orhankalyon / r-containers

docker and singularity containers for R

Docker and Apptainer images for R

Images

docker	description
radian	adds radian on rstudio (packages need to be installed by renv)
radian-ml	adds radian on ml (packages need to be installed by renv)
tinytex	R markdown + TinyTex + pandoc-crossref + quarto without Rstudio
rstan	adds rstan on geospatial
cmdstanr	adds cmdstanr on ml (GPU supported)

Push to a private repository

push_to_pr.sh <r-version> <ip>

./scripts/push_to_private.sh 4.2.1 xxx.xxx.xxx.xxx:xxxx

./scripts/pull_from_private.sh 4.1.3 4.2.1 xxx.xxx.xxx.xxx:xxxx

Example for Apptainer (Singularity)

This demonstration uses tictoc restored by renv to record elapsed time inside the radian container as an example.

1. Navigate to the tictoc directory.

cd tictoc

2. Change RENV_PATHS_CACHE in radian.def to your path (i.e., RENV_PATHS_CACHE=<your_path>" ).

3. Build an Apptainer image:

sudo apptainer build radian.sif radian.def

• Run a shell.

You can see renv being activated and the tictoc package can be restored:

apptainer shell radian.sif

Apptainer> radian
# Bootstrapping renv 0.15.4 --------------------------------------------------
* Downloading renv 0.15.4 ... OK
* Installing renv 0.15.4 ... Done!
* Successfully installed and loaded renv 0.15.4.

* Project '~/r-containers/tictoc' loaded. [renv 0.15.4]
* The project library is out of sync with the lockfile.
* Use `renv::restore()` to install packages recorded in the lockfile.
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Platform: x86_64-pc-linux-gnu (64-bit)

[ins] r$> renv::restore()
The following package(s) will be updated:

# GitHub =============================
- renv     [0.15.4 -> rstudio/renv@0.15.4]

# RSPM ===============================
- tictoc   [* -> 1.0.1]

[ins] Do you want to proceed? [y/N]: y
* Querying repositories for available source packages ... Done!
Retrieving 'https://packagemanager.rstudio.com/all/__linux__/focal/latest/src/contrib/tictoc_1.0.1.tar.gz' ...
        OK [downloaded 134.5 Kb in 0.4 secs]
Installing tictoc [1.0.1] ...
        OK [installed binary]
Moving tictoc [1.0.1] into the cache ...
        OK [moved to cache in 0.92 milliseconds]

[ins] r$> library(tictoc)

          tic()
          Sys.sleep(1)
          toc()
1.002 sec elapsed

• Or run an Rscript.

apptainer exec radian.sif Rscript check_time.R
1.002 sec elapsed

You can also specify the path to your renv cache when you start the container:

apptainer shell radian.sif --bind ~/renv:/usr/local/lib/R/etc/Renviron.site