Global Renvironment. PAT when installing from github.

04_copy_env.sh

@@ -1,3 +1,3 @@
 #!/usr/bin/with-contenv bash
 
-printenv >> /home/$USER/.Renviron
+printenv >> /etc/R/Renviron.site

Dockerfile

@@ -28,13 +28,18 @@ RUN for l in `cat /tmp/r_non_cran_pkgs.txt` ; do \
 
 # From github
 ADD https://code-repo.d4science.org/gCubeSystem/r-packages-list/raw/branch/master/r_github_pkgs.txt /tmp
-RUN for g in `cat /tmp/r_github_pkgs.txt` ; do \
-    Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
-    -e " require(devtools); devtools::install_github('$g')" ; done
+#RUN for g in `cat /tmp/r_github_pkgs.txt` ; do \
+#    Rscript --slave --no-site-file --no-init-file --no-save --no-restore-history \
+#    -e " require(devtools); devtools::install_github('$g')" ; done
+RUN export GITHUB_PAT ; for g in `cat /tmp/r_github_pkgs.txt` ; do installGithub.r -d TRUE -u FALSE -r https://packagemanager.rstudio.com/all/__linux__/focal/latest $g ; done
 
 RUN /rocker_scripts/install_rstudio.sh
 RUN /rocker_scripts/install_pandoc.sh
 
+# Remove the rstudio user's home directory and add the mountpoint for the workspace
+RUN rm -fr /home/rstudio
+RUN mkdir /workspace
+
 # This part comes from https://github.com/openanalytics/shinyproxy-rstudio-ide-demo/blob/master/Dockerfile
 RUN echo "www-frame-origin=disabled" >> /etc/rstudio/disable_auth_rserver.conf
 RUN echo "www-verify-user-agent=0" >> /etc/rstudio/disable_auth_rserver.conf