Something broken with seqinfo in latest rtracklayer update? #3
Description
I for the life of me cannot get around this issue when trying to renormalize my bigwigs to each other. I also fail during the runLILY script when it has to handle bigwigs. This did work two months ago...
total_densities = apply(files_info,1,get_peaks_density_commonPeaks)
Error: unable to find an inherited method for function ‘seqinfo’ for signature ‘x = "BigWigFile"’
R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/Toronto
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.68.0 GenomicRanges_1.62.0 Seqinfo_1.0.0 IRanges_2.44.0 S4Vectors_0.48.0 BiocGenerics_0.56.0 generics_0.1.4
loaded via a namespace (and not attached):
[1] Matrix_1.7-3 jsonlite_2.0.0 compiler_4.5.1 rjson_0.2.23 crayon_1.5.3
[6] SummarizedExperiment_1.40.0 Biobase_2.70.0 Rsamtools_2.24.1 bitops_1.0-9 Biostrings_2.78.0
[11] GenomicAlignments_1.44.0 parallel_4.5.1 BiocParallel_1.42.2 yaml_2.3.12 lattice_0.22-5
[16] R6_2.6.1 XVector_0.50.0 S4Arrays_1.10.0 curl_7.0.0 GenomeInfoDb_1.44.3
[21] XML_3.99-0.20 DelayedArray_0.36.0 MatrixGenerics_1.22.0 GenomeInfoDbData_1.2.14 SparseArray_1.10.3
[26] grid_4.5.1 rstudioapi_0.17.1 codetools_0.2-20 abind_1.4-8 RCurl_1.98-1.17
[31] restfulr_0.0.16 httr_1.4.7 matrixStats_1.5.0 tools_4.5.1 BiocIO_1.18.0
[36] UCSC.utils_1.4.0