R-3.4.0 and recommended packages

hello,

I just installed R-3.4.0 from scratch:

$ sudo apt install r-base

but when I try

 > library(survival, lib.loc = "/usr/lib/R/library")
 > fit <- coxph(Surv(exit, event) ~ x, data = mort)

I get

Error in fitter(X, Y, strats, offset, init, control, weights = weights,  :
   object 'Ccoxmart' not found

I was told on R-help that I need to

 > update.packages(checkBuilt = TRUE)

(and it works), but

1. I get two versions of recommended packages, one in
/usr/lib/R/library, and one in
~/R/x86_64-pc-linux-gnu-library/3.4
I could fix a write permission in /usr/lib/R or run R as root.

2. Installing from scratch should have this fixed automatically, right?

Thanks, G?ran