Code that was working under R wouldn't work under rpy2. I figured out that rpy2 was ignoring /etc/R/Renviron.site by default. (I was adding to R_LIBS, etc.) This is because rpy2 initializes R using its --vanilla option.
In my opinion, this choice of default does not follow the principle of least surprise. And ignoring /etc/R/Renviron.site (which is the file where the sysadmin can make local additions to R_LIBS, etc.) is not very convenient.
I'm proposing this patch, which removes the --vanilla from the default arguments passed to R, and add the --no-restore option (which was included in --vanilla and not part of the other options passed to R by rpy2). Please consider this patch for inclusion in the next release of rpy2. Thanks.