Greg (with apologies for the repeat for the benefit of the mailing list
-gmail is great up until it isn't!),
Please see below,
import _frozen_importlib # frozen
import imp # builtin
import sys # builtin
# installing zipimport hook
# installed zipimport hook
# /usr/lib/python3.4/encodings/__pycache__/__init__.cpython-34.pyc matches
/usr/lib/python3.4/encodings/__init__.py
# code object from '/usr/lib/python3.4/encodings/
__pycache__/__init__.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc matches
/usr/lib/python3.4/codecs.py
# code object from '/usr/lib/python3.4/__pycache__/codecs.cpython-34.pyc'
import 'codecs' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa7a14dd8>
# /usr/lib/python3.4/encodings/__pycache__/aliases.cpython-34.pyc matches
/usr/lib/python3.4/encodings/aliases.py
# code object from '/usr/lib/python3.4/encodings/
__pycache__/aliases.cpython-34.pyc'
import 'encodings.aliases' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa7a2a908>
import 'encodings' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa7a149b0>
# /usr/lib/python3.4/encodings/__pycache__/utf_8.cpython-34.pyc matches
/usr/lib/python3.4/encodings/utf_8.py
# code object from '/usr/lib/python3.4/encodings/
__pycache__/utf_8.cpython-34.pyc'
import 'encodings.utf_8' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79b75f8>
# /usr/lib/python3.4/encodings/__pycache__/latin_1.cpython-34.pyc matches
/usr/lib/python3.4/encodings/latin_1.py
# code object from '/usr/lib/python3.4/encodings/
__pycache__/latin_1.cpython-34.pyc'
import 'encodings.latin_1' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79b9160>
# /usr/lib/python3.4/__pycache__/io.cpython-34.pyc matches
/usr/lib/python3.4/io.py
# code object from '/usr/lib/python3.4/__pycache__/io.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/abc.cpython-34.pyc matches
/usr/lib/python3.4/abc.py
# code object from '/usr/lib/python3.4/__pycache__/abc.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/_weakrefset.cpython-34.pyc matches
/usr/lib/python3.4/_weakrefset.py
# code object from '/usr/lib/python3.4/__pycache_
_/_weakrefset.cpython-34.pyc'
import '_weakrefset' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79b9e48>
import 'abc' # <_frozen_importlib.SourceFileLoader object at 0x7f5aa79b9630>
import 'io' # <_frozen_importlib.SourceFileLoader object at 0x7f5aa79b9390>
# /usr/lib/python3.4/__pycache__/site.cpython-34.pyc matches
/usr/lib/python3.4/site.py
# code object from '/usr/lib/python3.4/__pycache__/site.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/os.cpython-34.pyc matches
/usr/lib/python3.4/os.py
# code object from '/usr/lib/python3.4/__pycache__/os.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/stat.cpython-34.pyc matches
/usr/lib/python3.4/stat.py
# code object from '/usr/lib/python3.4/__pycache__/stat.cpython-34.pyc'
import 'stat' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79e4390>
# /usr/lib/python3.4/__pycache__/posixpath.cpython-34.pyc matches
/usr/lib/python3.4/posixpath.py
# code object from '/usr/lib/python3.4/__pycache__/posixpath.cpython-34.pyc'
# /usr/lib/python3.4/__pycache__/genericpath.cpython-34.pyc matches
/usr/lib/python3.4/genericpath.py
# code object from '/usr/lib/python3.4/__pycache_
_/genericpath.cpython-34.pyc'
import 'genericpath' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79e5c50>
import 'posixpath' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79e45f8>
# /usr/lib/python3.4/__pycache__/_collections_abc.cpython-34.pyc matches
/usr/lib/python3.4/_collections_abc.py
# code object from '/usr/lib/python3.4/__pycache_
_/_collections_abc.cpython-34.pyc'
import '_collections_abc' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79e5b70>
import 'os' # <_frozen_importlib.SourceFileLoader object at 0x7f5aa79d0be0>
# /usr/lib/python3.4/__pycache__/_sitebuiltins.cpython-34.pyc matches
/usr/lib/python3.4/_sitebuiltins.py
# code object from '/usr/lib/python3.4/__pycache__/_sitebuiltins.cpython-34.
pyc'
import '_sitebuiltins' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79d0ba8>
# /usr/lib/python3.4/__pycache__/sysconfig.cpython-34.pyc matches
/usr/lib/python3.4/sysconfig.py
# code object from '/usr/lib/python3.4/__pycache__/sysconfig.cpython-34.pyc'
import 'sysconfig' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa799b710>
# /usr/lib/python3.4/__pycache__/_sysconfigdata.cpython-34.pyc matches
/usr/lib/python3.4/_sysconfigdata.py
# code object from '/usr/lib/python3.4/__pycache_
_/_sysconfigdata.cpython-34.pyc'
#
/usr/lib/python3.4/plat-x86_64-linux-gnu/__pycache__/_sysconfigdata_m.cpython-34.pyc
matches /usr/lib/python3.4/plat-x86_64-linux-gnu/_sysconfigdata_m.py
# code object from '/usr/lib/python3.4/plat-x86_64-linux-gnu/__pycache__/_
sysconfigdata_m.cpython-34.pyc'
import '_sysconfigdata_m' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa799d2b0>
import '_sysconfigdata' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa799d080>
# /usr/lib/python3.4/__pycache__/_bootlocale.cpython-34.pyc matches
/usr/lib/python3.4/_bootlocale.py
# code object from '/usr/lib/python3.4/__pycache_
_/_bootlocale.cpython-34.pyc'
import '_bootlocale' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa7900320>
