[R] Upgrade R?
Cem Girit
girit at comcast.net
Mon Nov 14 23:42:22 CET 2011
Hello all,
I received many emails to my post on this issue. None of the answers
were able to resolve all the issues experienced by many but helped me to
understand the issues. . But consıderıng the avaılable OSs to install on,
many packages to install, and the fact that R is a product of open source
effort, it is still impressive that it works. The desirable solution surely,
is to have a mnu entry in R GUI to update the whole while managing library
packages with a dialog.
The problem Kevin and I had in removing the old R version 2.13.1 is
not solved. We had to delete the old version and remove the registry entries
manually since the Window's uninstall program gives an error using the
available uninstall.dat file and does not uninstall it.
In order to help others in similar issues, I gathered all the
responses I received on this issue (thankfully from Kevin Burton, Bert
Gunter, Uwe Ligges, Eric Neuwirth, Richard M. Heiberger, David Wolfskill,
R. Michael Weylandt and Thomas Baier) and compiled them below. I hope, the
experts, in the light of these issues, would update the R-Manuals/Online
help etc. for successful updates.
Updating to the new version of R:
There are basically two strategies for R upgrading on windows.
A) The first is to install a new R version and copy paste all the packages
to the new R installation folder.
The following methods explain different ways to achieve this.
1. Run the following script in R-Console:
>update.packages(checkBuilt=TRUE)
This will update all the user installed packages to new version. But
it will overwrite the old versions of the packages.
Ref:
http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Window
2. First you install the new version, then run this in the old version:
#--run in the old version of R
setwd("C:/Temp/")
packages <- installed.packages()[,"Package"]
save(packages, file="Rpackages")
Followed by this in the new version:
#--run in the new version
setwd("C:/Temp/")
load("Rpackages")
for (p in setdiff(packages, installed.packages()[,"Package"]))
install.packages(p)
Ref:
http://stackoverflow.com/questions/1401904/painless-way-to-install-a-new-ver
sion-of-r
3. Run the following command on R-console:
>rownames(installed.packages())
This will tell you the names of all packages of the version of R in
which you are running the command.
Then compare this list with the list given at
http://cran.r-project.org/doc/FAQ/R-FAQ.html#R-Add_002dOn-Packages .
The installed package differences between these two lists are the
user installed packages.
4. The "Other" section on CRAN has an item called "batch files".
In there is copydir.bat which allows you to copy packages from one
version of R to another version.
It will respect already installed packages in the destination
directory and not overwrite them with possibly older versions.
Ref: http://cran.r-project.org/ . Download batchfiles_0.6-6.zip from
there.
5. If you want to install packages from SourceForge without overwriting them
from CRAN:
Ref:
http://stackoverflow.com/questions/3971815/automagically-update-packages-ins
talled-from-r-forge
6. If you also have statconnDCOM (rcom) installed, here are the recommend
steps:
a. Install the latest version of R
b. Copy your installed packages from the old version of R to the new
version of R.
copydir "c:\Program Files\R\R-2.3.1\library" "c:\Program
Files\R\R-2.14.0\library"
c. Start R with the -vanilla command line option:
"C:\Program files\R\R-2.14.0\bin\Rgui.exe" --vanilla
d. Update the packages:
update.packages(checkBuilt=TRUE, ask=FALSE)
e. Configure R with the latest version of rcom:
library(rcom)
comRegisterRegistry()
Ref:
http://learnserver.csd.univie.ac.at/rcomwiki/doku.php?id=wiki:how_to_upgrade
_r_with_our_packages_installed
Running comRegsterRegistry() gives NULL. Then the
application using statConn works fine.
B) The second is to have a global R package folder, each time synced to the
most current R installation (thus saving us the time of copying the package
library each we upgrade R)."How to upgrade R on windows XP - another
strategy" which explains how to upgrade R using the simple two-liner
codesource:
source("http://www.r-statistics.com/wp-content/uploads/2010/04/upgrading-R-o
n-windows.r.txt")
New.R.RunMe()
p.s: If this is the first time you are upgrading R using this
method, then first run the following two lines on your old R installation
(before running the above code in the new R intallation):
source("http://www.r-statistics.com/wp-content/uploads/2010/04/upgrading-R-o
n-windows.r.txt")
Old.R.RunMe()
Ref:
http://www.r-statistics.com/2010/04/changing-your-r-upgrading-strategy-and-t
he-r-code-to-do-it-on-windows/
http://www.r-statistics.com/2011/04/how-to-upgrade-r-on-windows-7/
This update leaves two library directories one in
the "C:\Program Files\R\library" directory and the other in the "C:\Program
Files\R\R-2.14.0\library" directory. Deleting the second makes R console
confused since it cannot find even the basic library. But undeleting it, is
extra ~0.5GB space.
Uninstalling the old version of R:
After all the packages are updated and the depended ones such as
rcom were registered, the old version can be uninstalled through "Programs
and Features" option of Windows.
Problems with installing the new version and uninstalling the old version:
There are many problems reported. Here are a few:
1. Windows 7 issues:
Windows security, UAC, installation directories etc. See:
Ref:
http://www.r-statistics.com/2011/04/how-to-upgrade-r-on-windows-7/
2. Uninstalling error "Internal error: Cannot find utCompiledCode record for
this version of uninstaller".
You can delete the old installation directory and remove the
registry entries manually or use a program such as CCleaner to remove the
registry entries.
Cem
-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Gene Leynes
Sent: Monday, November 14, 2011 4:43 PM
To: r-help at r-project.org
Cc: Kevin Burton
Subject: Re: [R] Upgrade R?
I have had similar problems.
