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

2018-05-22 Thread Greg Landrum
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  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 :
>
>> 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 :
>>
>>> 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 
>>> wrote:
>>>
 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)
>>   

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

2018-05-22 Thread alb greg
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 :

> 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 :
>
>> 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 
>> wrote:
>>
>>> 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/Ex
> ternal/CoordGen/maeparser
> -- Found coordgenlibs source in 

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

2018-05-17 Thread alb greg
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 :

> 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 
> wrote:
>
>> 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 

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
>>>
>>
>>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel


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
>>
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel


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
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel


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
>>
>>
>>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel


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
>
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel


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
>
>
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel


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

2018-05-03 Thread Greg Landrum
This is indeed almost certainly due to the version of boost being “too new”
for the version of cmake. I took advantage of a new cmake feature without
fully thinking through the consequences of how picky cmake is about it.

I’m going to revert this change to the build system before the 2018.03.2
release, which will happen sometime in the next couple of weeks. This
should allow older 3.x versions of cmake to work with newer boost versions.

-greg

On Thu, 3 May 2018 at 19:10, Andrew Dalke  wrote:

> 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
>
>
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Rdkit-devel mailing list
> Rdkit-devel@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>
--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot___
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel


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

2018-05-03 Thread 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



--
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
___
Rdkit-devel mailing list
Rdkit-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-devel