Trying to be helpful...
A few weeks ago I wrote a blog entry on how to install RDKit on Ubuntu
(tested on 12.04, 12.10):
http://blopig.com/blog/?p=315
-
Jean-Paul Ebejer
Early Stage Researcher
On 26 April 2013 03:39, Paul Emsley <[email protected]> wrote:
> On 25/04/13 23:43, hari jayaram wrote:
> > Hi
> > I did a
> > export RDBASE=/home/hari/RDKit_2012_09_1
> > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$RDBASE/lib
> >
> > Then cd into the build directory
> > Run cmake ..
> > Then run make
> >
> > At around 24% I get the following error ( see below)
> >
> > I installed the Ubuntu blessed libboost-python1.49-dev
> >
> > Any ideas how to get around this. On a related noted the Ubuntu
> > synaptic package repository did have a rdkit library but it does not
> > work and complains
> >
> > >>> from rdkit import Chem
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > File "/usr/local/lib/python2.7/dist-packages/rdkit/Chem/__init__.py",
> > line 18, in <module>
> > from rdkit import rdBase
> > ImportError: cannot import name rdBase
>
> Hmm... AFAIR, synaptic packages should not use files in /usr/local. Do
> you still get the same problem if you have not defined PYTHONPATH,
> PYTHONHOME or LD_LIBRARY_PATH?
>
> >
> >
> >
> > Linking CXX static library libCatalogs_static.a
> > [ 24%] Built target Catalogs_static
> > Scanning dependencies of target GraphMol
> > [ 25%] Building CXX object
> > Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o
> > [ 25%] Building CXX object
> > Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o
> > In file included from
> > /usr/local/include/boost/thread/detail/platform.hpp:17:0,
> > from /usr/local/include/boost/thread/mutex.hpp:12,
> > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryOps.h:20,
> > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.h:15,
> > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.cpp:11:
> > /usr/local/include/boost/config/requires_threads.hpp:29:4: error:
> > #error "Threading support unavaliable: it has been explicitly disabled
> > with BOOST_DISABLE_THREADS"
> > In file included from /usr/local/include/boost/thread/mutex.hpp:12:0,
> > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryOps.h:20,
> > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.h:15,
> > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.cpp:11:
> > /usr/local/include/boost/thread/detail/platform.hpp:67:9: error:
> > #error "Sorry, no boost threads are available for this platform."
> > In file included from
> > /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryOps.h:20:0,
> > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.h:15,
> > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.cpp:11:
> > /usr/local/include/boost/thread/mutex.hpp:18:2: error: #error "Boost
> > threads unavailable on this platform"
> > In file included from
> > /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.h:15:0,
> > from /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryAtom.cpp:11:
> > /home/hari/RDKit_2012_09_1/Code/GraphMol/QueryOps.h:313:5: error:
> > ‘mutex’ in namespace ‘boost’ does not name a type
> > make[2]: *** [Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o]
> > Error 1
> > make[1]: *** [Code/GraphMol/CMakeFiles/GraphMol.dir/all] Error 2
> > make: *** [all] Error 2
> >
> >
>
>
> There are 2 issues here:
>
> 1) "Threading support unavaliable: it has been explicitly disabled with
> BOOST_DISABLE_THREADS" (Someone at Boost Central can't spell :-) I doubt
> that compiling Boost without threads was a good idea.
>
> 2) and as this the above is unusual, this error:
> "/home/hari/RDKit_2012_09_1/Code/GraphMol/QueryOps.h:313:5: error:
> ‘mutex’ in namespace ‘boost’ does not name a type" was not trapped
> before. Ideally QueryOps (or anything else) should not use boost mutex
> if threads have been disabled (this might be a pain to code up).
>
>
> HTH,
>
> Paul.
>
>
>
>
>
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