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

[Greg L. <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/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 <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
>>>>
>>>
>>>
>