Fix Rprofile.site to point to correct mirror

yuvipanda · yuvipanda · commit bbf0ebabbdd8 · 2021-04-17T19:35:49.000+05:30
Earlier, interactive use of R somehow wasn't loading appropriate instructions on setting CRAN from Rprofile.site, resulting (partially) in errors like this: berkeley-dsep-infra/datahub#2255 (comment) My informed guess is that the `local{}` was scoping the effects, so it worked during build but not during interactive use. Removing that seems to make it work for both. Inspired by toolforge/paws#62
diff --git a/deployments/biology/image/Rprofile.site b/deployments/biology/image/Rprofile.site
@@ -1,6 +1,10 @@
-local({
-    r <- getOption("repos")
-    r["CRAN"] <- "https://packagemanager.rstudio.com/all/__linux__/focal/latest"
-    options(repos = r)
-    options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
-})
+# Use RStudio's CRAN mirror to get binary packages
+# 'latest' just means it has all available versions.
+# We can specify version numbers in devtools::install_version
+options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))
+
+# RStudio's CRAN mirror needs this to figure out which binary package to serve.
+# If not set properly, it will just serve up source packages
+# Quite hilarious, IMO.
+# See https://docs.rstudio.com/rspm/admin/binaries.html
+options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
diff --git a/deployments/datahub/images/default/Rprofile.site b/deployments/datahub/images/default/Rprofile.site
@@ -1,6 +1,10 @@
-local({
-    r <- getOption("repos")
-    r["CRAN"] <- "https://packagemanager.rstudio.com/all/__linux__/focal/latest"
-    options(repos = r)
-    options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
-})
+# Use RStudio's CRAN mirror to get binary packages
+# 'latest' just means it has all available versions.
+# We can specify version numbers in devtools::install_version
+options(repos = c(CRAN = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))
+
+# RStudio's CRAN mirror needs this to figure out which binary package to serve.
+# If not set properly, it will just serve up source packages
+# Quite hilarious, IMO.
+# See https://docs.rstudio.com/rspm/admin/binaries.html
+options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
