[BioC] Re : bug with AnnBuilder and parser

Nianhua Li nli at fhcrc.org
Fri May 11 23:35:32 CEST 2007

Hi Gregory,

I couldn't repeat your error with your base mapping file. I am using
linux though. The script I used was:
                 organism="Homo sapiens",
                   authors="Greg_Voisin, Amelie Ouellet",
                   maintainer="Greg_Voisin<voisingreg at yahoo.fr>"
But I didn't got any annotation at the beginning. It took me quite a
while, and with my colleague's help, to realize that your base mapping
file has "\r" at the end of each line. It caused some problems with
the perl scripts being invoked by ABPkgBuilder. You shouldn't have
this problem because you are using windows anyway. I have never used
AnnBuilder on windows, therefore can't give you more useful advices.
But I will send you the source package of "monPackageAnnoted" offline.



Hi Nianhua,

I have update version of R and Annbuilder ( on windows system, I wait
for the same update on my unix system)::

> sessionInfo()
R version 2.5.0 (2007-04-23)
attached base packages:
[1] "tools"     "stats"     "graphics"  "grDevices" "utils"
"datasets"  "methods"   "base"
other attached packages:
        GO AnnBuilder   annotate        XML    Biobase
  "1.16.0"   "1.14.0"   "1.14.1"    "1.7-1"   "1.14.0"

Then, I reload the same code ....but message error nd no creation of

> library (AnnBuilder)
Le chargement a nécessité le package : Biobase
Le chargement a nécessité le package : tools
Welcome to Bioconductor
  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.
Le chargement a nécessité le package : XML
Le chargement a nécessité le package : annotate
> data_gb = read.table("probeset_gb.txt" , sep = "\t", header=FALSE,
> mybase = file.path("probeset_gb.txt")
> mybasetype= "gb"
> mydir = getwd()
> LL_url  = getSrcUrl(src = "LL", organism = "Homo sapiens", xml =
TRUE, dateOnly = FALSE)
> KEGG_url = getSrcUrl(src = "KEGG", organism = "Homo sapiens", xml =
TRUE, dateOnly = FALSE)
> UG_url = getSrcUrl(src = "UG", organism = "Homo sapiens", xml =
TRUE, dateOnly = FALSE)
> mySrcUrls = c(LL_url, KEGG_url, UG_url)
> ABPkgBuilder(baseName= mybase, srcUrls= mySrcUrls, baseMapType =
mybasetype, pkgName = "monPackageAnnoted", pkgPath = mydir, organism =
"Homo sapiens", version = "1.0", author = list (authors =
"Greg_Voisin, Amelie Ouellet", maintainer = "voisingreg at ...."),
fromWeb =TRUE)
Attachement du package : 'GO'

        The following object(s) are masked from package:AnnBuilder :
Erreur dans function (classes, fdef, mtable)  :
        unable to find an inherited method for function "baseFile<-",
for signature "NULL"

I join my file input ( probeset /genbankID)

Can you try in your system?

Thanks ,Nianhua , for your help in R problems...


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