Hello, I am attempting to run a code analysis that works locally that uses R alongside Bioconductor Packages VariantAnnotation and Trio on a cloud computing service. To do so I am using Docker to containerize my environment (the website utilizes Docker in this fashion). I am having trouble installing the layers of dependencies for the Bioconductor Packages:

# FROM rocker/r-base
# RUN R -e "install.packages('BiocManager'); BiocManager::install(c('VariantAnnotation','Trio'))"

sessionInfo( )

I would really appreciate it if someone knew what I am doing wrong here and how to properly put the Bioconductor layers on top of this image. Thank you!

One thing I see when doing this manually in the latest r-base container is that many dependencies are missing, such as libcurl. I personally would recommend the Bioconductor Docker container which comes with all necessary dependencies to run any Bioconductor package out of the box. The latest one is bioconductor/bioconductor_docker:RELEASE_3_17 and in this the above install works fine for me, but changing Trio to trio (lowercase T) as this is what the package is called.

Generally, I like to test package installs in an interactive session first (docker run -it bioconductor/bioconductor_docker:RELEASE_3_17 bash) to see all logs hands-on, and then use the Dockerfile once I figured out whether it works or which dependencies need to be added first.