Updated: Oct-30-2025

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 4.5.1 Patched (2025-08-23 r88802)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              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: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] MotifPeeker_1.2.0
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3                   bitops_1.0-9               
##   [3] gridExtra_2.3               httr2_1.2.1                
##   [5] testthat_3.2.3              rlang_1.1.6                
##   [7] magrittr_2.0.4              matrixStats_1.5.0          
##   [9] compiler_4.5.1              RSQLite_2.4.3              
##  [11] vctrs_0.6.5                 pkgconfig_2.0.3            
##  [13] crayon_1.5.3                fastmap_1.2.0              
##  [15] dbplyr_2.5.1                XVector_0.50.0             
##  [17] memes_1.18.0                ca_0.71.1                  
##  [19] Rsamtools_2.26.0            rmarkdown_2.30             
##  [21] tzdb_0.5.0                  waldo_0.6.2                
##  [23] purrr_1.1.0                 bit_4.6.0                  
##  [25] xfun_0.53                   ggseqlogo_0.2              
##  [27] cachem_1.1.0                cigarillo_1.0.0            
##  [29] jsonlite_2.0.0              blob_1.2.4                 
##  [31] DelayedArray_0.36.0         BiocParallel_1.44.0        
##  [33] parallel_4.5.1              R6_2.6.1                   
##  [35] bslib_0.9.0                 RColorBrewer_1.1-3         
##  [37] rtracklayer_1.70.0          pkgload_1.4.1              
##  [39] brio_1.1.5                  GenomicRanges_1.62.0       
##  [41] jquerylib_0.1.4             Rcpp_1.1.0                 
##  [43] Seqinfo_1.0.0               assertthat_0.2.1           
##  [45] SummarizedExperiment_1.40.0 iterators_1.0.14           
##  [47] knitr_1.50                  R.utils_2.13.0             
##  [49] readr_2.1.5                 IRanges_2.44.0             
##  [51] Matrix_1.7-4                tidyselect_1.2.1           
##  [53] dichromat_2.0-0.1           abind_1.4-8                
##  [55] yaml_2.3.10                 viridis_0.6.5              
##  [57] TSP_1.2-5                   codetools_0.2-20           
##  [59] curl_7.0.0                  lattice_0.22-7             
##  [61] tibble_3.3.0                Biobase_2.70.0             
##  [63] S7_0.2.0                    evaluate_1.0.5             
##  [65] desc_1.4.3                  heatmaply_1.6.0            
##  [67] BiocFileCache_3.0.0         universalmotif_1.28.0      
##  [69] Biostrings_2.78.0           pillar_1.11.1              
##  [71] filelock_1.0.3              MatrixGenerics_1.22.0      
##  [73] DT_0.34.0                   foreach_1.5.2              
##  [75] stats4_4.5.1                plotly_4.11.0              
##  [77] generics_0.1.4              rprojroot_2.1.1            
##  [79] RCurl_1.98-1.17             S4Vectors_0.48.0           
##  [81] hms_1.1.4                   ggplot2_4.0.0              
##  [83] scales_1.4.0                glue_1.8.0                 
##  [85] lazyeval_0.2.2              tools_4.5.1                
##  [87] dendextend_1.19.1           BiocIO_1.20.0              
##  [89] data.table_1.17.8           BSgenome_1.78.0            
##  [91] webshot_0.5.5               GenomicAlignments_1.46.0   
##  [93] registry_0.5-1              XML_3.99-0.19              
##  [95] grid_4.5.1                  tidyr_1.3.1                
##  [97] seriation_1.5.8             cmdfun_1.0.2               
##  [99] restfulr_0.0.16             cli_3.6.5                  
## [101] rappdirs_0.3.3              S4Arrays_1.10.0            
## [103] viridisLite_0.4.2           dplyr_1.1.4                
## [105] gtable_0.3.6                R.methodsS3_1.8.2          
## [107] sass_0.4.10                 digest_0.6.37              
## [109] BiocGenerics_0.56.0         SparseArray_1.10.0         
## [111] rjson_0.2.23                htmlwidgets_1.6.4          
## [113] farver_2.1.2                R.oo_1.27.1                
## [115] memoise_2.0.1               htmltools_0.5.8.1          
## [117] lifecycle_1.0.4             httr_1.4.7                 
## [119] bit64_4.6.0-1               MASS_7.3-65