On Thu, Oct 6, 2011 at 1:19 PM, Terry Therneau <thern...@mayo.edu> wrote: > > On Thu, 2011-10-06 at 10:00 -0400, Kasper Daniel Hansen wrote: >> if you're using two packages that both define a diag function/method >> you absolutely _have_ to resolve this using your NAMESPACE. [Update: >> I see both are methods. I actually don't know what happens when you >> have the same generic in both packages] >> > > Your response made me look further, with some surprising results. > > 1. Sequential loading > tmt226% R --vanilla > R version 2.13.0 (2011-04-13) > >> library(bdsmatrix) >> tmat <- bdsmatrix(c(3,2,2,4), > c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, 8,14,9,10,13,11,12), > matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, > 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) >> tmat[1:7,1:7] [,1] [,2] [,3] [,4] [,5] [,6] [,7] > [1,] 22 1 2 0 0 0 0 > [2,] 1 21 3 0 0 0 0 > [3,] 2 3 20 0 0 0 0 > [4,] 0 0 0 19 4 0 0 > [5,] 0 0 0 4 18 0 0 > [6,] 0 0 0 0 0 17 5> > >> diag(tmat) > [1] 22 21 20 19 18 17 16 15 14 13 12 10 10 > >> library(Matrix) > Loading required package: lattice > > Attaching package: 'Matrix' > > The following object(s) are masked from 'package:base': > > det > >> diag(tmat) > [1] 22 21 20 19 18 17 16 15 14 13 12 10 10 > > Things to note: > in this case I did not get a message about overwriting the diag > method, > it works. > > This was not my experience with ranef(), an S3 generic that coxme, nlme, > and lme4 all define; there whichever library loaded last did not > discover existing methods. That is, if one loaded nlme after coxme, > then ranef(a coxme object) would not dispatch ranef.coxme. Our solution > (Doug Bates and I) was to have both coxme and lme4 import ranef and > fixef from the nlme library. > However, per above it appears to work with S4 generics. > Can I count on it though?
My _guess_ is that you cannot depend on this in general. What if the two generics have different signatures, say one uses x,y and the other uses x,y,z? Kasper > > ------------- > > Case 2: > > tmt229% R --vanilla > R version 2.13.0 (2011-04-13) > >> library(coxme) > Loading required package: survival > Loading required package: splines > Loading required package: bdsmatrix > Loading required package: nlme > Loading required package: Matrix > Loading required package: lattice > > Attaching package: 'Matrix' > > The following object(s) are masked from 'package:base': > > det > > Warning message: > replacing previous import ‘diag’ when loading ‘Matrix’ > >> tmat <- bdsmatrix(c(3,2,2,4), > c(22,1,2,21,3,20,19,4,18,17,5,16,15,6,7, > 8,14,9,10,13,11,12), > matrix(c(1,0,1,1,0,0,1,1,0,1,0,10,0, > 0,1,1,0,1,1,0,1,1,0,1,0,10), ncol=2)) >>diag(tmat) > [1] 22 21 20 19 18 17 16 15 14 13 12 10 10 > > > Things to note: > I now get a warning message about diag. Why only here? > Per the earlier comment I'm not importing all of nlme, just the two > generics > It still works > > (This example isn't reproducable for others: the coxme library on CRAN > does not yet have a Matrix dependency.) > > > > > > ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
