[Bioc-devel] Environment/RSqlite db interaction

[Seth Falcon]

Hi Jim,

Martin Morgan <mtmorgan at fhcrc.org> writes:
> John --

John?  Is that the original poster with drug problems?

>
> It's inherited from further up the search path
>
>> library("hgu95av2.db")
>> library("hgu95av2")
>> exists("db_conn", as.environment("package:hgu95av2"))
> [1] TRUE
>> exists("db_conn", as.environment("package:hgu95av2"), inherits=FALSE)
> [1] FALSE

Yes that is exactly the problem.  I've committed a quick fix to
annaffy so that inherits=FALSE is used.  This helper function should
move to AnnotationDbi so there is one place that has a
are-you-a-db-package helper function.

> This is probably a general issue when multiple packages with
> near-identical variables can be loaded.

Well, only sort of.  The real issue was my goof in not using exists
properly.

> I think seth will chime in with the future of db_conn, relating to
> issues like this.

Here I go:

Dispite it being possible, it really is a bad idea for all annotation
data packages to export the same symbols.  We will be changing these:
db_conn and db_file prior to the release and replace them with
accessor functions prefixed with the package name: hgu95av2_dbcon()
(name subject to change until implemented).

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
BioC: http://bioconductor.org/
Blog: http://userprimary.net/user/