For my system: Ubuntu 12.04 and R 3.03, whenever I install a custom package in R via
>install.packages()
the package is installed by default to
/home/USER/R/x86_64-pc-linus-gnu-library/3.0/
as opposed to system-wide in
/usr/local/lib/R/site-library/
which is needed for shiny-server to work with that package.
My temporary solution is to copy the packages to the correct folder after the fact.
Question: How can I set the default install path from the start to avoid this problem?
Yes -- I consider this to be a misfeature and disable my per-user directory.
Moreover, I mostly use a script install.r (of which a version is an example in the littler package you can install as part of Ubuntu) which simple explicitly set the /usr/local/lib/R/site-library directory as the default. With a patch we got into R 3.0.2 or 3.0.3, normal user can write into the directory and will now create group-writeable directories so other users can update and overwrite -- just make everybody a member of the same group, say staff or admin. And then you don't even need sudo or root.
I have essentially answered this same question a few times here over the years (minus the shiny angle, which is not really relevant) so feel free to search for the other for more details, examples, ...