Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
That thread does help and it provides enough information to solve most of my problem. However, it is not clear to me how to change the R_HOME directory so that it is not in the /Library/Frameworks/R.framework directory. This is important to me because I am providing a tool which will automatically install R and I don't want my tool to replace an existing version of R. I tried building from source, and immediately ran into two problems: 1) I don't know enough to know how to configure my build so that it doesn't use the Frameworks location 2) specifically to R 2.5, which I need, I get compiler errors. I'd like to simply take apart the framework build I get when install from the R-2.5.1.dmg. However, I'd also like this to work, even when I move this to a different location on my file system. I appreciate some guidance on this last step. Thanks, Peter ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
On Jan 26, 2012, at 4:44 PM, Peter Carr wrote: That thread does help and it provides enough information to solve most of my problem. However, it is not clear to me how to change the R_HOME directory so that it is not in the /Library/Frameworks/R.framework directory. This is important to me because I am providing a tool which will automatically install R and I don't want my tool to replace an existing version of R. I tried building from source, and immediately ran into two problems: 1) I don't know enough to know how to configure my build so that it doesn't use the Frameworks location You don't need to use the framework version of R if you don't need the GUI. If your copy will be private you can use --disable-R-framework and set rhome at install time to wherever you want (or alternatively you can set the path of the framework if you need it). Note that you'll have to re-compile all packages as well. 2) specifically to R 2.5, which I need, I get compiler errors. You'll have to share much more detail. Note that such an ancient version of R may not be buildable on your system without SDKs for older OS X versions (and note that recent Xcode tools default to 64-bit which was not supported back then so you may need to use 32-bit). I'd like to simply take apart the framework build I get when install from the R-2.5.1.dmg. It is possible, albeit convoluted. The easy part of to modify R_HOME - you simply do that in the R script. The harder part is that all binaries have absolute paths to libraries inside the framework. You will have to go through every single binary (package, module, executable) and change all paths to your new location using install_name_tool. To be honest, given how ancient your R is I wouldn't even bother and just keep it in its 2.5 folder since chances that it will clash on user's machine are close to zero. But if you choose to tackle this, you can take inspiration from this script (it uses @rpath which is a bit more flexible but requires more support from binaries): https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R-build/rpath.sh An alternative fix is to use DYLD_LIBRARY_PATH to prepend your new location of libraries. It may or may not work, depending on what you use from R. It is a bit fragile but is fairly easy to do so you can test whether it works for your particular setup of using R. However, I'd also like this to work, even when I move this to a different location on my file system. I appreciate some guidance on this last step. That is actually close to impossible unless you are ok with giving up package installation. The problem is that a) binary package have full paths encoded and b) if you compile a package it will get full path and they need a path to compile. However, if you are shipping a fixed R that will not be modified by adding packages, you can use the same idea as above with the special @executable_path prefix. You'll need to perform some gymnastics to infer R_HOME in the R script since it will by dynamic, but it's possible -- the following patch will give you an idea: https://svn.r-project.org/R-dev-web/trunk/QA/Simon/R-build/R-rpath-diff The executive summary is that what you want is possible, but not really easy. Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
I get compiler errors: ld: duplicate symbol _Rf_mkChar in CommandLineArgs.o and CConverters.o However, I did not explicitly use 32-bit. Is this a compiler flag? I will look into it. On 1/26/12 5:15 PM, Simon Urbanek wrote: 2) specifically to R 2.5, which I need, I get compiler errors. You'll have to share much more detail. Note that such an ancient version of R may not be buildable on your system without SDKs for older OS X versions (and note that recent Xcode tools default to 64-bit which was not supported back then so you may need to use 32-bit). ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
Corrected with the '-m32' flag for each of the compilers. On 1/26/12 5:22 PM, Peter Carr wrote: I get compiler errors: ld: duplicate symbol _Rf_mkChar in CommandLineArgs.o and CConverters.o However, I did not explicitly use 32-bit. Is this a compiler flag? I will look into it. On 1/26/12 5:15 PM, Simon Urbanek wrote: 2) specifically to R 2.5, which I need, I get compiler errors. You'll have to share much more detail. Note that such an ancient version of R may not be buildable on your system without SDKs for older OS X versions (and note that recent Xcode tools default to 64-bit which was not supported back then so you may need to use 32-bit). ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
