better strategy

images/Dockerfile

@@ -41,7 +41,8 @@ ENV PATH=$PATH:/usr/lib/rstudio-server/bin/quarto/bin
 COPY install.r install.r
 RUN Rscript install.r
 
-
+## switch from BSPM to r-universe for user default 
+COPY Rprofile /etc/R/Rprofile.site
 
 USER ${NB_USER}
 

images/Dockerfile.gpu

@@ -44,6 +44,10 @@ ENV PATH=$PATH:/usr/lib/rstudio-server/bin/quarto/bin
 COPY install.r install.r
 RUN Rscript install.r
 
+## switch from BSPM to r-universe for user default 
+COPY Rprofile /etc/R/Rprofile.site
+
+
 
 USER ${NB_USER}
 COPY spatial-env.yml spatial-env.yml

images/install.r

@@ -1,13 +1,2 @@
 install.packages(c('tidyverse', 'devtools', 'reticulate', 'nimble', 'duckdbfs', 'arrow', 'gdalcubes', 'rstac', 'terra', 'sf', 'stars', 'quarto', 'mapgl', 'neonstore', 'rfishbase', 'shiny', 'pak'))
 
-# NOTE: r-universe supports binaries only for latest R release and latest LTS, as follows:
-readr::write_lines("
-options(repos = c(
-  linux = 'https://cran.r-universe.dev/bin/linux/noble/4.4/',
-  sources = 'https://cran.r-universe.dev'
-))
-", 
-paste0(R.home(), "/etc/Rprofile.site"),
-append = TRUE)
-# NOTE: also, we omit an official cran repo to avoid more recent source version taking priority over install from binary.
-