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_6
>>> 4-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-package
>>> s/__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
>>>
>>> ------------------------------------------------------------
>>> ------------------
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>>> _______________________________________________
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>>> [email protected]
>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> ------------------------------------------------------------
>>> ------------------
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot______
>>> _________________________________________
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>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>>
>>
> ------------------------------------------------------------
> ------------------
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>
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>
>
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