Error when running Integrating scRNA-seq and scATAC-seq data vignette

[realmungmung]

Hi all,
I'm running this Integrating scRNA-seq and scATAC-seq data vignette and I was able to run through the tutorial until this command:
gene.activities <- GeneActivity(pbmc.atac, features = VariableFeatures(pbmc.rna))

where I got a huge error:

gene.activities <- GeneActivity(pbmc.atac, features = VariableFeatures(pbmc.rna))
Extracting gene coordinates
Extracting reads overlapping genomic regions
| | 0 % ~calculating [E::bgzf_read_block] Failed to read BGZF header at offset 1416828390
[E::hts_itr_next] Failed to seek to offset 92869838159767: Illegal seek
[E::hts_itr_next] Failed to seek to offset 92902743745887: Illegal seek
[E::hts_itr_next] Failed to seek to offset 92916919541141: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93381738192310: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93413213899239: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93516938894158: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93609721460164: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93629593997030: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93633988935576: Illegal seek
[E::hts_itr_next] Failed to seek to offset 93643503715391: Illegal seek
......

my session info is:

sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
[1] cowplot_1.1.3 ggplot2_3.5.1 EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.30.0 AnnotationFilter_1.30.0
[6] GenomicFeatures_1.58.0 AnnotationDbi_1.68.0 Biobase_2.66.0 GenomicRanges_1.58.0 GenomeInfoDb_1.42.1
[11] IRanges_2.40.1 S4Vectors_0.44.0 BiocGenerics_0.52.0 Signac_1.14.0 Seurat_5.1.0
[16] SeuratObject_5.0.2 sp_2.1-4 pbmcMultiome.SeuratData_0.1.4 SeuratData_0.2.2.9001

loaded via a namespace (and not attached):
[1] RcppAnnoy_0.0.22 splines_4.4.2 later_1.4.1 BiocIO_1.16.0 bitops_1.0-9 tibble_3.2.1
[7] polyclip_1.10-7 rpart_4.1.23 XML_3.99-0.18 fastDummies_1.7.4 lifecycle_1.0.4 globals_0.16.3
[13] lattice_0.22-6 MASS_7.3-63 backports_1.5.0 magrittr_2.0.3 rmarkdown_2.29 Hmisc_5.2-1
[19] plotly_4.10.4 yaml_2.3.10 httpuv_1.6.15 sctransform_0.4.1 spam_2.11-0 spatstat.sparse_3.1-0
[25] reticulate_1.40.0 pbapply_1.7-2 DBI_1.2.3 RColorBrewer_1.1-3 abind_1.4-8 zlibbioc_1.52.0
[31] Rtsne_0.17 purrr_1.0.2 biovizBase_1.54.0 RCurl_1.98-1.16 nnet_7.3-20 VariantAnnotation_1.52.0
[37] rappdirs_0.3.3 GenomeInfoDbData_1.2.13 ggrepel_0.9.6 irlba_2.3.5.1 listenv_0.9.1 spatstat.utils_3.1-1
[43] goftest_1.2-3 RSpectra_0.16-2 spatstat.random_3.3-2 fitdistrplus_1.2-1 parallelly_1.41.0 leiden_0.4.3.1
[49] codetools_0.2-20 DelayedArray_0.32.0 RcppRoll_0.3.1 tidyselect_1.2.1 UCSC.utils_1.2.0 farver_2.1.2
[55] base64enc_0.1-3 matrixStats_1.4.1 spatstat.explore_3.3-3 GenomicAlignments_1.42.0 jsonlite_1.8.9 Formula_1.2-5
[61] progressr_0.15.1 ggridges_0.5.6 survival_3.8-3 tools_4.4.2 ica_1.0-3 Rcpp_1.0.13-1
[67] glue_1.8.0 gridExtra_2.3 SparseArray_1.6.0 xfun_0.49 MatrixGenerics_1.18.0 dplyr_1.1.4
[73] withr_3.0.2 fastmap_1.2.0 digest_0.6.37 R6_2.5.1 mime_0.12 colorspace_2.1-1
[79] scattermore_1.2 tensor_1.5 dichromat_2.0-0.1 spatstat.data_3.1-4 RSQLite_2.3.9 tidyr_1.3.1
[85] generics_0.1.3 data.table_1.16.4 rtracklayer_1.66.0 httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.6.0
[91] uwot_0.2.2 pkgconfig_2.0.3 gtable_0.3.6 blob_1.2.4 lmtest_0.9-40 XVector_0.46.0
[97] htmltools_0.5.8.1 dotCall64_1.2 ProtGenerics_1.38.0 scales_1.3.0 png_0.1-8 spatstat.univar_3.1-1
[103] knitr_1.49 rstudioapi_0.17.1 reshape2_1.4.4 rjson_0.2.23 checkmate_2.3.2 nlme_3.1-166
[109] curl_6.0.1 zoo_1.8-12 cachem_1.1.0 stringr_1.5.1 KernSmooth_2.23-26 parallel_4.4.2
[115] miniUI_0.1.1.1 foreign_0.8-87 restfulr_0.0.15 pillar_1.10.0 grid_4.4.2 vctrs_0.6.5
[121] RANN_2.6.2 promises_1.3.2 xtable_1.8-4 cluster_2.1.8 htmlTable_2.4.3 evaluate_1.0.1
[127] cli_3.6.3 compiler_4.4.2 Rsamtools_2.22.0 rlang_1.1.4 crayon_1.5.3 future.apply_1.11.3
[133] labeling_0.4.3 plyr_1.8.9 stringi_1.8.4 viridisLite_0.4.2 deldir_2.0-4 BiocParallel_1.40.0
[139] munsell_0.5.1 Biostrings_2.74.1 lazyeval_0.2.2 spatstat.geom_3.3-4 Matrix_1.7-1 BSgenome_1.74.0
[145] RcppHNSW_0.6.0 patchwork_1.3.0 bit64_4.5.2 future_1.34.0 KEGGREST_1.46.0 shiny_1.10.0
[151] SummarizedExperiment_1.36.0 ROCR_1.0-11 igraph_2.1.2 memoise_2.0.1 fastmatch_1.1-6 bit_4.5.0.1

Please let me know if you have any suggestions thank you so much!