diff --git a/DESCRIPTION b/DESCRIPTION index 9e1b565f6..adc5fda52 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9258 +Version: 2.1.1.9259 Date: 2025-04-27 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index d59a44098..dc23e31dc 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9258 +# AMR 2.1.1.9259 *(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)* diff --git a/R/sir.R b/R/sir.R index 3a01951e9..4becfdbb2 100755 --- a/R/sir.R +++ b/R/sir.R @@ -680,7 +680,7 @@ as.sir.disk <- function(x, } #' @rdname as.sir -#' @param parallel A [logical] to indicate if parallel computing must be used, defaults to `FALSE`. This requires no additional packages, as the used `parallel` package is part of base \R. On Windows and on \R < 4.0.0 [parallel::parLapply()] will be used; in all other cases the most efficient [parallel::mclapply()] will be used. +#' @param parallel A [logical] to indicate if parallel computing must be used, defaults to `FALSE`. This requires no additional packages, as the used `parallel` package is part of base \R. On Windows and on \R < 4.0.0 [parallel::parLapply()] will be used, in all other cases the most efficient [parallel::mclapply()] will be used. #' @param max_cores Maximum number of cores to use if `parallel = TRUE`. Use a negative value to subtract that number from the available number of cores, e.g. a value of `-2` on an 8-core machine means that at most 6 cores will be used. Defaults to `-1`. There will never be used more cores than variables to analyse. The available number of cores are detected using [parallelly::availableCores()] if that package is installed, and base \R's [parallel::detectCores()] otherwise. #' @export as.sir.data.frame <- function(x, @@ -854,6 +854,12 @@ as.sir.data.frame <- function(x, # set up parallel computing n_cores <- get_n_cores(max_cores = max_cores) n_cores <- min(n_cores, length(ab_cols)) # never more cores than variables required + if (isTRUE(parallel) && .Platform$OS.type != "windows" && getRversion() < "4.0.0") { + n_cores <- 1 + if (isTRUE(info)) { + warning("Parallel computing is not available on unix in R < 4.0", call. = FALSE) + } + } run_as_sir_column <- function(i) { ab_col <- ab_cols[i] diff --git a/man/as.sir.Rd b/man/as.sir.Rd index e2c169412..00d0b3b78 100644 --- a/man/as.sir.Rd +++ b/man/as.sir.Rd @@ -138,7 +138,7 @@ The default \code{"standard"} setting ensures cautious handling of uncertain val \item{col_mo}{Column name of the names or codes of the microorganisms (see \code{\link[=as.mo]{as.mo()}}) - the default is the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} -\item{parallel}{A \link{logical} to indicate if parallel computing must be used, defaults to \code{FALSE}. This requires no additional packages, as the used \code{parallel} package is part of base \R. On Windows and on \R < 4.0.0 \code{\link[parallel:clusterApply]{parallel::parLapply()}} will be used; in all other cases the most efficient \code{\link[parallel:mclapply]{parallel::mclapply()}} will be used.} +\item{parallel}{A \link{logical} to indicate if parallel computing must be used, defaults to \code{FALSE}. This requires no additional packages, as the used \code{parallel} package is part of base \R. On Windows and on \R < 4.0.0 \code{\link[parallel:clusterApply]{parallel::parLapply()}} will be used, in all other cases the most efficient \code{\link[parallel:mclapply]{parallel::mclapply()}} will be used.} \item{max_cores}{Maximum number of cores to use if \code{parallel = TRUE}. Use a negative value to subtract that number from the available number of cores, e.g. a value of \code{-2} on an 8-core machine means that at most 6 cores will be used. Defaults to \code{-1}. There will never be used more cores than variables to analyse. The available number of cores are detected using \code{\link[parallelly:availableCores]{parallelly::availableCores()}} if that package is installed, and base \R's \code{\link[parallel:detectCores]{parallel::detectCores()}} otherwise.}