testing (blue).
+ }
+
+-\subsubsection{Local or mean dispersion fit}
+-
+-A local smoothed dispersion fit is automatically substitited in the case that
+-the parametric curve doesn't fit the observed dispersion mean relationship.
+-This can be prespecified by providing the argument
+-\Robject{fitType="local"} to either \Rfunction{DESeq} or \Rfunction{estimateDispersions}.
+-Additionally, using the mean of gene-wise disperion estimates as the
+-fitted value can be specified by providing the argument \Robject{fitType="mean"}.
+-
+ \subsubsection{Supply a custom dispersion fit}
+
+ Any fitted values can be provided during dispersion estimation, using
+--- r-bioc-deseq2.orig/DESCRIPTION
++++ r-bioc-deseq2/DESCRIPTION
+@@ -13,7 +13,7 @@
+ License: LGPL (>= 3)
+ VignetteBuilder: knitr
+ Imports: BiocGenerics (>= 0.7.5), Biobase, BiocParallel, genefilter,
+- methods, locfit, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0)
++ methods, geneplotter, ggplot2, Hmisc, Rcpp (>= 0.11.0)
+ Depends: S4Vectors (>= 0.9.25), IRanges, GenomicRanges,
+ SummarizedExperiment (>= 1.1.6)
+ Suggests: testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer,
+--- r-bioc-deseq2.orig/NAMESPACE
++++ r-bioc-deseq2/NAMESPACE
+@@ -86,7 +86,6 @@
+ importFrom(graphics,hist)
+ importFrom(graphics,plot)
+ importFrom(graphics,points)
+-importFrom(locfit,locfit)
+ importFrom(stats,Gamma)
+ importFrom(stats,as.formula)
+ importFrom(stats,coef)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..1040b84
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+remove-locfit
diff --git a/debian/rules b/debian/rules
index aeb12b3..fe409b4 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,4 +1,5 @@
#!/usr/bin/make -f
+export DEB_BUILD_MAINT_OPTIONS=hardening=+bindnow
debRreposname=bioc
include /usr/share/R/debian/r-cran.mk
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..d2aa55a
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
new file mode 100644
index 0000000..771fc61
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,16 @@
+#!/bin/sh -e
+
+pkg=r-bioc-deseq2
+if [ "$ADTTMP" = "" ] ; then
+ ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
+find . -name "*.gz" -exec gunzip \{\} \;
+export LC_ALL=C
+for test in *R
+do
+ R CMD BATCH ${test}
+ echo "Test ${test} passed"
+done
+rm -f $ADTTMP/*
--
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