On 16.02.2015 14:35, Duncan Murdoch wrote:
On 16/02/2015 8:20 AM, Therneau, Terry M., Ph.D. wrote:
> 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.
Duncan and Martin,
These are helpful comments. Let me start over and be more clear. It also helps
that I'm
not writing this second note when I am too tired, and trying to push coxme out
the door
before I had planned because of an interaction with one of the "survival" data
sets
("rats" got bigger, making one coxme test fail).
1. The heart of the issue is an attempt to follow the general advice of
"almost no
depends, only imports." For the S3 methods imported from nlme I now see this
as a bad
idea. The help page, vignettes, etc all tell the users of coxme to type
"ranef(fit)" to
get random effects. I do not want to force them to type "nlme::ranef(fit)". I
will
return nlme to the depends list.
I believe you can import it and then export it from your own package,
though I don't know if this will lead to other problems.
2. I depend on the S3 generics of nlme: both of you wrote "lme4" in your
response.
Freudian slip, or was there a reason?
Not for me: I just copied it from Martin's message.
I can include either, as long as it works. The
reason I don't define the generics myself is that it is quite possible for
someone to be
fitting both linear and Cox mixed effects models, and if two packages define
the generics
de novo then all methods for one of them disappear, or at least that was true
in prior
releases of R (the last one loaded wins). Any advice? Take it as a given
that survival
and coxme will remain firmly in the S3 camp.
3. Given 1 and 2, should the coxme function import all of nlme, or (as
present) only the
methods?
If you are depending on nlme, you don't need to also import it.
Well, you should import all the functionality that you actually want to
use (see Duncan's comment below). Otherwise R CMD check should yell.
Best,
Uwe
But it
is generally a good practice to avoid either modifying or relying on the
search list: as people get more packages there, there are more chances
for clashes.
Duncan
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