Compile R 3.2.2 on AIX 6.1

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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.

Build 32 bit R on 64 bit Ubuntu by utilizing chroot

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In the past, I’ve described how one could build multiarch (64 bit and 32 bit) versions of R on a 64 bit Ubuntu machine. The method based on this thread no longer works as of R 2.13 or 2.14 I believe. I received advice from someone on #R over on freenode (forgot who) a few months ago that suggested the chroot route (see this also). I recently tried it and wanted to document the procedures. Although the solution isn’t as nice as the previous multiarch route, it will suffice for now. With the chroot method, first compile the 64 bit version of R the usual way. For the 32 bit version of R, do: 

<pre class="src src-sh"><span style="color: #ff4500;">#### </span><span style="color: #ff4500;">change my.username to your username, or modify path per your taste</span>

### create chroot jail sudo apt-get install dchroot debootstrap sudo mkdir ~/chroot-R32 sudo emacs -q -nw /etc/schroot/schroot.conf ## paste the following in the file: (no quotes) “ [natty] description=Ubuntu Natty location=/home/my.username/chroot-R32 priority=3 users=my.username groups=sbuild root-groups=root “

## build a basic Ubuntu system in the chroot jail sudo debootstrap –variant=buildd –arch i386 natty /home/my.username/chroot-R32 http://ubuntu.cs.utah.edu/ubuntu/ ## pick a mirror from https://launchpad.net/ubuntu/+archivemirrors

## copy my source locations for apt sudo cp /etc/apt/sources.list /var/chroot/etc/apt/sources.list ## edit this new file if to reflect only the needed source

### do following steps whenever you need to access 32 bit R ## access to proc and dns sudo mount -o bind /proc /home/my.username/chroot-R32/proc sudo cp /etc/resolv.conf /home/my.username/chroot-R32/etc/resolv.conf ## go into jail; do this whenever you want sudo chroot /home/my.username/chroot-R32 dpkg-architecture ## make sure system is i386 ### now the root / location should reflect the jail

### following happens in jail ## tools needed to build R apt-get install gcc g++ gfortran libreadline-dev libx11-dev xorg-dev ## get svn to get latest r source code apt-get install git-core subversion

## compile 32 bit R cd home/ mkdir R32 cd R32 svn checkout https://svn.r-project.org/R/trunk/ r-devel cd r-devel/ apt-get install rsync ./tools/rsync-recommended ./configure make make install R

How big is my /home/my.username/chroot-R32 folder? It is at 791 MB after the above steps. Let me know if you have suggestions for having both 32 bit or 64 concurrently on Linux. I believe Windows and Mac ships and compiles both 32 bit and 64 bit versions of R. I’m surprised this isn’t the case for Linux.

Build multiarch R (32 bit and 64 bit) on Debian/Ubuntu

by ·1 Comment

I have the 64 bit version of R compiled from source on my Ubuntu laptop. I recently had a need for R based on 32 bit since a package I needed to compile and use only works in 32 bit. I thought it was readily available on Ubuntu since both 32 bit and 64 bit versions of R are shipped with the Windows and Mac OS X installers. I tried figuring out how to do so using the manual (R 2.13.1), but could not figure it out on my own. I seeked help on R-devel and received some helpful responses.

Here is a quick reminder for myself: 

<pre class="src src-sh"><span style="color: #ff4500;">## </span><span style="color: #ff4500;">download R source from tar ball or svn</span>

## working directory has R/trunk/ ## run in trunk ./tools/rsync-recommended sudo apt-get install ia32-libs lib32readline6-dev lib32ncurses5-dev lib32icu-dev gcc-multilib gfortran-multilib ## ubuntu does not have ia32-libs-dev # cd ../.. # mkdir R32 # cd R32 # ../R/trunk/configure r_arch=i386 CC=’gcc -std=gnu99 -m32′ CXX=’g++ -m32′ FC=’gfortran -m32′ F77=’gfortran -m32′ # make -j24 && sudo make install # cd .. # mkdir R64 # ../R/trunk/configure r_arch=amd64 # make -j24 && sudo make install ./configure r_arch=i386 CC=‘gcc -std=gnu99 -m32′ CXX=‘g++ -m32′ FC=‘gfortran -m32′ F77=‘gfortran -m32′ make -j24 && sudo make install make clean ./configure r_arch=amd64 make -j24 && sudo make install

You can build directly in the R/trunk, but make sure you execute make clean first to clear out any previous builds. Not doing so gave me errors like: 

 <pre class="src src-sh">/usr/bin/install: cannot create regular file

`../../include/i386/Rconfig.h': No such file or directory

Now, executing R will give me the 64 bit version of R (whatever was the last build). If I want to specify the arch, I can just issue the commands R --arch i386 or R --arch amd64. When launching R in emacs, do C-u M-x R and type in the --arch argument.

Do a make uninstall to remove R prior to installing a new version of R to the same location.