Using {pagedown} in Docker
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I’m building an automated reporting system which generates PDF reports. My approach is to use R Markdown to write the report and render to PDF using the excellent {pagedown} package.
Ultimately the system needs to be packaged in Docker and deployed in the cloud.
Setup
To illustrate what I’m doing, we’ll use a simple dummy document, test.Rmd.
--- title: "Test Document" output: html_document --- This is a test document.
To convert this into PDF run:
pagedown::chrome_print("test.Rmd")
I got this all running in my local environment quite easily. However, I ran into a snag when trying to package the code with Docker.
The Chrome Problem
I created a Dockerfile based on rocker/r-ver, adding Chrome and {pagedown}, then copying across test.Rmd.
FROM rocker/r-ver:4.1.0
RUN apt-get update -qq && \
apt-get install -y -qq --no-install-recommends \
libz-dev \
libpoppler-cpp-dev \
pandoc \
curl
RUN curl -L http://bit.ly/google-chrome-stable -o chrome.deb && \
apt-get -y install ./chrome.deb && \
rm chrome.deb
RUN install2.r --error --deps TRUE pagedown
COPY test.Rmd .
Running pagedown::chrome_print() from a container produces an error.
Error in is_remote_protocol_ok(debug_port, verbose = verbose) : Cannot find headless Chrome after 20 attempts
Bummer!
What’s going on here? Chrome is clearly installed, so why is R failing to find it? Well, I think what’s happening is R is actually finding Chrome it but it’s failing to run it.
And the problem appears to relate to Chrome’s sandbox. This is a safety feature built into Chrome. However, in this instance we need to circumvent it to get things working.
Cartoon from the Google Chrome Comic.
Print to PDF using Docker
The {pagedown} documentation suggests two approaches to solving the problem.
Use --no-sandbox Argument
One solution is to send --no-sandbox to Chrome via the extra_args argument.
pagedown::chrome_print("test.Rmd", extra_args = c("--no-sandbox"))
This is perfectly reasonable. And it works! So, from a pragmatic perspective, it’s perfect.
However, I’m going to be making a bunch of calls to pagedown::chrome_print() and, in the interests of simplicity, I’d prefer not to have to provide the extra argument every time.
Specify Security Options
An alternative is to use docker run with --security-opt to specify some custom security options. Again, this works, but it’s just added complexity! Also, I prefer a solution that’s actually baked into the Docker image.
A Chrome Solution
A Chrome Shim
I created a BASH script shim, google-chrome, with the following contents:
#!/bin/bash /usr/bin/google-chrome --no-sandbox $*
It basically executes Chrome, passing along all command line arguments plus --no-sandbox.
I made the script executable.
chmod u+x google-chrome
An Environment File
I also added the root folder, /, to the PATH environment variable in a file called Renviron.
PATH="/:${PATH}"
Tweaking the Dockerfile
The Dockerfile requires two small tweaks:
- copy the
google-chromescript across to/usr/local/bin/; and - copy
Renvironas.Renviron.
The revised Dockerfile looks like this:
FROM rocker/r-ver:4.1.0
RUN apt-get update -qq && \
apt-get install -y -qq --no-install-recommends \
libz-dev \
libpoppler-cpp-dev \
pandoc \
curl
RUN curl -L http://bit.ly/google-chrome-stable -o chrome.deb && \
apt-get -y install ./chrome.deb && \
rm chrome.deb
RUN install2.r --error --deps TRUE pagedown
COPY test.Rmd .
COPY Renviron /.Renviron
COPY google-chrome /usr/local/bin/
The actual Chrome executable is located at /usr/bin/google-chrome. But /usr/local/bin/ comes before /usr/bin/ in PATH, so when R looks for Chrome it finds the shim script first. This in turn adds in the --no-sandbox argument and my PDFs are then happily built by pagedown::chrome_print().
A Chromium Solution
How about using Chromium instead of Chrome? We need to make some changes to the Dockerfile to get Chromium installed.
FROM rocker/r-ver:4.1.0
# Install Chromium with apt not snap!
COPY bionic-updates.list /etc/apt/sources.list.d/
COPY chromium-deb-bionic-updates /etc/apt/preferences.d/
RUN apt-get update -qq && \
apt-get install -y -qq --no-install-recommends \
libz-dev \
libpoppler-cpp-dev \
pandoc \
chromium-browser
RUN install2.r --error --deps TRUE pagedown
COPY test.Rmd .
COPY Renviron /.Renviron
COPY chromium-browser /usr/local/bin/
Adding in a shim script which supplies the --no-sandbox option to Chromium and we’re sorted! ?
Admittedly this is a relatively deep rabbit hole for such a simple (and probably inconsequential) issue. But it was fun and instructive.
Resources
If you want to try this out yourself, here are the files you’ll need:
Chrome —
Chromium —
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