I have trouble running the AnnBuilder Vignette
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@richard-friedman-513
Last seen 7.1 years ago
Dear Bioconductor Users, I am trying to learn to use AnnBuilder in Bioconductor 1.5.0 under R2.0 under Windows XP Professional. Here is a transcript of my session: ################################################################### > library(XML) > library(AnnBuilder) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: annotate Warning message: 'addPDF2Vig' is deprecated. Use 'addVigs2WinMenu' instead. See help("Deprecated") > 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") > myBaseType <- "gb" > mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens") > mySrcUrls LL "ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz" GP "http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/" UG "ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz" GO "http://www.godatabase.org/dev/database/archive/2004-09-01/go_200409-t ermdb.xml.gz" KEGG "ftp://ftp.genome.ad.jp/pub/kegg/pathways" YG "http://www.yeastgenome.org/DownloadContents.shtml" HG "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp" > > myDir <- tempdir() > if(.Platform$OS.type != "windows" && interactive()){ + ABPkgBuilder(baseName = thgu95a, srcUrls = mySrcUrls, baseMapType = g, + pkgName = "myPkg", + pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", + makeXML = TRUE, author = list(author = "RichardFriedman", maintainer = + "friedman@cancercenter.columbia.edu"), fromWeb = TRUE) + } > ls() [1] "last.warning" "myBase" "myBaseType" "myDir" "mySrcUrls" "sourceURLs" > if(.Platform$OS.type != "windows" && interactive()){ + list.files(file.path(myDir, "myPkg")) + list.files(file.path(myDir, "myPkg", "data")) + list.files(file.path(myDir, "myPkg", "man")) + list.files(file.path(myDir, "myPkg", "R")) + } > > > list.files(file.path(myDir, "myPkg")) Warning: list.files: C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg is not a readable directory character(0) > list.files(file.path(myDir, "myPkg", "data")) Warning: list.files: C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg/data is not a readable directory character(0) ###################################################################### ######## Apparently the package was not created. Am I correct in this? If the package was created, how can I access it? If the package was not created, how can I create it? Thanks and best wieshes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "That was written by Felix Mendelsohn? Did he start Mendelsohn's Pizza?" -Rose Friedman, age 8
Cancer Organism AnnBuilder Cancer Organism AnnBuilder • 823 views
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John Zhang ★ 2.9k
@john-zhang-6
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The files were certainly not created since the code did not get to run under Windows. You have to remove "if(.Platform$OS.type != "windows" && interactive()){" when you rn ABPkgBuilder(...). Since human interference is required to finish the vignette, I have to put the checking there to make the vignette pass the building process under Windows. >Date: Wed, 10 Nov 2004 15:22:23 -0500 (EST) >From: Richard Friedman <friedman@cancercenter.columbia.edu> >To: bioconductor@stat.math.ethz.ch >MIME-Version: 1.0 >Received-SPF: none (hypatia: domain of bioconductor- bounces@stat.math.ethz.ch does not designate permitted sender hosts) >Received-SPF: none (hypatia: domain of friedman@cancercenter.columbia.edu does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] I have trouble running the AnnBuilder Vignette >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: > >Dear Bioconductor Users, > > I am trying to learn to use AnnBuilder in Bioconductor 1.5.0 >under R2.0 under Windows XP Professional. Here is a transcript >of my session: >################################################################### >> library(XML) >> library(AnnBuilder) >Loading required package: Biobase >Loading required package: tools >Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. >Loading required package: annotate >Warning message: >'addPDF2Vig' is deprecated. >Use 'addVigs2WinMenu' instead. >See help("Deprecated") >> 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") >> myBaseType <- "gb" >> mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens") >> mySrcUrls > >LL > >"ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz" > >GP > >"http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/" > >UG > >"ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz" > >GO >"http://www.godatabase.org/dev/database/archive/2004-09-01/go_200409- termdb.xml .gz" > >KEGG > >"ftp://ftp.genome.ad.jp/pub/kegg/pathways" > >YG > >"http://www.yeastgenome.org/DownloadContents.shtml" > >HG > >"ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp" >> >> myDir <- tempdir() >> if(.Platform$OS.type != "windows" && interactive()){ >+ ABPkgBuilder(baseName = thgu95a, srcUrls = mySrcUrls, >baseMapType = g, >+ pkgName = "myPkg", >+ pkgPath = myDir, organism = "Homo sapiens", version = >"1.1.0", >+ makeXML = TRUE, author = list(author = "RichardFriedman", >maintainer = >+ "friedman@cancercenter.columbia.edu"), >fromWeb = TRUE) >+ } >> ls() >[1] "last.warning" "myBase" "myBaseType" "myDir" >"mySrcUrls" "sourceURLs" >> if(.Platform$OS.type != "windows" && interactive()){ >+ list.files(file.path(myDir, "myPkg")) >+ list.files(file.path(myDir, "myPkg", "data")) >+ list.files(file.path(myDir, "myPkg", "man")) >+ list.files(file.path(myDir, "myPkg", "R")) >+ } >> >> >> list.files(file.path(myDir, "myPkg")) >Warning: list.files: C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg is >not a readable directory >character(0) >> list.files(file.path(myDir, "myPkg", "data")) >Warning: list.files: >C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg/data is not a readable >directory >character(0) >##################################################################### ######### > >Apparently the package was not created. >Am I correct in this? >If the package was created, how can I access it? >If the package was not created, how can I create it? > >Thanks and best wieshes, >Rich >------------------------------------------------------------ >Richard A. Friedman, PhD >Associate Research Scientist >Herbert Irving Comprehensive Cancer Center >Oncoinformatics Core >Lecturer >Department of Biomedical Informatics >Box 95, Room 130BB or P&S 1-420C >Columbia University Medical Center >630 W. 168th St. >New York, NY 10032 >(212)305-6901 (5-6901) (voice) >friedman@cancercenter.columbia.edu >http://cancercenter.columbia.edu/~friedman/ > >"That was written by Felix Mendelsohn? >Did he start Mendelsohn's Pizza?" >-Rose Friedman, age 8 > >_______________________________________________ >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
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Dear John (and Everyone), Thank you very much for your quick reply. I tried what you said, but I got a warrning and an error message but I still can't reachthe object. The warning was that gzip was not found. The error was Error in parseKEGGGenome() : Faild to obtain KEGG organism code I got a list of entries in AnnInfo but could not find the files: Here is what I did: ###################################################################### ##### > ABPkgBuilder(baseName = "thgu95a", srcUrls = mySrcUrls, baseMapType = "gb", + pkgName = "myPkg", + pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", + makeXML = TRUE, author = list(author = "RichardFriedman", maintainer = + "friedman@cancercenter.columbia.edu"), fromWeb = TRUE) Warning: gzip not found Warning: gzip not found Error in parseKEGGGenome() : Faild to obtain KEGG organism code > > ls() [1] "AnnInfo" "last.warning" "myBase" "myBaseType" "myDir" "mySrcUrls" [7] "sourceURLs" > library(gzip) Error in library(gzip) : There is no package called 'gzip' > ls(AnnInfo) [1] "#CHRNUM#END" "#CHRNUM#START" "#CHROMSEQ#" "#EXON#" "#HGID2GB#" [6] "#HGID2HGID#" "#HGID2LL#" "#HGID2PS#" "#HOMODATA#" "#ONETOMANYMAN#" [11] "#ONETOONEMAN#" "#REPLACEME#" "#SEQUENCE#" "ACCNUM" "AFFY" [16] "ALIAS" "AnnInfo" "ASSOCIATION" "BPANCESTOR" "BPCHILDREN" [21] "BPID2TERM" "BPOFFSPRING" "BPPARENTS" "CATEGORY" "CCANCESTOR" [26] "CCCHILDREN" "CCID2TERM" "CCOFFSPRING" "CCPARENTS" "CHR" [31] "CHRLENGTHS" "CHRLOC" "CHRORI" "CURRENTLOCUSID" "CYTOLOC" [36] "DESCRIPTION" "ENZYME" "ENZYME2PROBE" "ENZYMEID2GO" "ENZYMEID2NAME" [41] "EXTID2PATHID" "GENENAME" "GO" "GO2ALLLL" "GO2ALLPROBES" [46] "GO2ENZYMEID" "GO2EVIDENCE" "GO2LL" "GO2PROBE" "GRIF" [51] "HGID" "IMAGE" "LL2GO" "LL2HGID" "LOCUSID" [56] "LOCUSID2CHR" "LOCUSTYPE" "MAP" "MFANCESTOR" "MFCHILDREN" [61] "MFID2TERM" "MFOFFSPRING" "MFPARENTS" "NC" "NG" [66] "NM" "NP" "OMIM" "ONTOLOGY" "ORF" [71] "ORGANISM" "ORGCODE" "PATH" "PATH2PROBE" "PATHID2EXTID" [76] "PATHID2NAME" "PATHNAME2ID" "PMID" "PMID2PROBE" "PROBE" [81] "PROBECOUNTS" "PRODUCT" "REFSEQ" "SUMFUNC" "SUMMARY" [86] "SYMBOL" "TERM" "UNIGENE" > list.files(file.path(myDir, "myPkg")) Warning: list.files: C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg is not a readable directory character(0) > list.files(file.path(myDir, "myPkg", "data")) Warning: