[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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