GHA failing tests fails on WIndows: `index_tabix`?

Al-Murphy / MungeSumstats

Rapid standardisation and quality control of GWAS or QTL summary statistics

https://doi.org/doi:10.18129/B9.bioc.MungeSumstats

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GHA failing tests fails on WIndows: `index_tabix`? #78

Closed bschilder closed 2 years ago

bschilder commented 2 years ago

Issue

GHA is failing tests on Windows only, but it's not clear in which test or why.

https://github.com/neurogenomics/MungeSumstats/runs/4319268403?check_suite_focus=true#step:20:102

Screenshot 2021-12-13 at 15 37 02

Potential source

The report above suggests it may revolve around the index_tabix function, which relies on seqminer and Rsamtools. So it's possible this is a WIndows-specific bug in one of those softwares.

Temporary solution

I edited test-index_tabix.R file so that it doesn't run on Windows at all.

bschilder commented 2 years ago

This seems to have fixed itself. it may have been a bug in one of the dependencies, or simply GHA being finicky.

Either way, GHA is passing on all 3 platforms now.