AMR/.gitlab-ci.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)
# }
# }
}