Hugh, Thanks for the advice. I decided to go the route of using source debian packages this time around. Below is the basic script I used, adapted from the other replies I received. This was successful in getting the base R installed as well as an addition ~275 packages from CRAN, Omegahat, and BioConductor.
Unfortunately, I have not yet had luck with the following packages: [1] "affycoretools" "AnnBuilder" "biocViews" "biomaRt" [5] "GSEABase" "odfWeave" "RCurl" "Resourcerer" [9] "Rgraphviz" "RSPerl" "RSPython" "SBMLR" [13] "TMat" "XML" Some of which may depend on one another. In particular, I get errors from both curl and graphviz, I suspect a version problem as they are both on my PATH. I am going to work on them some more tomorrow and may be posting more specific error messages if I cannot get the problems fixed myself. The script below is what I believe I did, but this was not done on a virgin Ubuntu install as I have been futzing with this for a day or so. I am also not absolutely sure I have included every necessary step nor perhaps included some un-necessary ones. I am brand new to Debian/Ubuntu and just learning about the apt/synaptic system. If Johannes, Vincent, or Dirk could comment on what I did below, it would be helpful to me and perhaps other Debian newbies. Thanks again to all, Mark ######################################################### #Making R and BioC on Ubuntu Gutsy with AMD64-bit OS #Add this to /etc/apt/sources.list and update apt deb-src http://cran.r-project.org/bin/linux/debian etch/ apt-get update #make a directory for deb source files mkdir /home/USER/r-2.6.0-deb cd /home/USER/r-2.6.0-deb #get the source files and unpack them sudo apt-get source r-base sudo dpkg-source -x r-base_2.6.0-1~etchcran.1.dsc #cd into r-base-VERSION cd r-base-2.6.0 #compile the package, this may be un-necessary, but I did it sudo dpkg-buildpackage -rfakeroot -b #get some libraries need for building R apt-get install build-essential # fail and will produce a suggestion to do the following command, DO IT apt-get -f install #install the package from .deb sudo dpkg -i ../r-base-core_2.6.0-1~etchcran.1_amd64.deb ## to get rgl to install into R with Ubuntu Gutsy AMD64 apt-get install freeglut3 freeglut3-dev libgl1-mesa-dev libglu1-mesa-dev libice-dev libsm-dev libx11-dev libxau-dev libxdmcp-dev libxext-dev libxt-dev mesa-common-dev x11proto-core-dev x11proto-input-dev x11proto-kb-dev x11proto-xext-dev xlibmesa-gl-dev xtrans-dev #Now replace i686 site-library with an empty one for new packages cd R_HOME #if not made, make it mv site-library site-library-i686 #if you have an old site-library you want to save mkdir site-library #if have packages in old library that you want installed in new one cd site-library-i686 ls > ../my.packages.txt #to .Rprofile add at beginning: .libPaths(new= "~/R_HOME/site-library") #tell R where site-library is export PATH:$PATH:/usr #Start R #install.packages from appropriate repositories, may read in old package # names from old library using: packages.to.install <- read.delim("~/R_HOME/my.packages.txt", as.is = TRUE)[,1] source("http://bioconductor.org/biocLite.R") biocLite(packages.to.install) my.new.packages <- c( dir("~/R_HOME/site-library"), dir("/usr/lib/R/library")) yet.to.install <- setdiff(packages,my.new.packages) biocLite(yet.to.install, dependencies = TRUE) Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 204-4202 Home (no voice mail please) mwkimpel<at>gmail<dot>com ****************************************************************** hugh wrote: > Mark, > > I am also a relatively new user of Linux, so am not an expert and thus > am not responding to the whole R-sig-Debian group. I am running the > 64-bit version (intel Q6700 CPU) of Gutsy and was able to compile from > source file on CRAN. I am able to use 'install.packages(FOO)' within my > compiled R to successfully add packages. If building a shared library > is important to you, I was NOT successful in doing that (a shared > library appears to be important if you want to use GUI's like JGR). > > The only change/flag I used was LDFLAGS="-L/usr/local/lib64 > -L/usr/local/lib". You can edit your config.site file (e.g., sudo gedit > config.site) and search for LDFLAGS....uncomment it and use the line I > used. Alternately, you can just type sudo ./configure > LDFLAGS="-L/usr/local/lib64 -L/usr/local/lib" (that is how you can set > flags). > > My experience was that the "standard" Gutsy install was missing a number > of programs/librarys to compile R, so I had to add a lot of them. If > you are having compile problems, my guess is that you are missing some > of these libraries which you can install using the Synaptic Package > Manager. If you are still having problems, I can try to figure out how > to send a list of the packages/libraries I have installed if that is > helpful. > > I also found this site helpful: > http://idecide.mskcc.org/yl_home/linux.html > > > Best, > Hugh Whelan > > > > > > On Tue, 2007-10-30 at 11:26 -0400, Mark W Kimpel wrote: >> I have recently upgraded to Ubuntu Gutsy and, for the first time, am >> using a 64-bit installation. After failing miserably to install R from >> source, not a problem for me in the past with a 32-bit install, I went >> the route of using the Debian Etch build. This went smoothly, but I am >> unable to update my numerous R and BioConductor packages, getting >> non-zero exit status errors on each package. Is there a repository of >> pre-built packages for Debian Etch 64 besides the r-base and >> r-recommended? If not, could someone suggest how I might get things >> working installing from source? >> >> I have installed the ia32 library, which did help me build VMWare, but >> did not help with R. Reading the R-admin manual, there are some >> suggested compiler flags, but I don't know how to enter them as I am a >> relative new-comer to Linux. >> >> Thanks so much, >> Mark >> >> --- >> >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 663-0513 Home (no voice mail please) >> >> _______________________________________________ >> 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