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)