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List: r-sig-mac
Subject: Re: [R-SIG-Mac] R3.4.0 Upgrade from R3.3.3
From: Bryan Hanson <hanson () depauw ! edu>
Date: 2017-05-01 18:39:02
Message-ID: 611789AD-47BC-453D-A1AA-3995083D6606 () depauw ! edu
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Got it — the search box drop down menu is sort of non-standard I guess, you have to \
click in just the right place to see it (left edge of box, no up down arrow icon like \
on the repo selection). I've missed this for nearly 10 years!
Thanks for the details Roy.
Bryan
> On May 1, 2017, at 2:31 PM, Roy Mendelssohn - NOAA Federal \
> <roy.mendelssohn@noaa.gov> wrote:
> Hi Bryan:
>
> What you need to do is launch R-app and select the "Package Installer" GUI. Let \
> the usual list of CRAN binaries come up. The search field to the upper right has a \
> drop down menu if you look closely, and one option is to "Select packages from R \
> 3.3" , chose that. You think that this will appear in the search box, instead if \
> you look closely you will see that those packages have indeed been selected in the \
> list of packages. Then hit "Install Selected" and it will go.
> The main problem I had was more and more they are bricking our computers. I still \
> have R in /LIbrary/Frameworks/R, and my regular user does not have access to that. \
> I had to go in as an admin user, which in my case takes some work (you don't want \
> to know), and then it all worked fine.
> HTH,
>
> -Roy
>
>
>
> > On May 1, 2017, at 11:19 AM, Bryan Hanson <hanson@depauw.edu> wrote:
> >
> > Roy, I'm interested in how you got it to work. Can you elaborate? What do you \
> > select from where, and how did permissions affect what you see? Thanks, Bryan
> >
> > > On May 1, 2017, at 1:51 PM, Roy Mendelssohn - NOAA Federal \
> > > <roy.mendelssohn@noaa.gov> wrote:
> > > Ignore the previous email. I was having permission problems, got it to work.
> > >
> > > -Roy
> > >
> > > > On May 1, 2017, at 9:15 AM, Roy Mendelssohn - NOAA Federal \
> > > > <roy.mendelssohn@noaa.gov> wrote:
> > > > I am not getting this. In the drop down box where it usually defaults to \
> > > > CRAN (binaries) what do I select. I tried pasting in exactly what u=you \
> > > > said and don't get anything back.
> > > > Thanks for any help.
> > > >
> > > > -Roy
> > > >
> > > >
> > > > > On Apr 23, 2017, at 5:16 PM, Simon Urbanek <simon.urbanek@r-project.org> \
> > > > > wrote:
> > > > > Note that if you use R.app and standard locations you can simply select \
> > > > > "Select packages from R 3.3" in the package installer search box and hit \
> > > > > Install Selected.
> > > > > Cheers,
> > > > > Simon
> > > > >
> > > > >
> > > > >
> > > > > > On Apr 23, 2017, at 10:47 AM, Roy Mendelssohn - NOAA Federal \
> > > > > > <roy.mendelssohn@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@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@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@stats.ox.ac.uk
> > > > > > > Emeritus Professor of Applied Statistics, University of Oxford
> > > > > >
> > > > > > **********************
> > > > > > "The contents of this message do not reflect any position of the U.S. \
> > > > > > Government or NOAA."
> > > > > > **********************
> > > > > > Roy Mendelssohn
> > > > > > Supervisory Operations Research Analyst
> > > > > > NOAA/NMFS
> > > > > > Environmental Research Division
> > > > > > Southwest Fisheries Science Center
> > > > > > ***Note new street address***
> > > > > > 110 McAllister Way
> > > > > > Santa Cruz, CA 95060
> > > > > > Phone: (831)-420-3666
> > > > > > Fax: (831) 420-3980
> > > > > > e-mail: Roy.Mendelssohn@noaa.gov www: http://www.pfeg.noaa.gov/
> > > > > >
> > > > > > "Old age and treachery will overcome youth and skill."
> > > > > > "From those who have been given much, much will be expected"
> > > > > > "the arc of the moral universe is long, but it bends toward justice" -MLK \
> > > > > > Jr.
> > > > > > _______________________________________________
> > > > > > R-SIG-Mac mailing list
> > > > > > R-SIG-Mac@r-project.org
> > > > > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> > > > > >
> > > > >
> > > >
> > > > **********************
> > > > "The contents of this message do not reflect any position of the U.S. \
> > > > Government or NOAA."
> > > > **********************
> > > > Roy Mendelssohn
> > > > Supervisory Operations Research Analyst
> > > > NOAA/NMFS
> > > > Environmental Research Division
> > > > Southwest Fisheries Science Center
> > > > ***Note new street address***
> > > > 110 McAllister Way
> > > > Santa Cruz, CA 95060
> > > > Phone: (831)-420-3666
> > > > Fax: (831) 420-3980
> > > > e-mail: Roy.Mendelssohn@noaa.gov www: http://www.pfeg.noaa.gov/
> > > >
> > > > "Old age and treachery will overcome youth and skill."
> > > > "From those who have been given much, much will be expected"
> > > > "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
> > > >
> > >
> > > **********************
> > > "The contents of this message do not reflect any position of the U.S. \
> > > Government or NOAA."
> > > **********************
> > > Roy Mendelssohn
> > > Supervisory Operations Research Analyst
> > > NOAA/NMFS
> > > Environmental Research Division
> > > Southwest Fisheries Science Center
> > > ***Note new street address***
> > > 110 McAllister Way
> > > Santa Cruz, CA 95060
> > > Phone: (831)-420-3666
> > > Fax: (831) 420-3980
> > > e-mail: Roy.Mendelssohn@noaa.gov www: http://www.pfeg.noaa.gov/
> > >
> > > "Old age and treachery will overcome youth and skill."
> > > "From those who have been given much, much will be expected"
> > > "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
> > >
> > > _______________________________________________
> > > R-SIG-Mac mailing list
> > > R-SIG-Mac@r-project.org
> > > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
>
> **********************
> "The contents of this message do not reflect any position of the U.S. Government or \
> NOAA."
> **********************
> Roy Mendelssohn
> Supervisory Operations Research Analyst
> NOAA/NMFS
> Environmental Research Division
> Southwest Fisheries Science Center
> ***Note new street address***
> 110 McAllister Way
> Santa Cruz, CA 95060
> Phone: (831)-420-3666
> Fax: (831) 420-3980
> e-mail: Roy.Mendelssohn@noaa.gov www: http://www.pfeg.noaa.gov/
>
> "Old age and treachery will overcome youth and skill."
> "From those who have been given much, much will be expected"
> "the arc of the moral universe is long, but it bends toward justice" -MLK Jr.
>
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