[BioC] error with getBM function of biomaRt package

[James W. MacDonald]

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