I can not load sf in docker

Question

I'm deploying an application (on docker) that is totally dependent on sf but I'm having trouble loading it into docker :

FROM rocker/shiny

#Make a directory in the container
RUN mkdir /home/shiny-app

RUN R -e "install.packages('sf')"

RUN R -e "library('sf')"

COPY . /home/shiny-app/

This is the error message I received. I have no idea what caused this error. Probably GDAL? I need help to solve this problem.

Answer 1

When you want to add R packages to a new OS running R, you need to be aware of any underlying OS packages that are required. In this case, reading sf's DESCRIPTION, we see

SystemRequirements: GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0), sqlite3

It's not always intuitive how to know what these labels mean. One place you might look for a hint about this is Posit's Package Manager, which lists the following OS requirements on Ubuntu 22.04 (on which rocker/shiny is based).

apt-get install -y libgdal-dev
apt-get install -y gdal-bin
apt-get install -y libgeos-dev
apt-get install -y libproj-dev
apt-get install -y libsqlite3-dev
apt-get install -y libssl-dev
apt-get install -y libudunits2-dev

Many of those are likely already present.

First, let me reproduce the problem:

$ docker build -t quux .
$ docker run -it --rm quux R --quiet
> library("sf")
Error: package or namespace load failed for ‘sf’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/usr/local/lib/R/site-library/units/libs/units.so':
  libudunits2.so.0: cannot open shared object file: No such file or directory

Through experience, I know that Jammy (22.04) needs these packages for R's sf package, add these lines somewhere in your Dockerfile:

# ...
RUN apt-get update && \
  apt-get install -y libproj22 libudunits2-0 libgdal30 && \
  rm -rf /var/lib/apt/lists/*
RUN R -e "install.packages('sf')"

Notes:

1. Whether or not you join those with previous apt and install.packages(..) commands are up to you.
2. I encourage you to review https://docs.docker.com/develop/develop-images/instructions/ for "best practices", especially when installing OS-level packages, attempting to balance that with image size (ergo the rm -rf command).

It now works:

$ docker build -t quux .
$ docker run -it --rm quux R --quiet
> library("sf")
Linking to GEOS 3.10.2, GDAL 3.4.1, PROJ 8.2.1; sf_use_s2() is TRUE