WIP: move ChemmineOB to Suggests

Aariq commented 6 months ago

We think the CRAN pre-test is failing because OpenBabel isn't installed on their Debian runner and is making it impossible to install ChemmineOB. This PR moves ChemmineOB from Imports to Suggests and does a bunch of other things to make this work:

Prompts user to install ChemmineOB when they first run get_fx_groups() (or calc_vol()) using pak, which, if they are on linux, will also take care of OpenBabel installation (yay!). So, it's just macOS folks who will have to struggle with that now hopefully.
Only runs examples if ChemmineOB is installed (essentially skipping them on CRAN)
Precomputes the main volcalc vignette also, since ChemmineOB is needed to render it.
Skips all tests of get_fx_groups() and calc_vol() if ChemmineOB isn't installed (Question: would it be better to skip_on_cran() instead?). I think this means that no tests are run on CRAN because the KEGG tests are also skipped, and they might complain about that. Ugh!

I'm now questioning whether this will even work. I think CRAN tries to install Suggests dependencies as well and I'm not sure what happens if one of those errors.

We should run rhub::check_on_debian() and/or rhub::check_for_cran() on this branch before merging and re-submitting.

Aariq commented 5 months ago

This may not be needed. The CRAN error was due to the formatting of the License field in the DESCRIPTION file of ChemmineOB. Waiting for ChemmineOB to be updated on Bioconductor to try CRAN again (#103)

Aariq commented 3 months ago

Closing because this is likely not necessary, and definitely not necessary if it isn't going on CRAN. Also, it's out of date now.

Meredith-Lab / volcalc

WIP: move ChemmineOB to Suggests #102