Support `install.R` files

We should support R functionality. R handles dependencies differently from both Python and Julia, here are some thoughts from Carl:

Current proposal

• Use runtime.txt to specify the R version as a date.
  • We’ll expect a line with the format r-YYYY-MM-DD. E.g. 2017-01-21.
  • If that line is found, it will trigger and R build in r2d. This sets up a version of R that was current at that date, and sets the MRAN snapshot for that date as the default repo.
  • We’ll also set up an R kernel for jupyter to discover. This R will also make sure we are installing in a user-owned library path so stuff can be installed there at any point.
• Use install.R (must be executable) to execute with the installed R kernel (in the point above). This primarily lets people write R code that installs packages.
• If install.R is given without a r-YYYY-MM-DD line in runtime.txt then we raise an error.

Main to-do items

• How do users specify what servers contain what packages (e.g. rstudio vs. bioconductor)
• ~What about non-CRAN packages?~ outside of the standard R repositories, we can’t do much else other then tell people to clone a github repo of preference and install it with install.R or postBuild or something.
• How can we ensure versions are frozen, since R doesn’t easily handle specific version installs?
• Someone needs to actually implement this!

Notes

In an R package, the DESCRIPTION file plays the role of a requirements.txt in stating the dependencies, minimal version needed, and where get them (e.g. CRAN or additional cran-type repo like bioconductor).

This approach does not accommodate installing something that is not the most recent version of a package. (CRAN archives old sources, but because, unlike python or ruby gems distribution, CRAN is designed to provide binaries & you can’t guarantee binaries build for an old /archived source, the default install does not immediately support installing archived packages).

If you just have a list of packages you want, I recommend something along the lines of what we do with rocker, e.g.

install2.r cat deps.txt

Where deps.txt is just a list of package names you want to install. If these come from multiple repos (cran & bioconductor), just list those as arguments to -r:

install2.r -r “https://cran.rstudio.com” -r “https://bioconductor.org/pagkages/release” cat deps.txt

If you want to install the same version each time, just use an MRAN snapshot of the appropriate date.

[yuvipanda]

Me and @cboettig just talked about this!

1. Specify the R version as a date in runtime.txt. So a value like r-2017-01-21 needs to be set there to ‘trigger’ R. This sets up a version of R that was current at that date, and sets the MRAN snapshot for that date as the default repo. We’ll also set up R kernel for jupyter to discover. This R will also make sure we are installing in a user-owned library path so stuff can be installed there at any point.
2. If there’s an install.r executable script, that is then executed with the installed R. This lets people write R code that installs packages. This seems to be the most common & accepted way to install libraries.

We can deal with packrat later. This current solution seems like a good start to supporting the R community on binder/repo2docker.

[choldgraf]

I think that we should pivot this issue to be specifically about adding an R build pack (e.g. supporting install.R or something like this). Will change title to reflect this!