Rd markup.

git-svn-id: https://svn.r-project.org/R/trunk@84750 00db46b3-68df-0310-9c12-caf00c1e9a41

src/library/base/man/Memory-limits.Rd

@@ -32,7 +32,7 @@
  \item The environment may impose limitations on the resources
  available to a single process: Windows' versions of \R do so directly.
  }
- Error messages beginning \code{cannot allocate vector of size}
+ Error messages beginning \samp{cannot allocate vector of size}
  indicate a failure to obtain memory, either because the size exceeded
  the address-space limit for a process or, more likely, because the
  system was unable to provide the memory. Note that on a 32-bit build
@@ -41,7 +41,7 @@
 
  There are also limits on individual objects. The storage space
  cannot exceed the address limit, and if you try to exceed that limit,
- the error message begins \code{cannot allocate vector of length}.
+ the error message begins \samp{cannot allocate vector of length}.
  The number of bytes in a character string is limited to
  \eqn{2^{31} - 1 \approx 2\thinspace 10^9}{2^31 - 1 ~ 2*10^9},
  which is also the limit on each dimension of an array.

src/library/base/man/S3method.Rd

@@ -14,7 +14,7 @@
  \item{class}{a character string naming an S3 class.}
  \item{method}{a character string or function giving the S3 method to
  be registered. If not given, the function named
- \code{\var{generic}.\var{class}} is used.}
+ \samp{\var{generic}.\var{class}} is used.}
 }
 \details{
  This function should only be used in R scripts: for package code, one

src/library/base/man/connections.Rd

@@ -572,8 +572,8 @@ socketTimeout(socket, timeout = -1)
  use Unicode file names (such as NTFS but not FAT32).
 }
 
-\section{\code{ftp://} URLs}{
- Most modern browsers do not support such URLs, and \code{https://}
+\section{\samp{ftp://} URLs}{
+ Most modern browsers do not support such URLs, and \samp{https://}
  ones are much preferred for use in \R.
 
  It is intended that \R will continue to allow such URLs for as long as

src/library/base/man/curlGetHeaders.Rd

@@ -10,7 +10,7 @@
 }
 \description{
  Retrieve the headers for a URL for a supported protocol such as
- \code{http://}, \code{ftp://}, \code{https://} and \code{ftps://}.
+ \samp{http://}, \samp{ftp://}, \samp{https://} and \samp{ftps://}.
 }
 \usage{
 curlGetHeaders(url, redirect = TRUE, verify = TRUE,
@@ -26,7 +26,7 @@ curlGetHeaders(url, redirect = TRUE, verify = TRUE,
  allowed to take. Non-positive and invalid values are ignored
  (including the default). (Added in \R 4.1.0.)}
  \item{TLS}{character: the minimum version of the TLS protocol to be used
- for \code{https://} URLs: the default (\code{""}) is no restriction
+ for \samp{https://} URLs: the default (\code{""}) is no restriction
  beyond that of the underlying \code{libcurl} (usually 1.0). Other
  valid values are \code{"1.1"}, \code{"1.2"} (both for \code{libcurl}
  7.34.0 and later) and \code{"1.3"} (7.52.0 and later), if supported
@@ -37,7 +37,7 @@ curlGetHeaders(url, redirect = TRUE, verify = TRUE,
 
 \details{
  This reports what \command{curl -I -L} or \command{curl -I} would
- report. For a \code{ftp://} URL the \sQuote{headers} are a record of
+ report. For a \samp{ftp://} URL the \sQuote{headers} are a record of
  the conversation between client and server before data transfer.
 
  Only 500 header lines will be reported: there is a limit of 20

src/library/base/man/funprog.Rd

@@ -81,11 +81,11 @@ Position(f, x, right = FALSE, nomatch = NA_integer_)
  subset of \code{x} for which this gives true. Note that possible
  \code{NA} values are currently always taken as false; control over
  \code{NA} handling may be added in the future. \code{Filter}
- corresponds to \code{filter} in Haskell or \code{remove-if-not} in
+ corresponds to \code{filter} in Haskell or \samp{remove-if-not} in
  Common Lisp.
 
