Updated: Jun-02-2025

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 4.5.0 (2025-04-11)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 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_1.1.1
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3                   bitops_1.0-9               
##   [3] gridExtra_2.3               httr2_1.1.2                
##   [5] testthat_3.2.3              rlang_1.1.6                
##   [7] magrittr_2.0.3              matrixStats_1.5.0          
##   [9] compiler_4.5.0              RSQLite_2.4.0              
##  [11] vctrs_0.6.5                 pkgconfig_2.0.3            
##  [13] crayon_1.5.3                fastmap_1.2.0              
##  [15] dbplyr_2.5.0                XVector_0.49.0             
##  [17] memes_1.17.0                ca_0.71.1                  
##  [19] Rsamtools_2.25.0            rmarkdown_2.29             
##  [21] tzdb_0.5.0                  UCSC.utils_1.5.0           
##  [23] waldo_0.6.1                 purrr_1.0.4                
##  [25] bit_4.6.0                   xfun_0.52                  
##  [27] ggseqlogo_0.2               cachem_1.1.0               
##  [29] GenomeInfoDb_1.45.4         jsonlite_2.0.0             
##  [31] blob_1.2.4                  DelayedArray_0.35.1        
##  [33] BiocParallel_1.43.3         parallel_4.5.0             
##  [35] R6_2.6.1                    bslib_0.9.0                
##  [37] RColorBrewer_1.1-3          rtracklayer_1.69.0         
##  [39] pkgload_1.4.0               brio_1.1.5                 
##  [41] GenomicRanges_1.61.0        jquerylib_0.1.4            
##  [43] Rcpp_1.0.14                 assertthat_0.2.1           
##  [45] SummarizedExperiment_1.39.0 iterators_1.0.14           
##  [47] knitr_1.50                  R.utils_2.13.0             
##  [49] readr_2.1.5                 IRanges_2.43.0             
##  [51] Matrix_1.7-3                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_6.2.3                  lattice_0.22-7             
##  [61] tibble_3.2.1                Biobase_2.69.0             
##  [63] evaluate_1.0.3              desc_1.4.3                 
##  [65] heatmaply_1.5.0             BiocFileCache_2.99.5       
##  [67] universalmotif_1.27.2       Biostrings_2.77.1          
##  [69] pillar_1.10.2               filelock_1.0.3             
##  [71] MatrixGenerics_1.21.0       DT_0.33                    
##  [73] foreach_1.5.2               stats4_4.5.0               
##  [75] plotly_4.10.4               generics_0.1.4             
##  [77] rprojroot_2.0.4             RCurl_1.98-1.17            
##  [79] S4Vectors_0.47.0            hms_1.1.3                  
##  [81] ggplot2_3.5.2               scales_1.4.0               
##  [83] glue_1.8.0                  lazyeval_0.2.2             
##  [85] tools_4.5.0                 dendextend_1.19.0          
##  [87] BiocIO_1.19.0               data.table_1.17.4          
##  [89] BSgenome_1.77.0             webshot_0.5.5              
##  [91] GenomicAlignments_1.45.0    registry_0.5-1             
##  [93] XML_3.99-0.18               grid_4.5.0                 
##  [95] tidyr_1.3.1                 seriation_1.5.7            
##  [97] cmdfun_1.0.2                restfulr_0.0.15            
##  [99] cli_3.6.5                   rappdirs_0.3.3             
## [101] S4Arrays_1.9.1              viridisLite_0.4.2          
## [103] dplyr_1.1.4                 gtable_0.3.6               
## [105] R.methodsS3_1.8.2           sass_0.4.10                
## [107] digest_0.6.37               BiocGenerics_0.55.0        
## [109] SparseArray_1.9.0           rjson_0.2.23               
## [111] htmlwidgets_1.6.4           farver_2.1.2               
## [113] R.oo_1.27.1                 memoise_2.0.1              
## [115] htmltools_0.5.8.1           lifecycle_1.0.4            
## [117] httr_1.4.7                  bit64_4.6.0-1              
## [119] MASS_7.3-65