[Bioc-devel] strange error in Jenkins build for singleCellWorkflow

[Kevin RUE]

Hi all,

I had this same issue a few months ago (in the weeks leading up to the
release of R-3.4.0), when building an Rmarkdown website on my own laptop.
It seemed the session variables were cleaned up between markdown documents,
but that packages remained loaded and accumulated to the point that I hit
the '100 DLLs limit' (
http://r.789695.n4.nabble.com/Is-it-possible-to-increase-MAX-NUM-DLLS-in-future-R-releases-td4720352.html)
causing the same error message as Aaron.

At the time, I was using R-devel which was to become 3.4.0. After a couple
of days, updating to the latest nightly build of R-devel solved the error
(except if I inadvertently touched anything else in the process).

It may not be much of a clear bug fix, but I hope my experience can
somewhat help hint toward the source of the issue on Jenkins.

Best wishes,
Kevin

Fun fact:
at the time, that issue made me discover this amazing package:
https://github.com/romainfrancois/nothing (which didn't solve the issue!)
Enjoy ;)


On Tue, Jun 20, 2017 at 6:23 PM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> Thanks for the report Aaron. I'll take a look.
>
> Valerie
>
> On 06/20/2017 07:10 AM, Aaron Lun wrote:
> > Hi all,
> >
> >
> > I'm getting a curious error in the Jenkins log when I try to build the
> singleCellWorkflow:
> >
> >
> > http://docbuilder.bioconductor.org:8080/job/simpleSingleCell/48/label=
> master/console
> >
> >
> > The key part is at the bottom:
> >
> >
> > Error: package or namespace load failed for 'GenomicFeatures' in
> dyn.load(file, DLLpath = DLLpath, ...):
> >  unable to load shared object '/var/lib/jenkins/R/x86_64-pc-
> linux-gnu-library/3.4/Rsamtools/libs/Rsamtools.so':
> >   `maximal number of DLLs reached...
> >
> >
> > The workflow had previously been running fine on the build system; I'm
> not quite sure what's going on here, given that it's not even failing at
> the point where I made the latest changes.
> >
> > Cheers,
> >
> > Aaron
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
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