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
>
>
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