What does the error 'invalid class “DMNGroup” object' mean, how to resolve the problem?
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Entering edit mode
mschmidt ▴ 10
@mschmidt-18923
Last seen 9 hours ago
Poznan

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

ps. I have updated R to 4.0.3, but the error persists.


sessionInfo( )

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] xtable_1.8-4                lattice_0.20-41             readr_1.4.0                 BiocParallel_1.24.1        
 [5] magrittr_2.0.1              reshape2_1.4.4              survival_3.2-7              ggsci_2.9                  
 [9] dplyr_1.0.2                 ggpubr_0.4.0                knitr_1.30                  microbiome_1.10.0          
[13] ggplot2_3.3.3               phyloseq_1.32.0             DirichletMultinomial_1.30.0 IRanges_2.24.1             
[17] S4Vectors_0.28.1            BiocGenerics_0.36.0        

loaded via a namespace (and not attached):
 [1] Rtsne_0.15                  colorspace_2.0-0            ggsignif_0.6.0              ellipsis_0.3.1             
 [5] rio_0.5.16                  XVector_0.28.0              GenomicRanges_1.40.0        rstudioapi_0.13            
 [9] bit64_4.0.5                 AnnotationDbi_1.50.3        codetools_0.2-16            splines_4.0.3              
[13] geneplotter_1.66.0          ade4_1.7-16                 jsonlite_1.7.2              broom_0.7.3                
[17] annotate_1.66.0             cluster_2.1.0               compiler_4.0.3              backports_1.2.1            
[21] Matrix_1.2-18               prettyunits_1.1.1           tools_4.0.3                 igraph_1.2.6               
[25] gtable_0.3.0                glue_1.4.2                  GenomeInfoDbData_1.2.3      Rcpp_1.0.5                 
[29] carData_3.0-4               Biobase_2.48.0              cellranger_1.1.0            vctrs_0.3.6                
[33] Biostrings_2.56.0           rhdf5filters_1.2.0          multtest_2.44.0             ape_5.4-1                  
[37] nlme_3.1-149                iterators_1.0.13            xfun_0.20                   stringr_1.4.0              
[41] openxlsx_4.2.3              lifecycle_0.2.0             rstatix_0.6.0               XML_3.99-0.5               
[45] zlibbioc_1.34.0             MASS_7.3-53                 scales_1.1.1                hms_1.0.0                  
[49] MatrixGenerics_1.2.0        SummarizedExperiment_1.18.2 biomformat_1.16.0           rhdf5_2.34.0               
[53] RColorBrewer_1.1-2          curl_4.3                    memoise_1.1.0               stringi_1.5.3              
[57] RSQLite_2.2.2               genefilter_1.70.0           foreach_1.5.1               permute_0.9-5              
[61] zip_2.1.1                   GenomeInfoDb_1.24.2         rlang_0.4.10                pkgconfig_2.0.3            
[65] matrixStats_0.57.0          bitops_1.0-6                purrr_0.3.4                 Rhdf5lib_1.12.0            
[69] bit_4.0.4                   tidyselect_1.1.0            plyr_1.8.6                  DESeq2_1.28.1              
[73] R6_2.5.0                    generics_0.1.0              DelayedArray_0.16.0         DBI_1.1.0                  
[77] pillar_1.4.7                haven_2.3.1                 foreign_0.8-80              withr_2.3.0                
[81] mgcv_1.8-33                 abind_1.4-5                 RCurl_1.98-1.2              tibble_3.0.4               
[85] crayon_1.3.4                car_3.0-10                  progress_1.2.2              locfit_1.5-9.4             
[89] grid_4.0.3                  readxl_1.3.1                data.table_1.13.6           blob_1.2.1                 
[93] vegan_2.5-7                 forcats_0.5.0               digest_0.6.27               tidyr_1.1.2                
[97] munsell_0.5.0
DirichletMultinomial • 107 views
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0
Entering edit mode
mschmidt ▴ 10
@mschmidt-18923
Last seen 9 hours ago
Poznan

I have updated Bioconductor to version 3.12 for R version 4.0.3 I am using. Now it works. For similar problems check similar post findOverlaps() error after updating package

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