From Troy.Robertson at aad.gov.au  Tue Jun 30 01:39:32 2009
From: Troy.Robertson at aad.gov.au (Troy Robertson)
Date: Tue, 30 Jun 2009 09:39:32 +1000
Subject: [Rd] S4 and connection slot [Sec=Unclassified]
In-Reply-To: <4A49120D.7040605@fhcrc.org>
Message-ID: <42C7503E0B99F248B06BC65E7D2B4E020122C50FB2BB@EX2K7-CCR.AAD.GOV.AU>

Thanks guys,

I wasn't having a problem storing active connections in slots initially.  They were opened during initialisation of the object and then a routine ran through and closed them all before the program exited.

I have now implemented them as environment stored objects as a way around the slot problem (along with all the rest of the class data members so that object passing is more efficient without all the memcpying).  So much for S4 slots.

Troy


> -----Original Message-----
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> Sent: Tuesday, 30 June 2009 5:12 AM
> To: Stavros Macrakis
> Cc: Troy Robertson; r-devel at R-project.org
> Subject: Re: [Rd] S4 and connection slot [Sec=Unclassified]
>
> Stavros Macrakis wrote:
> > On Mon, Jun 29, 2009 at 9:19 AM, Martin Morgan <mtmorgan at fhcrc.org
> > <mailto:mtmorgan at fhcrc.org>> wrote:
> >
> >     ...I'm not sure that including a connection in a slot is going to be
> >     a good
> >     idea, though -- a connection has reference-like semantics, so you
> can
> >     end up with multiple objects pointing to the same connection, Also
> when
> >     an object is garbage collected the connection will not be closed
> >     automatically.
> >
> >
> > I'm not sure I understand your point here.  Having multiple objects
> > refer to the same connection seems like a perfectly reasonable and
> > useful thing, and garbage collection should work just fine -- when *all*
> > of the objects referring to that connection are unreachable, then the
> > connection is unreachable and will itself be garbage collected.  No?
>
> I meant that, in practice, there were enough additional pitfalls that I
> wouldn't choose this route (placing a connection in an S4 slot) for
> myself. These little experiments were enough to make me cautious...
>
> setOldClass(c("file", "connection"))
>
> ## Attempt one -- prototype
> setClass("Element",
>          representation=representation(conn="file"),
>          prototype=prototype(conn=file()))
>
> ## oops, all instances share a single connection
>
> close(new("Element")@conn)
> ## oops, all new instances now have a closed (invalid) connection
>
>
> ## Attempt two -- initialize
> setClass("Element",
>          representation=representation(conn="file"))
>
> setMethod(initialize, "Element", function(.Object, ..., conn=file()) {
>     callNextMethod(.Object, ..., conn=conn)
> })
>
> new("Element")
> ## oops, connection created but not closed; gc() closes (eventually)
> ## but with an ugly warning
> ## > gc()
> ##            used  (Mb) gc trigger  (Mb) max used  (Mb)
> ## Ncells   717240  38.4    1166886  62.4  1073225  57.4
> ## Vcells 37333395 284.9   63274729 482.8 60051033 458.2
> ## > gc()
> ##            used  (Mb) gc trigger  (Mb) max used  (Mb)
> ## Ncells   715906  38.3    1166886  62.4  1073225  57.4
> ## Vcells 37335626 284.9   63274729 482.8 60051033 458.2
> ## Warning messages:
> ## 1: closing unused connection 3 ()
>
> setClass("ElementX", contains="Element")
> ## oops, two connections opened (!)
> ## > showConnections()
> ##   description class  mode text   isopen   can read can write
> ## 3 ""          "file" "w+" "text" "opened" "yes"    "yes"
> ## 4 ""          "file" "w+" "text" "opened" "yes"    "yes"
>
> And while completely expected the action-at-a-distance of references has
> the usual risks
>
> > x <- y <- new("Element")
> > close(x at conn)
> > y
> An object of class "Element"
> Slot "conn":
> Error in summary.connection(x) : invalid connection
>
> One place I know where S4 and connections are used effectively is in the
> AnnotationDbi package in Bioconductor (I did not participate in
> developing this package, so am probably misrepresenting its
> implementation). Here there is a database connection. But it is stored
> in an environment in an S4 class. This part of the class is used
> essentially as a singleton -- AnnotationDbi creates packages containing
> instances, and users load the package and hence single instance; the
> interface never exposes the connection itself to copying. The database
> functionality exposed to the user is read-only, and querying the
> connection does not change it's state (other than opening it if it were
> closed). I think the underlying connection has C code to tidy itself up
> appropriately (and quietly) when eventually garbage collected. So yes,
> connections and multiple references to them can be useful.
>
> Martin
>
>
> >            -s
> >

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[Rd] S4 and connection slot [Sec=Unclassified]
Troy Robertson