feat: install R packages from CRAN

Author: ymarcon

Dockerfile

@@ -8,17 +8,20 @@ FROM obiba/rock:2.2.1-R4.5.3
 
 LABEL DataSHIELD=<info@datashield.ac.uk>
 
-ENV DSBASE_VERSION=6.3.5
-ENV DSTIDYVERSE_VERSION=v1.2.1
+# Uncomment the following lines to specify versions of dsBase and dsTidyverse to install from GitHub
+# ENV DSBASE_VERSION=6.3.5
+# ENV DSTIDYVERSE_VERSION=v1.2.1
 
 ENV ROCK_LIB=/var/lib/rock/R/library
 
 RUN \
   # Additional system dependencies
   apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y cmake && \
   # Update R packages
-  #Rscript -e "update.packages(ask = FALSE, repos = c('https://cloud.r-project.org'), instlib = '/usr/local/lib/R/site-library')" && \
+  # Rscript -e "update.packages(ask = FALSE, repos = c('https://cloud.r-project.org'), instlib = '/usr/local/lib/R/site-library')" && \
   # Install new R packages
-  Rscript -e "remotes::install_github('molgenis/ds-tidyverse', ref = '$DSTIDYVERSE_VERSION', repos = c('https://cloud.r-project.org', 'https://cran.datashield.org'), dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
-  Rscript -e "remotes::install_github('datashield/dsBase', ref = '$DSBASE_VERSION', repos = c('https://cloud.r-project.org', 'https://cran.datashield.org'), dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
+  Rscript -e "install.packages(c('dsBase', 'dsTidyverse'), repos = c('https://cloud.r-project.org'), dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
+  # Uncomment the following lines to install specific versions of dsBase and dsTidyverse from GitHub
+  # Rscript -e "remotes::install_github('molgenis/ds-tidyverse', ref = '$DSTIDYVERSE_VERSION', repos = c('https://cloud.r-project.org', 'https://cran.datashield.org'), dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
+  # Rscript -e "remotes::install_github('datashield/dsBase', ref = '$DSBASE_VERSION', repos = c('https://cloud.r-project.org', 'https://cran.datashield.org'), dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
   chown -R rock $ROCK_LIB