# Troubleshooting

Updated: Feb-03-2026

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.

#### 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 version 4.5.2 (2025-10-31)
    ## Platform: x86_64-pc-linux-gnu
    ## Running under: Ubuntu 24.04.3 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_1.2.0 rmarkdown_2.30
    ##
    ## loaded via a namespace (and not attached):
    ##   [1] DBI_1.2.3                   bitops_1.0-9
    ##   [3] gridExtra_2.3               httr2_1.2.2
    ##   [5] testthat_3.3.2              rlang_1.1.7
    ##   [7] magrittr_2.0.4              otel_0.2.0
    ##   [9] matrixStats_1.5.0           compiler_4.5.2
    ##  [11] RSQLite_2.4.5               vctrs_0.7.1
    ##  [13] pkgconfig_2.0.3             crayon_1.5.3
    ##  [15] fastmap_1.2.0               dbplyr_2.5.1
    ##  [17] XVector_0.50.0              memes_1.18.0
    ##  [19] ca_0.71.1                   Rsamtools_2.26.0
    ##  [21] tzdb_0.5.0                  waldo_0.6.2
    ##  [23] purrr_1.2.1                 bit_4.6.0
    ##  [25] xfun_0.56                   ggseqlogo_0.2.2
    ##  [27] cachem_1.1.0                cigarillo_1.0.0
    ##  [29] jsonlite_2.0.0              blob_1.3.0
    ##  [31] DelayedArray_0.36.0         BiocParallel_1.44.0
    ##  [33] parallel_4.5.2              R6_2.6.1
    ##  [35] bslib_0.10.0                RColorBrewer_1.1-3
    ##  [37] rtracklayer_1.70.1          pkgload_1.4.1
    ##  [39] brio_1.1.5                  GenomicRanges_1.62.1
    ##  [41] jquerylib_0.1.4             Rcpp_1.1.1
    ##  [43] Seqinfo_1.0.0               assertthat_0.2.1
    ##  [45] SummarizedExperiment_1.40.0 iterators_1.0.14
    ##  [47] knitr_1.51                  R.utils_2.13.0
    ##  [49] readr_2.1.6                 IRanges_2.44.0
    ##  [51] Matrix_1.7-4                tidyselect_1.2.1
    ##  [53] abind_1.4-8                 yaml_2.3.12
    ##  [55] viridis_0.6.5               TSP_1.2.6
    ##  [57] codetools_0.2-20            curl_7.0.0
    ##  [59] lattice_0.22-7              tibble_3.3.1
    ##  [61] Biobase_2.70.0              S7_0.2.1
    ##  [63] evaluate_1.0.5              desc_1.4.3
    ##  [65] heatmaply_1.6.0             BiocFileCache_3.0.0
    ##  [67] universalmotif_1.28.0       Biostrings_2.78.0
    ##  [69] pillar_1.11.1               filelock_1.0.3
    ##  [71] MatrixGenerics_1.22.0       DT_0.34.0
    ##  [73] foreach_1.5.2               stats4_4.5.2
    ##  [75] plotly_4.12.0               generics_0.1.4
    ##  [77] rprojroot_2.1.1             RCurl_1.98-1.17
    ##  [79] S4Vectors_0.48.0            hms_1.1.4
    ##  [81] ggplot2_4.0.1               scales_1.4.0
    ##  [83] glue_1.8.0                  lazyeval_0.2.2
    ##  [85] maketools_1.3.2             tools_4.5.2
    ##  [87] dendextend_1.19.1           BiocIO_1.20.0
    ##  [89] sys_3.4.3                   data.table_1.18.2.1
    ##  [91] BSgenome_1.78.0             webshot_0.5.5
    ##  [93] GenomicAlignments_1.46.0    registry_0.5-1
    ##  [95] buildtools_1.0.0            XML_3.99-0.20
    ##  [97] grid_4.5.2                  tidyr_1.3.2
    ##  [99] seriation_1.5.8             cmdfun_1.0.2
    ## [101] restfulr_0.0.16             cli_3.6.5
    ## [103] rappdirs_0.3.4              S4Arrays_1.10.1
    ## [105] viridisLite_0.4.2           dplyr_1.1.4
    ## [107] gtable_0.3.6                R.methodsS3_1.8.2
    ## [109] sass_0.4.10                 digest_0.6.39
    ## [111] BiocGenerics_0.56.0         SparseArray_1.10.8
    ## [113] rjson_0.2.23                htmlwidgets_1.6.4
    ## [115] farver_2.1.2                R.oo_1.27.1
    ## [117] memoise_2.0.1               htmltools_0.5.9
    ## [119] lifecycle_1.0.5             httr_1.4.7
    ## [121] MASS_7.3-65                 bit64_4.6.0-1