[BioC] GenomicFeatures Transcripts Retrieval Fails

[Steve Lianoglou]

On Sun, Oct 21, 2012 at 9:00 PM, Dario Strbenac
<D.Strbenac at garvan.org.au> wrote:
> I get FALSE, even after removing the typographical error on the end of your URL example.

Woops -- sorry about that, the URL I pasted was the one I used to see
what happens when you `url.exists` a phony URL. Good catch.

> Must be something odd with the network here at university.

Maybe -- but still might be a windows thing. Are you sure you're not
getting bit by something like this?:

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#The-Internet-download-functions-fail_002e

-steve

>
> ---- 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
>>
>>Hi,
>>
>>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
>>
>>--
>>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



-- 
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