# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2021 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # # some old R instances have trouble installing tinytest, so we ship it too install.packages("data-raw/tinytest_1.2.4.patched.tar.gz") descr <- readLines("AMR/DESCRIPTION") pkg_suggests <- gsub(".*Suggests: (.*)*?[A-Z].*", "\\1", paste0(descr, "*", collapse = ""), perl = FALSE) pkg_suggests <- unlist(strsplit(pkg_suggests, "[,* ]")) pkg_suggests <- pkg_suggests[pkg_suggests != ""] cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n") to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())] to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE) to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE] for (i in seq_len(length(to_install))) { cat("Installing package", to_install[i], "\n") tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE), # message = function(m) invisible(), warning = function(w) message(w$message), error = function(e) message(e$message)) } for (i in seq_len(length(to_update))) { cat("Updating package", to_update[i], "\n") tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE), # message = function(m) invisible(), warning = function(w) message(w$message), error = function(e) message(e$message)) }