[Bioc-devel] unexpected interaction of "exprSet" and "DBI" package
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. Bw, + seth
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org