[Bioc-devel] cyclic dependency bug in Rdbi

Hervé Pagès hpages at fhcrc.org
Wed Mar 23 19:24:31 CET 2011

Hi Philip,

Thanks again for your feedback. I've removed the "automatic reconnection 
to a
database from a saved object" feature from Rdbi. I totally agree with 
you that this
feature is not good design.

We've also decided to move forward and to deprecate Rdbi/RdbiPgSQL in favor
of DBI/RPostgreSQL. Note that Rdbi/RdbiPgSQL will still be available in 
the upcoming
release (BioC 2.8) but they will issue a warning at load time and point 
the user to
DBI/PostgreSQL. Then later, during the BioC 2.9 devel cycle, we will 
remove those
2 packages.

I hope this is OK.


On 03/22/2011 02:32 AM, Philip Lijnzaad wrote:
> Hi Hervé,
>> How many people are still using Rdbi?
> mmm ... no idea. The stats do show a downward sloping trend, that much is
> clear.
>> It has long been superseded by
>> DBI. One long standing reason for not moving to DBI was that there
>> was no support for PostgreSQL in the DBI world for a long time. But
>> this has changed recently with RPostgreSQL now available on CRAN.
>> Now the question is how good is RPostgreSQL these days? Is it mature
>> enough to be worth migrating apps from Rdbi/RdbiPgSQL to
>> DBI/RPostgreSQL? Is it something you've considered/tried?
> No, I wasn't aware of this, I will look into it.
>> Maybe it's time for us to deprecate Rdbi/RdbiPgSQL?
> I think that is probably the case, but at the same time I would argue that
> simply changing the .onLoad() function to an empty one (or deleting it, dunno
> what's best) solves a design error that would at least help the current
> users.
>> Feedback from
>> other "PostgreSQL within R" users would be appreciated.
> Certainly. Thanks,
>                                                                         Philip

Hervé Pagès

Program in Computational Biology
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