[Bioc-devel] unexpected interaction of "exprSet" and "DBI" package

Seth Falcon sfalcon at fhcrc.org
Sun Apr 15 02:32:25 CEST 2007

Wolfgang Huber <huber at ebi.ac.uk> writes:

> Hi
> has anybody seen the following phenomenon before or have an idea whether 
> it is to be considered a bug in either methods, Biobase or DBI?

Not until now.

> library("Biobase")
> new("exprSet", description = new("MIAME"))
> library("DBI")
> Error in .mergeMethodsTable(generic, mtable, get(tname, envir = env),  :
>          Invalid object in meta table of methods for "coerce", label 
> "list#Versions", had class "function"
> Thanks to Jelle Goeman, who pointed out a version of this problem. My 
> attempts to more closely locate the origin have so far not been 
> successul. The error does not occur when 'description = new("MIAME")' is 
> omitted.

Very odd.  The NAMESPACE file in DBI was exporting a coerce method
when it should not have (there is no call to setAs).  Removing the
coerce export from DBI seems to have made the problem go away.  I will
send an update to CRAN.

Still, this seems buggy to me: I would expect at least a warning about
exporting methods that you don't define in any way.  And not ending up
with a corrupt methods table would be nice.

Thanks for the report.


+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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