Rbind error during permutations

[plbngl]

Hello! Thanks for the tool! I am encountering an error that seems to be recurrent but should have been fixed according to the forums.

I am using dmrseq_1.26.0 , installed from BiocManager and having the following error (testCovariate is multi-factor):

blocks <- dmrseq(bs=bsseq_obj,
                 cutoff = 0.05,
                 testCovariate="Genotype",
                 adjustCovariate = 'Replicate',
                 block = TRUE,
                 minInSpan = 500,
                 bpSpan = 5e4,
                 maxGapSmooth = 1e6,
                 maxGap = 5e3)
 Beginning permutation 5
...Chromosome chr1: Smoothed (0.04 min). 430 regions scored (0.47 min). 
...Chromosome chr10: Smoothed (0.05 min). 272 regions scored (0.25 min). 
...Chromosome chr11: Smoothed (0.02 min). Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match

R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Red Hat Enterprise Linux 8.8 (Ootpa)

Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.12.so;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Rome
tzcode source: system (glibc)

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

other attached packages:
 [1] BiocParallel_1.40.2         data.table_1.17.0           RColorBrewer_1.1-3          dmrseq_1.26.0              
 [5] bsseq_1.42.0                SummarizedExperiment_1.36.0 Biobase_2.66.0              MatrixGenerics_1.18.1      
 [9] matrixStats_1.5.0           GenomicRanges_1.58.0        GenomeInfoDb_1.42.3         IRanges_2.40.1             
[13] S4Vectors_0.44.0            BiocGenerics_0.52.0        

loaded via a namespace (and not attached):
  [1] DBI_1.2.3                 bitops_1.0-9              permute_0.9-7             rlang_1.1.6              
  [5] magrittr_2.0.3            compiler_4.4.0            RSQLite_2.3.9             GenomicFeatures_1.58.0   
  [9] DelayedMatrixStats_1.28.1 png_0.1-8                 vctrs_0.6.5               reshape2_1.4.4           
 [13] stringr_1.5.1             pkgconfig_2.0.3           crayon_1.5.3              fastmap_1.2.0            
 [17] dbplyr_2.5.0              XVector_0.46.0            Rsamtools_2.22.0          tzdb_0.5.0               
 [21] UCSC.utils_1.2.0          bit_4.6.0                 zlibbioc_1.52.0           cachem_1.1.0             
 [25] jsonlite_2.0.0            blob_1.2.4                rhdf5filters_1.18.1       DelayedArray_0.32.0      
 [29] Rhdf5lib_1.28.0           parallel_4.4.0            R6_2.6.1                  stringi_1.8.7            
 [33] limma_3.62.2              rtracklayer_1.66.0        iterators_1.0.14          Rcpp_1.0.14              
 [37] R.utils_2.13.0            readr_2.1.5               splines_4.4.0             Matrix_1.7-0             
 [41] tidyselect_1.2.1          abind_1.4-8               yaml_2.3.10               codetools_0.2-20         
 [45] curl_6.2.2                doRNG_1.8.6.2             lattice_0.22-6            tibble_3.2.1             
 [49] regioneR_1.38.0           plyr_1.8.9                KEGGREST_1.46.0           BiocFileCache_2.14.0     
 [53] Biostrings_2.74.1         pillar_1.10.2             BiocManager_1.30.25       filelock_1.0.3           
 [57] rngtools_1.5.2            foreach_1.5.2             generics_0.1.3            RCurl_1.98-1.17          
 [61] BiocVersion_3.20.0        hms_1.1.3                 ggplot2_3.5.2             sparseMatrixStats_1.18.0 
 [65] munsell_0.5.1             scales_1.3.0              bumphunter_1.48.0         gtools_3.9.5             
 [69] glue_1.8.0                tools_4.4.0               AnnotationHub_3.14.0      BiocIO_1.16.0            
 [73] BSgenome_1.74.0           locfit_1.5-9.12           GenomicAlignments_1.42.0  XML_3.99-0.18            
 [77] rhdf5_2.50.2              grid_4.4.0                AnnotationDbi_1.68.0      colorspace_2.1-1         
 [81] nlme_3.1-164              GenomeInfoDbData_1.2.13   HDF5Array_1.34.0          restfulr_0.0.15          
 [85] annotatr_1.32.0           cli_3.6.4                 rappdirs_0.3.3            S4Arrays_1.6.0           
 [89] dplyr_1.1.4               gtable_0.3.6              outliers_0.15             R.methodsS3_1.8.2        
 [93] digest_0.6.37             SparseArray_1.6.2         rjson_0.2.23              memoise_2.0.1            
 [97] R.oo_1.27.0               lifecycle_1.0.4           httr_1.4.7                statmod_1.5.0            
[101] bit64_4.6.0-1            

This error did not occur when using just a subset of the regions to test. Can you please advise on how to fix it? Thank you!!