rdkit-devel — Developers information and discussion.

Re: [Rdkit-devel] Failing tests in Visual Studio build

[Greg L. <gre...@gm...>]

Hi Juuso,

Thanks for letting us know about this.

-greg


On Wed, May 30, 2018 at 10:28 AM Juuso Lehtivarjo <
juu...@gm...> wrote:

> Hi All,
>
> Just wanted to inform all Visual Studio users of some weirdness that
> we encountered after updating Visual Studio 2017 to version 15.7.2,
> that was, on release config, the following tests failed:
>
> 1>     53 - pyChemReactions (SEGFAULT)
> 1>     60 - pyFilterCatalog (SEGFAULT)
> 1>     72 - pyMolDescriptors (SEGFAULT)
> 1>    114 - pyGraphMolWrap (SEGFAULT)
>
> What caused the segfaults was direct touching of the __doc__ property
> of the python wrapper functions. The underlying reason for this was
> that at O2 level optimization, boost::python produced corrupted
> wrappers, apparently due to some changes in the VS optimizer. There is
> now a PR in boost/python for this issue at
> https://github.com/boostorg/python/pull/208.
>
> My setup was Python 3.6.5 and Boost 1.67.0.
>
> Cheers,
> Juuso
>
>
> ------------------------------------------------------------------------------
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> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

[Rdkit-devel] Failing tests in Visual Studio build

[Juuso L. <juu...@gm...>]

Hi All,

Just wanted to inform all Visual Studio users of some weirdness that
we encountered after updating Visual Studio 2017 to version 15.7.2,
that was, on release config, the following tests failed:

1>     53 - pyChemReactions (SEGFAULT)
1>     60 - pyFilterCatalog (SEGFAULT)
1>     72 - pyMolDescriptors (SEGFAULT)
1>    114 - pyGraphMolWrap (SEGFAULT)

What caused the segfaults was direct touching of the __doc__ property
of the python wrapper functions. The underlying reason for this was
that at O2 level optimization, boost::python produced corrupted
wrappers, apparently due to some changes in the VS optimizer. There is
now a PR in boost/python for this issue at
https://github.com/boostorg/python/pull/208.

My setup was Python 3.6.5 and Boost 1.67.0.

Cheers,
Juuso

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

[Greg L. <gre...@gm...>]

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 <agp...@gm...> 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 <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/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
>>>>>>>
>>>>>>
>>>>>>
>>>>
>>
>

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
>>>>>>
>>>>>
>>>>>
>>>
>

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

[alb g. <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/
>>>> 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
>>>>>
>>>>
>>>>
>>

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
>>>>
>>>
>>>
>

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

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

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
>>>
>>
>>

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

[Greg L. <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
>>
>
>

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

[Greg L. <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

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

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

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 <gre...@gm...>:

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

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

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

Thanks for your help Andrew!

My cmake is in version 3.5.1

2018-05-03 19:09 GMT+02:00 Andrew Dalke <da...@da...>:

> On May 3, 2018, at 18:44, alb greg <agp...@gm...> 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...@da...
>
>
>

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

[Greg L. <gre...@gm...>]

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

Re: [Rdkit-devel] bivariate_normal deprecation

[Greg L. <gre...@gm...>]

Thanks Kiran!

On Fri, May 4, 2018 at 5:08 PM Kiran Telukunta <
kir...@in...> wrote:

> Hello Greg,
>
> I have created the ticket <https://github.com/rdkit/rdkit/issues/1851>.
>
> Thanks,
> Kiran
>
> On 4 May 2018 at 09:13, Greg Landrum <gre...@gm...> wrote:
>
>> Hi Kira,
>>
>> I would rather not introduce a dependency on scipy (which is rather
>> large) here. I think it probably makes more sense to just add an RDKit
>> reimplementation of the function and use that.
>>
>> I need to check, but I would guess that the license on matplotlib would
>> probably allow us to just grab their current implementation and use that.
>>
>> Regardless, there should be an RDKit GitHub ticket for this. Do you want
>> to create that or shall I?
>>
>> Best,
>> -greg
>>
>>
>>
>> On Fri, 4 May 2018 at 06:19, Kiran Telukunta <
>> kir...@in...> wrote:
>>
>>> Hi All,
>>>
>>>
>>> What is the best way to rewrite in rdkit.Chem.Draw import SimilarityMaps
>>>
>>> def calcAtomGaussians(mol, a=0.03, step=0.02, weights=None):
>>>
>>> As  mlab.bivariate_normal
>>> <https://matplotlib.org/api/mlab_api.html#matplotlib.mlab.bivariate_normal>
>>> ​​
>>> is deprecated.
>>>
>>> Should we use scipy multivarate function
>>> <https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.multivariate_normal.html#scipy.stats.multivariate_normal>
>>> or is there any other best method?
>>>
>>> I was trying to use SimilarityMaps.GetSimilarityMapForFingerprint, and
>>> got the error:
>>>
>>> home/kiran/anaconda3/envs/rdkit-2018_03_1/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py:285:
>>> MatplotlibDeprecationWarning: The bivariate_normal function was deprecated
>>> in version 2.2.
>>>   Z = mlab.bivariate_normal(X, Y, a, a, mol._atomPs[0][0],
>>> mol._atomPs[0][1]) * weights[0]
>>> /home/kiran/anaconda3/envs/rdkit-2018_03_1/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py:287:
>>> MatplotlibDeprecationWarning: The bivariate_normal function was deprecated
>>> in version 2.2.
>>>   Zp = mlab.bivariate_normal(X, Y, a, a, mol._atomPs[i][0],
>>> mol._atomPs[i][1])
>>>
>>> I was using latest RDKit 2018.03.1.
>>>
>>> Thanks,
>>> Kiran
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> 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
>>> Rdk...@li...
>>> 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
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

Re: [Rdkit-devel] bivariate_normal deprecation

[Kiran T. <kir...@in...>]

Hello Greg,

I have created the ticket <https://github.com/rdkit/rdkit/issues/1851>.