list.files: C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg/data is not a readable directory character(0) > ###################################################################### ####### I would appreciate any suggestion that you might have about building the annotation files. Best wishes. Rich On Wed, 10 Nov 2004, John Zhang wrote: > The files were certainly not created since the code did not get to run under > Windows. You have to remove "if(.Platform$OS.type != "windows" && > interactive()){" when you rn ABPkgBuilder(...). Since human interference is > required to finish the vignette, I have to put the checking there to make the > vignette pass the building process under Windows. > > > >Date: Wed, 10 Nov 2004 15:22:23 -0500 (EST) > >From: Richard Friedman <friedman@cancercenter.columbia.edu> > >To: bioconductor@stat.math.ethz.ch > >MIME-Version: 1.0 > >Received-SPF: none (hypatia: domain of bioconductor- bounces@stat.math.ethz.ch > does not designate permitted sender hosts) > >Received-SPF: none (hypatia: domain of friedman@cancercenter.columbia.edu does > not designate permitted sender hosts) > >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch > >Subject: [BioC] I have trouble running the AnnBuilder Vignette > >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: > > > >Dear Bioconductor Users, > > > > I am trying to learn to use AnnBuilder in Bioconductor 1.5.0 > >under R2.0 under Windows XP Professional. Here is a transcript > >of my session: > >################################################################### > >> library(XML) > >> library(AnnBuilder) > >Loading required package: Biobase > >Loading required package: tools > >Welcome to Bioconductor > > Vignettes contain introductory material. To view, > > simply type: openVignette() > > For details on reading vignettes, see > > the openVignette help page. > >Loading required package: annotate > >Warning message: > >'addPDF2Vig' is deprecated. > >Use 'addVigs2WinMenu' instead. > >See help("Deprecated") > >> 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") > >> myBaseType <- "gb" > >> mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens") > >> mySrcUrls > > > >LL > > > >"ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz" > > > >GP > > > >"http://hgdownload.cse.ucsc.edu/goldenPath/hg17/database/" > > > >UG > > > >"ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz" > > > >GO > >"http://www.godatabase.org/dev/database/archive/2004-09-01/go_20040 9-termdb.xml > .gz" > > > >KEGG > > > >"ftp://ftp.genome.ad.jp/pub/kegg/pathways" > > > >YG > > > >"http://www.yeastgenome.org/DownloadContents.shtml" > > > >HG > > > >"ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp" > >> > >> myDir <- tempdir() > >> if(.Platform$OS.type != "windows" && interactive()){ > >+ ABPkgBuilder(baseName = thgu95a, srcUrls = mySrcUrls, > >baseMapType = g, > >+ pkgName = "myPkg", > >+ pkgPath = myDir, organism = "Homo sapiens", version = > >"1.1.0", > >+ makeXML = TRUE, author = list(author = "RichardFriedman", > >maintainer = > >+ "friedman@cancercenter.columbia.edu"), > >fromWeb = TRUE) > >+ } > >> ls() > >[1] "last.warning" "myBase" "myBaseType" "myDir" > >"mySrcUrls" "sourceURLs" > >> if(.Platform$OS.type != "windows" && interactive()){ > >+ list.files(file.path(myDir, "myPkg")) > >+ list.files(file.path(myDir, "myPkg", "data")) > >+ list.files(file.path(myDir, "myPkg", "man")) > >+ list.files(file.path(myDir, "myPkg", "R")) > >+ } > >> > >> > >> list.files(file.path(myDir, "myPkg")) > >Warning: list.files: C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg is > >not a readable directory > >character(0) > >> list.files(file.path(myDir, "myPkg", "data")) > >Warning: list.files: > >C:\DOCUME~1\Richard\LOCALS~1\Temp\Rtmp30648/myPkg/data is not a readable > >directory > >character(0) > >################################################################### ########### > > > >Apparently the package was not created. > >Am I correct in this? > >If the package was created, how can I access it? > >If the package was not created, how can I create it? > > > >Thanks and best wieshes, > >Rich > >------------------------------------------------------------ > >Richard A. Friedman, PhD > >Associate Research Scientist > >Herbert Irving Comprehensive Cancer Center > >Oncoinformatics Core > >Lecturer > >Department of Biomedical Informatics > >Box 95, Room 130BB or P&S 1-420C > >Columbia University Medical Center > >630 W. 168th St. > >New York, NY 10032 > >(212)305-6901 (5-6901) (voice) > >friedman@cancercenter.columbia.edu > >http://cancercenter.columbia.edu/~friedman/ > > > >"That was written by Felix Mendelsohn? > >Did he start Mendelsohn's Pizza?" > >-Rose Friedman, age 8 > > > >_______________________________________________ > >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 > > ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "That was written by Felix Mendelsohn? Did he start Mendelsohn's Pizza?" -Rose Friedman, age 8
