allow binary installs for users

Author: cboettig

Dockerfile

@@ -10,6 +10,9 @@ RUN curl -s https://raw.githubusercontent.com/boettiger-lab/repo2docker-r/refs/h
 COPY install.r install.r
 RUN Rscript install.r
 
+## switch from BSPM to r-universe for user default, only after BSPM does install.r! 
+COPY Rprofile /usr/lib/R/etc/Rprofile.site
 USER ${NB_USER}
+
 COPY environment.yml environment.yml
 RUN conda env update -f environment.yml

Rprofile

@@ -0,0 +1,31 @@
+# Based on Jeroen's config: 
+# https://github.com/r-universe-org/base-image/blob/f20ec9fc6f51ef8a89aad489206a43790bd9bf77/Rprofile
+
+local({
+rver <- getRversion()
+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(CRAN = sprintf("https://packagemanager.rstudio.com/all/__linux__/%s/latest", distro)))
+
+# Enable BioConductor repos
+utils::setRepositories(ind = 1:4, addURLs = c(fallback = "https://cloud.r-project.org"))
+
+# Enable universe repo(s)
+my_universe <- Sys.getenv("MY_UNIVERSE", "https://cran.r-universe.dev")
+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")))
+}
+
+# Other settings
+options(crayon.enabled = TRUE)
+Sys.unsetenv(c("CI", "GITHUB_ACTIONS"))
+
+# Dummy token for API limits
+if(is.na(Sys.getenv("GITHUB_PAT", NA))){
+  dummy <- c('ghp_SXg', 'LNM', 'Tu4cnal', 'tdqkZtBojc3s563G', 'iqv')
+  Sys.setenv(GITHUB_PAT = paste(dummy, collapse = 'e'))
+}
+})
+