Re: [R] Can one get a list of recommended packages?
On 13.06.2010 01:09, Dr. David Kirkby wrote: On 06/12/10 05:27 PM, Douglas Bates wrote: On Sat, Jun 12, 2010 at 8:37 AM, Dr. David Kirkby david.kir...@onetel.net wrote: R 2.10.1 is used in the Sage maths project. Several recommended packages (Matrix, class, mgcv, nnet, rpart, spatial, and survival) are failing to build on Solaris 10 (SPARC). Have you checked the dependencies for those packages? Some require GNU make. We used GNU make. We would like to be able to get a list of the recommended packages for R 2.10.1, but ideally via a call to R, so it is not necessary to update that list every time a new version of R is released. We do not want to access the Internet to get this information. Is there a way in R to list the recommended packages? I'm not sure I understand the logic of this. If you are going to build R then presumably you have the tar.gz file which contains the sources for the recommended packages in the subdirectory src/library/Recommended/. Why not get the list from there? The reason is when the version of R gets updated in Sage, then someone will have to check that list again, and more than likely fail to do so, with the result tests will fail since packages do not exist, or worst still we will be unaware they have failed to build properly. Therefore, being able to get them from a command would be useful, but can understand if that is not possible. $ cd ~/src/R-devel/src/library/Recommended/ $ ls *.tgz boot.tgz codetools.tgz lattice.tgz mgcv.tgz rpart.tgz class.tgz foreign.tgz MASS.tgz nlme.tgz spatial.tgz cluster.tgz KernSmooth.tgz Matrix.tgz nnet.tgz survival.tgz OK, thank you for that list. Better still, is there a way to list the recommended packages which have not been installed, so getting a list of any failures? Again, this seems to be a rather convoluted approach. Why not check why the packages don't install properly? R had built, and the failure of the packages to build was not very obvious, since it did not cause make to exit with a non-zero exit code. Nobody had noticed until very recently that there was a problem. Therefore I proposed to make a test of the packages that should have been installed, and ensure they actually all had. You need to be aware that R is just one part of Sage. Building the whole of Sage takes a long time (24 hours on some computers) so needless to say, people will not view every line of error messages. The fact that 'make' succeeded left us a false sense of security, when later it was realsed there were problems when R run its self-tests. Dave But if you really want to sense some security, you should really run make check-all after the installation, particularly since you are on a platform that is not really mainstream any more. Uwe Ligges __ R-help@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] Can one get a list of recommended packages?
R 2.10.1 is used in the Sage maths project. Several recommended packages (Matrix, class, mgcv, nnet, rpart, spatial, and survival) are failing to build on Solaris 10 (SPARC). We would like to be able to get a list of the recommended packages for R 2.10.1, but ideally via a call to R, so it is not necessary to update that list every time a new version of R is released. We do not want to access the Internet to get this information. Is there a way in R to list the recommended packages? Better still, is there a way to list the recommended packages which have not been installed, so getting a list of any failures? Dave __ R-help@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.
Re: [R] Can one get a list of recommended packages?
Hello David, I am not sure I understood your question. Are you asking what are the packages that the R release comes with? Or are you asking what recommended packages one should have when installing R? (There is a good list to start with herehttp://stackoverflow.com/questions/54763/what-r-package-do-you-use-most ) Also, are you asking how to not need to install new packages when upgrading R? (For that, you can have a look at a post I wrote on an alternative way for upgrading R on windowshttp://www.r-statistics.com/2010/04/changing-your-r-upgrading-strategy-and-the-r-code-to-do-it-on-windows/, which might give relevant ideas for your case as well) Best, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Sat, Jun 12, 2010 at 4:37 PM, Dr. David Kirkby david.kir...@onetel.netwrote: R 2.10.1 is used in the Sage maths project. Several recommended packages (Matrix, class, mgcv, nnet, rpart, spatial, and survival) are failing to build on Solaris 10 (SPARC). We would like to be able to get a list of the recommended packages for R 2.10.1, but ideally via a call to R, so it is not necessary to update that list every time a new version of R is released. We do not want to access the Internet to get this information. Is there a way in R to list the recommended packages? Better still, is there a way to list the recommended packages which have not been installed, so getting a list of any failures? Dave __ R-help@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@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.
Re: [R] Can one get a list of recommended packages?
