[Bioc-devel] Bioconductor time out in Windows while building vignettes

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Fri Jun 11 07:29:11 CEST 2021

Hi Nuno,

When I go on riesling1 and run 'R CMD build' on psichomics, the 
evaluation of the CLI_tutorial.Rmd vignette gets stuck at the call to 
plotSplicingEvent(). This call fires up the browser to display the 
alternate splicing event and the evaluation of the vignette resumes only 
after I shutdown the browser.

Note that, strangely enough, this doesn't happen all the time. After 
being able to reproduce this a couple of times, my further attempts failed!

One more thing: this call to plotSplicingEvent() doesn't actually inject 
anything in the final HTML vignette. Take a look at the vignette linked 
from the landing page of the package (first vignette listed at 
https://bioconductor.org/packages/3.13/psichomics) and you'll see that 
only the next plot (produced by plotDistribution()) shows up in the 

That's all I was able to find out, sorry. Hopefully you'll still be able 
to somehow make some sense of this information.


On 09/06/2021 07:35, Nuno Agostinho wrote:
> Hey all,
> I have a Bioconductor package named psichomics <https://bioconductor.org/packages/psichomics> that is timing out according to the Bioconductor R CMD build reports for Windows (both release and devel versions). This time out occurs after ~40 minutes while trying to create the package vignettes.
> In my local Windows virtual machine (running the latest Windows 10 Enterprise 20H2 <https://developer.microsoft.com/en-us/windows/downloads/virtual-machines/> in VMware Fusion 12.1.2 using R 4.1.0 and Bioconductor 3.13), it takes ~2m30 to finish building the package using the same command shown in the Bioconductor build report <http://bioconductor.org/checkResults/release/bioc-LATEST/psichomics/tokay2-buildsrc.html>:
> R.exe CMD build --keep-empty-dirs --no-resave-data psichomics
> How can I replicate the environment used in Bioconductor build reports to test what is going on?
> My package hasn't built once for Windows since the new release of Bioconductor 3.13 and I have no idea how to solve this... Any help would be greatly appreciated. Thanks!
> Best regards,
> Nuno Agostinho
> PhD student
> Nuno Morais Lab
> 	[[alternative HTML version deleted]]
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Hervé Pagès

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

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