# /usr/lib/python3.4/__pycache__/sitecustomize.cpython-34.pyc matches
/usr/lib/python3.4/sitecustomize.py
# code object from '/usr/lib/python3.4/__pycache__/sitecustomize.cpython-34.
pyc'
# /usr/lib/python3/dist-packages/__pycache__/apport_python_hook.cpython-34.pyc
matches /usr/lib/python3/dist-packages/apport_python_hook.py
# code object from '/usr/lib/python3/dist-packages/__pycache__/apport_
python_hook.cpython-34.pyc'
import 'apport_python_hook' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa7907c18>
import 'sitecustomize' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa7907160>
import 'site' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa79cb710>
Python 3.4.3 (default, Sep 14 2016, 12:36:27)
[GCC 4.8.4] on linux
Type "help", "copyright", "credits" or "license" for more information.
# /home/padler1/Downloads/rdkit-Release_2016_03_1/rdkit/__
pycache__/__init__.cpython-34.pyc matches /home/padler1/Downloads/rdkit-
Release_2016_03_1/rdkit/__init__.py
# code object from '/home/padler1/Downloads/rdkit-Release_2016_03_1/rdkit/
__pycache__/__init__.cpython-34.pyc'
import 'rdkit' # <_frozen_importlib.SourceFileLoader object at
0x7f5aa790d6d8>
Segmentation fault (core dumped)
Thanks again,
Phil
On Mon, Oct 3, 2016 at 11:53 AM, Greg Landrum <[email protected]>
wrote:
> Yeah, but that ldd output indicates that python2.7 is being pulled in. As
> is, curiously, the python2.7 version of boost.
> Can you please try:
> python3.4 -v -c 'from rdkit import rdBase'
> and send the command and output from that?
>
> -greg
>
>
>
> On Mon, Oct 3, 2016 at 5:45 PM, Philip Adler <[email protected]>
> wrote:
>
>> Python2.7 is the default install for Ubuntu 14.04, but I ran the first
>> command using python3.4
>>
>> On Mon, Oct 3, 2016 at 11:43 AM, Greg Landrum <[email protected]>
>> wrote:
>>
>>> You built against python3.4, but it looks like you are running python2.7
>>>
>>> -greg
>>>
>>>
>>> On Mon, Oct 3, 2016 at 5:39 PM, Philip Adler <[email protected]>
>>> wrote:
>>>
>>>> Greg,
>>>>
>>>> The output of the commands is as follows:
>>>>
>>>> Segmentation fault (core dumped)
>>>>
>>>> and
>>>>
>>>> linux-vdso.so.1 => (0x00007fff3d6be000)
>>>> libRDGeneral.so.1 => /usr/lib/libRDGeneral.so.1 (0x00007f03d51df000)
>>>> libRDBoost.so.1 => /usr/lib/libRDBoost.so.1 (0x00007f03d4fdc000)
>>>> libpython3.4m.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython3.4m.so.1.0
>>>> (0x00007f03d49a7000)
>>>> libboost_python-py34.so.1.54.0 =>
>>>> /usr/lib/x86_64-linux-gnu/libboost_python-py34.so.1.54.0
>>>> (0x00007f03d475b000)
>>>> libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
>>>> (0x00007f03d4457000)
>>>> libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1
>>>> (0x00007f03d4241000)
>>>> libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f03d3e7c000)
>>>> libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f03d3b76000)
>>>> libpython2.7.so.1.0 => /usr/lib/x86_64-linux-gnu/libpython2.7.so.1.0
>>>> (0x00007f03d3612000)
>>>> libboost_python-py27.so.1.54.0 =>
>>>> /usr/lib/x86_64-linux-gnu/libboost_python-py27.so.1.54.0
>>>> (0x00007f03d33c5000)
>>>> libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>>>> (0x00007f03d31a7000)
>>>> libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1
>>>> (0x00007f03d2f7d000)
>>>> libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f03d2d64000)
>>>> libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f03d2b60000)
>>>> libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1
>>>> (0x00007f03d295d000)
>>>> /lib64/ld-linux-x86-64.so.2 (0x00007f03d56fc000)
>>>>
>>>> Thanks,
>>>>
>>>> Phil
>>>>
>>>>
>>>> On Mon, Oct 3, 2016 at 11:34 AM, Greg Landrum <[email protected]>
>>>> wrote:
>>>>
>>>>> Hi Phil,
>>>>>
>>>>> I can't think of any particular reason that Ubuntu 14.04 should be a
>>>>> problem, so this should be solvable.
>>>>>
>>>>> This kind of thing (every python test failing) is typically a problem
>>>>> with either the python version or the boost libraries.
