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
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