Changes between Version 5 and Version 6 of cypress/RunningRStudioWithSingularity

Timestamp:

02/05/26 16:34:28 (12 hours ago)

Author:

Carl Baribault

Comment:

Added tidyvverse alternative to bare RStudio

cypress/RunningRStudioWithSingularity

@@ -48 +48 @@
 }}}
 
-
 == Construct and check the image file for RStudio ==
 Then proceed as follows to construct the container image file '''rstudio_latest.sif''' and check the R version.
@@ -70 +69 @@
 }}}
 
+== Alternative for tidyverse ==
+As an alternative to just the base RStudio container, you can construct the container image file '''tidyverse_latest.sif''' and run RStudio server with the '''tidyverse''' package suite pre-installed.
+
+To do so, here and in the following, simply substitute '''tidyverse_latest.sif''' for '''rstudio_latest.sif'''.
+
+{{{
+[tulaneID@cypress01-060 ~]$module load singularity/3.9.0 # load the singularity module
+[tulaneID@cypress01-060 ~]$singularity pull docker://rocker/tidyverse:latest # takes a few minutes to construct file r-base_latest.sif
+...
+[tulaneID@cypress01-060 ~]$singularity exec tidyverse_latest.sif R --version # check the version of R
+R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
+Copyright (C) 2025 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under the terms of the
+GNU General Public License versions 2 or 3.
+For more information about these matters see
+https://www.gnu.org/licenses/.
+
+[tulaneID@cypress01-060 ~]$
+}}}
+
 == Start the RStudio server ==
-
 
  * Setup local authentication
@@ -89 +110 @@
 
 {{{
-[tulaneID@cypress01-060 ~]$singularity exec -B /lustre:/lustre --scratch /run,/var/lib/rstudio-server --workdir $(mktemp -d) tidyverse_latest.sif  rserver --www-address=0.0.0.0 --www-port=8888 --server-user=$(whoami) --database-config-file $PWD/database.conf
+[tulaneID@cypress01-060 ~]$singularity exec -B /lustre:/lustre --scratch /run,/var/lib/rstudio-server --workdir $(mktemp -d) rstudio_latest.sif  rserver --www-address=0.0.0.0 --www-port=8888 --server-user=$(whoami) --database-config-file $PWD/database.conf
 }}}