Simple process for sharing R code via Docker

Author
Affiliation

Ronald (Ryy) Glenn Thomas

UCSD

Published

August 22, 2024

1 Motivation

We have code we want to send to a colleague to run and/or edit. In doing this we need to avoid the problem of potentially different R and R-package versions. We also need to avoid needing to install pandoc and latex as well as supplemental files, e.g. bibtex, latex preamble, logo graphics files.

In sum, we want out colleague to simply have to download a github repository and pull a docker image from dockerhub and then run the command:

docker run  -v "$(pwd):/home/joe" -v "$(pwd)/output:/home/joe/output" rgt47/penguins1

inside the repo to get access to the identical R environment. And


vim peng1.Rmd

to edit

and

R -e "library(rmarkdown); render('peng1.Rmd')"

to process code through R, pandoc, and latex.

2 Introduction

Its often the case that two research collaborators want to work on the same R codebase. Unfortunately, to accomplish this, its often not as simple as one researcher sending a text file containing the code to the other colleague.

For example, a number of elements of the computing environment can differ between collaborators, such as: the version of R, the operating system(macos vs. windows vs Linus vs Other), R packages installed, the versions of the packages, startup files (e.g. .Rprofile) and environment variables. Any of these can cause code working for one reseracher to break when run by a second.

3 Methods

Lets assume you have some R program code in a file, say peng.R, that you’re written to analyze some “Palmer Penguin” data. You want to share the code with a colleague, we’ll call him Joe. How to proceed?

The simplest option is simply to send Joe the R file containing the code via the most convenient method (e.g. email)

The next step is for for Joe to (attempt to) run the code with the idea of expanding the analysis. Typically he would do this either using an IDE, such as Rstudio, or run the code from the command line in the terminal with the command:

> R -e "source('peng1.Rmd')"

Sometimes this approach works. When it does, Joe can add comments or expand the code and relay it back to you, “rince and repeat” and all is well. Frequently, however, this simple approach will fail for any of several reasons. Even when it runs, unless care is taken, its not guaranteed that Joe will get the same results you do.

Ideally to facilitate reproducibility your colleague Joe will have a computing environment as similar to yours as possible. This can be difficult to achieve, especially given the dynamic nature of open source software. For example, Joe may have an older version of R installed on his workstation, or his R environment may be missing a necessary package to run the code or it may be the wrong version. Additiional potential problems include: the program may need to source an additional file or load data that’s missing.

All of these problems go away if instead of sending the program as a standalone text file you send it as a docker image. In this post we’ll walk through the process of dockerizing the R code.

4 Methods

Assume we have a simple R file that we want to share with Joe such as the following:

---
title: "\\includegraphics[width=2cm, right]{sudoku_apple.pdf}\\newline 
  New Penguin plot"
author: "R.G. Thomas"
date: "`r format(Sys.time(), '%B %d, %Y')`"
fontsize: 11pt
geometry: "left=3cm,right=5cm,top=2cm,bottom=2cm"
output:
  pdf_document:
    keep_tex: true 
    includes:
header-includes:
   - \usepackage{lipsum}
   - \usepackage[export]{adjustbox}
   - \usepackage{currfile}
   - \usepackage{fancyhdr}
   - \pagestyle{fancy}
   - \setlength{\headheight}{14pt}
   - \fancyfoot[L]{\currfilename} %put date in header
   - \fancyfoot[R]{\includegraphics[width=.8cm]{sudoku_apple.pdf}}
   - \fancyhead[L]{\today} %put current file in footer
   - \fancyhead[R]{Penguins RGT Lab report}
latex_engine: xelatex
---

```{r  echo=F}
# clear env: objects and packages
library(pacman)
p_load(palmerpenguins, rmarkdown, knitr)

opts_chunk$set(
  warning = FALSE, message = FALSE, echo = FALSE, fig.width = 5.2,
  fig.height = 3, results = "asis", dev = "pdf"
)
```

# Introduction

\lipsum[1-5]

Draft report examining Penguin characteristics. Data from Alison Horst article
in the `R journal` 
@m.horstPalmerArchipelagoPenguins2022

```{r }
attach(penguins)
plot(flipper_length_mm, bill_length_mm, col = sex)
legend("topleft", legend = levels(sex), pch = 16, col = unique(sex))
```