  \code{Find} and \code{Position} are patterned after Common Lisp's
- \code{find-if} and \code{position-if}, respectively. If there is an
+ \samp{find-if} and \samp{position-if}, respectively. If there is an
  element for which the predicate function gives true, then the first or
  last such element or its position is returned depending on whether
  \code{right} is false (default) or true, respectively. If there is no

src/library/base/man/srcfile.Rd

@@ -127,7 +127,7 @@ srcref(srcfile, lloc)
  is made to read the file, and the original line numbers of the
  \code{srcref} record (i.e., elements 1 and 3) are used. If an error
  occurs (e.g., the file no longer exists), text like
- \code{<srcref: "file" chars 1:1 to 2:10>} will be returned instead,
+ \samp{<srcref: "file" chars 1:1 to 2:10>} will be returned instead,
  indicating the \code{line:column} ranges of the first and last
  character. The \code{summary} method defaults to this type of
  display.
@@ -138,7 +138,7 @@ srcref(srcfile, lloc)
  \code{\link{print.default}} using the associated \code{srcref}. To
  see deparsed code instead, call \code{\link{print}} with argument
  \code{useSource = FALSE}. If a \code{srcref} object
- is printed with \code{useSource = FALSE}, the \code{<srcref: \dots>}
+ is printed with \code{useSource = FALSE}, the \samp{<srcref: \dots>}
  record will be printed.
 
  \code{.isOpen} is intended for internal use: it checks whether the

src/library/base/man/system.Rd

@@ -110,7 +110,7 @@ system(command, intern = FALSE,
 
 #ifdef unix
  Timeouts cannot be used with interactive commands: the command is run with
- standard input redirected from \code{/dev/null} and it must not modify
+ standard input redirected from \file{/dev/null} and it must not modify
  terminal settings. As long as tty \code{tostop} option is disabled, which
  it usually is by default, the executed command may write to standard
  output and standard error. One cannot rely on that the execution time of

src/library/stats/man/formula.Rd

@@ -98,7 +98,7 @@ as.formula(object, env = parent.frame())
  including the function \code{\link{offset}} to indicate terms with a
  fixed coefficient of one. Some functions accept other
  \sQuote{specials} such as \code{strata} or \code{cluster} (see the
- \code{specials} argument of \code{\link{terms.formula})}.
+ \code{specials} argument of \code{\link{terms.formula}}).
 
  There are two special interpretations of \code{.} in a formula. The
  usual one is in the context of a \code{data} argument of model

src/library/tools/man/CRANtools.Rd

@@ -78,7 +78,7 @@ summarize_CRAN_check_status(packages,
  environment variable \env{R_CRAN_WEB}, defaulting to one specified in
  the \code{"repos"} option. Otherwise the entry in the
  \file{repositories} file (see \code{\link{setRepositories}}) is used:
- if that specifies \code{@CRAN@} (the default) or does not contain an
+ if that specifies \samp{@CRAN@} (the default) or does not contain an
  entry for CRAN then \url{https://CRAN.R-project.org} is used.
 
  The mirror to be used is reported by

src/library/tools/man/Rdiff.Rd

@@ -33,7 +33,7 @@ Rdiff(from, to, useDiff = FALSE, forEx = FALSE,
  on Windows, Windows' so-called \sQuote{smart quotes}, are mapped to
  a simple quote. Addresses of environments, compiled bytecode and
  other exotic types expressed as hex addresses
- (e.g., \code{<environment: 0x12345678>}) are mapped to
+ (e.g., \samp{<environment: 0x12345678>}) are mapped to
  \code{0x00000000}. The files are then compared line-by-line. If
  there are the same number of lines and \code{useDiff} is false, a
  simple \command{diff -b} -like display of differences is printed

src/library/tools/man/buildVignette.Rd

@@ -31,7 +31,7 @@ buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, tangle = TRUE,
  \item{keep}{a list of file names to keep in any case when cleaning. Note
  that \dQuote{target} files are kept anyway.}
  \item{engine}{\code{NULL} or character; name of vignette engine to
- use. Overrides any \code{\\VignetteEngine\{\}} markup in the vignette.}
+ use. Overrides any \samp{\\VignetteEngine\{\}} markup in the vignette.}
  \item{buildPkg}{\code{NULL} or a character vector; optional packages
  in which to find the vignette engine.}
  \item{encoding}{the encoding to assume for the file. If not
@@ -56,7 +56,7 @@ buildVignette(file, dir = ".", weave = TRUE, latex = TRUE, tangle = TRUE,
  the vignette is processed and will be used as the default packages in
  the search for a vignette engine, but an explicitly specified package
  in the vignette source (e.g., using
- \code{\\VignetteEngine\{utils::Sweave\}} to specify the \code{Sweave}
+ \samp{\\VignetteEngine\{utils::Sweave\}} to specify the \code{Sweave}
  engine in the \pkg{utils} package) will override it. In contrast, if
  the \code{engine} argument is given, it will override the vignette
  source.

