[BioC] GenomicFeatures Transcripts Retrieval Fails

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Oct 22 02:14:22 CEST 2012


On Sun, Oct 21, 2012 at 8:00 PM, Dario Strbenac
<D.Strbenac at garvan.org.au> wrote:
> Hello,
> makeTranscriptDbFromUCSC isn't working for me. I can download R packages from CRAN and Bioconductor using install.packages or biocLite, so it's not a proxy issue. I can also paste the URL http://hgdownload.cse.ucsc.edu/goldenPath into a web browser and I get to the website fine.
>> tx19 <- makeTranscriptDbFromUCSC(genome = "hg19", tablename = "refGene")
> Error in function (type, msg, asError = TRUE)  : couldn't connect to host

This doesn't help you too much, but it's working for me -- my
sessionInfo is the same as yours except for the fact that I'm not
running windows.

You say accessing the URL via your browser works, but does the
following call to url.exists return `TRUE`?

R> library(RCurl)
R> url.exists("http://hgdownload.cse.ucsc.edu/goldenPaths")


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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