In o2r-project/containerit: Package R in Docker Containers

Introduction

Containerit is also available itself as a ready-to-use Docker image from Docker Hub. This is useful if you do not want to install a full stack of packages in your local machine, but still trace a specific R session/script/document using a regular command line interface.

tl;dr - pull image and show Dockerfile on console

The following example pulls the geospatial variant of the containerit images, runs two R commands, and prints out the created Dockerfile to the console.

```{bash tldr} docker pull o2rproject/containerit:geospatial docker run --rm o2rproject/containerit:geospatial R -e "library(sf); the_dockerfile <- containerit::dockerfile(); print(the_dockerfile);"

## Control output

By default the containerit images print the session info before R is terminated.
You can disable this by setting the environment variable `CONTAINERIT_SILENT`.
Combined with the `--quiet` option for R, this reduces the output to merely the Dockerfile

```{bash log_silent, eval=FALSE}
docker run --rm -e CONTAINERIT_SILENT=true o2rproject/containerit:geospatial R -q -e "the_dockerfile <- dockerfile(); print(the_dockerfile);"

You can set the futile.logger threshold with the environment variable CONTAINERIT_FLOG_THRESHOLD to ERROR, WARN or DEBUG; default is INFO.

```{bash log_threshold, eval=FALSE} docker run --rm -e CONTAINERIT_SILENT=true -e CONTAINERIT_FLOG_THRESHOLD=WARN o2rproject/containerit:geospatial R -q -e "the_dockerfile <- dockerfile(); print(the_dockerfile);"

## Save file

You can of course also mount a directory with write permissions and save the Dockerfile.
The default directory in the container is `/containerit`, so you can mount to this location and write the Dockerfile object:

```{bash save_file, eval=FALSE}
mkdir /tmp/containerit
docker run --rm -v /tmp/containerit:/containerit -e CONTAINERIT_SILENT=true -e CONTAINERIT_FLOG_THRESHOLD=WARN o2rproject/containerit:geospatial R -q -e "the_dockerfile <- dockerfile(); write(the_dockerfile);"
echo Directory contents:
ls -l /tmp/containerit
rm -r /tmp/containerit

Or you can use full paths, as shown below. The next example also sets the user of the container, so that the file on the host has a more convenient user and permissions.

```{bash save_file_user_fullpath, eval=FALSE} mkdir /tmp/containerit docker run --rm -v /tmp/containerit:/my_dir -e CONTAINERIT_SILENT=true -e CONTAINERIT_FLOG_THRESHOLD=WARN --user=1000 o2rproject/containerit:geospatial R -q -e "the_dockerfile <- dockerfile(); write(the_dockerfile,file = '/my_dir/Dockerfile');" echo Directory contents: ls -l /tmp/containerit rm -r /tmp/containerit

## Example: package script

```{bash script, eval=FALSE}
mkdir /tmp/containerit
echo "install.packages('fortunes', repos = 'https://cran.r-project.org'); fortunes::fortune();" >> /tmp/containerit/script.R

docker run --rm -v /tmp/containerit:/data o2rproject/containerit R -q -e "setwd('/data'); scriptFile <- 'script.R'; write(dockerfile(from = scriptFile, cmd = CMD_Rscript(basename(scriptFile))));"

cat /tmp/containerit/Dockerfile
rm -r /tmp/containerit

Build image locally

With the following commands you can build an image from the local source code. The following commands executed in the containerit source directory create an image containerit:geo-manual and run it to create a Dockerfile:

```{bash build_local, eval=FALSE} docker build --file ../inst/docker/geospatial/Dockerfile --tag containerit:geo-manual . docker run --rm containerit:geo-manual R -e "library(sf); the_dockerfile <- containerit::dockerfile(); print(the_dockerfile);"

You can try the `predetect` feature by packaging the R Markdown file of the second spacetime vignette with the non-`geospatial` image of containerit that was just built.
The following command will install missing packages before running the file, namely `sf` itself, but it's installation will fail due to missing system dependencies, which are not covered by predetection.

```{bash predetect, eval=FALSE}
docker run --rm -i -v $(pwd)/tests/testthat/package_markdown/sfr:/erc -e CONTAINERIT_FLOG_THRESHOLD=DEBUG containerit R --quiet -e "setwd('/erc'); list.files(); print(dockerfile(from = '.'))"