On 16/02/2015 4:32 AM, Martin Maechler wrote:
>>>>>> Therneau, Terry M , Ph D <thern...@mayo.edu>
>>>>>> on Sun, 15 Feb 2015 17:31:00 -0600 writes:
>
> > I'm testing out a new version of coxme and R CMD check fails with
> "could not find function
> > ranef" (or random.effects or fixef, or anything from nlme). The
> NAMESPACE file has the
> > line below
>
> > importFrom(nlme, ranef, random.effects, fixef, fixed.effects, VarCorr)
>
> > and nlme is declared in the DESCRIPTION file as an import. I feel that
> I must be staring
> > at some obvious (but invisible to me) mistake.
>
> are you using them in (help page) examples, demos, or vignettes
> ?
>
> In that case, as you no longer 'Depend' on lme4, you need a
> require(lme4)
> before the corresponding code.
Or use it with the prefix, lme4::ranef. This is somewhat preferred, as
it doesn't modify the user's search list.
Duncan Murdoch
>
> > Users are very likely to use "ranef" as well.
>
> Well, and you are sure that you do not want them to see the help
> file for ranef() ?
>
> If a user of coxme() should typically use ranef() in her own code,
> you should rather *depend* on lme4 than only *import* it.
>
> > Second question. The files now declare bdsmatrix as an import rather
> than a depends. If
> > one of my test files has an explicit call to a bdsmatrix function, I
> assume that I will
> > need to put an explicit "require" there.
>
> Sure. See above
>
> > Third: How should "methods" be listed? I'm getting a message from CMD
> check if I leave it
> > in or leave it out.
>
> this is not precise enough for me to help, rather we need exact details.
>
> > An update to the survival package is forcing an update to one of the
> tests in coxme (the
> > "rats" data set in survival now has both male and female, prompted by a
> user, but the test
> > assumed the old version with only female). An update of the include vs
> update material
> > seemed in order as well.
>
> ??? {"nix verstahn" we'd say here}
>
> > Terry Therneau
>
> Martin Maechler
>
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