[R] Packages 'effects' loads 'name' which conflicts with 'lme4' [corrected subject: Package 'effects' loads 'nlme' which conflicts with 'lme4']

Spencer Graves spencer.graves at structuremonitoring.com
Thu Mar 8 17:10:47 CET 2012

Dear John, et al.:

       What happens with import(foo) and importFrom(foo, f, g) with foo 
in suggests?  Does foo appear in the search path?  If no, then it may be 
wise to specify all uses in package "mine" of objects from package 
"other" using import and importFrom with "other" in suggests.

       If this is accurate, then users of "mine" will never have to 
worry about secondary conflicts like "effects" using "name" from either 
"nlme" or "lme4":  The use of "name" from "nlme" in "effects" will not 
cause "nlme" to be loaded.  That means that it won't matter to "effects" 
whether and where "lme4" is loaded, and it won't matter to the user, 

       Might it be good to modify section "1.6.1 Specifying imports and 
exports" of "Writing R Extensions" to make this clear?  I just read it 
now, and it seemed quite clear to me except for this point.


On 3/8/2012 7:50 AM, John Fox wrote:
> Dear Spencer,
>> -----Original Message-----
>> From: Spencer Graves [mailto:spencer.graves at prodsyse.com]
>> Sent: March-08-12 10:29 AM
>> To: Michael Kubovy
>> Cc: John Fox; r-help
>> Subject: Re: [R] Packages 'effects' loads 'name' which conflicts with
>> 'lme4' [corrected subject: Package 'effects' loads 'nlme' which
>> conflicts with 'lme4']
>> Dear John, et al.:
>>         What happens if lme4 is loaded before the effect package?
> Then some functions in it will be masked by nlme, which is loaded along with
> effects.
> Sandy Weisberg and I are discussing moving nlme from "Depends" to "Suggests"
> in the effects package Description file to avoid this potential problem.
> Although we'll have to check more carefully, I don't at this point see a
> reason not to do that.
>>         Is this an issue of a user wanting to use two different packages
>> with potentially conflicting names?  What are the standard
>> recommendations for handling issues like this?  Just to test my
>> comprehension, I assume that the key is that users should routinely
>> watch for warnings of name conflicts and follow the advice of sect.
>> "1.6.1 Specifying imports and exports" of "Writing R Extensions" when
>> that occurs?  (This is another reason for writing R packages and using
>> namespaces, so users can record appropriately what they want in
>> situations like this and not have to worry about name conflicts later?)
> The name conflicts are in lme4 and nlme, which share an author. I think that
> it's inevitable with 3000+ CRAN packages that there will be name conflicts,
> even if packages only export objects meant for the user.
> Best,
>   John
>>         Thanks,
>>         Spencer
>> On 3/8/2012 4:19 AM, Michael Kubovy wrote:
>>> Dear John,
>>> Thanks for the quick response. It works perfectly.
>>> Michael
>>> On Mar 7, 2012, at 9:19 PM, John Fox wrote:
>>>> Dear Michael,
>>>> effect() works with lmer(). Just load lme4 after the effect package.
>> See the penultimate example in ?effect.
>>>> I hope this helps,
>>>> John
>>>> ------------------------------------------------
>>>> John Fox
>>>> Sen. William McMaster Prof. of Social Statistics Department of
>>>> Sociology McMaster University Hamilton, Ontario, Canada
>>>> http://socserv.mcmaster.ca/jfox/
>>>> On Wed, 7 Mar 2012 20:53:20 -0500
>>>> Michael Kubovy<kubovy at virginia.edu>   wrote:
>>>>> Hi,
>>>>> I would like to use the effect() function (actually a slightly
>> modified version of it) on the output of the lmer() function in the
>> lme4 package. But the effects package requires the nlme pacvkage, which
>> is incompatible with lme4. Workaround?
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