mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:46:11 +01:00
96 lines
4.5 KiB
R
96 lines
4.5 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# CITE AS #
|
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
|
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
|
|
# Data. Journal of Statistical Software, 104(3), 1-31. #
|
|
# doi:10.18637/jss.v104.i03 #
|
|
# #
|
|
# 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(getwd(), repos = NULL, type = "source")
|
|
|
|
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 = "")
|
|
}
|