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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Jeff Newmiller
2016-Feb-16 20:53 UTC
[R] Recommendation for updating packages such as nlme
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* > > > [[alternative HTML version deleted]] > >______________________________________________ >R-help at r-project.org 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]]