Thanks,
Kiran

On 4 May 2018 at 09:13, Greg Landrum <gre...@gm...> wrote:

> Hi Kira,
>
> I would rather not introduce a dependency on scipy (which is rather large)
> here. I think it probably makes more sense to just add an RDKit
> reimplementation of the function and use that.
>
> I need to check, but I would guess that the license on matplotlib would
> probably allow us to just grab their current implementation and use that.
>
> Regardless, there should be an RDKit GitHub ticket for this. Do you want
> to create that or shall I?
>
> Best,
> -greg
>
>
>
> On Fri, 4 May 2018 at 06:19, Kiran Telukunta <kiran.telukunta@indiayouth.
> info> wrote:
>
>> Hi All,
>>
>>
>> What is the best way to rewrite in rdkit.Chem.Draw import SimilarityMaps
>>
>> def calcAtomGaussians(mol, a=0.03, step=0.02, weights=None):
>>
>> As  mlab.bivariate_normal
>> <https://matplotlib.org/api/mlab_api.html#matplotlib.mlab.bivariate_normal>
>> ​​
>> is deprecated.
>>
>> Should we use scipy multivarate function
>> <https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.multivariate_normal.html#scipy.stats.multivariate_normal>
>> or is there any other best method?
>>
>> I was trying to use SimilarityMaps.GetSimilarityMapForFingerprint, and
>> got the error:
>>
>> home/kiran/anaconda3/envs/rdkit-2018_03_1/lib/python3.5/
>> site-packages/rdkit/Chem/Draw/__init__.py:285:
>> MatplotlibDeprecationWarning: The bivariate_normal function was deprecated
>> in version 2.2.
>>   Z = mlab.bivariate_normal(X, Y, a, a, mol._atomPs[0][0],
>> mol._atomPs[0][1]) * weights[0]
>> /home/kiran/anaconda3/envs/rdkit-2018_03_1/lib/python3.5/
>> site-packages/rdkit/Chem/Draw/__init__.py:287:
>> MatplotlibDeprecationWarning: The bivariate_normal function was deprecated
>> in version 2.2.
>>   Zp = mlab.bivariate_normal(X, Y, a, a, mol._atomPs[i][0],
>> mol._atomPs[i][1])
>>
>> I was using latest RDKit 2018.03.1.
>>
>> Thanks,
>> Kiran
>>
>> ------------------------------------------------------------
>> ------------------
>> 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
>> Rdk...@li...
>> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>>
>

Re: [Rdkit-devel] bivariate_normal deprecation

[Greg L. <gre...@gm...>]

Hi Kira,

I would rather not introduce a dependency on scipy (which is rather large)
here. I think it probably makes more sense to just add an RDKit
reimplementation of the function and use that.

I need to check, but I would guess that the license on matplotlib would
probably allow us to just grab their current implementation and use that.

Regardless, there should be an RDKit GitHub ticket for this. Do you want to
create that or shall I?

Best,
-greg



On Fri, 4 May 2018 at 06:19, Kiran Telukunta <
kir...@in...> wrote:

> Hi All,
>
>
> What is the best way to rewrite in rdkit.Chem.Draw import SimilarityMaps
>
> def calcAtomGaussians(mol, a=0.03, step=0.02, weights=None):
>
> As  mlab.bivariate_normal
> <https://matplotlib.org/api/mlab_api.html#matplotlib.mlab.bivariate_normal>
> ​​
> is deprecated.
>
> Should we use scipy multivarate function
> <https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.multivariate_normal.html#scipy.stats.multivariate_normal>
> or is there any other best method?
>
> I was trying to use SimilarityMaps.GetSimilarityMapForFingerprint, and got
> the error:
>
> home/kiran/anaconda3/envs/rdkit-2018_03_1/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py:285:
> MatplotlibDeprecationWarning: The bivariate_normal function was deprecated
> in version 2.2.
>   Z = mlab.bivariate_normal(X, Y, a, a, mol._atomPs[0][0],
> mol._atomPs[0][1]) * weights[0]
> /home/kiran/anaconda3/envs/rdkit-2018_03_1/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py:287:
> MatplotlibDeprecationWarning: The bivariate_normal function was deprecated
> in version 2.2.
>   Zp = mlab.bivariate_normal(X, Y, a, a, mol._atomPs[i][0],
> mol._atomPs[i][1])
>
> I was using latest RDKit 2018.03.1.
>
> Thanks,
> Kiran
>
>
> ------------------------------------------------------------------------------
> 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
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

[Rdkit-devel] bivariate_normal deprecation

[Kiran T. <kir...@in...>]

Hi All,


What is the best way to rewrite in rdkit.Chem.Draw import SimilarityMaps

def calcAtomGaussians(mol, a=0.03, step=0.02, weights=None):

As  mlab.bivariate_normal
<https://matplotlib.org/api/mlab_api.html#matplotlib.mlab.bivariate_normal>
​​
is deprecated.

Should we use scipy multivarate function
<https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.multivariate_normal.html#scipy.stats.multivariate_normal>
or is there any other best method?

I was trying to use SimilarityMaps.GetSimilarityMapForFingerprint, and got
the error:

home/kiran/anaconda3/envs/rdkit-2018_03_1/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py:285:
MatplotlibDeprecationWarning: The bivariate_normal function was deprecated
in version 2.2.
  Z = mlab.bivariate_normal(X, Y, a, a, mol._atomPs[0][0],
mol._atomPs[0][1]) * weights[0]
/home/kiran/anaconda3/envs/rdkit-2018_03_1/lib/python3.5/site-packages/rdkit/Chem/Draw/__init__.py:287:
MatplotlibDeprecationWarning: The bivariate_normal function was deprecated
in version 2.2.
  Zp = mlab.bivariate_normal(X, Y, a, a, mol._atomPs[i][0],
mol._atomPs[i][1])

I was using latest RDKit 2018.03.1.

Thanks,
Kiran

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

[Greg L. <gre...@gm...>]

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 <da...@da...> wrote:

> On May 3, 2018, at 18:44, alb greg <agp...@gm...> 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...@da...
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> Rdk...@li...
> https://lists.sourceforge.net/lists/listinfo/rdkit-devel
>

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

[Andrew D. <da...@da...>]

On May 3, 2018, at 18:44, alb greg <agp...@gm...> 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...@da...

