On Apr 23, 2017, at 10:47 AM, Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote:
Thanks to all, particularly the script to aid in the update. In the past when I just copied, I had problems with some packages.
-Roy
On Apr 23, 2017, at 7:09 AM, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
Note that at the moment there are many missing binary packages for 3.4.0, and BioC will update all their versions when BioC 3.5 is released this coming week. So I would wait a few days before updating, especially if you prefer to use binary packages.
nrow(available.packages(, type="source"))
nrow(available.packages(, type="binary"))
[1] 9779
whereas for 3.3.3 10356 are available.
On 23/04/2017 09:35, peter dalgaard wrote:
Yes, especially this time, since the toolchain has been updated.
My favourite procedure for this goes like
(pkgs <- .libPaths())
(pkgs.old <- sub("3.4", "3.3", pkgs, fixed=TRUE))
(pkgs.new <- setdiff(list.files(pkgs.old), list.files(pkgs)))
Check for sanity(!), then install.packages(pkgs.new). Things may need modification if yor setup involves personalized libraries, multiple repos, etc.
Just copying the entire directory followed by update.packages(checkBuilt=TRUE) will overwrite packages from the installation of 3.4 and not all of those are CRAN based.
[To tell the truth, I don't usually practice what I preach. I just install the missing packages when it turns out that I need them...]
-pd
On 23 Apr 2017, at 05:49 , Roy Mendelssohn - NOAA Federal <roy.mendelssohn at noaa.gov> wrote:
I keep forgetting. So if I jump from R3.3.3 to R3.4.0 is it necessary (or at least advisable) to re-install packages?
Thanks,
-Roy
--
Brian D. Ripley, ripley at stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford
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Roy Mendelssohn
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Environmental Research Division
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