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

2018-05-16 Thread alb greg 
The system boost? You're talking about libboost?



2018-05-16 14:54 GMT+02:00 Greg Landrum :

> cmake is finding boost v1.67, not the system boost.
>
>
> On Wed, May 16, 2018 at 2:34 PM alb greg 
> 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 :
>>
>>> On Wed, May 16, 2018 at 12:53 PM alb greg 
>>> 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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Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

2018-05-16 Thread Greg Landrum 
cmake is finding boost v1.67, not the system boost.


On Wed, May 16, 2018 at 2:34 PM alb greg  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 :
>
>> On Wed, May 16, 2018 at 12:53 PM alb greg 
>> 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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Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

2018-05-16 Thread Greg Landrum 
On Wed, May 16, 2018 at 12:53 PM alb greg  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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Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

2018-05-16 Thread alb greg 
I followed the instructions in this dockerfile but it failed with an error
2 during "make -j3 .. install" command.




2018-05-07 4:47 GMT+02:00 Greg Landrum :

> For what it's worth:
> I put together a Dockerfile to demonstrate how to build the RDKit under
> Ubuntu 16.04 here:
> https://github.com/rdkit/rdkit_containers/blob/master/
> docker/ubuntu_xenial/Dockerfile
>
> Aside from the RDkit itself, this uses only software that is part of the
> Ubuntu distribution (including the Ubuntu-supplied versions of boost and
> Python).
>
> -greg
>
>
> On Thu, May 3, 2018 at 6:44 PM alb greg  wrote:
>
>> Hello everyone,
>>
>> I'm an IT and I'm writing in connection with the installation process of
>> RDKit.
>>
>> I have to install the latest version of RDKit (2018.03.1) on several
>> workstations running on Ubuntu 16.04 but the building sequence systematically
>> went wrong on the "cmake .." step (see logs below).
>>
>> I installed cmake, python-dev, libsqlite3-dev, NumPy and Boost as
>> required.
>>
>> I tried to specify options like boost and python directories but it
>> didn't solve anything.
>>
>> Could you please take a look on my logs and give me some help?
>>
>> Thanks you very much.
>>
>> Best regards
>>
>>
>>
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Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

2018-05-16 Thread alb greg 
Thanks for your help Andrew!

My cmake is in version 3.5.1

2018-05-03 19:09 GMT+02:00 Andrew Dalke :

> On May 3, 2018, at 18:44, alb greg  wrote:
> > I installed cmake, python-dev, libsqlite3-dev, NumPy and Boost as
> required.
> >
> > I tried to specify options like boost and python directories but it
> didn't solve anything.
>
> > CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
> >   Target "maeparser_static" links to target "Boost::boost" but the
> target was
> >   not found.  Perhaps a find_package() call is missing for an IMPORTED
> >   target, or an ALIAS target is missing?
> > Call Stack (most recent call first):
> >   External/CoordGen/CMakeLists.txt:21 (rdkit_library)
>
>
> That looks similar to a problem I had when I tried to build the most
> recent RDKit.
>
> The problem for me was the installed version of cmake on my system was too
> old.
>
> Once I upgraded from 3.7.2 to 3.11.1, the problem went away.
>
> What version of cmake did you install? Use "cmake --version" to find out.
>
> Cheers,
>
> Andrew
> da...@dalkescientific.com
>
>
>
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