[BioC] ABPkgBuilder Error;

[Barry Henderson]

Yes I am sure.  The sessionInfo from the linux installation (using the
zip you emailed) is:

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:
AnnBuilder   annotate        XML    Biobase
 "1.6.8-4"   "1.5.16"   "0.97-7"   "1.5.12"


I installed 1.6.8-4 listed on the developers page form bioconductor (I
just re-downloaded and re-installed it to make sure).  The session info
there is:

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:
AnnBuilder   annotate        XML    Biobase 
   "1.6.8"   "1.5.16"   "0.97-7"   "1.5.12" 

Note that there were a couple of warnings on windows installation:

>package 'AnnBuilder' successfully unpacked and MD5 sums checked
>updating HTML package descriptions
>Warning messages:
>1: no package 'file15700' was found in: packageDescription(i, fields =
"Title", lib.loc = lib) 
>2: no package 'file27003' was found in: packageDescription(i, fields =
"Title", lib.loc = lib) 



-----Original Message-----
From: John Zhang [mailto:jzhang at jimmy.harvard.edu] 
Sent: Thursday, August 04, 2005 7:57 AM
To: jzhang at jimmy.harvard.edu; bioconductor at stat.math.ethz.ch; Barry
Henderson
Subject: Re: [BioC] ABPkgBuilder Error;


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]]
>>
>>_______________________________________________
>>Bioconductor mailing list
>>Bioconductor at stat.math.ethz.ch
>>https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>Jianhua Zhang
>Department of Medical Oncology
>Dana-Farber Cancer Institute
>44 Binney Street
>Boston, MA 02115-6084
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch 
>https://stat.ethz.ch/mailman/listinfo/bioconductor

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