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(v1.6.0.9050) printing NA in custom_eucast_rules()

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dr. M.S. (Matthijs) Berends
2021-05-20 10:10:40 +02:00
parent 9a2879cba9
commit 04ef5b28e7
21 changed files with 71 additions and 64 deletions
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data-raw/AMR_latest.tar.gz
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data-raw/_install_deps.R
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@ -23,32 +23,31 @@
# 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
install.packages("data-raw/tinytest_1.2.4.patched.tar.gz")
pkg_suggests <- AMR:::trimws(unlist(strsplit(packageDescription("AMR")$Suggests, ",(\n)?")))
descr <- readLines("AMR/DESCRIPTION")
pkg_suggests <- gsub(".*Suggests: (.*)*?[A-Z].*", "\\1", paste0(descr, "*", collapse = ""), perl = FALSE)
pkg_suggests <- unlist(strsplit(pkg_suggests, "[,* ]"))
pkg_suggests <- pkg_suggests[pkg_suggests != ""]
cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")
to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
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))
}
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))
}
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))
}