Hi I want to use a special package (openMx: http://openmx.psyc.virginia.edu/installing-openmx) that runs currently only on R 2.9 but I have R 2.10 installed (from CRAN). How can I do to have the two versions ( 2.9 and czrrent 2.10) running? Is there a trick with apt-get or should I compile 2.9 from the sources? And if yes, how can I specify a special path for R 2.9 so that by default 2.10 is used? Thanks a lot! Matthieu Stigler
How to have multiple versions of R on Ubuntu 8.04
6 messages · Michael Rutter, Matthieu Stigler, Paul Johnson
Matthieu, Have you tried installing it? We have just updated the versions of R on CRAN and maybe the bug the package website mentions have been fixed. In order to have multiple version of R installed, you will need to build the second version from source. Here are the details: http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Unix_002dalikes You must be very careful to install R in a different location and have a different location for the lib files. Read carefully through the section of Unix-like systems to see which options you need to set. The good news is that you can always reinstall R 2.10 from apt-get or synaptic if the versions cross. Another option to consider is using a virtual machine (I use Virtual Box, which is open source) with the needed version of R on it. You can share data files between the host and virtual machine, if needed. Hope this helps, Michael
Matthieu Stigler wrote:
Hi I want to use a special package (openMx: http://openmx.psyc.virginia.edu/installing-openmx) that runs currently only on R 2.9 but I have R 2.10 installed (from CRAN). How can I do to have the two versions ( 2.9 and czrrent 2.10) running? Is there a trick with apt-get or should I compile 2.9 from the sources? And if yes, how can I specify a special path for R 2.9 so that by default 2.10 is used? Thanks a lot! Matthieu Stigler
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Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College Station Road Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter
Dear Michael Thanks a lot for your quick answer! Michael Rutter a ?crit :
Matthieu, Have you tried installing it? We have just updated the versions of R on CRAN and maybe the bug the package website mentions have been fixed.
Yes I tried and unfortunately it does not solve the prob: checking gcc version... 4.2.4 checking for gawk... /usr/bin/awk checking for inst/npsol/linux/x86/gcc4.2/libnpsol.a... no configure: error: npsol library not found ERROR: configuration failed for package ?OpenMx?
In order to have multiple version of R installed, you will need to build the second version from source. Here are the details: http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Unix_002dalikes You must be very careful to install R in a different location and have a different location for the lib files. Read carefully through the section of Unix-like systems to see which options you need to set. The good news is that you can always reinstall R 2.10 from apt-get or synaptic if the versions cross.
Ok, so I need to compile :-( I'll try it, thanks for info!
Another option to consider is using a virtual machine (I use Virtual Box, which is open source) with the needed version of R on it. You can share data files between the host and virtual machine, if needed.
Oh also? Mmh this would be something to do, but as I don't have any knowledge of it I think I'll try first to compile... Thanks again for help!
Hope this helps, Michael Matthieu Stigler wrote:
Hi I want to use a special package (openMx: http://openmx.psyc.virginia.edu/installing-openmx) that runs currently only on R 2.9 but I have R 2.10 installed (from CRAN). How can I do to have the two versions ( 2.9 and czrrent 2.10) running? Is there a trick with apt-get or should I compile 2.9 from the sources? And if yes, how can I specify a special path for R 2.9 so that by default 2.10 is used? Thanks a lot! Matthieu Stigler
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Matthieu, The problem is the lack of the npsol library on Ubuntu boxes. Google was not helpful in finding an easy way to install this. Part of the problem may be that you are using an older version of Ubuntu and the OpenMx group may not be supporting it anymore. I would search the OpenMx forums for a possible solution, since it seems to only effect that package. Michael
Matthieu Stigler wrote:
Dear Michael Thanks a lot for your quick answer! Michael Rutter a ?crit :
Matthieu, Have you tried installing it? We have just updated the versions of R on CRAN and maybe the bug the package website mentions have been fixed.
Yes I tried and unfortunately it does not solve the prob: checking gcc version... 4.2.4 checking for gawk... /usr/bin/awk checking for inst/npsol/linux/x86/gcc4.2/libnpsol.a... no configure: error: npsol library not found ERROR: configuration failed for package ?OpenMx?
In order to have multiple version of R installed, you will need to build the second version from source. Here are the details: http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Unix_002dalikes You must be very careful to install R in a different location and have a different location for the lib files. Read carefully through the section of Unix-like systems to see which options you need to set. The good news is that you can always reinstall R 2.10 from apt-get or synaptic if the versions cross.
Ok, so I need to compile :-( I'll try it, thanks for info!
