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Bioconductor / BiocParallel

Bioconductor facilities for parallel evaluation
https://bioconductor.org/packages/BiocParallel
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'offset' contains negative indices #214

Closed TheFirstAdrien closed 2 years ago

TheFirstAdrien commented 2 years ago

Hi all, Currently trying to work with Rcardinal package. I have installed all the required packages, but when I wish to open a file, the following error pops up while processing the 5th chunk;

Error: BiocParallel errors 1 remote errors, element index: 5 15 unevaluated and other errors first remote error: Error in validObject(x): invalid class “atoms” object: 'offset' contains negative indices

I had just used the > readMSIData() command. Any experience with this kind of error? Is it due to the file itself?

Cheers, Adrien

mtmorgan commented 2 years ago

This looks like a problem in the Cardinal package, rather than BiocParallel. Ask on https://support.bioconductor.org or perhaps if there is a support forum at https://cardinalmsi.org/.

You could try to debug this by using 'serial evaluation, perhaps with setCardinalBPPARAM(SerialParam()). The error would then occur in a way that you could use traceback() or options(error=recover) to debug. I cannot help further with debugging Cardinal.