Browse code

Fix links in Rd files to quieten R CMD check on Windows

- FWIW Martin Morgan calls this the "complicated and not-best-practice solution" (https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016552.html)

Peter Hickey authored on 01/06/2020 09:35:56
Showing8 changed files

... ...
@@ -35,14 +35,18 @@ BSmooth(BSseq,
35 35
     monitoring' and 'Realization backends' for further details.}
36 36
   \item{chunkdim}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
37 37
     The dimensions of the chunks to use for writing the data to
38
-    disk. By default, \code{\link[HDF5Array]{getHDF5DumpChunkDim}()} using the
39
-    dimensions of the returned \linkS4class{BSseq} object will be used. See
40
-    \code{?\link[HDF5Array]{getHDF5DumpChunkDim}} for more information.}
38
+    disk. By default,
39
+    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}()}
40
+    using the dimensions of the returned \linkS4class{BSseq} object will be
41
+    used. See \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}}
42
+    for more information.}
41 43
   \item{level}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
42 44
     The compression level to use for writing the data to disk. By
43
-    default, \code{\link[HDF5Array]{getHDF5DumpCompressionLevel}()} will be
44
-    used. See \code{?\link[HDF5Array]{getHDF5DumpCompressionLevel}} for more
45
-    information.}
45
+    default,
46
+    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}()}
47
+    will be used. See
48
+    \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}}
49
+    for more information.}
46 50
   \item{verbose}{A \code{logical(1)} indicating whether progress messages
47 51
     should be printed (default \code{TRUE}).}
48 52
 }
... ...
@@ -64,7 +68,7 @@ BSmooth(BSseq,
64 68
 
65 69
   The choice of realization backend is controlled by the \code{BACKEND}
66 70
   argument, which defaults to the current value of
67
-  \code{DelayedArray::\link[DelayedArray]{getRealizationBackend}()}.
71
+  \code{DelayedArray::\link[DelayedArray:RealizationSink]{getRealizationBackend}()}.
68 72
 
69 73
   \code{BSmooth} supports the following realization backends:
70 74
 
... ...
@@ -134,8 +134,8 @@ slots for representing smoothed data. This class is an extension of
134 134
       matrices (the latter two can only be combined if all objects have the
135 135
       same rowRanges). The default, \code{BACKEND = NULL}, corresponds to using
136 136
       \link[base]{matrix} objects. See
137
-      \code{?DelayedArray::\link[DelayedArray]{setRealizationBackend}} for
138
-      alternative backends.
137
+      \code{?DelayedArray::\link[DelayedArray:RealizationSink]{setRealizationBackend}}
138
+      for alternative backends.
139 139
       }
140 140
 