src/library/tools/man/make_translations_pkg.Rd

@@ -16,7 +16,7 @@ make_translations_pkg(srcdir, outDir = ".", append = "-1")
  \item{srcdir}{The \R source directory.}
  \item{outDir}{The directory into which to place the prepared package.}
  \item{append}{The suffix for the package version number,
- e.g.\sspace{}\code{3.0.0-1} will be the default in \R 3.0.0.}
+ e.g.\sspace{}\samp{3.0.0-1} will be the default in \R 3.0.0.}
 }
 \details{
  This extracts the translations in a current \R source distribution and
@@ -27,7 +27,7 @@ make_translations_pkg(srcdir, outDir = ".", append = "-1")
  \samp{R-patched}, even by a user without administrative privileges.
 
  The package has a \samp{Depends} field which restricts it to versions
- \code{3.x.*} for a single \code{x}.
+ \samp{3.x.*} for a single \code{x}.
 }
 
 \keyword{utilities}

src/library/tools/man/package_native_routine_registration_skeleton.Rd

@@ -54,7 +54,7 @@ package_native_routine_registration_skeleton(dir, con = stdout(),
  routines: they should be checked against the C/Fortran source code,
  not least as the number of arguments is taken from the \R code. For
  \code{.Call} and \code{.External} calls they will often suffice, but
- for \code{.C} and \code{.Fortran} calls the \code{void *} arguments
+ for \code{.C} and \code{.Fortran} calls the \samp{void *} arguments
  would ideally be replaced by the actual types. Otherwise declarations
  need to be included (they may exist earlier in that file if appending
  to a file, or in a header file which can be included in

src/library/tools/man/startDynamicHelp.Rd

@@ -22,7 +22,7 @@ startDynamicHelp(start = TRUE)
 }
 \details{
  This function starts the internal HTTP server, which runs on the
- loopback interface (\code{127.0.0.1}). If \code{options("help.ports")}
+ loopback interface (\samp{127.0.0.1}). If \code{options("help.ports")}
  is set to a vector of non-zero integer values, \code{startDynamicHelp} will try
  those ports in order; otherwise, it tries up to 10 random ports to
  find one not in use. It can be disabled by setting the environment
@@ -43,7 +43,7 @@ startDynamicHelp(start = TRUE)
  The browser in use does need to be able to connect to the loopback
  interface: occasionally it is set to use a proxy for HTTP on all
  interfaces, which will not work -- the solution is to add an exception
- for \code{127.0.0.1}.
+ for \samp{127.0.0.1}.
 }
 \value{
  The chosen port number is returned invisibly (which will be \code{0}

src/library/tools/man/xgettext.Rd

@@ -48,7 +48,7 @@ xgettext2pot(dir, potFile, name = "R", version, bugs)
 }
 \details{
  Leading and trailing white space (space, tab and linefeed
- (aka newline, i.e., \code{\\n})) is removed
+ (aka newline, i.e., \samp{\\n})) is removed
  for all the calls extracted by \code{xgettext()}, see
  \sQuote{Description} above,
  as it is by the internal code that passes strings for translation.

src/library/utils/man/browseURL.Rd

@@ -79,9 +79,9 @@ browseURL(url, browser = getOption("browser"),
  \code{NULL}.
  To suppress showing URLs altogether, use the value \code{"false"}.
 
- Some browsers have required \code{:} be replaced by \code{|} in file
- paths: others do not accept that. All seem to accept \code{\\} as a
- path separator even though the RFC1738 standard requires \code{/}.
+ Some browsers have required \samp{:} be replaced by \samp{|} in file
+ paths: others do not accept that. All seem to accept \samp{\\} as a
+ path separator even though the RFC1738 standard requires \samp{/}.
 
