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! Best, Nuno > On 11 Jun 2021, at 06:29, Hervé Pagès <hpages.on.git...@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@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
