How to install dependencies when using "R CMD INSTALL" to install R packages?
RDependenciesPackageR Problem Overview
I'm developing my first R package (using R 2.13, Ubuntu 10.10). Let's call it foo and let's say that the code in the R/ directory begins with the line library(bar), where bar is an existing package, in CRAN, on which foo depends. My DESCRIPTION file contains the line:
Depends: bar
When package foo is ready for testing, I install it locally using:
R CMD INSTALL foo_1.0.tar.gz
However, if bar is not installed, I see:
ERROR: dependency ‘bar’ is not available for package ‘foo’
Obviously, if my foo were installed from CRAN using install.packages(), bar would be installed at the same time. So my question is: how can I ensure that CRAN package bar is installed, if required, when I install my package foo using R CMD INSTALL? Is this a job for a configuration script?
R Solutions
Solution 1 - R
Actually, re-reading the R extensions guide, it doesn't say that R CMD INSTALL will get dependencies from CRAN. The install.packages() method from within R will do that, but at first glance I don't think R CMD INSTALL does.
You can use install.packages to install from a .tar.gz, but you have to set repos=NULL, and then this applies:
dependencies: logical indicating to also install uninstalled packages
on which these packages depend/suggest/import (and so on
recursively). Not used if repos = NULL.
I suspect the thing to do is to get the dependencies out of the DESCRIPTION file and then run R and do an install.packages() on those when you are testing your build in a clean environment.
Solution 2 - R
Fortunately Devtools provides an easy solution: install_deps()
> install_deps(pkg = ".", dependencies = logical, threads = getOption("Ncpus",1))
> Arguments:
> pkg: package description, can be path or package name. See
> ‘as.package’ for more information
> dependencies: ‘logical’ indicating to also install uninstalled packages > which this ‘pkg’ depends on/links to/suggests. See argument > ‘dependencies’ of ‘install.packages’.
> threads: number of concurrent threads to use for installing > dependencies. It defaults to the option ‘"Ncpus"’ or ‘1’ if > unset.
Examples:
install_deps(".")
install_deps("/path/to/package",dependencies="logical")
Solution 3 - R
I ended up just using a bash here-document and specifying the cloud mirror to find the dependencies:
sudo R --vanilla <<EOF
install.packages('forecast', repos='http://cran.us.r-project.org')
q()
EOF
the R package is "forecast", the cloud mirror I used was http://cran.us.r-project.org. If you want to use a different mirror, here they all are: https://cran.r-project.org/mirrors.html
The above worked for me in getting R packages into an AWS EMR bootstrap shell script.
Solution 4 - R
Similar to @Jonathan Le, but better for script usage :
sudo R --vanilla -e 'install.packages("forecast", repos="http://cran.us.r-project.org")'
Solution 5 - R
Update; as of Feb 2021, the remotes package does the trick and has a much smaller footprint than devtools:
R -e "install.packages('remotes')"
R -e "remotes::install_local('/path/to/mypackage.tar.gz', dependencies=T)"
Solution 6 - R
Following Romain Rossi's idea, here is a simple shell script which installs every argument you send it's way (assuming it's a package):
#!/bin/sh
for f in $*
do
sudo R --vanilla -e "install.packages('"$f"', repos='http://cran.us.r-project.org')"
done
Solution 7 - R
The mechanism to do this is to add an entry in the depends field in your DESCRIPTION file.
Depends: bar
This will load the bar library if already installed, otherwise will install it from CRAN.
This is described in section 1.1.1 of the Writing R extensions manual: http://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file