Native R package support

Last modified: 28 August 2023

This chapter describes the specifics of working with public and private R packages repositories.

Environment tool

Use the tool (Environment > Packages) to install and manage R packages (install.packages, remove.packages, and available.packages commands supported).

This method records the applied changes to the environment.yml file of the respective notebook. As a result, the new configuration is automatically applied when opening the notebook.

.Rprofile files

To configure a custom R package repository, add an .Rprofile file to the notebook's Attached data or the home directory in a custom agent image (applicable for Datalore Enterprise).

If you want to use R Studio Package Manager you can set it up it there (or in other supported places if you use a custom docker image). If no CRAN url is specified, https://cloud.r-project.org is used by default.

The .Rprofile file will be respected when installing environment for the notebook.

Custom R environment without Anaconda (for Datalore Enterprise users)

This custom environment sets a non-conda default environment with the R kernel.

note

At the moment this solution adds this environment to /opt/anaconda/envs. Therefore, this option will be offered as a conda-based environment when creating a notebook. Such a restriction will be removed in the next release.

FROM jetbrains/datalore-agent:2023.4
ENV CUSTOM_ENV_NAME myenv
USER root
RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y -q --no-install-recommends libzmq3-dev libcurl4-openssl-dev libssl-dev r-base make g++ libharfbuzz-dev libfribidi-dev libtiff-dev apt-file && \
Rscript -e "install.packages(c('repr', 'IRdisplay', 'IRkernel'), type = 'source')" && \
rm -rf /var/lib/apt/lists/* && apt-get clean
RUN sudo chown -R datalore:datalore /home/datalore
USER datalore
RUN mkdir -p /opt/anaconda3/envs/$CUSTOM_ENV_NAME
RUN /opt/python/bin/python -m venv /opt/anaconda3/envs/$CUSTOM_ENV_NAME
RUN /opt/anaconda3/envs/$CUSTOM_ENV_NAME/bin/pip install ipykernel==5.5.3 ipython==7.31.1 ipython_genutils==0.2.0 jedi==0.17.2
RUN PATH=/opt/anaconda3/envs/$CUSTOM_ENV_NAME/bin/:$PATH Rscript -e "IRkernel::installspec(sys_prefix=TRUE)"
RUN /opt/datalore/build_code_insight_data.sh /opt/anaconda3/envs/$CUSTOM_ENV_NAME