[Bioc-devel] issue to open a file from UCSC
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 at 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 [[alternative HTML version deleted]]
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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