R and Rdevel share some libpaths about rocker

[eddelbuettel]

It is on purpose as we do not want to install everything twice.

The other three entries are the standard Debian layout we had since 2003 or so and which is documented elsewhere.

[eddelbuettel]

@wch here is a brief 'what is where and why'

• /usr/local/lib/R/site-library/: Packages installed by the user, and we share this on purpose between R and Rdevel.
• /usr/lib/R/site-library/: By convention, use for .deb package not part of Base R. We just don't have any installed in this image, as soon as you apt-get or dpkg one you see it here
• /usr/lib/R/library/: As you noted, base packages for R installed via .deb like r-cran-mass.
• /usr/local/lib/R/library/ The build-local directory for Rdevel.

I consider the Docker containers to be 'temporary' enough so that one focused on R-devel will see use primarily of R-devel -- so this version of R can easily re-use earlier/other packages from R-release. This strikes me as easier and more lightweight than forcing each package in twice. Which you can still do simply by changing the .libPath() -- but this strikes me as a worse default.

[wch]

@eddelbuettel thanks for the explanation. The rationale for sharing /usr/local/lib/R/site-library makes sense (especially with the idea that containers are disposable), though it does result in the occasional problem where a package installed in one version of R is broken in another version.

You could still allow packages installed on R-release to be used on R-devel, while also ensuring that packages installed on R-devel aren't used on R-release, by setting the libpath to: /usr/local/lib/R/site-library-devel, /usr/local/lib/R/site-library, /usr/local/lib/R/library, /usr/lib/R/library. This seems to me to be a better strategy, and the cost is negligible.

We've been bitten by R version changes in the past: when R 3.0.1 was released and CRAN started building binary packages on it, any package that contained reference class objects (including Shiny) would no longer run on R 3.0.0. This is because in R 3.0.1, they added and used a function named .setDummyField: https://github.com/SurajGupta/r-source/blame/master/src/library/methods/R/refClass.R#L748. If you google for that string, you'll see a lot of references to problems that people had.

But as you said, this isn't a huge deal if you treat the containers as disposable, so I don't feel super strongly about it.