You should be able to use Python 2.7 as well, but I do strongly recommend
Python 3 if you can possibly use it.
-greg
On Tue, May 22, 2018 at 2:01 PM alb greg <agparis7dide...@gmail.com> wrote:
> Hi Greg,
>
> I'd like to know one thing : is it mandatory to use python 3 to install
> RDKit (as in your dockerfile) or is there a similar process in python 2.7 ?
>
> BR
>
>
>
> 2018-05-17 19:20 GMT+02:00 alb greg <agparis7dide...@gmail.com>:
>
>> Thanks, Greg!
>>
>> Installation is okay now but ctest ends with these 2 failed :
>>
>> 118 - pyGraphMolWrap (Failed)
>> 136 - pythonTestDirChem (Failed)
>>
>> Any idea?
>>
>>
>>
>> 2018-05-16 15:08 GMT+02:00 Greg Landrum <greg.land...@gmail.com>:
>>
>>> Yeah, the dockerfile that I pointed you to installs the ubuntu version
>>> of boost. That is what ends up being used to build the RDKit.
>>> You have a copy of boost 1.67 installed; this is too new for the version
>>> of cmake you have (and has additional problems anyway); the system boost
>>> solves this problem.
>>>
>>> On Wed, May 16, 2018 at 3:03 PM alb greg <agparis7dide...@gmail.com>
>>> wrote:
>>>
>>>> The system boost? You're talking about libboost?
>>>>
>>>>
>>>>
>>>> 2018-05-16 14:54 GMT+02:00 Greg Landrum <greg.land...@gmail.com>:
>>>>
>>>>> cmake is finding boost v1.67, not the system boost.
>>>>>
>>>>>
>>>>> On Wed, May 16, 2018 at 2:34 PM alb greg <agparis7dide...@gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Ubuntu 16.04
>>>>>>
>>>>>> *CmakeMessages :*
>>>>>>
>>>>>> -- The C compiler identification is GNU 5.4.0
>>>>>> -- The CXX compiler identification is GNU 5.4.0
>>>>>> -- Check for working C compiler: /usr/bin/cc
>>>>>> -- Check for working C compiler: /usr/bin/cc -- works
>>>>>> -- Detecting C compiler ABI info
>>>>>> -- Detecting C compiler ABI info - done
>>>>>> -- Detecting C compile features
>>>>>> -- Detecting C compile features - done
>>>>>> -- Check for working CXX compiler: /usr/bin/c++
>>>>>> -- Check for working CXX compiler: /usr/bin/c++ -- works
>>>>>> -- Detecting CXX compiler ABI info
>>>>>> -- Detecting CXX compiler ABI info - done
>>>>>> -- Detecting CXX compile features
>>>>>> -- Detecting CXX compile features - done
>>>>>> -- Check if the system is big endian
>>>>>> -- Searching 16 bit integer
>>>>>> -- Looking for sys/types.h
>>>>>> -- Looking for sys/types.h - found
>>>>>> -- Looking for stdint.h
>>>>>> -- Looking for stdint.h - found
>>>>>> -- Looking for stddef.h
>>>>>> -- Looking for stddef.h - found
>>>>>> -- Check size of unsigned short
>>>>>> -- Check size of unsigned short - done
>>>>>> -- Using unsigned short
>>>>>> -- Check if the system is big endian - little endian
>>>>>> -- Found PythonInterp: /usr/bin/python3 (found version "3.5.2")
>>>>>> -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.5m.so
>>>>>> (found version "3.5.2")
>>>>>> -- Found Eigen3: /usr/include/eigen3 (Required is at least version
>>>>>> "2.91.0")
>>>>>> -- Looking for pthread.h
>>>>>> -- Looking for pthread.h - found
>>>>>> -- Looking for pthread_create
>>>>>> -- Looking for pthread_create - not found
>>>>>> -- Looking for pthread_create in pthreads
>>>>>> -- Looking for pthread_create in pthreads - not found
>>>>>> -- Looking for pthread_create in pthread
>>>>>> -- Looking for pthread_create in pthread - found
>>>>>> -- Found Threads: TRUE
>>>>>> -- Boost version: 1.67.0
>>>>>> -- Found the following Boost libraries:
>>>>>> -- serialization
>>>>>> == Done updating pains files
>>>>>> -- Configuring done
>>>>>> -- Generating done
>>>>>> -- Build files have been written to: /home/user/src/rdkit/rdkit/build
>>>>>>
>>>>>> *CmakeErrors :*
>>>>>>
>>>>>> CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725
>>>>>> (message):
>>>>>> Imported targets not available for Boost version 106700
>>>>>> Call Stack (most recent call first):
>>>>>> /usr/share/cmake-3.5/Modules/FindBoost.cmake:763
>>>>>> (_Boost_COMPONENT_DEPENDENCIES)
>>>>>> /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332
>>>>>> (_Boost_MISSING_DEPENDENCIES)
>>>>>> CMakeLists.txt:194 (find_package)
>>>>>>
>>>>>>
>>>>>> CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725
>>>>>> (message):
>>>>>> Imported targets not available for Boost version 106700
>>>>>> Call Stack (most recent call first):
>>>>>> /usr/share/cmake-3.5/Modules/FindBoost.cmake:763
>>>>>> (_Boost_COMPONENT_DEPENDENCIES)
>>>>>> /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332
>>>>>> (_Boost_MISSING_DEPENDENCIES)
>>>>>> CMakeLists.txt:194 (find_package)
>>>>>>
>>>>>>
>>>>>> PYTHON Py_ENABLE_SHARED: 1
>>>>>> PYTHON USING LINK LINE: -pthread -shared -Wl,-O1
>>>>>> -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro
>>>>>> CMake Warning at /usr/share/cmake-3.5/Modules/FindBoost.cmake:725
>>>>>> (message):
>>>>>> Imported targets not available for Boost version 106700
>>>>>> Call Stack (most recent call first):
>>>>>> /usr/share/cmake-3.5/Modules/FindBoost.cmake:763
>>>>>> (_Boost_COMPONENT_DEPENDENCIES)
>>>>>> /usr/share/cmake-3.5/Modules/FindBoost.cmake:1332
>>>>>> (_Boost_MISSING_DEPENDENCIES)
>>>>>> CMakeLists.txt:303 (find_package)
>>>>>>
>>>>>>
>>>>>> == Using strict rotor definition
>>>>>> -- Found MAEParser source in
>>>>>> /home/labbe/src/rdkit/rdkit/External/CoordGen/maeparser
>>>>>> -- Found coordgenlibs source in
>>>>>> /home/labbe/src/rdkit/rdkit/External/CoordGen/coordgenlibs
>>>>>> == Updating Filters.cpp from pains file
>>>>>> -- Found RapidJSON source in /home/labbe/src/rdkit/rdkit/External
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> 2018-05-16 13:05 GMT+02:00 Greg Landrum <greg.land...@gmail.com>:
>>>>>>
>>>>>>> On Wed, May 16, 2018 at 12:53 PM alb greg <agparis7dide...@gmail.com>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> I followed the instructions in this dockerfile but it failed with
>>>>>>>> an error 2 during "make -j3 .. install" command.
>>>>>>>>
>>>>>>>>
>>>>>>> In order to be able to help I need a bit more information than that.
>>>>>>> What was the error you encountered? What version of Ubuntu? etc.
>>>>>>>
>>>>>>> -greg
>>>>>>>
>>>>>>
>>>>>>
>>>>
>>
>
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