[BioC] AnnBuilder: problem with kegg url?

[Marc Carlson]

Matthias E. Futschik wrote:
> hi all,
> I try to use ABPkgBuilder (session info below)
> with following code (partly from the vignette)
>
> #####
> library(AnnBuilder)
> read.table(file.path(.path.package("AnnBuilder"), "data", "thgu95a"),
>            sep = "\t", header = FALSE, as.is = TRUE)
> myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a")
> myBaseType <- "gb"
> myDir <- tempdir()
> ABPkgBuilder(baseName = myBase, baseMapType = myBaseType,
>  pkgName = "myPkg", pkgPath = myDir,
> organism = "Homo sapiens", version = "1.1.0", author = list(authors =
> "myname",
> maintainer = "myname at myemail.com"), fromWeb = TRUE)
> #####
>
> The last command however failed:
>
> Error in parseKEGGGenome(url = kegggenomeUrl) :
>         Faild to obtain KEGG organism code
>
> Checking for the url gives
>
>  getOption("AnnBuilderSourceUrls")$KEGGGENOME
> [1] "ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/genome"
>
> However, this directory does not exist anymore!
> Which should be the correct one? And how do I fix this
> within the ABPkgBuilder command?
>
> thanks,
> Matthias.
>
> ps: I could save my troubles if there is an annotation package for
> the complete set of human entrezids (which includes go + kegg + pfam) -
> is there?
>
>   
>> sessionInfo()
>>     
> R version 2.4.1 (2006-12-18)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252
>
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets"
>  "methods"   "base"
>
> other attached packages:
>         GO AnnBuilder    RSQLite        DBI   annotate        XML    Biobase
>   "1.14.1"   "1.12.0"    "0.5-4"    "0.2-3"   "1.12.1"    "1.6-0"   "1.12.2"
>   
>
>
>
> ***************************************************
> Matthias E. Futschik
> Institute for Theoretical Biology
> Charite - Medical School
> Humboldt-University
> Invalidenstrasse 43
> 10115 Berlin
> Germany
>
> email: m.futschik at biologie.hu-berlin.de
> phone: + 49-30-2093 9106
> fax:   + 49-30-2093 8801
> URL:  
> http://itb.biologie.hu-berlin.de/~futschik	***************************************************
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>   

I believe that the package that you desire is called:  org.Hs.eg.db

And it can be found here:

http://www.bioconductor.org/packages/2.1/data/annotation/


Please let us know how this works for you.  And if you need any help
using it, please let me know that too.

    Marc