  To suppress showing URLs altogether, set \code{browser = "false"}.
  }

src/library/utils/man/cite.Rd

@@ -35,7 +35,7 @@ Additional arguments to pass to the \code{cite()} function for the
 default style.
 }
  \item{textual}{
-Produce a \dQuote{textual} style of citation, i.e.\sspace{}what \code{\\citet} would
+Produce a \dQuote{textual} style of citation, i.e.\sspace{}what \samp{\\citet} would
 produce in LaTeX.
 }
  \item{before}{

src/library/utils/man/download.file.Rd

@@ -154,13 +154,13 @@ download.file(url, destfile, method, quiet = FALSE, mode = "w",
 
  The choice of binary transfer (\code{mode = "wb"} or \code{"ab"}) is
  important on Windows, since unlike Unix-alikes it does distinguish
- between text and binary files and for text transfers changes \code{\\n}
- line endings to \code{\\r\\n} (aka \file{CRLF}).
+ between text and binary files and for text transfers changes \samp{\\n}
+ line endings to \samp{\\r\\n} (aka \file{CRLF}).
 
  On Windows, if \code{mode} is not supplied (\code{\link{missing}()})
- and \code{url} ends in one of \code{.gz}, \code{.bz2}, \code{.xz},
- \code{.tgz}, \code{.zip}, \code{.jar}, \code{.rda}, \code{.rds},
- \code{.RData} or \code{.pdf}, \code{mode = "wb"} is set so that a binary
+ and \code{url} ends in one of \samp{.gz}, \samp{.bz2}, \samp{.xz},
+ \samp{.tgz}, \samp{.zip}, \samp{.jar}, \samp{.rda}, \samp{.rds},
+ \samp{.RData} or \samp{.pdf}, \code{mode = "wb"} is set so that a binary
  transfer is done to help unwary users.
 
  Code written to download binary files must use \code{mode = "wb"} (or
@@ -252,7 +252,7 @@ download.file(url, destfile, method, quiet = FALSE, mode = "w",
  available.
 }
 
-\section{\code{ftp://} URLs}{
+\section{\samp{ftp://} URLs}{
  Most modern browsers do not support such URLs, and \samp{https://}
  ones are much preferred for use in \R. \samp{ftps://} URLs have always
  been rare, and are nowadays even less supported.

src/library/utils/man/glob2rx.Rd

@@ -23,13 +23,13 @@ glob2rx(pattern, trim.head = FALSE, trim.tail = TRUE)
 }
 \details{
  This takes a wildcard as used by most shells and returns an equivalent
- regular expression. \code{?} is mapped to \code{.} (match a single
- character), \code{*} to \code{.*} (match any string, including an
+ regular expression. \samp{?} is mapped to \samp{.} (match a single
+ character), \samp{*} to \samp{.*} (match any string, including an
  empty one), and the pattern is anchored (it must start at the
  beginning and end at the end). Optionally, the resulting regexp is
  simplified.
 
- Note that now even \code{(}, \code{[} and \code{\{} can be used
+ Note that now even \samp{(}, \samp{[} and \samp{\{} can be used
  in \code{pattern}, but \code{glob2rx()} may not work correctly with
  arbitrary characters in \code{pattern}.
 }

src/library/utils/man/help.search.Rd

@@ -122,7 +122,7 @@ help.search(pattern, fields = c("alias", "concept", "title"),
 
  Vignettes are searched as follows. The \code{"name"} and
  \code{"alias"} are both the base of the vignette filename, and the
- \code{"concept"} entries are taken from the \code{\\VignetteKeyword}
+ \code{"concept"} entries are taken from the \samp{\\VignetteKeyword}
  entries. Vignettes are not classified using the help system
  \code{"keyword"} classifications. Demos are handled
  similarly to vignettes, without the \code{"concept"} search.

src/library/utils/man/install.packages.Rd

@@ -30,15 +30,15 @@ install.packages(pkgs, lib, repos = getOption("repos"),
  \describe{
  \item{on Windows,}{
  file paths of \file{.zip} files containing binary builds of
- packages. (\code{http://} and \code{file://} URLs are also accepted
+ packages. (\samp{http://} and \samp{file://} URLs are also accepted
  and the files will be downloaded and installed from local copies.)
  Source directories or file paths or URLs of archives may be
  specified with \code{type = "source"}, but some packages need
  suitable tools installed (see the \sQuote{Details} section).
  }
  \item{On Unix-alikes,}{these file paths can be source directories or archives
  or binary package archive files (as created by \command{R CMD build
- --binary}). (\code{http://} and \code{file://} URLs are also
+ --binary}). (\samp{http://} and \samp{file://} URLs are also
  accepted and the files will be downloaded and installed from local
  copies.) On a CRAN build of \R for macOS these can be \file{.tgz}
  files containing binary package archives.
@@ -147,7 +147,7 @@ install.packages(pkgs, lib, repos = getOption("repos"),
  install of more than one source package. Values greater than one
  are supported if the \command{make} command specified by
  \code{Sys.getenv("MAKE", "make")} accepts argument
- \code{-k -j \var{Ncpus}}.
+ \option{-k -j \var{Ncpus}}.
  }
  \item{verbose}{
  a logical indicating if some \dQuote{progress report} should be given.
@@ -305,15 +305,15 @@ install.packages(pkgs, lib, repos = getOption("repos"),
 
