Hi Dennis, Just to clarify; I took your post as an opportunity to answer a (related) question I have seen one or twice - about running the current AND development versions of R on the same machine.
You should NOT do this unless you really need R2.10 (and BioC 2.5). The HIGHLY prefered method of installing ANY software on linux is via a packet manager like apt or synaptic so all the dependencies can be taken care easily and updates are then easy to do. Cheers Paul Email: p....@uq.edu.au Web: http://www.di.uq.edu.au -----Original Message----- From: Paul Leo <p....@uq.edu.au> To: Dirk Eddelbuettel <e...@debian.org> Cc: Dennis Fisher <fis...@plessthan.com>, r-sig-debian@r-project.org Subject: Re: [R-sig-Debian] Updating R for Linux Date: Thu, 24 Sep 2009 10:12:33 +1000 I don't know if this will help you, I run the current version of R which is installed via Synaptic as described below. I also install the development version and run the two simultaneously. There is some advantage to this is you want to do bioinformatics with R and bioconductor...so I figure some may be interested The most recent version of R can be obtained from the subversion library . These are the command on the terminal window is you want to install : I will assume you want to make downloads to a directory /media/Bioinform-D/Research/R_latest_install and install R2.10 in /home/pleo/R_latest ###################as follows in a terminal window ################### svn checkout https://svn.r-project.org/R/trunk/ /media/Bioinform-D/Research/R_latest_install cd /media/Bioinform-D/Research/R_latest_install ## get recommed packages ./tools/rsync-recommended ################ build it! cd /home/pleo/R_latest /media/Bioinform-D/Research/R_latest_install/configure --prefix=/home/pleo/R_latest ##### This is the only tricky bit; but you only need to do this once. The above command will get lots of info on required packages ##### look for "any no's" ##### you will probably need tcl8.5-dev , tk8.5.dev , tex , gfortran and gcc compilers redo the above command and see if you fixed ##### the configure error, note some "nos" are ok, use common sense , even with some "no"s it with make an excutable in most cases make make check ### a very few tests may fail, don't worry about those ! ##### optional: make vignettes ## now modify /home/pleo/.emacs to set exec path i.e add line: (setq inferior-R-program-name "/home/pleo/R_latest/bin/R") make dvi make pdf make info your done , you can use the R2.9.2 AND R.10 at the same time if needed. All this is from the R admin pdf avaliable from CRAN ############################## Note if you want to stick to the current version of R- use as Dirk suggested as it will make updates easier. PS I do this on ubuntu 8.1 not that that sound make a difference .. Cheers PAul -----Original Message----- From: Dirk Eddelbuettel <e...@debian.org> To: Dennis Fisher <fis...@plessthan.com> Cc: r-sig-debian@r-project.org Subject: Re: [R-sig-Debian] Updating R for Linux Date: Wed, 23 Sep 2009 10:39:08 -0500 On 23 September 2009 at 08:17, Dennis Fisher wrote: | Colleagues, | | Please forgive my ignorance of this topic. I am experienced with the | installation/use of R in OSX and Windows, much less so with Linux. Welcome! We're here to help. | I just created a virtual machine of Ubuntu 9.0.4. Using the Synaptic | Package Manager, I installed R 2.8.1. I would like to obtain 2.9.x | and I am having trouble doing so using the tools available within | Ubuntu. | | I tried | apt-get install r-base | The system replied that the newest version was already installed and | no changes were made. Right. But you want apt-get update # to refresh information apt-get dist-upgrade # to upgrade to newer versions # incl. possible dependencies after you have done this: | I also added | dev http://cran.cnr.berkeley.edu/bin/linux/debian etch-cran Wrong repo. You copied this from the _Debian_ README but there is also one for _Ubuntu_ in the neighboring directory (ie $CRAN/bin/linux/ubuntu/). Use that instead. | to | /etc/apt/sources.list | Running apt-get install r-base again yielded no response. Very close. | Can anyone advise on the simplest means to update to 2.9.x. I need | only the basic packages, nothing special. Thanks in advance. The above will get you fresh and shiny R 2.9.2 packages courtesy of Vincent and Michael (for the Ubuntu port). Debian via CRAN works thanks to Johannes, and yours truly looks after things in Debian itself which provides the basis for these so-called 'ports'. Keep posting with questions, you're very close. Dirk | | Dennis | | Dennis Fisher MD | P < (The "P Less Than" Company) | Phone: 1-866-PLessThan (1-866-753-7784) | Fax: 1-415-564-2220 | www.PLessThan.com | | _______________________________________________ | R-SIG-Debian mailing list | R-SIG-Debian@r-project.org | https://stat.ethz.ch/mailman/listinfo/r-sig-debian _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian