r4ds bookdown

Build the image

docker build -t r4ds .

What the Dockerfile does:

1. Pull the image for R-3.6.3

   # BUILD_DATE for R-3.6.3 is 2020-04-24
   FROM rocker/verse:3.6.3
   

2. Create folder /home/rstudio/r4ds inside the image

   RUN . /etc/environment \
       && mkdir /home/rstudio/r4ds
   

3. Copy the book source files under local folder book to image folder /home/rstudio/r4ds/book/:

   # when copying a folder we have to specify the destination folder as well
   COPY book /home/rstudio/r4ds/book/
   

4. Copy the DESCRIPTION file to image folder /home/rstudio/r4ds/:

   # we don't copy everything because we have a single file left at the end
   COPY DESCRIPTION /home/rstudio/r4ds/
   

5. Install book dependencies using DESCRIPTION as a dummy package constructor

   RUN R -e "devtools::install(\
       '/home/rstudio/r4ds', \
       keep_source=TRUE, \
       args='--install-tests', \
       dependencies=TRUE)"
   

6. Change default folder to /home/rstudio/r4ds/book

   # output folder for the book
   WORKDIR /home/rstudio/r4ds/book
   

7. Build the book

   # build gitbook with bookdown
   RUN Rscript -e 'bookdown::render_book(input = "index.Rmd",\
                         output_format = "bookdown::gitbook",\
                         output_dir = "public", clean_envir = FALSE)'
   

8. Assign user permissions to the public output folder under /home/rstudio/r4ds/book/.

   RUN chown -R 1001:1001 public
   

9. From the local folder, copy the script copy_gitbook.sh to the image folder /home/rstudio/r4ds. This script will take care of copying the public folder in the container to the local machine.

   #!/bin/bash
   # copy_gitbook.sh
   #
   echo "Will start copying output files to share folder ..."
   cp -avr public/ ../../share/

Figure: This is how it looks at the end of the Docker build process. The last Docker operation is copying the script copy_gitbook.sh.

Run the container

There are several options to get access to the book and the output generated by bookdown in the Docker container by means of running a container of the image.

• Option 1: This command will copy the public folder to the share folder. Note that this command doesn't require to load RStudio in a browser; it only executes a script.

  docker run --rm \
  	-v $PWD/share:/home/rstudio/share \
  	r4ds \
  	../copy_gitbook.sh
  

  • -v $PWD/share:/home/rstudio/share: connect the container folder /home/rstudio/share with the local folder $PWD/share. The environment variable $PWD contains the name of the current directory.
  • r4ds: is the the name of the image
  • ../copy_gitbook.sh: location of the script to execute

• Option 2: With the next command we set up the /home/rstudio/share folder in the container that can be shared with the host machine under the current project folder. This is the classic way of sharing a container folder with a local folder. This command will enable an RStudio session to the project via http://localhost:58787.

docker run --rm -p 58787:8787 \
    -v $PWD/share:/home/rstudio/share  \
    -e USERID=$UID -e PASSWORD=r4ds \
    r4ds

• Option 3: With this other command, we will be sharing the book with the volume bookdown-r4ds. Also we are making available a local share to the current project folder. This command requires that we have created the volume bookdown-r4ds in advance withdocker volume create bookdown-r4ds.

docker run --rm -p 58787:8787 \
    -v $PWD/share:/home/rstudio/share  \
    --mount source=bookdown-r4ds,destination=/home/rstudio/r4ds \
    -e USERID=$UID -e PASSWORD=r4ds \
    r4ds

NOTE The following command will not allow us to share the book that was built in the image because it overwrites the output folder r4ds. It will show empty.

docker run --rm -p 58787:8787 \
    -v $PWD/share:/home/rstudio/r4ds  \
    -e USERID=$UID -e PASSWORD=r4ds \
    r4ds

Scripts

The following shell script copies the output of the bookdown::gitbook to the folder /home/rstudio/share which is linked to the share folder under our current project.

#!/bin/bash
# copy_gitbook.sh
#
echo "Will start copying output files to share folder ..."
cp -avr public/ ../../share/

Errors

* checking for file ‘r4ds.book/DESCRIPTION’ ... ERROR

Required fields missing or empty:

  ‘License’ ‘Description’ ‘Author’ ‘Maintainer’