install_packages.R

#' @title Function to install sets of R packages
#'
#' The `install_packages()` function installs sets of R packages defined in
#' (tab separated) text files.
#'
#' @param path `character(1)` with the path to the directory containing the txt
#'     files from which package lists should be read.
#'
#' @param files optional `character` vector with the actual file names from
#'     which to read package definition.
#'
#' @export
install_packages <- function(path = ".", files = dir(path, pattern = ".txt$")) {
    if (!length(files))
        stop("No files provided or found in the specified path")
    pkg <- character()
    for (i in seq_along(files)) {
        message("Installing packages defined in \"", files[i], "\"")
        pkgs <- read.table(files[i])[, 1L]
        BiocManager::install(pkgs, ask = FALSE)
        pkg <- c(pkg, pkgs)
    }
    pkgi <- installed.packages()[, "Package"]
    pkg <- vapply(strsplit(pkg, "/"), function(z) z[length(z)], NA_character_)
    pkgn <- pkg[!pkg %in% pkgi]
    if (length(pkgn)) {
        message("\n\nThe following packages failed to install:")
        message(paste0(pkgn, collapse = "\n"))
        message("You might want to install them manually\n\n")
    }
}

## RUn the installation.
install_packages()