To be very clear: you do not need *any* of these packages to install the RDKit.
-greg On Wed, Feb 23, 2011 at 10:53 AM, JP <jeanpaul.ebe...@inhibox.com> wrote: > Great wiki - I wonder how I missed that. > But the first instruction > sudo yum install atlas, atlas-devel, blas blas-devel lapack lapack-devel > > Gives me the following error: > No package atlas, available. > No package atlas-devel, available. > No package blas available. > No package lapack available. > Is there a repos I have to add to /etc/yum.repos.d/ ? > > > On 22 February 2011 18:41, Robert DeLisle <rkdeli...@gmail.com> wrote: >> >> What are your environment settings? You should have at minimum, these: >> >> $RDBASE = <the directory where you have installed the RDKit code> >> >> >> $LD_LIBRARY_PATH = /usr/local/lib:/$RDBASE/lib >> >> $PYTHONPATH = $RDBASE >> >> >> At least this worked for me for a CentOS installation, detailed here - >> http://code.google.com/p/rdkit/wiki/BuildingOnCentOS >> >> >> >> Another possibility is your PATH variable. Make sure that /usr/local >> pathnames precede any /usr options. >> This will ensure looking into /usr/local first. >> >> There also may be options for cmake that will force it into the correct >> directory. I've found in the past that even though >> >> >> it says in the initial output that is looking in the correct location for >> boost and python, it doesn't necessarily follow its >> own advice. >> >> -Kirk >> >> >> >> >> On Tue, Feb 22, 2011 at 9:44 AM, JP <jeanpaul.ebe...@inhibox.com> wrote: >>> >>> I ended up not using yum to install Numpy - I installed it from source, >>> which was only slightly painful. >>> >>> import platform; print platform.python_version() >>> # /usr/local/lib/python2.7/platform.pyc matches >>> /usr/local/lib/python2.7/platform.py >>> import platform # precompiled from /usr/local/lib/python2.7/platform.pyc >>> 2.7.0 >>> >>> import numpy as N >>> >>> a=N.random.randn(10, 10) >>> >>> >>> In /usr/lib64/ I can find some libpython2.4.so, libpython2.4.so.1.0 >>> What should I do? >>> >>> On 22 February 2011 16:23, <rkdeli...@gmail.com> wrote: >>>> >>>> Are you sure that your NumPy installation is going to the correct Python >>>> instance? I see from the logs that you have Python 2.7 installed, or at >>>> least that is what cmake is finding at /usr/local/lib. You use yum to >>>> install NumPy, but the standard installation of Python on CentOS 5.x is 2.4 >>>> and it is located in /usr/lib. Which version of Python has NumPy? >>>> >>>> >>>> -Kirk >>>> >>>> >>>> >>>> >>>> >>>> >>>> On Feb 22, 2011 9:14am, JP <jeanpaul.ebe...@inhibox.com> wrote: >>>> > I've installed Atlas, Numpy, Boostand everything works fine until I >>>> > try: >>>> > >>>> > >>>> > >>>> > cmake .. -DBOOST_ROOT=/share/apps/boost_1_45_0/ >>>> > sudo make VERBOSE=1 >>>> > >>>> > >>>> > >>>> > At which point everything fails as follows:: >>>> > >>>> > >>>> > >>>> > [ 3%] Building CXX object >>>> > Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o >>>> > >>>> > cd /share/apps/RDKit_2010_12_1/build/Code/RDBoost && /usr/bin/c++ >>>> > -DRDBoost_EXPORTS -O3 -DNDEBUG -fPIC -I/usr/local/include/python2.7 >>>> > -I/usr/local/lib/python2.7/site-packages/numpy/core/include >>>> > -I/share/apps/boost_1_45_0/include -I/share/apps/RDKit_2010_12_1/Code >>>> > -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -o >>>> > CMakeFiles/RDBoost.dir/Wrap.cpp.o -c >>>> > /share/apps/RDKit_2010_12_1/Code/RDBoost/Wrap.cpp >>>> > >>>> > Linking CXX shared library ../../lib/libRDBoost.so >>>> > cd /share/apps/RDKit_2010_12_1/build/Code/RDBoost && >>>> > /usr/local/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt >>>> > --verbose=1 >>>> > >>>> > /usr/bin/c++ -fPIC -O3 -DNDEBUG -shared -Wl,-soname,libRDBoost.so.1 >>>> > -o ../../lib/libRDBoost.so.1.2010.12.1 CMakeFiles/RDBoost.dir/Wrap.cpp.o >>>> > -L/usr/local/lib/libpython2.7.a -L/share/apps/boost_1_45_0/lib >>>> > /usr/local/lib/libpython2.7.a >>>> > /share/apps/boost_1_45_0/lib/libboost_python.so >>>> > -Wl,-rpath,/usr/local/lib/libpython2.7.a:/share/apps/boost_1_45_0/lib: >>>> > >>>> > /usr/bin/ld: /usr/local/lib/libpython2.7.a(exceptions.o): relocation >>>> > R_X86_64_32 against `_Py_NoneStruct' can not be used when making a shared >>>> > object; recompile with -fPIC >>>> > >>>> > /usr/local/lib/libpython2.7.a: could not read symbols: Bad value >>>> > collect2: ld returned 1 exit status >>>> > >>>> > make[2]: *** [lib/libRDBoost.so.1.2010.12.1] Error 1 >>>> > make[2]: Leaving directory `/share/apps/RDKit_2010_12_1/build' >>>> > >>>> > make[1]: *** [Code/RDBoost/CMakeFiles/RDBoost.dir/all] Error 2 >>>> > make[1]: Leaving directory `/share/apps/RDKit_2010_12_1/build' >>>> > >>>> > make: *** [all] Error 2 >>>> > >>>> > >>>> > >>>> > >>>> > Note that all env variables have been set: >>>> > >>>> > [jpebe@caio build]$ echo $LD_LIBRARY_PATH >>>> > >>>> > >>>> > /share/apps/boost_1_45_0/lib:/share/apps/openbabel-2.3.0/lib:/usr/lib64/atlas/sse2:/share/apps/RDKit_2010_12_1/lib:/opt/gridengine/lib/lx26-amd64 >>>> > >>>> > >>>> > Any ideas? I spent the whole day on this... >>>> > >>>> > >>>> > And its freaking me out... >>>> > >>> >>> >>> -- >>> >>> Jean-Paul Ebejer >>> Early Stage Researcher >>> InhibOx Ltd >>> Pembroke House >>> 36-37 Pembroke Street >>> Oxford >>> OX1 1BP >>> UK >>> (+44 / 0) 1865 262 034 >>> >>> >>> This email and any files transmitted with it are confidential and >>> intended solely for the use of the individual or entity to whom they are >>> addressed. Any unauthorised dissemination or copying of this email or its >>> attachments, and any use or disclosure of any information contained in them, >>> is strictly prohibited and may be illegal. 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