I am trying to run this line:

clusters <- DECIPHER::IdClusters( d, method = "complete", cutoff = 0.03, # use cutoff = 0.03 for a 97% OTU processors = nproc)

but I received "Error: 'IdClusters' is not an exported object from 'namespace:DECIPHER'"

I tried to install several times DECIPHER with this BiocManager::install("DECIPHER") and it does not mark any error in the installation. I am using R 4.2.2. Is anybody having the same trouble?

Hi Julieta,

It looks like the maintainer has removed the function without deprecating it. It was last available in RELEASE_3_15.

https://code.bioconductor.org/browse/DECIPHER/blob/RELEASE_3_15/R/IdClusters.R

The author should follow the guidelines shown here:

http://contributions.bioconductor.org/deprecation.html?q=De#deprecate-function

Best regards,

Marcel

for ref https://github.com/benjjneb/dada2/issues/947#issuecomment-1277776614

clusters <- DECIPHER::TreeLine(
  myDistMatrix=d,
  method = "complete",
  cutoff = 0.03, # use `cutoff = 0.03` for a 97% OTU
  type = "clusters",
  processors = nproc)

That's not an exported function for DECIPHER, although there is IdConsensus. Is that what you are looking for?

The IdClusters() function was split into two functions, Clusterize() and TreeLine(), in the latest version of DECIPHER.