R help - Aug 2007 - use AnnBuilderSourceUrls with local path insted of ftp adress

Hallo everybody.

I want to build my own GO package using the function GOPkgBuilder of AnnBuilder.
It uses AnnBuilderSourceUrls to collect data from different ftp sites. These
data are not complete for my organism, so I would like to change the ftp
adresses to a local one. The changing itself is working but when I run the
script I get the following Error:

Error in loadFromUrl(file.path(sourceURLs[["EG"]],
"gene2go.gz")) :
 URL /path/to/file/gene2go.gz is incorrect or the target site is not responding!

The full code of the script is this:

library(AnnBuilder)
list<-options("AnnBuilderSourceUrls") 
list$AnnBuilderSourceUrls$EG<-"/path/to/file/"
options("AnnBuilderSourceUrls"=list$AnnBuilderSourceUrls)

GOPkgBuilder(pkgName = "GO", pkgPath = ".", filename =
"go_200706-termdb.obo-xml.gz", version = "v.1.0", author =
list(author = "author", maintainer = "maintainer <main.tainer
at mail.net>") )

Thanks in advance for any help.

Daniela Albrecht


-- 
Psssst! Schon vom neuen GMX MultiMessenger geh?rt?
Der kanns mit allen: http://www.gmx.net/de/go/multimessenger

>
>I want to build my own GO package using the function GOPkgBuilder of 
AnnBuilder. It uses AnnBuilderSourceUrls to collect data from different ftp 
sites. These data are not complete for my organism, so I would like to change 
the ftp adresses to a local one. The changing itself is working but when I run 
the script I get the following Error:
>
>Error in loadFromUrl(file.path(sourceURLs[["EG"]],
"gene2go.gz")) :
> URL /path/to/file/gene2go.gz is incorrect or the target site is not 
>responding!

First of all, please post questions about BioConductor packages in BioConductor 
mailing list instead of R.

Is /path/to/file a real local path? If so, you may also need to modify 
GOPkgBuilder a little. Try to change the line

eg = EG(srcUrl = sourceURLs[["EG"]]) to
eg = EG(srcUrl = sourceURLs[["EG"]], fromWeb = FALSE)

>
>The full code of the script is this:
>
>library(AnnBuilder)
>list<-options("AnnBuilderSourceUrls") 
>list$AnnBuilderSourceUrls$EG<-"/path/to/file/"
>options("AnnBuilderSourceUrls"=list$AnnBuilderSourceUrls)
>
>GOPkgBuilder(pkgName = "GO", pkgPath = ".", filename = 
"go_200706-termdb.obo-xml.gz", version = "v.1.0", author =
list(author =
"author", maintainer = "maintainer <main.tainer at
mail.net>") )
>
>Thanks in advance for any help.
>
>Daniela Albrecht
>
>
>-- 
>Psssst! Schon vom neuen GMX MultiMessenger geh?rt?
>Der kanns mit allen: http://www.gmx.net/de/go/multimessenger
>
>______________________________________________
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>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084