"CI" tag for system dependencies only

[noamross]

A draft PR addressing #311, starting with just the script to install tidyverse/verse/geospatial system dependencies.

@eitsupi, I'm a bit confused as to where I would add a new image type to test. build/make-stacks.R both reads from and writes to the JSON files in stacks/. To add a new tag (I'm thinking rocker/ci), should I modify the stack files manually and then also add code to build/make-stacks.R for tagging?

[noamross]

@cboettig Not sure what is needed in this section

[cboettig]

yeah, this is a bit of a mess. debian/ubuntu ship a few different versions of libcurl (specifically, gnutils vs openssl), which conflict. (Some packages can bind either one, but don't necessarily play nicely with both -- e.g. I believe curl R package doesn't fail but does some unexpected things with the non-openssl version iirc?)

The redland R package needs librdf0-dev which depends on gnutils, meaning that line 64 will uninstalls the openssl version and potentially breaks things. So if we're going to install librdf0-dev, I think it is necessary to reinstall libcurl4-openssl-dev after we finish building redland from source (maybe not necessary now that we can get binaries??)

Anyway, long story short, I've always been very confused about the libcurl conflict. @eddelbuettel or @jeroen probably have a much better handle on this; maybe one of them could advise what's the best way to support both redland and curl R packages?

[eddelbuettel]

Sorry, do not have a fix. There are alternative implementations, which in turn are use by different packages, so you could indeed end up with 'graph' with conflicts. Best solution might be to locally rebuild packages using, say, gnutls to use openssl. Not something I tried though.

[eitsupi]

Is this image supposed to set a specific date snapshot as CRAN?
Or do you expect to use the "latest" for all R versions?

I'm a bit confused as to where I would add a new image type to test. build/make-stacks.R both reads from and writes to the JSON files in stacks/. To add a new tag (I'm thinking rocker/ci), should I modify the stack files manually and then also add code to build/make-stacks.R for tagging?

Yes, you need to run the script after editing stacks/devel.json and build/make-stacks.R to update stacks/4.1.2.json and stacks/4.1.1.json.
Only the part of stacks/devel.json that is related to the R version is rewritten by the script to become stacks/4.1.2.json and stacks/4.1.1.json.

To update stack files with version <= 4.1.0, we will need to temporarily fix the version limit of the script and transcribe devel.json, or update them manually.

rocker-versioned2/build/make-stacks.R

Line 540 in f3f9caf

dplyr::slice_max(r_release_date, n = 2, with_ties = FALSE) |>

If you can show me the structure of the Dockerfile you want, I can update the script for you.

[eitsupi]

I think it would be better to set an option in each script to skip installation of R packages and call each script instead of copying the apt install command into this script to avoid code duplication.