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

2017-04-23 Thread Roy Mendelssohn - NOAA Federal 
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  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 
>>>  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,  rip...@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.mendelss...@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

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

2017-04-23 Thread Prof Brian Ripley 
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 
 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,  rip...@stats.ox.ac.uk
Emeritus Professor of Applied Statistics, University of Oxford

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac

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

2017-04-23 Thread peter dalgaard 
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 
>  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
> 
> **
> "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.mendelss...@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

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

___
R-SIG-Mac mailing list
R-SIG-Mac@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-mac