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.
utils::sessionInfo()## R version 4.5.1 Patched (2025-09-10 r88807)
## Platform: x86_64-apple-darwin20
## Running under: macOS Monterey 12.7.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## 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] RColorBrewer_1.1-3 jsonlite_2.0.0
## [3] magrittr_2.0.4 farver_2.1.2
## [5] rmarkdown_2.30 fs_1.6.6
## [7] BiocIO_1.20.0 vctrs_0.6.5
## [9] memoise_2.0.1 Rsamtools_2.26.0
## [11] RCurl_1.98-1.17 base64enc_0.1-3
## [13] webshot_0.5.5 htmltools_0.5.8.1
## [15] S4Arrays_1.10.0 curl_7.0.0
## [17] SparseArray_1.10.0 sass_0.4.10
## [19] bslib_0.9.0 htmlwidgets_1.6.4
## [21] desc_1.4.3 plyr_1.8.9
## [23] testthat_3.2.3 httr2_1.2.1
## [25] lubridate_1.9.4 plotly_4.11.0
## [27] cachem_1.1.0 GenomicAlignments_1.46.0
## [29] mime_0.13 downloadthis_0.5.0
## [31] lifecycle_1.0.4 iterators_1.0.14
## [33] pkgconfig_2.0.3 Matrix_1.7-4
## [35] R6_2.6.1 fastmap_1.2.0
## [37] MatrixGenerics_1.22.0 digest_0.6.37
## [39] S4Vectors_0.48.0 ps_1.9.1
## [41] rprojroot_2.1.1 pkgload_1.4.1
## [43] crosstalk_1.2.2 GenomicRanges_1.62.0
## [45] RSQLite_2.4.3 seriation_1.5.8
## [47] bsplus_0.1.5 labeling_0.4.3
## [49] filelock_1.0.3 timechange_0.3.0
## [51] httr_1.4.7 abind_1.4-8
## [53] compiler_4.5.1 bit64_4.6.0-1
## [55] withr_3.0.2 S7_0.2.0
## [57] BiocParallel_1.44.0 viridis_0.6.5
## [59] DBI_1.2.3 heatmaply_1.6.0
## [61] dendextend_1.19.1 R.utils_2.13.0
## [63] MASS_7.3-65 rappdirs_0.3.3
## [65] DelayedArray_0.36.0 rjson_0.2.23
## [67] tools_4.5.1 zip_2.3.3
## [69] ggseqlogo_0.2 R.oo_1.27.1
## [71] glue_1.8.0 restfulr_0.0.16
## [73] grid_4.5.1 reshape2_1.4.4
## [75] generics_0.1.4 gtable_0.3.6
## [77] BSgenome_1.78.0 tzdb_0.5.0
## [79] R.methodsS3_1.8.2 ca_0.71.1
## [81] tidyr_1.3.1 data.table_1.17.8
## [83] hms_1.1.4 xml2_1.4.1
## [85] XVector_0.50.0 BiocGenerics_0.56.0
## [87] memes_1.18.0 foreach_1.5.2
## [89] pillar_1.11.1 stringr_1.5.2
## [91] vroom_1.6.6 dplyr_1.1.4
## [93] BiocFileCache_3.0.0 lattice_0.22-7
## [95] rtracklayer_1.70.0 bit_4.6.0
## [97] universalmotif_1.28.0 tidyselect_1.2.1
## [99] BSgenome.Hsapiens.UCSC.hg38_1.4.5 registry_0.5-1
## [101] Biostrings_2.78.0 knitr_1.50
## [103] gridExtra_2.3 IRanges_2.44.0
## [105] Seqinfo_1.0.0 SummarizedExperiment_1.40.0
## [107] cmdfun_1.0.2 stats4_4.5.1
## [109] xfun_0.53 Biobase_2.70.0
## [111] brio_1.1.5 matrixStats_1.5.0
## [113] DT_0.34.0 stringi_1.8.7
## [115] UCSC.utils_1.6.0 lazyeval_0.2.2
## [117] yaml_2.3.10 evaluate_1.0.5
## [119] codetools_0.2-20 cigarillo_1.0.0
## [121] archive_1.1.12 tibble_3.3.0
## [123] cli_3.6.5 processx_3.8.6
## [125] jquerylib_0.1.4 dichromat_2.0-0.1
## [127] Rcpp_1.1.0 GenomeInfoDb_1.46.0
## [129] emoji_16.0.0 dbplyr_2.5.1
## [131] XML_3.99-0.19 parallel_4.5.1
## [133] ggplot2_4.0.0 readr_2.1.5
## [135] assertthat_0.2.1 blob_1.2.4
## [137] bitops_1.0-9 viridisLite_0.4.2
## [139] scales_1.4.0 purrr_1.1.0
## [141] crayon_1.5.3 rlang_1.1.6
## [143] TSP_1.2-5 waldo_0.6.2