Building R Binary Packages for Linux

And how Docker makes them useful

Photo: Matt Pike on Unsplash

Background

One of the challenges of producing a performant build environment for linux, such as what might be used to have developers test software in identical environments, is the need to compile R packages from source on linux. If, however, one had an identical set of installed libraries, kernel version, compiler, etc., we could use binary packages in linux as well.

Docker provides just such a shareable and identical environment for linux. Recent work by Levi Waldron and Nitesh Turaga to produce the bioconductor_full docker image will allow for nearly all bioconductor packages to be installed, as the underlying system dependencies are all included.

Docs from R on building binaries

docs on building binary R packages

The recommended method of building binary packages is to use R CMD INSTALL --build pkg where pkg is either the name of a source tarball (in the usual .tar.gz format) or the location of the directory of the package source to be built.

R CMD INSTALL --build operates by first installing the package and then packing the installed binaries into the appropriate binary package file for the particular platform.

By default, R CMD INSTALL --build will attempt to install the package into the default library tree for the local installation of R. This has two implications:

If the installation is successful, it will overwrite any existing installation of the same package. The default library tree must have write permission; if not, the package will not install and the binary will not be created. To prevent changes to the present working installation or to provide an install location with write access, create a suitably located directory with write access and use the -l option to build the package in the chosen location. The usage is then

R CMD INSTALL -l location --build pkg

where location is the chosen directory with write access. The package will be installed as a subdirectory of location, and the package binary will be created in the current directory.

Walkthrough

With that background in place, by starting a docker container from bioconductor_full, we can build binary packages that can be shared with others who are also running using bioconductor_full.

The next command assumes that docker is running.

docker run -v PATH_TO_LOCAL_STORAGE_DIRECTORY:/data \
  --name bioc_full \
  -e PASSWORD=<YOUR_PASSWORD_OF_CHOICE> \
  -p 8787:8787 \
  bioconductor/bioconductor_full:devel 

The PATH_TO_LOCAL_STORAGE_DIRECTORY should be replaced with the local directlry where the binary packages will land as they are built inside the container. Packages can then be reused or copied somewhere else for installation as binaries.

After running the docker run command above, you should be able to navigate to https://localhost:8787/ (or whatever your docker host address is). You will be presented with an Rstudio login. Login with username=rstudio and password=YOUR_PASSWORD_OF_CHOICE as set above.

Install and build binaries

Binary packages, after being installed and built, will be placed in the current working directory. I switch to the directory that is mapped back to the host so that I can keep the binary packages around after the container stops.

setwd('/data') # to drop binary tarballs into this directory

After logging into Rstudio, execute the following command. Note the INSTALL_opts.

# Biocmanager will be installed already for bioconductor_full
BiocManager::install('limma', INSTALL_opts='--build')

These installation options will copy the installed binary package(s) to /data. These will end up on the docker host machine in the PATH_TO_LOCAL_STORAGE_DIRECTORY

Bioconductor version 3.10 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'limma'
trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/limma_3.41.18.tar.gz'
Content type 'application/x-gzip' length 1493044 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

* installing *source* package ‘limma’ ...
** using staged installation
** libs
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c normexp.c -o normexp.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c weighted_lowess.c -o weighted_lowess.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o limma.so init.o normexp.o weighted_lowess.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-limma/00new/limma/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* creating tarball
packaged installation of ‘limma’ as ‘limma_3.41.18_R_x86_64-pc-linux-gnu.tar.gz’
* DONE (limma)

Check what we created:

dir('/data')

Your version of limma may differ.

[1] "limma_3.41.18_R_x86_64-pc-linux-gnu.tar.gz"

These binary packages can be installed just like any .tar.gz package but will be intalled very quickly like on Mac OS and Windows.

Remember to kill the docker container after you are done.

Avatar
Sean Davis
Senior Associate Scientist

My interests include biomedical data science, open data, genomics, and cancer research.

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