[Rdkit-devel] RDKit 2018.03.1 Build and Installation

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

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 at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "coordgenlib_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:41 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testCoordGen" 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:57 (rdkit_test)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdCoordGen" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  External/CoordGen/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdCoordGen" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  External/CoordGen/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdCoordGen" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  External/CoordGen/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdCoordGen" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  External/CoordGen/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdCoordGen" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  External/CoordGen/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testDict" 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):
  Code/RDGeneral/CMakeLists.txt:59 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "RDGeneral_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):
  Code/RDGeneral/CMakeLists.txt:4 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "RDGeneral" 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):
  Code/RDGeneral/CMakeLists.txt:4 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testRDValue" 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):
  Code/RDGeneral/CMakeLists.txt:60 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "RDBoost" 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):
  Code/RDBoost/CMakeLists.txt:2 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "RDBoost" links to target "Boost::python" 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):
  Code/RDBoost/CMakeLists.txt:2 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "RDBoost" links to target "Boost::serialization" 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):
  Code/RDBoost/CMakeLists.txt:2 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "RDBoost_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):
  Code/RDBoost/CMakeLists.txt:2 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "RDBoost_static" links to target "Boost::python" 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):
  Code/RDBoost/CMakeLists.txt:2 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "RDBoost_static" links to target "Boost::serialization" 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):
  Code/RDBoost/CMakeLists.txt:2 (rdkit_library)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdBase" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/RDBoost/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdBase" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/RDBoost/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdBase" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/RDBoost/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdBase" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/RDBoost/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdBase" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/RDBoost/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testFPB" 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):
  Code/DataStructs/CMakeLists.txt:29 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "DataStructs_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):
  Code/DataStructs/CMakeLists.txt:5 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "DataStructs" 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):
  Code/DataStructs/CMakeLists.txt:5 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testMultiFPB" 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):
  Code/DataStructs/CMakeLists.txt:32 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testDataStructs" 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):
  Code/DataStructs/CMakeLists.txt:26 (rdkit_test)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "cDataStructs" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/DataStructs/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "cDataStructs" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/DataStructs/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "cDataStructs" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/DataStructs/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "cDataStructs" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/DataStructs/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "cDataStructs" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/DataStructs/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testGrid" 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):
  Code/Geometry/CMakeLists.txt:16 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "RDGeometryLib_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):
  Code/Geometry/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testTransforms" 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):
  Code/Geometry/CMakeLists.txt:15 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "RDGeometryLib" 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):
  Code/Geometry/CMakeLists.txt:1 (rdkit_library)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdGeometry" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/Geometry/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdGeometry" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/Geometry/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdGeometry" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/Geometry/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdGeometry" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/Geometry/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdGeometry" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/Geometry/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testMatrices" 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):
  Code/Numerics/CMakeLists.txt:10 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "Alignment_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):
  Code/Numerics/Alignment/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "Alignment" 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):
  Code/Numerics/Alignment/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testAlignment" 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):
  Code/Numerics/Alignment/CMakeLists.txt:5 (rdkit_test)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdAlignment" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/Numerics/Alignment/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdAlignment" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/Numerics/Alignment/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdAlignment" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/Numerics/Alignment/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdAlignment" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/Numerics/Alignment/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdAlignment" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/Numerics/Alignment/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "EigenSolvers" 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):
  Code/Numerics/EigenSolvers/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "EigenSolvers_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):
  Code/Numerics/EigenSolvers/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "Optimizer" 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):
  Code/Numerics/Optimizer/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "Optimizer_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):
  Code/Numerics/Optimizer/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testOptimizer" 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):
  Code/Numerics/Optimizer/CMakeLists.txt:7 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "ForceField" 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):
  Code/ForceField/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "ForceField_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):
  Code/ForceField/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testUFFForceField" 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):
  Code/ForceField/UFF/CMakeLists.txt:1 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testMMFFForceField" 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):
  Code/ForceField/MMFF/CMakeLists.txt:9 (rdkit_test)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdForceField" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/ForceField/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdForceField" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/ForceField/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdForceField" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/ForceField/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdForceField" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/ForceField/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "rdForceField" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/ForceField/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "DistGeometry_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):
  Code/DistGeom/CMakeLists.txt:3 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "DistGeometry" 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):
  Code/DistGeom/CMakeLists.txt:3 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "testDistGeom" 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):
  Code/DistGeom/CMakeLists.txt:16 (rdkit_test)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "DistGeom" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/DistGeom/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "DistGeom" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/DistGeom/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "DistGeom" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/DistGeom/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "DistGeom" links to target "Boost::python" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/DistGeom/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at /usr/share/cmake-3.5/Modules/FindPythonLibs.cmake:292
(add_library):
  Target "DistGeom" links to target "Boost::serialization" 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):
  Code/cmake/Modules/RDKitUtils.cmake:116 (PYTHON_ADD_MODULE)
  Code/DistGeom/Wrap/CMakeLists.txt:1 (rdkit_python_extension)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "Catalogs_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):
  Code/Catalogs/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "Catalogs" 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):
  Code/Catalogs/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "graphmoltestChirality" 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):
  Code/GraphMol/CMakeLists.txt:112 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "molBundleTest" 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):
  Code/GraphMol/CMakeLists.txt:133 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "graphmoltestCanon" 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):
  Code/GraphMol/CMakeLists.txt:109 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "graphmolIterTest" 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):
  Code/GraphMol/CMakeLists.txt:122 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "graphmoltestPickler" 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):
  Code/GraphMol/CMakeLists.txt:116 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "graphmolMolOpsTest" 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):
  Code/GraphMol/CMakeLists.txt:105 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "GraphMol" 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):
  Code/GraphMol/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "graphmoltestPicklerGlobalSetting" 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):
  Code/GraphMol/CMakeLists.txt:119 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "graphmolqueryTest" 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):
  Code/GraphMol/CMakeLists.txt:103 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "hanoiTest" 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):
  Code/GraphMol/CMakeLists.txt:124 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "GraphMol_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):
  Code/GraphMol/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "graphmolcpTest" 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):
  Code/GraphMol/CMakeLists.txt:101 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "test-valgrind" 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):
  Code/GraphMol/CMakeLists.txt:136 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "graphmolTest1" 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):
  Code/GraphMol/CMakeLists.txt:98 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "graphmolMemTest1" 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):
  Code/GraphMol/CMakeLists.txt:128 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:155 (add_executable):
  Target "resMolSupplierTest" 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):
  Code/GraphMol/CMakeLists.txt:130 (rdkit_test)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:57 (add_library):
  Target "Depictor_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):
  Code/GraphMol/Depictor/CMakeLists.txt:1 (rdkit_library)


CMake Error at Code/cmake/Modules/RDKitUtils.cmake:51 (add_library):
  Target "Depictor" 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):
  Code/GraphMol/Depictor/CMakeLists.txt:1 (rdkit_library)

(...)