  Note that it is possible for the package installation to fail so badly
  that the lock directory is not removed: this inhibits any further
- installs to the library directory (or for \code{--pkglock}, of the
+ installs to the library directory (or for \option{--pkglock}, of the
  package) until the lock directory is removed manually.
 }
 
 \section{Parallel installs}{
  Parallel installs are attempted if \code{pkgs} has length greater than
  one and \code{Ncpus > 1}. It makes use of a parallel \command{make},
  so the \code{make} specified (default \command{make}) when \R was
- built must be capable of supporting \code{make -j \var{n}}: GNU make,
+ built must be capable of supporting \option{make -j \var{n}}: GNU make,
  \command{dmake} and \command{pmake} do, but Solaris \command{make} and
  older FreeBSD \command{make} do not: if necessary environment variable
  \env{MAKE} can be set for the current session to select a suitable

src/library/utils/man/package.skeleton.Rd

@@ -31,7 +31,7 @@ package.skeleton(name = "anRpackage", list,
  \item{code_files}{a character vector with the paths to R code files to
  build the package around. See \sQuote{Details}.}
  \item{encoding}{optionally a \code{\link{character}} string with an
- encoding for an optional \code{Encoding:} line in
+ encoding for an optional \samp{Encoding:} line in
  \file{DESCRIPTION} when non-ASCII characters will be used; typically
  one of \code{"latin1"}, \code{"latin2"}, or \code{"UTF-8"}; see the
  WRE manual.}

src/library/utils/man/rtags.Rd

@@ -26,7 +26,7 @@ rtags(path = ".", pattern = "\\\\.[RrSs]$",
  \item{path, pattern, recursive}{
  Arguments passed on to \code{\link{list.files}} to determine the
  files to be tagged. By default, these are all files with extension
- \code{.R}, \code{.r}, \code{.S}, and \code{.s} in the current
+ \file{.R}, \file{.r}, \file{.S}, and \file{.s} in the current
  directory. These arguments are ignored if \code{src} is specified.
  }
  \item{src}{
@@ -35,7 +35,7 @@ rtags(path = ".", pattern = "\\\\.[RrSs]$",
  \item{keep.re}{ A regular expression further restricting \code{src}
  (the files to be indexed). For example, specifying
  \code{keep.re = "/R/[^/]*\\\\.R$"} will only retain files with
- extension \code{.R} inside a directory named \code{R}.
+ extension \file{.R} inside a directory named \file{R}.
  }
 
  \item{ofile}{ Passed on to \code{\link{cat}} as the \code{file}
@@ -75,7 +75,7 @@ rtags(path = ".", pattern = "\\\\.[RrSs]$",
  \PR{17214}.
 
  It may be more convenient to use the command-line wrapper script
- \code{R CMD rtags}.
+ \command{R CMD rtags}.
 }
 
 \references{

src/library/utils/man/shortPathName.Rd

@@ -24,7 +24,7 @@ shortPathName(path)
  path names when the long-name path will be returned instead.
 }
 \value{
- A character vector. The path separator will be \code{\\}. If a
+ A character vector. The path separator will be \samp{\\}. If a
  file path does not exist, the supplied path will be returned with slashes
  replaced by backslashes.
 }

src/library/utils/man/tar.Rd

@@ -175,7 +175,7 @@ tar(tarfile, files = NULL,
  specified by e.g.\sspace{}\code{extra_flags = "-I lz4"}.
  Some versions of \command{bsdtar} accept options such as
  \option{--lz4}, \option{--lzop} and \option{--lrzip} or an external
- compressor \emph{via} \code{--use-compress-program lz4}: these could
+ compressor \emph{via} \option{--use-compress-program lz4}: these could
  be supplied in \code{extra_flags}.
 
  NetBSD prior to 8.0 used flag \option{--xz} rather than \option{-J},