Thanks JP and Paul,
I noticed that I did not modify the pythonpath...I also noticed on the
googlecode build page (https://code.google.com/p/rdkit/wiki/WorkingBuilds) that
Greg had built it on Ubuntu 12.04 LTS with boost 1.53.
I tried to remove the dpkg installed boost files on 12.10 and go with boost
1.53.. but strangely the cmake is still locating boost 1.49 probably from a
previous manual non dpkg install...I will track that down and remove it and
try with 1.53 ..that is assuming JPs instructions don't get the compile
done.
It's strange as Paul pointed out that Ubuntu didnt put the rdkit package
into /usr/local
I'll report back once I get either of two suggested approaches to work.
Thanks for your help
Hari
On Friday, April 26, 2013, JP wrote:
> 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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