rstats

Building R Binary Packages for Linux

Background One of the challenges of producing a performant build environment for linux, such as what might be used to have developers test software in identical environments, is the need to compile R packages from source on linux. If, however, one had an identical set of installed libraries, kernel version, compiler, etc., we could use binary packages in linux as well. Docker provides just such a shareable and identical environment for linux.

Single cell packages and dependencies in Bioconductor using BiocPkgTools

The Bioconductor package ecosystem continues to grow at an exponential rate (check it–I am right). We have recently completed the BiocPkgtools package that can mine package metadata, build reports, dependencies and can produce interesting plots of package dependencies. I was recently asked about the dependency structure of packages labeled by the package authors (using biocViews) as “SingleCell”. I am posting the code here, just for fun.