general status query on DBI etc
Here's my understanding of the R-RDBMS interface situation, after poking around CRAN and the SIG page/mailing list. 1) DBI is available on CRAN but it is not clear if any compliant drivers are on hand; of particular interest are postgres and oracle drivers 2) Rdbi is available on sourceforge; Rdbi.PgSQL is also available there and the latter provides the postgres driver for the Rdbi (not DBI) API. Tim Keitt indicates that all the C code that would be necessary for a postgres driver for DBI is present in Rdbi.PgSQL, but DBI-compliant R code needs to be written 3) ROracle is available on CRAN, and 0.3-3 DESCRIPTION identifies it as transitional; the next version will satisfy the DBI API. 4) RODBC is at CRAN devel (not on the main package distribution page) and the RS-DBI.pdf document suggests that unix ODBC is inadequately developed. Based on my limited web searching, ODBC does not seem a viable approach for unix at present. Note: Bioconductor has made substantial use of RPgSQL for databasing genomic annotation data. The fact that RPgSQL has been abandoned by its maintainer is a source of concern. We are starting to strategize on the problem of storing and analyzing large quantities of expression data in RDBMS and we look to the DB-SIG for guidance on resources related to this problem. Questions 1) How far off is the DBI-compliant ROracle? Are there risks that code developed using the transitional version will require substantial reworking when the new version emerges? 2) Is anyone working on the postgres driver for DBI? Apparently most of the C code is available. 3) RS-DBI.pdf suggests a number of alternative architectures (e.g., ODBC, JDBC). Is the slow emergence of drivers for DBI ascribable to uncertainty about the long-term viability of the DBI approach? Has RSJava matured to the point where one might prefer a JDBC-centered approach? Thanks
--- Vince Carey, PhD Ass't Prof Med (Biostatistics) Harvard Medical School Channing Laboratory - ph 6175252265 fa 6177311541 cell 8572126768 181 Longwood Ave Boston MA 02115 USA stvjc at channing.harvard.edu