How do you keep track of per-pkg system libraries?

[jasonh-logic2020]

I'm building custom images containing R libs (among other things) using GoogleContainerTools/distroless/package_manager. I have worked though collecting and adding R deps to packages.csv so all of my R world dependencies are fine.

But those R libraries have system library dependencies. When you load the R libraries in R code, they look for the system libraries they use, and throw at the first one they can't find.

I am not a native R person, so please forgive me if this is a stupid question: is there any way to find the native deps of R libraries? Iterating over this is really time consuming at scale.

Any help appreciated.

[siddharthab]

Hi, unfortunately there is no easy way. You could parse the DESCRIPTION files of all the packages in your workspace, and look at the list of SystemRequirements, but that is also not a guarantee.

To parse the DESCRIPTION file of all the packages, you can use this command.
Before running the command, you need to ensure all remote repos are fetched using bazel fetch or bazel sync.

bazel query 'kind(r_repository, //external:*)' | sed -e "s@.*:R_\(.*\)@$(bazel info output_base)/external/R_\1/\1/DESCRIPTION@" | xargs grep SystemRequirements

At GRAIL, installing these apt packages allow us to build 400+ packages from CRAN and Bioconductor.

libcurl4-openssl-dev
python3-pip
libgsl-dev
libmariadb-client-lgpl-dev
libomp-dev
libpq-dev
librsvg2-2
libssl-dev
libxml2-dev
libv8-3.14-dev

For r_markdown rules, you will also need pandoc and texlive-latex-extra.

Please feel free to close this issue when you feel like your question has been answered.

Thanks!

[siddharthab]

Closing because of no activity.