Skip to content

Latest commit

 

History

History
87 lines (60 loc) · 4.44 KB

installation.md

File metadata and controls

87 lines (60 loc) · 4.44 KB
Raw

Installing RCall.jl

RCall.jl can simply be installed with

Pkg.add("RCall")

RCall.jl will automatically install R for you using Conda if it doesn't detect that you have R 3.4.0 or later installed already.

Customizing the R installation

Before installing its own copy of R, the RCall build script (run by Pkg.add) will check for an existing R installation by looking in the following locations, in order.

  • The R_HOME environment variable, if set, should be the location of the R home directory.
  • Otherwise, it runs the R HOME command, assuming R is located in your PATH.
  • Otherwise, on Windows, it looks in the Windows registry.
  • Otherwise, it installs the r-base package.

To change which R installation is used for RCall, set the R_HOME environment variable and run Pkg.build("RCall"). Once this is configured, RCall remembers the location of R in future updates, so you don't need to set R_HOME permanently.

You can set R_HOME to the empty string "" to force Pkg.build to re-run the R HOME command, e.g. if you change your PATH:

ENV["R_HOME"]=""
ENV["PATH"]="....directory of R executable..."
Pkg.build("RCall")

When R HOME doesn't return a valid R library or R_HOME is set to "*", RCall will use its own Conda installation of R.

Should you experience problems with any of these methods, please open an issue.

Standard installations

If you want to install R yourself, rather than relying on the automatic Conda installation, you can use one of the following options:

Windows

The current Windows binary from CRAN.

OS X

The CRAN .pkg or the homebrew/science tap.

Linux

Most Linux distributions allow installation of R from their package manager, however these are often out of date, and may not work with RCall.jl. We recommend that you use the updated repositories from CRAN.

Ubuntu

The following will update R on recent versions of Ubuntu:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo add-apt-repository -y "deb http://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -s -c)/"
sudo apt-get update -y
sudo apt-get install -y r-base r-base-dev

Failure on recent Linux distributions

The version of libstdc++ shipped by Julia might be outdated if you are using a recent Linux distribution (e.g. Ubuntu 19.10) and make use of certain R packages (e.g. Rcpp). In this case RCall will fail with an error message looking similar to this:

Error: package or namespace load failed for ‘package’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/libs/Rcpp.so':
/home/user/julia-1.3.1/bin/../lib/julia/libstdc++.so.6: version `GLIBCXX_3.4.26' not found 
(required by /home/user/R/x86_64-pc-linux-gnu-library/3.6/Rcpp/libs/Rcpp.so)

Until this issue is fixed in Julia (see JuliaLang/julia#34276) a workaround is to replace Julias libstdc++ with the one of your OS:

# works for Ubuntu 19.10 64bit - match your locations accordingly!
cp /usr/lib/x86_64-linux-gnu/libstdc++.so.6 $JULIA_HOME/lib/julia/

Other methods

If you have installed R by some other method (e.g. building from scratch, or files copied but not installed in the usual manner), which often happens on cluster installations, then you may need to set R_HOME or your PATH as described above before running Pkg.build("RCall") in order for the build script to find your R installation. RCall requries R to be installed with its shared library. It could be done with the flag --enable-R-shlib, consult your server administrator if see if it was the caase.

For some environments, you might also need to specify LD_LIBRARY_PATH

export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:`R RHOME`/lib"

Updating R

If you have updated your R installation, you may need to re-run Pkg.build("RCall") as described above, possibly changing the R_HOME environment variable first.