From 7ea68dc24d0e62e4a7856e29f23091580a2acce7 Mon Sep 17 00:00:00 2001
From: Jeroen Ooms <jeroenooms@gmail.com>
Date: Thu, 12 Sep 2024 21:57:31 +0200
Subject: [PATCH] Update default repos to include all the things possible

---
 Rprofile | 34 +++++++++++++++++++++-------------
 1 file changed, 21 insertions(+), 13 deletions(-)

diff --git a/Rprofile b/Rprofile
index bb03048..2a64ed5 100644
--- a/Rprofile
+++ b/Rprofile
@@ -1,21 +1,29 @@
-# Enable CRAN and BIOC
-options(repos = c(CRAN = "https://cloud.r-project.org"))
-utils::setRepositories(ind = 1:4)
-
 local({
-  # Enable RSPM
-  rver <- getRversion()
+  r_branch <- substr(getRversion(), 1, 3)
   distro <- system2('lsb_release', '-sc', stdout = TRUE)
-  options(HTTPUserAgent = sprintf("R/%s R (%s)", rver, paste(rver, R.version$platform, R.version$arch, R.version$os)))
-  options(repos = c(P3M = sprintf("https://p3m.dev/all/__linux__/%s/latest", distro), getOption("repos")))
+  binary_universe <- function(universe){
+    sprintf("%s/bin/linux/%s/%s", universe, distro, r_branch)
+  }
+  bioc_urls <- function(){
+    ver <- utils:::.BioC_version_associated_with_R_version();
+    c(
+      BioCsoft = sprintf("https://bioconductor.org/packages/%s/bioc", ver),
+      BioCann = sprintf("https://bioconductor.org/packages/%s/data/annotation", ver),
+      BioCexp = sprintf("https://bioconductor.org/packages/%s/data/experiment", ver)
+    )
+  }
+  options(repos = c(
+    P3M = sprintf("https://p3m.dev/all/__linux__/%s/latest", distro),
+    BIOC = binary_universe("https://bioc.r-universe.dev"),
+    CRAN = "https://cloud.r-project.org",
+    CRANHAVEN = binary_universe("https://cranhaven.r-universe.dev"),
+    bioc_urls()
+  ))
+  options(HTTPUserAgent = sprintf("R/%s R (%s)", getRversion(), paste(getRversion(), R.version$platform, R.version$arch, R.version$os)))
 
-  # Enable universe repo(s)
   my_universe <- Sys.getenv("MY_UNIVERSE")
   if(nchar(my_universe)){
-    my_repos <- trimws(strsplit(my_universe, ';')[[1]])
-    binaries <- sprintf('%s/bin/linux/%s/%s', my_repos[1], distro, substr(rver, 1, 3))
-    options(repos = c(binaries = binaries, universe = my_repos, getOption("repos")))
+    options(repos = c(binaries = binary_universe(my_universe), universe = my_universe, getOption("repos")))
   }
 })
 
-#print(options('repos'))