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

[Dan Tenenbaum]

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Mike" <wjiang2 at fhcrc.org>
> Cc: Bioc-devel at r-project.org
> Sent: Tuesday, January 20, 2015 5:01:52 PM
> Subject: Re: [Bioc-devel] Latest R-devel revision breaks flowCore and other flow	packages
> 
> Hi Mike,
> 
> ----- Original Message -----
> > From: "Mike" <wjiang2 at fhcrc.org>
> > To: Bioc-devel at r-project.org
> > Cc: "Dan Tenenbaum" <dtenenba at fhcrc.org>
> > Sent: Tuesday, January 20, 2015 4:56:43 PM
> > Subject: [Bioc-devel] Latest R-devel revision breaks flowCore and
> > other flow	packages
> > 
> > Dan,
> > 
> > First of all, Thanks to the bioconductor |docker container| project
> > that
> > allows me to quickly troubleshoot within the exactly same
> > environment
> > that |bioc| has.
> > 
> 
> I want to be very clear that the docker containers we maintain
> do NOT have exactly the same environment as the build systems. Maybe
> a little closer, but not the same.
> We are not attempting to replicate the build environment, just to
> create an environment that
> is useful to users. In particular, we try and build the docker
> containers daily with the latest R-devel, whereas
> we do not update R-devel daily on the build systems. There are many
> other differences.
> 
> > 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()
> >            })
> > |
> > 
> > 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)
> 


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.

Dan



> 
> OK, thanks for letting us know. Michael, if/when this is addressed
> can you let us know?
> 
> Thanks,
> Dan
> 
> 
> 
> > 
> > Best,
> > 
> > Mike
> > 
> > ​
> > 
> > 	[[alternative HTML version deleted]]
> > 
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> 
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