Welcome to the 29th post in the randomly repeating R recommendations series or R4 for short. Our last post #28 introduced RSPM, and just before that we also talked in #27 about binary installations on Ubuntu (which was also a T4 video). This post is joined with Iñaki Ucar and mainly about work we have done with his bspm package.
CRAN has been a cornerstone of the success of R in recent years. As a well-maintained repository with stringent quality control, it ensures users have access to highest-quality statistical / analytical software that “just works”. Users on Windows and macOS also benefit from faster installation via pre-compiled binary packages.
Linux users generally install from source, which can be more tedious and, often, much slower. Those who know where to look have had access to (at least some) binaries for years as well (and one of us blogged and vlogged about this at length). Debian users get close to 1000 CRAN and BioConductor packages (and, true to Debian form, for well over a dozen hardware platforms). Michael Rutter maintains a PPA with 4600 binaries for three different Ubuntu flavors (see c2d4u4.0+). More recently, Fedora joined the party with 16000 (!!) binaries, essentially all of CRAN, via a Copr repository (see iucar/cran).
The buzz currently is however with RSPM, a new package manager by RStudio. An audacious project, it provides binaries for several Linux distributions and releases. It has already been tested in many RStudio Cloud sessions (including with some of our students) as well as some CI integrations.
RSPM cuts “across” and takes the breadth of CRAN across several Linux distributions, bringing installation of pre-built CRAN packages a binaries under their normal CRAN package names. Another nice touch is the integration with
install.packages(): these binaries are installed in a way that is natural for R users—but as binaries. It is however entirely disconnected from the system package management. This means that the installation of a package requiring an external library may “succeed” and still fail, as a required library simply cannot be pulled in directly by RSPM.
So what is needed is a combination. We want binaries that are aware of their system dependencies but accessible directly from R just like RSPM offers it. Enter BSPM—the Bridge to System Package Manager package (also on CRAN).
The first illustration (using Ubuntu 18.04) shows RSPM on the left, and BSPM on the right, both installing the graphics package Cairo (and both using custom Rocker containers).
This fails for RSPM as no binary is present and a source build fails for the familiar lack of a
-dev package. It proceeds just fine on the right under BSPM.
A second illustration shows once again RSPM on the left, and BSPM on the right (this time on Fedora), both installing the units package without a required system dependency.
The installation of units works for BSPM as the dependency
libudunits is brought in, but fails under RSPM. The binary installation succeeds in both cases, but the missing dependency (the UDUNITS2 library) is brought in only by BSPM. Consequently, the package fails to load under RSPM.
To conclude, highlights of BSPM are:
This offers easy, reliable, fast installation of R packages, and we invite you to pick all three. We recommend usage with either Ubuntu with the 4.6k packages via the Rutter PPA, or Fedora via the even more complete Copr repository (which already includes a specially-tailored version of BSPM called CoprManager).
We hope this short note wets your appetite to learn more about bspm (which is itself on CRAN) and the two sets of Rocker containers shown. The rocker/r-rspm container comes in two two flavours for Ubuntu 18.04 and 20.04. Similarly, the rocker/r-bspm container comes in the same two two flavours for Ubuntu 18.04 and 20.04, as well as in a Debian testing variant.