Upgrading R means I lose my packages

This is actually an R-sig-mac question so I am responding there.


In general, if you want to install a new version without losing the previous 
packages,  using the finder, go to Library/Receipts and remove the R.app and 
R.Gui receipts.  Then install the new version. That will keep the previous 
packages.  This is not mysterious, this is R.


Thanks to Simon et al. for the upgrade.

Bill



At 11:00 PM -0400 8/27/08, Charilaos Skiadas wrote:

On Aug 27, 2008, at 10:40 PM, Rolf Turner wrote:

On 28/08/2008, at 2:02 PM, James Milks wrote:

The title says it all.  Does anyone know of a way to save your packages 
when you upgrade to a new version of R?  This may seem petty, but I'm 
accumulating enough packages that having to download and install each of 
them anew every time I install a new version of R is rather of a pain. 
Ideally, I would like the new version of R to recognize the packages I've 
installed on the previous version without needing to reinstall the 
packages.  Is that possible?

My system: Mac OS 10.5.4.
Current R version: 2.7.1

Mac OS moves in mysterious ways, but apparently your installation moves in 
more mysterious
ways than most.

I also (by necessity, not by choice) run Mac OS.  But I certainly don't 
lose my
packages when I update R.  The new version of R certainly ``recognizes'' 
the packages
that I have installed.  No action required.

There may be something funny about *where* you have your packages 
installed, and
what environment variables you have set.

To answer your question ``Is that possible?'' --- Yes.  Not just possible,
but universal.  Except, it would seem, in your case.  What have you done
to offend the gods? :-)

Actually have had the same problem as James. By default, unless I'm 
mistaken, R will save installed packages within the "R.framework" framework 
(system-wide installation). This framework gets completely replaced when a 
new version is installed. In my system, the location of these packages is:
/Library/Frameworks/R.framework/Resources/library

So unless I am mistaken you have to take some action to prevent packages 
from being installed there. I do hope I am wrong.

	cheers,

		Rolf Turner

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

-- 
William Revelle		http://personality-project.org/revelle.html
Professor 
http://personality-project.org/personality.html
Department of Psychology             http://www.wcas.northwestern.edu/psych/
Northwestern University	http://www.northwestern.edu/
Attend  ISSID/ARP:2009               http://issid.org/issid.2009/

The standard R mechanisms for installing packages into a different  
library
apply on Mac OS X just as anywhere else.  It was not said that R was  
being run from the R.app GUI, but I'll assume that is the case.

The rw-FAQ provides detailed advice for Windows users: see

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#I-don_0027t-have-permission-to-write-to-the-R_002d2_002e7_002e2_005clibrary-directory

The differences for Mac OS users are small -- some of the names and  
how to set the library path via R_LIBS.

We arrange not to install packages within .Library on any of our  
systems -- and for most users they do not have permission to do so.

On Wed, 27 Aug 2008, William Revelle wrote:

This is actually an R-sig-mac question so I am responding there.


In general, if you want to install a new version without losing the  
previous packages,  using the finder, go to Library/Receipts and  
remove the R.app and R.Gui receipts.  Then install the new version.  
That will keep the previous packages.  This is not mysterious, this  
is R.


Thanks to Simon et al. for the upgrade.

Bill



At 11:00 PM -0400 8/27/08, Charilaos Skiadas wrote:

On Aug 27, 2008, at 10:40 PM, Rolf Turner wrote:

On 28/08/2008, at 2:02 PM, James Milks wrote:

The title says it all.  Does anyone know of a way to save your  
packages when you upgrade to a new version of R?  This may seem  
petty, but I'm accumulating enough packages that having to  
download and install each of them anew every time I install a  
new version of R is rather of a pain. Ideally, I would like the  
new version of R to recognize the packages I've installed on the  
previous version without needing to reinstall the packages.  Is  
that possible?
My system: Mac OS 10.5.4.
Current R version: 2.7.1

