Hello everybody, I have some trouble with Resourcerer package. I want to convert the Agilent_Human1Av2 array to a BioC meta-data package as described in "How to use Resourcerer". Everything goes fine (except the kegg errors) until this error: library(Resourcerer) resourcerer2BioC("Agilent_Human1Av2.zip", organism="human", destDir=file.path(.path.package("Resourcerer"), "temp"), pkgName=("AgilentHuman1Av2"), srcUrls=getSrcUrl("all","Homo sapiens"), pkgPath=file.path(.path.package("Resourcerer"),"temp"), otherSrc=NULL,baseMapType="gbNRef", version="1.0.0", makeXML=TRUE, fromWeb=True, baseUrl="ftp://ftp.tigr.org/pub/data/tgi/Resourcerer", check=FALSE, author=list(author="Anonymous",maintainer="mortema@medisin.uio")) Error in author[["authors"]] : subscript out of bounds [1] "Unsuccessful" I use R 2.1.0 and Resourcerer 1.1.1 on Linux Cant seem to figure this one out (its seems kinda trivial). Anyone knows what I am doing wrong? morten

It was caused by a bug in AnnBuilder. I will fix that. Thanks. >X-Original-To: jzhang@jimmy.harvard.edu >Delivered-To: jzhang@jimmy.harvard.edu >Date: Tue, 07 Jun 2005 14:37:09 +0200 >From: Morten Mattingsdal <morten.mattingsdal@student.uib.no> >User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) >X-Accept-Language: en-us, en >MIME-Version: 1.0 >To: bioconductor@stat.math.ethz.ch >Content-Transfer-Encoding: 7bit >X-UiO-Spam-info: not spam, SpamAssassin (score=-6.827, required 12, autolearn=disabled, ALL_TRUSTED -2.82, AWL 0.99, UIO_MAIL_IS_INTERNAL -5.00) >Received-SPF: pass hypatia.math.ethz.ch: 129.132.145.15 is authenticated by a trusted mechanism) >Received-SPF: none (hypatia: domain of morten.mattingsdal@student.uib.no does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] Resourcerer, Error in author[["authors"]] >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=BAYES_00 autolearn=ham version=3.0.1 > >Hello everybody, > >I have some trouble with Resourcerer package. I want to convert the >Agilent_Human1Av2 array to a BioC meta-data package as described in "How to use >Resourcerer". Everything goes fine (except the kegg errors) until this error: > >library(Resourcerer) >resourcerer2BioC("Agilent_Human1Av2.zip", organism="human", >destDir=file.path(.path.package("Resourcerer"), "temp"), >pkgName=("AgilentHuman1Av2"), srcUrls=getSrcUrl("all","Homo sapiens"), >pkgPath=file.path(.path.package("Resourcerer"),"temp"), >otherSrc=NULL,baseMapType="gbNRef", version="1.0.0", makeXML=TRUE, fromWeb=True, >baseUrl="ftp://ftp.tigr.org/pub/data/tgi/Resourcerer", check=FALSE, >author=list(author="Anonymous",maintainer="mortema@medisin.uio")) > > >Error in author[["authors"]] : subscript out of bounds >[1] "Unsuccessful" > > >I use R 2.1.0 and Resourcerer 1.1.1 on Linux > >Cant seem to figure this one out (its seems kinda trivial). Anyone knows what I am doing wrong? > >morten > >_______________________________________________ >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

The bug was actually in Resourcerer and has been fixed. Version 1.2.2 has the bug fix and should be up soon. Thanks. >X-Original-To: jzhang@jimmy.harvard.edu >Delivered-To: jzhang@jimmy.harvard.edu >Date: Tue, 07 Jun 2005 14:37:09 +0200 >From: Morten Mattingsdal <morten.mattingsdal@student.uib.no> >User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) >X-Accept-Language: en-us, en >MIME-Version: 1.0 >To: bioconductor@stat.math.ethz.ch >Content-Transfer-Encoding: 7bit >X-UiO-Spam-info: not spam, SpamAssassin (score=-6.827, required 12, autolearn=disabled, ALL_TRUSTED -2.82, AWL 0.99, UIO_MAIL_IS_INTERNAL -5.00) >Received-SPF: pass hypatia.math.ethz.ch: 129.132.145.15 is authenticated by a trusted mechanism) >Received-SPF: none (hypatia: domain of morten.mattingsdal@student.uib.no does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] Resourcerer, Error in author[["authors"]] >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=BAYES_00 autolearn=ham version=3.0.1 > >Hello everybody, > >I have some trouble with Resourcerer package. I want to convert the >Agilent_Human1Av2 array to a BioC meta-data package as described in "How to use >Resourcerer". Everything goes fine (except the kegg errors) until this error: > >library(Resourcerer) >resourcerer2BioC("Agilent_Human1Av2.zip", organism="human", >destDir=file.path(.path.package("Resourcerer"), "temp"), >pkgName=("AgilentHuman1Av2"), srcUrls=getSrcUrl("all","Homo sapiens"), >pkgPath=file.path(.path.package("Resourcerer"),"temp"), >otherSrc=NULL,baseMapType="gbNRef", version="1.0.0", makeXML=TRUE, fromWeb=True, >baseUrl="ftp://ftp.tigr.org/pub/data/tgi/Resourcerer", check=FALSE, >author=list(author="Anonymous",maintainer="mortema@medisin.uio")) > > >Error in author[["authors"]] : subscript out of bounds >[1] "Unsuccessful" > > >I use R 2.1.0 and Resourcerer 1.1.1 on Linux > >Cant seem to figure this one out (its seems kinda trivial). Anyone knows what I am doing wrong? > >morten > >_______________________________________________ >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

On 7 Jun 2005, jzhang@jimmy.harvard.edu wrote: > The bug was actually in Resourcerer and has been fixed. Version > 1.2.2 has the bug fix and should be up soon. Thanks. I will merge this bug fix into the release branch. The version in the release branch will be 1.1.2. Resourcerer 1.2.2 will be available in the devel repository soon. + seth