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

[Mike]

Sorry, I just want to clarify some more on this.(maybe useful for others 
as well)
What you actually mean is callNextMethod() used to drop both |...| and 
the other arguments explicitly supplied from the parent call (in my 
case, |parameters| argument).
And now after your fix, both gets passed on and that’s why I should 
explicitly select the argument for callNextMethod?

Thanks.

Mike

On 01/23/2015 11:30 AM, Michael Lawrence wrote:

> The bug has existed forever. The commit log may be confusing. The
> actual bug (or at least a very undesirable behavior) was in
> match.call(), not callNextMethod().
>
> I think it's still true that callNextMethod() is the natural
> invocation. When adding arguments to initialize that you do not want
> to pass on (and thus set as slots), it's necessary to use explicit
> args. There are other cases where callNextMethod() is exactly what you
> want. Like the case in rtracklayer that motivated this fix.
>
>
> On Fri, Jan 23, 2015 at 11:23 AM, Mike <wjiang2 at fhcrc.org> wrote:
>> Michael,
>>
>> Thanks for the confirmation of the issue. I see you were trying to tackle it
>> in the latest commits r67467:67472 which apparently haven’t fixed the bug
>> yet (instead it triggers the error of the existing legacy code in other R
>> packages like flowCore). I can certainly change the code to explicitly pass
>> on all the arguments to callNextMethod as you and Martin suggested. I just
>> wonder if the documentation should drop the sentence of Calling with no
>> arguments is often the natural way to use callNextMethod and change the
>> example code (at least before the bug is eventually fixed.) so that users
>> won’t be misusing it.
>>
>>
>>
>> Mike
>>
>> On 01/23/2015 10:55 AM, Martin Morgan wrote:
>>
>> On 01/23/2015 10:52 AM, Michael Lawrence wrote:
>>
>> First let me apologize for my failure to read emails. There was a
>> long-standing bug in the methods package where arguments passed as
>> "..." to a method would be dropped by callNextMethod(). It turns out
>> that in all known cases this affects calls to initialize(), probably
>> because there are many initialize() methods, and new() calls
>> initialize with "...".
>>
>> This case is a very typical one, and Martin's fix is the right one,
>> according to the (unchanged) documentation of callNextMethod().
>>
>> It's in general impossible to detect these cases from static analysis,
>> since we do not know how the user is calling a method. But catching
>> them in initialize() should be easy, with some false positives. Just
>> look for callNextMethod().
>>
>> Is it OK for me to checkout all of Bioconductor so that I can perform
>> that analysis, or will that stress the servers too much? I have a
>> package that embeds GNU Global to index and search
>> CRAN/Bioconductor-size repositories for these cases.
>>
>>
>> Hi Michael -- there is no problem checking out all
>> (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks presumably) of
>> Bioc.
>>
>> Thanks! Martin
>>
>>
>> Michael
>>
>> On Thu, Jan 22, 2015 at 6:15 AM, Martin Morgan <mtmorgan at fredhutch.org>
>> wrote:
>>
>> 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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>>
>>
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>>
>>
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