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Richard Friedman wrote: > Dear John (and Everyone), > > Thank you very much for your quick reply. I tried what you said, > but I got a warrning and an error message but I still can't reachthe > object. The warning was that gzip was not found. > The error was Error in parseKEGGGenome() : Faild to obtain KEGG organism > code You need to download the tool set found here (http://www.murdoch-sutherland.com/Rtools/tools.zip ) and make sure that you add the directory where you place the tools to your PATH variable, preferably before your windows folder. In other words, download the tools, unzip in e.g., C:\Rtools, and then add this to your PATH by right clicking My Computer --> Properties/Advanced/Environment Variables/System variables. Click on the path variable, then the edit button and add C:\Rtools. As an example, my PATH looks like this: .;C:\Perl\bin\;C:\Rtools;C:\Program Files\TeXLive\bin\win32;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\Syst em32\Wbem;c:\mingw\bin;C:\Program Files\HTML Help Workshop;C:\Program Files\GNU\WinCvs 1.3\CVSNT;C:\Program Files\PuTTY;C:\RW1091\bin;C:\Program Files\Subversion\bin Note that C:\Rtools comes *before* C:\WINDOWS HTH, Jim -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
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Dear Jim (and John and Everybody): What you wrote helps considerably. I have another question before I proceed. In your note below, the second entry in the path file is C:\Perl\bin\ The AnnBuilder documentation states thatit requires Perl to run. The only Perl I have on my PC is C:\Documents and Settings\Richard\Local Settings\Temp\R-2.0.0\share\perl Is this sufficient, or do I have to download Perl and place it in a directory for AnnBuilder to run? Thanks and best wishes, Rich On Thu, 11 Nov 2004, James W. MacDonald wrote: > Richard Friedman wrote: > > Dear John (and Everyone), > > > > Thank you very much for your quick reply. I tried what you said, > > but I got a warrning and an error message but I still can't reachthe > > object. The warning was that gzip was not found. > > The error was Error in parseKEGGGenome() : Faild to obtain KEGG organism > > code > You need to download the tool set found here > (http://www.murdoch-sutherland.com/Rtools/tools.zip ) and make sure that > you add the directory where you place the tools to your PATH variable, > preferably before your windows folder. > > In other words, download the tools, unzip in e.g., C:\Rtools, and then > add this to your PATH by right clicking My Computer --> > Properties/Advanced/Environment Variables/System variables. Click on the > path variable, then the edit button and add C:\Rtools. As an example, my > PATH looks like this: > > .;C:\Perl\bin\;C:\Rtools;C:\Program > Files\TeXLive\bin\win32;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\Sy stem32\Wbem;c:\mingw\bin;C:\Program > Files\HTML Help Workshop;C:\Program Files\GNU\WinCvs > 1.3\CVSNT;C:\Program Files\PuTTY;C:\RW1091\bin;C:\Program > Files\Subversion\bin > > Note that C:\Rtools comes *before* C:\WINDOWS > > HTH, > > Jim > > > -- > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "That was written by Felix Mendelsohn? Did he start Mendelsohn's Pizza?" -Rose Friedman, age 8
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I have the ActiveState perl port, which is what you need to build R libraries from source. If that is what you have then you should be alright. Note that your path should point to the bin directory of your perl installation. Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Richard Friedman <friedman@cancercenter.columbia.edu> 11/11/04 4:57 PM >>> Dear Jim (and John and Everybody): What you wrote helps considerably. I have another question before I proceed. In your note below, the second entry in the path file is C:\Perl\bin\ The AnnBuilder documentation states thatit requires Perl to run. The only Perl I have on my PC is C:\Documents and Settings\Richard\Local Settings\Temp\R-2.0.0\share\perl Is this sufficient, or do I have to download Perl and place it in a directory for AnnBuilder to run? Thanks and best wishes, Rich On Thu, 11 Nov 2004, James W. MacDonald wrote: > Richard Friedman wrote: > > Dear John (and Everyone), > > > > Thank you very much for your quick reply. I tried what you said, > > but I got a warrning and an error message but I still can't reachthe > > object. The warning was that gzip was not found. > > The error was Error in parseKEGGGenome() : Faild to obtain KEGG organism > > code > You need to download the tool set found here > (http://www.murdoch-sutherland.com/Rtools/tools.zip ) and make sure that > you add the directory where you place the tools to your PATH variable, > preferably before your windows folder. > > In other words, download the tools, unzip in e.g., C:\Rtools, and then > add this to your PATH by right clicking My Computer --> > Properties/Advanced/Environment Variables/System variables. Click on the > path variable, then the edit button and add C:\Rtools. As an example, my > PATH looks like this: > > .;C:\Perl\bin\;C:\Rtools;C:\Program > Files\TeXLive\bin\win32;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\Syst em32\Wbem;c:\mingw\bin;C:\Program > Files\HTML Help Workshop;C:\Program Files\GNU\WinCvs > 1.3\CVSNT;C:\Program Files\PuTTY;C:\RW1091\bin;C:\Program > Files\Subversion\bin > > Note that C:\Rtools comes *before* C:\WINDOWS > > HTH, > > Jim > > > -- > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "That was written by Felix Mendelsohn? Did he start Mendelsohn's Pizza?" -Rose Friedman, age 8 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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@richard-friedman-513
Last seen 7.1 years ago
Jim, How do I know if I have that. Otherwise where do I get it? Thanks and best wishes, Rich On Nov 11, 2004, at 7:08 PM, James MacDonald wrote: > I have the ActiveState perl port, which is what you need to build R > libraries from source. If that is what you have then you should be > alright. Note that your path should point to the bin directory of your > perl installation. > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 >>>> Richard Friedman <friedman@cancercenter.columbia.edu> 11/11/04 4:57 > PM >>> > Dear Jim (and John and Everybody): > > > What you wrote helps considerably. I have another question > before > I proceed. In your note below, the second entry in the path file is > > C:\Perl\bin\ > > The AnnBuilder documentation states thatit requires Perl to run. > The only Perl I have on my PC is > C:\Documents and Settings\Richard\Local > Settings\Temp\R-2.0.0\share\perl > > Is this sufficient, or do I have to download Perl and place it in a > directory for AnnBuilder to run? > > > Thanks and best wishes, > Rich > > > On Thu, 11 Nov 2004, James W. MacDonald wrote: > >> Richard Friedman wrote: >>> Dear John (and Everyone), >>> >>> Thank you very much for your quick reply. I tried what you said, >>> but I got a warrning and an error message but I still can't reachthe >>> object. The warning was that gzip was not found. >>> The error was Error in parseKEGGGenome() : Faild to obtain KEGG > organism >>> code >> You need to download the tool set found here >> (http://www.murdoch-sutherland.com/Rtools/tools.zip ) and make sure > that >> you add the directory where you place the tools to your PATH variable, >> preferably before your windows folder. >> >> In other words, download the tools, unzip in e.g., C:\Rtools, and then >> add this to your PATH by right clicking My Computer --> >> Properties/Advanced/Environment Variables/System variables. Click on > the >> path variable, then the edit button and add C:\Rtools. As an example, > my >> PATH looks like this: >> >> .;C:\Perl\bin\;C:\Rtools;C:\Program >> > Files\TeXLive\bin\win32;C:\WINDOWS\system32;C:\WINDOWS;C: > \WINDOWS\System32\Wbem;c:\mingw\bin;C:\Program >> Files\HTML Help Workshop;C:\Program Files\GNU\WinCvs >> 1.3\CVSNT;C:\Program Files\PuTTY;C:\RW1091\bin;C:\Program >> Files\Subversion\bin >> >> Note that C:\Rtools comes *before* C:\WINDOWS >> >> HTH, >> >> Jim >> >> >> -- >> James W. MacDonald >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> > > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist > Herbert Irving Comprehensive Cancer Center > Oncoinformatics Core > Lecturer > Department of Biomedical Informatics > Box 95, Room 130BB or P&S 1-420C > Columbia University Medical Center > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) > friedman@cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "That was written by Felix Mendelsohn? > Did he start Mendelsohn's Pizza?" > -Rose Friedman, age 8 > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues. > > ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "That was written by Felix Mendelsohn? Did he start Mendelsohn's Pizza?" -RoseFriedman, age 8
