https://github.com/f0nzie/r4ds-over-docker
Book r4ds with Dockerfile to build it with Docker
https://github.com/f0nzie/r4ds-over-docker
Last synced: 4 months ago
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Book r4ds with Dockerfile to build it with Docker
- Host: GitHub
- URL: https://github.com/f0nzie/r4ds-over-docker
- Owner: f0nzie
- Created: 2020-10-11T17:19:20.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2020-10-12T15:26:35.000Z (over 4 years ago)
- Last Synced: 2024-08-13T07:14:02.659Z (8 months ago)
- Language: R
- Size: 25.8 MB
- Stars: 1
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- jimsghstars - f0nzie/r4ds-over-docker - Book r4ds with Dockerfile to build it with Docker (R)
README
# 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.
```bash
#!/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](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 with`docker 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.
```bash
#!/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’
```