[BioC] AnnBuilder links to unigene
John Zhang
jzhang at jimmy.harvard.edu
Thu Aug 19 14:31:17 CEST 2004
I have no problem accessing the URL with both the devel and release version.
Would it be possible that the web site was down when you were trying the code?
>From: "Margaret Gardiner-Garden" <m.gardiner-garden at garvan.org.au>
>To: <bioconductor at stat.math.ethz.ch>
>Date: Thu, 19 Aug 2004 17:01:20 +1000
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>Subject: [BioC] AnnBuilder links to unigene
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>
>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 at 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 at 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 at 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()
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
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