AMR/.gitlab-ci.R

59 lines
2.6 KiB
R

# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://gitlab.com/msberends/AMR #
# #
# LICENCE #
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
# #
# 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. #
# #
# This R package was created for academic research and was publicly #
# released in the hope that it will be useful, but it comes WITHOUT #
# ANY WARRANTY OR LIABILITY. #
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
# ==================================================================== #
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...")
if (pkg == "cleaner") {
devtools::install_github("msberends/cleaner")
} else {
install.packages(pkg, repos = repos, quiet = quiet)
}
}
}
gl_update_pkg_all <- function(repos = "https://cran.rstudio.com",
quiet = TRUE,
install_pkgdown = FALSE,
install_lintr = 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)
}
if (install_lintr == TRUE) {
install_if_needed(pkg = "lintr", repos = repos, quiet = quiet)
}
install_if_needed(pkg = "cleaner", repos = repos, quiet = quiet)
devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE)
cat("INSTALLED:\n")
instld <- as.data.frame(installed.packages())
rownames(instld) <- NULL
print(instld[, c("Package", "Version")])
return(invisible(TRUE))
}