[BioC] ABPkgBuilder question

[Marc Carlson]

Kamila Naxerova wrote:
> Hi all,
>
> I am - not very successfully - playing with AnnBuilder and would
> appreciate any comments on the error I am getting (system info below).
> Confusingly, the same code *seems* to work fine on my windows machine,
> only here I don't want to deal with unzipping problems. Sorry if this is
> something obvious.
>
> platform       x86_64-unknown-linux-gnu
> arch           x86_64
> os             linux-gnu
> system         x86_64, linux-gnu
> status
> major          2
> minor          7.1
> year           2008
> month          06
> day            23
> svn rev        45970
> language       R
>
>
> library(hgu133plus2.db)
> x=hgu133plus2ENTREZID
> xx=as.list(x)
> basefile=data.frame(names(xx),as.character(unlist(xx)))
> write.table(basefile,"Basefile.txt",sep="\t",row.names=F)
>
> library(AnnBuilder)
> mySrcUrls=getSrcUrl("all",organism="Homo sapiens")
>
> ABPkgBuilder(baseName = read.table("Basefile.txt",header=F,sep="\t"),
> srcUrls = mySrcUrls, baseMapType ="ll", pkgName = "hgu133plus2",
> pkgPath = getwd(), organism = "Homo sapiens", version = "1.1.0",author =
> list(authors = "K"),fromWeb=TRUE)
>
> Error in validObject(.Object) :
>   invalid class "UG" object: invalid object for slot "baseFile" in class
> "UG": got class "data.frame", should be or extend class "character"
> Calls: ABPkgBuilder ... UG -> new -> initialize -> initialize -> validObject
> Execution halted
>
>
> Thanks,
> Kamila
>   
Hi Kamila,


It looks like you might be trying to make a customized annotation 
package for human?  If so, then instead of AnnBuilder, please use the 
SQLForge functions inside of AnnotationDbi to make custom annotation 
packages.  This will allow you to make a more modern ".db" style 
annotation package.  You can find the instructions here: 

http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html

If you have further questions, please feel free to ask,


  Marc