[Bioc-devel] Wrong skipping of tests when builidng on Bioconductor and R CMD check timeout

[Jacopo Ronchi]

Dear Developers,

I am currently in the process of submitting my package on Bioconductor and
I am facing some issues during the R CMD check on the Bioconductor Build
System. Since I was not able to find any answers to my doubts, I decided to
ask for your help before doing anything wrong.

The build report for my package is available here:
http://bioconductor.org/spb_reports/MIRit_buildreport_20231211095232.html

In particular, my package includes some functions where it accesses remote
resources. Therefore, I included some "skip_on_bioc()" chunks at the
beginning of these tests since I don't want my package to fail during the
build process because of occasional down times. However, when I look at the
build report, I notice that the relevant tests are not skipped.
Furthermore, other tests that should be run are instead skipped on CRAN. I
am referring to these lines:

Skipped tests (2)
   On CRAN (2): 'test-topological-integration.R:23:5', 'test-utils.R:20:5'

Lastly, I have an error during R CMD check on macOS, and I really don't
know how to reduce the running time on this operating system. Currently, I
have reshaped the testing suite to reduce the time spent on unit tests.
However, on macOS, i guess that most of the time consumed is due to
examples. Nevertheless, the most time consuming functions retrieve
gene-sets from external resources and I can't reduce the download size of
KEGG pathways, for example. What should I do?

Sorry again for bothering you,
Best regards,
Jacopo

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