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

[Mike]

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.
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>
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>


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