On 25/01/2012 01:22, Steve Lianoglou wrote: Hi Peter, On Tue, Jan 24, 2012 at 8:06 PM, Peter Carrpc...@broadinstitute.org wrote: I, too, would like to run multiple versions of R, via command line, on Mac OS X. I have looked in vain for a clear explanation of why there can be one and only one 'Current' version of R running at a time. That is simply untrue, and would be crippling for the R developers if it were true. Assuming you have multiple R versions installed, all you need to do is to invoke their 'R' scripts directly. There is a problem caused by the way Simon installs these scripts in frameworks, so e.g. /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R starts #!/bin/sh # Shell wrapper for R executable. R_HOME_DIR=/Library/Frameworks/R.framework/Resources but all you have to do is make a copy and change that to e.g. R_HOME_DIR=/Library/Frameworks/R.framework/Versions/2.13/Resources [Which is in the thread mentioned.] And of course, no one said you have to use that particular build of R, and for serious users of command-line R a personal build will be more convenient (just like any other platform). If you have packages which use compiled code they are tied (on OS X only) to a particular 2.x.* set of R versions, but you can overcome that easily enough by using different library directories for different versions of R. You can dig up some info from this thread: https://stat.ethz.ch/pipermail/r-sig-mac/2011-September/008582.html I believe the take home message is that if you want to do this (running different R versions *simultaneously*), you can do some symlink mojo (you'll find links to examples in that thread) that will let you do so, and (for the most part), it will work. The problem arises when you have to install R packages that need be source compiled. This limitation holds if we are talking about running R versions that were released as binaries on CRAN (I'm not sure if this is true when you compile R as a framework build yourself (but my guess is that it will still be a problem in that scenario, as well)). I can link you straight to the email that says that (w/ more details), but you'd probably better be served by just going through the entirety of that thread. Hope that helps, -steve -- Brian D. Ripley, rip...@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, UKFax: +44 1865 272595 ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
Hi Peter, On Tue, Jan 24, 2012 at 8:06 PM, Peter Carr pc...@broadinstitute.org wrote: I, too, would like to run multiple versions of R, via command line, on Mac OS X. I have looked in vain for a clear explanation of why there can be one and only one 'Current' version of R running at a time. You can dig up some info from this thread: https://stat.ethz.ch/pipermail/r-sig-mac/2011-September/008582.html I believe the take home message is that if you want to do this (running different R versions *simultaneously*), you can do some symlink mojo (you'll find links to examples in that thread) that will let you do so, and (for the most part), it will work. The problem arises when you have to install R packages that need be source compiled. This limitation holds if we are talking about running R versions that were released as binaries on CRAN (I'm not sure if this is true when you compile R as a framework build yourself (but my guess is that it will still be a problem in that scenario, as well)). I can link you straight to the email that says that (w/ more details), but you'd probably better be served by just going through the entirety of that thread. Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
[R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
Hi, I have multiple R versions installed and would like to switch between them via setting the symblic link Current. To make this a bit more convenient, I defined two aliases in .bashrc: alias R2.13='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -s $d/2.13 $d/Current' alias R2.14='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -s $d/2.14 $d/Current' On executing R2.13 in the terminal, I get: rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied ln: /Library/Frameworks/R.framework/Versions/Current/2.13: Permission denied If I chown Current, I still get: rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied I (bad) solution is to put in sudo in the alias... How is it done correctly? Cheers, Marius PS: I also posted it for future reference, I've only found the idea of using ln -s on the help pages/FAQ, but not how to get around the permission issue. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
