GVIZ on R not loading hg38 from UCSC

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> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.3.1
> packageVersion("Gviz")
[1] '1.36.2'
> packageVersion("GenomicRanges")
[1] '1.44.0'

I am trying to visualize some ATAC-seq data that were processed on hg38. GVIZ will not load hg38 data the error provided is:

> itrack <- IdeogramTrack(genome = "hg38", chromosome = "chr4")
Error in value[[3L]](cond) : 
  There doesn't seem to be any chromosome length data available for genome 'hg38' at UCSC or the service is temporarily down.
In addition: Warning message:
In value[[3L]](cond) :
  There doesn't seem to be any cytoband data available for genome 'hg38' at UCSC or the service is temporarily down. Trying to fetch the chromosome length data.

I had a similar problem last October trying to load the mm10 genome and I followed all the suggestions from before. I update the Gviz and GenomicRanges packages using:

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("Gviz")
BiocManager::install("GenomicRanges")

I also updated R. Does anyone have any suggestions? Thank you so much for your help.

r
1 Answers

updating the package with:

    if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")
    remotes::install_github("ivanek/Gviz")

seemed to fix this error.

user_96880840
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