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
>>>>> Therneau, Terry M , Ph D <therneau at 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. > 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
On 16/02/2015 4:32 AM, Martin Maechler wrote:>>>>>> Therneau, Terry M , Ph D <therneau at 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 > > ______________________________________________ > R-devel at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel >