Yes, NCBI has moved files around. The fix will be included in a new version of AnnBuilder. Meanwhile, if you replace srcUrls of resourcer2BioC with mySrcUrls that has the correct urls, the code should work. >X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >Date: Tue, 12 Jul 2005 12:46:56 +0200 >From: Morten <morten.mattingsdal at="" student.uib.no=""> >To: Bioconductor at stat.math.ethz.ch >MIME-Version: 1.0 >User-Agent: Internet Messaging Program (IMP) 3.1-cvs >X-checked-clean: by exiscan on noralf >X-Scanner: 119d673d3adba89491d5fea5a36a7728 http://tjinfo.uib.no/virus.html >X-UiB-SpamFlag: NO UIB: -9 hits, 8.0 required >X-UiB-SpamReport: spamassassin found; -9.0 Message received from UIB >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 at student.uib.no does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] Resourcerer, UniGene and getSrcUrl >X-BeenThere: bioconductor at stat.math.ethz.ch >X-Mailman-Version: 2.1.6 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> >Content-Transfer-Encoding: 7bit >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 > >Hello everyone. > >Im puzzled (and maybe abit stupid). When i try to use Resourcerer with: > >resourcerer2BioC("Agilent_HumanGenome.zip",organism="human",destDir=f ile.path(. path.package("Resourcerer"),"temp"), >pkgName=("AgilentHumanGenome"), srcUrls=getSrcUrl("all","Homo sapiens"), >pkgPath=file.path(.path.package("Resourcerer"),"temp"),otherSrc=NULL, baseMapTyp e="gbNRef", >version="1.0.0",fromWeb=True,baseUrl="ftp://ftp.tigr.org/pub/data/tgi /Resourcer er", >check=TRUE,author=list(author="Anonymous",maintainer="<morten.matting sdal="" at="" medis="" in.uio.no="">")) > >i get: >Error in loadFromUrl(srcUrls[i]) : URL >ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz is incorrect or the target >site is not responding! >[1] "Unsuccessful" > >After trying the ftp adress above, Resourcerer is correct cause there is no >Hs.data.gz there. The correct one is > >ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/ > >Have ncbi recently moved their data or am I just confused? Is this a way to >surpass this? i have tried to manualy set the url by: > >mySrcUrls <- c( >GP="ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sapi ens/databa se/", >UG="ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/", >KEGG="ftp://ftp.genome.ad.jp/pub/kegg/pathways", >EG="ftp://ftp.ncbi.nlm.nih.gov/gene/DATA", >HG="ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp", >GO="http://www.godatabase.org/dev/database/archive/latest/go_200506-t ermdb.rdf- xml.gz", >YG="ftp://genome-ftp.stanford.edu/pub/yeast/data_download/") > >but i still get >Error in loadFromUrl(srcUrls[i]) : URL >ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/ is incorrect or the >target site is not responding! > >anyone got any hints ? > >morten > > >with: >R 2.1.0 >Resourcerer 1.1.2 >AnnBuilder 1.5.31 > >_______________________________________________ >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

Hi.. yes, I saw I was using the wrong: ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/ instead of the correct ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/Hs.data.gz in mySrcUrls when i do, everything goes fine for a while but then i get: Error in readURL(infoURL): Can't read from ulr:ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.info [1] Unsuccessful Which is abit strange since I have already specified the correct url where both Hs.data.gz and Hs.info is located. Ill just wait for the new realease of AnnBuilder :) morten >Yes, NCBI has moved files around. The fix will be included in a new version of >AnnBuilder. Meanwhile, if you replace srcUrls of resourcer2BioC with mySrcUrls >that has the correct urls, the code should work. > > > >>X-Original-To: jzhang at jimmy.harvard.edu >>Delivered-To: jzhang at jimmy.harvard.edu >>Date: Tue, 12 Jul 2005 12:46:56 +0200 >>From: Morten <morten.mattingsdal at="" student.uib.no=""> >>To: Bioconductor at stat.math.ethz.ch >>MIME-Version: 1.0 >>User-Agent: Internet Messaging Program (IMP) 3.1-cvs >>X-checked-clean: by exiscan on noralf >>X-Scanner: 119d673d3adba89491d5fea5a36a7728 http://tjinfo.uib.no/virus.html >>X-UiB-SpamFlag: NO UIB: -9 hits, 8.0 required >>X-UiB-SpamReport: spamassassin found; -9.0 Message received from UIB >>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 at student.uib.no does >> >> >not designate permitted sender hosts) > > >>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >>Subject: [BioC] Resourcerer, UniGene and getSrcUrl >>X-BeenThere: bioconductor at stat.math.ethz.ch >>X-Mailman-Version: 2.1.6 >>List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >>List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> >> ><mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> > > >>List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >>List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >>List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >>List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, >> >> ><mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> > > >>Content-Transfer-Encoding: 7bit >>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 > > >>Hello everyone. >> >>Im puzzled (and maybe abit stupid). When i try to use Resourcerer with: >> >>resourcerer2BioC("Agilent_HumanGenome.zip",organism="human",destDir= file.path(. >> >> >path.package("Resourcerer"),"temp"), > > >>pkgName=("AgilentHumanGenome"), srcUrls=getSrcUrl("all","Homo sapiens"), >>pkgPath=file.path(.path.package("Resourcerer"),"temp"),otherSrc=NULL ,baseMapTyp >> >> >e="gbNRef", > > >>version="1.0.0",fromWeb=True,baseUrl="ftp://ftp.tigr.org/pub/data/tg i/Resourcer >> >> >er", > > >>check=TRUE,author=list(author="Anonymous",maintainer="<morten.mattin gsdal="" at="" medis="">> >> >in.uio.no>")) > > >>i get: >>Error in loadFromUrl(srcUrls[i]) : URL >>ftp://ftp.ncbi.nih.gov/repository/UniGene/Hs.data.gz is incorrect or the target >>site is not responding! >>[1] "Unsuccessful" >> >>After trying the ftp adress above, Resourcerer is correct cause there is no >>Hs.data.gz there. The correct one is >> >>ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/ >> >>Have ncbi recently moved their data or am I just confused? Is this a way to >>surpass this? i have tried to manualy set the url by: >> >>mySrcUrls <- c( >>GP="ftp://hgdownload.cse.ucsc.edu/goldenPath/currentGenomes/Homo_sap iens/databa >> >> >se/", > > >>UG="ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/", >>KEGG="ftp://ftp.genome.ad.jp/pub/kegg/pathways", >>EG="ftp://ftp.ncbi.nlm.nih.gov/gene/DATA", >>HG="ftp://ftp.ncbi.nih.gov/pub/HomoloGene/old/hmlg.ftp", >>GO="http://www.godatabase.org/dev/database/archive/latest/go_200506- termdb.rdf- >> >> >xml.gz", > > >>YG="ftp://genome-ftp.stanford.edu/pub/yeast/data_download/") >> >>but i still get >>Error in loadFromUrl(srcUrls[i]) : URL >>ftp://ftp.ncbi.nih.gov/repository/UniGene/Homo_sapiens/ is incorrect or the >>target site is not responding! >> >>anyone got any hints ? >> >>morten >> >> >>with: >>R 2.1.0 >>Resourcerer 1.1.2 >>AnnBuilder 1.5.31 >> >>_______________________________________________ >>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 > > >