Troubleshooting

Updated: Jan-22-2026

This vignette provides troubleshooting tips for common issues encountered when using the MotifPeeker package.

If you encounter an issue that is not covered, please open an issue on the GitHub repository.


Session Info

utils::sessionInfo()
## R version 4.5.2 (2025-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 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] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [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       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] MotifPeeker_1.3.1 rmarkdown_2.30   
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3                         bitops_1.0-9                     
##   [3] gridExtra_2.3                     httr2_1.2.2                      
##   [5] rlang_1.1.7                       magrittr_2.0.4                   
##   [7] otel_0.2.0                        matrixStats_1.5.0                
##   [9] compiler_4.5.2                    RSQLite_2.4.5                    
##  [11] vctrs_0.7.0                       pkgconfig_2.0.3                  
##  [13] crayon_1.5.3                      fastmap_1.2.0                    
##  [15] dbplyr_2.5.1                      XVector_0.51.0                   
##  [17] memes_1.19.1                      ca_0.71.1                        
##  [19] Rsamtools_2.27.0                  tzdb_0.5.0                       
##  [21] UCSC.utils_1.7.1                  purrr_1.2.1                      
##  [23] bit_4.6.0                         BSgenome.Hsapiens.UCSC.hg38_1.4.5
##  [25] xfun_0.56                         cachem_1.1.0                     
##  [27] cigarillo_1.1.0                   GenomeInfoDb_1.47.2              
##  [29] jsonlite_2.0.0                    blob_1.3.0                       
##  [31] DelayedArray_0.37.0               BiocParallel_1.45.0              
##  [33] parallel_4.5.2                    R6_2.6.1                         
##  [35] bslib_0.9.0                       RColorBrewer_1.1-3               
##  [37] rtracklayer_1.71.3                GenomicRanges_1.63.1             
##  [39] jquerylib_0.1.4                   Rcpp_1.1.1                       
##  [41] Seqinfo_1.1.0                     assertthat_0.2.1                 
##  [43] SummarizedExperiment_1.41.0       iterators_1.0.14                 
##  [45] knitr_1.51                        readr_2.1.6                      
##  [47] IRanges_2.45.0                    Matrix_1.7-4                     
##  [49] tidyselect_1.2.1                  abind_1.4-8                      
##  [51] yaml_2.3.12                       viridis_0.6.5                    
##  [53] TSP_1.2.6                         codetools_0.2-20                 
##  [55] curl_7.0.0                        lattice_0.22-7                   
##  [57] tibble_3.3.1                      Biobase_2.71.0                   
##  [59] S7_0.2.1                          evaluate_1.0.5                   
##  [61] heatmaply_1.6.0                   BiocFileCache_3.1.0              
##  [63] universalmotif_1.29.0             Biostrings_2.79.4                
##  [65] pillar_1.11.1                     filelock_1.0.3                   
##  [67] MatrixGenerics_1.23.0             DT_0.34.0                        
##  [69] foreach_1.5.2                     stats4_4.5.2                     
##  [71] plotly_4.11.0                     generics_0.1.4                   
##  [73] RCurl_1.98-1.17                   S4Vectors_0.49.0                 
##  [75] hms_1.1.4                         ggplot2_4.0.1                    
##  [77] scales_1.4.0                      glue_1.8.0                       
##  [79] lazyeval_0.2.2                    maketools_1.3.2                  
##  [81] tools_4.5.2                       dendextend_1.19.1                
##  [83] BiocIO_1.21.0                     sys_3.4.3                        
##  [85] data.table_1.18.0                 BSgenome_1.79.1                  
##  [87] webshot_0.5.5                     GenomicAlignments_1.47.0         
##  [89] registry_0.5-1                    buildtools_1.0.0                 
##  [91] XML_3.99-0.20                     grid_4.5.2                       
##  [93] tidyr_1.3.2                       seriation_1.5.8                  
##  [95] restfulr_0.0.16                   cli_3.6.5                        
##  [97] rappdirs_0.3.4                    S4Arrays_1.11.1                  
##  [99] viridisLite_0.4.2                 dplyr_1.1.4                      
## [101] gtable_0.3.6                      sass_0.4.10                      
## [103] digest_0.6.39                     BiocGenerics_0.57.0              
## [105] SparseArray_1.11.10               rjson_0.2.23                     
## [107] htmlwidgets_1.6.4                 farver_2.1.2                     
## [109] memoise_2.0.1                     htmltools_0.5.9                  
## [111] lifecycle_1.0.5                   httr_1.4.7                       
## [113] MASS_7.3-65                       bit64_4.6.0-1