Thanks to the instructions from Jean-Paul Ebejer at
http://blopig.com/blog/?p=315
I got the rdkit RDKit_2013_03_1 build to work on 64 bit Ubuntu 13.04 .
My previous errors were caused due to older versions of rdkit which were
still in the path. Once I purged the older versions and went with Ubuntu
supplied numpy, blas , lapack and boost..I could build Rdkit by following
Jean-Pauls instructions
Thanks for your help everyone
Hari
On Fri, Apr 26, 2013 at 6:51 AM, hari jayaram <[email protected]> wrote:
> 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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