Error: 'IdClusters'
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@d16504ea
Last seen 14 months ago
Mexico

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?

DECIPHER • 1.6k views
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@marcel-ramos-7325
Last seen 10 days ago
United States

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

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Ling-Hsiu ▴ 10
@b3f7034e
Last seen 10 months ago
United States

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)
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@james-w-macdonald-5106
Last seen 3 days ago
United States

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

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Erik Wright ▴ 150
@erik-wright-14386
Last seen 12 weeks ago
United States

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

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As Marcel noted above, it is considered bad form to just remove (or split) functions without a deprecation/defunction cycle. At the very least you should add a deprecation warning to point end users to the new functions.

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