I am trying to dockerize a shiny project and am having getting an error when running the docker image:
Error: package or namespace load failed for ‘rgdal’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/usr/local/lib/R/site-library/rgdal/libs/rgdal.so':
libgdal.so.26: cannot open shared object file: No such file or directory
For context my file structure is as follows:
.
├── shiny-app
│ ├── App.R
│ └── data
├── .gitignore
├── Dockerfile
├── README.md
└── my-project.Rproj
My shiny-app has the following library dependencies:
library(shiny)
library(shinythemes)
library(textdata)
library(tidyverse)
library(leaflet)
library(rgdal)
library(viridis)
(I know I could defiantly narrow down the dependency size by selecting only the packages within tidyverse that I am using but that's a problem for later).
Finally, my Dockerfile contains the following commands:
# get shiny server and R from the rocker project
FROM rocker/shiny:latest
# system libraries of general use
## install debian packages
RUN apt-get update -qq && apt-get -y --no-install-recommends install \
libxml2-dev \
libcairo2-dev \
libsqlite3-dev \
libmariadbd-dev \
libpq-dev \
libssh2-1-dev \
unixodbc-dev \
libcurl4-openssl-dev \
libssl-dev
## update system libraries
RUN apt-get update && \
apt-get upgrade -y && \
apt-get clean
# copy necessary files
## app folder
COPY /shiny-app ./app
# install R packages required
RUN R -e 'install.packages(c(\
"shiny", \
"shinythemes", \
"textdata", \
"tidyverse", \
"rgdal", \
"leaflet", \
"viridis", \
), \
repos="https://packagemanager.rstudio.com/cran/__linux__/focal/2021-04-23"\
)'
# run app on container start
CMD ["R", "-e", "shiny::runApp('/app')"]
I am able to build the image with docker build -t my-app .. However, when I try to run the docker image I get the error as I mentioned above. The weirdest part though is that shiny, tidyverse, and other packages are able to load. I am not sure why, then, docker is unable to access and use the installed package of rgdal if it can access the others.
Would love to hear any ideas! Thanks!