fix Rd warnings

.dev/CRAN_Release.cmd

@@ -127,7 +127,7 @@ install.packages("xml2")   # to check the 150 URLs in NEWS.md under --as-cran be
 q("no")
 R CMD build .
 R CMD check data.table_1.12.7.tar.gz --as-cran
-R CMD INSTALL data.table_1.12.7.tar.gz
+R CMD INSTALL data.table_1.12.7.tar.gz --html
 
 # Test C locale doesn't break test suite (#2771)
 echo LC_ALL=C > ~/.Renviron

NEWS.md

@@ -10,6 +10,8 @@
 
 ## NOTES
 
+1. Links in the manual were creating warnings when installing HTML, [#4000](https://github.com/Rdatatable/data.table/issues/4000). Thanks to Morgan Jacob.
+
 
 # data.table [v1.12.6](https://github.com/Rdatatable/data.table/milestone/18?closed=1)  (18 Oct 2019)
 

man/fread.Rd

@@ -42,11 +42,11 @@ yaml=FALSE, autostart=NA, tmpdir=tempdir()
   \item{skip}{ If 0 (default) start on the first line and from there finds the first row with a consistent number of columns. This automatically avoids irregular header information before the column names row. \code{skip>0} means ignore the first \code{skip} rows manually. \code{skip="string"} searches for \code{"string"} in the file (e.g. a substring of the column names row) and starts on that line (inspired by read.xls in package gdata). }
   \item{select}{ A vector of column names or numbers to keep, drop the rest. \code{select} may specify types too in the same way as \code{colClasses}; i.e., a vector of \code{colname=type} pairs, or a \code{list} of \code{type=col(s)} pairs. In all forms of \code{select}, the order that the columns are specified determines the order of the columns in the result. }
   \item{drop}{ Vector of column names or numbers to drop, keep the rest. }
-  \item{colClasses}{ As in \code{\link[utils]{read.csv}}; i.e., an unnamed vector of types corresponding to the columns in the file, or a named vector specifying types for a subset of the columns by name. The default, \code{NULL} means types are inferred from the data in the file. Further, \code{data.table} supports a named \code{list} of vectors of column names \emph{or numbers} where the \code{list} names are the class names; see examples. The \code{list} form makes it easier to set a batch of columns to be a particular class. When column numbers are used in the \code{list} form, they refer to the column number in the file not the column number after \code{select} or \code{drop} has been applied.
+  \item{colClasses}{ As in \code{\link[utils:read.table]{utils::read.csv}}; i.e., an unnamed vector of types corresponding to the columns in the file, or a named vector specifying types for a subset of the columns by name. The default, \code{NULL} means types are inferred from the data in the file. Further, \code{data.table} supports a named \code{list} of vectors of column names \emph{or numbers} where the \code{list} names are the class names; see examples. The \code{list} form makes it easier to set a batch of columns to be a particular class. When column numbers are used in the \code{list} form, they refer to the column number in the file not the column number after \code{select} or \code{drop} has been applied.
     If type coercion results in an error, introduces \code{NA}s, or would result in loss of accuracy, the coercion attempt is aborted for that column with warning and the column's type is left unchanged. If you really desire data loss (e.g. reading \code{3.14} as \code{integer}) you have to truncate such columns afterwards yourself explicitly so that this is clear to future readers of your code.
   }
-  \item{integer64}{ "integer64" (default) reads columns detected as containing integers larger than 2^31 as type \code{bit64::integer64}. Alternatively, \code{"double"|"numeric"} reads as \code{base::read.csv} does; i.e., possibly with loss of precision and if so silently. Or, "character". }
-  \item{dec}{ The decimal separator as in \code{base::read.csv}. If not "." (default) then usually ",". See details. }
+  \item{integer64}{ "integer64" (default) reads columns detected as containing integers larger than 2^31 as type \code{bit64::integer64}. Alternatively, \code{"double"|"numeric"} reads as \code{utils::read.csv} does; i.e., possibly with loss of precision and if so silently. Or, "character". }
+  \item{dec}{ The decimal separator as in \code{utils::read.csv}. If not "." (default) then usually ",". See details. }
   \item{col.names}{ A vector of optional names for the variables (columns). The default is to use the header column if present or detected, or if not "V" followed by the column number. This is applied after \code{check.names} and before \code{key} and \code{index}. }
   \item{check.names}{default is \code{FALSE}. If \code{TRUE} then the names of the variables in the \code{data.table} are checked to ensure that they are syntactically valid variable names. If necessary they are adjusted (by \code{\link{make.names}}) so that they are, and also to ensure that there are no duplicates.}
   \item{encoding}{ default is \code{"unknown"}. Other possible options are \code{"UTF-8"} and \code{"Latin-1"}.  Note: it is not used to re-encode the input, rather enables handling of encoded strings in their native encoding. }
@@ -63,7 +63,7 @@ yaml=FALSE, autostart=NA, tmpdir=tempdir()
   \item{keepLeadingZeros}{If TRUE a column containing numeric data with leading zeros will be read as character, otherwise leading zeros will be removed and converted to numeric.}
   \item{yaml}{ If \code{TRUE}, \code{fread} will attempt to parse (using \code{\link[yaml]{yaml.load}}) the top of the input as YAML, and further to glean parameters relevant to improving the performance of \code{fread} on the data itself. The entire YAML section is returned as parsed into a \code{list} in the \code{yaml_metadata} attribute. See \code{Details}. }
   \item{autostart}{ Deprecated and ignored with warning. Please use \code{skip} instead. }
-  \item{tmpdir}{ Directory to use as the \code{tmpdir} argument for any \code{tempfile} calls, e.g. when the input is a URL or a shell command. The default is \code{tempdir()} which can be controlled by setting \code{TMPDIR} before starting the R session; see \code{\link[base]{tempdir}}. }
+  \item{tmpdir}{ Directory to use as the \code{tmpdir} argument for any \code{tempfile} calls, e.g. when the input is a URL or a shell command. The default is \code{tempdir()} which can be controlled by setting \code{TMPDIR} before starting the R session; see \code{\link[base:tempfile]{base::tempdir}}. }
 }
 \details{
 

