[Bioc-devel] issue to open a file from UCSC

[Robert Castelo]

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 using 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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>>
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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
E-08003 Barcelona, Spain
telf: +34.933.160.514