r - What does the error 'invalid class “DMNGroup” object' mean, how to resolve the problem?

Question

I am trying to replicate the workflow from library(DirichletMultinomial). I have large matrix containing counts count and vector of factors pheno. I made a subset of count into countp based on pheno (division into groups) as in the example in vignettes shows countp <- count[pheno %in% c("group1", "group2"), ] after executing the next step for Dirichlet-multinominal model for each group:

bestgrp <- dmngroup(countp, pheno, k=1:15, simplify = FALSE, verbose=TRUE, .lapply = parallel::mclapply)

the process was working for 8-12 hours and crashed reporting:

invalid class “DMNGroup” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")

I know for sure that the process took several hours since crashed because I have following code

if(exists('bestgrp')) {
  save(bestgrp, file = "NRR_DMM_bestgrp.Rda")
} else {
  write(geterrmessage(), file = "!!!ERROR.txt") }

and have the time the error message was saved. Since verbose=TRUE doesn't work in parallel multiple core computing I don't have more specific point when it crashed. The whole dataset count when processed with dmn goes smooth. I am not a bioinformatician, and new in R computing therefore as Google returns NULL results for the error message I am totally lost. Can anyone help? Best regards, Marcin

question from:https://stackoverflow.com/questions/65936924/what-does-the-error-invalid-class-dmngroup-object-mean-how-to-resolve-the-p

Answer 1

I have updated Bioconductor to version 3.12 for R version 4.0.3 I am using. Now it works. For similar problems check support.bioconductor.org/p/92281