[R] Recommendation for updating packages such as nlme

[Jeff Newmiller]

Isn't /usr/local for software your sysadmin (you, when you wear that hat) have compiled, while /usr/lib is managed by the system package manager (apt-get for Ubuntu)?

FWIW I usually only manage my personal R library and ignore the system R library... I never specify instLib myself, and never run R as root. There might be advantages to specifying instLib, but I have not encountered them. 
-- 
Sent from my phone. Please excuse my brevity.

On February 16, 2016 12:01:22 PM PST, Frank Harrell <f.harrell at vanderbilt.edu> wrote:
>I use this function to update my installed R packages:
>
>updatePac <- function (checkBuilt = FALSE, ...)
>update.packages(repos = "http://cran.rstudio.com", instlib = 
>"/usr/local/lib/R/site-library",
>     checkBuilt = checkBuilt, ...)
>
>When I type updatePac() I get:
>
>Warning: package 'MASS' 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 'mgcv' 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
>
>Should I not try to update recommended packages in 
>/usr/local/lib/R/site-library on my Ubuntu system but specify 
>/usr/lib/R/library instead?
>
>-- 
>------------------------------------------------------------------------
>Frank E Harrell Jr 	Professor and Chairman 	School of Medicine
>
>	Department of *Biostatistics* 	*Vanderbilt University*
>
>
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>
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