I'm not sure if you're already aware of RSwitch (available at http://r.research.att.com/), but it seems like it might be useful for what you're trying to do. Cheers, Martin On 11 October 2011 11:24, Marius Hofert marius.hof...@math.ethz.ch wrote: Hi, I have multiple R versions installed and would like to switch between them via setting the symblic link Current. To make this a bit more convenient, I defined two aliases in .bashrc: alias R2.13='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -s $d/2.13 $d/Current' alias R2.14='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -s $d/2.14 $d/Current' On executing R2.13 in the terminal, I get: rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied ln: /Library/Frameworks/R.framework/Versions/Current/2.13: Permission denied If I chown Current, I still get: rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied I (bad) solution is to put in sudo in the alias... How is it done correctly? Cheers, Marius PS: I also posted it for future reference, I've only found the idea of using ln -s on the help pages/FAQ, but not how to get around the permission issue. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
Hi Martin, thanks, but I'm aware of that. I was looking for the command-line approach :-) Cheers, Marius On 2011-10-11, at 12:43 , Martin Ellis wrote: I'm not sure if you're already aware of RSwitch (available at http://r.research.att.com/), but it seems like it might be useful for what you're trying to do. Cheers, Martin On 11 October 2011 11:24, Marius Hofert marius.hof...@math.ethz.ch wrote: Hi, I have multiple R versions installed and would like to switch between them via setting the symblic link Current. To make this a bit more convenient, I defined two aliases in .bashrc: alias R2.13='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -s $d/2.13 $d/Current' alias R2.14='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -s $d/2.14 $d/Current' On executing R2.13 in the terminal, I get: rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied ln: /Library/Frameworks/R.framework/Versions/Current/2.13: Permission denied If I chown Current, I still get: rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied I (bad) solution is to put in sudo in the alias... How is it done correctly? Cheers, Marius PS: I also posted it for future reference, I've only found the idea of using ln -s on the help pages/FAQ, but not how to get around the permission issue. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
On Oct 11, 2011, at 6:24 AM, Marius Hofert wrote: Hi, I have multiple R versions installed and would like to switch between them via setting the symblic link Current. To make this a bit more convenient, I defined two aliases in .bashrc: alias R2.13='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -s $d/2.13 $d/Current' alias R2.14='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -s $d/2.14 $d/Current' Try ln -sfn 2.13 /Library/Frameworks/R.framework/Versions/Current You'll need to be admin of the computer, otherwise you'll need sudo or change permissions. Note that for symlinks you'll need extra -h in chown otherwise you're changing ownership of the target not the link. If in doubt (ie., you messed with permissions before), run sudo chmod g+w -R /Library/Frameworks/R.framework Cheers, Simon On executing R2.13 in the terminal, I get: rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied ln: /Library/Frameworks/R.framework/Versions/Current/2.13: Permission denied If I chown Current, I still get: rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied I (bad) solution is to put in sudo in the alias... How is it done correctly? Cheers, Marius PS: I also posted it for future reference, I've only found the idea of using ln -s on the help pages/FAQ, but not how to get around the permission issue. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
On Oct 11, 2011, at 10:35 AM, Marius Hofert wrote: On 2011-10-11, at 16:19 , Simon Urbanek wrote: On Oct 11, 2011, at 6:24 AM, Marius Hofert wrote: Hi, I have multiple R versions installed and would like to switch between them via setting the symblic link Current. To make this a bit more convenient, I defined two aliases in .bashrc: alias R2.13='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -s $d/2.13 $d/Current' alias R2.14='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -s $d/2.14 $d/Current' Try ln -sfn 2.13 /Library/Frameworks/R.framework/Versions/Current Dear Simon, thanks, I put it in the alias. It now looks like this: alias R2.13='d=/Library/Frameworks/R.framework/Versions; rm $d/Current; ln -sfn $d/2.13 $d/Current' (and similarly for R 2.14) You'll need to be admin of the computer, otherwise you'll need sudo If I execute (in a new shell, as usual) R2.13, I (still) get: bash-3.2$ R2.13 rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied ln: /Library/Frameworks/R.framework/Versions/Current: Permission denied So the obvious would be to sudo R2.13, but I obtain: bash-3.2$ sudo R2.13 Password: sudo: R2.13: command not found or change permissions. Note that for symlinks you'll need extra -h in chown otherwise you're changing ownership of the target not the link. This I also realized :-) I tried that: sudo chown -h myuser /Library/Frameworks/R.framework/Versions/Current bash-3.2$ ls -al total 8 drwxrwxr-x 5 root wheel 170 Oct 11 15:54 . drwxrwxr-x 9 root wheel 306 Oct 11 11:38 .. drwxrwxr-x 8 root wheel 272 Oct 11 12:16 2.13 drwxrwxr-x 6 root wheel 204 Oct 11 11:38 2.14 lrwxr-xr-x 1 myuser wheel 45 Oct 11 15:54 Current - /Library/Frameworks/R.framework/Versions/2.13 bash-3.2$ You permissions are odd - this is not what installed