Entering edit mode
Margaret Gardiner-Garden
▴
160
@margaret-gardiner-garden-426
Last seen 10.2 years ago
Hi,
I am using AnnBuilder for the first time and am having trouble getting
GenBank identifiers to find LocusLink and Unigene IDs from the NCBI
server.
The error I get is
Failed to create a data connection
Error in readURL(infoUrl) : Can't read from url:
ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.info
I have checked that I can access this site using my browser (outside
the
AnnBuilder program).
I tried using the data sets in the "How to use AnnBuilder tutorial"
and got
the same error.
When I tried to leave out unigene and just go for locuslink on the
NCBI
server I got a different error
Error in toupper(x) : non-character argument to toupper()
I have put a text version of my session using the tutorial data below.
I was wondering if anyone might have any idea where I am going wrong.
Any
help would be greatly appreciated!
Thanks
Marg Gardiner-Garden (Garvan Institue of Medical Research)
read.table(file.path(.path.package("AnnBuilder"),"data", "thgu95a"),
sep="\t", header= FALSE, as.is=TRUE)
V1 V2
1 32468_f_at D90278
2 32469_at L00693
3 32481_at AL031663
4 33825_at X68733
5 35730_at X03350
6 36512_at L32179
7 38912_at D90042
8 38936_at M16652
9 39368_at AL031668
myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a")
myBase #[1] "C:/PROGRA~1/R/RW1090~1/library/AnnBuilder/data/thgu95a"
myBaseType <- "gb" #this was the second column in the file
mySrcUrls <-
c(LL="http://www.bioconductor.org/datafiles/wwwsources/T11_tmp1.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)
# V1 V2
#1 32468_f_at NA
#2 32469_at 2
#3 32481_at NA
#4 33825_at 9
#5 35730_at 1576r
#6 36512_at NA
#7 38912_at 10
#8 38936_at NA
#9 39368_at NA
read.table(file.path(.path.package("AnnBuilder"), "data", "srcb"),
sep="\t",
header=FALSE, as.is=TRUE)
V1 V2
#1 32468_f_at NA
#2 32469_at NA
#3 32481_at 7051
#4 33825_at NA
#5 35730_at NA
#6 36512_at 1084
#7 38912_at NA
#8 38936_at NA
# 39368_at 89
myOtherSrc <- c(srcone=file.path(.path.package("AnnBuilder"), "data",
"srca"), srctwo= file.path(.path.package("AnnBuilder"), "data",
"srcb"))
myOtherSrc
# srcone
# srctwo
#"C:/PROGRA~1/R/RW1090~1/library/AnnBuilder/data/srca"
"C:/PROGRA~1/R/RW1090~1/ #library/AnnBuilder/data/srcb"
myDir <- tempdir()
myDir #[1] "C:\\DOCUME~1\\margar\\LOCALS~1\\Temp\\Rtmp23936"
if (.Platform$OS.type !="windows"){
ABPkgBuilder(baseName=myBase, srcUrls= mySrcUrls, baseMapType=
myBaseType,
otherSrc= myOtherSrc, pkgName ="myPkg", pkgPath=myDir,
organism="human",
version ="1.9.0", makeXML= TRUE, author=list(author="MGG",
maintainer="m.gardiner-garden@garvan.org.au"),fromWeb= TRUE)
}
#didn't seem to process so tried without the if statement
#The folder "C:\\DOCUME~1\\margar\\LOCALS~1\\Temp\\Rtmp23936"
existed but
there #was no myPkg in it
ABPkgBuilder(baseName=myBase, srcUrls= mySrcUrls, baseMapType=
myBaseType,
otherSrc= myOtherSrc, pkgName ="myPkg", pkgPath=myDir,
organism="human",
version ="1.9.0", makeXML= TRUE, author=list(author="MGG",
maintainer="m.gardiner-garden@garvan.org.au"),fromWeb= TRUE)
#[1] "It may take me a while to process the data. Be patient!"
#Warning message:
#Failed to create a data connection
#Error in readURL(infoUrl) : Can't read from url:
ftp://ftp.ncbi.nih.gov/
#repository/UniGene/Hs.info
#Try it without the unigene (ie just getting LocusLink from
NCBI)
mySrcUrls <- getSrcUrl(src = "LL", organism = "human", xml = TRUE,
dateOnly
= FALSE)
mySrcUrls
#[1] "ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz"
ABPkgBuilder(baseName=myBase, srcUrls= mySrcUrls, baseMapType=
myBaseType,
otherSrc= myOtherSrc, pkgName ="myPkg", pkgPath=myDir,
organism="human",
version ="1.9.0", makeXML= TRUE, author=list(author="MGG",
maintainer="m.gardiner-garden@garvan.org.au"),fromWeb= TRUE)
#[1] "It may take me a while to process the data. Be patient!"
#Error in toupper(x) : non-character argument to toupper()