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

Mon May 1 20:39:02 CEST 2017

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 at 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 at 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 at 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 at 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 at 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 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"))
>>>>>>> [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
>>>>>> 
>>>>>> **********************
>>>>>> "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 at 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 at 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 at 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 at 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 at 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 at 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.
> 