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:
install.packages("mcmcpack")
and later on apt-get install r-cran-mcmcpack
- should I expect trouble?apt-get install r-cran-mcmcpack
and later on install.packages("mcmcpack")
- should I expect trouble?Comprehensive R Archive Network (CRAN) It contains an archive of the latest and previous versions of the R distribution, documentation, and contributed R packages. It includes both source packages and pre-compiled binaries for Windows and macOS. As of November 2020, more than 16,000 packages are available.
You only need to install packages the first time you use R (or after updating to a new version). **R Tip:** You can just type this into the command line of R to install each package. Once a package is installed, you don't have to install it again while using the version of R!
Installing the CRAN packages with the menuIn RStudio go to Tools → Install Packages and in the Install from option select Repository (CRAN) and then specify the packages you want. In classic R IDE go to Packages → Install package(s) , select a mirror and install the package.
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.
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