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

[Hervé Pagès]

Hi Jacopo,

testthat::skip_on_bioc() relies on the IS_BIOC_BUILD_MACHINE environment 
variable to know whether it's on a BioC build machine or not.

This environment variable is defined during the daily build via the 
Renviron.bioc file. Note that a link to this file is provided on the 
individual build reports e.g. here 
https://bioconductor.org/checkResults/3.19/bioc-LATEST/Biobase/ 
("Renviron settings" link).

Maybe this environment variable is not defined on the Single Package 
Builder (SPB)? The SPB is the build system used during the package 
submission process. It runs on the same machines as the daily builds but 
my understanding is that it uses a slightly different set of variables. 
Maybe Lori can shed some light?

As for the timeout on merida1 (Intel Mac), have you considered using 
BiocFileCache to cache the data that you download in your examples? You 
might still get a timeout the next time 'R CMD check' will run on our 
build machines, but it should go significantly faster after that.

Best,

H.

On 12/12/23 07:22, Jacopo Ronchi wrote:
> 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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>
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-- 
Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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