bsseq: Failing to reproduce the results

Question

[Mithil Gaikwad]

Hi everyone, I am reproducing my collaborator's bsseq analysis results. But I do not understand what possible reason could be to have different results when our script, threshold input files and package and dependency version (except packages via namespace) is identical?

My collaborator's sessionInfo()

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
 [1] bsseq_1.22.0                SummarizedExperiment_1.16.0
 [3] DelayedArray_0.12.0         BiocParallel_1.20.0        
 [5] matrixStats_0.55.0          Biobase_2.46.0             
 [7] GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
 [9] IRanges_2.20.0              S4Vectors_0.24.0           
[11] BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2               compiler_3.6.1           XVector_0.26.0          
 [4] R.methodsS3_1.7.1        bitops_1.0-6             R.utils_2.9.0           
 [7] tools_3.6.1              DelayedMatrixStats_1.8.0 zlibbioc_1.32.0         
[10] rhdf5_2.30.0             lattice_0.20-38          BSgenome_1.54.0         
[13] Matrix_1.2-17            GenomeInfoDbData_1.2.2   rtracklayer_1.46.0      
[16] Biostrings_2.54.0        gtools_3.8.1             locfit_1.5-9.1          
[19] grid_3.6.1               data.table_1.14.2        HDF5Array_1.14.0        
[22] XML_3.98-1.20            limma_3.42.0             Rhdf5lib_1.8.0          
[25] scales_1.0.0             Rsamtools_2.2.0          GenomicAlignments_1.22.0
[28] permute_0.9-5            colorspace_1.4-1         RCurl_1.95-4.12         
[31] munsell_0.5.0            R.oo_1.23.0           

My sessionInfo()

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

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

other attached packages:
 [1] bsseq_1.22.0                SummarizedExperiment_1.16.0
 [3] DelayedArray_0.12.0         BiocParallel_1.20.0        
 [5] matrixStats_0.58.0          Biobase_2.46.0             
 [7] GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
 [9] IRanges_2.20.0              S4Vectors_0.24.0           
[11] BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6               compiler_3.6.3           XVector_0.26.0          
 [4] R.methodsS3_1.8.1        R.utils_2.10.1           bitops_1.0-7            
 [7] tools_3.6.3              DelayedMatrixStats_1.8.0 zlibbioc_1.32.0         
[10] lifecycle_1.0.0          rhdf5_2.30.0             lattice_0.20-44         
[13] BSgenome_1.54.0          rlang_0.4.11             Matrix_1.3-3            
[16] GenomeInfoDbData_1.2.2   rtracklayer_1.46.0       Biostrings_2.54.0       
[19] gtools_3.8.2             locfit_1.5-9.4           grid_3.6.3              
[22] data.table_1.14.0        R6_2.5.0                 HDF5Array_1.14.0        
[25] XML_3.99-0.3             limma_3.42.0             Rhdf5lib_1.8.0          
[28] GenomicAlignments_1.22.0 scales_1.1.1             Rsamtools_2.2.0         
[31] permute_0.9-5            colorspace_2.0-1         RCurl_1.98-1.3          
[34] munsell_0.5.0            R.oo_1.24.0             
> 

You may find the attached picture for your reference purpose:

Would anyone like to share their intuition?

Thank you for your time and consideration.