Dear bioconductor users,
 
I'm trying to use Annbuilder to make an annotation package for chicken data. Last week (23 april 2007) I downloaded R 2.5.0 (under windows XP) and have downloaded the Annbuilder package.
When running my script (see at the end of the mail) all files are downloaded (a directory "bartkip" is generated with 3 sub-directories "data" , "man", "R")
 
But when I try to call this package in R using library(bartkip), it is not working.
 
Then I have tried the following options:
1> copied the complete directory "bartkip", under the library folder of R, and run library(bartkip) : Not working
 
2> in the "R" folder under "bartkip" there is an R-script generated in the Annbuilder run. I tried to run that but got the following error message:
 
bartkip <- function() cat(bartkipQC)
 .no_S3_generics = TRUE
 ns <- asNamespace("bartkip")

#! Error in loadNamespace(name) : there is no package called 'bartkip'

 bartkipLOCUSIDfunc <- function() {
 bartkipLOCUSID <- function(){
 .Deprecated("bartkipENTREZID")
 }
 bartkipLOCUSID()
 bartkipENTREZID
 }
 makeActiveBinding("bartkipLOCUSID", bartkipLOCUSIDfunc, ns)

#! Error in makeActiveBinding("bartkipLOCUSID", bartkipLOCUSIDfunc, ns) : 
        object "ns" not found

 
Does anyone have a suggestion?
 
Best regards,
Bart
 
#=============== Begin Script=================================================
setwd("H:/FP/experiment1/Microarrays/annotation")
#!memory.limit(size=2000)
 
################################################################################
#set up to annotate the genes for the chicken array in a window environment
# R-version 2.5.0 / 2.4.1
# Install on PC:
# 1> RTools:      http://www.murdoch-sutherland.com/Rtools/
# 2> Active Perl: http://www.perl.com/download.csp
# 3> gzip:        http://www.gzip.org/
# Set these programmes to the PATH on your PC
################################################################################
 
#! Annbuilder
library(AnnBuilder)
 
#File book2.txt is a txt file with information of the spots on the chicken array. The
#columns are "OLIGO_ID" and "Unigene_ID" (Gga.####), missing values are
#noted as '.'
 
myBase <- "H:/FP/experiment1/Microarrays/annotation/Book2.txt"
myBase
 
myBaseRead <- read.table(myBase, sep = "\t", header = FALSE, as.is = TRUE)
myBaseRead[1:10,]

myBaseType <- "ug"
myBaseType
mySrcUrls  <- getSrcUrl("all", "Gallus gallus")
mySrcUrls
 
myDir <- "H:/FP/experiment1/Microarrays/annotation/kip"

myPkg      <- "bartkip"
myname     <- "Bart Buitenhuis"
myemail    <- "bart.buitenhuis@agrsci.dk"
.Platform$OS.type
#![1] "windows"
interactive()
#![1] TRUE
 
if (.Platform$OS.type == "windows" && interactive()) {
 ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType,
 pkgName = myPkg, pkgPath = myDir, organism = "Gallus gallus", 
 version = "1.1.0", author = list(authors = myname,
 maintainer = myemail), fromWeb = TRUE)
 }

#========================END SCRIPT=================================
 

Med venlig hilsen / Regards

Bart Buitenhuis
Projektleder / Project manager


 	
 	 AARHUS UNIVERSITET / UNIVERSITY OF AARHUS	
Det Jordbrugsvidenskabelige Fakultet / Faculty of Agricultural Sciences	
Inst. for Genetik og Bioteknologi / Dept. of Genetics and Biotechnology	
Blichers Allé 20, P.O. BOX 50	
DK-8830 Tjele	
 	
Tel:	 +45 8999 1900	
Direct:	 +45 8999 1316	
Mobile:	 +45 	
E-mail:	 Bart.Buitenhuis@agrsci.dk <mailto:Bart.Buitenhuis@agrsci.dk> 	
Web:	 www.agrsci.dk <http://www.agrsci.dk/> 	
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