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Add remaining system packages for Codespaces R packages #81

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remlapmot
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This adds the system packages required at runtime for the following R packages: sf, rgdal, rgeos, units, tcltk, odbc.

Also two other minor tweaks

@lucyb
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lucyb commented Dec 9, 2024

There are some good fixes in here, thanks for doing them @remlapmot. I spotted this PR because it's in a Team REX repo. I assume it's still open because it's still relevant.

Can I ask why support for the extra R packages (sf, rgdal, rgeos, units, tcltk and odbc) is needed, please? Who is likely to use them?

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I guess there hasn't been any demand for these. These R packages are in the current r image and hence in the Codespaces RStudio. But currently if you try to load any of these packages in Codespaces RStudio the loading fails (which I guess a user would find confusing because they load in the r image).

The packages sf, rgdal, and rgeos are for spatial statistics. I guess whomever was using spatial statistics hasn't used OpenSAFELY in a while (or they don't use Codespaces).

Essentially I had a look at this for completeness after we'd added the dd4d and dagitty packages to the r image for Will and Becky's workshop at the conference. We then realised a dependency of dagitty, V8, required a system library (libnode-dev); and then it occurred to me that there were likely other packages that required some system libraries at runtime.

So I don't have a strong preference whether this is merged. At least if a user ever needs them you have a record of what's needed.

In the forthcoming v2 r image we've removed the odbc package, so the system library for that won't be needed soon in any case.

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