[BioC] annotate htmlpage error

[James W. MacDonald]

Hi Georg,

On 3/19/2012 11:24 AM, Georg Otto wrote:
> "James W. MacDonald"<jmacdon at uw.edu>  writes:
>
>> Hi Martin,
>>
>> On 3/14/2012 4:36 PM, Martin Morgan wrote:
>>> On 03/14/2012 01:13 PM, Georg Otto wrote:
>>>> Hi,
>>>>
>>>> after updating the annotate package from 1.32.1 to 1.32.2 I get an error
>>>> using the htmlpage function. Here with the old version:
>>> Sorry, probably my fault; I've tried to update this in v. 1.32.3. If
>>> you provide a fully reproducible example (deg$id, othernames,
>>> table.head as necessary to reproduce just the bug) I could be more
>>> sure of the fix. Martin
>> library(annotate)
>> library(org.Hs.eg.db)
>> gnlst2<- list(egs = head(Rkeys(org.Hs.egENSEMBL),3))
>> example(htmlpage)
>> htmlpage(gnlst2, "test.html","Some gene expression data", otherdata,
>> c("Ens", table.head[-c(1:3)]), repository=list("ens"), species =
>> "Homo_sapiens")
>>
>>
> Thanks Jim. I can confirm tah Martin's fix works. However it generates a
> dead link. In getQuery4ENSEMBL() the link is created like this:
>
> out<- paste("http://www.ensembl.org/", species, "/Search/Summary?species=",
>                   species, ";idx=;q=", ids, sep = "")
>
> However (dependant on where you exactly want to point the link to) it
> should read like this:
>
> out<- paste("http://www.ensembl.org/", species, "/Gene/Summary?g=",
>                   ids, sep = "")

It was already updated in version 1.33.6, but was pointing to the 
transcript variation page. I have now updated it to point to the summary 
page as you request. This is in version 1.33.8, which will propagate to 
the download server in a day or so.

Best,

Jim


>
>
> Best,
>
> Georg
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099