[Bioc-devel] BiocParallel Error in SingleCellAlleleExperiment on palomino7/8

[Jonas Schuck]

Dear Community,


Im running into an error in the vignette of the “
*SingleCellAlleleExperiment*” Software package on the *palomino7/8* windows
distribution.

Error report in short:

Quitting from lines 229-238 [unnamed-chunk-8] (scae_intro.Rmd)

Error: processing vignette 'scae_intro.Rmd' failed with diagnostics:
BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in file(file, "rt"): cannot open the connection


I was not yet able to reproduce the error locally.

In the vignette, we load example data from the "*scaeData*" ExperimentHub
package. Since I can see `scaeData` listed among the installed packages on
palomino7/8 and the vignette runs as expected locally on a windows system,
I assume its not the actual lack of files that throw this error. Could
someone please confirm whether *scaeData* is actually available in the
palomino testing distributions?

Additionally, I’ve read that windows-based systems may run into issues with
parallelization using BiocParallel, however the function where the error
supposedly arises uses *BiocParallel::SerialParam()* by default.

Since this error occurs only on the windows distribution, I wanted to ask
if anyone has encountered a similar issue or has insights / suggestions on
how to best debug this error?


Any help would be much appreciated!

Best,
Jonas

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