\lipsum[1-5]
\bibliography{penguins.bib}
\bibliographystyle{plain}
\nocite{*}

5 Share program code with Joe.

Joe downloads the attachment. Opens a working directory and attempts to run the Rmd file

with the command

> R -e "source('peng1.Rmd')"

Joe has a linux mint desktop

> mkdir peng1
> cd peng1
> R -e "render('peng1.Rmd')"

Linux can’t find R

Joe can fix this by installing R

> sudo apt install r-base-core

So install R…. to fix

sudo apt install r-base-core Try again…

R -e “render(‘peng1.Rmd’)” Result: R loads but gives error: could not find function “render”

Search google “R render”

Result: https://pkgs.rstudio.com/rmarkdown/reference/render.html

Looks like render is a function inside rmarkdown package. so install package


R> install.packages("rmarkdown")

Try again.


> R -e "library(rmarkdown); render('peng1.Rmd')"

Result: error. pandoc version 1.12.3 or higher required.

Now try to install pandoc Try again. > R -e “library(rmarkdown); render(‘peng1.Rmd’)” Result: error. there is no called pacman

so install pacman R> install.packages(“pacman”) Try again…

R -e “library(rmarkdown); render(‘peng1.Rmd’)” result: failed pandoc could not find /Users/zenn/shr/preamble.tex

This makes sense we forgot to send the preamble.tex file to researcher 2. Lets send it now. Also we need to adjust its location from a macos style file name to a linux based one.

To edit peng1.Rmd we need vim > sudo apt install vim

Try again Result: pandoc error “pdflatex not found” Lets install tinytex. First in R and then in mint R> install.packages(“tinytex”) R> tinytex::install_tinytex() # to uninstall TinyTeX, run # tinytex::uninstall_tinytex()

Try again:

R -e “library(rmarkdown); render(‘peng1.Rmd’)” result: pandoc error: file sudoku_apple.pdf not found.

This makes sense we forgot to send the logo file. Lets send the file and try again.

R -e “library(rmarkdown); render(‘peng1.Rmd’)” Result: error no bibliography file found.

This makes sense we forgot to send the bib file. Lets send the file and try again. Also need to edit the location of bib file.

Try again:

R -e “library(rmarkdown); render(‘peng1.Rmd’)”

results: minor error. Some packages weren’t loading via pacman.

Try removing janitor, kableExtra, tidyverse, readxl and add ggplot2.

Try again:

R -e “library(rmarkdown); render(‘peng1.Rmd’)”

Success!

Lesson learned: The program peng1.Rmd needs access to three external files: 1. preamble.tex 2. penguins.bib 3. sudoku_apple.pdf

6 Docker approach

Alternatively, consider the “Docker” approach.

Before sending peng.Rmd to Joe we’ll dockerize it.

  • Prepare a work directory: peng1. We want to prepare a repo and a docker image that has a standardized computing environment set up including R, the R packages and all the preliminaries taken care of, so that all Joe has to do is clone the repo and run the image from dockerhub.

Steps for Joe:

  • install docker on his machine.
  • download docker image from dockerhub
  • run image

Here is the docker file


FROM rocker/r-devel
RUN apt-get update -qq && apt-get -y --no-install-recommends install \
    libxml2 \
    libxml2-dev \
    libcairo2-dev \
    libsqlite3-dev \
    libpq-dev \
    libssh2-1-dev \
    unixodbc-dev \
    r-cran-v8 \
    libv8-dev \
    net-tools \
    libprotobuf-dev \
    protobuf-compiler \
    libjq-dev \
    libudunits2-0 \
    libudunits2-dev \
    libgdal-dev \
    libssl-dev
## update system libraries
RUN apt-get update && \
    apt-get upgrade -y && \
    apt-get clean
RUN apt-get install pandoc -y
RUN groupadd --system joe
RUN useradd --system --gid joe -m joe
RUN chown joe:joe -R /home/joe
USER joe
WORKDIR /home/joe
COPY renv.lock renv.lock
RUN R -e "install.packages('renv', repos = c(CRAN = 'https://cloud.r-project.org'))"
COPY renv/settings.json renv/settings.json
RUN R -e "renv::restore()"
CMD ["/bin/bash"]

run docker

docker build -t rgt47/penguins1 --platform=linux/amd64 .