Mac OS moves in mysterious ways, but apparently your installation  
moves in more mysterious
ways than most.
I also (by necessity, not by choice) run Mac OS.  But I certainly  
don't lose my
packages when I update R.  The new version of R certainly  
``recognizes'' the packages
that I have installed.  No action required.
There may be something funny about *where* you have your packages  
installed, and
what environment variables you have set.
To answer your question ``Is that possible?'' --- Yes.  Not just  
possible,
but universal.  Except, it would seem, in your case.  What have  
you done
to offend the gods? :-)

Actually have had the same problem as James. By default, unless  
I'm mistaken, R will save installed packages within the  
"R.framework" framework (system-wide installation). This framework  
gets completely replaced when a new version is installed. In my  
system, the location of these packages is:
/Library/Frameworks/R.framework/Resources/library
So unless I am mistaken you have to take some action to prevent  
packages from being installed there. I do hope I am wrong.

	cheers,

		Rolf Turner

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

-- 
William Revelle		http://personality-project.org/revelle.html
Professor http://personality-project.org/personality.html
Department of Psychology             http://www.wcas.northwestern.edu/psych/
Northwestern University	http://www.northwestern.edu/
Attend  ISSID/ARP:2009               http://issid.org/issid.2009/

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

So, what it boils down to is that I'm installing my packages at too  
high of a level (I'm an administrator for my system) and should  
save them in places other than the R framework folder.

Thanks too all for the tips and links.

Jim Milks

On Aug 28, 2008, at 5:08 AM, Prof Brian Ripley wrote:

The standard R mechanisms for installing packages into a different  
library
apply on Mac OS X just as anywhere else.  It was not said that R  
was being run from the R.app GUI, but I'll assume that is the case.

The rw-FAQ provides detailed advice for Windows users: see

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s- 
the-best-way-to-upgrade_003f
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#I-don_0027t- 
have-permission-to-write-to-the-R_002d2_002e7_002e2_005clibrary- 
directory

The differences for Mac OS users are small -- some of the names  
and how to set the library path via R_LIBS.

We arrange not to install packages within .Library on any of our  
systems -- and for most users they do not have permission to do so.

On Wed, 27 Aug 2008, William Revelle wrote:

This is actually an R-sig-mac question so I am responding there.


In general, if you want to install a new version without losing  
the previous packages,  using the finder, go to Library/Receipts  
and remove the R.app and R.Gui receipts.  Then install the new  
version. That will keep the previous packages.  This is not  
mysterious, this is R.


Thanks to Simon et al. for the upgrade.

Bill



At 11:00 PM -0400 8/27/08, Charilaos Skiadas wrote:

On Aug 27, 2008, at 10:40 PM, Rolf Turner wrote:

On 28/08/2008, at 2:02 PM, James Milks wrote:

The title says it all.  Does anyone know of a way to save your  
packages when you upgrade to a new version of R?  This may  
seem petty, but I'm accumulating enough packages that having  
to download and install each of them anew every time I install  
a new version of R is rather of a pain. Ideally, I would like  
the new version of R to recognize the packages I've installed  
on the previous version without needing to reinstall the  
packages.  Is that possible?
My system: Mac OS 10.5.4.
Current R version: 2.7.1

Mac OS moves in mysterious ways, but apparently your  
installation moves in more mysterious
ways than most.
I also (by necessity, not by choice) run Mac OS.  But I  
certainly don't lose my
packages when I update R.  The new version of R certainly  
``recognizes'' the packages
that I have installed.  No action required.
There may be something funny about *where* you have your  
packages installed, and
what environment variables you have set.
To answer your question ``Is that possible?'' --- Yes.  Not  
just possible,
but universal.  Except, it would seem, in your case.  What have  
you done
to offend the gods? :-)

Actually have had the same problem as James. By default, unless  
I'm mistaken, R will save installed packages within the  
"R.framework" framework (system-wide installation). This  
framework gets completely replaced when a new version is  
installed. In my system, the location of these packages is:
/Library/Frameworks/R.framework/Resources/library
So unless I am mistaken you have to take some action to prevent  
packages from being installed there. I do hope I am wrong.

