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Bioconductor / Biostrings

Efficient manipulation of biological strings
https://bioconductor.org/packages/Biostrings
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segfault error when saving Biostrings output #103

Closed gevro closed 11 months ago

gevro commented 11 months ago

Hi, I'm getting a strange segfault error that happens reproducibly for a specific chunk of my data when in my pipeline I do this:

layered.seq <- sequenceLayer(bam$seq,bam$cigar) saveRDS(layered.seq,outputfile)

Error:

 *** caught segfault ***
address (nil), cause 'memory not mapped'

Using the latest version of Biostring 2.68.1.

Strangely, it happens only when running as an Rscript (non-interactive) but doesn't happen when interactive, so it is very hard to debug.

And it happens to only a small number of chunks that I break my dataset into, i.e. most chunks run fine.

Has anyone seen this before?

gevro commented 11 months ago

Note, I traced it to specific prior functions from Biostrings. But seems that upgrading from R 4.2.0 to R 4.3.1 just fixed it.

hpages commented 11 months ago

Glad you were able to make it work @gevro. Not much we were going to be able to do without seeing your sessionInfo() and having a minimal reproducible example.

Best, H.