[med-svn] [r-bioc-deseq2] 05/06: Refresh patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-deseq2.

commit 00859d12f6890b26328a39cf11a85f60befd9480
Author: Andreas Tille <tille at debian.org>
Date:   Fri Nov 10 09:18:38 2017 +0100

    Refresh patches
---
 debian/patches/remove-locfit | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/debian/patches/remove-locfit b/debian/patches/remove-locfit
index 649642d..b01adec 100644
--- a/debian/patches/remove-locfit
+++ b/debian/patches/remove-locfit
@@ -2,7 +2,7 @@ Author: Michael R. Crusoe <michael.crusoe at gmail.com>
 Description: r-cran-locfit is non-free and not yet packaged for Debian
 --- a/R/core.R
 +++ b/R/core.R
-@@ -156,7 +156,7 @@ NULL
+@@ -159,7 +159,7 @@ NULL
  #' 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}})
@@ -11,15 +11,15 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian
  #' 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
-@@ -206,7 +206,6 @@ NULL
- #' 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}
+@@ -210,7 +210,6 @@ NULL
+ #' 
  #' @import BiocGenerics BiocParallel S4Vectors IRanges GenomicRanges SummarizedExperiment Biobase Rcpp methods
  #'
 -#' @importFrom locfit locfit
  #' @importFrom genefilter rowVars filtered_p
  #' @importFrom Hmisc wtd.quantile
  #' 
-@@ -242,14 +241,14 @@ NULL
+@@ -246,14 +245,14 @@ NULL
  #'
  #' @export
  DESeq <- function(object, test=c("Wald","LRT"),
@@ -36,7 +36,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian
    stopifnot(is.logical(quiet))
    stopifnot(is.numeric(minReplicatesForReplace))
    stopifnot(is.logical(parallel))
-@@ -507,7 +506,7 @@ estimateSizeFactorsForMatrix <- function
+@@ -511,7 +510,7 @@ estimateSizeFactorsForMatrix <- function
  #' examples below.
  #'
  #' @param object a DESeqDataSet
@@ -45,7 +45,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian
  #' 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
-@@ -721,7 +720,7 @@ estimateDispersionsGeneEst <- function(o
+@@ -728,7 +727,7 @@ estimateDispersionsGeneEst <- function(o
  
  #' @rdname estimateDispersionsGeneEst
  #' @export
@@ -54,7 +54,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian
                                     minDisp=1e-8, quiet=FALSE) {
  
    if (is.null(mcols(object)$allZero)) {
-@@ -738,7 +737,7 @@ estimateDispersionsFit <- function(objec
+@@ -745,7 +744,7 @@ estimateDispersionsFit <- function(objec
    ...then continue with testing using nbinomWaldTest or nbinomLRT")
    }
    
@@ -63,7 +63,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian
    stopifnot(length(fitType)==1)
    stopifnot(length(minDisp)==1)
    if (fitType == "parametric") {
-@@ -752,18 +751,18 @@ estimateDispersionsFit <- function(objec
+@@ -759,18 +758,18 @@ estimateDispersionsFit <- function(objec
        fitType <- "local"
      }
    }
@@ -88,7 +88,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian
      stop("unknown fitType")
    }
   
-@@ -1838,16 +1837,17 @@ parametricDispersionFit <- function( mea
+@@ -1849,16 +1848,17 @@ parametricDispersionFit <- function( mea
  
  # Local fit of dispersion to the mean intensity
  # fitting is done on log dispersion, log mean scale
@@ -136,7 +136,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian
    
    noReps <- checkForExperimentalReplicates(object, modelMatrix)
    if (noReps) {
-@@ -628,7 +628,7 @@ checkForExperimentalReplicates <- functi
+@@ -630,7 +630,7 @@ checkForExperimentalReplicates <- functi
  #' @rdname estimateDispersions
  #' @aliases estimateDispersions estimateDispersions,DESeqDataSet-method
  #' @param object a DESeqDataSet
@@ -145,7 +145,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian
  #' for the type of fitting of dispersions to the mean intensity.
  #' \itemize{
  #'   \item parametric - fit a dispersion-mean relation of the form:
-@@ -636,10 +636,6 @@ checkForExperimentalReplicates <- functi
+@@ -638,10 +638,6 @@ checkForExperimentalReplicates <- functi
  #'     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.
@@ -193,7 +193,7 @@ Description: r-cran-locfit is non-free and not yet packaged for Debian
  Suggests: testthat, knitr, BiocStyle, vsn, pheatmap, RColorBrewer, IHW,
 --- a/NAMESPACE
 +++ b/NAMESPACE
-@@ -88,7 +88,6 @@ importFrom(graphics,axis)
+@@ -92,7 +92,6 @@ importFrom(graphics,axis)
  importFrom(graphics,hist)
  importFrom(graphics,plot)
  importFrom(graphics,points)

-- 
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