Error running functional_enrichment

[msierk]

When I try to run functional_enrichment, I get the error below a couple seconds after it starts running.

> functional_enrichment(rl, k=2) 
-----------------------------------------------------------
* enrich signature genes (k = 2) to BP terms for SD:skmeans on org.Hs.eg.db, 1/20
  - 80/376 significant genes are taken from 2-group comparisons
  - on k-means group 1/2, 48 genes
Error in .local(object, ...) : 
  formal argument "prefix" matched by multiple actual arguments

[jokergoo]

What is your cola version? >= 2.0.0? Can you also provide the output from traceback()?

[msierk]

Yes, cola 2.00. traceback and session info below. Thanks!

> functional_enrichment(rl) 
* enrich signature genes (k = 2) to BP terms for SD:skmeans on org.Hs.eg.db, 1/20
- 1163/6923 significant genes are taken from 2-group comparisons
 - on k-means group 1/2, 431 genes
Error in .local(object, ...) : 
  formal argument "prefix" matched by multiple actual arguments
In addition: Warning messages:
1: Quick-TRANSfer stage steps exceeded maximum (= 170850) 
2: Quick-TRANSfer stage steps exceeded maximum (= 150500) 
3: Quick-TRANSfer stage steps exceeded maximum (= 214050) 
4: Quick-TRANSfer stage steps exceeded maximum (= 182650) 
5: Quick-TRANSfer stage steps exceeded maximum (= 180050) 
6: Quick-TRANSfer stage steps exceeded maximum (= 204200) 
7: Quick-TRANSfer stage steps exceeded maximum (= 185150) 
8: Quick-TRANSfer stage steps exceeded maximum (= 183100) 

> traceback()
12: functional_enrichment(sig_gene[l], id_mapping = id_mapping, org_db = org_db, 
        ontology = ontology, min_set_size = min_set_size, max_set_size = max_set_size, 
        verbose = verbose, prefix = paste0(prefix, "  "), ...)
11: functional_enrichment(sig_gene[l], id_mapping = id_mapping, org_db = org_db, 
        ontology = ontology, min_set_size = min_set_size, max_set_size = max_set_size, 
        verbose = verbose, prefix = paste0(prefix, "  "), ...)
10: .local(object, ...)
9: functional_enrichment(object@list[[i]], gene_fdr_cutoff = gene_fdr_cutoff, 
       id_mapping = id_mapping, org_db = org_db, min_set_size = min_set_size, 
       max_set_size = max_set_size, prefix = "  ", ontology = ontology, 
       ...)
8: functional_enrichment(object@list[[i]], gene_fdr_cutoff = gene_fdr_cutoff, 
       id_mapping = id_mapping, org_db = org_db, min_set_size = min_set_size, 
       max_set_size = max_set_size, prefix = "  ", ontology = ontology, 
       ...)
7: .local(object, ...)
6: functional_enrichment(rl)
5: functional_enrichment(rl) at cola.R#49
4: eval(ei, envir)
3: eval(ei, envir)
2: withVisible(eval(ei, envir))
1: source("~/Library/CloudStorage/OneDrive-NationalInstitutesofHealth/Krauze/Glioma_Andra_Krauze_Lab/cola.R", 
       echo = TRUE)`

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] tibble_3.1.7                  dplyr_1.0.9                   ssgsea.GBM.classification_1.0
 [4] devtools_2.4.3                usethis_2.1.6                 genefilter_1.76.0            
 [7] ComplexHeatmap_2.11.1         markdown_1.1                  knitr_1.39                   
[10] cola_2.0.0                    Biobase_2.54.0                BiocGenerics_0.40.0          

[jokergoo]

Now it is fixed. Please update from GitHub.

[msierk]

Thanks for the quick fix! And thanks for all the great packages you provide!