[BioC] Bioconductor/R on AIX?

Mark W Kimpel mwkimpel at gmail.com
Thu Feb 14 20:52:48 CET 2008

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 
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)



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

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