[BioC] GenomicFeatures Transcripts Retrieval Fails

[Dario Strbenac]

Turns out that setting was wrongly specified.

---- Original message ----
>Date: Sun, 21 Oct 2012 22:27:16 -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 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