R looks like, you should see ginaz:Versions$ ls -l total 8 drwxrwxr-x 6 root admin 204 Mar 26 2010 2.12 drwxrwxr-x 6 root admin 204 Jul 12 15:44 2.13 drwxrwxr-x 6 root admin 204 Oct 2 11:01 2.14 drwxrwxr-x 6 root admin 204 Oct 3 12:05 2.15 lrwxr-xr-x 1 root admin4 Oct 3 12:05 Current - 2.15 so run chown -Rh root:admin /Library/Frameworks/R.framework/ followed by to fix that. Cheers, Simon = okay, root was changed to myuser, that's good. But again, I get bash-3.2$ R2.13 rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied ln: /Library/Frameworks/R.framework/Versions/Current: Permission denied If in doubt (ie., you messed with permissions before), run sudo chmod g+w -R /Library/Frameworks/R.framework okay, thanks a lot, that's good to know. Cheers, Simon On executing R2.13 in the terminal, I get: rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied ln: /Library/Frameworks/R.framework/Versions/Current/2.13: Permission denied If I chown Current, I still get: rm: /Library/Frameworks/R.framework/Versions/Current: Permission denied I (bad) solution is to put in sudo in the alias... How is it done correctly? Cheers, Marius PS: I also posted it for future reference, I've only found the idea of using ln -s on the help pages/FAQ, but not how to get around the permission issue. ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ETH Zurich Dr. Marius Hofert RiskLab, Department of Mathematics HG E 65.2 Rämistrasse 101 8092 Zurich Switzerland Phone +41 44 632 2423 marius.hof...@math.ethz.ch http://www.math.ethz.ch/~hofertj ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
You permissions are odd - this is not what installed R looks like, you should see ginaz:Versions$ ls -l total 8 drwxrwxr-x 6 root admin 204 Mar 26 2010 2.12 drwxrwxr-x 6 root admin 204 Jul 12 15:44 2.13 drwxrwxr-x 6 root admin 204 Oct 2 11:01 2.14 drwxrwxr-x 6 root admin 204 Oct 3 12:05 2.15 lrwxr-xr-x 1 root admin4 Oct 3 12:05 Current - 2.15 so run chown -Rh root:admin /Library/Frameworks/R.framework/ followed by to fix that. followed by what? With chown -Rh root:admin /Library/Frameworks/R.framework/ I get a lot of output of the form: ... chown: /Library/Frameworks/R.framework//library/Rcpp/unitTests/runit.Module.client.package.R: Operation not permitted ... Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
On Oct 11, 2011, at 10:46 AM, Marius Hofert wrote: You permissions are odd - this is not what installed R looks like, you should see ginaz:Versions$ ls -l total 8 drwxrwxr-x 6 root admin 204 Mar 26 2010 2.12 drwxrwxr-x 6 root admin 204 Jul 12 15:44 2.13 drwxrwxr-x 6 root admin 204 Oct 2 11:01 2.14 drwxrwxr-x 6 root admin 204 Oct 3 12:05 2.15 lrwxr-xr-x 1 root admin4 Oct 3 12:05 Current - 2.15 so run chown -Rh root:admin /Library/Frameworks/R.framework/ followed by to fix that. followed by what? With chown -Rh root:admin /Library/Frameworks/R.framework/ I get a lot of output of the form: ... chown: /Library/Frameworks/R.framework//library/Rcpp/unitTests/runit.Module.client.package.R: Operation not permitted ... I should have said run as root or simply sudo chown ... Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
You'll need to run the chown command using sudo, if the files are owned by root. Martin On 11 October 2011 15:46, Marius Hofert marius.hof...@math.ethz.ch wrote: You permissions are odd - this is not what installed R looks like, you should see ginaz:Versions$ ls -l total 8 drwxrwxr-x 6 root admin 204 Mar 26 2010 2.12 drwxrwxr-x 6 root admin 204 Jul 12 15:44 2.13 drwxrwxr-x 6 root admin 204 Oct 2 11:01 2.14 drwxrwxr-x 6 root admin 204 Oct 3 12:05 2.15 lrwxr-xr-x 1 root admin 4 Oct 3 12:05 Current - 2.15 so run chown -Rh root:admin /Library/Frameworks/R.framework/ followed by to fix that. followed by what? With chown -Rh root:admin /Library/Frameworks/R.framework/ I get a lot of output of the form: ... chown: /Library/Frameworks/R.framework//library/Rcpp/unitTests/runit.Module.client.package.R: Operation not permitted ... Cheers, Simon ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
Re: [R-SIG-Mac] Multiple R versions: set Current via symbolic link: permissions?
*thanks* a lot, it now works! Cheers, Marius On 2011-10-11, at 16:48 , Simon Urbanek wrote: On Oct 11, 2011, at 10:46 AM, Marius Hofert wrote: You permissions are odd - this is not what installed R looks like, you should see ginaz:Versions$ ls -l total 8 drwxrwxr-x 6 root admin 204 Mar 26 2010 2.12 drwxrwxr-x 6 root admin 204 Jul 12 15:44 2.13 drwxrwxr-x 6 root admin 204 Oct 2 11:01 2.14 drwxrwxr-x 6 root admin 204 Oct 3 12:05 2.15 lrwxr-xr-x 1 root admin4 Oct 3 12:05 Current - 2.15 so run chown -Rh root:admin /Library/Frameworks/R.framework/ followed by to fix that. followed by what? With chown -Rh root:admin /Library/Frameworks/R.framework/ I get a lot of output of the form: ... chown: /Library/Frameworks/R.framework//library/Rcpp/unitTests/runit.Module.client.package.R: Operation not permitted ... I should have said run as root or simply sudo chown ... Cheers, Simon ETH Zurich Dr. Marius Hofert RiskLab, Department of Mathematics HG E 65.2 Rämistrasse 101 8092 Zurich Switzerland Phone +41 44 632 2423 marius.hof...@math.ethz.ch http://www.math.ethz.ch/~hofertj ___ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac
