Troubleshooting

Updated: Apr-29-2026

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 4.6.0 (2026-04-24)
## 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] 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_1.4.0 rmarkdown_2.31   
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.3.0                         bitops_1.0-9                     
##   [3] gridExtra_2.3                     httr2_1.2.2                      
##   [5] rlang_1.2.0                       magrittr_2.0.5                   
##   [7] otel_0.2.0                        matrixStats_1.5.0                
##   [9] compiler_4.6.0                    RSQLite_2.4.6                    
##  [11] vctrs_0.7.3                       pkgconfig_2.0.3                  
##  [13] crayon_1.5.3                      fastmap_1.2.0                    
##  [15] dbplyr_2.5.2                      XVector_0.52.0                   
##  [17] memes_1.18.0                      ca_0.71.1                        
##  [19] Rsamtools_2.28.0                  tzdb_0.5.0                       
##  [21] UCSC.utils_1.8.0                  purrr_1.2.2                      
##  [23] bit_4.6.0                         BSgenome.Hsapiens.UCSC.hg38_1.4.5
##  [25] xfun_0.57                         ggseqlogo_0.2.2                  
##  [27] cachem_1.1.0                      cigarillo_1.2.0                  
##  [29] GenomeInfoDb_1.48.0               jsonlite_2.0.0                   
##  [31] blob_1.3.0                        DelayedArray_0.38.0              
##  [33] BiocParallel_1.46.0               parallel_4.6.0                   
##  [35] R6_2.6.1                          bslib_0.10.0                     
##  [37] RColorBrewer_1.1-3                rtracklayer_1.72.0               
##  [39] GenomicRanges_1.64.0              jquerylib_0.1.4                  
##  [41] Rcpp_1.1.1-1.1                    Seqinfo_1.2.0                    
##  [43] assertthat_0.2.1                  SummarizedExperiment_1.42.0      
##  [45] iterators_1.0.14                  knitr_1.51                       
##  [47] readr_2.2.0                       IRanges_2.46.0                   
##  [49] Matrix_1.7-5                      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_7.1.0                       
##  [57] lattice_0.22-9                    tibble_3.3.1                     
##  [59] Biobase_2.72.0                    S7_0.2.2                         
##  [61] evaluate_1.0.5                    heatmaply_1.6.0                  
##  [63] BiocFileCache_3.2.0               universalmotif_1.30.0            
##  [65] Biostrings_2.80.0                 pillar_1.11.1                    
##  [67] filelock_1.0.3                    MatrixGenerics_1.24.0            
##  [69] DT_0.34.0                         foreach_1.5.2                    
##  [71] stats4_4.6.0                      plotly_4.12.0                    
##  [73] generics_0.1.4                    RCurl_1.98-1.18                  
##  [75] S4Vectors_0.50.0                  hms_1.1.4                        
##  [77] ggplot2_4.0.3                     scales_1.4.0                     
##  [79] glue_1.8.1                        lazyeval_0.2.3                   
##  [81] maketools_1.3.2                   tools_4.6.0                      
##  [83] dendextend_1.19.1                 BiocIO_1.22.0                    
##  [85] sys_3.4.3                         data.table_1.18.2.1              
##  [87] BSgenome_1.80.0                   webshot_0.5.5                    
##  [89] GenomicAlignments_1.48.0          registry_0.5-1                   
##  [91] buildtools_1.0.0                  XML_3.99-0.23                    
##  [93] grid_4.6.0                        tidyr_1.3.2                      
##  [95] seriation_1.5.8                   restfulr_0.0.16                  
##  [97] cli_3.6.6                         rappdirs_0.3.4                   
##  [99] S4Arrays_1.12.0                   viridisLite_0.4.3                
## [101] dplyr_1.2.1                       gtable_0.3.6                     
## [103] sass_0.4.10                       digest_0.6.39                    
## [105] BiocGenerics_0.58.0               SparseArray_1.12.0               
## [107] rjson_0.2.23                      htmlwidgets_1.6.4                
## [109] farver_2.1.2                      memoise_2.0.1                    
## [111] htmltools_0.5.9                   lifecycle_1.0.5                  
## [113] httr_1.4.8                        MASS_7.3-65                      
## [115] bit64_4.8.0