On Sat, Jun 12, 2010 at 8:37 AM, Dr. David Kirkby david.kir...@onetel.net wrote: R 2.10.1 is used in the Sage maths project. Several recommended packages (Matrix, class, mgcv, nnet, rpart, spatial, and survival) are failing to build on Solaris 10 (SPARC). Have you checked the dependencies for those packages? Some require GNU make. We would like to be able to get a list of the recommended packages for R 2.10.1, but ideally via a call to R, so it is not necessary to update that list every time a new version of R is released. We do not want to access the Internet to get this information. Is there a way in R to list the recommended packages? I'm not sure I understand the logic of this. If you are going to build R then presumably you have the tar.gz file which contains the sources for the recommended packages in the subdirectory src/library/Recommended/. Why not get the list from there? $ cd ~/src/R-devel/src/library/Recommended/ $ ls *.tgz boot.tgz codetools.tgz lattice.tgz mgcv.tgz rpart.tgz class.tgzforeign.tgz MASS.tgz nlme.tgz spatial.tgz cluster.tgz KernSmooth.tgz Matrix.tgz nnet.tgz survival.tgz Better still, is there a way to list the recommended packages which have not been installed, so getting a list of any failures? Again, this seems to be a rather convoluted approach. Why not check why the packages don't install properly? __ R-help@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.
Re: [R] Can one get a list of recommended packages?
On 06/12/10 03:31 PM, Tal Galili wrote: Hello David, I am not sure I understood your question. Sorry, perhaps I should have rephrased it better. Are you asking what are the packages that the R release comes with? Sort of. When R is configured, there is an option --with-recommended-packages use/install recommended R packages [yes] which defaults to yes. So I assume that installs some recommended, but not essential packages. We are building R in Sage with no options, so various non-essential packages are building because that is the default, though some (Matrix being one of them), is not building on Solaris. So when R is tested a failure occurs. The build of R apppears to succeed, but a check shows some problems - see here http://sage.math.washington.edu/home/mpatel/trac/8306/r-2.10.1.p2.log What I'd like to find is a list of packages (like Matrix) which would be installed with a default installation of R, but are missing from my installation. We would like something that can quickly check if it is built or not - we don't wish to run an extensive time-consuming test suite. Or are you asking what recommended packages one should have when installing R? (There is a good list to start with herehttp://stackoverflow.com/questions/54763/what-r-package-do-you-use-most ) No, Also, are you asking how to not need to install new packages when upgrading R? No (For that, you can have a look at a post I wrote on an alternative way for upgrading R on windowshttp://www.r-statistics.com/2010/04/changing-your-r-upgrading-strategy-and-the-r-code-to-do-it-on-windows/, which might give relevant ideas for your case as well) Best, Tal Thank you. __ R-help@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.
Re: [R] Can one get a list of recommended packages?
On 06/12/10 05:27 PM, Douglas Bates wrote: On Sat, Jun 12, 2010 at 8:37 AM, Dr. David Kirkby david.kir...@onetel.net wrote: R 2.10.1 is used in the Sage maths project. Several recommended packages (Matrix, class, mgcv, nnet, rpart, spatial, and survival) are failing to build on Solaris 10 (SPARC). Have you checked the dependencies for those packages? Some require GNU make. We used GNU make. We would like to be able to get a list of the recommended packages for R 2.10.1, but ideally via a call to R, so it is not necessary to update that list every time a new version of R is released. We do not want to access the Internet to get this information. Is there a way in R to list the recommended packages? I'm not sure I understand the logic of this. If you are going to build R then presumably you have the tar.gz file which contains the sources for the recommended packages in the subdirectory src/library/Recommended/. Why not get the list from there? The reason is when the version of R gets updated in Sage, then someone will have to check that list again, and more than likely fail to do so, with the result tests will fail since packages do not exist, or worst still we will be unaware they have failed to build properly. Therefore, being able to get them from a command would be useful, but can understand if that is not possible. $ cd ~/src/R-devel/src/library/Recommended/ $ ls *.tgz boot.tgz codetools.tgz lattice.tgz mgcv.tgz rpart.tgz class.tgzforeign.tgz MASS.tgz nlme.tgz spatial.tgz cluster.tgz KernSmooth.tgz Matrix.tgz nnet.tgz survival.tgz OK, thank you for that list. Better still, is there a way to list the recommended packages which have not been installed, so getting a list of any failures? Again, this seems to be a rather convoluted approach. Why not check why the packages don't install properly? R had built, and the failure of the packages to build was not very obvious, since it did not cause make to exit with a non-zero exit code. Nobody had noticed until very recently that there was a problem. Therefore I proposed to make a test of the packages that should have been installed, and ensure they actually all had. You need to be aware that R is just one part of Sage. Building the whole of Sage takes a long time (24 hours on some computers) so needless to say, people will not view every line of error messages. The fact that 'make' succeeded left us a false sense of security, when later it was realsed there were problems when R run its self-tests. Dave __ R-help@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.
