If you're not directly accessing this URL, but through GenomeInfoDb as
an upstream dependency, this has been recently fixed a couple of days ago:
https://github.com/Bioconductor/GenomeInfoDb/commit/77f3c97cb78607a169b24ab1f827453e04cdd6a0
and the updated version 1.39.6 of GenomeInfoDb should become available
in the next few hours via BiocManager::install().
robert.
On 2/8/24 21:49, Zuguang Gu wrote:
You can use
https://hgdownload2.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz
instead.
On Thu, 8 Feb 2024 at 20:03, Martin, Tiphaine via Bioc-devel <
bioc-devel@r-project.org> wrote:
Hi,
I have an error in the package compilation because of issues accessing a
file from UCSC.
Are you aware of such type of issue? What do I need to do?
Quitting from lines 337-345 [cometwebPlot] (coMET.Rnw)
Error: processing vignette 'coMET.Rnw' failed with diagnostics:
error in evaluating the argument 'object' in selecting a method for
function 'getTable': cannot open URL '
https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz'
Thanks,
Tiphaine
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Robert Castelo, PhD
Associate Professor
Dept. of Medicine and Life Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
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telf: +34.933.160.514
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