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

[Jacopo Ronchi]

Dear Hervé,

Thank you very much for your answer. Regarding the issue that my package
encounters during the building on SPB i had the same doubt. Indeed when i
include that variable locally in my Renviron file everything works as
expected (tests that should be skipped on Bioconductor are indeed ignored).
So maybe the slight differences in variables between the two build systems
might be the answer.

On the other hand, i did not consider the caching of resources used in
examples. Since i already use BiocFileCache in my package, i will extend
this also for other features used in examples! Thank you very much for this
very useful suggestion.

Kind regards,
Jacopo

Il mer 13 dic 2023, 00:00 Hervé Pagès <hpages.on.github using gmail.com> ha
scritto:

> 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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>
> _______________________________________________Bioc-devel using r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> --
> Hervé Pagès
>
> Bioconductor Core Teamhpages.on.github using gmail.com
>
>

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