Troubleshooting

Updated: Dec-19-2024

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.

MEME Suite Related

1. Error: Cannot find MEME Suite
   If You have ensured that the MEME Suite is installed, but still encounter this error, set the path to the MEME suite binaries (.../meme/bin/) using the meme_path parameter in the MotifPeeker() function call.

2. Error: Failed to generate .html file.
   Please ensure that the Perl dependencies required by the MEME Suite are installed, particularly XML::Parser, which can be installed using the following command in the terminal:
   bash cpan install XML::Parser

MotifPeeker() Related

1. Function takes too long to run
   It is likely motif discovery is what is taking too long to run. Try reducing the number of workers if you are running out of memory while running the MotifPeeker() function.
   Additionally, follow the runtime guidance for MotifPeeker().

Session Info

utils::sessionInfo()

## R Under development (unstable) (2024-10-21 r87258)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.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_0.99.13
## 
## loaded via a namespace (and not attached):
##   [1] DBI_1.2.3                   bitops_1.0-9               
##   [3] gridExtra_2.3               testthat_3.2.2             
##   [5] rlang_1.1.4                 magrittr_2.0.3             
##   [7] matrixStats_1.4.1           compiler_4.5.0             
##   [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_0.47.0              memes_1.15.0               
##  [17] ca_0.71.1                   Rsamtools_2.23.1           
##  [19] rmarkdown_2.29              tzdb_0.4.0                 
##  [21] UCSC.utils_1.3.0            waldo_0.6.1                
##  [23] purrr_1.0.2                 bit_4.5.0.1                
##  [25] xfun_0.49                   zlibbioc_1.53.0            
##  [27] ggseqlogo_0.2               cachem_1.1.0               
##  [29] GenomeInfoDb_1.43.2         jsonlite_1.8.9             
##  [31] blob_1.2.4                  DelayedArray_0.33.3        
##  [33] BiocParallel_1.41.0         parallel_4.5.0             
##  [35] R6_2.5.1                    bslib_0.8.0                
##  [37] RColorBrewer_1.1-3          rtracklayer_1.67.0         
##  [39] pkgload_1.4.0               brio_1.1.5                 
##  [41] GenomicRanges_1.59.1        jquerylib_0.1.4            
##  [43] Rcpp_1.0.13-1               assertthat_0.2.1           
##  [45] SummarizedExperiment_1.37.0 iterators_1.0.14           
##  [47] knitr_1.49                  R.utils_2.12.3             
##  [49] readr_2.1.5                 IRanges_2.41.2             
##  [51] Matrix_1.7-1                tidyselect_1.2.1           
##  [53] abind_1.4-8                 yaml_2.3.10                
##  [55] viridis_0.6.5               TSP_1.2-4                  
##  [57] codetools_0.2-20            curl_6.0.1                 
##  [59] lattice_0.22-6              tibble_3.2.1               
##  [61] Biobase_2.67.0              evaluate_1.0.1             
##  [63] desc_1.4.3                  heatmaply_1.5.0            
##  [65] BiocFileCache_2.15.0        universalmotif_1.25.1      
##  [67] Biostrings_2.75.3           pillar_1.10.0              
##  [69] filelock_1.0.3              MatrixGenerics_1.19.0      
##  [71] DT_0.33                     foreach_1.5.2              
##  [73] stats4_4.5.0                plotly_4.10.4              
##  [75] generics_0.1.3              rprojroot_2.0.4            
##  [77] RCurl_1.98-1.16             S4Vectors_0.45.2           
##  [79] hms_1.1.3                   ggplot2_3.5.1              
##  [81] munsell_0.5.1               scales_1.3.0               
##  [83] glue_1.8.0                  lazyeval_0.2.2             
##  [85] tools_4.5.0                 dendextend_1.19.0          
##  [87] BiocIO_1.17.1               data.table_1.16.4          
##  [89] BSgenome_1.75.0             webshot_0.5.5              
##  [91] GenomicAlignments_1.43.0    registry_0.5-1             
##  [93] XML_3.99-0.17               grid_4.5.0                 
##  [95] tidyr_1.3.1                 seriation_1.5.7            
##  [97] cmdfun_1.0.2                colorspace_2.1-1           
##  [99] GenomeInfoDbData_1.2.13     restfulr_0.0.15            
## [101] cli_3.6.3                   S4Arrays_1.7.1             
## [103] viridisLite_0.4.2           dplyr_1.1.4                
## [105] gtable_0.3.6                R.methodsS3_1.8.2          
## [107] sass_0.4.9                  digest_0.6.37              
## [109] BiocGenerics_0.53.3         SparseArray_1.7.2          
## [111] rjson_0.2.23                htmlwidgets_1.6.4          
## [113] R.oo_1.27.0                 memoise_2.0.1              
## [115] htmltools_0.5.8.1           lifecycle_1.0.4            
## [117] httr_1.4.7                  MASS_7.3-61                
## [119] bit64_4.5.2