I just came back from a vacation. Another user has complained about this. I will take a look when I get to the office on Monday. Thanks >X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >X-IronPort-Anti-Spam-Filtered: true >X-IronPort-Anti-Spam-Result: AmABAMfC8kmBhJEPlGdsb2JhbACNNIkhAQEBAQkLCAkRBadGBYZdiE2CRoEuBQ >X-IronPort-AV: E=Sophos;i="4.40,246,1238990400"; d="scan'208";a="232440995" >X-SBRS: 4.8 >X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on hypatia.math.ethz.ch >X-Spam-Level: >X-Spam-Status: No, score=-4.6 required=5.0 tests=AWL, BAYES_00, RCVD_IN_DNSWL_MED autolearn=unavailable version=3.2.5 >From: Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> >To: Philip Lijnzaad <p.lijnzaad at="" umcutrecht.nl=""> >Mime-Version: 1.0 (Apple Message framework v930.3) >Date: Sat, 25 Apr 2009 08:02:37 -0700 >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >X-Virus-Status: Clean >X-Tag-Only: YES >X-Filter-Node: phil3.ethz.ch >X-USF-Spam-Level: -- >X-USF-Spam-Status: hits=-2.6 tests=BAYES_00 >X-USF-Spam-Flag: NO >Cc: Bioconductor at stat.math.ethz.ch >Subject: Re: [BioC] RdbiPgSQL problem: SET_VECTOR_ELT() can only be applied to a 'list', not a 'character' >X-BeenThere: bioconductor at stat.math.ethz.ch >X-Mailman-Version: 2.1.11 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" options="" 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 > >This is most likely a bug in RdbiPgSQL, related to more stringent >check of SET_VECTOR_ELT (C code) in R. > >It is probably easy to fix, but I don't have access to a PostGres >database, so I would be unable to check. > >Contact the maintainer and complain :) > >Kasper > >On Apr 25, 2009, at 2:26 , Philip Lijnzaad wrote: > >> Dear all, >> >> I'm having difficulty using RdbiPgSQL. This is using R 2.9.1, >> RdbiPgSQL >> 1.18.0, both R client and server at 8.3. >> >> If I do >> >> conn=dbConnect(PgSQL(), >> host=db.host, >> dbname=db.name, >> user=db.user, >> password=db.password) >> >> >> I keep getting this: >> >> SET_VECTOR_ELT() can only be applied to a 'list', not a 'character' >> Calls: dbConnect ... dbConnectionInfo -> >> dbConnectionInfo.PgSQL.conn -> .Call >> >> This used to work fine under R 2.7 >> >> I see that the RdbiPgSQL compiles properly, but is the actual >> connectivity >> against a real database really checked? In an ideal world this would >> be the >> case, as the current version is unusuable. >> >> This is very unfortunate, since we really rely on this code. >> >> Any suggestions are welcome. >> Philip >> >> -- >> Philip Lijnzaad, PhD >> Holstege Genomics Laboratory >> Dept. of Biomedical Genetics >> University Medical Center (UMC), Utrecht >> Stratenum room 2.211 (on Mondays and Thursdays not in after 15.00) >> MSN chat (*NOT* email): philip_lijnzaad at hotmail.com >> P.O. Box 85060, 3508 AB Utrecht >> (Universiteitsweg 100, 3584 CG Utrecht) >> The Netherlands >> tel: +31 (0)8875 68464 >> fax: +31 (0)8875 68479 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084