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

[Vincent J. Carey, Jr.]

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