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I run Debian, and I do a mix of two paths: install using apt-get and install using install.packages() under R. Both work and it's safe to use both together. However, as has been pointed out, you tend to get dumped with multiple copies of some packages since the two channels lead to two different directories (/usr/local/lib/R/site-library for install.packages() and /usr/lib/R/site-library for