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

Tue Dec 26 14:21:45 CET 2023

Thank you very much for your effort!

Best regards and happy new year!
Jacopo

Il mar 26 dic 2023, 12:59 Kern, Lori <Lori.Shepherd using roswellpark.org> ha
scritto:

> Sorry for the delay. These environment variables should be set now on the
> Single Package Builder.
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
> ------------------------------
> *From:* Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Kern,
> Lori via Bioc-devel <bioc-devel using r-project.org>
> *Sent:* Friday, December 15, 2023 9:36 AM
> *To:* Jacopo Ronchi <jacopo.ronchi using unimib.it>; Hervé Pagès <
> hpages.on.github using gmail.com>
> *Cc:* bioc-devel using r-project.org <bioc-devel using r-project.org>
> *Subject:* Re: [Bioc-devel] Wrong skipping of tests when builidng on
> Bioconductor and R CMD check timeout
>
> I can update the SPB to have that environment variable set.  I will also
> cross check it with the current variables set on the daily builder.
> It may not be until next week that it is implemented.
>
> Cheers,
>
>
> Lori Shepherd - Kern
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive Cancer Center
>
> Department of Biostatistics & Bioinformatics
>
> Elm & Carlton Streets
>
> Buffalo, New York 14263
>
> ________________________________
> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Jacopo
> Ronchi <jacopo.ronchi using unimib.it>
> Sent: Friday, December 15, 2023 8:47 AM
> To: Herv�ag�<hpages.on.github using gmail.com>
> Cc: bioc-devel using r-project.org <bioc-devel using r-project.org>
> Subject: Re: [Bioc-devel] Wrong skipping of tests when builidng on
> Bioconductor and R CMD check timeout
>
> Regarding the Renviron file i have seen on the GitHub repository of SPB
> that indeed it is not using the IS_BIOC_BUILD_MACHINE env variable. How
> should i do in order to pass the checks without errors for my package in
> submission?
>
> Kind regards,
> Jacopo
>
> Il mer 13 dic 2023, 00:48 Jacopo Ronchi <jacopo.ronchi using unimib.it> ha
> scritto:
>
> > Dear Herv�>
> > 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 Herv�ag�<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://secure-web.cisco.com/1VAUfQTzP732tzYFyWRl9R-VpUe0qcrj11ANCzhi1M7PXdmEUq8BM7_xAJMn24SuX7fWWohKPYZhB0230fNWhTyL4DmAVWLPvmLQrY5ekH9gk0wIeUU8p_IHNHwooLmCYzg1EM9sBSbHTBa-lYfH_5RxRsfe9G46Fzgh4qD9LOMpVZH1EVerXKPfVHgQIJIXjWIkiyjvKSPcnIEXFgTHXVrklHZnSW_X7ba5yCvjOLPEAsUhPpIdJdDbYUEhR37AlDIl7CI6ww6vt95xFIBwEpTv8AsSrGIUY7opOomIPbtZTZiiznEYRC6gZQPGmhUrd/https%3A%2F%2Fbioconductor.org%2FcheckResults%2F3.19%2Fbioc-LATEST%2FBiobase%2F
> >> ("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://secure-web.cisco.com/1Rk_soQiHKHVPFUyxQEVFg-vcGG0WAJR6XK9z24AVEnrYfyKPY9vQ4_mh_dSEWnq5yhsoMSsoBYGZdR9X6XGeGTieTjRz0eFyhxsZ6EwtJp5WanZk4hoMSYlCzTQlbWTrp0W0U3GNKSqDkKWI9JcB6yDgdJkYsz3_A3DTSPZ5utwV_dF7MrGbC9_ccpBq33AGenBIHH43zCquE-F0QDPTJI85Sufi4xzh9O0DjBTFaGekjHHCm2WVF406Ga6Ij_IBAQBNBO78-SU9THFiK386l4E_sv0N9hiMQM-6BU7wXBS8dtxYQfa7Z42RMzZ_6Rax/http%3A%2F%2Fbioconductor.org%2Fspb_reports%2FMIRit_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
> >>
> >>       [[alternative HTML version deleted]]
> >>
> >> _______________________________________________Bioc-devel using r-project.org
> mailing listhttps://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >> --
> >> Herv�ag�>>
> >> Bioconductor Core Teamhpages.on.github using gmail.com
> >>
> >>
>
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