[Rdkit-devel] Apologies for the delays processing pull requests

[Greg L. <gre...@gm...>]

Dear all,

There's something of a backlog of unprocessed pull requests for the RDKit.
Putting (what I hope were) the final touches on the release ended up being
a time consuming slog and didn't leave me much time for looking at PRs. I'm
sorry for this; it's great to have the contributions coming in and I feel
bad about not being able to process them in a timely manner.

Having said that, it's going to get a bit worse before it gets better.
After finishing the release, I'm going to celebrate by giving myself a
short "vacation" from bug fixes, the vagaries of conda, and such tings.I
plan to spend the next week or so using my "RDKit time" to work on a fun
project or two.

Best,
-greg

[Rdkit-devel] 2018.03.1 RDKit release

[Greg L. <gre...@gm...>]

 I'm pleased to announce that the next version of the RDKit - 2018.03 - is
released. The release notes are below.

The release files are on the github release page:
https://github.com/rdkit/rdkit/releases/tag/Release_2018_03_1

Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit).
The available conda binaries for this release are:
Linux 64bit: python 2.7, 3.5, 3.6
Mac OS 64bit: python 2.7, 3.5, 3.6
Windows 64bit: python 3.5, 3.6

The missing binary for python 2.7 on windows is explained here:
https://www.mail-archive.com/rdk...@li.../msg07850.html

Some things that will be finished over the next couple of days:
- The conda build scripts will be updated to reflect the new version and
new conda builds will be available in the RDKit channel at anaconda.org (
https://anaconda.org/rdkit).
- The homebrew script
- The online version of the documentation at rdkit.org (I'm traveling this
week, so this is unlikely to be done before next weekend).

Thanks to everyone who submitted code, bug reports, and suggestions for
this release!

Please let me know if you find any problems with the release or have
suggestions for the next one, which is scheduled for Octobera 2018.

Best Regards,
-greg

# Release_2018.03.1
(Changes relative to Release_2017.09.1)

## C++11 notes

Starting with this release, the RDKit core C++ code is written in modern
C++;
for this release that means C++11. This means that the compilers used to
build
it cannot be completely ancient. Here are the minimum tested versions:
- g++ v4.8: though note that the SLN parser code cannot be built with v4.8.
It
  will automatically be disabled when this older compiler is used.
- clang v3.9: it may be that older versions of the compiler also work, but
we
  haven't tested them.
- Visual Studio 2015: it may be that older versions of the compiler also
work,
  but we haven't tested them.

## Backwards incompatible changes

This release includes a set of changes to make the default arguments to
common
functions less error prone (github #1679).
- MolToSmiles() now generates isomeric SMILES by default.
- The embedding code now uses the ETKDG method by default.
- MolToMolBlock() will now by default generate a set of 2D coordinates for
  molecules when the includeStereo option is set to True. The changes are
made
  to a copy of the molecule; the molecule itself will not be modified.
- The Mol file (and SDF) parser now determines atomic stereochemisty based
on
  the 3D coordinates provided (if 3D coordinates are provided).
- The SMILES parser now supports CXSMILES by default (assuming that
additional
  text that looks like CXSMILES extensions is there).

In every case the old behavior can be obtained by providing an optional
argument
to the function(s) mentioned.

## Acknowledgements:
Boran Adas, José Emilio Sánchez Aparicio, Patrick Avery, Jason Biggs, Brian
Cole, Andrew Dalke, JW Feng, Peter Gedeck, Guillaume Godin, Richard Hall,
Thomas
Heavy, Gareth Jones, Brian Kelley, Karl Leswing, Susan Leung, Chris Morris,
Dan
Nealschneider, Noel O'Boyle, Axel Pahl, Pavel Polishchuk, Sereina Riniker,
Jeff
van Santen, Roger Sayle, Martin Šícho, Matt Swain, Paolo Tosco, Sam Webb,
Maciej
Wójcikowski, Nicola Zonta, 'clinntt', 'hjuinj', 'iwatobipen',

## Highlights:
  - An initial version of an integration with Schrodinger's coordgen
library is
    included. This produces much better 2D coordinates for complex
molecules.
  - Thanks to the move to modern C++ the RDKit is now faster and uses less
    memory
  - A number of improvements were made to the PDB reader
  - v2 of the ETKDG torsions and potentials is now available

## Contrib updates:
  - Implementation of Peter Ertl's IFG method for identifying functional
groups
    from Guillaume Godin and Richard Hall
  (github pull #1813 from thegodone)

