@@ -1,5 +1,5 @@

 Package: bsseq

-Version: 1.11.1

+Version: 1.11.2

 Encoding: UTF-8

 Title: Analyze, manage and store bisulfite sequencing data

 Description: A collection of tools for analyzing and visualizing bisulfite

@@ -35,8 +35,7 @@ importFrom(R.utils, "isGzipped", "gunzip")

 import(limma)

 importFrom(permute, "shuffleSet", "how")

 importClassesFrom(DelayedArray, "DelayedArray", "DelayedMatrix")

-importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2",

-           "setRealizeBackend", "type")

+importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2")

 ##

 ## Exporting

@@ -134,7 +134,7 @@ slots for representing smoothed data. This class is an extension of

       matrices (the latter two can only be combined if all objects have the

       same rowRanges). The default, \code{BACKEND = NULL}, corresponds to using

       \link[base]{matrix} objects. See

-      \code{?DelayedArray::\link[DelayedArray]{setRealizeBackend}} for

+      \code{?DelayedArray::\link[DelayedArray]{setRealizationBackend}} for

       alternative backends.

       }

@@ -32,10 +32,10 @@

     \code{mc.cores} to a value greater than 1 is not  supported on MS

     Windows, see the help page for \code{mclapply}.}

   \item{verbose}{Make the function verbose.}

-  \item{BACKEND}{Which backend should be used for the 'M' and 'Cov' matrices?

-    The default, \code{NULL}, corresponds to using \link[base]{matrix}

-    objects. See \code{?DelayedArray::\link[DelayedArray]{setRealizeBackend}}

-    for alternative backends.}

+  \item{BACKEND}{The backend used for the 'M' and 'Cov' matrices. The default,

+  \code{NULL}, corresponds to using \link[base]{matrix} objects. See

+    \code{?DelayedArray::\link[DelayedArray]{setRealizationBackend}} for

+    alternative backends.}

 }

 \note{

   Input files can either be gzipped or not.

@@ -118,7 +118,7 @@

   # An example constructing a HDF5Array-backed BSseq object

   #

   library(HDF5Array)

-  # See ?DelayedArray::setRealizeBackend for details

+  # See ?DelayedArray::setRealizationBackend for details

   hdf5_bismarkBSseq <- read.bismark(files = infile,

                                     sampleNames = "test_data",

                                     rmZeroCov = FALSE,