Errors with populationRanges(grl, density=0.1, est.recur=TRUE) and cnvOncoPrint(grl, cgenes)

[FL512]

Hi:
Thank you very much for sharing a very useful tool, I really appreciate it.

First of all, I followed your instructions (https://bioconductor.org/packages/devel/bioc/vignettes/AnnotationHub/inst/doc/AnnotationHub-HOWTO.html),
and all worked well.

Then, I started to anlyze my data and got two errors.
1.
cnvrs <- populationRanges(grl, density=0.1, est.recur=TRUE)
seq.default(1, length(both.scores) - 1, by = 2) error:
wrong sign in "by" argument

This is sort of weird to me, because the default paremter (est.recur=FALSE) ran without any errors , which is for the "Trimming low-density areas" accourding to your website.
cnvrs <- populationRanges(grl, density=0.1)

On top of that, I have encountered the second error when I performed the below code to visualize the oncoprint.
2.
cnvOncoPrint(grl, cgenes)
normalizeDoubleBracketSubscript(i, x, exact = exact, allow.NA = TRUE, error:
subscript is out of bounds

I am analyzing human data and my session info are as follows.
3.

sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=Japanese_Japan.utf8 LC_CTYPE=Japanese_Japan.utf8 LC_MONETARY=Japanese_Japan.utf8
[4] LC_NUMERIC=C LC_TIME=Japanese_Japan.utf8

time zone: Asia/Tokyo
tzcode source: internal

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

other attached packages:
[1] SummarizedExperiment_1.32.0 MatrixGenerics_1.14.0
[3] matrixStats_1.2.0 BSgenome.Hsapiens.UCSC.hg38_1.4.5
[5] BSgenome_1.70.2 rtracklayer_1.62.0
[7] BiocIO_1.12.0 Biostrings_2.70.3
[9] XVector_0.42.0 regioneR_1.34.0
[11] ensembldb_2.26.0 AnnotationFilter_1.26.0
[13] GenomicFeatures_1.54.4 AnnotationDbi_1.64.1
[15] Biobase_2.62.0 AnnotationHub_3.10.0
[17] BiocFileCache_2.10.1 dbplyr_2.5.0
[19] Gviz_1.46.1 CNVRanger_1.18.1
[21] RaggedExperiment_1.26.0 GenomicRanges_1.54.1
[23] GenomeInfoDb_1.38.8 IRanges_2.36.0
[25] S4Vectors_0.40.2 BiocGenerics_0.48.1
[27] dplyr_1.1.4

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 shape_1.4.6.1 rstudioapi_0.15.0
[4] magrittr_2.0.3 rmarkdown_2.26 GlobalOptions_0.1.2
[7] zlibbioc_1.48.2 vctrs_0.6.5 memoise_2.0.1
[10] Rsamtools_2.18.0 RCurl_1.98-1.14 base64enc_0.1-3
[13] BiocBaseUtils_1.4.0 htmltools_0.5.7 S4Arrays_1.2.1
[16] progress_1.2.3 curl_5.2.1 SparseArray_1.2.4
[19] Formula_1.2-5 htmlwidgets_1.6.4 cachem_1.0.8
[22] GenomicAlignments_1.38.2 iterators_1.0.14 mime_0.12
[25] lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.6-1.1
[28] R6_2.5.1 fastmap_1.1.1 clue_0.3-65
[31] GenomeInfoDbData_1.2.11 shiny_1.8.0 digest_0.6.35
[34] colorspace_2.1-0 Hmisc_5.1-2 RSQLite_2.3.5
[37] filelock_1.0.3 fansi_1.0.6 httr_1.4.7
[40] abind_1.4-5 compiler_4.3.2 doParallel_1.0.17
[43] bit64_4.0.5 withr_3.0.0 htmlTable_2.4.2
[46] backports_1.4.1 BiocParallel_1.36.0 DBI_1.2.2
[49] biomaRt_2.58.2 rappdirs_0.3.3 DelayedArray_0.28.0
[52] rjson_0.2.21 tools_4.3.2 foreign_0.8-85
[55] interactiveDisplayBase_1.40.0 httpuv_1.6.14 nnet_7.3-19
[58] glue_1.7.0 restfulr_0.0.15 promises_1.2.1
[61] checkmate_2.3.1 cluster_2.1.4 generics_0.1.3
[64] gtable_0.3.4 data.table_1.15.2 hms_1.1.3
[67] xml2_1.3.6 utf8_1.2.4 foreach_1.5.2
[70] BiocVersion_3.18.1 pillar_1.9.0 stringr_1.5.1
[73] later_1.3.2 circlize_0.4.16 lattice_0.21-9
[76] deldir_2.0-4 bit_4.0.5 biovizBase_1.50.0
[79] tidyselect_1.2.1 ComplexHeatmap_2.18.0 knitr_1.45
[82] gridExtra_2.3 ProtGenerics_1.34.0 xfun_0.42
[85] stringi_1.8.3 lazyeval_0.2.2 yaml_2.3.8
[88] evaluate_0.23 codetools_0.2-19 interp_1.1-6
[91] tibble_3.2.1 BiocManager_1.30.22 cli_3.6.2
[94] rpart_4.1.21 xtable_1.8-4 munsell_0.5.0
[97] dichromat_2.0-0.1 Rcpp_1.0.12 png_0.1-8
[100] XML_3.99-0.16.1 parallel_4.3.2 ellipsis_0.3.2
[103] ggplot2_3.5.0 blob_1.2.4 prettyunits_1.2.0
[106] jpeg_0.1-10 latticeExtra_0.6-30 bitops_1.0-7
[109] VariantAnnotation_1.48.1 scales_1.3.0 purrr_1.0.2
[112] crayon_1.5.2 GetoptLong_1.0.5 rlang_1.1.3
[115] KEGGREST_1.42.0

Thank you in advance!