Hi,
I'm using cardinal 3.8 with
bpparam <- MulticoreParam(workers=35)
register(bpparam)
m55657 <- readMSIData(file)
m55657 <- normalize(m55657, method="tic")
m55657 <- smooth(m55657, method="gaussian")
m55657 <- reduceBaseline(m55657, method="locmin")
m55657 <- peakProcess(m55657, method="diff", SNR=3,sampleSize=0.3,BPPARAM=bpparam)
and when the process went to
aligned to 69522 reference peaks with relative tolerance 2.5e-05 (25 ppm)
filtering to keep only peaks with counts > 1 (0.01% of considered spectra)
processed to 69493 peaks
extracting reference peaks from all spectra
queued: height peak picking
processing: intensity normalization, smoothing, baseline reduction, height peak picking
...
# processing chunk 20/20 (2484 items | 3.64 GB)
I got
Error in reducer$value.cache[[as.character(idx)]] <- values :
wrong args for environment subassignment
In addition: Warning message:
In parallel::mccollect(wait = FALSE, timeout = 1) :
1 parallel job did not deliver a result
It seems to be a biocparallel error, but I'm not sure how to fix it from cardinal setting, do you have any suggestion?Thank you very much for your help.
Weichen Song