[BioC] ABPkgBuilder Error;

[John Zhang]

Are you sure you have installed AnnBuilder 1.6.8-4 as your sessionInfo still 
showed 1.6.8?



>John et al.
>
>I tried AnnBuilder 1.6.8-4 and it solved the "invalid class.." error but
>it still fails building the package.  Results from windows install is
>below (same results on linux):
>
>> library(AnnBuilder)
>Loading required package: Biobase
>Loading required package: tools
>Welcome to Bioconductor 
>         Vignettes contain introductory material.  To view, 
>         simply type: openVignette() 
>         For details on reading vignettes, see
>         the openVignette help page.
>Loading required package: XML
>Loading required package: annotate
>Warning message:
>package 'AnnBuilder' was built under R version 2.2.0 
>> myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a")
>> datadir <- "c:/rc2/curren~1/RCAnno~1"
>> myDir <- tempdir()
>> myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"),
>"data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), "data",
>"srcb"))
>> myBaseType="gb"
>> mySrcUrls <- getSrcUrl("all", "Homo sapiens")
>> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
>myBaseType,
>+ pkgName = "hsRiboChipv2", pkgPath = datadir, organism = "Homo
>sapiens",
>+ version = "1.0.0",
>+ author = list(author = "Barry Henderson", maintainer =
>"barry.henderson at ribonomics.com"),
>+ fromWeb = TRUE)
>
>Attaching package: 'GO'
>
>
>        The following object(s) are masked from package:AnnBuilder :
>
>         GO 
>
>Error in if (is.na(built) || is.null(built) || built == "") { : 
>        missing value where TRUE/FALSE needed
>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"
>"datasets" 
>[8] "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
>with 
>ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls solves
>the 
>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.
>
>>
>>System:
>> 
>>Windows XP
>>R 2.1.1
>>Current release of BioC packages (downloaded via getBioC yesterday)
>> 
>>Any ideas?
>> 
>>Thanks
>>Barry
>>
>>	[[alternative HTML version deleted]]
>>
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>
>Jianhua Zhang
>Department of Medical Oncology
>Dana-Farber Cancer Institute
>44 Binney Street
>Boston, MA 02115-6084
>
>_______________________________________________
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>Bioconductor at stat.math.ethz.ch
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084