GitHub Actions: check lesson template (#489)

[rnaseq-cwl-training.git] / bin / dependencies.R

diff --git a/bin/dependencies.R b/bin/dependencies.R
new file mode 100644 (file)
index 0000000..b710558
--- /dev/null
+++ b/bin/dependencies.R
@@ -0,0 +1,68 @@
+find_root <- function() {
+  if (!requireNamespace("rprojroot", quietly = TRUE)) {
+    install.packages("rprojroot", lib = lib, repos = repos)
+  }
+
+  cfg  <- rprojroot::has_file_pattern("^_config.y*ml$")
+  root <- rprojroot::find_root(cfg)
+
+  root
+}
+
+identify_dependencies <- function(lib = NULL, repos = getOption("repos")) {
+
+  if (is.null(lib)) {
+    lib <- .libPaths()
+  }
+
+  if (!requireNamespace("renv", quietly = TRUE)) {
+    install.packages("renv", lib = lib, repos = repos)
+  }
+
+  root <- find_root()
+
+  required_pkgs <- unique(c(
+    ## Packages for episodes
+    renv::dependencies(file.path(root, "_episodes_rmd"), progress = FALSE, error = "ignore")$Package,
+    ## Packages for tools
+    renv::dependencies(file.path(root, "bin"), progress = FALSE, error = "ignore")$Package
+  ))
+
+  required_pkgs
+}
+
+install_dependencies <- function(required_pkgs,
+                                 lib = NULL, repos = getOption("repos"),
+                                 update = FALSE, ...) {
+
+  if (missing(lib))  {
+    lib <- .libPaths()
+  }
+
+  missing_pkgs <- setdiff(required_pkgs, rownames(installed.packages()))
+
+  if (length(missing_pkgs)) {
+    message("Installing missing required packages: ",
+      paste(missing_pkgs, collapse=", "))
+    install.packages(missing_pkgs, lib = lib, repos = repos)
+  }
+
+  if (update) {
+    update.packages(
+      lib.loc = lib, repos = repos,
+      ask = FALSE, checkBuilt = TRUE, ...
+    )
+  }
+
+  if (require("knitr") && packageVersion("knitr") < '1.9.19') {
+    stop("knitr must be version 1.9.20 or higher")
+  }
+
+}
+
+create_description <- function(required_pkgs) {
+  require("desc")
+  d <- description$new("!new")
+  lapply(required_pkgs, function(x) d$set_dep(x))
+  d$write("DESCRIPTION")
+}