[BioC] ABPkgBuilder Error;

[Barry Henderson]

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