Issue with DECIPHER::IdTaxa
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@sebastianmynott-7437
Last seen 9 months ago
United Kingdom

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!

DECIPHER IdTaxa • 454 views
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UPDATE: I've done a clean reinstall of the latest version of R and reinstalled the latest versions only the packages that are used in my script (and their dependencies).

At first I had the same problem but then I removed the packages spdep, ape, pegas and ade4, which got IdTaxa running again.

However, now it won't multithread! I've checked parallel is correctly loaded.

Again, any assistance would be appreciated.

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Hi Sebastian. If you are using a Mac, the compiler was changed so that multi-threading is no longer supported by default. See the recent thread here for how to enable it.

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Erik,

Thanks for posting the link to these workarounds. I've followed the steps you used via Homebrew. My install path (Step 2) was the same as yours but Step 3 didn't work for me. I restarted RStudio and R. I also tried using these lines from http://mac.r-project.org/openmp:

CPPFLAGS += -Xclang -fopenmp
LDFLAGS += -lomp

Strangely enough, multithreading in other packages seems to be working. Do you have any suggestions for what I might try next?

Many thanks! Seb

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Using Homebrew worked for me, but this is not the recommended way of enabling OpenMP. I haven't tried the recommended way, so I can't help you there.

Note that not all multithreaded packages use OpenMP, which might be why you observed multithreading on the Mac working in some of your other packages.

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Ok. I'll keep trying options on my end to get it multithreading again.

The recommended way you mention is clearly intended as a workaround which could stop working at any point. Are you planning on updating DECIPHER to use another multithreading package that doesn't require OpenMP support?

Cheers, Seb

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So it seems this issue has been affecting other packages, namely multithreading in data.table. So finally this solution has worked for me: https://github.com/Rdatatable/data.table/wiki/Installation#openmp-enabled-compiler-for-mac.

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