[BioC] running AnnBuilder Vignette:Error in baseFile

Xue Lin xlin at ams.jhu.edu
Wed Apr 5 04:18:24 CEST 2006


I am trying to run the following codes from AnnBuilder Vignette in R 2.2.1 
under Windows XP,

#########################################################################
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"


mySrcUrls<-c(LL="http://www.bioconductor.org/datafiles/wwwsources/Tll_tmpl.gz",
             
UG="http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz",
GO="http://www.bioconductor.org/datafiles/wwwsources/Tgo.xml")

read.table(file.path(.path.package("AnnBuilder"), "data", "srca"), 
sep="\t",
 header=FALSE,as.is=TRUE)

read.table(file.path(.path.package("AnnBuilder"), "data", "srcB"), 
sep="\t",
 header=FALSE,as.is=TRUE)

myOtherSrc<-c(srcone=file.path(.path.package("AnnBuilder"), "data", 
"srca"),
 srctwo=file.path(.path.package("AnnBuilder"), "data","srcb"))

myDir<-tempdir()


ABPkgBuilder(baseName=myBase, srcUrls=mySrcUrls, baseMapType=myBaseType,
otherSrc=myOtherSrc, pkgName="myPkg", pkgPath=myDir, organism= "Homo 
sapiens",
version="1.1.0", author=list(author="myname", 
maintainer="myname at myemail.com"), fromWeb=TRUE)

######################################################################
And I got an error message, 

Warning message:
cannot open: HTTP status was '404 Not Found' 
Error in loadFromUrl(srcUrls[i]) : URL 
http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz is incorrect 
or the target site is not responding!


So I delete 
UG="http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz",
from mySrcUrls and run again, and this time I got another error message,

Error in "baseFile<-"(`*tmp*`, value = 
"C:\\DOCUME~1\\Owner\\LOCALS~1\\Temp/Rtmp2j5Apb\\tempFile5f906952") : 
        no direct or inherited method for function 'baseFile<-' for this 
call


I found that myDir is  "C:\\DOCUME~1\\Owner\\LOCALS~1\\Temp/Rtmp2j5Apb"
I change myDir to 
"C:\\DOCUME~1\\Owner\\LOCALS~1\\Temp/Rtmp2j5Apb\\tempFile5f906952"
and got an error message 

Error in "baseFile<-"(`*tmp*`, value = 
"C:\\DOCUME~1\\Owner\\LOCALS~1\\Temp/Rtmp2j5Apb\\tempFile6df11649") : 
        no direct or inherited method for function 'baseFile<-' for this 
call

Could someone tell me how to solve this problem? 

Thanks
Mary



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