----- Original Message -----
> From: "Dan Tenenbaum" <dtene...@fredhutch.org>
> To: "Mike" <wjia...@fhcrc.org>
> Cc: Bioc-devel@r-project.org
> Sent: Tuesday, January 20, 2015 5:01:52 PM
> Subject: Re: [Bioc-devel] Latest R-devel revision breaks flowCore and other
> flow packages
>
> Hi Mike,
>
> ----- Original Message -----
> > From: "Mike" <wjia...@fhcrc.org>
> > To: Bioc-devel@r-project.org
> > Cc: "Dan Tenenbaum" <dtene...@fhcrc.org>
> > Sent: Tuesday, January 20, 2015 4:56:43 PM
> > Subject: [Bioc-devel] Latest R-devel revision breaks flowCore and
> > other flow packages
> >
> > Dan,
> >
> > First of all, Thanks to the bioconductor |docker container| project
> > that
> > allows me to quickly troubleshoot within the exactly same
> > environment
> > that |bioc| has.
> >
>
> I want to be very clear that the docker containers we maintain
> do NOT have exactly the same environment as the build systems. Maybe
> a little closer, but not the same.
> We are not attempting to replicate the build environment, just to
> create an environment that
> is useful to users. In particular, we try and build the docker
> containers daily with the latest R-devel, whereas
> we do not update R-devel daily on the build systems. There are many
> other differences.
>
> > Here is the |initialize|method for |parameterFilter| which causes
> > the
> > various errors from flow package vignettes.
> >
> > |setMethod("initialize",
> > signature=signature(.Object="parameterFilter"),
> > definition=function(.Object, parameters,...)
> > {
> > if (!missing(parameters))
> > parameters(.Object) <- parameters
> > callNextMethod()
> > })
> > |
> >
> > The error goes away after |callNextMethod| call is removed.
> >
> > I suspect it has to do with a bug introduced by the latest
> > |R-devel|
> > based on its svn history.
> >
> > | ~/R/r-devel/src$ svn log |grep callNextMethod -C3
> > ------------------------------------------------------------------------
> > r67472 | lawrence |2015-01-14 20:11:30 -0800 (Wed,14 Jan2015)
> > |3 lines
> >
> > callNextMethod no longer drops arguments named"..." (bug
> > introduced
> > in r67468)
> >
> > ------------------------------------------------------------------------
> > --
> > ------------------------------------------------------------------------
> > r67468 | lawrence |2015-01-14 09:57:53 -0800 (Wed,14 Jan2015)
> > |3 lines
> >
> > remove hack from C part of callNextMethod that should no longer
> > be
> > necessary given the dots fixes
> >
> > ------------------------------------------------------------------------
> > r67467 | lawrence |2015-01-14 07:38:41 -0800 (Wed,14 Jan2015)
> > |3 lines
> >
> > fix PR#16141 and other issues related to "..." forwarding in
> > callGeneric() and callNextMethod()
> >
> > ------------------------------------------------------------------------
> > |
> >
> > If so, it should get fixed by the next run of updating |R-devel|
> > from
> > |bioc| (hopefully coming soon)
>
I'm not sure if you were implying that this has already been fixed in R-devel.
Note that the devel build machines currently have r67501 installed, which is
later than all the commits you cite above, yet the flow packages are still
broken.
Dan
>
> OK, thanks for letting us know. Michael, if/when this is addressed
> can you let us know?
>
> Thanks,
> Dan
>
>
>
> >
> > Best,
> >
> > Mike
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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