[Bioc-devel] imageMap in package genplotter has wrong signature

Florian Hahne fhahne at gmx.de
Mon Mar 6 13:52:29 CET 2006

Hi Seth,

Seth Falcon schrieb:
> Hi Florian,
> Not sure I understand what's going on, but the graph package defines a
> method fromGXL that has a connection object as part of its signature.
> Here's what the code does there:
>     setIs("file", "connection")
This doesn't work here, only produces another error.  And as far as I
understand, it can be used to set up inheritance via a subclass but what
is needed here is rather a virtual S4 class "connection" to allow for
method dispatching. Since
setOldClass(c("file", "connection"))
works interactively but not in the source code, this could also be a
namespace issue.  There is a paramter "which" to setOldClass and the
documentation states, that it can be used to specify the search path
position to assign the virtual class to, but playing around with it
didn't help either. As a solution for myself I now changed the signature to
signature(object="matrix", con="ANY", tags="list",
but this is definitely not the most beautiful way to solve the problem.
If you want I can check in the fix, but I'm not the maintainer of the
package and don't want to mess with other people's code...


PS: Thanks for adding another one of my numerous email adresses to the
mailing list ;)

>     setMethod("fromGXL", signature(con="connection"),
>               function(con) { ... }
> So you could give that a try.
> + seth
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Florian Hahne
Abt. Molekulare Genomanalyse (B050)
Deutsches Krebsforschungszentrum (DKFZ)
Im Neuenheimer Feld 580
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phone: 0049 6221 424764
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web: www.dkfz.de/mga

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