## New Features and Enhancements:
  - Support InChi 1.05
 (github issue #1533 from greglandrum)
  - Update CPack to create .deb files correctly
 (github pull #1580 from psavery)
  - Initial commit of EnumerateHeterocycles
 (github pull #1588 from coleb)
  - Version 2 of ETKDG
 (github pull #1597 from sriniker)
  - GetMolFrags now optionally returns atom indices along with mols
 (github pull #1602 from ptosco)
  - NP Likeness with confidence value
 (github pull #1608 from apahl)
  - Adding an option to EnumerateStereoisomers to only return unique isomers
 (github pull #1612 from coleb)
  - Add function wedgeBond()
  (github issue #1615 from greglandrum)
  - Dev/substructlibrary docs
 (github pull #1620 from bp-kelley)
  - Turns off exception throwing for certain classes Rlabel sanitization.
 (github pull #1621 from bp-kelley)
  - Add an "MDL" aromaticity model
 (github issue #1622 from hjuinj)
  - Add support for %(NNN) notation for ring closures
 (github pull #1624 from baoilleach)
  - Enable windows build that uses cairo
 (github pull #1628 from greglandrum)
  - [MRG] Fix PDB reader + add argument to toggle proximity bonding
 (github pull #1629 from mwojcikowski)
  - Improve AddHs for molecules read from PDB
 (github pull #1647 from mwojcikowski)
  - Improved regression test for ETKDG version 2
 (github pull #1640 from sriniker)
  - RDKit interpretation of atom stereo SMILES is different from 4 other
toolkits
 (github issue #1652 from coleb)
  - Treat bonds in PDB CONECT records explicitly, but make blacklisted ones
zero-order.
 (github pull #1658 from mwojcikowski)
  - There is no need to enforce that (i, j) and (k, l) be bonded when
setting a i, j, k, l dihedral
 (github pull #1673 from ptosco)
  - Make default arguments to common functions less error prone
 (github issue #1679 from greglandrum)
  - Add Fast cluster script
 (github pull #1683 from iwatobipen)
  - Update embedded InChI to v1.05
 (github pull #1684 from mcs07)
  - Add `AllChem.MMFFGetMoleculeForceField().CalcGradient()` to Python
wrappers
 (github issue #1688 from theavey)
  - Play nice with naughty MOL blocks
 (github issue #1689 from jw-feng)
  - Make the defaults for some functions less error prone.
 (github pull #1690 from greglandrum)
  - implemented Python wrappers for computing PMI axes and moments
 (github pull #1700 from ptosco)
  - Enable range-based for loops for molecules
 (github pull #1701 from bp-kelley)
  - Support some cactvs extensions to SMARTS
 (github pull #1704 from greglandrum)
  - Integrate Coordgen
 (github pull #1708 from greglandrum)
  - Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
 (github pull #1713 from greglandrum)
  - Set atomic properties from SMARTS
 (github pull #1716 from greglandrum)
  - Allow installation of Python tests to facilitate testing installations
 (github pull #1724 from greglandrum)
  - setAromaticity() should work even if there are aromatic atoms present
 (github issue #1730 from greglandrum)
  - Use uint32 atom and bond indices
 (github pull #1742 from greglandrum)
  - Switch from boost::thread to std::thread
 (github pull #1745 from greglandrum)
  - switch to using std::regex in the SLN parser
 (github pull #1746 from greglandrum)
  - replace the usage of rdk_auto_ptr with std::unique_ptr
 (github pull #1752 from greglandrum)
  - getMolBoundsMatrix() should do triangle bound smoothing by default
 (github issue #1763 from greglandrum)
  - Added Morgan feature fingerprints to Java API
 (github pull #1764 from jones-gareth)
  - Reaction fingerprints not exposed in Java wrapper
 (github issue #1776 from webbres)
  - add Tversky index calculation for shapes
 (github pull #1777 from susanhleung)
  - Add MolToInchiKey function()
 (github pull #1784 from greglandrum)
  - speedup the NumBitsInCommon operation
 (github pull #1785 from greglandrum)
  - Stop putting brackets around * atoms in SMILES
 (github pull #1788 from greglandrum)
  - Support for a JSON-based molecule interchange format
 (github pull #1798 from greglandrum)

## Bug Fixes:
  - Fixes Java wrapper build error with Boost 1.64
 (github pull #1613 from ptosco)
  - AssignStereochemistry cleanIt=True incorrectly removing new CIS/TRANS
bond stereo
 (github issue #1614 from coleb)
  - switch to using a specific freesasa version
 (github pull #1619 from greglandrum)
  - Add support for %(NNN) notation for ring closures
 (github pull #1624 from baoilleach)
  - Draw._moltoSVG() raises an exception
 (github issue #1625 from greglandrum)
  - MolDrawCairo2D does not build on windows
 (github issue #1627 from greglandrum)
  - Enable windows build that uses cairo
 (github pull #1628 from greglandrum)
  - don't always download the FreeSASA source
 (github issue #1630 from greglandrum)
  - Make sure EmbedMultipleConfs is deterministic for very large seeds and
a seed of 0
 (github pull #1635 from coleb)
  - from rdkit.Chem import AllChem has grown a six dependency
 (github issue #1637 from bp-kelley)
  - Fixing bug in IPythonConsole SVG rendering introduced in
1027d4469545653180fff9a38dc8224bd50e8b0d
 (github pull #1641 from coleb)
  - changes required to allow replacing the obsolete __conda_version__ in
conda-rdkit
 (github pull #1644 from ptosco)
  - GetConformerRMSMatrix does not work if some conformers were removed
 (github issue #1650 from DrrDom)
  - EnumerateLibrary with initFromString called twice doesn't clear the
reaction
 (github issue #1657 from bp-kelley)
  - Missed symmetrization in R-Group decomposition
 (github issue #1659 from greglandrum)
  - Use numpy not numeric for boost 1.65+ - fixes #1581
 (github pull #1664 from mcs07)
  - Support valence 7 for As, Sb, and Bi
 (github issue #1668 from greglandrum)
  - Fix: GetDonor2FeatVects heavy atoms confusion
 (github pull #1676 from josan82)
  - Acetylenic hydrogens not given appropriate 2D coordinates
 (github issue #1691 from jasondbiggs)
  - Warning on import of rgroup decomposition package
 (github issue #1695 from greglandrum)
  - AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is
required
 (github issue #1702 from baoilleach)
  - Dative bonds interfere with kekulization and the perception of
aromaticity
 (github issue #1703 from greglandrum)
  - Fix/rgroup prefer matching nonhs over hs
 (github pull #1707 from bp-kelley)
  - bonds that are STEREOCIS or STEREOTRANS cannot be depickled
 (github issue #1710 from greglandrum)
  - Get queries from the new cactvs SMARTS extensions to pickle correctly
 (github pull #1712 from greglandrum)
  - fix an irritating cmake problem
 (github pull #1715 from greglandrum)
  - Added dependency from Boost headers to PgSQL CMakeLists.txt
 (github pull #1717 from ptosco)
  - Updates python test runner to always use sys.executable
 (github pull #1721 from bp-kelley)
  - - make bond stereo detection in rings consistent
 (github pull #1727 from ptosco)
  - xlocale.h not needed to compile with clang
 (github issue #1728 from adalke)
 - BreakBRICSBonds() not preserving stereochemistry
 (github issue #1734 from greglandrum)
  - rdmolfiles.CanonicalRankAtoms segfaults on 0 atom molecules
 (github issue #1735 from lilleswing)
  - deprecated apply() function causes GetRDKFingerprint to fail in Python 3
 (github issue #1747 from clinntt)
  - Stop dereferencing end() iterators
 (github pull #1748 from greglandrum)
  - out of range fromAtom causes GetMorganFingerprintAsBitVect to segfault
 (github issue #1749 from adalke)
  - Generated SMARTS does not contain atomic chiral tags
 (github issue #1756 from greglandrum)
  - make the build work even if boost::serialization is disabled
 (github pull #1767 from greglandrum)
  - Fix typo in GetBoolProp documentation
 (github pull #1770 from jvansan)
  - Fingerprint segfaults with branchedPaths=False and useHs=False
 (github issue #1793 from chrishmorris)
  - Fix python linkage (primarily for conda builds)
 (github pull #1808 from greglandrum)
  - removeHs() should not remove H atoms that are contributing to the
definition of a stereo bond
 (github pull #1810 from d-b-w)
  - global EmbedParameters objects should not be writeable in SWIG wrappers
 (github issue #1826 from greglandrum)
  - RDKit crashes when MolsToGridImage function is called with an empty
iterable.
 (github issue #1829 from martin-sicho)

