[BioC] postForm in RCurl

[Ovokeraye Achinike-Oduaran]

Sorted. My bad. I had re-installed R and hadn't taken the proxy
setting into account. Sorry for the hassle.

Thanks again.

Regards

-Avoks

On Thu, Oct 13, 2011 at 11:05 AM, Ovokeraye Achinike-Oduaran
<ovokeraye at gmail.com> wrote:
> Hi Duncan,
>
> I forgot to add that to add that I'm using a proxy but that was kind
> of sorted out with my R installation, I think, because I had to adjust
> the settings on that. Everything else has worked fine.
>
> -Avoks
>
> On Wed, Oct 12, 2011 at 7:49 PM, Duncan Temple Lang
> <duncan at wald.ucdavis.edu> wrote:
>> Hi Ovokeraye
>>
>>  Your script is  okay. It works for me.
>> Somehow the communication between the server and RCurl
>> fell apart at some point.
>> You should try it again now and see if it works now.
>> Otherwise, are you behind some sort of firewall? proxy? etc.?
>>
>> While your query works, it gives no results in the table.
>>
>> I simplified the query to just one disease.
>>
>>  data = postForm("http://www.genome.gov/GWAStudies/#searchForm",
>>                   disease = c("Fasting glucose-related traits"),
>>                   submit = "Search")
>>
>>  tbl = readHTMLTable(htmlParse(data, asText = TRUE), which = 5, header = TRUE)
>>
>> and tbl contains the result.
>>
>>  D.
>>
>> On 10/12/11 4:26 AM, Ovokeraye Achinike-Oduaran wrote:
>>> Hi all,
>>>
>>> I was trying to retrieve some information from the GWAS catalog using
>>> the postForm() function. I get an error (below the script). I can't
>>> seem to figure out where I went wrong in my script. Please help.
>>>
>>> -Avoks
>>>
>>>>  data = postForm("http://www.genome.gov/GWAStudies/#searchForm",
>>> + disease = c("Fasting glucose-related traits",
>>> + "Fasting insulin-related traits",
>>> + "Fasting plasma glucose",
>>> + "Insulin resistance/response",
>>> + "Insulin traits",
>>> + "Type 2 diabetes",
>>> + "Type 2 diabetes and 6 quantitative traits",
>>> + "Type 2 diabetes and other traits"),
>>> + submit = "Search")
>>>
>>> Error in postForm("http://www.genome.gov/GWAStudies/#searchForm",
>>> disease = c("Fasting glucose-related traits",  :
>>>   Failure when receiving data from the peer
>>>
>>>> sessionInfo()
>>> R version 2.13.2 (2011-09-30)
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_xxx  LC_CTYPE=English_xxx
>>> [3] LC_MONETARY=English_xxx LC_NUMERIC=C
>>> [5] LC_TIME=English_xxx
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] RCurl_1.6-10.1  bitops_1.0-4.1  puma_2.4.0      mclust_3.4.10
>>> [5] affy_1.30.0     limma_3.8.3     GEOquery_2.19.4 Biobase_2.12.2
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affyio_1.20.0         preprocessCore_1.14.0 tools_2.13.2
>>> [4] XML_3.4-2.2
>>>
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>>
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>