I keep all my R packages in a specific location that is not my home directory.

For some reason when ExperimentHub was downloading (through biocLite call) it decided to push files to ~/.ExperimentHub... but my server doesn't allow users to surpass a certain amount of space (in their homes) so that process got nuked.

I don't feel like a package should be writing to somewhere that wasn't originally specified? It is also not the R tempdir() or .libPaths()

I'm not sure if this is the right place to report something like this... please let me know where to I should post this if not. Maybe the github page?

We agree and have actually just pushed changes this past week in devel that uses the rappdirs::user_cache_dir to decide the directory. This function utilizes "Typical user cache directories" now as default. Keep in mind the directory (of the older versions of ExperimentHub and new) can be altered by specifying the directory in the constructor.