[R-sig-Debian] R-3.4.0 and recommended packages

[Göran Broström]

On 2017-04-25 15:50, Dirk Eddelbuettel wrote:
>
> On 25 April 2017 at 14:58, Göran Broström wrote:
> | 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
>
> That is from apt / dpkg -- ie pre-packaged.
>
> | ~/R/x86_64-pc-linux-gnu-library/3.4
> | I could fix a write permission in /usr/lib/R or run R as root.
>
> That is from you.
>
> The two have ALWAYS been independent.

I understand that, but what is then the best practice to avoid having 
duplicates of the recommended packages? I tried running R as root and

 > update.packages(checkBuilt=TRUE)
--- Please select a CRAN mirror for use in this session ---
Warning: package 'class' in library '/usr/lib/R/library' will not be updated
Warning: package 'cluster' in library '/usr/lib/R/library' will not be 
updated
Warning: package 'codetools' in library '/usr/lib/R/library' will not be 
updated
Warning: package 'foreign' in library '/usr/lib/R/library' will not be 
updated
Warning: package 'KernSmooth' in library '/usr/lib/R/library' will not 
be updated
Warning: package 'lattice' in library '/usr/lib/R/library' will not be 
updated
Warning: package 'Matrix' in library '/usr/lib/R/library' will not be 
updated
Warning: package 'nlme' in library '/usr/lib/R/library' will not be updated
Warning: package 'nnet' in library '/usr/lib/R/library' will not be updated
Warning: package 'spatial' in library '/usr/lib/R/library' will not be 
updated
Warning: package 'survival' in library '/usr/lib/R/library' will not be 
updated
 >

Not possible?

I also tried

$ sudo apt install --reinstall r-cran-survival

to no avail.
>
> | 2. Installing from scratch should have this fixed automatically, right?
>
> False.

Thanks. Maybe better to install R from source then.

Göran