Hi I'd like to build an Annotation package for the (custom made rat) array that i'm using. I'm running R 1.9.1 on mac osx and have an installation failure of AnnBuilder 1.4.13 I installed the devel versions of biobase and annotate as well, xml 0.95-6 is also installed. install.from.file(pkg="/Users/fjstam/Desktop/AnnBuilder") npackage installation failed If i go back to the current versions of annotate and biobase i get the same error. If i install AnnBuilder 1.4.2 i get it installed but then the same thing happens that was reported earlier, see mail below. > 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") > 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 = "testPkg", pkgPath = myDir, organism = "human", version = "1.1.0", makeXML = TRUE, author = list(author = "kees", maintainer = "kees@myemail.com"), fromWeb = TRUE) [1] "It may take me a while to process the data. Be patient!" Error in url(sourceURLs[["GO"]], open = "r") : Object "sourceURLs" not found So if i want the ABPkgBuilder to work, -which version of AnnBuilder should i install? -Should i upgrade any other package to devel or have everything at the current level? Earlier this week i tried the code from the ABPkgPrimer vignette (see mail below) in R 1.9.0, and then i got an error at the end, after my computer had been thinking about things for a while, which said something like: cannot parse rows and cannot open blabla.xml. The same thing happened when i used the 'real' urls and my own base file (it's just that it took my poor laptop an hour or so instead of a few minutes to give the error message). I decided that going to R 1.9.1 would probably solve my problem so i did not save the text from this session, and can therefore not be more exact (i don't feel like going back to R 1.9.0 unless it is really necessary). i hope anyone can help me with the installation and/or the source url problem. When these things are fixed i will probably have the parsing/opening xml problem again but we'll cross that bridge when we get there. floor _______________________________________________________ Floor Stam Vrije Universiteit Amsterdam Faculty of Earth and Life Sciences Department of Molecular and Cellular Neurobiology De Boelelaan 1085 1081HV Amsterdam The Netherlands Ph: +31-20-4447114 +31-20-5665512 Fax: +31-20-4447112 e-mail: fjstam@bio.vu.nl _______________________________________________________ On 25 Aug 2004 , at 18:20, John Zhang wrote: > >> I'm running R 1.9.1 on Windows 2000 and tried to test some of the >> code in >> the AnnBuilder (1.4.2) package from the vignette. >> I'm encountering an error, which I'm not clear on how to fix. Code and >> error are copied below. Note that I've tried to run the same code on >> Linux >> (R version 1.9.0) and got the same error. >> Any advice on this? > > I just noticed this bug and will have it fixed today. Thanks. > > >> Thanks, >> Elisabetta >> >> --- >>> 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") >>> ABPkgBuilder(baseName=myBase, srcUrls=mySrcUrls, >>> baseMapType=myBaseType, >> pkgName="myPkg", pkgPath="C:\tmp", organism="human", makeXML=F) >> [1] "It may take me a while to process the data. Be patient!" >> Error in url(sourceURLs[["GO"]], open = "r") : >> Object "sourceURLs" not found >> --- >> >> _______________________________________________ >> 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

>If i install AnnBuilder 1.4.2 i get it installed but then the same >thing happens that was reported earlier, see mail below. > > > 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") > > 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 = "testPkg", pkgPath = >myDir, organism = "human", version = "1.1.0", makeXML = TRUE, author = >list(author = "kees", maintainer = "kees@myemail.com"), fromWeb = TRUE) >[1] "It may take me a while to process the data. Be patient!" >Error in url(sourceURLs[["GO"]], open = "r") : > Object "sourceURLs" not found The bug has been fixed but not pushed to the release vresion yet. You may try > getSrcUrl("GO") before running your code. Let me know if this does not work for you. Thanks.

I'm running R 1.9.1 on mac OSX using AnnBuilder 1.4.2. When i try to build an annotation package using AnnBuilder i get an error using the following code: > myDir<-("/Data_analyse") > myBase<-file.path("GBbase.txt") > myBaseType<-"gb" ShowmyBase<-read.table("GBbase.txt") ShowmyBase[1:5,] V1 V2 1 91 NM_013184 2 92 NM_019255 3 93 NM_031055 4 94 AI236115 5 95 BI283260 > mySrcUrls LL "ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz" UG "ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.data.gz" GO "http://www.godatabase.org/dev/database/archive/2004-07-01/go_200407- termdb.xml.gz" KEGG "ftp://ftp.genome.ad.jp/pub/kegg/pathways" > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = + myBaseType, pkgName = "GOFloor", pkgPath=myDir, organism = "rat", version = "1.1.0", makeXML = F, author = + list(author = "fjstam", maintainer = "fjstam@bio.vu.nl"), fromWeb = TRUE) [1] "It may take me a while to process the data. Be patient!" Error in file(con, "r") : All connections are in use Error in ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, : Parsing LocusLink data failed because of: Error in file(con, "r") : All connections are in use The error happens after about half an hour of processing. Using the urls and base file from the Vignette (except for the GO url that i was reporting about yesterday), this code does produce a package. Can anyone tell me what's happening here? is there anything wrong with the source urls? the LL url points to an existing file on the ftp server but this file does not seem to contain rat information. If i point it to LL.out_rn.gz which does contain rat data then i get Error in file(file, "r") : All connections are in use after a few seconds. Running the scirpt (with the LL_tmpl.gz url), a huge textfile (>200MB) that ends with _tmpl is created in the temp subdir of the AnnBuilder package. This file contains lots of info per LL ID and starts with LLID 1 and goes on for ages. Also a perl file (? .pl ) is created. But no package. Floor _______________________________________________________ Floor Stam Vrije Universiteit Amsterdam Faculty of Earth and Life Sciences Department of Molecular and Cellular Neurobiology De Boelelaan 1085 1081HV Amsterdam The Netherlands Ph: +31-20-4447114 +31-20-5665512 Fax: +31-20-4447112 e-mail: fjstam@bio.vu.nl _______________________________________________________ On 7 Sep 2004 , at 12:29, Floor Stam wrote: > Hi > > I'd like to build an Annotation package for the (custom made rat) > array that i'm using. > > I'm running R 1.9.1 on mac osx and have an installation failure of > AnnBuilder 1.4.13 > I installed the devel versions of biobase and annotate as well, xml > 0.95-6 is also installed. > > install.from.file(pkg="/Users/fjstam/Desktop/AnnBuilder") > npackage installation failed > > If i go back to the current versions of annotate and biobase i get the > same error. > If i install AnnBuilder 1.4.2 i get it installed but then the same > thing happens that was reported earlier, see mail below. > > > 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") > > 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 = "testPkg", pkgPath = > myDir, organism = "human", version = "1.1.0", makeXML = TRUE, author > = list(author = "kees", maintainer = "kees@myemail.com"), fromWeb = > TRUE) > [1] "It may take me a while to process the data. Be patient!" > Error in url(sourceURLs[["GO"]], open = "r") : > Object "sourceURLs" not found > > So if i want the ABPkgBuilder to work, > -which version of AnnBuilder should i install? > -Should i upgrade any other package to devel or have everything at the > current level? > > Earlier this week i tried the code from the ABPkgPrimer vignette (see > mail below) in R 1.9.0, and then i got an error at the end, after my > computer had been thinking about things for a while, which said > something like: cannot parse rows and cannot open blabla.xml. The same > thing happened when i used the 'real' urls and my own base file (it's > just that it took my poor laptop an hour or so instead of a few > minutes to give the error message). I decided that going to R 1.9.1 > would probably solve my problem so i did not save the text from this > session, and can therefore not be more exact (i don't feel like going > back to R 1.9.0 unless it is really necessary). > > i hope anyone can help me with the installation and/or the