[Rdkit-devel] The 2018.03 release, python 2.7, and Windows

[Greg L. <gre...@gm...>]

Dear all,

In finalizing the details for the 2018.03.1 release, I hit a problem with
python v2.7 on Windows that is likely to result in there being no conda
builds available for the Windows version of python 2.7.

The problem is that extension modules for python 2.7 “are supposed to be”
built with a 10+ year old version of visual C++. This ancient compiler
can’t handle modern C++ and thus can no longer build the RDKit. It is
possible, though somewhat risky, to use other compilers, but conda-build
makes that challenging.

I have already spent a fair amount of time on this without making
significant progress, so I’m going to give up with apologies to anyone who
is still using Python 2.7 on Windows. I may have end up having alternate
ideas to try out later, but if anyone else knows how to force recent
versions of conda-build to use a more modern compiler on Windows, I’d love
to hear about it.

A reminder for people who are still using python 2.7: it's a very good idea
to read this and start figuring out a plan for migrating to Python 3:
https://python3statement.org


 Best,
-greg

Re: [Rdkit-devel] [Rdkit-discuss] [Announcement] 7th RDKit UGM in Cambridge UK

[Greg L. <gre...@gm...>]

The optional training events will have separate registration pages (or
maybe just one). I will post the link for those "soon" (hopefully in the
next week).

-greg


On Tue, Apr 10, 2018 at 11:03 AM, Paul Czodrowski <
Pau...@me...> wrote:

> Great idea about the optional training on the day before.
>
>
>
> However, I could not see any link (on the eventbrite page) regarding this
> event. There was an option for the dinner & reception, but no training..
>
>
>
> Or is the “main UGM registration” a different place than the evenbrite
> page?
>
>
>
>
>
> Paul
>
>
>
> *Von:* Greg Landrum [mailto:gre...@gm...]
> *Gesendet:* Samstag, 7. April 2018 07:14
> *An:* RDKit Discuss <rdk...@li...>; RDKit
> Developers List <rdk...@li...>
> *Cc:* Andreas Bender, PhD <ab...@ca...>
> *Betreff:* [Rdkit-devel] [Announcement] 7th RDKit UGM in Cambridge UK
>
>
>
> Dear all,
>
>
>
> This year's RDKit User Group Meeting will take place from 19-21 September
> in Cambridge, UK and is being hosted by Andreas Bender at Cambridge
> University.
>
>
>
> Registration for the RDKit UGM is free:
>
> https://www.eventbrite.com/e/7th-rdkit-ugm-2018-tickets-44883066460
>
>
>
> We will once again mostly stick to what has become a tried and true format:
>
> Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, poster
> sessions, and talktorials. For those who haven’t attended before,
> talktorials are somewhere between a talk and a tutorial, they cover
> something interesting done with the RDKit and include the code used to do
> the work. During the presentation you'll give an overview of what you did
> and also show the pieces of the code that are central to the work. The idea
> is to mix the science up with the tutorial aspects.
>
>
>
> Day 3 will be a hackathon: those who choose to stay will spend an intense
> day working in small groups to produce useful artifacts: new bits of code,
> KNIME nodes, KNIME workflows, tutorials, documentation, IPython notebooks,
> etc. We will once again try to structure this a bit by collecting a bunch
> of ideas for things to work on in advance. Two years ago we also did
> extended tutorials on Day 3; if there are volunteers to do tutorials and
> people interested in attending them, we'll repeat that this year as well.
>
>
>
> As an experiment this year there will be an optional training day on
> Tuesday the 18th. Andrew Dalke (Dalke Scientific) will offer a course on
> Python and the RDKit and Daria Goldmann (KNIME) will offer a course on
> KNIME and the RDKit. Space for both of these is limited, so we'll do
> separate registrations for them (links will be included on the main UGM
> registration page). Many thanks to Andrew for coming up with the idea to do
> this!
>
>
>
> There will also be, of course, social activities. This year we have the
> special opportunity to have the dinner on the 19th in the Old Library of
> Pembroke College. I can't wait for that. :-)
>
>
>
> A more detailed announcement with additional information about place,
> hotels and logistics will follow soon.
>
>
>
> We are looking for people who are willing to do presentations, talktorials
> or posters on the first two days. If you're interested in contributing,
> please send Greg and Andreas an email.
>
>
>
> Lightning talks don't need to be arranged too far in advance; we will
> start collecting the list of people interested in doing those shortly
> before the event.
>
>
>
> Best Regards,
>
> Greg and Andreas
>
>
>
> This message and any attachment are confidential and may be privileged or
> otherwise protected from disclosure. If you are not the intended recipient,
> you must not copy this message or attachment or disclose the contents to
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>
>
> Click http://www.merckgroup.com/disclaimer to access the German, French,
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>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
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>
>

[Rdkit-devel] [Announcement] 7th RDKit UGM in Cambridge UK

[Greg L. <gre...@gm...>]

Dear all,

This year's RDKit User Group Meeting will take place from 19-21 September
in Cambridge, UK and is being hosted by Andreas Bender at Cambridge
University.

