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[Bioc-devel] orthogene: killed while reading tree

3 messages · Brian Schilder, Shepherd, Lori

#
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/>
Twitter | twitter.com/BMSchilder<http://www.twitter.com/BMSchilder>
Lab | neurogenomics.co.uk<http://neurogenomics.co.uk>
UK DRI | www.ukdri.ac.uk<http://www.ukdri.ac.uk/>
4 days later
#
I'm not sure what caused it but it looks like it was intermittent as the build report is now showing all OK


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263
#
Indeed, thanks!

___________
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/>
Twitter | twitter.com/BMSchilder<http://www.twitter.com/BMSchilder>
Lab | neurogenomics.co.uk<http://neurogenomics.co.uk>
UK DRI | www.ukdri.ac.uk<http://www.ukdri.ac.uk/>

From: Kern, Lori <Lori.Shepherd at RoswellPark.org>
Date: Monday, 10 April 2023 at 13:03
To: Brian Schilder <brian_schilder at alumni.brown.edu>, bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: orthogene: killed while reading tree
I'm not sure what caused it but it looks like it was intermittent as the build report is now showing all OK


Lori Shepherd - Kern

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263