I have several installations of R and now I have no control over which one
opens when I try opening a RData file. The RGUI is registered more than
once, but they all have the exact same appearance in the "choose programs"
menu.
It's become particularly annoying now that new versions of R seem to be
published with ever increasing frequency.
On Mon, Nov 14, 2011 at 10:11 AM, Kevin Burton
<rkevinburton at charter.net>wrote:
> I am also using statConn so I will let you know if I hear anything new.
>
> -----Original Message-----
> From: Cem Girit [mailto:girit at comcast.net]
> Sent: Monday, November 14, 2011 8:52 AM
> To: 'Kevin Burton'
> Cc: r-help at r-project.org
> Subject: RE: [R] Upgrade R?
>
> Hello Kevin,
>
> Thank you. I will delete the folder and run an application
> called CCleaner (free). That will remove all the broken registry entries.
>
> There should be a problem free update path for R installation.
> As you rightfully mentioned the R- manual is not clear about package
> update issues. I received many helpful suggestions on the update path
> but some of the them were contradictory in the order of steps to be
> taken. I am also using statConn (DCOM) interface for programming. So
> my problems are multifold. I will compile the answers I received on
> the R version update issue and publish them so that that the experts
> could put them into more effective use.
>
> Sincerely,
>
> Cem
>
>
> -----Original Message-----
> From: Kevin Burton [mailto:rkevinburton at charter.net]
> Sent: Sunday, November 13, 2011 4:11 PM
> To: 'Cem Girit'
> Subject: RE: [R] Upgrade R?
>
> I don't know if it was correct but I just removed the directory and
> then searched and removed all instances in the registry that referred
> to 2.13.1 (in my case searching for this seemed to only return
> references to 'R'). I have since been given some links that address
> specific registry entries but I haven't had any problem yet with my
> 'slash and burn' approach. It removed it from the 'Install/Uninstall'
> list with windows so it seems to have be removed and the disk space that
2.13.2 took up has been reclaimed.
>
> Hope this helps. Let me know if you find any more definitive answers.
>
> Thanks.
>
> Kevin
>
> -----Original Message-----
> From: Cem Girit [mailto:girit at comcast.net]
> Sent: Saturday, November 12, 2011 6:33 PM
> To: 'Kevin Burton'
> Subject: RE: [R] Upgrade R?
>
> Hello Kevin,
>
> I am getting the same error "utCompiledCode..." since I
> installed
> R2.14 while R2.13 existed. How did you get rid of R2.13 eventually?
> Did you just delete it? If so, how did you clean the registry?
>
> Thank you,
>
> Cem
>
> -----Original Message-----
> From: r-help-bounces at r-project.org
> [mailto:r-help-bounces at r-project.org]
> On
> Behalf Of Kevin Burton
> Sent: Thursday, November 10, 2011 11:54 AM
> To: 'jose Bartolomei'; 'R Help'
> Subject: Re: [R] Upgrade R?
>
> The problem with this documentation is two-fold. One it seems to
> concentrate on building from source which I don't need. Two it doesn't
> address the upgade. I have a number of packages and so I need to do
> what has been suggested and install the latest version *first*. Then
> copy the libraries (packages). Then uninstall the previous version. It
> is on this last step that I am stuck on right now. The last link on
> uninstalling R manually was what I needed. Thank you.
>
>
>
> Kevin
>
>
>
> From: jose Bartolomei [mailto:surfprjab at hotmail.com]
> Sent: Thursday, November 10, 2011 10:19 AM
> To: rkevinburton at charter.net; R Help
> Subject: RE: [R] Upgrade R?
>
>
>
> Hi,
> Don't know if this will help you but...
> In my short experience and following the guidelines you should first
> uninstall R.
>
>
> http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-
> Window
> s
>
> Unistall it from the Windows control panel.
>
> The old R version libraries file will be kept on machine.
> For example : C:\Program Files\R\R-2.13.0\library
>
> Then install the new version via:
>
> http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-
> Window
> s
>
> You can copy/paste libraries from the old version R library file to
> the new one.
> C:\Program Files\R\R-2.14.0\library
>
> There is too an function named:
> ?update.packagee
>
> If above was what you did, then there is a post on Uninstalling R
manually:
>
>
> http://learnserver.csd.univie.ac.at/rcomwiki/doku.php?id=wiki:uninstal
> ling_r
> _manually
>
> Regards,
> Jose
>
>
> > From: rkevinburton at charter.net
> > To: r-help at r-project.org
> > Date: Thu, 10 Nov 2011 09:07:20 -0600
> > Subject: Re: [R] Upgrade R?
> >
> > Since apparently there is no one familiar with this error message
> > let me rephrase the question. Is there a 'manual' process to fully
> > remove a
> version
> > of 'R' from my machine? This is a Window PC running Windows 7.
> >
> >
> >
> > Thank you.
> >
> >
> >
> > Kevin
> >
> >
> >
> > From: Kevin Burton [mailto:rkevinburton at charter.net]
> > Sent: Monday, November 07, 2011 2:23 PM
> > To: 'r-help at r-project.org'
> > Subject: Upgrade R?
> >
> >
> >
> > I am trying to upgrade to R 2.14 from R 2.13.1 I have compied all
> > the libraries from the 'library' directory in my existing
> > installation
> (2.13.1)
> > to the installed R 2.14. Now I want to uninstall the old
> > installation (R
> > 2.13.1) and I get the error:
> >
> >
> >
> > Internal Error: Cannot find utCompiledCode record for this version
> > of the uninstaller.
> >
> >
> >
> > Any ideas?
> >
> >
> >
> > Kevin
> >
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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