From: Zhian N. Kamvar <zkamvar@gmail.com>
Date: Wed, 2 Dec 2020 17:35:13 +0000 (-0800)
Subject: set CRAN url if default is "@CRAN@"
X-Git-Url: https://git.arvados.org/rnaseq-cwl-training.git/commitdiff_plain/ca16e0be7110e18c1cef47544698141fefdb53af

set CRAN url if default is "@CRAN@"

This will fix #526
---

diff --git a/bin/dependencies.R b/bin/dependencies.R
index ad5afe7..640b3e2 100644
--- a/bin/dependencies.R
+++ b/bin/dependencies.R
@@ -9,6 +9,12 @@ install_required_packages <- function(lib = NULL, repos = getOption("repos", def
     c("rprojroot", "desc", "remotes", "renv"),
     rownames(installed.packages(lib.loc = lib))
   )
+  # The default installation of R will have "@CRAN@" as the default repository, which directs contrib.url() to either
+  # force the user to choose a mirror if interactive or fail if not. Since we are not interactve, we need to force the
+  # mirror here.
+  if ("@CRAN@" %in% repos) {
+    repos <- c(CRAN = "https://cran.rstudio.com/")
+  }
 
   install.packages(missing_pkgs, lib = lib, repos = repos)