[Bioc-devel] printing GRanges fails

[Hervé Pagès]

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]]
> 
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-- 
Hervé Pagès

Bioconductor Core Team
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