From therneau at mayo.edu  Mon Feb 16 00:31:00 2015
From: therneau at mayo.edu (Therneau, Terry M., Ph.D.)
Date: Sun, 15 Feb 2015 17:31:00 -0600
Subject: [Rd] Imports problem
Message-ID: <1e7ee5$2f7or@ironport10.mayo.edu>

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



[Rd] Imports problem
Therneau, Terry M., Ph.D.