AMR/data-raw/_install_deps.R

57 lines
3.1 KiB
R

# ==================================================================== #
# 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/ #
# ==================================================================== #
install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
# some old R instances have trouble installing tinytest, so we ship it too
# R < 3.2 does not contain trimws(), which is part of this script and of a tinytest script
trimws <- AMR:::trimws
intall.packages("data-raw/tinytest_1.2.4.tar.gz")
pkg_suggests <- trimws(unlist(strsplit(packageDescription("AMR")$Suggests, ",(\n)?")))
to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
for (i in seq_len(length(to_install))) {
if (isTRUE(is.character(to_install[i]))) {
cat("Installing package", to_install[i], "\n")
tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE),
# message = function(m) invisible(),
warning = function(w) message(w$message),
error = function(e) message(e$message))
}
}
for (i in seq_len(length(to_update))) {
if (isTRUE(is.character(to_update[i]))) {
cat("Updating package", to_update[i], "\n")
tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
# message = function(m) invisible(),
warning = function(w) message(w$message),
error = function(e) message(e$message))
}
}