Compile R 3.2.2 on AIX 6.1

Here are my notes compiling 64-bit R 3.2.2 on AIX 6.1. As a pre-requisite, read the AIX notes from R-admin. Like the notes, I had GCC installed from here by our admin, along with many other pre-requisites. These were installed prior to compiling R. Note that you could grab newer versions of each package by going to http://www.oss4aix.org/download/RPMS/ (needed for R-dev).

## list of packages

http://www.oss4aix.org/download/RPMS/info/info-5.2-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/less/less-458-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/screen/screen-4.0.3-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/parallel/parallel-20140122-1.aix5.1.ppc.rpm

http://www.bullfreeware.com/download/bin/1464/readline-6.2-3.aix6.1.ppc.rpm


http://www.bullfreeware.com/download/bin/1465/readline-devel-6.2-3.aix6.1.ppc.rpm

http://www.oss4aix.org/download/RPMS/gmp/gmp-5.1.3-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gmp/gmp-devel-5.1.3-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/mpfr/mpfr-3.1.2-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/mpfr/mpfr-devel-3.1.2-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/libmpc/libmpc-1.0.2-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/libmpc/libmpc-devel-1.0.2-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gcc/gcc-4.8.2-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gcc/gcc-c++-4.8.2-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gcc/gcc-cpp-4.8.2-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gcc/gcc-gfortran-4.8.2-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gcc/libgcc-4.8.2-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gcc/libgomp-4.8.2-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gcc/libstdc++-4.8.2-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gcc/libstdc++-devel-4.8.2-1.aix6.1.ppc.rpm

http://www.oss4aix.org/download/RPMS/libiconv/libiconv-1.14-2.aix5.1.ppc.rpm

## conversting unicode, ascii, etc; aix version is not compatible with
R

http://download.icu-project.org/files/icu4c/54.1/icu4c-54_1-AIX7_1-VA2.tgz

## dependency for unicode support; just need to extract to root /
http://www.oss4aix.org/download/RPMS/make/make-4.1-1.aix5.3.ppc.rpm ##
need the gnu version of make

## libm
https://www.ibm.com/developerworks/community/forums/html/topic?id=72e62875-0603-4d93-a9bf-9d80c6cdc6ea
http://www-01.ibm.com/support/docview.wss?uid=isg1fileset-1318926131

https://www.ibm.com/developerworks/java/jdk/aix/service.html ## jre

http://www.oss4aix.org/download/RPMS/libpng/libpng-1.6.12-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/libpng/libpng-devel-1.6.12-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/libjpeg/libjpeg-9a-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/libjpeg/libjpeg-devel-9a-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/icu/icu-gcc-4.8.1.1-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/icu/libicu-gcc-4.8.1.1-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/icu/libicu-gcc-devel-4.8.1.1-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/icu/libicu-gcc-doc-4.8.1.1-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gdb/gdb-7.8.1-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/expat/expat-2.1.0-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/curl/curl-7.27.0-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/curl/curl-devel-7.27.0-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/libxml2/libxml2-2.9.1-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/libxml2/libxml2-devel-2.9.1-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/ncurses/ncurses-5.9-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/ncurses/ncurses-devel-5.9-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gdbm/gdbm-1.11-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/gdbm/gdbm-devel-1.11-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/libtool/libtool-1.5.26-2.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/libtool/libtool-ltdl-1.5.26-2.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/libtool/libtool-ltdl-devel-1.5.26-2.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/zlib/zlib-1.2.8-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/zlib/zlib-devel-1.2.8-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/bzip2/bzip2-1.0.6-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/bzip2/bzip2-devel-1.0.6-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/pcre/pcre-8.37-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/pcre/pcre-devel-8.37-1.aix5.1.ppc.rpm

#### python

http://www.oss4aix.org/download/RPMS/python-setuptools/python-setuptools-0.6.24-1.aix5.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/python/python-2.7.5-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/python/python-devel-2.7.5-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/python/python-libs-2.7.5-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/python/python-test-2.7.5-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/python/python-tools-2.7.5-1.aix6.1.ppc.rpm


http://www.oss4aix.org/download/RPMS/python/tkinter-2.7.5-1.aix6.1.ppc.rpm

Add /opt/freeware/bin to PATH.

Now, download the R source tarball, extract, and cd.