source url > problem. > > When these things are fixed i will probably have the parsing/opening > xml problem again but we'll cross that bridge when we get there. > > floor > > _______________________________________________________ Floor Stam Vrije Universiteit Amsterdam Faculty of Earth and Life Sciences Department of Molecular and Cellular Neurobiology De Boelelaan 1085 1081HV Amsterdam The Netherlands Ph: +31-20-4447114 +31-20-5665512 Fax: +31-20-4447112 e-mail: fjstam@bio.vu.nl _______________________________________________________ > On 25 Aug 2004 , at 18:20, John Zhang wrote: > >> >>> I'm running R 1.9.1 on Windows 2000 and tried to test some of the >>> code in >>> the AnnBuilder (1.4.2) package from the vignette. >>> I'm encountering an error, which I'm not clear on how to fix. Code >>> and >>> error are copied below. Note that I've tried to run the same code on >>> Linux >>> (R version 1.9.0) and got the same error. >>> Any advice on this? >> >> I just noticed this bug and will have it fixed today. Thanks. >> >> >>> Thanks, >>> Elisabetta >>> >>> --- >>>> 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") >>>> ABPkgBuilder(baseName=myBase, srcUrls=mySrcUrls, >>>> baseMapType=myBaseType, >>> pkgName="myPkg", pkgPath="C:\tmp", organism="human", makeXML=F) >>> [1] "It may take me a while to process the data. Be patient!" >>> Error in url(sourceURLs[["GO"]], open = "r") : >>> Object "sourceURLs" not found >>> --- >>> >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

Could you start a new R and try the code again to see if the problem persists? >Mime-Version: 1.0 (Apple Message framework v619) >From: Floor Stam <fjstam@bio.vu.nl> >Subject: Re: [BioC] AnnBuilder/ABPkgBuilder: lots of Errors >Date: Wed, 8 Sep 2004 15:39:34 +0200 >To: "'bioconductor@stat.math.ethz.ch'" <bioconductor@stat.math.ethz.ch> >Received-SPF: none (hypatia: domain of bioconductor- bounces@stat.math.ethz.ch does not designate permitted sender hosts) >Received-SPF: none (hypatia: domain of fjstam@bio.vu.nl does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Content-Transfer-Encoding: 7bit >X-Content-Filtered-By: Mailman/MimeDel 2.1.5 >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> >X-Spam-Checker-Version: SpamAssassin 2.60-rc1 (1.197-2003-08-21-exp) on blaise.dfci.harvard.edu >X-Spam-Status: No, hits=0.0 required=5.0 tests=none autolearn=ham version=2.60-rc1 >X-Spam-Level: > >I'm running R 1.9.1 on mac OSX using AnnBuilder 1.4.2. >When i try to build an annotation package using AnnBuilder i get an >error using the following code: > > > myDir<-("/Data_analyse") > > myBase<-file.path("GBbase.txt") > > myBaseType<-"gb" > > >ShowmyBase<-read.table("GBbase.txt") >ShowmyBase[1:5,] > V1 V2 >1 91 NM_013184 >2 92 NM_019255 >3 93 NM_031055 >4 94 AI236115 >5 95 BI283260 > > > > mySrcUrls > > LL > >"ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz" > > UG > >"ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.data.gz" > > GO >"http://www.godatabase.org/dev/database/archive/2004-07-01/go_200407- >termdb.xml.gz" > > KEGG > >"ftp://ftp.genome.ad.jp/pub/kegg/pathways" > > > > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >+ myBaseType, pkgName = "GOFloor", pkgPath=myDir, organism = "rat", >version = "1.1.0", makeXML = F, author = >+ list(author = "fjstam", maintainer = "fjstam@bio.vu.nl"), fromWeb = >TRUE) >[1] "It may take me a while to process the data. Be patient!" >Error in file(con, "r") : All connections are in use >Error in ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, >baseMapType = myBaseType, : > Parsing LocusLink data failed because of: > > Error in file(con, "r") : All connections are in use > >The error happens after about half an hour of processing. Using the >urls and base file from the Vignette (except for the GO url that i was >reporting about yesterday), this code does produce a package. > >Can anyone tell me what's happening here? is there anything wrong with >the source urls? the LL url points to an existing file on the ftp >server but this file does not seem to contain rat information. If i >point it to LL.out_rn.gz which does contain rat data then i get > >Error in file(file, "r") : All connections are in use > >after a few seconds. > > >Running the scirpt (with the LL_tmpl.gz url), a huge textfile (>200MB) >that ends with _tmpl is created in the temp subdir of the AnnBuilder >package. This file contains lots of info per LL ID and starts with LLID >1 and goes on for ages. Also a perl file (? .pl ) is created. But no >package. > >Floor > >_______________________________________________________ >Floor Stam > >Vrije Universiteit Amsterdam >Faculty of Earth and Life Sciences >Department of Molecular and Cellular Neurobiology >De Boelelaan 1085 >1081HV Amsterdam >The Netherlands > >Ph: +31-20-4447114 > +31-20-5665512 >Fax: +31-20-4447112 >e-mail: fjstam@bio.vu.nl >_______________________________________________________ >On 7 Sep 2004 , at 12:29, Floor Stam wrote: > >> Hi >> >> I'd like to build an Annotation package for the (custom made rat) >> array that i'm using. >> >> I'm running R 1.9.1 on mac osx and have an installation failure of >> AnnBuilder 1.4.13 >> I installed the devel versions of biobase and annotate as well, xml >> 0.95-6 is also installed. >> >> install.from.file(pkg="/Users/fjstam/Desktop/AnnBuilder") >> npackage installation failed >> >> If i go back to the current versions of annotate and biobase i get the >> same error. >> If i install AnnBuilder 1.4.2 i get it installed but then the same >> thing happens that was reported earlier, see mail below. >> >> > 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") >> > 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 = "testPkg", pkgPath = >> myDir, organism = "human", version = "1.1.0", makeXML = TRUE, author >> = list(author = "kees", maintainer = "kees@myemail.com"), fromWeb = >> TRUE) >> [1] "It may take me a while to process the data. Be patient!" >> Error in url(sourceURLs[["GO"]], open = "r") : >> Object "sourceURLs" not found >> >> So if i want the ABPkgBuilder to work, >> -which version of AnnBuilder should i install? >> -Should i upgrade any other package to devel or have everything at the >> current level? >> >> Earlier this week i tried the code from the ABPkgPrimer vignette (see >> mail below) in R 1.9.0, and then i got an error at the end, after my >> computer had been thinking about things for a while, which said >> something like: cannot parse rows and cannot open blabla.xml. The same >> thing happened when i used the 'real' urls and my own base file (it's >> just that it took my poor laptop an hour or so instead of a few >> minutes to give the error message). I decided that going to R 1.9.1 >> would probably solve my problem so i did not save the text from this >> session, and can therefore not be more exact (i don't feel like going >> back to R 1.9.0 unless it is really necessary). >> >> i hope anyone can help me with the installation and/or the source url >> problem. >> >> When these things are fixed i will probably have the parsing/opening >> xml problem again but we'll cross that bridge when we get there. >> >> floor >> >> >_______________________________________________________ >Floor Stam > >Vrije Universiteit Amsterdam >Faculty of Earth and Life Sciences >Department of Molecular and Cellular Neurobiology >De Boelelaan 1085 >1081HV Amsterdam >The Netherlands > >Ph: +31-20-4447114 > +31-20-5665512 >Fax: +31-20-4447112 >e-mail: fjstam@bio.vu.nl >_______________________________________________________ >> On 25 Aug 2004 , at 18:20, John Zhang wrote: >> >>> >>>> I'm running R 1.9.1 on Windows 2000 and tried to test some of the >>>> code in >>>> the AnnBuilder (1.4.2) package from the vignette. >>>> I'm encountering an error, which I'm not clear on how to fix. Code >>>> and >>>> error are copied below. Note that I've tried to run the same code on >>>> Linux >>>> (R version 1.9.0) and got the same error. >>>> Any advice on this? >>> >>> I just noticed this bug and will have it fixed today. Thanks. >>> >>> >>>> Thanks, >>>> Elisabetta >>>> >>>> --- >>>>> 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") >>>>> ABPkgBuilder(baseName=myBase, srcUrls=mySrcUrls, >>>>> baseMapType=myBaseType, >>>> pkgName="myPkg", pkgPath="C:\tmp", organism="human", makeXML=F) >>>> [1] "It may take me a while to process the data. Be patient!" >>>> Error in url(sourceURLs[["GO"]], open = "r") : >>>> Object "sourceURLs" not found >>>> --- >>>> >>>> _______________________________________________ >>>> 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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > >_______________________________________________ >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