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
