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
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