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

3 messages · Martin, Tiphaine, Zuguang Gu, Robert Castelo

Martin, Tiphaine
# 
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
Zuguang Gu
# 
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 at r-project.org> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      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: