R SIG Debian - Apr 2017 - 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

On 25 April 2017 at 14:58, G?ran Brostr?m 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.
 
| 2. Installing from scratch should have this fixed automatically, right?

False.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

On 2017-04-25 15:50, Dirk Eddelbuettel wrote:
>
> On 25 April 2017 at 14:58, G?ran Brostr?m 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.

G?ran

Am Dienstag, 25. April 2017, 08:50:34 schrieb Dirk
Eddelbuettel:
> On 25 April 2017 at 14:58, G?ran Brostr?m 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
This looks similar to what I got this morning when I tested my (unreleased) 
backport of R 3.4.0 to Debian jessie. My test was

library(MASS)
example(rlm)

and there was an object that was not found. I am on a train on the way to a 
meeting right now, so I can not look into it at the moment. Maybe a side effect 
of the new registration requirements for compiled objects?


Cheers,

Johannes