Registration for the RDKit UGM is free:
https://www.eventbrite.com/e/7th-rdkit-ugm-2018-tickets-44883066460

We will once again mostly stick to what has become a tried and true format:
Days 1 and 2: Talks, lightning talks, roundtable(s), discussion, poster
sessions, and talktorials. For those who haven’t attended before,
talktorials are somewhere between a talk and a tutorial, they cover
something interesting done with the RDKit and include the code used to do
the work. During the presentation you'll give an overview of what you did
and also show the pieces of the code that are central to the work. The idea
is to mix the science up with the tutorial aspects.

Day 3 will be a hackathon: those who choose to stay will spend an intense
day working in small groups to produce useful artifacts: new bits of code,
KNIME nodes, KNIME workflows, tutorials, documentation, IPython notebooks,
etc. We will once again try to structure this a bit by collecting a bunch
of ideas for things to work on in advance. Two years ago we also did
extended tutorials on Day 3; if there are volunteers to do tutorials and
people interested in attending them, we'll repeat that this year as well.

As an experiment this year there will be an optional training day on
Tuesday the 18th. Andrew Dalke (Dalke Scientific) will offer a course on
Python and the RDKit and Daria Goldmann (KNIME) will offer a course on
KNIME and the RDKit. Space for both of these is limited, so we'll do
separate registrations for them (links will be included on the main UGM
registration page). Many thanks to Andrew for coming up with the idea to do
this!

There will also be, of course, social activities. This year we have the
special opportunity to have the dinner on the 19th in the Old Library of
Pembroke College. I can't wait for that. :-)

A more detailed announcement with additional information about place,
hotels and logistics will follow soon.

We are looking for people who are willing to do presentations, talktorials
or posters on the first two days. If you're interested in contributing,
please send Greg and Andreas an email.

Lightning talks don't need to be arranged too far in advance; we will start
collecting the list of people interested in doing those shortly before the
event.

Best Regards,
Greg and Andreas

[Rdkit-devel] Beta of the 2018.03 release available

[Greg L. <gre...@gm...>]

 Dear all,

The beta of the 2018.03 RDKit release has been tagged in github:
https://github.com/rdkit/rdkit/releases/tag/Release_2018_03_1b1

I will try to get some conda builds for python 3.6 up over the next day or
so. These will use the beta label so that they do not install by default;
you'll need to run "conda install" as follows:

conda install -c rdkit/label/beta rdkit python=3.6

Be sure to confirm that it's installing the right version when you are
prompted (if there's no build available, it will pick the current
production release instead).

You can check to see if a build is available for your platform/python
version here:
https://anaconda.org/rdkit/rdkit/files?version=2018.03.1.b1

About the builds:
- These will be done using the most recent version of conda.
- I will do the conda builds somewhat differently than I've done them
before due to the transition to modern C++ on the backend. If you encounter
problems with the beta builds, particularly the windows or linux builds,
please let me know. It is, of course, also really nice to hear if you try
things and they work!

The relevant section of the release notes is below.

As usual, if you have time to try out the new release I would love
feedback. If nothing major comes up, I plan to do the actual release
sometime next week.

Best,
-greg

# Release_2018.03.1
(Changes relative to Release_2017.09.1)

## C++11 notes
Starting with this release, the RDKit core C++ code is written in
modern C++; for this release that means C++11.
This means that the compilers used to build it cannot be completely
ancient. Here are the minimum tested versions:

- g++ v4.8: though note that the SLN parser code cannot be built with
v4.8. It will automatically be disabled when this older compiler is
used.
- clang v3.9: it may be that older versions of the compiler also work,
but we haven't tested them.
- Visual Studio 2015: it may be that older versions of the compiler
also work, but we haven't tested them.

## Backwards incompatible changes
This release includes a set of changes to make the default arguments
to common functions less error prone (github #1679).
- MolToSmiles() now generates isomeric SMILES by default.
- The embedding code now uses the ETKDG method by default.
- MolToMolBlock() will now by default generate a set of 2D coordinates
for molecules when the includeStereo option is set to True. The
changes are made to a copy of the molecule; the molecule itself will
not be modified.
- The Mol file (and SDF) parser now determines atomic stereochemisty
based on the 3D coordinates provided (if 3D coordinates are provided).
- The SMILES parser now supports CXSMILES by default (assuming that
additional text that looks like CXSMILES extensions is there).

In every case the old behavior can be obtained by providing an
optional argument to the function(s) mentioned.

## Acknowledgements:
Boran Adas, José Emilio Sánchez Aparicio, Patrick Avery, Jason Biggs,
Brian Cole, Andrew Dalke, JW Feng, Peter Gedeck, Thomas Heavy, Gareth
Jones, Brian Kelley, Karl Leswing, Susan Leung, Chris Morris, Noel
O'Boyle, Axel Pahl, Pavel Polishchuk, Sereina Riniker, Jeff van
Santen, Roger Sayle, Matt Swain, Palo Tosco, Sam Webb, Maciej
Wójcikowski, Nicola Zonta, 'clinntt', 'hjuinj', 'iwatobipen',

## Highlights:
  - A number of improvements were made to the PDB reader
  - Thanks to the move to modern C++ the RDKit is now faster and uses
less memory

