Installing R-devel on Linux (Ubuntu/Mint)

October 24, 2015
By

(This article was first published on Computational Psychology - Henrik Singmann, and kindly contributed to R-bloggers)

This post has been updated:

  • 1. March 2018: Removed `bash ./tools/rsync-recommended` and  `bash ./tools/link-recommended`. They should not be needed anymore.
  • 15. November 2017: Removed installing of recommended packages from build script. Those packages are now simply installed in the local library path which is also added to the `LIB_SITE`. This also allows that checked packages depend on recommended packages and those will also be updated with update.packages().
  • 1. July 2016: Updates thanks to comment of Frederik Eaton
  • 2. April 2016: Included downloading and building recommended package (I couldn’t check packages requiring recommended packages without that).
  • 29. March 2016: Updated r-devel.sh script as it stopped working (Thanks to Matt Flor for noticing that).

 

Before submitting an R package to CRAN the CRAN policies require that a package runs R CMD check --as-cran without any warnings or notes. More specifically, the policies demand that “[t]his should be done with the current version of R-devel”.  Previously I have done this on Windows, but even with the latest R-devel there are always issues that just do not pop up there (e.g., checking of URLs). Consequently, I have recently (finally) switched to Linux. But as a total Linux noob setting up R-devel was not trivial. This post shows how to set up R-devel next to the latest regular R and how to use it to test packages.

To install R-devel you first need to make sure you are able to install R, R-packages, and have a working LaTeX installation (e.g., texlive). Please follow the instructions here: https://cran.rstudio.com/bin/linux/ubuntu/README

Then you will also need subversion (for getting the latest source) and I also needed to install xorg (in case you get some unexpected errors it may be necessary to also install the suggestions given here):

sudo apt-get install subversion ccache
sudo apt-get install xorg-dev

Now you need to get a current version of the source code via svn (i.e., subversion). For this, first create a folder svn in your home directory, change to this directory, and then checkout the latest version of the source code.

cd ~
mkdir svn
cd svn
svn co https://svn.r-project.org/R/trunk r-devel/R

You also need to download and link the recommended packages for using them in R CMD check as described in the R installation manual (this needs to happen in the correct folder).

cd r-devel/R/

Following a comment from Martin Maechler we do not build R in the svn directory, but rather in a newly created build directory:

mkdir ~/svn/R-devel-build

Next you need to build R-devel, preferably in a different location then your usual R installation. We do this with a script courtesy of Dirk Eddelbuettel (which I changed so it uses the correct path and --with-recommended-packages). Simply create a new file build-R-devel with the following content. It makes a lot of sense to put this file in a location that is in the $PATH, I recommend /usr/local/bin (which requires root/sudo). At the end of this, we automatically run make install which we also add to the script (which is in contrast to the recommendations of Martin Macheler from above, but it works just fine).

## ~/bin/build-R-devel

#!/bin/sh

cd ~/svn/R-devel-build

# R_PAPERSIZE=letter                \
# R_BATCHSAVE="--no-save --no-restore"         \
# R_BROWSER=xdg-open                \
# PAGER=/usr/bin/pager                \
# PERL=/usr/bin/perl                \
# R_UNZIPCMD=/usr/bin/unzip            \
# R_ZIPCMD=/usr/bin/zip                \
# R_PRINTCMD=/usr/bin/lpr                \
# LIBnn=lib                    \
# AWK=/usr/bin/awk                                \
# CC="ccache gcc"                    \
# CFLAGS="-ggdb -pipe -std=gnu99 -Wall -pedantic -DTESTING_WRITE_BARRIER" \
# CXX="ccache g++"                \
# CXXFLAGS="-ggdb -std=c++0x -pipe -Wall -pedantic" \
# FC="ccache gfortran"                \
# FCFLAGS="-ggdb -pipe -Wall -pedantic"        \
# F77="ccache gfortran"                \
# FFLAGS="-ggdb -pipe -Wall -pedantic"        \
# MAKE="make -j4"                    \
# ./configure                     \
#     --prefix=/usr/local/lib/R-devel         \
#     --enable-R-shlib                 \
#     --enable-strict-barrier             \
#     --with-blas                 \
#     --with-lapack                 \
#     --with-readline                 \
#     --without-recommended-packages

R_PAPERSIZE=letter                \
R_BATCHSAVE="--no-save --no-restore"         \
R_BROWSER=xdg-open                \
PAGER=/usr/bin/pager                \
PERL=/usr/bin/perl                \
R_UNZIPCMD=/usr/bin/unzip            \
R_ZIPCMD=/usr/bin/zip                \
R_PRINTCMD=/usr/bin/lpr                \
LIBnn=lib                    \
AWK=/usr/bin/awk                                \
CC="ccache gcc"                    \
CFLAGS="-ggdb -pipe -std=gnu99 -Wall -pedantic" \
CXX="ccache g++"                \
CXXFLAGS="-ggdb -pipe -Wall -pedantic"         \
FC="ccache gfortran"                   \
F77="ccache gfortran"                \
MAKE="make -j4"                    \
../r-devel/R/configure                     \
    --prefix=/usr/local/lib/R-devel         \
    --enable-R-shlib                 \
    --with-blas                 \
    --with-lapack                 \
    --with-readline                 \
    --without-recommended-packages

#CC="clang -O3"                                  \
#CXX="clang++ -03"                \


#make svnonly
make 

echo "*** Done -- now run 'make install'"

make install

echo "*** All Done -- start R-devel with 'bash R-devel'"

Next, you need to install R-devel using this script which automatically changes to the correct directory. Note that this step requires sudo.

sudo bash build-R-devel

Now we only need a custom run script to actually run R-devel. Again this script is based on one written by Dirk Eddelbuettel and it should also be in a folder which is in the path such as /usr/local/bin. Note that we need to export the local library path for this installation as well. Below this is ~/R/x86_64-pc-linux-gnu-library/3.5, but this might need updating depending on your setup.

## ~/bin/R-devel.sh

#!/bin/bash

export R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R-devel/lib/R/library:~/R/x86_64-pc-linux-gnu-library/3.5'}
export PATH="/usr/local/lib/R-devel/bin:$PATH"
R "[email protected]"

To finally run R-devel simply call it as a script: bash R-devel
It should show you that it is the current development version: R Under development (unstable) (CURRENT DATE)
As this is a vanilla version of R, you will have to install all the packages you need.

The R-devel script can also be used to build or check your package:

bash R-devel CMD build your-package-directory
bash R-devel CMD check --as-cran your-package.tar.gz

Once all this is set up, the steps of updating your R-devel installation to the latest version only involves calling the scripts in the right order:

cd ~/svn/r-devel/R
svn update
sudo bash build-R-devel

After doing so, it is probably a good idea to update the packages:

bash R-devel
update.packages(ask=FALSE, checkBuilt = TRUE)

I have used the following sources to compile this post:

 

To leave a comment for the author, please follow the link and comment on their blog: Computational Psychology - Henrik Singmann.

R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...



If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.

Search R-bloggers

Sponsors

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)