Install R packages using docker file

Question

I have installed R using below line in my docker file. Please suggest how do I specify now packages to be installed in my docker file.

RUN yum -y install R-core R-devel 

I'm doing something like this:

RUN R -e "install.packages('methods',dependencies=TRUE, repos='http://cran.rstudio.com/')"\     && R -e "install.packages('jsonlite',dependencies=TRUE, repos='http://cran.rstudio.com/')" \     && R -e "install.packages('tseries',dependencies=TRUE, repos='http://cran.rstudio.com/')"  

Is this the right way to do?

Answer 1

As suggested by @Cameron Kerr's comment, Rscript does not give you a build failure. As of now, the recommended way is to do as the question suggests.

RUN R -e "install.packages('methods',dependencies=TRUE, repos='http://cran.rstudio.com/')" RUN R -e "install.packages('jsonlite',dependencies=TRUE, repos='http://cran.rstudio.com/')" RUN R -e "install.packages('tseries',dependencies=TRUE, repos='http://cran.rstudio.com/')"  

If you're fairly certain of no package failures then use this one-liner -

RUN R -e "install.packages(c('methods', 'jsonlite', 'tseries'),                            dependencies=TRUE,                             repos='http://cran.rstudio.com/')" 

---

EDIT: If you're don't use the Base-R image, you can use rocker-org's r-ver or r-studio or tidyverse images. Here's the repo. Here's an example Dockerfile -

FROM rocker/tidyverse:latest  # Install R packages RUN install2.r --error \     methods \     jsonlite \     tseries 

The --error flag is optional, it makes install.packages() throw an error if the package installation fails (which will cause the docker build command to fail). By default, install.packages() only throws a warning, which means that a Dockerfile can build successfully even if it has failed to install the package.

All rocker-org's basically installs the littler package for the install2.R functionality

Answer 2

Yes, your solution should work. I came across the same problem and found the solution here https://github.com/glamp/r-docker/blob/master/Dockerfile.

In short, use: RUN Rscript -e "install.packages('PACKAGENAME')". I have tried it and it works.

As others have mentioned in the comments, this solution will not raise an error if the package could not be installed.