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

[Dan Tenenbaum]

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)


OK, thanks for letting us know. Michael, if/when this is addressed can you let us know?

Thanks,
Dan



> 
> Best,
> 
> Mike
> 
> ​
> 
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> 
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