Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

[alb g. <agp...@gm...>]

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 <agp...@gm...>:

> 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 <gre...@gm...>:
>
>> 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 <agp...@gm...>
>> wrote:
>>
>>> The system boost? You're talking about libboost?
>>>
>>>
>>>
>>> 2018-05-16 14:54 GMT+02:00 Greg Landrum <gre...@gm...>:
>>>
>>>> cmake is finding boost v1.67, not the system boost.
>>>>
>>>>
>>>> On Wed, May 16, 2018 at 2:34 PM alb greg <agp...@gm...>
>>>> 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/Ex
>>>>> ternal/CoordGen/maeparser
>>>>> -- Found coordgenlibs source in /home/labbe/src/rdkit/rdkit/Ex
>>>>> ternal/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 <gre...@gm...>:
>>>>>
>>>>>> On Wed, May 16, 2018 at 12:53 PM alb greg <agp...@gm...>
>>>>>> 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
>>>>>>
>>>>>
>>>>>
>>>
>