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gagneurlab / FRASER

FRASER - Find RAre Splicing Events in RNA-seq
MIT License
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Error: useNames = NA is defunct #77

Open deb0612 opened 9 months ago

deb0612 commented 9 months ago

Dear sir, I ran the test dataset, and got the error below image

drewjbeh commented 8 months ago

Hi there,

I cannot recreate this error. My environment with a recently installation of FRASER handles the test data perfectly. What verison of FRASER are you running? (take a look at sessionInfo() in the R session producing the error you posted).

Aokht17 commented 6 months ago

Hello,

It is not the FRASER version. Latest version of FRASER (1.99.0) also crushes with this error. The issue is (as far as I understood) in countRNAData --> extractSplitCountRanges --> return(rowRanges(splitCounts[passed,])) } else{ return(rowRanges(splitCounts)) rowRanges function from matrixStats version 1.2.0 has a deprecated useNames = NA option. You need to specify TRUE or FALSE.

That is why downgrading matrixStats to 1.1.0 solves the issue (also discussed here https://github.com/satijalab/seurat/issues/7501#issuecomment-1854571904).

Just a small modification to fix compatibility with new versions of matrixStats

AtaJadidAhari commented 4 weeks ago

Hi @deb0612 , as mentioned by @Aokht17 there was an issue with matrixStats versions which is fixed in the new FRASER versions >= 1.99.4 I will close the issue in two weeks if it stays inactive since it's resolved in newer FRASER versions.