[Bioc-devel] Fw: MungeSumstats Bioconductor

[alan murphy]

Hi,

I'm the maintainer of the MungeSumstats package which is currently failing on the devel nebbiolo1 Linux platform because of RAM requirements of the unit tests. These tests use large reference datasets (like BSgenome.Hsapiens.1000genomes.hs37d5::BSgenome.Hsapiens.1000genomes.hs37d5) which cause the issue, e.g. from the output of the devel linux test<https://bioconductor.org/checkResults/3.19/bioc-LATEST/MungeSumstats/nebbiolo1-checksrc.html>:

```

Validating RSIDs of 92 SNPs using BSgenome::snpsById...
Killed

```
which is from this function: https://github.com/neurogenomics/MungeSumstats/blob/cccf77b2249f52be59fe1749f13a386ffaaae528/R/load_ref_genome_data.R#L49

I would like to keep these units tests as they are very important for me to know if things have gone wrong. I can't scale down the RAM usage, it is only using a few rows of data as it, the issue is that the reference sets are massive rather than the actual set being tested. I currently don't have a lot of these tests set to run on windows/mac platforms so I rely on the Linux machines to run this. I am not sure what has changed but a few releases back, the same tested were not causing this issue and would complete on linux - has the machine spec changed? Is there any chance RAM could be increased for these tests or is there a way to specify not to run the specific unit tests on the Bioconductor server so I can at least keep these for my github actions workflows? See below for the automated message I got about these errors.

Any other suggestions on ways around this would be greatly appreciated!

Thanks,
Alan.
________________________________
From: CoreTeam Bioconductor <bioconductorcoreteam using gmail.com>
Sent: Friday 2 February 2024 16:43
To: alanmurph94 using hotmail.com <alanmurph94 using hotmail.com>
Subject: MungeSumstats Bioconductor

Hello Package Maintainer,

We would like to bring to your attention that your package is failing in devel on the linux platform. This is very problematic. Please investigate the issues and fix the package to avoid deprecation.

https://bioconductor.org/checkResults/devel/bioc-LATEST/
<https://bioconductor.org/checkResults/3.17/workflows-LATEST/TCGAWorkflow>

If you have further questions or concerns please reach out on the bioc-devel using r-project.org<mailto:bioc-devel using r-project.org>

We appreciate your quick attention to this matter

Cheers,
On behalf of the Bioconductor Core Team

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