Hi everyone, There's a bug in resourcerer2BioC in the Resourcerer package version 1.0.4 (I'm using R 2.0.0 and all packages were current ). The parameter organism has to be either "human", "mouse" or "rat" and it's changed to the full name ("Homo sapiens" in this case). All of the other functions afterwards expect to have "human", "mouse" or "rat" as the organism. Using debug(resourcerer2BioC) and setting organism back to "human" in the browser solves the problem. The first 2 lines of resourcerer2BioC: { organism <- match.arg(organism) switch(toupper(organism), HUMAN = organism <- "Homo sapiens", MOUSE = organism <- "Mus musculus", RAT = organism <- "Rattus norvegicus") The command (from the vignette) along with the traceback(): > resourcerer2BioC("Agilent_Human1_cDNA.zip", organism = "human", destDir = file.path(.path.package("Resourcerer"), "temp"), pkgName = "AgilentHsa1", srcUrls = getSrcUrl("all", "Homo sapiens"), pkgPath = file.path(.path.package("Resourcerer"), "temp"), otherSrc = NULL, baseMapType = "gb", version = "1.1.0", makeXML = TRUE, fromWeb = TRUE, baseUrl = "ftp://ftp.tigr.org/pub/data/tgi/Resourcerer", check = TRUE,author = list(author = "Anonymous", maintainer = "anonymous@email.com")) Error in match.arg(organism) : ARG should be one of human, mouse, rat >traceback() 4: stop(paste("ARG should be one of", paste(choices, collapse = ", "), sep = " ")) 3: match.arg(organism) 2: loadResourcerer(which, organism, destDir, baseUrl, exten) 1: resourcerer2BioC("Agilent_Human1_cDNA.zip", organism = "human", destDir = file.path(.path.package("Resourcerer"), "temp"), pkgName = "AgilentHsa1", srcUrls = getSrcUrl("all", "Homo sapiens"), pkgPath = file.path(.path.package("Resourcerer"), "temp"), otherSrc = NULL, baseMapType = "gb", version = "1.1.0", makeXML = TRUE, fromWeb = TRUE, baseUrl = "ftp://ftp.tigr.org/pub/data/tgi/Resourcerer", check = TRUE, author = list(author = "Anonymous", maintainer = "anonymous@email.com")) Francois Pepin

Thank you for reporting! >From: Francois Pepin <fpepin@cs.mcgill.ca> >To: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> >Mime-Version: 1.0 >Date: Sat, 27 Nov 2004 14:57:06 -0500 >Content-Transfer-Encoding: 7bit >Received-SPF: none (hypatia: domain of bioconductor- bounces@stat.math.ethz.ch does not designate permitted sender hosts) >Received-SPF: none (hypatia: domain of fpepin@cs.mcgill.ca does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] bug in resourcerer2BioC in Resourcerer package >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=TO_ADDRESS_EQ_REAL autolearn=ham version=2.60-rc1 >X-Spam-Level: > >Hi everyone, > >There's a bug in resourcerer2BioC in the Resourcerer package version >1.0.4 (I'm using R 2.0.0 and all packages were current ). > >The parameter organism has to be either "human", "mouse" or "rat" and >it's changed to the full name ("Homo sapiens" in this case). All of the >other functions afterwards expect to have "human", "mouse" or "rat" as >the organism. > >Using debug(resourcerer2BioC) and setting organism back to "human" in >the browser solves the problem. > >The first 2 lines of resourcerer2BioC: >{ > organism <- match.arg(organism) > switch(toupper(organism), HUMAN = organism <- "Homo sapiens", > MOUSE = organism <- "Mus musculus", RAT = organism <- "Rattus >norvegicus") > >The command (from the vignette) along with the traceback(): >> resourcerer2BioC("Agilent_Human1_cDNA.zip", organism = "human", >destDir = file.path(.path.package("Resourcerer"), "temp"), pkgName = >"AgilentHsa1", srcUrls = getSrcUrl("all", "Homo sapiens"), pkgPath = >file.path(.path.package("Resourcerer"), "temp"), otherSrc = NULL, >baseMapType = "gb", version = "1.1.0", makeXML = TRUE, fromWeb = TRUE, >baseUrl = "ftp://ftp.tigr.org/pub/data/tgi/Resourcerer", check = >TRUE,author = list(author = "Anonymous", maintainer = >"anonymous@email.com")) >Error in match.arg(organism) : ARG should be one of human, mouse, rat > >>traceback() >4: stop(paste("ARG should be one of", paste(choices, collapse = ", "), > sep = " ")) >3: match.arg(organism) >2: loadResourcerer(which, organism, destDir, baseUrl, exten) >1: resourcerer2BioC("Agilent_Human1_cDNA.zip", organism = "human", > destDir = file.path(.path.package("Resourcerer"), "temp"), > pkgName = "AgilentHsa1", srcUrls = getSrcUrl("all", "Homo >sapiens"), > pkgPath = file.path(.path.package("Resourcerer"), "temp"), > otherSrc = NULL, baseMapType = "gb", version = "1.1.0", makeXML = >TRUE, > fromWeb = TRUE, baseUrl = >"ftp://ftp.tigr.org/pub/data/tgi/Resourcerer", > check = TRUE, author = list(author = "Anonymous", maintainer = >"anonymous@email.com")) > >Francois Pepin > >_______________________________________________ >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