[BioC] biomaRt doesn't load RCurl automatically

[James W. MacDonald]

Hi Tao,

Works for me:

 > library(biomaRt)
 > mart <- useMart("snp", "hsapiens_snp")
Checking attributes and filters ... ok
 > snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart)
Warning message:
The getSNP function will be removed in the next release of biomaRt.  Use 
the getBM function instead.  The biomaRt vignette contains examples of 
retrieving SNP data
 > sessionInfo()
R version 2.8.0 (2008-10-20)
x86_64-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] biomaRt_1.16.0

loaded via a namespace (and not attached):
[1] RCurl_0.91-0 XML_1.98-1

Although it looks like you have a really old version of RCurl.

Best,

Jim



Shi, Tao wrote:
> Hi list,
> 
> This only happened after I switched to R-2.8.0 and the latest biomaRt and RCurl.  I was using R-2.7.0 before and everything worked fine.  Currently, manually loading RCurl after loading biomaRt solves the problem.  Please see the R outputs below.  Many thanks!
> 
> ##==============================================================
> R version 2.8.0 (2008-10-20)
> Copyright (C) 2008 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
> 
> R is free software and comes with ABSOLUTELY NO WARRANTY.
> You are welcome to redistribute it under certain conditions.
> Type 'license()' or 'licence()' for distribution details.
> 
>   Natural language support but running in an English locale
> 
> R is a collaborative project with many contributors.
> Type 'contributors()' for more information and
> 'citation()' on how to cite R or R packages in publications.
> 
> Type 'demo()' for some demos, 'help()' for on-line help, or
> 'help.start()' for an HTML browser interface to help.
> Type 'q()' to quit R.
> 
>> library(biomaRt)
>> ?getSNP
>> mart <- useMart("snp",dataset="hsapiens_snp")
> Error in curlPerform(curl = curl, .opts = opts, .encoding = .encoding) : 
>   could not find function "findHTTPHeaderEncoding"
>> snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart)
> Error in martCheck(mart, "snp") : object "mart" not found
> In addition: Warning message:
> The getSNP function will be removed in the next release of biomaRt.  Use the getBM function instead.  The biomaRt vignette contains examples of retrieving SNP data 
>> show(snp)
> Error: object "snp" not found
> Error in show(snp) : 
>   error in evaluating the argument 'object' in selecting a method for function 'show'
>> ?findHTTPHeaderEncoding
> No documentation for 'findHTTPHeaderEncoding' in specified packages and libraries:
> you could try '??findHTTPHeaderEncoding'
>> library(RCurl)
>> mart <- useMart("snp",dataset="hsapiens_snp")
> Checking attributes and filters ... ok
>> snp = getSNP(chromosome = 8, start = 148350, end = 148612, mart = mart)
> Warning message:
> The getSNP function will be removed in the next release of biomaRt.  Use the getBM function instead.  The biomaRt vignette contains examples of retrieving SNP data 
>> snp
>     refsnp_id allele chrom_start chrom_strand
> 1     rs13291    C/T      148462            1
> 2   rs1134186    T/C      148569            1
> 3   rs1134187    G/A      148539           -1
> 4   rs1134189    G/A      148535           -1
> 5   rs1134190    C/T      148533           -1
> 6   rs1134191    C/T      148499           -1
> 7   rs1134192    G/A      148462           -1
> 8   rs1134195    G/T      148394           -1
> 9   rs3965587    C/T      148535            1
> 10  rs4046274    C/A      148394            1
> 11  rs4046275    A/G      148411            1
> 12  rs4046276    C/T      148462            1
> 13  rs4046277    G/A      148499            1
> 14  rs4046278    G/A      148533            1
> 15  rs4378731    G/A      148601            1
> 16 rs11136408    G/A      148525            1
> 17 rs12019378    T/G      148471            1
>> sessionInfo()
> R version 2.8.0 (2008-10-20) 
> i386-pc-mingw32 
> 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] RCurl_0.9-4    biomaRt_1.16.0
> 
> loaded via a namespace (and not attached):
> [1] XML_1.96-0
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-5646
734-936-8662