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

[Martin Morgan]

On 01/22/2015 12:26 AM, Martin Maechler wrote:
>>>>>> 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
>        callNextMethod()
> inside an  initialize method.
>
> I'm pretty sure that if you change (the same as I)
>
>             callNextMethod()
> to
>             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.
>

I also pinged Michael??

What's a precise statement of the problem -- no-argument callNextMethod() inside 
initialize? Any suggestions on ways to discover these without relying on package 
break during build / check / install?

Martin Morgan

> 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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