mirror of https://github.com/msberends/AMR.git
57 lines
2.4 KiB
R
57 lines
2.4 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# AUTHORS #
|
|
# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# LICENCE #
|
|
# This package is free software; you can redistribute it and/or modify #
|
|
# it under the terms of the GNU General Public License version 2.0, #
|
|
# as published by the Free Software Foundation. #
|
|
# #
|
|
# This R package is distributed in the hope that it will be useful, #
|
|
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
|
|
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
|
|
# GNU General Public License version 2.0 for more details. #
|
|
# ==================================================================== #
|
|
|
|
install_if_needed <- function(pkg, repos, quiet) {
|
|
package_path <- find.package(pkg, quiet = quiet)
|
|
if (length(package_path) == 0) {
|
|
message("NOTE: pkg ", pkg, " missing, installing...")
|
|
install.packages(pkg, repos = repos, quiet = quiet)
|
|
}
|
|
}
|
|
|
|
gl_update_pkg_all <- function(repos = "https://cran.rstudio.com",
|
|
quiet = TRUE,
|
|
install_pkgdown = FALSE) {
|
|
# update existing
|
|
update.packages(ask = FALSE, repos = repos, quiet = quiet)
|
|
|
|
install_if_needed(pkg = "devtools", repos = repos, quiet = quiet)
|
|
if (install_pkgdown == TRUE) {
|
|
install_if_needed(pkg = "pkgdown", repos = repos, quiet = quiet)
|
|
}
|
|
|
|
devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE)
|
|
|
|
cat("\nINSTALLED:\n\n")
|
|
instld <- as.data.frame(installed.packages())
|
|
rownames(instld) <- NULL
|
|
print(instld[, c("Package", "Version")])
|
|
|
|
return(invisible(TRUE))
|
|
|
|
# which ones are needed now?
|
|
# pkg_needed <-
|
|
|
|
# if (length(pkg_needed) > 0) {
|
|
# # install them
|
|
# for (i %in% 1:length(pkg_needed)) {
|
|
# install_if_needed(pkg = pkg_needed[i], repos = repos, quiet = quiet)
|
|
# }
|
|
# }
|
|
}
|