Troubleshooting

Updated: Mar-08-2025

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 4.4.3 (2025-02-28)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 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_0.99.13 rmarkdown_2.29     
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3                   bitops_1.0-9               
##   [3] gridExtra_2.3               testthat_3.2.3             
##   [5] rlang_1.1.5                 magrittr_2.0.3             
##   [7] matrixStats_1.5.0           compiler_4.4.3             
##   [9] RSQLite_2.3.9               vctrs_0.6.5                
##  [11] pkgconfig_2.0.3             crayon_1.5.3               
##  [13] fastmap_1.2.0               dbplyr_2.5.0               
##  [15] XVector_0.47.2              memes_1.15.0               
##  [17] ca_0.71.1                   Rsamtools_2.23.1           
##  [19] tzdb_0.4.0                  UCSC.utils_1.3.1           
##  [21] waldo_0.6.1                 purrr_1.0.4                
##  [23] bit_4.6.0                   xfun_0.51                  
##  [25] ggseqlogo_0.2               cachem_1.1.0               
##  [27] GenomeInfoDb_1.43.4         jsonlite_1.9.1             
##  [29] blob_1.2.4                  DelayedArray_0.33.6        
##  [31] BiocParallel_1.41.2         parallel_4.4.3             
##  [33] R6_2.6.1                    bslib_0.9.0                
##  [35] RColorBrewer_1.1-3          rtracklayer_1.67.1         
##  [37] pkgload_1.4.0               brio_1.1.5                 
##  [39] GenomicRanges_1.59.1        jquerylib_0.1.4            
##  [41] Rcpp_1.0.14                 assertthat_0.2.1           
##  [43] SummarizedExperiment_1.37.0 iterators_1.0.14           
##  [45] knitr_1.49                  R.utils_2.13.0             
##  [47] readr_2.1.5                 IRanges_2.41.3             
##  [49] Matrix_1.7-2                tidyselect_1.2.1           
##  [51] abind_1.4-8                 yaml_2.3.10                
##  [53] viridis_0.6.5               TSP_1.2-4                  
##  [55] codetools_0.2-20            curl_6.2.1                 
##  [57] lattice_0.22-6              tibble_3.2.1               
##  [59] Biobase_2.67.0              evaluate_1.0.3             
##  [61] desc_1.4.3                  heatmaply_1.5.0            
##  [63] BiocFileCache_2.15.1        universalmotif_1.25.1      
##  [65] Biostrings_2.75.4           pillar_1.10.1              
##  [67] filelock_1.0.3              MatrixGenerics_1.19.1      
##  [69] DT_0.33                     foreach_1.5.2              
##  [71] stats4_4.4.3                plotly_4.10.4              
##  [73] generics_0.1.3              rprojroot_2.0.4            
##  [75] RCurl_1.98-1.16             hms_1.1.3                  
##  [77] S4Vectors_0.45.4            ggplot2_3.5.1              
##  [79] munsell_0.5.1               scales_1.3.0               
##  [81] glue_1.8.0                  lazyeval_0.2.2             
##  [83] maketools_1.3.2             tools_4.4.3                
##  [85] dendextend_1.19.0           BiocIO_1.17.1              
##  [87] sys_3.4.3                   data.table_1.17.0          
##  [89] BSgenome_1.75.1             webshot_0.5.5              
##  [91] GenomicAlignments_1.43.0    registry_0.5-1             
##  [93] buildtools_1.0.0            XML_3.99-0.18              
##  [95] grid_4.4.3                  tidyr_1.3.1                
##  [97] seriation_1.5.7             cmdfun_1.0.2               
##  [99] colorspace_2.1-1            GenomeInfoDbData_1.2.13    
## [101] restfulr_0.0.15             cli_3.6.4                  
## [103] S4Arrays_1.7.3              viridisLite_0.4.2          
## [105] dplyr_1.1.4                 gtable_0.3.6               
## [107] R.methodsS3_1.8.2           sass_0.4.9                 
## [109] digest_0.6.37               BiocGenerics_0.53.6        
## [111] SparseArray_1.7.6           rjson_0.2.23               
## [113] htmlwidgets_1.6.4           R.oo_1.27.0                
## [115] memoise_2.0.1               htmltools_0.5.8.1          
## [117] lifecycle_1.0.4             httr_1.4.7                 
## [119] MASS_7.3-65                 bit64_4.6.0-1