[Bioc-devel] orthogene: killed while reading tree

[Brian Schilder]

Hi everyone,

After some pushes upstream to my package orthogene<https://bioconductor.org/packages/release/bioc/html/orthogene.html>, I noticed that the release version (3.16) is failing on the server because it was �Killed� midway through. But I can�t see any details that explain why or how it was killed.
http://bioconductor.org/checkResults/release/bioc-LATEST/orthogene/nebbiolo2-checksrc.html

The only thing I know is that is occurs at the step where a large tree (147k species, stored as a 5.3Mb newick file) is being read into R with ape::read.tree
https://github.com/neurogenomics/orthogene/blob/4e41e6322507a929562fc77cbdc602bc084a34bf/R/prepare_tree.R#L115

Oddly, this same code seems to work fine on devel (3.17):
http://bioconductor.org/packages/3.17/bioc/html/orthogene.html

Anyone know why this might be?

Thanks in advance,
Brian
___________
Brian Schilder
PhD Candidate
UK Dementia Research Institute at Imperial College London
Faculty of Medicine, Department of Brain Sciences, Neurogenomics Lab
CV | https://bschilder.github.io/CV/CV<https://bschilder.github.io/CV/CV.html>
LinkedIn | linkedin.com/in/brian-schilder<https://www.linkedin.com/in/brian-schilder/>
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UK DRI | www.ukdri.ac.uk<http://www.ukdri.ac.uk/>

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