phyloseq_mult_raref throwing warnings

[Skirnir3141]

Hey there, I'm running the phyloseq_mult_raref function on a fairly small phyloseq object and it's throwing some warnings. Trying to figure out why.

phyloseq-class experiment-level object
otu_table()   OTU Table:          [ 322 taxa and 9 samples ]:
sample_data() Sample Data:        [ 9 samples by 6 sample variables ]:
tax_table()   Taxonomy Table:     [ 322 taxa by 8 taxonomic ranks ]:
refseq()      DNAStringSet:       [ 322 reference sequences ]

metagMisc::phyloseq_mult_raref(
  ps.idataxa.t1,
  SampSize = 26049,
  MinSizeThreshold = 26049,
  iter = 1000,
  multithread = T,
  replace = F)

Warnings:

Warning messages: 1: : ... may be used in an incorrect context: ‘.fun(piece, ...)’

2: : ... may be used in an incorrect context: ‘.fun(piece, ...)’

I have the following libraries loaded:

library(SimpleMetaPackage)
library(dplyr)
library(decontam)
library(phyloseq)
library(ggplot2)
library(microViz)
library(metagMisc)
library(speedyseq)

Using R version 4.4.2 on a machine running Ubuntu 22.04.5 LTS.

Any idea what's causing the warning?

Thanks!

• Mike

[vmikk]

Hello Mike, you may safely ignore this warning (and it will not appear if you set multithread = FALSE).

The warning comes from the support of additional arguments (...) that phyloseq_mult_raref may pass to phyloseq::rarefy_even_depth. It occurs because ... argument is being handled withing nested functions.

I will think how to remove it, but it does not impact the results in any way.

With kind regards, Vladimir