# Creates a file with specified text
file_create <- function(txt, filename){
if(!file.exists(filename)){
writeLines(txt, filename)
}
}
# helpers
some <- function (x) {
length(x) > 0
}
none <- function (x) {
!some(x)
}
one <- function (x) {
length(x) == 1
}
# nicely format the number of file changes or line additions / deletions
paste_num <- function (number, item, event, fallback = NULL) {
if (number == 0) {
text <- fallback
} else if (number == 1) {
text <- sprintf("%i %s %s", number, item, event)
} else {
text <- sprintf("%i %ss %s", number, item, event)
}
text
}
Sys_which <- function(x) {
ret <- Sys.which(x)
if (ret == "") {
stop(sprintf("%s not found in $PATH", x))
}
ret
}
#' Function imported from callr package; makes it easy to call a
#' system command from R and have it behave.
#'
#' This function uses \code{system2} to call a system command fairly
#' portably. What it adds is a particular way of dealing with
#' errors. \code{call_system} runs the command \code{command} with
#' arguments \code{args} (and with optionally set environment
#' variables \code{env}) and hides \emph{all} produced output to
#' stdout and stderr. If the command fails (currently any nonzero
#' exit code is counted as a failure) then \code{call_system} will
#' throw an R error giving
#' \itemize{
#' \item the full string of the command run
#' \item the exit code of the command
#' \item any \code{errmsg} attribute that might have been returned
#' \item all output that the program produced to either stdout and
#' stderr
#' }
#'
#' This means that a successful invocation of a program produces no
#' output while the unsuccessful invocation throws an error and
#' prints all information to the screen (though this is delayed until
#' failure happens).
#'
#'
#' \code{call_system} also returns the contents of both stderr and
#' stdout \emph{invisibly} so that it can be inspected if needed.
#'
#' The function \code{run_system} does the same thing and will be
#' removed as soon as code that depends on it is out of use.
#'
#' @title Run a system command, stopping on error
#' @param command The system command to be invoked, as a character
#' string. \code{\link{Sys.which}} is useful here.
#' @param args A character vector of arguments to \code{command}
#' @param env A character vector of name=value pairs to be set as
#' environment variables (see \code{\link{system2}}).
#' @param max_lines Maximum number of lines of program output to
#' print with the error message. We may prune further to get the
#' error message under \code{getOption("warn.length")}, however.
#' @param p Fraction of the error message to show from the tail of
#' the output if truncating on error (default is 20\% lines are head,
#' 80\% is tail).
#' @param stdout,stderr Passed to \code{system2}. Set one of these
#' to \code{FALSE} to avoid capturing output from that stream. Setting
#' both to \code{FALSE} is not recommended.
#' @noRd
#' @importFrom utils head tail
#' @author Rich FitzJohn
call_system <- function(command, args, env=character(), max_lines=20,
p=0.8, stdout=TRUE, stderr=TRUE) {
res <- suppressWarnings(system2(command, args,
env=env, stdout=stdout, stderr=stderr))
ok <- attr(res, "status")
if (!is.null(ok) && ok != 0) {
max_nc <- getOption("warning.length")
cmd <- paste(c(env, shQuote(command), args), collapse = " ")
msg <- sprintf("Running command:\n %s\nhad status %d", cmd, ok)
errmsg <- attr(cmd, "errmsg")
if (!is.null(errmsg)) {
msg <- c(msg, sprintf("%s\nerrmsg: %s", errmsg))
}
sep <- paste(rep("-", getOption("width")), collapse="")
## Truncate message:
if (length(res) > max_lines) {
n <- ceiling(max_lines * p)
res <- c(head(res, ceiling(max_lines - n)),
sprintf("[[... %d lines dropped ...]]", length(res) - max_lines),
tail(res, ceiling(n)))
}
## compute the number of characters so far, including three new lines:
nc <- (nchar(msg) + nchar(sep) * 2) + 3
i <- max(1, which(cumsum(rev(nchar(res) + 1L)) < (max_nc - nc)))
res <- res[(length(res) - i + 1L):length(res)]
msg <- c(msg, "Program output:", sep, res, sep)
stop(paste(msg, collapse="\n"))
}
invisible(res)
}
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