Recommendation for updating packages such as nlme

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Recommendation for updating packages such as nlme

Frank Harrell
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*


        [[alternative HTML version deleted]]

______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Frank Harrell
Department of Biostatistics, Vanderbilt University
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Re: 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 <[hidden email]> 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*
>
>
> [[alternative HTML version deleted]]
>
>______________________________________________
>[hidden email] mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.