Question

GVIZ giving error with loading hg38 genome

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RUser743 • 0

@f82ed440

Last seen 23 months ago

United States

I am trying to use GVIZ to visualize some sequencing data. GVIZ is giving an error when loading the hg38 genome. I tried upgrading R and the Gviz package but I still see the error. Does anyone have any suggestions? Thank you!

> library(GenomicRanges)
> library(rtracklayer)
> 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.

> 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’

R Gviz • 1.8k views

ADD COMMENT • link 2.0 years ago RUser743 • 0

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updating the package with

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

Seemed to fix this error.

ADD REPLY • link 2.0 years ago RUser743 • 0

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Hi,

you do not need to install devel version of Gviz to create IdeogramTrack. It works fine in release. There had to be an internet connection issue at the time you issued the command.

Best, Robert

ADD REPLY • link 2.0 years ago Robert Ivanek ▴ 730

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Thank you for your help Robert!

ADD REPLY • link 2.0 years ago RUser743 • 0