GitHub Actions failure

[artur-sannikov]

Also see #741.

It's been a few months now that the GHA of Neurogenomics rworkflows is failing.

The issues is with these packages:

2026-01-14T08:46:35.2295893Z * checking package namespace information ... OK
2026-01-14T08:46:35.8669710Z * checking package dependencies ... ERROR
2026-01-14T08:46:35.8670298Z Packages suggested but not available:
2026-01-14T08:46:35.8670791Z   'IntegratedLearner', 'Maaslin2', 'MMUPHin'
2026-01-14T08:46:35.8674677Z The suggested packages are required for a complete check.
2026-01-14T08:46:35.8675956Z Checking can be attempted without them by setting the environment
2026-01-14T08:46:35.8678667Z variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
2026-01-14T08:46:35.8681542Z See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
2026-01-14T08:46:35.8682183Z manual.
2026-01-14T08:46:35.8682466Z * DONE

Maaslin2 has failing builds: https://bioconductor.org/checkResults/release/bioc-LATEST/Maaslin2/

However, IntegratedLeaner and MMUPHin seem to be fine.

The issue with MMUPHin is related to to its import of Maaslin2: https://github.com/biobakery/MMUPHin/blob/master/DESCRIPTION.

IntegratedLearner does build fine, I think, but its Docker image fails (but I want to remove it anyway).

[TuomasBorman]

Thanks, this is noted. The book is getting so big that it is getting hard to maintain; previously different packages were failing.

Have to check what to do with this

[artur-sannikov]

Can we use Maaslin3 instead of 2?

[TuomasBorman]

Not currently, the algorithms are different. Juho Pelto made nice updates to the chapters, but because of these rendering issues, it is not up yet.