This post has been updated:
- 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.shscript as it stopped working (Thanks to Matt Flor for noticing that).
Before submitting an R package to CRAN the CRAN policies demand 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 and R-packages. 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/ bash ./tools/rsync-recommended bash ./tools/link-recommended
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 \ # --with-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 \ --with-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 (I have updated this script based on the comments below).
## ~/bin/R-devel.sh
#!/bin/bash
export R_LIBS_SITE=${R_LIBS_SITE-'/usr/local/lib/R-devel/lib/R/library:/usr/local/lib/R/site-library:/usr/lib/R/site-library'}
export PATH="/usr/local/lib/R-devel/bin:$PATH"
R "$@"
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 bash ./tools/rsync-recommended bash ./tools/link-recommended 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)
I have used the following sources to compile this post:
- https://stat.ethz.ch/pipermail/r-sig-debian/2012-August/001937.html
- http://sites.psu.edu/theubunturblog/2012/08/09/installing-the-development-version-of-r-on-ubuntu-alongside-the-current-version-of-r/
- http://stackoverflow.com/q/17473547/289572
- http://serverfault.com/q/139451
- https://stat.ethz.ch/pipermail/r-devel/2016-May/072777.html
Thanks for that fantastic guide! That went very smoothly.
However, I encountered a weird error when installing packages. Some went fine, others threw a
object 'checkCompilerOptions' not founderror, like here: http://stackoverflow.com/questions/35503633/r-devel-object-checkcompileroptions-not-found-when-installing-magrittrSo, to anyone also seeing this: I finally managed to solve the issue after reading https://github.com/rocker-org/drd/issues/3
All I had to do was removing the
/usr/lib/R/librarypath inR-devel.sh:Matt, thanks for your comment. I also needed to make this change to get it to work now. I have updated the guide accordingly.
Thanks for this manual! It all worked pretty well
Interesting post, thank you!
you configure –without-recommended-packages, but you first do ./tools/rsync-recommended, why?
you configure with –prefix=/usr/local/lib/R-devel, but the script to run R points to /usr/lib/R-devel, why?
Martin Maechler suggested using a “build directory”, see https://stat.ethz.ch/pipermail/r-devel/2016-May/072777.html
Hi Frederik,
Thanks a lot for your comments. I have finally found the time to update the guide accordingly. I also have removed the step to call
make installseparately and added it to the script.Thanks and let me know if you see other problems.
Henrik
Hi Henrik,
the rsync stage does not wor on my ubuntu 16.04 distribution. I did the command
bash ./tools/rsync-recommended
There is the shell output:
rsync: failed to connect to cran.r-project.org (137.208.57.37): No route to host (113)
rsync error: error in socket IO (code 10) at clientserver.c(128) [Receiver=3.1.1]
*** rsync failed to update Recommended files ***
The error message suggests it is actually a problem with your internet connection. Perhaps it was temporary down or the SVN server unavailable. It still works on my machine.
On the r-help ML, I was told there were issues with the Vienna servers. However, I still got the same output. Can it be a firewall? I am connecting from my university.