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Changes due to renaming in DelayedArray package

Peter Hickey authored on 11/04/2017 11:56:48
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@@ -1,5 +1,5 @@
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 Package: bsseq
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-Version: 1.11.1
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+Version: 1.11.2
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 Encoding: UTF-8
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 Title: Analyze, manage and store bisulfite sequencing data
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 Description: A collection of tools for analyzing and visualizing bisulfite
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@@ -35,8 +35,7 @@ importFrom(R.utils, "isGzipped", "gunzip")
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 import(limma)
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 importFrom(permute, "shuffleSet", "how")
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 importClassesFrom(DelayedArray, "DelayedArray", "DelayedMatrix")
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-importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2",
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-           "setRealizeBackend", "type")
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+importFrom(DelayedArray, "DelayedArray", "plogis", "pmin2", "pmax2")
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 ##
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 ## Exporting
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@@ -134,7 +134,7 @@ slots for representing smoothed data. This class is an extension of
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       matrices (the latter two can only be combined if all objects have the
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       same rowRanges). The default, \code{BACKEND = NULL}, corresponds to using
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       \link[base]{matrix} objects. See
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-      \code{?DelayedArray::\link[DelayedArray]{setRealizeBackend}} for
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+      \code{?DelayedArray::\link[DelayedArray]{setRealizationBackend}} for
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       alternative backends.
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       }
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@@ -32,10 +32,10 @@
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     \code{mc.cores} to a value greater than 1 is not  supported on MS
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     Windows, see the help page for \code{mclapply}.}
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   \item{verbose}{Make the function verbose.}
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-  \item{BACKEND}{Which backend should be used for the 'M' and 'Cov' matrices?
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-    The default, \code{NULL}, corresponds to using \link[base]{matrix}
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-    objects. See \code{?DelayedArray::\link[DelayedArray]{setRealizeBackend}}
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-    for alternative backends.}
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+  \item{BACKEND}{The backend used for the 'M' and 'Cov' matrices. The default,
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+  \code{NULL}, corresponds to using \link[base]{matrix} objects. See
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+    \code{?DelayedArray::\link[DelayedArray]{setRealizationBackend}} for
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+    alternative backends.}
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 }
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 \note{
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   Input files can either be gzipped or not.
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@@ -118,7 +118,7 @@
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   # An example constructing a HDF5Array-backed BSseq object
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   #
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   library(HDF5Array)
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-  # See ?DelayedArray::setRealizeBackend for details
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+  # See ?DelayedArray::setRealizationBackend for details
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   hdf5_bismarkBSseq <- read.bismark(files = infile,
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                                     sampleNames = "test_data",
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                                     rmZeroCov = FALSE,