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smoothest way to upgrade R, say from 2.6.1 to 2.6.2?
5 messages · Galkowski, Jan, Stefan Grosse, Gabor Grothendieck +1 more
On Thursday 13 March 2008 06:05:15 pm Galkowski, Jan wrote:
GJ> (1) How do people manage an upgrade, from 2.6.1, say, to 2.6.2? 2.6.2 GJ> will create its own subdirectory, obliging a copy of library contents to GJ> the new spot. The documents are easier. You forgot to enlighten us about your system. From what you are telling I would guess its Windows (XP?). On my windows machine I install R in the very same directory of the old R. So you could create programs/R and there install your R but of course you must then alternate the suggested directory during the installation. GJ> GJ> (2) The problem with simply copying library contents is a fear of upward GJ> incompatibilities. Am I worrying for naught here? Are packages upward GJ> compatible but possibly not downwardly so? There is no problem within minor releases like 2.6.1 -> 2.6.2 but on greater "jumps" update.packages offers the option checkbuilt which if set TRUE updates the packages to their next built. So if 2.7.0 is released and you install that are over your old you should enable this option. GJ> (3) What about changing shortcuts, places for .Rprofile and the like? GJ> Do people have scripts that do all these things at once? See above GJ> GJ> It would be nice to have a single control file where R binaries and GJ> libraries and the like could be specified. That way, all that would GJ> need to be done is edit one file with an uptick on a point release GJ> number, say, and things would be fine. I don't think this is necessary. Cheers Stefan
Microeconomics University of Erfurt
I think Stefan has answered this so I will just add this about batchfiles. In the batchfiles distrirbution: http://batchfiles.googlecode.com is a file Rgui.bat. If you put that anywhere in your path and make your shortcut to that instead of to R itself then it will find the most recent version of R from the registry and start that so you don't have to update shortcuts each time you change R versions. There are also Rcmd.bat, sweave.bat and similar versions for the corresponding tasks. Using those you never have to set your path to R when installing or upgrading R on Windows. The most recent version of batchfiles is for Vista and the next to most recent is for XP as per home page. If you do want to move or copy your packages from one library to another movedir.bat and copydir.bat will do that. You can then use checkbuilt if its a major version change. There are also some other methods described in the Links on the home page.
On Thu, Mar 13, 2008 at 1:23 PM, Stefan Grosse <singularitaet at gmx.net> wrote:
On Thursday 13 March 2008 06:05:15 pm Galkowski, Jan wrote: GJ> (1) How do people manage an upgrade, from 2.6.1, say, to 2.6.2? 2.6.2 GJ> will create its own subdirectory, obliging a copy of library contents to GJ> the new spot. The documents are easier. You forgot to enlighten us about your system. From what you are telling I would guess its Windows (XP?). On my windows machine I install R in the very same directory of the old R. So you could create programs/R and there install your R but of course you must then alternate the suggested directory during the installation. GJ> GJ> (2) The problem with simply copying library contents is a fear of upward GJ> incompatibilities. Am I worrying for naught here? Are packages upward GJ> compatible but possibly not downwardly so? There is no problem within minor releases like 2.6.1 -> 2.6.2 but on greater "jumps" update.packages offers the option checkbuilt which if set TRUE updates the packages to their next built. So if 2.7.0 is released and you install that are over your old you should enable this option. GJ> (3) What about changing shortcuts, places for .Rprofile and the like? GJ> Do people have scripts that do all these things at once? See above GJ> GJ> It would be nice to have a single control file where R binaries and GJ> libraries and the like could be specified. That way, all that would GJ> need to be done is edit one file with an uptick on a point release GJ> number, say, and things would be fine. I don't think this is necessary. Cheers Stefan -- Microeconomics University of Erfurt
______________________________________________ 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.
If this _is_ Windows, the question is discussed in detail in the rw-FAQ. That document also discusses how to install packages into a site or personal library which can make upgrading easier. Another consideration not told to us was whether one wants to keep around a working copy of the older version. My dept does so (so students can use a consistent version when preparing their theses, for example), and that affects the choice of strategy.
