I've encountered an issue which hasn't occurred previously. I’m running DECIPHER v2.16.1 in R v4.0.2 and RStudio v1.3.959. and have managed to downgrade to R v3.6.3 to see if it made any difference but it hasn't.
I get the following error, even when running the Examples from the IdTaxa function:
data("TrainingSet_16S") fas <- system.file("extdata", "Bacteria_175seqs.fas", package="DECIPHER") dna <- readDNAStringSet(fas) dna <- RemoveGaps(dna) ids <- IdTaxa(dna, TrainingSet_16S, strand="top") Error in getMethod(f, c("XRawList", "XRawList")) : no method found for function 'match' and signature XRawList, XRawList
The issue seems to present itself as a result of certain packages loading and getting in the way of the IdTaxa function but I can't seem to figure out a workaround. I've noticed that I can sometimes get the IdTaxa function to run if I restart the R session, load the DECIPHER library and run it before loading other libraries. However, even this fails if the last bits of the restart (see below) manage to run before I can run the function.
Registered S3 method overwritten by 'spdep': method from plot.mst ape Registered S3 method overwritten by 'pegas': method from print.amova ade4
I've also tried explicitly loading the
XVector package as suggested here but to no avail.
Any assistance would be very much appreciated!