I'm using R 1.7.1 and Bioconductor release 1.2 under Redhat Linux 8. The package SAGElyzer (which is version 1.1.17 in BioC 1.2) requires the library Rdbi, when running under UNIX. This package is not available from CRAN anymore. You may still get it from http://rdbi.sourceforge.net/. Rdbi seems to have been replaced by the package DBI, which is available from CRAN. I have looked at the development sources for SAGElyzer (v 1.2.4) and it seems to have the same requirements as v1.1.17. Questions/thoughts: 1) Is DBI sufficiently developed to replace Rdbi? If so, I guess it needs to be fixed in SAGElyzer. 2) Otherwise I think a mention of this issue ought to be placed in the FAQ since Rdbi seems to have disappeared from CRAN. -- Kasper Daniel Hansen, Research Assistent Department of Biostatistics, University of Copenhagen

> I'm using R 1.7.1 and Bioconductor release 1.2 under Redhat Linux 8. > > The package SAGElyzer (which is version 1.1.17 in BioC 1.2) requires the > library Rdbi, when running under UNIX. This package is not available from > CRAN anymore. You may still get it from http://rdbi.sourceforge.net/. Rdbi > seems to have been replaced by the package DBI, which is available from CRAN. > I have looked at the development sources for SAGElyzer (v 1.2.4) and it seems > to have the same requirements as v1.1.17. > > Questions/thoughts: > 1) Is DBI sufficiently developed to replace Rdbi? If so, I guess it needs to > be fixed in SAGElyzer. DBI is pretty mature, the problem is that no one has written DBI-compliant drivers for postgres. ROracle and RMySQL from CRAN do satisfy DBI. > 2) Otherwise I think a mention of this issue ought to be placed in the FAQ > since Rdbi seems to have disappeared from CRAN. agreed. And anyone with an interest in/time to write a DBI-compliant RPostgres is encouraged to do this!

>From: Kasper Daniel Hansen <k.hansen@biostat.ku.dk> >To: bioconductor@stat.math.ethz.ch >Date: Wed, 8 Oct 2003 12:00:18 +0200 >User-Agent: KMail/1.4.3 >MIME-Version: 1.0 >Content-Transfer-Encoding: 8bit >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Spam-Checker-Version: SpamAssassin 2.60 (1.212-2003-09-23-exp) on hypatia >X-Spam-Status: No, hits=-4.6 required=5.0 tests=AWL, BAYES_00 autolearn=ham version=2.60 >Questions/thoughts: >1) Is DBI sufficiently developed to replace Rdbi? If so, I guess it needs to >be fixed in SAGElyzer. I am evaluating DBI and will make a decision on that soon. >2) Otherwise I think a mention of this issue ought to be placed in the FAQ >since Rdbi seems to have disappeared from CRAN. I have included the source for Rdbi and Rdbi.PgSQL in the vignette. Thank you for your comments. >-- >Kasper Daniel Hansen, Research Assistent >Department of Biostatistics, University of Copenhagen > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084