[Bioc-devel] orthogene: evolving dependencies

[Brian Schilder]

Hello everyone, 

I’m the developer of orthogene <https://github.com/neurogenomics/orthogene>, a package for inter-species gene mapping.

Despite orthogene passing all CRAN and Bioc checks on GitHub Actions <https://github.com/neurogenomics/orthogene/actions/runs/2079508299> (including when using the official Bioc devel Docker container <https://github.com/neurogenomics/orthogene/runs/5794025048?check_suite_focus=true> with Bioc 3.15 and R 4.2), it is consistently failing on Bioc’s VMs <http://bioconductor.org/checkResults/devel/bioc-LATEST/orthogene/>. Most if not all of these errors seem to be due to corrupted .rda files from babelgene (a central dependency of orthogene):
Error in `load(filename)`: bad restore file magic number (file may be corrupted) -- no data loaded
The developer of babelgene <https://github.com/igordot/babelgene/> has recently been making quite a few changes/updates to their package. They last submitted an update to CRAN on March 30th 2022 <https://cran.r-project.org/web/packages/babelgene/index.html>. Hopefully these will be complete soon so I can make any necessary adjustments to orthogene. Still, I’m not sure why I’ve been unable to replicate the errors seen on Bioc’s VMs over the past several weeks.

In addition, I just received a message that the old version of orthogene on Bioc 3.14 is now failing <https://master.bioconductor.org/checkResults/3.14/bioc-LATEST/orthogene/nebbiolo2-checksrc.html> for the first time because of these changes. I hadn’t specified a version of babelgene in 3.14 because I designed my unit tests to pass after slight changes (e.g. varying numbers of mapped orthologs between mouse and human) but not failures (e.g. corrupted .rda files).

So my questions are two-fold:
Why am I unable to replicate the errors seen on Bioc’s VMs on my local machine (both within a Bioc 3.15 Docker container and outside of it) or on GHA (both within a Bioc 3.15 Docker container and outside of it).
Since Bioc 3.14 is now frozen, how can I prevent orthogene from failing Bioc checks  <https://master.bioconductor.org/checkResults/3.14/bioc-LATEST/orthogene/nebbiolo2-checksrc.html>failing <https://master.bioconductor.org/checkResults/3.14/bioc-LATEST/orthogene/nebbiolo2-checksrc.html> Bioc checks due to the changes to babelgene?

Many 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
Profile | bit.ly/imperial_profile <https://bit.ly/imperial_profile>
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/>


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