[Bioc-devel] Environment/RSqlite db interaction

[Laurent Gautier]

2007/9/13, Seth Falcon <sfalcon at fhcrc.org>:
> 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).

Several packages exporting the same symbol has already bitten us.
Couldn't namespaces be used here, with something like
hgu95av2:::dbcon() instead ?

That would allow to have identical code within these annotation packages
(since these packages are generated programatically, code duplication
is presumably acceptable).


Just an idea,


L.


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