[BioC] error with getBM function of biomaRt package

[T Joshi]

Hi,
Thank you James, Installing RCurl package again solved the problem.

Josh

On Wed, Dec 3, 2008 at 2:25 PM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> Hi Josh,
>
> The version of RCurl that you have seems to be really old to me. The version
> used by BioC 2.3 is 0.92-0. You might try biocLite("RCurl"), or better yet,
> upgrade to R-2.8.0 and BioC 2.3.
>
> Best,
>
> Jim
>
>
>
> T Joshi wrote:
>>
>> Hi,
>> I was running the example in getBM and got the following error:
>>
>>
>> getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name","band"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at"),
>> mart=mart)
>> Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol",
>> "chromosome_name",  :
>>  could not find function "postForm"
>>
>> Here is the sessionInfo:
>>>
>>> sessionInfo()
>>
>> R version 2.7.1 (2008-06-23)
>> ia64-unknown-linux-gnu
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>>  [1] GOstats_2.6.0       Category_2.6.0      genefilter_1.20.1
>>  [4] survival_2.34-1     RBGL_1.18.0         annotate_1.18.0
>>  [7] xtable_1.5-4        GO.db_2.2.0         AnnotationDbi_1.2.2
>> [10] RSQLite_0.6-9       DBI_0.2-4           Biobase_2.0.1
>> [13] graph_1.18.1        biomaRt_1.14.1      RCurl_0.0.666
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.11 tcltk_2.7.1     XML_1.96-0
>>
>> I also tried with some other data, but it doesn't seem to work anyway.
>> I have attached the output of debug to this mail. Please let me know
>> what's happening here.
>>
>> regards,
>> Josh
>>
>>
>> ------------------------------------------------------------------------
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-0646
> 734-936-8662
>