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.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.
R3.4.0 Upgrade from R3.3.3
7 messages · Brian Ripley, Simon Urbanek, Roy Mendelssohn - NOAA Federal +1 more
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 ********************** "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.
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Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
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
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.
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.
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Thanks. Very nice touch. -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.
Missed that one, Simon. Usually I go straight for the Terminal or the Rstudio embedding. Do we have a command line variant of this already? -pd
On 24 Apr 2017, at 02:16 , 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
_______________________________________________ R-SIG-Mac mailing list R-SIG-Mac at 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.mes at cbs.dk Priv: PDalgd at gmail.com