Dear Seth and John,
 
Thank you for your reply. I have studied the suggestions in the manual
you suggested, but now I'm at a stage I'm not quite sure how to proceed
further.
 
This is what I have done so far:
 
1: I have downloaded all the suggested programmes and files from the
http://www.murdoch-sutherland.com/Rtools/ webside
 
2: Used the Annbuilder package to make an annotation package for chicken
data with R 2.5.0 under windows XP (see script in the bottom of this
mail)... OK
(a directory "bartkip" is generated with 3 sub-directories "data" ,
"man", "R")
 
Now I'd like to make this Annotation package suitable to be read in R
2.5.0 under windows.
 
3: Set the dos prompt to the directory where 'bartkip' is situated.
 
4:  R CMD build --binary bartkip
This gives the following message:
 
* checking for file 'bartkip/DESCRIPTION' ... OK
* preparing 'bartkip'
* checking DESCRIPTION meta-information ... OK
* remove junk files
* checking for LF line-endings in source files
* checking for empty and unneeded directories
* building binary distribution
 WARNING
* some HTML links may not be found
installing R.css in c:/TEMP/Rinst333285638
 
Using auto-selected zip options 'bartkip-HELP=ziponly'
make[2]: *** [zzzfirst] Error 57
make[1]: *** [All] Error 2
*** installation of bartkip failed ***
 
Removing 'c:/TEMP/Rinst333285638/bartkip'
ERROR
*installation failed
 
I have checked the command: R CMD check bartkip, this does not give
anything more then the error message above.
 
I have checked all the links in the files in the 'man' directory and
found that the link to KEGG was not correct in the files:
 
bartkipENZYME.Rd and bartkipENZYME2PROBE.Rd
 
ftp://ftp.genome.ad.jp/pub/kegg/pathways should be
ftp://ftp.genome.ad.jp/pub/kegg/pathway
 
Also in the file bartkipSUMFUNC.Rd, the link
http://www.ncbi.nlm.nih.gov/LocusLink is automatically further linked
to:
www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
<http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene> 
 
But unfortunately changing these links in these three files did not
help.
 
I hope that someone could give me a hint how to proceed.
 
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
# Install on PC:
# 1> RTools:      http://www.murdoch-sutherland.com/Rtools/
<http://www.murdoch-sutherland.com/Rtools/> 
# 2> Active Perl: http://www.perl.com/download.csp
<http://www.perl.com/download.csp> 
# 3> gzip:        http://www.gzip.org/ <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 <bart.buitenhuis@agrsci.dk
<mailto: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=================================
 

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