Resourcerer, Error in author[["authors"]]
3
0
Entering edit mode
Morten ▴ 300
@morten-929
Last seen 9.6 years ago
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
convert Resourcerer convert Resourcerer • 889 views
ADD COMMENT
0
Entering edit mode
John Zhang ★ 2.9k
@john-zhang-6
Last seen 9.6 years ago
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
ADD COMMENT
0
Entering edit mode
John Zhang ★ 2.9k
@john-zhang-6
Last seen 9.6 years ago
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
ADD COMMENT
0
Entering edit mode
Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
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
ADD COMMENT

Login before adding your answer.

Traffic: 687 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6