installer using BiocManager

release_process/update_biocmanager.R

@@ -0,0 +1,77 @@
+options(repos = "http://cran.r-project.org", width = 100)
+install.packages(c("BiocManager", "cli"), type = "source")
+
+library(BiocManager)
+library(cli)
+library(tools)
+
+# ------------------------------------------------------------------------------
+
+## Get the names of all CRAN related packages references by caret.
+## Exclude orphaned and Bioconductor packages for now
+
+# install.packages(c("devtools"), repos = "http://cran.r-project.org", type = "source")
+#
+# library(devtools)
+# install_github("topepo/caret", subdir = "pkg/caret")
+
+library(caret)
+
+mods <- getModelInfo()
+
+libs <- unlist(lapply(mods, function(x) x$library))
+libs <- libs[!(libs %in% c("caret", "vbmp", "gpls", "logicFS", "SDDA"))]
+libs <- c(libs, package_dependencies("caret", reverse = TRUE)$caret)
+libs <- unique(libs)
+
+# Don't install rJava in case it borks the existing system
+libs <- libs[libs != "rJava"]
+
+# ------------------------------------------------------------------------------
+
+## Check to see if any packages are not on CRAN
+
+options(repos = "http://cran.r-project.org")
+all_pkg <- rownames(available.packages(type = "source"))
+
+diffs <- libs[!(libs %in% all_pkg)]
+if (length(diffs) > 0) print(diffs)
+
+# ------------------------------------------------------------------------------
+## Install the files. This might re-install caret so beware.
+
+libs <- sort(libs)
+n <- length(libs)
+iters <- format(1:n)
+libs_chr <- format(libs)
+
+for (i in seq_along(libs)) {
+  cli::cli_rule(paste0(libs_chr[i], " (", iters[i], "/", n, ")"))
+
+  res <- try(
+    BiocManager::install(
+      libs[i],
+      type = "both",
+      dependencies = c("Depends", "Imports"),
+      update = FALSE,
+      ask = FALSE
+    ),
+    silent = TRUE
+  )
+
+  if (inherits(res, "try-error")) {
+    cat("Failed to install", libs[i], "\n\n")
+    print(as.character(res))
+  }
+
+  cat("\n\n")
+}
+
+# ------------------------------------------------------------------------------
+# exceptions:
+
+install.packages("CHAID", repos="http://R-Forge.R-project.org")
+
+# ------------------------------------------------------------------------------
+
+q("no")