man/like.Rd

@@ -22,13 +22,13 @@ vector \%flike\% pattern
    \item{fixed}{ \code{logical}; should \code{pattern} be interpreted as a literal string (i.e., ignoring regular expressions)? }
 }
 \details{
-  Internally, \code{like} is essentially a wrapper around \code{\link[base]{grepl}}, except that it is smarter about handling \code{factor} input (\code{base::grep} uses slow \code{as.character} conversion).
+  Internally, \code{like} is essentially a wrapper around \code{\link[base:grep]{base::grepl}}, except that it is smarter about handling \code{factor} input (\code{base::grep} uses slow \code{as.character} conversion).
 }
 \value{
     Logical vector, \code{TRUE} for items that match \code{pattern}.
 }
 \note{ Current implementation does not make use of sorted keys. }
-\seealso{ \code{\link[base]{grepl}} }
+\seealso{ \code{\link[base:grep]{base::grepl}} }
 \examples{
 DT = data.table(Name=c("Mary","George","Martha"), Salary=c(2,3,4))
 DT[Name \%like\% "^Mar"]

man/openmp-utils.Rd

@@ -19,7 +19,7 @@
   A length 1 \code{integer}. The old value is returned by \code{setDTthreads} so you can store that prior value and pass it to \code{setDTthreads()} again after the section of your code where you control the number of threads.
 }
 \details{
-  \code{data.table} automatically switches to single threaded mode upon fork (the mechanism used by \code{\link[parallel]{mclapply}} and the foreach package). Otherwise, nested parallelism would very likely overload your CPUs and result in much slower execution. As \code{data.table} becomes more parallel internally, we expect explicit user parallelism to be needed less often. The \code{restore_after_fork} option controls what happens after the explicit fork parallelism completes. It needs to be at C level so it is not a regular R option using \code{options()}. By default \code{data.table} will be multi-threaded again; restoring the prior setting of \code{getDTthreads()}. But problems have been reported in the past on Mac with Intel OpenMP libraries whereas success has been reported on Linux. If you experience problems after fork, start a new R session and change the default behaviour by calling \code{setDTthreads(restore_after_fork=FALSE)} before retrying. Please raise issues on the data.table GitHub issues page.
+  \code{data.table} automatically switches to single threaded mode upon fork (the mechanism used by \code{parallel::mclapply} and the foreach package). Otherwise, nested parallelism would very likely overload your CPUs and result in much slower execution. As \code{data.table} becomes more parallel internally, we expect explicit user parallelism to be needed less often. The \code{restore_after_fork} option controls what happens after the explicit fork parallelism completes. It needs to be at C level so it is not a regular R option using \code{options()}. By default \code{data.table} will be multi-threaded again; restoring the prior setting of \code{getDTthreads()}. But problems have been reported in the past on Mac with Intel OpenMP libraries whereas success has been reported on Linux. If you experience problems after fork, start a new R session and change the default behaviour by calling \code{setDTthreads(restore_after_fork=FALSE)} before retrying. Please raise issues on the data.table GitHub issues page.
 
   The number of logical CPUs is determined by the OpenMP function \code{omp_get_num_procs()} whose meaning may vary across platforms and OpenMP implementations. \code{setDTthreads()} will not allow more than this limit. Neither will it allow more than \code{omp_get_thread_limit()} nor the current value of \code{Sys.getenv("OMP_THREAD_LIMIT")}. Note that CRAN's daily test system (results for data.table \href{https://cran.r-project.org/web/checks/check_results_data.table.html}{here}) sets \code{OMP_THREAD_LIMIT} to 2 and should always be respected; e.g., if you have written a package that uses data.table and your package is to be released on CRAN, you should not change \code{OMP_THREAD_LIMIT} in your package to a value greater than 2.