[R-sig-DB] general status query on DBI etc

[Timothy H. Keitt]

The intention, as far as I can tell, is to support DBI, and I imagine we
will have drivers available sometime in the next year. I do think
progress has been slowed by the transition to v4 methods, which are
considerably more complex to implement and not many developers are
familiar with the new approach. David did a nice job putting together
the DBI core. It will make a strong and stable base for future
development. But we all have day jobs, so to speak, so its hard to
predict when new code will get written. (I can only really work on
coding when my research projects demand it.)

Tim

On Fri, 2002-07-19 at 20:58, Vincent J. Carey, Jr. wrote:
> 
> 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 using channing.harvard.edu
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