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()

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@garvan.org.au> >To: <bioconductor@stat.math.ethz.ch> >Date: Thu, 19 Aug 2004 17:01:20 +1000 >MIME-Version: 1.0 >Content-Transfer-Encoding: 7bit >X-Priority: 3 (Normal) >X-MSMail-Priority: Normal >Importance: Normal >X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2800.1441 >Received-SPF: none (hypatia: domain of bioconductor- bounces@stat.math.ethz.ch does not designate permitted sender hosts) >Received-SPF: none (hypatia: domain of m.gardiner- garden@garvan.org.au does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >X-Spam-Checker-Version: SpamAssassin 2.63 (2004-01-11) on hypatia.math.ethz.ch >X-Spam-Level: >X-Spam-Status: No, hits=0.0 required=5.0 tests=none autolearn=no version=2.63 >Subject: [BioC] AnnBuilder links to unigene >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.1.5 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> > >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() > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084