[BioC] ABPkgBuilder Error;

Thu Aug 4 16:52:09 CEST 2005

I installed the version you sent me on the linux system.  Same error.

>From the web site:

Package: AnnBuilder

Description: Processing annotation date from public data repositories and building annoation data packages or XML data documents using the source data.
Version: 1.6.8-4
Author: J. Zhang 
Maintainer: J. Zhang 
Dependencies: R (>= 2.1.0), methods, Biobase, XML, annotate, utils
Suggests: None
SystemRequirements: None
License: LGPL
URL: None available

	-----Original Message----- 
	From: John Zhang [mailto:jzhang at jimmy.harvard.edu] 
	Sent: Thu 8/4/2005 10:38 AM 
	To: jzhang at jimmy.harvard.edu; bioconductor at stat.math.ethz.ch; Barry Henderson 
	Cc: 
	Subject: RE: [BioC] ABPkgBuilder Error;

	>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