Next, update src/main/dcf.c from the R-dev as a bug that causes readDCF to segfault when using install.packages; no need to do this for future versions of R. Then apply this patch from here to fix the following error:

gcc -maix64 -pthread -std=gnu99 -I../../../../include -DNDEBUG
-I../../../include -I../../../../src/include -DHAVE_CONFIG_H
-I../../../../src/main -I/usr/local/include  -mminimal-toc    -O2 -g
-mcpu=power6  -c gramRd.c -o gramRd.o

gcc -maix64 -pthread -std=gnu99 -shared -Wl,-brtl -Wl,-G -Wl,-bexpall
-Wl,-bnoentry -lc -L/usr/local/lib -o tools.so text.o init.o Rmd5.o
md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o -lm
-lintl

make[6]: Entering directory '/sas/data04/vinh/R-3.2.2/src/library/tools/src'

mkdir -p -- ../../../../library/tools/libs

make[6]: Leaving directory '/sas/data04/vinh/R-3.2.2/src/library/tools/src'

make[5]: Leaving directory '/sas/data04/vinh/R-3.2.2/src/library/tools/src'

make[4]: Leaving directory '/sas/data04/vinh/R-3.2.2/src/library/tools'

make[4]: Entering directory '/sas/data04/vinh/R-3.2.2/src/library/tools'

installing 'sysdata.rda'

Error: Line starting 'Package: tools ...' is malformed!

Execution halted

../../../share/make/basepkg.mk:150: recipe for target 'sysdata' failed

make[4]: *** [sysdata] Error 1

make[4]: Leaving directory '/sas/data04/vinh/R-3.2.2/src/library/tools'

Makefile:30: recipe for target 'all' failed

make[3]: *** [all] Error 2

make[3]: Leaving directory '/sas/data04/vinh/R-3.2.2/src/library/tools'

Makefile:36: recipe for target 'R' failed

make[2]: *** [R] Error 1

make[2]: Leaving directory '/sas/data04/vinh/R-3.2.2/src/library'

Makefile:28: recipe for target 'R' failed

make[1]: *** [R] Error 1

make[1]: Leaving directory '/sas/data04/vinh/R-3.2.2/src'

Makefile:59: recipe for target 'R' failed

make: *** [R] Error 1

Hopefully, this patch will make it to R-dev so that it is no longer needed for future versions of R.

export OBJECT_MODE=64
export CC="gcc -maix64 -pthread"
export CXX="g++ -maix64 -pthread"
export FC="gfortran -maix64 -pthread"
export F77="gfortran -maix64 -pthread"
export CFLAGS="-O2 -g -mcpu=power6"
export FFLAGS="-O2 -g -mcpu=power6"
export FCFLAGS="-O2 -g -mcpu=power6"
./configure --prefix=/path/to/opt ## custom location so I don't need root
make -j 16
make install
## add /path/to/opt/bin to PATH

The last step may complain about NEWS.pdf not found in a directory and a certain directory is not found in the destination. For the former, just do touch NEWS.pdf to where it’s supposed to be; for the latter, create the directory yourself.

R from source

The following are notes for myself.

I like to use the bleeding edge version of R:

<pre class="example">svn checkout https://svn.r-project.org/R/trunk/ r-devel

cd r-devel ./tools/rsync-recommended

use the following to update sources: svn update

pre-reqs

sudo apt-get build-dep r-base

sudo apt-get install gcc g++ gfortran libreadline-dev libx11-dev xorg-dev

sudo apt-get install texlive texinfo

./configure make sudo make install

flags for compiling source code: pkg-config command

so i was trying to compile some C code on my server at school that involves the math and the GNU Scientific Library (gsl) libraries. that is, the source has the following lines:

 <pre class="src src-C"><span style="color: #b0c4de;">#include</span> <span style="color: #ffa07a;">&lt;stdio.h&gt;</span>

#include <math.h> #include <gsl/gsl_integration.h>

those link the header files. however, when compiling, gcc would complain that they can’t see functions such as sqrt, abs, etc, from the math library. it also complains about my call to a function from the gsl library. i googled the math library stuff and realized i need to pass the ‘-lm’ argument in gcc for the math library. similarly, i saw somewhere that refers to the ‘-gsl’ argument. however, this did not work for me. i tried many things. some more googling, i found this thread that shows the ‘pkg-config’ command that shows exactly what arguments u need for which library.

So, i get:

 <pre class="src src-sh">$ pkg-config --libs gsl

-lgsl -lgslcblas -lm

so i just need to execute:

 <pre class="src src-sh">gcc -lgsl -lgslcblas -lm myprogram.c

i really don’t understand how the GNU compilers work. on my mac, i don’t have to pass those arguments. on my debian server, i need to. at first i thought that including the header was enough. will need to learn more about this stuff.

PS I also remember using this command when i had a hard time compiling shell-fm on my mac os x.

UPDATE: so on my mac os x, after installing gsl, i need to use ‘gcc -lgsl myprog.c’ to use the gsl library. things are fine now. I also want to note that i could not compile GSL form source on my debian server…had to rely on apt-get.