[R-SIG-Mac] R3.4.0 Upgrade from R3.3.3

Roy Mendelssohn - NOAA Federal roy.mendelssohn at noaa.gov
Sun Apr 23 16:47:55 CEST 2017

Thanks to all, particularly the script to aid in the update.  In the past when I just copied,  I had problems with some packages.


> 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"))
> [1] 10477
> > 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
Supervisory Operations Research Analyst
Environmental Research Division
Southwest Fisheries Science Center
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