Error in seqinfo(con): UCSC library operation failed: Windows error importing bigwigs

[bschilder]

rtracklayer::import.bw seems to be having a number of issues. This one seems most relevant to the error below:
lawremi/rtracklayer#65

--- re-building 'peakyfinders.Rmd' using rmarkdown
Quitting from lines 71-82 (peakyfinders.Rmd) 
Error: Error: processing vignette 'peakyfinders.Rmd' failed with diagnostics:
BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error:
Error in seqinfo(con): UCSC library operation failed
--- failed re-building 'peakyfinders.Rmd'
SUMMARY: processing the following file failed:
  'peakyfinders.Rmd'
Error: Error: Vignette re-building failed.
Execution halted
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted
Error: Process completed with exit code 1.

The error only comes up with bigwig files on Windows; other file types like broad/narrowPeaks work fine with the rtracklayer::import function (including on Windows).

[bschilder]

Possible alternative method: plyranges::read_bigwig
https://www.bioconductor.org/packages/release/bioc/html/plyranges.html

Same errors, i think it relies on rtracklayer under the hood.

[bschilder]

Seems this is a known issue, though not sure why a more informative error message isn't given in that case.

Even so, still seems to be failing on Mac too:

query_granges <- PeakyFinders::get_genome(keep.chr = "chr22", style = "NCBI")
    bw.file <- paste0(
        "https://www.encodeproject.org",
        "/files/ENCFF103JOZ/@@download/ENCFF103JOZ.bigWig"
    )
    bw.filt <- plyranges::read_bigwig(file = bw.file,
                                      genome_info = query_granges)

Tried both UCSC and NCBI chromosome format, but same error as before.

This doesn't help either:

 query_granges <- rtracklayer::BigWigSelection(ranges = query_granges,
                                                  colnames = "score")

[bschilder]

Also appears to be some differences in how rtracklayer performs in R vs. Rstudio:
https://support.bioconductor.org/p/p133244/

[bschilder]

Same error after downloading the whole bigwig and trying to import the local version

 tmp <- tempfile()
    download.file(bw.file, tmp)
bw.filt <- rtracklayer::import.bw(
        con = tmp,
        selection = query_granges
    )

Noticed it seems to be compressed but doesn't have a ".gz" suffix. Renaming local file with ".gz" suffix doesn't seem to have any effect.

[bschilder]

Tried import.wig for a longshot. Diff error (expected):

[bschilder]

Temporary solution: Run rtracklayer_bigwig_error whenever relevant function called.

rtracklayer_bigwig_error <- function(){
    is_windows <- .Platform$OS.type=="windows"
    if(is_windows){
        stop(
            "rtracklayer::import.bw() does not work on Windows.",
            "Please contact the rtracklayer developers to address this issue.")
    }
    return(is_windows)
}