141 141
     \item{\code{strandCollapse(BSseq, shift = TRUE)}}{
... ...
@@ -31,7 +31,7 @@ BSseq(M = NULL, Cov = NULL, coef = NULL, se.coef = NULL,
31 31
 \details{
32 32
   The 'M', 'Cov', 'coef', and 'se.coef' matrix-like objects will be coerced to
33 33
   \linkS4class{DelayedMatrix} objects; see
34
-  \code{?DelayedArray::\link[DelayedArray]{DelayedMatrix}} for the full list of
34
+  \code{?DelayedArray::\linkS4class{DelayedMatrix}} for the full list of
35 35
   supported matrix-like objects. We recommend using \link[base]{matrix} objects
36 36
   for in-memory storage of data and \linkS4class{HDF5Matrix} for on-disk
37 37
   storage of data.
... ...
@@ -24,7 +24,7 @@
24 24
 \details{
25 25
   The matrix-like elements of the list in the 'stats' slot will be coerced to
26 26
   \linkS4class{DelayedMatrix} objects; see
27
-  \code{?DelayedArray::\link[DelayedArray]{DelayedMatrix}} for the full list of
27
+  \code{?DelayedArray::\linkS4class{DelayedMatrix}} for the full list of
28 28
   supported matrix-like objects. We recommend using \link[base]{matrix} objects
29 29
   for in-memory storage of data and \linkS4class{HDF5Matrix} for on-disk
30 30
   storage of data.
... ...
@@ -24,7 +24,7 @@
24 24
 \details{
25 25
   The 'stats' matrix-like object will be coerced to a
26 26
   \linkS4class{DelayedMatrix} object; see
27
-  \code{?DelayedArray::\link[DelayedArray]{DelayedMatrix}} for the full list of
27
+  \code{?DelayedArray::\linkS4class{DelayedMatrix}} for the full list of
28 28
   supported matrix-like objects. We recommend using \link[base]{matrix} objects
29 29
   for in-memory storage of data and \linkS4class{HDF5Matrix} for on-disk
30 30
   storage of data.
... ...
@@ -41,8 +41,12 @@ findLoci(pattern,
41 41
   }
42 42
 }
43 43
 \details{
44
-  This function provides a convenience wrapper for finding methylation loci in a genome, based on running \code{\link[Biostrings]{vmatchPattern}()}.
45
-  Users requiring finer-grained control should directly use the \code{\link[Biostrings]{vmatchPattern}()} function and coerce the result to a \linkS4class{GRanges} object.
44
+  This function provides a convenience wrapper for finding methylation loci in
45
+  a genome, based on running
46
+  \code{\link[Biostrings:matchPattern]{vmatchPattern}()}.
47
+  Users requiring finer-grained control should directly use the
48
+  \code{\link[Biostrings:matchPattern]{vmatchPattern}()} function and coerce
49
+  the result to a \linkS4class{GRanges} object.
46 50
 }
47 51
 \value{
48 52
   A \linkS4class{GRanges} object storing the found loci.
... ...
@@ -52,7 +56,7 @@ findLoci(pattern,
52 56
 }
53 57
 \seealso{
54 58
   \itemize{
55
-    \item \code{Biostrings::\link[Biostrings]{vmatchPattern}()}
59
+    \item \code{Biostrings::\link[Biostrings:matchPattern]{vmatchPattern}()}
56 60
     \item \code{?BSgenome::`\link[BSgenome]{BSgenome-utils}`}
57 61
     }
58 62
 }
... ...
@@ -20,7 +20,7 @@ fisherTests(BSseq, group1, group2, lookup = NULL,
20 20
   \item{returnLookup}{Should a \sQuote{lookup} object be returned, see
21 21
     details.}
22 22
   \item{mc.cores}{The number of cores used.  Note that setting
23
-    \code{mc.cores} to a value greater than 1 is not  supported on MS
23
+    \code{mc.cores} to a value greater than 1 is not supported on MS
24 24
     Windows, see the help page for \code{mclapply}.}
25 25
   \item{verbose}{Should the function be verbose.}
26 26
 }
... ...
@@ -52,7 +52,7 @@ fisherTests(BSseq, group1, group2, lookup = NULL,
52 52
 }
53 53
 \seealso{
54 54
   \link[stats]{fisher.test} for information about Fisher's test.
55
-  \link[parallel]{mclapply} for the \code{mc.cores} argument.
55
+  \code{\link{mclapply}} for the \code{mc.cores} argument.
56 56
 }
57 57
 \examples{
58 58
 M <- matrix(1:9, 3,3)
... ...
@@ -33,7 +33,7 @@
33 33
     If \code{loci = NULL}, then \code{read.bismark()} will perform a first pass over the Bismark file to identify candidate loci.
34 34
     If \code{loci} is a \linkS4class{GenomicRanges} instance, then these form the candidate loci.
35 35
     In either case, the candidate loci will be filtered if
36
-    \code{rmZeroCov = TRUE} and collapsed if \code{strandCollapse = TRUE} to form the final set of methylation loci that form the \code{\link[SummarizedExperiment]{rowRanges}} of the returned \linkS4class{BSseq} object.
36
+    \code{rmZeroCov = TRUE} and collapsed if \code{strandCollapse = TRUE} to form the final set of methylation loci that form the \code{\link[SummarizedExperiment:RangedSummarizedExperiment-class]{rowRanges}} of the returned \linkS4class{BSseq} object.
37 37
     See section 'Efficient use of \code{read.bismark()}' for further details.}
38 38
   \item{colData}{An optional \linkS4class{DataFrame} describing the samples.
39 39
     Row names, if present, become the column names of the \linkS4class{BSseq}
... ...
@@ -70,14 +70,18 @@
70 70
     with a new one? The content of the existing directory will be lost!}
71 71
   \item{chunkdim}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
72 72
     The dimensions of the chunks to use for writing the data to
73
-    disk. By default, \code{\link[HDF5Array]{getHDF5DumpChunkDim}()} using the
74
-    dimensions of the returned \linkS4class{BSseq} object will be used. See
75
-    \code{?\link[HDF5Array]{getHDF5DumpChunkDim}} for more information.}
73
+    disk. By default,
74
+    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}()}
75
+    using the dimensions of the returned \linkS4class{BSseq} object will be
76
+    used. See \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpChunkDim}}
77
+    for more information.}
76 78
   \item{level}{\strong{Only applicable if \code{BACKEND == "HDF5Array"}.}
77 79
     The compression level to use for writing the data to disk. By
78
-    default, \code{\link[HDF5Array]{getHDF5DumpCompressionLevel}()} will be
79
-    used. See \code{?\link[HDF5Array]{getHDF5DumpCompressionLevel}} for more
80
-    information.}
80
+    default,
81
+    \code{\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}()}
82
+    will be used. See
83
+    \code{?\link[HDF5Array:HDF5-dump-management]{getHDF5DumpCompressionLevel}}
84
+    for more information.}
81 85
   \item{nThread}{The number of threads used by \code{\link[data.table]{fread}}
82 86
     when reading the \code{files}. Be careful when combining a parallel backend
83 87
     specified with \code{BPPARAM} with \code{nThread} > 1 because each worker
... ...
@@ -88,7 +92,7 @@
88 92
 
