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

Fri Dec 15 15:36:52 CET 2023

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� Pag�s <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� Pag�s <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� Pag�s
>>
>> Bioconductor Core Teamhpages.on.github using gmail.com
>>
>>

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