On Thu, 13 Mar 2008, Stefan Grosse wrote:
On Thursday 13 March 2008 06:05:15 pm Galkowski, Jan wrote: GJ> (1) How do people manage an upgrade, from 2.6.1, say, to 2.6.2? 2.6.2 GJ> will create its own subdirectory, obliging a copy of library contents to GJ> the new spot. The documents are easier. You forgot to enlighten us about your system. From what you are telling I would guess its Windows (XP?). On my windows machine I install R in the very same directory of the old R. So you could create programs/R and there install your R but of course you must then alternate the suggested directory during the installation. GJ> GJ> (2) The problem with simply copying library contents is a fear of upward GJ> incompatibilities. Am I worrying for naught here? Are packages upward GJ> compatible but possibly not downwardly so? There is no problem within minor releases like 2.6.1 -> 2.6.2 but on greater "jumps" update.packages offers the option checkbuilt which if set TRUE updates the packages to their next built. So if 2.7.0 is released and you install that are over your old you should enable this option. GJ> (3) What about changing shortcuts, places for .Rprofile and the like? GJ> Do people have scripts that do all these things at once? See above GJ> GJ> It would be nice to have a single control file where R binaries and GJ> libraries and the like could be specified. That way, all that would GJ> need to be done is edit one file with an uptick on a point release GJ> number, say, and things would be fine. I don't think this is necessary. Cheers Stefan -- Microeconomics University of Erfurt
______________________________________________ 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.
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
Thanks to Stefan Grosse, Gabor Grothendieck, and Professor Ripley for all this guidance. I have collected the details, concatenating them below, for future reference. Sorry if attributions got muddled. It is WinXP Pro in the primary, and there's no need to keep around older versions. But there are (Debian) Linux users here interested in both the same question, and any caches of R-related shell goodies that might be out there, comparable to "batchfiles", both for upgrades and other things, like maybe spawning multiple R processes and the like, or running headless Rs on several servers at once. I apologize for leaving that out, but I thought putting out a wild guess on this might draw comment and help. It did. Thanks much, again. -----Original Message----- From: Prof Brian Ripley [mailto:ripley at stats.ox.ac.uk] Sent: Thursday, March 13, 2008 2:12 PM To: Stefan Grosse Cc: r-help at r-project.org; Galkowski, Jan Subject: Re: [R] smoothest way to upgrade R, say from 2.6.1 to 2.6.2? If this _is_ Windows, the question is discussed in detail in the rw-FAQ. That document also discusses how to install packages into a site or personal library which can make upgrading easier. Another consideration not told to us was whether one wants to keep around a working copy of the older version. My dept does so (so students can use a consistent version when preparing their theses, for example), and that affects the choice of strategy.
On Thu, 13 Mar 2008, Stefan Grosse wrote:
On Thursday 13 March 2008 06:05:15 pm Galkowski, Jan wrote: GJ> (1) How do people manage an upgrade, from 2.6.1, say, to 2.6.2? GJ> 2.6.2 will create its own subdirectory, obliging a copy of library
GJ> contents to the new spot. The documents are easier. You forgot to enlighten us about your system. From what you are telling I would guess its Windows (XP?). On my windows machine I install R in the very same directory of the old R. So you could create
programs/R and there install your R but of course you must then alternate the suggested directory during the installation. GJ> GJ> (2) The problem with simply copying library contents is a fear of GJ> upward incompatibilities. Am I worrying for naught here? Are GJ> packages upward compatible but possibly not downwardly so? There is no problem within minor releases like 2.6.1 -> 2.6.2 but on greater "jumps" update.packages offers the option checkbuilt which if set TRUE updates the packages to their next built. So if 2.7.0 is released and you install that are over your old you should enable this
option.
GJ> (3) What about changing shortcuts, places for .Rprofile and the
like?
GJ> Do people have scripts that do all these things at once? See above GJ> GJ> It would be nice to have a single control file where R binaries GJ> and libraries and the like could be specified. That way, all that
GJ> would need to be done is edit one file with an uptick on a point GJ> release number, say, and things would be fine.
[snip]
GJ> Where does this "update.packages" with the "checkbuilt" live? just type update.packages() in case of a major version change update.packages(checkbuilt=T) GJ> Is all this described on the Wiki some place? Or in the docs? In the docs run ?update.packages or have a look at the admin guide http://cran.r-project.org/doc/manuals/R-admin.html
[snip]
I think Stefan has answered this so I will just add this about batchfiles. In the batchfiles distrirbution: http://batchfiles.googlecode.com is a file Rgui.bat. If you put that anywhere in your path and make your shortcut to that instead of to R itself then it will find the
most
recent version of R from the registry and start that so you don't have to update shortcuts each time you change R versions. There are also Rcmd.bat, sweave.bat and similar versions for the corresponding tasks. Using those you never have to set your path to R when installing or upgrading R on Windows. The most recent version of batchfiles is for Vista and the next to most recent is for XP as per home page. If you do want to move or copy your packages from one library to another movedir.bat and copydir.bat will do that. You can then use checkbuilt if its a major version change. There are also some other methods described in the Links on the home page.