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

2018-05-06 Thread 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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[Rdkit-devel] RDKit 2018.03.1 Build and Installation

2018-05-03 Thread alb greg 
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

*CmakeMessages.log :*

-- 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/python (found version "2.7.12")
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython2.7.so (found
version "2.7.12")
-- Boost version: 1.67.0
-- Found the following Boost libraries:
--   python
-- Could NOT find Eigen3 (missing:  EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
(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/rdkit-Release_2018_03_1/build

*Errors.log :*

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:197 (find_package)


PYTHON Py_ENABLE_SHARED: 1
PYTHON USING LINK LINE: -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions
-Wl,-Bsymbolic-functions -Wl,-z,relro -fno-strict-aliasing -DNDEBUG -g
-fwrapv -O2 -Wall -Wstrict-prototypes -Wdate-time -D_FORTIFY_SOURCE=2 -g
-fstack-protector-strong -Wformat -Werror=format-security
Eigen3 not found, disabling the Descriptors3D build.
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:305 (find_package)


== Using strict rotor definition
-- Found MAEParser source in
/home/user/rdkit-Release_2018_03_1/External/CoordGen/maeparser
-- Found coordgenlibs source in
/home/user/rdkit-Release_2018_03_1/External/CoordGen/coordgenlibs
== Updating Filters.cpp from pains file
-- Found RapidJSON source in /home/user/rdkit-Release_2018_03_1/External
CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "coordgenlib" 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:41 (rdkit_library)


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)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "maeparser" 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)


CMake Error