[Bioc-devel] Latest R-devel revision breaks flowCore and other flow packages

Martin Maechler maechler at stat.math.ethz.ch
Thu Jan 22 09:26:12 CET 2015

>>>>> Mike  <wjiang2 at fhcrc.org>
>>>>>     on Tue, 20 Jan 2015 17:16:37 -0800 writes:

    > I don't think it has been addressed yet in the later commits of R-devel. 
    > And that piece of code in flowCore package was written long time ago and 
    > there is nothing wrong with it as far as I can see.

You are right.

I thought Michael Lawrence (member of R Core since last summer!)
was also reading Bioc-devel, so wonder why he has not yet
replied --> CC'ing him

The changes to R-devel also did break the Matrix package in
exactly the same way.  You said 

> > 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()
> >            })
> > |

and I also had  a  _no argument_ call
inside an  initialize method.

I'm pretty sure that if you change (the same as I)

           callNextMethod(.Object, ...)

you'll have a version of the code that works both in current R 3.1.2
(and older versions)  *and* in the R-devel version.

Michael L and I were not sure how many other packages or R code this
would influence and he was expecting very very few.

Best regards,

Martin Maechler, ETH Zurich

    > On 01/20/2015 05:06 PM, Dan Tenenbaum wrote:
    >> 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.

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