Task 10: pH, min.per.group = 9, overdispersion = MN, hi.perc = 99.9, cores = 32
uniting...
two groups detected:
 will calculate methylation difference as the difference of
treatment (group: 1) - control (group: 0)
Warning message:
In max(i) : no non-missing arguments to max; returning -Inf
R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0

locale:
[1] C

time zone: Etc/UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] methylKit_1.32.1     GenomicRanges_1.58.0 GenomeInfoDb_1.42.3 
 [4] IRanges_2.40.1       S4Vectors_0.44.0     BiocGenerics_0.52.0 
 [7] lubridate_1.9.4      forcats_1.0.0        stringr_1.5.1       
[10] dplyr_1.1.4          purrr_1.0.4          readr_2.1.5         
[13] tidyr_1.3.1          tibble_3.2.1         ggplot2_3.5.2       
[16] tidyverse_2.0.0     

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1            R.utils_2.13.0             
 [3] Biostrings_2.74.1           bitops_1.0-9               
 [5] RCurl_1.98-1.19             GenomicAlignments_1.42.0   
 [7] XML_3.99-0.18               timechange_0.3.0           
 [9] lifecycle_1.0.4             statmod_1.5.2              
[11] magrittr_2.0.3              compiler_4.4.3             
[13] rlang_1.1.5                 tools_4.4.3                
[15] yaml_2.3.10                 data.table_1.17.0          
[17] rtracklayer_1.66.0          S4Arrays_1.6.0             
[19] bit_4.6.0                   mclust_6.1.3               
[21] curl_6.2.2                  DelayedArray_0.32.0        
[23] plyr_1.8.9                  abind_1.4-8                
[25] BiocParallel_1.40.2         withr_3.0.2                
[27] numDeriv_2016.8-1.1         R.oo_1.27.1                
[29] grid_4.4.3                  colorspace_2.1-1           
[31] scales_1.3.0                gtools_3.9.5               
[33] MASS_7.3-65                 SummarizedExperiment_1.36.0
[35] bbmle_1.0.25.1              cli_3.6.4                  
[37] mvtnorm_1.4-1               crayon_1.5.3               
[39] generics_0.1.3              httr_1.4.7                 
[41] reshape2_1.4.4              tzdb_0.5.0                 
[43] rjson_0.2.23                bdsmatrix_1.3-7            
[45] qvalue_2.38.0               zlibbioc_1.52.0            
[47] splines_4.4.3               parallel_4.4.3             
[49] XVector_0.46.0              restfulr_0.0.17            
[51] matrixStats_1.5.0           vctrs_0.6.5                
[53] Matrix_1.7-3                jsonlite_2.0.0             
[55] hms_1.1.3                   bit64_4.6.0-1              
[57] fastseg_1.52.0              limma_3.62.2               
[59] glue_1.8.0                  emdbook_1.3.14             
[61] codetools_0.2-20            stringi_1.8.7              
[63] gtable_0.3.6                BiocIO_1.16.0              
[65] UCSC.utils_1.2.0            munsell_0.5.1              
[67] pillar_1.10.2               GenomeInfoDbData_1.2.13    
[69] R6_2.6.1                    vroom_1.6.5                
[71] lattice_0.22-7              Biobase_2.66.0             
[73] R.methodsS3_1.8.2           Rsamtools_2.22.0           
[75] Rcpp_1.0.14                 nlme_3.1-168               
[77] SparseArray_1.6.2           coda_0.19-4.1              
[79] mgcv_1.9-3                  MatrixGenerics_1.18.1      
[81] pkgconfig_2.0.3