Unable to find an inherited method for function ‘bg’ for signature ‘"PFMatrix"’

[alkurowska]

I am trying get motifs positions within ATAC-Seq peaks:

motif_ranges <- matchMotifs(my_PFMatrixList, peak_granges, genome = "hg38", out = "positions")

And I get the following error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘bg’ for signature ‘"PFMatrix"’

> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 9.1 (Blue Onyx)

Matrix products: default
BLAS/LAPACK: /home/kurowsaa/miniconda3/envs/chromVAR_env/lib/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=en_US.UTF-8
[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: Asia/Riyadh
tzcode source: system (glibc)

attached base packages:
[1] stats4 grid stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] BiocManager_1.30.22 lubridate_1.9.3
[3] forcats_1.0.0 stringr_1.5.1
[5] dplyr_1.1.4 purrr_1.0.2
[7] readr_2.1.5 tidyr_1.3.1
[9] tibble_3.2.1 ggplot2_3.5.0
[11] tidyverse_2.0.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5
[13] BSgenome_1.70.1 rtracklayer_1.62.0
[15] BiocIO_1.12.0 Biostrings_2.70.1
[17] XVector_0.42.0 GenomicRanges_1.54.1
[19] GenomeInfoDb_1.38.1 IRanges_2.36.0
[21] S4Vectors_0.40.2 BiocGenerics_0.48.1
[23] TFBSTools_1.40.0 chromVAR_1.24.0
[25] motifmatchr_1.24.0 ComplexHeatmap_2.18.0
[27] learnMotifs_0.1.0

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.8
[3] shape_1.4.6.1 magrittr_2.0.3
[5] GlobalOptions_0.1.2 zlibbioc_1.48.0
[7] vctrs_0.6.5 memoise_2.0.1
[9] Rsamtools_2.18.0 RCurl_1.98-1.14
[11] base64enc_0.1-3 htmltools_0.5.8
[13] S4Arrays_1.2.0 CNEr_1.38.0
[15] SparseArray_1.2.2 pracma_2.4.4
[17] htmlwidgets_1.6.4 plyr_1.8.9
[19] plotly_4.10.4 cachem_1.0.8
[21] GenomicAlignments_1.38.0 whisker_0.4.1
[23] mime_0.12 lifecycle_1.0.4
[25] iterators_1.0.14 pkgconfig_2.0.3
[27] Matrix_1.6-5 R6_2.5.1
[29] fastmap_1.1.1 GenomeInfoDbData_1.2.11
[31] MatrixGenerics_1.14.0 shiny_1.8.1
[33] clue_0.3-65 digest_0.6.35
[35] colorspace_2.1-0 TFMPvalue_0.0.9
[37] AnnotationDbi_1.64.1 RSQLite_2.3.4
[39] seqLogo_1.68.0 timechange_0.3.0
[41] fansi_1.0.6 tfruns_1.5.2
[43] httr_1.4.7 abind_1.4-5
[45] compiler_4.3.3 withr_3.0.0
[47] bit64_4.0.5 doParallel_1.0.17
[49] BiocParallel_1.36.0 DBI_1.2.2
[51] R.utils_2.12.3 tensorflow_2.15.0
[53] poweRlaw_0.80.0 DelayedArray_0.28.0
[55] rjson_0.2.21 gtools_3.9.5
[57] caTools_1.18.2 tools_4.3.3
[59] httpuv_1.6.15 ggseqlogo_0.2
[61] R.oo_1.26.0 glue_1.7.0
[63] restfulr_0.0.15 promises_1.2.1
[65] keras_2.13.0 cluster_2.1.6
[67] reshape2_1.4.4 generics_0.1.3
[69] gtable_0.3.4 tzdb_0.4.0
[71] R.methodsS3_1.8.2 data.table_1.15.2
[73] hms_1.1.3 utf8_1.2.4
[75] ggrepel_0.9.5 foreach_1.5.2
[77] pillar_1.9.0 later_1.3.2
[79] circlize_0.4.16 lattice_0.22-6
[81] bit_4.0.5 annotate_1.80.0
[83] tidyselect_1.2.1 DirichletMultinomial_1.44.0
[85] GO.db_3.18.0 miniUI_0.1.1.1
[87] SummarizedExperiment_1.32.0 Biobase_2.62.0
[89] matrixStats_1.2.0 DT_0.32
[91] stringi_1.8.3 lazyeval_0.2.2
[93] yaml_2.3.8 codetools_0.2-19
[95] cli_3.6.2 xtable_1.8-4
[97] reticulate_1.35.0 munsell_0.5.0
[99] Rcpp_1.0.12 zeallot_0.1.0
[101] png_0.1-8 XML_3.99-0.16.1
[103] parallel_4.3.3 blob_1.2.4
[105] bitops_1.0-7 viridisLite_0.4.2
[107] scales_1.3.0 crayon_1.5.2
[109] GetoptLong_1.0.5 rlang_1.1.3
[111] KEGGREST_1.42.0