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@james-w-macdonald-5106
Last seen 17 hours ago
United States
If I type perl --version at a command prompt, I get the following This is perl, v5.8.2 built for MSWin32-x86-multi-thread (with 25 registered patches, see perl -V for more detail) Copyright 1987-2003, Larry Wall Binary build 808 provided by ActiveState Corp. http://www.ActiveState.com ActiveState is a division of Sophos. Built Dec 9 2003 10:19:40 Perl may be copied only under the terms of either the Artistic License or the GNU General Public License, which may be found in the Perl 5 source kit. Complete documentation for Perl, including FAQ lists, should be found on this system using `man perl' or `perldoc perl'. If you have access to the Internet, point your browser at http://www.perl.com/, the Perl Home Page. As noted in the version information, you can get this port of perl at www.activestate.com. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Richard Friedman <friedman@cancercenter.columbia.edu> 11/15/04 4:48 PM >>> Jim, How do I know if I have that. Otherwise where do I get it? Thanks and best wishes, Rich On Nov 11, 2004, at 7:08 PM, James MacDonald wrote: > I have the ActiveState perl port, which is what you need to build R > libraries from source. If that is what you have then you should be > alright. Note that your path should point to the bin directory of your > perl installation. > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 >>>> Richard Friedman <friedman@cancercenter.columbia.edu> 11/11/04 4:57 > PM >>> > Dear Jim (and John and Everybody): > > > What you wrote helps considerably. I have another question > before > I proceed. In your note below, the second entry in the path file is > > C:\Perl\bin\ > > The AnnBuilder documentation states thatit requires Perl to run. > The only Perl I have on my PC is > C:\Documents and Settings\Richard\Local > Settings\Temp\R-2.0.0\share\perl > > Is this sufficient, or do I have to download Perl and place it in a > directory for AnnBuilder to run? > > > Thanks and best wishes, > Rich > > > On Thu, 11 Nov 2004, James W. MacDonald wrote: > >> Richard Friedman wrote: >>> Dear John (and Everyone), >>> >>> Thank you very much for your quick reply. I tried what you said, >>> but I got a warrning and an error message but I still can't reachthe >>> object. The warning was that gzip was not found. >>> The error was Error in parseKEGGGenome() : Faild to obtain KEGG > organism >>> code >> You need to download the tool set found here >> (http://www.murdoch-sutherland.com/Rtools/tools.zip ) and make sure > that >> you add the directory where you place the tools to your PATH variable, >> preferably before your windows folder. >> >> In other words, download the tools, unzip in e.g., C:\Rtools, and then >> add this to your PATH by right clicking My Computer --> >> Properties/Advanced/Environment Variables/System variables. Click on > the >> path variable, then the edit button and add C:\Rtools. As an example, > my >> PATH looks like this: >> >> .;C:\Perl\bin\;C:\Rtools;C:\Program >> > Files\TeXLive\bin\win32;C:\WINDOWS\system32;C:\WINDOWS;C: > \WINDOWS\System32\Wbem;c:\mingw\bin;C:\Program >> Files\HTML Help Workshop;C:\Program Files\GNU\WinCvs >> 1.3\CVSNT;C:\Program Files\PuTTY;C:\RW1091\bin;C:\Program >> Files\Subversion\bin >> >> Note that C:\Rtools comes *before* C:\WINDOWS >> >> HTH, >> >> Jim >> >> >> -- >> James W. MacDonald >> Affymetrix and cDNA Microarray Core >> University of Michigan Cancer Center >> 1500 E. Medical Center Drive >> 7410 CCGC >> Ann Arbor MI 48109 >> > > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist > Herbert Irving Comprehensive Cancer Center > Oncoinformatics Core > Lecturer > Department of Biomedical Informatics > Box 95, Room 130BB or P&S 1-420C > Columbia University Medical Center > 630 W. 168th St. > New York, NY 10032 > (212)305-6901 (5-6901) (voice) > friedman@cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > "That was written by Felix Mendelsohn? > Did he start Mendelsohn's Pizza?" > -Rose Friedman, age 8 > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues. > > ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Oncoinformatics Core Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman@cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "That was written by Felix Mendelsohn? Did he start Mendelsohn's Pizza?" -RoseFriedman, age 8 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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