Troubleshooting

Updated: Sep-09-2026

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 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04 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-r0.3.32.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=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       
## 
## time zone: Etc/UTC
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] MotifPeeker_1.5.1 rmarkdown_2.32   
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.3.0                         bitops_1.1-0                     
##   [3] gridExtra_2.3.1                   httr2_1.3.0                      
##   [5] rlang_1.3.0                       magrittr_2.0.5                   
##   [7] otel_0.2.0                        matrixStats_1.5.0                
##   [9] compiler_4.6.1                    RSQLite_3.53.3                   
##  [11] vctrs_0.7.3                       pkgconfig_2.0.3                  
##  [13] crayon_1.5.3                      fastmap_1.2.0                    
##  [15] dbplyr_2.6.0                      XVector_0.53.0                   
##  [17] memes_1.21.0                      ca_0.71.1                        
##  [19] Rsamtools_2.29.0                  tzdb_0.5.0                       
##  [21] UCSC.utils_1.9.0                  purrr_1.2.2                      
##  [23] bit_4.6.0                         BSgenome.Hsapiens.UCSC.hg38_1.4.5
##  [25] xfun_0.60                         cachem_1.1.0                     
##  [27] cigarillo_1.3.1                   GenomeInfoDb_1.49.1              
##  [29] jsonlite_2.0.0                    blob_1.3.0                       
##  [31] DelayedArray_0.39.6               BiocParallel_1.47.0              
##  [33] parallel_4.6.1                    R6_2.6.1                         
##  [35] bslib_0.12.0                      RColorBrewer_1.1-3               
##  [37] rtracklayer_1.73.0                GenomicRanges_1.65.4             
##  [39] jquerylib_0.1.4                   Rcpp_1.1.2                       
##  [41] Seqinfo_1.3.2                     assertthat_0.2.1                 
##  [43] SummarizedExperiment_1.43.0       iterators_1.0.14                 
##  [45] knitr_1.52                        readr_2.2.0                      
##  [47] IRanges_2.47.5                    BiocBaseUtils_1.15.1             
##  [49] Matrix_1.7-6                      tidyselect_1.2.1                 
##  [51] abind_1.4-8                       yaml_2.3.12                      
##  [53] viridis_0.6.5                     TSP_1.2.7                        
##  [55] codetools_0.2-20                  curl_8.0.0                       
##  [57] lattice_0.23-1                    tibble_3.3.1                     
##  [59] Biobase_2.73.2                    S7_0.2.2                         
##  [61] evaluate_1.0.5                    heatmaply_1.6.0                  
##  [63] BiocFileCache_3.3.0               universalmotif_1.31.48           
##  [65] Biostrings_2.81.9                 pillar_1.11.1                    
##  [67] filelock_1.0.3                    MatrixGenerics_1.25.0            
##  [69] DT_0.34.0                         foreach_1.5.2                    
##  [71] stats4_4.6.1                      plotly_4.12.1                    
##  [73] generics_0.1.4                    RCurl_1.98-1.20                  
##  [75] S4Vectors_0.51.9                  hms_1.1.4                        
##  [77] ggplot2_4.0.3                     scales_1.4.0                     
##  [79] glue_1.8.1                        maketools_1.3.2                  
##  [81] tools_4.6.1                       dendextend_1.19.1                
##  [83] BiocIO_1.23.3                     sys_3.4.3                        
##  [85] data.table_1.18.6.1               BSgenome_1.81.1                  
##  [87] webshot_0.5.5                     GenomicAlignments_1.49.2         
##  [89] registry_0.5-1                    buildtools_1.0.0                 
##  [91] XML_3.99-0.24                     grid_4.6.1                       
##  [93] tidyr_1.3.2                       seriation_1.5.8                  
##  [95] restfulr_0.0.17                   cli_3.6.6                        
##  [97] S4Arrays_1.13.0                   viridisLite_0.4.3                
##  [99] dplyr_1.2.1                       gtable_0.3.6                     
## [101] sass_0.4.10                       digest_0.6.39                    
## [103] BiocGenerics_0.59.12              SparseArray_1.13.2               
## [105] rjson_0.2.23                      htmlwidgets_1.6.4                
## [107] farver_2.1.2                      memoise_2.0.1                    
## [109] htmltools_0.5.9                   lifecycle_1.0.5                  
## [111] httr_1.4.9                        MASS_7.3-66                      
## [113] bit64_4.8.6