[BioC] ABPkgBuilder Error;

[Barry Henderson]

I just tried the same code on an linux system with the same results.

R version 2.1.1, 2005-06-20, i686-pc-linux-gnu
 
attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
[7] "datasets"  "base"
 
other attached packages:
        GO AnnBuilder   annotate        XML    Biobase
   "1.8.2"   "1.5.31"   "1.5.16"   "0.97-7"   "1.5.12"

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Barry
Henderson
Sent: Wednesday, August 03, 2005 10:27 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] ABPkgBuilder Error;


Reposted with sessionInfo() output:

> 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") 
> myDir <- tempdir() myOtherSrc <- c(srcone = 
> file.path(.path.package("AnnBuilder"),
"data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), "data",
"srcb"))
> myBaseType="gb"
> mySrcUrls <- getOption("AnnBuilderSourceUrls") ABPkgBuilder(baseName =

> myBase, srcUrls = mySrcUrls, baseMapType =
myBaseType,
+ otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, organism = 
+ "Homo sapiens", version = "1.1.0", author = list(author = "myname", 
+ maintainer = "myname at myemail.com"), fromWeb = TRUE)

Attaching package: 'GO'


        The following object(s) are masked from package:AnnBuilder :

         GO 

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"
> 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: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Barry
Henderson
Sent: Wednesday, August 03, 2005 9:40 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] ABPkgBuilder Error;


Hi All
 
I am trying to build the test annotation package from the AnnBuilder
primer but I keep getting an "invald class "GO" object" error.  
The code I am using is straight from the vignette with a couple of
modifications for path and package naming
 
>library(AnnBuilder)
>datadir <- "/rc2/current project storage/RCAnnotation"
>setwd(datadir)
 
>myDir <- tempdir()
>myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a")
>myBaseType="gb" mySrcUrls <- getOption("AnnBuilderSourceUrls")
>myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), "data",
"srca"), srctwo = file.path(.path.package("AnnBuilder"), "data",
"srcb"))

>ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType =
myBaseType,
+otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, organism =
+"Homo sapiens", version = "1.1.0", author = list(author = "myname", 
+maintainer = "myname at myemail.com"), fromWeb = TRUE)
 
 
>From here ABPkgBuilder downloads gene2accession.gz, runs gzip and dumps
out with the following 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"

System:
 
Windows XP
R 2.1.1
Current release of BioC packages (downloaded via getBioC yesterday)
 
Any ideas?
 
Thanks
Barry

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