From jfox at mcmaster.ca  Mon Nov 28 00:57:29 2011
From: jfox at mcmaster.ca (John Fox)
Date: Sun, 27 Nov 2011 18:57:29 -0500
Subject: [Rd] How to deal with package conflicts
In-Reply-To: <7366_1322239705_pAPGm4IM009763_000501ccab91$d0092690$701b73b0$@mcmaster.ca>
References: <mailman.21.1322218808.15358.r-devel@r-project.org>	<1322230252.5806.15.camel@nemo>
	<4ECFB773.2060106@yorku.ca>
	<7366_1322239705_pAPGm4IM009763_000501ccab91$d0092690$701b73b0$@mcmaster.ca>
Message-ID: <003001ccad60$52bd5ff0$f8381fd0$@mcmaster.ca>

Hi Michael,

As promised, I've moved survival to Suggests in the development version of
the car package on R-Forge. AFAICS, this doesn't cause any problems (and
should solve your problem). 

I incidentally added Anova() and linearHypothesis() methods for svyglm
objects, and placed the survey package under Suggests.

Best,
 John

> -----Original Message-----
> From: r-devel-bounces at r-project.org [mailto:r-devel-bounces at r-
> project.org] On Behalf Of John Fox
> Sent: November-25-11 11:47 AM
> To: 'Michael Friendly'
> Cc: 'Terry Therneau'; r-devel at r-project.org
> Subject: Re: [Rd] How to deal with package conflicts
> 
> Hi Michael,
> 
> I'll look into moving survival to suggests (this weekend, if I have
> time), but that doesn't address the more general issue.
> 
> Best,
>  John
> 
> > -----Original Message-----
> > From: Michael Friendly [mailto:friendly at yorku.ca]
> > Sent: November-25-11 10:43 AM
> > To: Terry Therneau
> > Cc: r-devel at r-project.org; John Fox; Duncan Murdoch
> > Subject: Re: [Rd] How to deal with package conflicts
> >
> > On 11/25/2011 9:10 AM, Terry Therneau wrote:
> > > The ridge() function was put into the survival package as a simple
> > > example of what a user could do with penalized functions.  It's not
> > > a "serious" function, and I'd be open to any suggestions for
> change.
> > >
> > > Actually, for any L2 penalty + Cox model one is now better off
> using
> > > coxme as the maximization process is much better thought out there.
> > > I'd be happy to remove ridge from survival -- except that there are
> > > bound to be lots of folks using the function and any such changes
> > > (even good
> > > ones) to the survival package are fraught with peril.
> > Duncan provided one suggestion:  make ridge() an S3 generic, and
> > rename
> > ridge()
> > to ridge.coxph(), but this won't work, since you use ridge() inside
> > coxph() and
> > survreg() to add a penalty term in the model formula.
> > Another idea might be simply to not export ridge(), but I have the
> > feeling this will break your R CMD checks.
> >
> > Alternatively, my particular problem (wanting to use car::vif in my
> > package documentation) would be solved if John Fox considered making
> > making survival a Suggests:
> > package rather than a
> > Depends: one.  This might work, since survival is only referenced in
> > car by providing Anova() methods for coxph models.
> >
> > I think all of this raises a general issue of unintended consequences
> > of "package bloat," where
> > (a) Depends: packages are forced to load by require()/library(),
> > whether they are really needed or not;
> > (b) There is nothing like require(car, depends=FALSE) to circumvent
> > this;
> > (c) Once a require()'d package is loaded, it cannot be unloaded;
> > (d) AFAIK, there is no way for a package author to override the
> > masking of functions or data provided by other other packages, except
> > by using
> > mypackage::myfun() calls.
> >
> > To me this seems to be a flaw in the namespace mechanism.
> >
> > best,
> > -Michael
> >
> >
> >
> >
> >
> >
> >
> > --
> > Michael Friendly     Email: friendly AT yorku DOT ca
> > Professor, Psychology Dept.
> > York University      Voice: 416 736-5115 x66249 Fax: 416 736-5814
> > 4700 Keele Street    Web:   http://www.datavis.ca
> > Toronto, ONT  M3J 1P3 CANADA
> 
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[Rd] How to deal with package conflicts
John Fox