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

Michael Lawrence lawrence.michael at gene.com
Fri Jan 23 19:52:08 CET 2015

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.


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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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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