Hi Patrick,

I had a similar problem with RDKit 2017.09.03 on MacOS, using rdkit channel
in anaconda.
Using the conda-forge channel with python 3.5.5 and ipython 6.2 works fine.

I can post my env tomorrow from work.

Best,

Christos

Christos Kannas

Chem[o]informatics Researcher & Software Developer

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On 16 April 2018 at 18:57, Brian Cole <col...@gmail.com> wrote:

> Pat, the beta for 2018.03 seems to work fine:
>
> conda install -c rdkit/label/beta rdkit
>
> My current guess is that there is a boost python dependency problem with
> RDKit 2017 for Python 3. I've twiddled between a few different boost
> versions in the conda environment, but to no success in getting 2017
> working.
>
> -Brian
>
>
> On Mon, Apr 16, 2018 at 1:20 PM, Brian Cole <col...@gmail.com> wrote:
>
>> I can reproduce the problem, and the issue does appear to be different
>> than the previous issue. Reproducible with the following on OSX:
>>
>> $ conda create -c rdkit -n rdkit_2017 rdkit python=3.5
>> $ source activate rdkit_2017
>> $ python -c 'import rdkit.rdBase'
>> Segmentation fault: 11
>>
>> $ lldb -- python -c 'import rdkit.rdBase'
>> (lldb) target create "python"
>> Current executable set to 'python' (x86_64).
>> (lldb) settings set -- target.run-args  "-c" "import rdkit.rdBase"
>> (lldb) run
>> Process 14929 launched: '/Users/coleb/anaconda2/envs/rdkit_2017/bin/python'
>> (x86_64)
>> Process 14929 stopped
>> * thread #1, queue = 'com.apple.main-thread', stop reason =
>> EXC_BAD_ACCESS (code=1, address=0xa9)
>>     frame #0: 0x00000001001c301d python`visit_decref + 13
>> python`visit_decref:
>> ->  0x1001c301d <+13>: testb  $0x40, 0xa9(%rax)
>>     0x1001c3024 <+20>: jne    0x1001c302f               ; <+31>
>>     0x1001c3026 <+22>: xorl   %eax, %eax
>>     0x1001c3028 <+24>: addq   $0x8, %rsp
>> Target 0: (python) stopped.
>> (lldb) bt
>> * thread #1, queue = 'com.apple.main-thread', stop reason =
>> EXC_BAD_ACCESS (code=1, address=0xa9)
>>   * frame #0: 0x00000001001c301d python`visit_decref + 13
>>     frame #1: 0x00000001000a07a7 python`tupletraverse + 55
>>     frame #2: 0x00000001001c1eb3 python`collect + 291
>>     frame #3: 0x0000000100196972 python`Py_Finalize + 226
>>     frame #4: 0x00000001001bfbc8 python`Py_Main + 3096
>>     frame #5: 0x0000000100001301 python`main + 497
>>     frame #6: 0x00007fff5fe23015 libdyld.dylib`start + 1
>>     frame #7: 0x00007fff5fe23015 libdyld.dylib`start + 1
>> (lldb) info threads
>>
>>
>>
>> On Mon, Apr 16, 2018 at 1:11 PM, Brian Cole <col...@gmail.com> wrote:
>>
>>> An issue like this was fixed in the past: https://github.com/rdkit
>>> /rdkit/commit/009dd580527caa662de8bac5ad0c60f1e9bc90cd
>>>
>>> Will see if I can reproduce this.
>>>
>>> -Brian
>>>
>>> On Mon, Apr 16, 2018 at 12:09 PM, Patrick Walters <wpwalt...@gmail.com>
>>> wrote:
>>>
>>>> Hi All,
>>>>
>>>> I installed the latest RDKit using conda
>>>>
>>>> conda create -c rdkit -n rdkit_2017 rdkit
>>>>
>>>> When I import Chem I get a seg fault
>>>>
>>>> ➜  ~ source activate rdkit_2017
>>>> (rdkit_2017) ➜  ~ python
>>>> Python 3.5.5 |Anaconda, Inc.| (default, Mar 12 2018, 16:25:05)
>>>> [GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)] on darwin
>>>> Type "help", "copyright", "credits" or "license" for more information.
>>>> >>> from rdkit import Chem
>>>> [1]    85097 segmentation fault  python
>>>>
>>>> Has anyone else encountered this?
>>>>
>>>> Thanks,
>>>>
>>>> Pat
>>>>
>>>>
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>>>>
>>>
>>
>
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