Hi, Last year our systems group tried to install Bioconductor/R on an IBM p5-570 machine (16 nodes, 256 GB shared RAM), running AIX 5.3. They ran into all sorts of difficulties and finally gave up. I am interested in trying again (and working with an IBM support group if necessary), but before embarking on this odyssey I was wondering if anyone on this list has ever successfully run Bioconductor/R on a similar architecture/AIX OS? If so, is there any kind of cribsheet or other underground documentation that we could consult to get around any AIX peculiarities? Given IBM's long-term interest in the Life Sciences, it seems hard to believe that Bioconductor/R would not be supported on this platform, but that is what we heard through the grapevine. Thanks for any thoughts/help with this. - Susan -- ------------------------------------------------------------------ Susan R. Atlas Research Associate Professor, Physics and Astronomy Director, Cancer Research and Treatment Center Shared Resource for Bioinformatics and Computational Biology Department of Physics & Astronomy MSC07 4220 p: 505.277.1509 1 University of New Mexico e: susie at sapphire.phys.unm.edu Albuquerque, NM 87131-0001 n: www.phys.unm.edu/CompMaterials

You should ask this question on R-devel - you will be able to get much better help there. Once you have R running I doubt it will be hard to install Bioconductor (of course certain packages might not work if they depend on external libraries that do not work - for example Rgraphviz). Kasper On Feb 14, 2008, at 11:09 AM, Susan R. Atlas wrote: > Hi, > Last year our systems group tried to install Bioconductor/R on > an IBM > p5-570 machine (16 nodes, 256 GB shared RAM), running AIX 5.3. They > ran into all sorts of difficulties and finally gave up. > I am interested in trying again (and working with an IBM support > group if necessary), but before embarking on this odyssey I was > wondering if anyone on this list has ever successfully run > Bioconductor/R on a similar architecture/AIX OS? If so, is there any > kind of cribsheet or other underground documentation that we could > consult to get around any AIX peculiarities? > Given IBM's long-term interest in the Life Sciences, it seems > hard to > believe that Bioconductor/R would not be supported on this > platform, but > that is what we heard through the grapevine. > Thanks for any thoughts/help with this. > - Susan > > -- > > ------------------------------------------------------------------ > Susan R. Atlas > Research Associate Professor, Physics and Astronomy > Director, Cancer Research and Treatment Center Shared Resource for > Bioinformatics and Computational Biology > > Department of Physics & Astronomy > MSC07 4220 p: 505.277.1509 > 1 University of New Mexico e: susie at sapphire.phys.unm.edu > Albuquerque, NM 87131-0001 n: www.phys.unm.edu/CompMaterials > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

Susan, my sysAdmin helped me get R installed on AIX 5.3 with the power arch. Here is my script. You will need to modify some of the paths, especially the install directory. I'm not an expert on this, but hopefully this will get you started in the right direction. Mark #make R on Libra AIX 5.3 #################### wget ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz gunzip R-devel.tar.gz tar -xf R-devel.tar cd ~/R_HOME/R-devel mkdir R-build cd R-build # export CC=xlc_r # export CXX=xlC_r # export F77=xlf_r # export F90=xlf90_r # export FC=xlf95_r export CC=gcc export CXX=g++ export F77=g77 export F90=gfortran export FC=gfortran export OBJECT_MODE=64 export CFLAGS="-qstrict -O3 -q64 -qmaxmem=-1" export CXXFLAGS="-qstrict -O3 -q64 -qmaxmem=-1" export FCFLAGS="-qstrict -O3 -q64 -qmaxmem=-1" export FFLAGS="-qstrict -O3 -q64 -qmaxmem=-1" export BLAS_LIBS="-L/usr/lib/ -lessl" export LAPACK_LIBS="-L/libapps/lapack3.0 -llapack64" export DYLIB_EXT=".a" export MAIN_LDFLAGS="-brtl -bexpall" export SHLIB_LDFLAGS="-bexpall -bnoentry" export CPPFLAGS="-I/software/gnu/include -I/opt/freeware/include" export LDFLAGS="-L/software/gnu/lib -L/opt/freeware/lib -lintl" export TCLTK_LIBS="-L/miscapps/gnu/lib -ltcl8.4 -ltk8.4" export TCLTK_CPPFLAGS="-I/miscapps/gnu/include" export R_LIBS=/N/u/mkimpel/Libra/R_HOME/R-devel/site-library/ export PATH=$PATH:/usr/bin/:/miscapps ../configure --prefix=/N/u/mkimpel/Libra/R_HOME/R-devel/R-build --without-x --without-readline --without-iconv --with-tcltk --with-tcl-config=/miscapps/gnu/lib/tclConfig.sh --with-tk-config=/miscapps/gnu/lib/tkConfig.sh gmake gmake install # 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 ****************************************************************** Susan R. Atlas wrote: > Hi, > Last year our systems group tried to install Bioconductor/R on an IBM > p5-570 machine (16 nodes, 256 GB shared RAM), running AIX 5.3. They > ran into all sorts of difficulties and finally gave up. > I am interested in trying again (and working with an IBM support > group if necessary), but before embarking on this odyssey I was > wondering if anyone on this list has ever successfully run > Bioconductor/R on a similar architecture/AIX OS? If so, is there any > kind of cribsheet or other underground documentation that we could > consult to get around any AIX peculiarities? > Given IBM's long-term interest in the Life Sciences, it seems hard to > believe that Bioconductor/R would not be supported on this platform, but > that is what we heard through the grapevine. > Thanks for any thoughts/help with this. > - Susan >