Fix R runtime

[lorenzwalthert]

#346 removed libblas3 and liblapack3 from the apt list. R doesn’t need those, but liblapack3 depended on libgfortran5, so removing it also removed libgfortran.so.5. R’s stats.so links against that library, so R now fails when calling the {stats} package, a base R package (i.e. shipped with R, like the python standard library):

library(stats)
unable to load shared object '/opt/r/lib/R/library/stats/libs/stats.so':
  libgfortran.so.5: cannot open shared object file

This breaks most language: r hook environments (renv::install fails while loading stats). We first add a call to {stats} package to demonstrate the behavior in the R tests and later add libgfortran.so back to the main image.

[lorenzwalthert]

You can see that d1564d7 shows the problematic behavior. Also for some reasons, the conda tests fail, that's why I temporarily deactivated all tests except the R tests (for speed).

[lorenzwalthert]

I can confirm that this PR runs successfully on all my hooks as I have created an integration test with it in my fork: lorenzwalthert#1
I have re-activated all tests. Unfortunately, there seems to be an unrelated failure of the conda test that I don't understand / fix in this PR.

[asottile]

[lorenzwalthert]

Still fails on the conda test...

[asottile]

yeah I'm trying to upgrade conda to fix that. for now I've rolled back to the previous image

[lorenzwalthert]

Thanks for the quick rollback response.

[lorenzwalthert]

I still see failures when pushing just now. Seems like pre-commit.ci did not pick it up yet?

[asottile]

I haven't had a chance to deploy it yet. had some unrelated issues last night to resolve. should be in a couple hours and then I'll let you know here!

[lorenzwalthert]

No worries, tomorrow is also fine or any time you get to it. A heads up here would be appreciated. Also, do you have an indication of how many runs this broke?

[asottile]

I've just deployed the newest image

[lorenzwalthert]

Hooray ,it worked. 🥳