relay image to Joe via dockerhub.

docker push rgt47/penguins1

or

docker save rgt47/penguins1 | gzip > penguins1_transfer.tgz
docker load -i penguins1_transfer.tgz
> docker pull rgt47/penguins1

docker run -it --rm \
-v "$(pwd):/home/joe" -v "$(pwd)/output:/home/joe/output" rgt47/penguins1


> cd output
> library(rmarkdown); render('peng1.Rmd')

Important to include the association between the /home/joe/output directory in the container with the output directory on the local workstation. Thats where the results of the analysis will be saved.

> R -e "library(rmarkdown); render('peng1.Rmd')"

and if he wants to edit peng.Rmd

> vim peng1.Rmd

7 REFERENCES

Running your R script in Docker

docker run --rm -p 8787:8787 -e PASSWORD=z rocker/rstudio

j share
cd peng1

docker build -t rgt47/penguin1 .
docker run --rm -it rgt47/penguin1

droot="${PWD}"

docker run -it --rm -v $droot:/home/joe/output rgt47/penguin1 

Problem
☔ docker run -it --rm -v $droot:/home/joe rgt47/penguins1

Unable to find image 'rgt47/penguins1:latest' locally
docker: Error response from daemon: manifest for rgt47/penguins1:latest not found: manifest unknown: manifest unknown.
See 'docker run --help'.
share_R_code_via_docker/peng1 ☔ echo $droot
/Users/zenn/prj/qblog/posts/share_R_code_via_docker/peng1
share_R_code_via_docker/peng1 ☕ mkdir output
share_R_code_via_docker/peng1 ☕ f

Need a base R that includes dev tools

Try rocker/r-devel

docker build -t rgt47/penguin2 . --platform linux/amd64


docker run --rm \
  -e DISABLE_AUTH=true -e ROOT=true \
  -v "$(pwd):/home/rstudio/project:rw" \
  -p 8787:8787 \
  --name rstudio rocker/verse:3.6.3

docker run -it --rm -v “$(pwd):/home/joe” rgt47/penguins1

Dockerfile with R code


FROM rocker/r-devel
RUN apt-get update && \
    apt-get upgrade -y && \
    apt-get clean
RUN apt-get install terminator tree eza ssh zsh git fzf ripgrep vim curl \
autojump  zsh-autosuggestions sudo pandoc -y
RUN Rscript -e 'install.packages("renv")'
COPY renv.lock renv.lock
RUN  Rscript -e 'renv::restore()'
RUN groupadd --system joe
RUN useradd --system --gid joe -m joe
RUN usermod -aG sudo joe
RUN echo joe:z | chpasswd
RUN chown joe:joe -R /home/joe
RUN chown joe:joe -R /usr/local/lib/R/site-library
RUN chsh -s $(which zsh) joe
WORKDIR /home/joe/
COPY .vimrc .vimrc
COPY .zshrc .zshrc
RUN chown joe:joe -R /home/joe
RUN mkdir -p  /home/joe/output
USER joe
RUN curl -fLo ~/.vim/autoload/plug.vim --create-dirs \
    https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
CMD ["/bin/zsh"]
docker build -t rgt47/penguins1 . --platform linux/amd64
docker pull rgt47/penguins 
docker run -it --rm -v "$(pwd):/home/joe/peng2" -v "$(pwd)/out:/home/joe/output" rgt47/penguins1

Reuse

Citation

BibTeX citation:
@online{(ryy)_glenn_thomas2024,
  author = {(Ryy) Glenn Thomas, Ronald},
  title = {Simple Process for Sharing {R} Code via {Docker}},
  date = {2024-08-22},
  url = {https://focusonr.org/posts/share_R_code_via_docker},
  langid = {en}
}
For attribution, please cite this work as:
(Ryy) Glenn Thomas, Ronald. 2024. “Simple Process for Sharing R Code via Docker.” August 22, 2024. https://focusonr.org/posts/share_R_code_via_docker.