[BioC] GenomicFeatures Transcripts Retrieval Fails

Dario Strbenac D.Strbenac at garvan.org.au
Mon Oct 22 03:00:21 CEST 2012

I get FALSE, even after removing the typographical error on the end of your URL example. Must be something odd with the network here at university.

---- Original message ----
>Date: Sun, 21 Oct 2012 20:14:22 -0400
>From: Steve Lianoglou <mailinglist.honeypot at gmail.com>  
>Subject: Re: [BioC] GenomicFeatures Transcripts Retrieval Fails  
>To: D.Strbenac at garvan.org.au
>Cc: bioconductor at r-project.org
>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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