89 93
 \section{File formats}{
90 94
   The format of each file is automatically detected using the internal function \code{bsseq:::.guessBismarkFileType()}.
91
-  Files ending in \code{.gz}, \code{.bz2}, \code{.xz}, or \code{.zip} will be automatically decompressed to \code{\link[base]{tempdir}()}.
95
+  Files ending in \code{.gz}, \code{.bz2}, \code{.xz}, or \code{.zip} will be automatically decompressed to \code{\link{tempdir}()}.
92 96
   \subsection{Supported file formats}{
93 97
     Bismark's 'genome wide cytosine report' (\url{https://github.com/FelixKrueger/Bismark/tree/master/Docs#the-genome-wide-cytosine-report-optional-is-tab-delimited-in-the-following-format-1-based-coords}) and 'coverage' (\url{https://github.com/FelixKrueger/Bismark/tree/master/Docs#the-coverage-output-looks-like-this-tab-delimited-1-based-genomic-coords}) formats are both supported.
94 98
     If setting \code{loci = NULL}, then we strongly recommend using the 'genome wide cytosine report' output format because this includes strand information for each locus.
... ...
@@ -174,7 +178,7 @@
174 178
 \section{Realization backends}{
175 179
   The \code{read.bismark()} function creates a \linkS4class{BSseq} object with two assays, \code{M} and \code{Cov}.
176 180
   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.
177
-  The choice of realization backend is controlled by the \code{BACKEND} argument, which defaults to the current value of \code{DelayedArray::\link[DelayedArray]{getRealizationBackend}()}.
181
+  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}()}.
178 182
 
179 183
   \code{read.bismark()} supports the following realization backends:
180 184