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. Users are very likely to use "ranef" as well.
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.
Third: How should "methods" be listed? I'm getting a message from CMD check if I leave it
in or leave it out.
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.
Terry Therneau
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