From mtmorgan at fhcrc.org  Wed Mar  2 04:36:47 2011
From: mtmorgan at fhcrc.org (Martin Morgan)
Date: Tue, 01 Mar 2011 19:36:47 -0800
Subject: [Rd] changes in recent R-devel revisions?
In-Reply-To: <AANLkTi=UipvSvxCmzgORy=QAbgGW+2kA5eJw8DziBmsN@mail.gmail.com>
References: <AANLkTi=UipvSvxCmzgORy=QAbgGW+2kA5eJw8DziBmsN@mail.gmail.com>
Message-ID: <4D6DBB4F.7010009@fhcrc.org>

On 03/01/2011 03:19 PM, Benilton Carvalho wrote:
> Hi,
> 
> I have a BioC infra-structure package that works fine (I can build,
> check and load it successfully) on revision r53950. The very same
> package fails on r54591 with the error below:
> 
> Error in loadNamespace(package, c(which.lib.loc, lib.loc), keep.source
> = keep.source) :
>   cyclic name space dependency detected when loading ?oligoClasses?,
> already loading ?oligoClasses?
> 
> I don't see anything obvious in the name space that would indicate
> cyclic dependency and I wonder:

For what it's worth, saying

> trace(stop, recover)

prior to library(oligoClasses) leads to

 7: loadNamespace(package, c(which.lib.loc, lib.loc), keep.source =
keep.source
 8: methods:::cacheMetaData(ns, TRUE, ns)
 9: getGeneric(f, FALSE, searchWhere, fpkg)
10: tryCatch(loadNamespace(package), error = function(e) e)

where 'package' is oligoClasses in lines 7 and 10, and the 'f' in 9 is
'relocateObject'. Line 10 is evaluated when methods:::.getGeneric
returns NULL.

In oligoClasses we have

oligoClasses/R> grep relocateObject *
AllGenerics.R:setGeneric("relocateObject", function(object, ...)
standardGeneric("relocateObject"))
methods-CNSet.R:relocateObject <- function(object, to){

which I guess is not as intended.

My guess is that setGeneric adds the generic to a cache of some sort
when the name space is created, but doesn't remove it when the generic
is overwritten by a plain function.

No idea why this shows up in the current R revision.

Martin

> 
> a) if there were changes that were meant to affect this;
> 
> b) what is the recommended strategy to solve this issue.
> 
> Thank you very much for any suggestion,
> 
> benilton
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


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[Rd] changes in recent R-devel revisions?
Martin Morgan