[BioC] ABPkgBuilder Error;

John Zhang jzhang at jimmy.harvard.edu
Wed Aug 3 19:33:29 CEST 2005

>That helped a little but now I get the following error:
>> mySrcUrls <- getSrcUrl("all", "Homo sapiens")
>> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
>+ otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
>+ organism = "Homo sapiens", version = "1.1.0", 
>+ author = list(author = "myname", maintainer = "myname at myemail.com"),
>+ fromWeb = TRUE)
>Error in if (is.na(built) || is.null(built) || built == "") { : 
>        missing value where TRUE/FALSE needed

Yes, that was because the code failed to get the built information from KEGG due 
to changes in the web interface. The fix has been checked in and a new version 
of AnnBuilder will be available when it is pushed out to the download site. 

>In addition: Warning message:
>data length [932] is not a sub-multiple or multiple of the number of
>rows [311] in matrix 
>> sessionInfo()
>R version 2.1.1, 2005-07-31, i386-pc-mingw32 
>attached base packages:
>[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
>[7] "datasets"  "base"     
>other attached packages:
>        GO AnnBuilder   annotate        XML    Biobase 
>   "1.8.2"    "1.6.8"   "1.5.16"   "0.97-7"   "1.5.12" 
>-----Original Message-----
>From: John Zhang [mailto:jzhang at jimmy.harvard.edu] 
>Sent: Wednesday, August 03, 2005 11:36 AM
>To: bioconductor at stat.math.ethz.ch; Barry Henderson
>Subject: Re: [BioC] ABPkgBuilder Error;
>>>Error in validObject(.Object) : invalid class "GO" object: invalid
>>object for slot "srcUrl" in class "GO": got class "list", should be or 
>>extend class "character"
>The return of getOption("AnnBuilderSourceUrls") does not work too well
>ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls solves
>problem. However, KEGG changed some of the web pages that caused the
>code to 
>fail. I have fixed the problem and will check in the fixes. It may take
>a few 
>days for the revised version to be available though.
>>Windows XP
>>R 2.1.1
>>Current release of BioC packages (downloaded via getBioC yesterday)
>>Any ideas?
>>	[[alternative HTML version deleted]]
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch 
>Jianhua Zhang
>Department of Medical Oncology
>Dana-Farber Cancer Institute
>44 Binney Street
>Boston, MA 02115-6084

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

More information about the Bioconductor mailing list