>>>>>
>>>>> The first check is to see what error message you get when you do:
>>>>> python -c 'from rdkit import rdBase'
>>>>>
>>>>> That will hopefully point to a particular library that is the problem.
>>>>> Another useful diagnosis command is:
>>>>> ldd $RDBASE/rdkit/rdBase.so
>>>>>
>>>>> That will show which dynamic libraries are being pulled in.
>>>>>
>>>>> -greg
>>>>>
>>>>>
>>>>> On Mon, Oct 3, 2016 at 5:05 PM, Philip Adler <[email protected]>
>>>>> wrote:
>>>>>
>>>>>> Dear All,
>>>>>>
>>>>>> I am trying to compile rdkit to run with Python3.4 on Ubuntu 14.04
>>>>>> as per the instructions at http://www.rdkit.org/docs/Install.html
>>>>>> For reasons which I don't really want to get into we would prefer to
>>>>>> avoid
>>>>>> anaconda for the time being.
>>>>>>
>>>>>> That being said, when I try to test the build, I get a number of
>>>>>> errors and failed tests (the build does not work when called from Python,
>>>>>> which is unsurprising).
>>>>>>
>>>>>> For reference, the cmake command I issued was:
>>>>>>
>>>>>> cmake -DRDK_BUILD_INCHI_SUPPORT=ON -D PYTHON_LIBRARY=/usr/lib/python
>>>>>> 3.4/config-3.4m-x86_64-linux-gnu/libpython3.4.so -D
>>>>>> PYTHON_INCLUDE_DIR=/usr/include/python3.4/ -D
>>>>>> PYTHON_EXECUTABLE=/usr/bin/python3.4
>>>>>> -DBOOST_ROOT=/usr/lib/x86_64-linux-gnu/
>>>>>> ..
>>>>>>
>>>>>> The tests which fail are as follows:
>>>>>>
>>>>>> The following tests FAILED:
>>>>>> 5 - pyBV (SEGFAULT)
>>>>>> 6 - pyDiscreteValueVect (SEGFAULT)
>>>>>> 7 - pySparseIntVect (SEGFAULT)
>>>>>> 8 - pyFPB (SEGFAULT)
>>>>>> 11 - testPyGeometry (SEGFAULT)
>>>>>> 14 - pyAlignment (Failed)
>>>>>> 18 - pyForceFieldConstraints (SEGFAULT)
>>>>>> 20 - pyDistGeom (Failed)
>>>>>> 33 - pyDepictor (SEGFAULT)
>>>>>> 45 - pyChemReactions (SEGFAULT)
>>>>>> 50 - pyFilterCatalog (SEGFAULT)
>>>>>> 52 - pyFragCatalog (SEGFAULT)
>>>>>> 54 - pyMolDescriptors (SEGFAULT)
>>>>>> 57 - pyPartialCharges (SEGFAULT)
>>>>>> 59 - pyMolTransforms (SEGFAULT)
>>>>>> 63 - pyForceFieldHelpers (SEGFAULT)
>>>>>> 65 - pyDistGeom (SEGFAULT)
>>>>>> 67 - pyMolAlign (SEGFAULT)
>>>>>> 69 - pyChemicalFeatures (SEGFAULT)
>>>>>> 71 - pyShapeHelpers (SEGFAULT)
>>>>>> 73 - pyMolCatalog (SEGFAULT)
>>>>>> 75 - pyMolDraw2D (SEGFAULT)
>>>>>> 77 - pyFMCS (SEGFAULT)
>>>>>> 80 - pyMolHash (SEGFAULT)
>>>>>> 82 - pyMMPA (SEGFAULT)
>>>>>> 84 - pyReducedGraphs (SEGFAULT)
>>>>>> 86 - pySLNParse (SEGFAULT)
>>>>>> 87 - pyGraphMolWrap (SEGFAULT)
>>>>>> 88 - pyTestConformerWrap (SEGFAULT)
>>>>>> 89 - pyTestThreads (SEGFAULT)
>>>>>> 92 - pyMatCalc (SEGFAULT)
>>>>>> 93 - pySimDivPickers (SEGFAULT)
>>>>>> 94 - pyRanker (Failed)
>>>>>> 96 - pyFeatures (SEGFAULT)
>>>>>> 97 - pythonTestDbCLI (Failed)
>>>>>> 98 - pythonTestDirML (Failed)
>>>>>> 99 - pythonTestDirDataStructs (Failed)
>>>>>> 101 - pythonTestDirSimDivFilters (Failed)
>>>>>> 102 - pythonTestDirVLib (Failed)
>>>>>> 103 - pythonTestDirChem (SEGFAULT)
>>>>>>
>>>>>> I must confess I'm a little out of my depth right now, so I don't
>>>>>> even know where to begin debugging this. Any advice would be greatly
>>>>>> appreciated,
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Phil
>>>>>>
>>>>>> ------------------------------------------------------------
>>>>>> ------------------
>>>>>> Check out the vibrant tech community on one of the world's most
>>>>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>>>>> _______________________________________________
>>>>>> Rdkit-discuss mailing list
>>>>>> [email protected]
>>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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