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

Nuno Agostinho nunod@n|e|@go@t|nho @end|ng |rom gm@||@com
Fri Jun 11 16:51:30 CEST 2021

Hi Hervé,

Many thanks for your help! I modified plotSplicingEvent() to run differently in non-interactive R sessions. Now, it correctly prints the output in the vignette without opening the browser! Still, I find it weird that this issue is only a problem since Bioconductor 3.13 and for Windows only...

Anyway, just updated the new version in Bioconductor, let's see if it solves the timeout issue. Thanks again!


> On 11 Jun 2021, at 06:29, Hervé Pagès <hpages.on.github using gmail.com> wrote:
> 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 vignette.
> That's all I was able to find out, sorry. Hopefully you'll still be able to somehow make some sense of this information.
> Best,
> H.
> 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]]
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> -- 
> Hervé Pagès
> Bioconductor Core Team
> hpages.on.github using gmail.com

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