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Update R, keep packages

3 messages · Wilmar Igl, Uwe Ligges, Eric Archer

Original
Wilmar Igl
# 
Hi,

when updating R I continuously face the problem that I have to reinstall 
packages or copy them into the new R library path.

Is there a smart way of configuring R (.Rprofile) so the packages 
installed under older R versions (different lib paths) are 
included/found by newer R versions (e.g. R site archive).
What problems due to version conflicts/out-of-date packages can arise?

I am working with R on a Linux server.

Thanks in advance,

Will
Uwe Ligges
#
Will wrote:
See the manual R Installation and Administration on how to use library 
trees and how to update all packages for the recent version of R. If you 
do not recompile / update for a new major release of R, some packages 
(and packages that depend on them) may not work anymore (due to API 
changes, changes in S4 classes and so on).

Uwe Ligges
Eric Archer
# 
Will,

Below are the contents of my Rprofile.site file.  It makes sure that I 
have all of the packages I use regularly always up to date every time I 
start R.
I don't know if it is the "smart" way, but it works for me.  I'd be more 
than happy to get suggestions on improvements from the expeRts.

Cheers,
eric


local({
  repos <- getOption("repos")
  repos["CRAN"] <- "http://cran.stat.ucla.edu"
  options(digits = 3, stringsAsFactors = FALSE, repos = repos)
  library(grDevices)
  windows.options(record = TRUE)
  library(utils)
  update.packages(ask = FALSE)
  my.packages <- c("adapt", "ade4", "ape", "BRugs", "cluster", "coda", 
"fields", "gpclib",
    "Geneland", "genetics", "gpclib", "Hmisc", "lattice", "mapproj", 
"maps", "maptools",     "MASS",
    "R.oo", "R.utils", "randomForest", "rmetasim", "rpart", "sgeostat", 
"shapefiles",
    "sm", "sp", "spatial", "spatstat", "splancs")
  to.download <- which(!my.packages %in% rownames(installed.packages()))
  if(length(to.download) > 0) install.packages(my.packages[to.download], 
clean = TRUE)
})
Will wrote: