[Bioc-devel] Build error - C stack usage is too close to the limit

Aaron Lun |n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Fri Aug 2 04:36:28 CEST 2019

One possibility is that this is due to a regression in 
SingleCellExperiment, caused by the altexp updates and other 
refactoring. This should be fixed in 1.7.3, you can check this for 
yourself by installing drisso/SingleCellExperiment off GitHub.

The other moral of the story is to not use serialized high-level 
objects. Serializing basic objects is fine, but the higher up you go, 
the more fragile your code becomes to refactoring. See, for example, the 
scRNAseq data package for how to deliver a SingleCellExperiment to an R 
session without relying on serialized SingleCellExperiments.


On 8/1/19 7:14 PM, Kevin Wang wrote:
> Hi all,
> I am getting a strange build error message for scMerge (http://bioconductor.org/checkResults/devel/bioc-LATEST/scMerge/malbec1-buildsrc.html) that reads
> + "C stack usage is too close to the limit” on Linux and Mac and
> + "evaluation nested too deeply: infinite recursion” on Windows, when building the vignette file “scMerge.Rmd”.
> However, when I was building the Rmd locally and also on Travis + pkgdown under BioC3.10 (https://travis-ci.org/SydneyBioX/scMerge/builds/566753523), I had no errors. This file has not been edited for 2 months (https://github.com/SydneyBioX/scMerge/blob/master/vignettes/scMerge.Rmd).
> Any help would be appreciated.
> Thank you
> Best Wishes
> Kevin
> PhD Candidate
> Faculty of Science, School of Mathematics and Statistics
> 	[[alternative HTML version deleted]]
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