Hi everyone, I'm trying to rebuild my annotation package for an Agilent chip using Resourcerer and it's not finder one of the parsers. The basic error is: >resourcerer2BioC("Agilent_HumanGenome.zip", organism="human") Warning: cannot open file `NA' Warning in unifyMappings(base, eg, ug, otherSrc) : Failed to get or parse Entrez Gene data because of: Error in file(con, "r") : unable to open connection The missing file in question is the parser from Genbank to Entrez Gene (The Agilent annotations are based on GenBank). > getBaseParsers("gb") LL "/usr/local/lib/R/library/AnnBuilder/scripts/egAccParser" UG "/usr/local/lib/R/library/AnnBuilder/scripts/gbUGParser" I've convinced it to use the LocusLink parser instead as the IDs should be the same, and the code runs for about an hour and at the very end: ... [21] "/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsW gREFSEQ.rda" [22] "/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsW gSYMBOL.rda" [23] "/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsW gUNIGENE.rda" exiting from: ABPkgBuilder(baseFile, srcUrls, baseMapType, otherSrc, pkgName, pkgPath, organism, version, makeXML, author, fromWeb) Warning: cannot open compressed file `/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHsW gLOCUSID.rda' Error in open.connection(con, "rb") : unable to open connection At which point I assume I'll need a proper parser for it. Any suggestions on what to do next? Having since learned my lesson: > sessionInfo() R version 2.0.0, 2004-10-04, x86_64-unknown-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: Resourcerer AnnBuilder annotate XML Biobase "1.1.0" "1.5.12" "1.5.1" "0.95-6" "1.5.0" Francois

I will have a look to see what might be wrong. Due to a recent switch from LocusLink to Entrez Gene, AnnBuilder and other packages that depend on AnnBuilder may not work as expected. We are in the process of fixing the problems. Sorry! >X-Original-To: jzhang@jimmy.harvard.edu >Delivered-To: jzhang@jimmy.harvard.edu >From: Francois Pepin <fpepin@cs.mcgill.ca> >To: bioconductor@stat.math.ethz.ch >Mime-Version: 1.0 >Date: Fri, 08 Apr 2005 14:37:36 -0400 >Content-Transfer-Encoding: 7bit >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] missing AnnBuilder parser >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 3.0.1 (2004-10-22) on pascal.dfci.harvard.edu >X-Spam-Level: >X-Spam-Status: No, score=-2.6 required=3.0 tests=AWL,BAYES_00 autolearn=ham version=3.0.1 > >Hi everyone, > >I'm trying to rebuild my annotation package for an Agilent chip using >Resourcerer and it's not finder one of the parsers. > >The basic error is: >>resourcerer2BioC("Agilent_HumanGenome.zip", organism="human") > >Warning: cannot open file `NA' >Warning in unifyMappings(base, eg, ug, otherSrc) : > Failed to get or parse Entrez Gene data because of: > > Error in file(con, "r") : unable to open connection > > >The missing file in question is the parser from Genbank to Entrez Gene >(The Agilent annotations are based on GenBank). > >> getBaseParsers("gb") > LL >"/usr/local/lib/R/library/AnnBuilder/scripts/egAccParser" > UG > "/usr/local/lib/R/library/AnnBuilder/scripts/gbUGParser" > > >I've convinced it to use the LocusLink parser instead as the IDs should >be the same, and the code runs for about an hour and at the very end: > >... >[21] >"/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHs WgREFSEQ.r da" >[22] >"/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHs WgSYMBOL.r da" >[23] >"/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHs WgUNIGENE. rda" >exiting from: ABPkgBuilder(baseFile, srcUrls, baseMapType, otherSrc, >pkgName, > pkgPath, organism, version, makeXML, author, fromWeb) >Warning: cannot open compressed file >`/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHs WgLOCUSID. rda' >Error in open.connection(con, "rb") : unable to open connection > >At which point I assume I'll need a proper parser for it. Any >suggestions on what to do next? > >Having since learned my lesson: >> sessionInfo() >R version 2.0.0, 2004-10-04, x86_64-unknown-linux-gnu > >attached base packages: >[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" >[7] "datasets" "base" > >other attached packages: >Resourcerer AnnBuilder annotate XML Biobase > "1.1.0" "1.5.12" "1.5.1" "0.95-6" "1.5.0" > >Francois > >_______________________________________________ >Bioconductor mailing list >Bioconductor@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

>I'm trying to rebuild my annotation package for an Agilent chip using >Resourcerer and it's not finder one of the parsers. > >The basic error is: >>resourcerer2BioC("Agilent_HumanGenome.zip", organism="human") I have checked in the bug fixes. Please look for a new build (1.1.1) of Resourcerer in the next few days. Meanwhile, you may try to fix the bug yourself by changing the argument baseMapType = c("gb", "ug", "ll") to baseMapType = c("gbNRef", "gb", "ug") of resourcerer2BioC and call the function by setting baseMapType = "gbNRef" (resourcerer2BioC("Agilent_HumanGenome.zip", organism = "human", baseMapType = "gbNRef")) Let me know if you run into any problem. Thanks. > >Warning: cannot open file `NA' >Warning in unifyMappings(base, eg, ug, otherSrc) : > Failed to get or parse Entrez Gene data because of: > > Error in file(con, "r") : unable to open connection > > >The missing file in question is the parser from Genbank to Entrez Gene >(The Agilent annotations are based on GenBank). > >> getBaseParsers("gb") > LL >"/usr/local/lib/R/library/AnnBuilder/scripts/egAccParser" > UG > "/usr/local/lib/R/library/AnnBuilder/scripts/gbUGParser" > > >I've convinced it to use the LocusLink parser instead as the IDs should >be the same, and the code runs for about an hour and at the very end: > >... >[21] >"/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHs WgREFSEQ.r da" >[22] >"/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHs WgSYMBOL.r da" >[23] >"/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHs WgUNIGENE. rda" >exiting from: ABPkgBuilder(baseFile, srcUrls, baseMapType, otherSrc, >pkgName, > pkgPath, organism, version, makeXML, author, fromWeb) >Warning: cannot open compressed file >`/usr/local/lib/R/library/Resourcerer/temp/AgilentHsWg/data/AgilentHs WgLOCUSID. rda' >Error in open.connection(con, "rb") : unable to open connection > >At which point I assume I'll need a proper parser for it. Any >suggestions on what to do next? > >Having since learned my lesson: >> sessionInfo() >R version 2.0.0, 2004-10-04, x86_64-unknown-linux-gnu > >attached base packages: >[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" >[7] "datasets" "base" > >other attached packages: >Resourcerer AnnBuilder annotate XML Biobase > "1.1.0" "1.5.12" "1.5.1" "0.95-6" "1.5.0" > >Francois > >_______________________________________________ >Bioconductor mailing list >Bioconductor@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