	cheers,

		Rolf Turner

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

-- 
William Revelle		http://personality-project.org/revelle.html
Professor http://personality-project.org/personality.html
Department of Psychology             http:// 
www.wcas.northwestern.edu/psych/
Northwestern University	http://www.northwestern.edu/
Attend  ISSID/ARP:2009               http://issid.org/issid.2009/

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

So, what it boils down to is that I'm installing my packages at too  
high of a level (I'm an administrator for my system) and should save  
them in places other than the R framework folder.

Thanks too all for the tips and links.

Jim Milks

On Aug 28, 2008, at 5:08 AM, Prof Brian Ripley wrote:

The standard R mechanisms for installing packages into a different  
library
apply on Mac OS X just as anywhere else.  It was not said that R  
was being run from the R.app GUI, but I'll assume that is the case.

The rw-FAQ provides detailed advice for Windows users: see

http://cran.r-project.org/bin/windows/base/rw-FAQ.html#What_0027s-the-best-way-to-upgrade_003f
http://cran.r-project.org/bin/windows/base/rw-FAQ.html#I-don_0027t-have-permission-to-write-to-the-R_002d2_002e7_002e2_005clibrary-directory

The differences for Mac OS users are small -- some of the names and  
how to set the library path via R_LIBS.

We arrange not to install packages within .Library on any of our  
systems -- and for most users they do not have permission to do so.

On Wed, 27 Aug 2008, William Revelle wrote:

This is actually an R-sig-mac question so I am responding there.


In general, if you want to install a new version without losing  
the previous packages,  using the finder, go to Library/Receipts  
and remove the R.app and R.Gui receipts.  Then install the new  
version. That will keep the previous packages.  This is not  
mysterious, this is R.


Thanks to Simon et al. for the upgrade.

Bill



At 11:00 PM -0400 8/27/08, Charilaos Skiadas wrote:

On Aug 27, 2008, at 10:40 PM, Rolf Turner wrote:

On 28/08/2008, at 2:02 PM, James Milks wrote:

The title says it all.  Does anyone know of a way to save your  
packages when you upgrade to a new version of R?  This may seem  
petty, but I'm accumulating enough packages that having to  
download and install each of them anew every time I install a  
new version of R is rather of a pain. Ideally, I would like the  
new version of R to recognize the packages I've installed on  
the previous version without needing to reinstall the  
packages.  Is that possible?
My system: Mac OS 10.5.4.
Current R version: 2.7.1

Mac OS moves in mysterious ways, but apparently your  
installation moves in more mysterious
ways than most.
I also (by necessity, not by choice) run Mac OS.  But I  
certainly don't lose my
packages when I update R.  The new version of R certainly  
``recognizes'' the packages
that I have installed.  No action required.
There may be something funny about *where* you have your  
packages installed, and
what environment variables you have set.
To answer your question ``Is that possible?'' --- Yes.  Not just  
possible,
but universal.  Except, it would seem, in your case.  What have  
you done
to offend the gods? :-)

Actually have had the same problem as James. By default, unless  
I'm mistaken, R will save installed packages within the  
"R.framework" framework (system-wide installation). This  
framework gets completely replaced when a new version is  
installed. In my system, the location of these packages is:
/Library/Frameworks/R.framework/Resources/library
So unless I am mistaken you have to take some action to prevent  
packages from being installed there. I do hope I am wrong.

	cheers,

		Rolf Turner

Haris Skiadas
Department of Mathematics and Computer Science
Hanover College

-- 
William Revelle		http://personality-project.org/revelle.html
Professor http://personality-project.org/personality.html
Department of Psychology             http://www.wcas.northwestern.edu/psych/
Northwestern University	http://www.northwestern.edu/
Attend  ISSID/ARP:2009               http://issid.org/issid.2009/

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595