I just finished writing a manuscript for publication in a scientific journal. I want my research to be reproducible, so besides sharing my original and compiled R markdown notebooks on Github, I would like to save the environment in which I was analysing my data (including the data, notebooks and specific R and package versions) in a Docker container. Moreover, I would like anyone trying to reproduce my work to be able to execute this code in an interactive Rstudio session.
I was able to create a Dockerfile with the correct environment. Here is a toy example:
FROM rocker/r-ver:3.5.1
RUN mkdir /home/working_directory
RUN mkdir /home/working_directory/bin
RUN R -e 'options(repos = \
list(CRAN = "http://mran.revolutionanalytics.com/snapshot/2019-01-01")); \
install.packages("ggplot2")'
COPY current/0[1-8]-*.Rmd /home/working_directory/
COPY current/bin/utils.R /home/working_directory/bin/
RUN R
However, this doesn't allow the users to read the Rmd notebooks and execute the code line by line. A workaround is to run the image rocker/rstudio, and install the packages from there, but I would like to be able to do so from a single docker build call. Unfortunately, I wasn't able to do so.
Cheers!
The Rocker RStudio image should have what you need - RStudio on top R. If you want specifically R 3.5.1, you can find the source here:
For more details on how to use it read https://hub.docker.com/r/rocker/rstudio.
To just use the pre-built images with a specific R version
# with R version 3.5.1:
docker pull rocker/rstudio:3.5.1
To investigate the image interactively:
docker run --rm -it rocker/rstudio:3.5.1 bash
Now we can run for example:
# Check R version
Rscript -e "sessionInfo()[['R.version']][['version.string']]"
# [1] "R version 3.5.1 (2018-07-02)"
# Check RStudio Server version
rstudio-server version
# 1.1.463
# Exit when done
exit