Hi John Just getting back to AnnBuilder after vacation. 1.6.8.5 worked like a champ on Linux with ABPkgBuilder. But I need/would prefer the package on a windows xp system. When I tried the same process on XP, ABPkgBuilder dies complaining about not finding a temp file. I think it may be related to the parser/perl based on the information below. ActiveState Perl v5.8.7 is installed, in the path and runs. Can you offer any suggestions as to why this might be failing and how to proceed? Thanks Barry After AnnPkgBuilder failed I tried to manually build the package on XP based on code derived from the vignette. The srcfiles download and unzip ok. But when I call parseData on the EG object it fails with the same error I get with ABPkgBuilder: > llMapping <- parseData(eg, eg at accession) + Error in file(file, "r") : unable to open connection + In addition: Warning message: + cannot open file + 'C:/PROGRA~1/R/RW2011~1/library/AnnBuilder/temp/tempOut24672' The above command downloads gene2accession.gz, launches a cmd window and unzips the archive, then launches another cmd window and exits. The final cmd window closes so fast I can not see what is returned. SessionInfo, full code/errors, traceback and debug runs are pasted below. > sessionInfo() R version 2.1.1, 2005-07-31, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: GO AnnBuilder annotate XML Biobase "1.8.2" "1.6.8-5" "1.5.16" "0.97-7" "1.5.12" > ##################################Beginning of Code block > datadir <- "c:\\rc2\\curren~1\\RCAnno~1" > setwd(datadir) > 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: XML Loading required package: annotate > # > # > # First create a text file called baseName with two columns > # col1 = ProbeID > # col2 = GB > # > # call that file RC2baseName.txt# > # > # > # Actually, first is to download the XML package from cran.r-project.org > # and install into windows R > # > ###################################################################### ## #### > > myBase <- file.path(datadir, "RC2baseName.txt") > myDir <- datadir > showmyBase <- read.table(myBase) > myBaseType="gbNRef" > mySrcUrls <- getSrcUrl("all", "Homo sapiens") # ############Predownloaded src files to speed the process # > mySrcUrls["EG"] <- "ftp://192.168.0.4/pub/data/" > mySrcUrls["UG"] <- "ftp://192.168.0.4/pub/data/Hs.data.gz" > mySrcUrls["HG"] <- "ftp://192.168.0.4/pub/data/hmlg.ftp" > mySrcUrls["GO"] <- "ftp://192.168.0.4/pub/data/go_200507-termdb.rdf-xml" > baseName = myBase > srcUrls = mySrcUrls > baseMapType = myBaseType > pkgName = "hsRCv2" > pkgPath = datadir > organism = "Homo sapiens" > version = "1.0.0" > author = list(author = "Barry Henderson", maintainer = "barry.henderson at ribonomics.com") > fromWeb = TRUE > otherSrc = NULL > pkgpath <- .find.package("AnnBuilder") > # Begin disecting BPPkgBuilder > > require("GO", quietly = TRUE) || stop("GO is needed to build data package") Attaching package: 'GO' The following object(s) are masked from package:AnnBuilder : GO [1] TRUE > > makeSrcInfo() > srcObjs <- list() > eg <- EG(srcUrl = mySrcUrls["EG"], parser = file.path(pkgpath, "scripts", + "gbLLParser"), baseFile = baseName, accession = "gene2accession.gz", + built = "N/A", fromWeb = TRUE) > ug <- UG(srcUrl = mySrcUrls["UG"], parser = file.path(pkgpath, + "scripts", "gbUGParser"), baseFile = baseName, + organism = "Homo sapiens", built = "N/A", fromWeb = TRUE) > > srcObjs[["eg"]] <- eg > srcObjs[["ug"]] <- ug > > llMapping <- parseData(eg, eg at accession) Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file 'C:/PROGRA~1/R/RW2011~1/library/AnnBuilder/temp/tempOut12498' > traceback() 7: file(file, "r") 6: scan(fileMuncher(tempOut, baseFile(object), srcData, parser(object)), what = "character", sep = sep, quote = "", quiet = TRUE, strip.white = TRUE, comment.char = "") 5: as.vector(data) 4: matrix(scan(fileMuncher(tempOut, baseFile(object), srcData, parser(object)), what = "character", sep = sep, quote = "", quiet = TRUE, strip.white = TRUE, comment.char = ""), ncol = ncol, byrow = TRUE) 3: .local(object, ...) 2: parseData(eg, eg at accession) 1: parseData(eg, eg at accession) > ?fileMuncher > debug(parseData) > llMapping <- parseData(eg, eg at accession) debugging in: parseData(eg, eg at accession) debug: standardGeneric("parseData") Browse[1]> Error in file(file, "r") : unable to open connection In addition: Warning message: cannot open file 'C:/PROGRA~1/R/RW2011~1/library/AnnBuilder/temp/tempOut4328' -----Original Message----- From: John Zhang [mailto:jzhang@jimmy.harvard.edu] Sent: Friday, August 05, 2005 9:43 AM To: Barry Henderson Subject: RE: [BioC] ABPkgBuilder Error; Hi Barry, 1.6.8-4 should work for Linux but did have problems for Windows. I have fixed the bug and am attaching both the zip and gz files. I have tested the code under both platforms. John >I installed the version you sent me on the linux system. Same error. > >From the web site: > >Package: AnnBuilder > > >Description: Processing annotation date from public data repositories >and building annoation data packages or XML data documents using the source data. >Version: 1.6.8-4 >Author: J. Zhang >Maintainer: J. Zhang >Dependencies: R (>= 2.1.0), methods, Biobase, XML, annotate, utils >Suggests: None >SystemRequirements: None >License: LGPL >URL: None available > > > > -----Original Message----- > From: John Zhang [mailto:jzhang at jimmy.harvard.edu] > Sent: Thu 8/4/2005 10:38 AM > To: jzhang at jimmy.harvard.edu; bioconductor at stat.math.ethz.ch; Barry Henderson > Cc: > Subject: RE: [BioC] ABPkgBuilder Error; > > > > > >I installed 1.6.8-4 listed on the developers page form bioconductor (I > >just re-downloaded and re-installed it to make sure). The session info > >there is: > > 1.6.8-4 is not even available from the web and this still gives you 1.6.8 as > shown below. That was why I sent you the package I built. > > > > > >R version 2.1.1, 2005-07-31, i386-pc-mingw32 > > > >attached base packages: > >[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > > > >[7] "datasets" "base" > > > >other attached packages: > >AnnBuilder annotate XML Biobase > > "1.6.8" "1.5.16" "0.97-7" "1.5.12" > > > >Note that there were a couple of warnings on windows installation: > > > >>package 'AnnBuilder' successfully unpacked and MD5 sums checked > >>updating HTML package descriptions > >>Warning messages: > >>1: no package 'file15700' was found in: packageDescription(i, fields = > >"Title", lib.loc = lib) > >>2: no package 'file27003' was found in: packageDescription(i, fields = > >"Title", lib.loc = lib) > > > > > > > >-----Original Message----- > >From: John Zhang [mailto:jzhang at jimmy.harvard.edu] > >Sent: Thursday, August 04, 2005 7:57 AM > >To: jzhang at jimmy.harvard.edu; bioconductor at stat.math.ethz.ch; Barry > >Henderson > >Subject: Re: [BioC] ABPkgBuilder Error; > > > > > >Are you sure you have installed AnnBuilder 1.6.8-4 as your sessionInfo > >still > >showed 1.6.8? > > > > > > > >>John et al. > >> > >>I tried AnnBuilder 1.6.8-4 and it solved the "invalid class.." error > >>but it still fails building the package. Results from windows install > >>is below (same results on linux): > >> > >>> 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: XML > >>Loading required package: annotate > >>Warning message: > >>package 'AnnBuilder' was built under R version 2.2.0 > >>> myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") > >>> datadir <- "c:/rc2/curren~1/RCAnno~1" myDir <- tempdir() > >>> myOtherSrc <- c(srcone = file.path(.path.package("AnnBuilder"), > >>"data", "srca"), srctwo = file.path(.path.package("AnnBuilder"), > >>"data", > >>"srcb")) > >>> myBaseType="gb" > >>> mySrcUrls <- getSrcUrl("all", "Homo sapiens") >ABPkgBuilder(baseName = > > > >>> myBase, srcUrls = mySrcUrls, baseMapType = > >>myBaseType, > >>+ pkgName = "hsRiboChipv2", pkgPath = datadir, organism = "Homo > >>sapiens", > >>+ version = "1.0.0", > >>+ author = list(author = "Barry Henderson", maintainer = > >>"barry.henderson at ribonomics.com"), > >>+ fromWeb = TRUE) > >> > >>Attaching package: 'GO' > >> > >> > >> The following object(s) are masked from package:AnnBuilder : > >> > >> GO > >> > >>Error in if is.na(built) || is.null(built) || built == "") { : > >> missing value where TRUE/FALSE needed > >>In addition: Warning message: > >>data length [932] is not a sub-multiple or multiple of the number of > >>rows [311] in matrix > >>> sessionInfo() > >>R version 2.1.1, 2005-07-31, i386-pc-mingw32 > >> > >>attached base packages: > >>[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" > >>"datasets" > >>[8] "base" > >> > >>other attached packages: > >> GO AnnBuilder annotate XML Biobase > >> "1.8.2" "1.6.8" "1.5.16" "0.97-7" "1.5.12" > >>> > >> > >> > >> > >> > >>-----Original Message----- > >>From: John Zhang [mailto:jzhang at jimmy.harvard.edu] > >>Sent: Wednesday, August 03, 2005 11:36 AM > >>To: bioconductor at stat.math.ethz.ch; Barry Henderson > >>Subject: Re: [BioC] ABPkgBuilder Error; > >> > >> > >> > >>>>Error in validObject(.Object) : invalid class "GO" object: invalid > >>>object for slot "srcUrl" in class "GO": got class "list", should be or > >>>extend class "character" > >> > >>The return of getOption("AnnBuilderSourceUrls") does not work too well > >>with ABPkgBuilder. Using getSrcUrl("all", "Homo sapiens") for srcUrls > >>solves the > >>problem. However, KEGG changed some of the web pages that caused the > >>code to > >>fail. I have fixed the problem and will check in the fixes. It may take > >>a few > >>days for the revised version to be available though. > >> > >>> > >>>System: > >>> > >>>Windows XP > >>>R 2.1.1 > >>>Current release of BioC packages (downloaded via getBioC yesterday) > >>> > >>>Any ideas? > >>> > >>>Thanks > >>>Barry > >>> > >>> [[alternative HTML version deleted]] > >>> > >>>_______________________________________________ > >>>Bioconductor mailing list > >>>Bioconductor at stat.math.ethz.ch > >>>https://stat.ethz.ch/mailman/listinfo/bioconductor > >> > >>Jianhua Zhang > >>Department of Medical Oncology > >>Dana-Farber Cancer Institute > >>44 Binney Street > >>Boston, MA 02115-6084 > >> > >>_______________________________________________ > >>Bioconductor mailing list > >>Bioconductor at stat.math.ethz.ch > >>https://stat.ethz.ch/mailman/listinfo/bioconductor > > > >Jianhua Zhang > >Department of Medical Oncology > >Dana-Farber Cancer Institute > >44 Binney Street > >Boston, MA 02115-6084 > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > > > Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084