[Bioc-devel] Latest R-devel revision breaks flowCore and other flow packages
mtmorgan at fredhutch.org
Thu Jan 22 15:15:28 CET 2015
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.
>>> definition=function(.Object, parameters,...)
>>> if (!missing(parameters))
>>> parameters(.Object) <- parameters
> and I also had a _no argument_ call
> inside an initialize method.
> I'm pretty sure that if you change (the same as I)
> 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?
> 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.
> Bioc-devel at r-project.org mailing list
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