Another option to consider is using a virtual machine (I use Virtual Box, which is open source) with the needed version of R on it. You can share data files between the host and virtual machine, if needed.
Oh also? Mmh this would be something to do, but as I don't have any knowledge of it I think I'll try first to compile... Thanks again for help!
Hope this helps, Michael Matthieu Stigler wrote:
Hi I want to use a special package (openMx: http://openmx.psyc.virginia.edu/installing-openmx) that runs currently only on R 2.9 but I have R 2.10 installed (from CRAN). How can I do to have the two versions ( 2.9 and czrrent 2.10) running? Is there a trick with apt-get or should I compile 2.9 from the sources? And if yes, how can I specify a special path for R 2.9 so that by default 2.10 is used? Thanks a lot! Matthieu Stigler
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Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College Station Road Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter
1 day later
Hi Michael Thanks that you looked for the error!
The problem is the lack of the npsol library on Ubuntu boxes. Google was not helpful in finding an easy way to install this. Part of the problem may be that you are using an older version of Ubuntu and the OpenMx group may not be supporting it anymore. I would search the OpenMx forums for a possible solution, since it seems to only effect that package.
It seems the solution has ben found, but is still not available: In order to install OpenMx, you will need R version 2.9.x. R versions, 2.9.0 through 2.9.2 work fine. Unfortunately there is a bug in 2.10.0 that prevents the use of our automatic installer. There is a patch for this bug available from CRAN <http://cran.r-project.org/>, but it requires you to compile R, so we don't recommend it for most people. For now, we are recommending R version 2.9.2 for use with OpenMx. We expect that the next version of R will include the bug fix and at that point we will begin official support for R 2.10. So I think I just compile R 2.9, though I could compile 2.10 with the patch but thought the first solution is easier... Thanks again!
Michael Matthieu Stigler wrote:
Dear Michael Thanks a lot for your quick answer! Michael Rutter a ?crit :
Matthieu, Have you tried installing it? We have just updated the versions of R on CRAN and maybe the bug the package website mentions have been fixed.
Yes I tried and unfortunately it does not solve the prob: checking gcc version... 4.2.4 checking for gawk... /usr/bin/awk checking for inst/npsol/linux/x86/gcc4.2/libnpsol.a... no configure: error: npsol library not found ERROR: configuration failed for package ?OpenMx?
In order to have multiple version of R installed, you will need to build the second version from source. Here are the details: http://cran.r-project.org/doc/manuals/R-admin.html#Installing-R-under-Unix_002dalikes You must be very careful to install R in a different location and have a different location for the lib files. Read carefully through the section of Unix-like systems to see which options you need to set. The good news is that you can always reinstall R 2.10 from apt-get or synaptic if the versions cross.
Ok, so I need to compile :-( I'll try it, thanks for info!
Another option to consider is using a virtual machine (I use Virtual Box, which is open source) with the needed version of R on it. You can share data files between the host and virtual machine, if needed.
Oh also? Mmh this would be something to do, but as I don't have any knowledge of it I think I'll try first to compile... Thanks again for help!
Hope this helps, Michael Matthieu Stigler wrote:
Hi I want to use a special package (openMx: http://openmx.psyc.virginia.edu/installing-openmx) that runs currently only on R 2.9 but I have R 2.10 installed (from CRAN). How can I do to have the two versions ( 2.9 and czrrent 2.10) running? Is there a trick with apt-get or should I compile 2.9 from the sources? And if yes, how can I specify a special path for R 2.9 so that by default 2.10 is used? Thanks a lot! Matthieu Stigler
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2 days later
On Thu, Dec 17, 2009 at 1:42 PM, Michael Rutter <mar36 at psu.edu> wrote:
Matthieu, The problem is the lack of the npsol library on Ubuntu boxes. ?Google was not helpful in finding an easy way to install this. ?Part of the problem may be that you are using an older version of Ubuntu and the OpenMx group may not be supporting it ?anymore. I would search the OpenMx forums for a possible solution, since it seems to only effect that package.
I've been monitoring OpenMX and I think I can answer this question. OpenMx uses a commercial library called N-poly-solve. That's missing on your system, of course, since you probably did not buy it. The OpenMx authors don't require users to buy that library, they provide a shared library along with OpenMx source code. I've wondered why the OpenMx folks don't use an optimizer native to R, but they don't, and that's the way it is. if the version of the Shared library npolysol.la does not match the gcc version you have, then you are "stuck" until the OpenMx folks rebuild the shared library to match the gcc you have. I think that the CRAN rules on openness of code should prevent the redistribution of the commercial npsolv library. If you get the source code by joining the OpenMx beta tester program, this will all be more apparent to you. Hope This Helps.
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