[BioC] Problem with library(SSPA)

[Martin Morgan]

On 06/09/2010 01:35 PM, Samuel Okoye wrote:
> 
> Hello,
> 
> I have the fellowing problem and I am thankful for any advice!
> 
> Regards,
> Samuel
> 
> ################################################################
>>    source("http://bioconductor.org/biocLite.R")
> BioC_mirror = http://www.bioconductor.org
> Change using chooseBioCmirror().
>>      biocLite("SSPA")
> Using R version 2.11.0, biocinstall version 2.6.7.
> Installing Bioconductor version 2.6 packages:
> [1] "SSPA"
> Please wait...
> 
> trying URL 'http://www.bioconductor.org/packages/2.6/bioc/bin/windows/contrib/2.11/SSPA_1.4.0.zip'
> Content type 'application/zip' length 305310 bytes (298 Kb)
> opened URL
> downloaded 298 Kb
> 
> package 'SSPA' successfully unpacked and MD5 sums checked
> 
>> library(SSPA)
> Loading required package: qvalue
> Loading
>  required package: tcltk
> Loading Tcl/Tk interface ... done
> Error : .onAttach failed in attachNamespace() for 'SSPA', details:
>   call: fun(...)
>   error: could not find function "addVigs2WinMenu"
> Error: package/namespace load failed for 'SSPA'

Hi Samuel

my best guess is a package, other than SSPA, installed incorrectly. I'd
make sure to start R so that it doesn't load any .Rdata or other files
(e.g., with something like c:\Program Files\R\R-2.11\bin\Rgui --vanilla
from the DOS shell) and then try updating packages as outlined at
http://bioconductor.org/install. If that fails traceback() after the
error occurs might help, as might trace(attachNamespace,
browser=quote(print(nm))) before running the command.

Martni


>> sessionInfo()
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
> 
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252   
> 
> attached base packages:
> [1] tcltk     stats     graphics  grDevices utils     datasets  methods   base    
> 
> other attached
>  packages:
> [1] qvalue_1.22.0
> 
> loaded via a namespace (and not attached):
> [1] limma_3.4.3  SSPA_1.4.0   tools_2.11.0
> 
> ##########################################################################
> 
> 
> 
> 
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> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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