Phillip, if you run
ctest --debug
This may help us diagnose the issue with paths and such. Note that you will
get a LOT of output.
----
Brian Kelley
> On Oct 3, 2016, at 4:05 PM, Philip Adler <[email protected]> wrote:
>
> it does not seem that I am missing any dependencies.
>
>> On Mon, Oct 3, 2016 at 3:55 PM, Paolo Tosco <[email protected]> wrote:
>> Hi Philip,
>>
>> Just wondering if CMake is pulling in Python 2.7 because you are missing
>> some Python dependencies on 3.4 (e.g., NumPy)?
>>
>> p.
>>
>>> On 3 Oct 2016, at 20:47, Philip Adler <[email protected]> wrote:
>>>
>>> Those variables were set correctly in my CMakeCache.txt.
>>>
>>>> On Mon, Oct 3, 2016 at 2:47 PM, Peter Gedeck <[email protected]>
>>>> wrote:
>>>> You can also check the CMakeCache.txt file in the build directory. When I
>>>> last compiled for 3.5 on the Mac, I had to correct the PYTHON_INCLUDE_DIR.
>>>>
>>>> Greg, PYTHON_INCLUDE_DIR was incorrectly set after "cmake ..". Executable
>>>> and library correctly found.
>>>>
>>>> --------
>>>> //Path to a program.
>>>> PYTHON_EXECUTABLE:FILEPATH=/Users/peter/miniconda3/bin/python
>>>> //Path to a file.
>>>> PYTHON_INCLUDE_DIR:PATH=/System/Library/Frameworks/Python.framework/Headers
>>>> //Path to a library.
>>>> PYTHON_LIBRARY:FILEPATH=/Users/peter/miniconda3/lib/libpython3.5m.dylib
>>>> --------
>>>>
>>>> Best,
>>>>
>>>> Peter
>>>>
>>>>
>>>>
>>>>
>>>>> On Mon, Oct 3, 2016 at 2:00 PM Philip Adler <[email protected]> wrote:
>>>>> 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/python3.4/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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>>>>> engaging tech sites, SlashDot.org!
>>>>> http://sdm.link/slashdot_______________________________________________
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>>>>> [email protected]
>>>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
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>
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