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

Mike wjiang2 at fhcrc.org
Wed Jan 21 01:56:43 CET 2015


First of all, Thanks to the bioconductor |docker container| project that 
allows me to quickly troubleshoot within the exactly same environment 
that |bioc| has.

Here is the |initialize|method for |parameterFilter| which causes the 
various errors from flow package vignettes.

           definition=function(.Object, parameters,...)
             if  (!missing(parameters))
               parameters(.Object) <- parameters

The error goes away after |callNextMethod| call is removed.

I suspect it has to do with a bug introduced by the latest |R-devel| 
based on its svn history.

|  ~/R/r-devel/src$ svn log |grep callNextMethod -C3
  r67472 | lawrence |2015-01-14  20:11:30  -0800  (Wed,14  Jan2015) |3  lines

  callNextMethod no longer drops arguments named"..."  (bug introduced
  in  r67468)

  r67468 | lawrence |2015-01-14  09:57:53  -0800  (Wed,14  Jan2015) |3  lines

  remove hack from C part of callNextMethod that should no longer be
  necessary given the dots fixes

  r67467 | lawrence |2015-01-14  07:38:41  -0800  (Wed,14  Jan2015) |3  lines

  fix PR#16141 and other issues related to "..." forwarding in
  callGeneric() and callNextMethod()


If so, it should get fixed by the next run of updating |R-devel| from 
|bioc| (hopefully coming soon)




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