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# ==================================================================== #
# 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_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
pkg_suggests <- gsub("[^a-zA-Z0-9]+", "",
unlist(strsplit(unlist(packageDescription("AMR",
fields = c("Suggests", "Enhances", "LinkingTo"))),
split = ", ?")))
pkg_suggests <- unname(pkg_suggests[!is.na(pkg_suggests)])
cat("################################################\n")
cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
cat("################################################\n")
if (.Platform$OS.type != "unix") {
# no compiling on Windows here
options(install.packages.compile.from.source = FALSE)
}
to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
if (length(to_install) == 0) {
message("\nNothing to install\n")
}
for (i in seq_len(length(to_install))) {
cat("Installing package", to_install[i], "\n")
tryCatch(install.packages(to_install[i],
type = "source",
repos = "https://cran.rstudio.com/",
dependencies = c("Depends", "Imports", "LinkingTo"),
quiet = FALSE),
# message = function(m) invisible(),
warning = function(w) message(w$message),
error = function(e) message(e$message))
if (.Platform$OS.type != "unix" && !to_install[i] %in% rownames(utils::installed.packages())) {
tryCatch(install.packages(to_install[i],
type = "binary",
repos = "https://cran.rstudio.com/",
dependencies = c("Depends", "Imports", "LinkingTo"),
quiet = FALSE),
# message = function(m) invisible(),
warning = function(w) message(w$message),
error = function(e) message(e$message))
}
}
to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
if (length(to_update) == 0) {
message("\nNothing to update\n")
}
for (i in seq_len(length(to_update))) {
cat("Updating package '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
# message = function(m) invisible(),
warning = function(w) message(w$message),
error = function(e) message(e$message))
cat("Updated to '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
}