Dear all,
I'm trying to build RDKit_2012_03_1 on a machine running CentOS 5.8. After
finally getting the build to complete, almost all Python-related tests fail.
I'll try to provide all the relevant details of my system and the steps
I've taken so far. I must say that I have little control over the machine;
all I can do is to get our IT department to install packages for me. I've
had all the required packages installed/updated to the latest available
version from the official repository.
The system is running a fairly old python version as the default:
$ python -V
Python 2.4.3
But python 2.6 is also available, as is the corresponding numpy:
$ python26 -V
Python 2.6.8
....
The boost version installed via the package repository is too old:
$ yum list boost
Loaded plugins: fastestmirror
Installed Packages
boost.x86_64 1.33.1-15.el5
installed
Available Packages
boost.i386 1.33.1-15.el5 base
so I had to build boost myself:
$ tar tvzf boost_1_49_0.tar.gz
$ cd boost_1_49_0
$ ./bootstrap.sh --prefix=$installbase/boost --with-libraries=python,regex
$ ./bjam address-model=64 cflags=-fPIC cxxflags=-fPIC install
$ export LD_LIBRARY_PATH=$installbase/boost/lib:$LD_LIBRARY_PATH
$ export CMAKE_INCLUDE_PATH=$installbase/boost/include
The flex package install on the system is also too old, so I had to build a
newer one:
$ tar xvzf flex-2.5.35.tar.gz
$ cd flex-2.5.35
$ ./configure --prefix=$installbase
$ make
$ make check
$ make install
$ alias flex="$installbase/bin/flex"
I had to add a missing include to Code/RDBoost/Wrap.h, as described in
http://sourceforge.net/tracker/?func=detail&aid=3527061&group_id=160139&atid=814650
I also had to change PYTHONPATH to make sure the default python 2.4
packages were not picked up:
$ export PYTHONPATH=/usr/lib/python2.6/site-packages
Finally:
$ cd $RDBASE
$ mkdir build
$ cd build
$ cmake -DBOOST_ROOT=$installbase/boost -D
PYTHON_EXECUTABLE=/usr/bin/python2.6 ..
$ make
$ make install
$ ctest
All python-related tests fail (py*, except for the last ones:
pythonTest*). Any suggestions for what to try are highly appreciated!
Thanks in advance,
Leo
--
Leonardo Trabuco, Postdoctoral fellow (Russell group)
CellNetworks, University of Heidelberg, Germany
http://www.russelllab.org/people/leo/
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