[BioC] Error with AnnBuilder ABPkgBuilder

[Ting-Yuan Liu]

Hi Sylvain,

Could you remove the argument "srcUrls = mySrcUrls" and try again?  
ABPkgBuilder will find the srcUrls automatically.  If this cannot solve 
the problem, you can send me the "ProbeIdToLL.txt" file and I am happy to 
test it for you.

Moreover, the argument author should be

author = list(authors = "sylvain", maintainer = 
"sylvain <sylvain at sdsc.edu>")

See the difference?

HTH,
Ting-Yuan
______________________________________
Ting-Yuan Liu
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
Seattle, WA, USA
______________________________________

On Fri, 20 Jan 2006, Sylvain Pradervand wrote:

> 
> Hi,
> 
> I am having a problem with AnnBuilder:
> 
> Error in "[.data.frame"(annotation, , 1:3) : 
>         undefined columns selected
> 
> The code that generate this error is below:
> 
> > myBase <- "ProbeIdToLL.txt"
> > myBaseType <- "ll"
> > myDir <- tempdir()
> > mySrcUrls <- getSrcUrl("all", "Mus musculus")
> > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
> myBaseType, pkgName = "agilentOligo", pkgPath = myDir, organism = "Mus
> musculus", version = "1.1.0", author = list(author = "sylvain",
> maintainer = "sylvain at sdsc.edu"), fromWeb = TRUE)
> 
> Error in "[.data.frame"(annotation, , 1:3) : 
>         undefined columns selected
> In addition: Warning message:
> Built for UCSC is not valid! in: getUCSCBuilt(organism)
> 
> > sessionInfo()
> R version 2.2.0, 2005-10-06, i386-pc-mingw32 
> 
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"  "base"     
> 
> other attached packages:
>         GO AnnBuilder   annotate        XML    Biobase 
>   "1.10.0"    "1.8.0"    "1.8.0"   "0.99-5"    "1.8.0"
> 
> 
> Thanks.
> 
> Sylvain
> 
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