[BioC] AnnBuilder: problem with kegg url?

[Herve Pages]

Hi Matthias,

Just an additional comment to Marc's answer: you must use R-2.6.0 (just
released yesterday) if you want to be able to install and use org.Hs.eg.db
(and this is currently true for any other .db package). Also, as with any
Bioconductor package, the recommended way to install a package is to use
biocLite (from R-2.6.0 ):

  > source("http://bioconductor.org/biocLite.R")
  > biocLite("org.Hs.eg.db")

Those org.*.*.db packages are new in Bioconductor 2.1 (BioC 2.1 will be
released tomorrow but you can start using it right now). Please let us
now if you find any problem or need help with this package. Thanks!

H.


Marc Carlson wrote:
> 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
> 
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