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Another attempt to fix links in Rd files to quieten R CMD check on Windows

- According to Martin, this is the 'simplest solution', which lets the help system resolve the location dynamically (https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016552.html)

Peter Hickey authored on 04/06/2020 03:06:19
Showing3 changed files

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@@ -35,18 +35,13 @@ BSmooth(BSseq,
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     monitoring' and 'Realization backends' for further details.}
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   \item{chunkdim}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
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     The dimensions of the chunks to use for writing the data to
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-    disk. By default,
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-    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}()}
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-    using the dimensions of the returned \linkS4class{BSseq} object will be
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-    used. See \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}}
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-    for more information.}
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+    disk. By default, \code{\link{getHDF5DumpChunkDim}()} using the dimensions
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+    of the returned \linkS4class{BSseq} object will be used. See
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+    \code{?{getHDF5DumpChunkDim}} for more information.}
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   \item{level}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
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     The compression level to use for writing the data to disk. By
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-    default,
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-    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}()}
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-    will be used. See
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-    \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}}
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-    for more information.}
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+    default, \code{\link{getHDF5DumpCompressionLevel}()} will be used. See
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+    \code{?\link{getHDF5DumpCompressionLevel}} for more information.}
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   \item{verbose}{A \code{logical(1)} indicating whether progress messages
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     should be printed (default \code{TRUE}).}
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 }
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@@ -67,8 +62,7 @@ BSmooth(BSseq,
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   \linkS4class{HDF5Array}, for example.
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   The choice of realization backend is controlled by the \code{BACKEND}
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-  argument, which defaults to the current value of
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-  \code{DelayedArray::\link[DelayedArray:RealizationSink]{getRealizationBackend}()}.
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+  argument, which defaults to the current value of \code{DelayedArray::\link{getRealizationBackend}()}.
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   \code{BSmooth} supports the following realization backends:
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@@ -134,9 +134,8 @@ 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:RealizationSink]{setRealizationBackend}}
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-      for alternative backends.
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-      }
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+      \code{?DelayedArray::\link{setRealizationBackend}} for alternative
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+      backends.}
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     \item{\code{strandCollapse(BSseq, shift = TRUE)}}{
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... ...
@@ -71,17 +71,14 @@
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   \item{chunkdim}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
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     The dimensions of the chunks to use for writing the data to
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     disk. By default,
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-    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}()}
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-    using the dimensions of the returned \linkS4class{BSseq} object will be
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-    used. See \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}}
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-    for more information.}
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+    \code{\link{getHDF5DumpChunkDim}()} using the dimensions of the returned
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+    \linkS4class{BSseq} object will be used. See
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+    \code{?\link{getHDF5DumpChunkDim}} for more information.}
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   \item{level}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
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     The compression level to use for writing the data to disk. By
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     default,
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-    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}()}
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-    will be used. See
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-    \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}}
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-    for more information.}
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+    \code{\link{getHDF5DumpCompressionLevel}()} will be used. See
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+    \code{?\link{getHDF5DumpCompressionLevel}} for more information.}
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   \item{nThread}{The number of threads used by \code{\link[data.table]{fread}}
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     when reading the \code{files}. Be careful when combining a parallel backend
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     specified with \code{BPPARAM} with \code{nThread} > 1 because each worker
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@@ -178,7 +175,7 @@
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 \section{Realization backends}{
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   The \code{read.bismark()} function creates a \linkS4class{BSseq} object with two assays, \code{M} and \code{Cov}.
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   The choice of \emph{realization backend} controls whether these assays are stored in-memory as an ordinary \link[base]{matrix} or on-disk as a \linkS4class{HDF5Array}, for example.
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-  The choice of realization backend is controlled by the \code{BACKEND} argument, which defaults to the current value of \code{DelayedArray::\link[DelayedArray:RealizationSink]{getRealizationBackend}()}.
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+  The choice of realization backend is controlled by the \code{BACKEND} argument, which defaults to the current value of \code{DelayedArray::\link{getRealizationBackend}()}.
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   \code{read.bismark()} supports the following realization backends:
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