[Bioc-devel] printing GRanges fails

[Oleksii Nikolaienko]

Ok, thanks very much Herve. I didn't know about these changes.

Best,
Oleksii

On Sun, 21 Nov 2021 at 20:17, Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> Hi Oleksii,
>
> This was caused by the serialized object in ramr/data/ramr.rda being
> out-of-sync with the latest changes in S4Vectors (DataFrame became a
> virtual class in S4Vectors 0.33.3). See
>
>
>
> https://bioconductor.org/help/course-materials/2019/BiocDevelForum/02-DataFrame.pdf
>
> for the motivation behind this change.
>
> Many packages contain serialized S4 objects with this problem. Most of
> them got fixed in devel already. Yours was fixed today (ramr 1.3.1,
> commit 6f30c30) so the error should clear on tomorrow's build report.
>
> Make sure to resync your GitHub repo with the ramr repo at
> git.bioconductor.org by following the instructions described here:
>
>    https://bioconductor.org/developers/how-to/git/
>
> Cheers,
> H.
>
>
> On 21/11/2021 07:28, Oleksii Nikolaienko wrote:
> > Hi,
> > devel branch of my package (ramr) cannot be built due to an error which I
> > don't understand. Package has sample data of class GRanges, but when I
> try
> > to print it I get the following:
> >> library(ramr)
> >> data(ramr)
> >> class(ramr.data)
> > [1] "GRanges"
> > attr(,"package")
> > [1] "GenomicRanges"
> >> ramr.data
> > GRanges object with 3000 ranges and 100 metadata columns:
> > Error: C stack usage  7954616 is too close to the limit
> >
> > This object seems to be ok in the release branch. Could anyone advise me
> on
> > further steps, please?
> >
> > Best regards,
> > Oleksii Nikolaienko
> >
> >       [[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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