Hello and thank you for anyone willing to spare a moment to help.

I am really struggling trying to execute a pipeline that worked two months ago but has since stopped.

https://github.com/BoevaLab/LILY

It fails when trying to import a BigWigFile using rtracklayer. Trying to troubleshoot with the good'ol chatbot, it says that a bioconductor update has broken an internal methods call.

Below is the function call at which it is failing and the main function itself...

It's the import.bw that is failing. I can load these bigwigs into IGV and visualize them, so I don't think it's the file itself...

> total_densities = apply(files_info,1,get_peaks_density_commonPeaks)
Error: unable to find an inherited method for function ‘seqinfo’ for signature ‘x = "BigWigFile"’

get_peaks_density_commonPeaks <- function(info){
  peaks = import.bed3(info["peak"])
  rangeToConsider=c(100:5000)
  peaks = peaks[rangeToConsider]
  peaks= peaks[which(countOverlaps(peaks,commonPeaks)>0)]
  densities = import.bw(info["density"])
  peak_density = subsetByOverlaps(densities,peaks)  
  total_density = median(peak_density$score)
  gc()
  return(total_density)
}





sessionInfo( )

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    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             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              BiocManager_1.30.27         compiler_4.5.1              rjson_0.2.23               
 [6] crayon_1.5.3                SummarizedExperiment_1.40.0 Biobase_2.70.0              Rsamtools_2.24.1            bitops_1.0-9               
[11] Biostrings_2.78.0           GenomicAlignments_1.44.0    parallel_4.5.1              BiocParallel_1.42.2         yaml_2.3.12                
[16] lattice_0.22-5              R6_2.6.1                    XVector_0.50.0              S4Arrays_1.10.0             curl_7.0.0                 
[21] GenomeInfoDb_1.44.3         XML_3.99-0.20               DelayedArray_0.36.0         MatrixGenerics_1.22.0       GenomeInfoDbData_1.2.14    
[26] rlang_1.1.6                 pkgload_1.4.1               cli_3.6.5                   SparseArray_1.10.3          grid_4.5.1                 
[31] rstudioapi_0.17.1           codetools_0.2-20            abind_1.4-8                 RCurl_1.98-1.17             restfulr_0.0.16            
[36] httr_1.4.7                  matrixStats_1.5.0           tools_4.5.1                 BiocIO_1.18.0               UCSC.utils_1.4.0