Hi Greg,
Thanks for the quick reply---you are absolutely right, the new version
builds just fine. However, I now have the following issue:
>>> from rdkit import Chem
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/RDKit/rdkit/Chem/__init__.py",
line 18, in <module>
from rdkit import rdBase
ImportError: /usr/lib/python2.7/dist-packages/RDKit/rdkit/rdBase.so:
undefined symbol: _ZN5InvarlsERSoRKNS_9InvariantE
running ldd gives me:
linux-vdso.so.1 => (0x00007fff79de4000)
libRDGeneral.so.1 => /usr/lib/libRDGeneral.so.1 (0x00007fec6c99d000)
libRDBoost.so.1 => /usr/lib/libRDBoost.so.1 (0x00007fec6c79a000)
libpython2.7.so.1.0 =>
/usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0 (0x00007fec6c232000)
libboost_python-py27.so.1.54.0 =>
/usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.54.0
(0x00007fec6bfe5000)
libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
(0x00007fec6bce1000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
(0x00007fec6baca000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fec6b704000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fec6b3fe000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00007fec6b1df000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fec6afc6000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fec6adc2000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1
(0x00007fec6abbe000)
/lib64/ld-linux-x86-64.so.2 (0x00007fec6cedb000)
Is there a the wrong version of something being pointed to here? Thanks in
advance, I'm afraid my Ubuntu knowledge isn't very good...
Dante
On Tue, Feb 10, 2015 at 11:08 PM, Greg Landrum <greg.land...@gmail.com>
wrote:
> Hi Dante,
>
> Looks like you are trying to build a fairly old version of the RDKit.
> Newer versions no longer require the flex/bison step, so if you could
> switch to one of those I think it would make your life easier.
>
> -greg
>
> On Wed, Feb 11, 2015 at 4:35 AM, Dante <dante.esgrimi...@gmail.com> wrote:
>
>> Hello,
>>
>> I am trying to install rdkit on Ubuntu 14.04, and am building from source
>> so I can get the inchi functionality. When I run make, I get:
>>
>> [ 24%] Building CXX object
>> Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o
>>
>> smiles.yy:25:1: warning: "YYDEBUG" redefined
>>
>> In file included from smiles.yy:21:
>>
>> /sw64/src/fink.build/rdkit-2013.06.1-5/RDKit_2013_06_1/Code/GraphMol/SmilesParse/smiles.tab.hpp:37:1:
>> warning: this is the location of the previous definition
>>
>> smiles.yy: In function 'int yysmiles_parse(const char*,
>> std::vector<RDKit::RWMol*, std::allocator<RDKit::RWMol*> >*,
>> std::list<unsigned int, std::allocator<unsigned int> >*, void*)':
>>
>> smiles.yy:23: error: too few arguments to function 'int
>> yysmiles_lex(YYSTYPE*, void*)'
>>
>> /sw64/src/fink.build/rdkit-2013.06.1-5/RDKit_2013_06_1/Code/GraphMol/SmilesParse/smiles.tab.cpp:1245:
>> error: at this point in file
>>
>> make[2]: ***
>> [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o]
>> Error 1
>>
>> make[1]: *** [Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/all]
>> Error 2
>>
>> make: *** [all] Error 2
>>
>> I've seen on previous messages that one potential fix to this is to
>> downgrade to bison 2.7.1, which I've done, but this error persists. Any
>> ideas?
>>
>> Thanks,
>>
>> DP
>>
>>
>>
>>
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