[BioC] ABPkgBuilder Error;

[John Zhang]

>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:

1.6.8-4 is not even available from the web and this still gives you 1.6.8 as 
shown below. That was why I sent you the package I built.


>
>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

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