Home > Uncategorized > Hadoop 0.20.2-cdh3u3 R-2.15.2 statistics language libraries custom install

Hadoop 0.20.2-cdh3u3 R-2.15.2 statistics language libraries custom install

I will not describe here the R language install,
in general there is a default R installed at the default location
but the R latest is compiled and installed at /opt/R-2.15.2/ with –enable-R-shlib –with-x=no flags.

How install R 2.15.2 libraries requested by the devs :

Example : someone needs fastICA

Go to the Table of available R packages, sorted by name
Locate the package, download it and do not compile it, just use R to install it using the CMD INSTALL R feature:
Example :

alias R=/opt/R-2.15.2/bin/R
mkdir /tmp/tickt.HDP22212
cd /tmp/tickt.HDP22212
wget http://cran.r-project.org/src/contrib/fastICA_1.1-16.tar.gz
root@hadoop:[Mon Feb 25 09:06:39]:[/tmp/tickt.HDP22212]$ R CMD INSTALL fastICA_1.1-16.tar.gz 
* installing to library ‘/opt/R-2.15.2/library’
* installing *source* package ‘fastICA’ ...
** package ‘fastICA’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for scopy in -L/opt/R-2.15.2/lib -lRblas... no
configure: WARNING: could not find scopy in your BLAS library, using our BLAS and LAPACK routines
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/opt/R-2.15.2/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ica.c -o ica.o
gfortran   -fpic  -g -O2  -c lsame.f -o lsame.o
gfortran   -fpic  -g -O2  -c sblas.f -o sblas.o
gfortran   -fpic  -g -O2 -ffloat-store -c -o slamc.o slamc.f
gfortran   -fpic  -g -O2  -c slapack.f -o slapack.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o fastICA.so ica.o lsame.o sblas.o slamc.o slapack.o -L/opt/R-2.15.2/lib -lRblas -lgfortran -lm
installing to /opt/R-2.15.2/library/fastICA/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (fastICA)
root@hadoop:[Mon Feb 25 09:06:53]:[/tmp/tickt.HDP22212]$
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  1. dragkh
    June 21, 2013 at 11:13 am

    note, now the fastICA for R 2.15.2 is considered old, so its being moved here :
    http://cran.r-project.org/src/contrib/Archive/fastICA/fastICA_1.1-16.tar.gz

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