The problem is that a "~" directory is created in my home, when using the *Hub packages.
First of all, this is only an issue for me using R-devel, which I build from source. Using the Mac binary for R 3.3.1 this does not present the problem.
I can trace it to path.expand()'s behavior, which I know is used to create the location of the *Hub cache directories:
> path.expand("~")  "/Users/love/~"
BTW, it seems like adding a slash fixes this:
> path.expand("~/")  "/Users/love/"
One solution that I've used is to put the following lines in my .Rprofile:
However, when I build software packages that use the *Hub packages, I believe the init files aren't used and I again end up with a "~" dir in my home.
My session info:
R Under development (unstable) (2016-08-22 r71129) Platform: x86_64-apple-darwin15.5.0 (64-bit) Running under: OS X El Capitan 10.11.5 locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  parallel stats graphics grDevices utils datasets methods  base other attached packages:  ExperimentHub_0.101.12 AnnotationHub_2.5.11 BiocGenerics_0.19.2 loaded via a namespace (and not attached):  Rcpp_0.12.6 IRanges_2.7.14  digest_0.6.10 mime_0.5  R6_2.1.3 xtable_1.8-2  DBI_0.5 stats4_3.4.0  RSQLite_1.0.0 BiocInstaller_1.23.6  httr_1.2.1 S4Vectors_0.11.13  Biobase_2.33.0 shiny_0.13.2  httpuv_1.3.3 AnnotationDbi_1.35.4  htmltools_0.3.5 interactiveDisplayBase_1.11.3