R: apt-get install r-cran-foo vs. install.packages("foo")
cran, debian, r, ubuntu
Solution
Update (some thirteens years later): It is now as easy as it seems if you use for example the wonderful and powerful r2u system I set up last year, and which now provides over 20k binary .deb packages for each of twi Ubuntu LTS releases (currently: 20.04 and 22.04), and is also accessible via `install.packages()` thanks top `bspm`. Follow the link to r2u for more.
It's not as easy as it seems.
`apt-get update` is good if and when
packages exist -- but there are only around 150 or so `r-cran-*` packages out of a pool of 2100+ packages on CRAN, so rather sparse coverage
packages are maintained, bug free and current
you are happy enough with the bi-annual releases by Ubuntu
`install.packages()` and later `update.packages()` is good if and when
you know what it takes to have built-time dependencies (besides `r-base-dev`) installed
you don't mind running `update.packages()` by hand as well as the `apt-get` updates.
On my Ubuntu machine at work, I go with the second solution. But because the first one is better if you have enough coverage, we have built cran2deb which provides 2050+ binary deb packages for amd64 and i386 --- but only for Debian testing. That is what I use at home.
As for last question of whether you 'should you expect trouble': No, because `R_LIBS_SITE` is set in `/etc/R/Renvironment` to be
# edd Apr 2003 Allow local install in /usr/local, also add a directory for
# Debian packaged CRAN packages, and finally the default dir
# edd Jul 2007 Now use R_LIBS_SITE, not R_LIBS
R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R/site-library:\
/usr/lib/R/site-library:/usr/lib/R/library'}
which means that your packages go into `/usr/local/lib/R/site-library` whereas those managed by `apt` go into `/usr/lib/R/site-library` and (in the case of base packages) `/usr/lib/R/library`.
Hope that clarifies matters. The r-sig-debian mailing list is a more informed place for questions like this.
Problem
When installing R packages (say `mcmcpack` in this example) under Ubuntu I have the choice between the following two methods of installation: ``` # Let the distribution's packaging system take care of installation/upgrades apt-get install r-cran-mcmcpack # Let R take care of installation/upgrades install.packages("mcmcpack") ``` Questions: - Is any of the two ways of installing R packages considered "best practice"? - Assume that I first `install.packages("mcmcpack")` and later on `apt-get install r-cran-mcmcpack` - should I expect trouble? - Assume that I first `apt-get install r-cran-mcmcpack` and later on `install.packages("mcmcpack")` - should I expect trouble?