## New Features and Enhancements:
  - Support InChi 1.05
 (github issue #1533 from greglandrum)
  - Update CPack to create .deb files correctly
 (github pull #1580 from psavery)
  - Initial commit of EnumerateHeterocycles
 (github pull #1588 from coleb)
  - Version 2 of ETKDG
 (github pull #1597 from sriniker)
  - GetMolFrags now optionally returns atom indices along with mols
 (github pull #1602 from ptosco)
  - NP Likeness with confidence value
 (github pull #1608 from apahl)
  - Adding an option to EnumerateStereoisomers to only return unique isomers
 (github pull #1612 from coleb)
  - Add function wedgeBond()
  (github issue #1615 from greglandrum)
  - Dev/substructlibrary docs
 (github pull #1620 from bp-kelley)
  - Turns off exception throwing for certain classes Rlabel sanitization.…
 (github pull #1621 from bp-kelley)
  - Add an "MDL" aromaticity model
 (github issue #1622 from hjuinj)
  - Add support for %(NNN) notation for ring closures
 (github pull #1624 from baoilleach)
  - Enable windows build that uses cairo
 (github pull #1628 from greglandrum)
  - [MRG] Fix PDB reader + add argument to toggle proximity bonding
 (github pull #1629 from mwojcikowski)
  - Improve AddHs for molecules read from PDB
 (github pull #1647 from mwojcikowski)
  - Improved regression test for ETKDG version 2
 (github pull #1640 from sriniker)
  - RDKit interpretation of atom stereo SMILES is different from 4
other toolkits
 (github issue #1652 from coleb)
  - Treat bonds in PDB CONECT records explicitly, but make blacklisted
ones zero-order.
 (github pull #1658 from mwojcikowski)
  - There is no need to enforce that (i, j) and (k, l) be bonded when
setting a i, j, k, l dihedral
 (github pull #1673 from ptosco)
  - Make default arguments to common functions less error prone
 (github issue #1679 from greglandrum)
  - Add Fast cluster script
 (github pull #1683 from iwatobipen)
  - Update embedded InChI to v1.05
 (github pull #1684 from mcs07)
  - Add `AllChem.MMFFGetMoleculeForceField().CalcGradient()` to Python wrappers
 (github issue #1688 from theavey)
  - Play nice with naughty MOL blocks
 (github issue #1689 from jw-feng)
  - Make the defaults for some functions less error prone.
 (github pull #1690 from greglandrum)
  - implemented Python wrappers for computing PMI axes and moments
 (github pull #1700 from ptosco)
  - Enable range-based for loops for molecules
 (github pull #1701 from bp-kelley)
  - Support some cactvs extensions to SMARTS
 (github pull #1704 from greglandrum)
  - Integrate Coordgen
 (github pull #1708 from greglandrum)
  - Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
 (github pull #1713 from greglandrum)
  - Set atomic properties from SMARTS
 (github pull #1716 from greglandrum)
  - Allow installation of Python tests to facilitate testing installations
 (github pull #1724 from greglandrum)
  - setAromaticity() should work even if there are aromatic atoms present
 (github issue #1730 from greglandrum)
  - Use uint32 atom and bond indices
 (github pull #1742 from greglandrum)
  - Switch from boost::thread to std::thread
 (github pull #1745 from greglandrum)
  - switch to using std::regex in the SLN parser
 (github pull #1746 from greglandrum)
  - replace the usage of rdk_auto_ptr with std::unique_ptr
 (github pull #1752 from greglandrum)
  - getMolBoundsMatrix() should do triangle bound smoothing by default
 (github issue #1763 from greglandrum)
  - Added Morgan feature fingerprints to Java API
 (github pull #1764 from jones-gareth)
  - Reaction fingerprints not exposed in Java wrapper
 (github issue #1776 from webbres)
  - add Tversky index calculation for shapes
 (github pull #1777 from susanhleung)
  - Add MolToInchiKey function()
 (github pull #1784 from greglandrum)
  - speedup the NumBitsInCommon operation
 (github pull #1785 from greglandrum)
  - Stop putting brackets around * atoms in SMILES
 (github pull #1788 from greglandrum)
  - Support for a JSON-based molecule interchange format
 (github pull #1798 from greglandrum)

## Bug Fixes:
  - Fixes Java wrapper build error with Boost 1.64
 (github pull #1613 from ptosco)
  - AssignStereochemistry cleanIt=True incorrectly removing new
CIS/TRANS bond stereo
 (github issue #1614 from coleb)
  - switch to using a specific freesasa version
 (github pull #1619 from greglandrum)
  - Add support for %(NNN) notation for ring closures
 (github pull #1624 from baoilleach)
  - Draw._moltoSVG() raises an exception
 (github issue #1625 from greglandrum)
  - MolDrawCairo2D does not build on windows
 (github issue #1627 from greglandrum)
  - Enable windows build that uses cairo
 (github pull #1628 from greglandrum)
  - don't always download the FreeSASA source
 (github issue #1630 from greglandrum)
  - Make sure EmbedMultipleConfs is deterministic for very large seeds
and a seed of 0
 (github pull #1635 from coleb)
  - from rdkit.Chem import AllChem has grown a six dependency
 (github issue #1637 from bp-kelley)
  - Fixing bug in IPythonConsole SVG rendering introduced in
1027d4469545653180fff9a38dc8224bd50e8b0d
 (github pull #1641 from coleb)
  - changes required to allow replacing the obsolete __conda_version__
in conda-rdkit
 (github pull #1644 from ptosco)
  - GetConformerRMSMatrix does not work if some conformers were removed
 (github issue #1650 from DrrDom)
  - EnumerateLibrary with initFromString called twice doesn't clear the reaction
 (github issue #1657 from bp-kelley)
  - Missed symmetrization in R-Group decomposition
 (github issue #1659 from greglandrum)
  - Use numpy not numeric for boost 1.65+ - fixes #1581
 (github pull #1664 from mcs07)
  - Support valence 7 for As, Sb, and Bi
 (github issue #1668 from greglandrum)
  - Fix: GetDonor2FeatVects heavy atoms confusion
 (github pull #1676 from josan82)
  - Acetylenic hydrogens not given appropriate 2D coordinates
 (github issue #1691 from jasondbiggs)
  - Warning on import of rgroup decomposition package
 (github issue #1695 from greglandrum)
  - AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required
 (github issue #1702 from baoilleach)
  - Dative bonds interfere with kekulization and the perception of aromaticity
 (github issue #1703 from greglandrum)
  - Fix/rgroup prefer matching nonhs over hs
 (github pull #1707 from bp-kelley)
  - bonds that are STEREOCIS or STEREOTRANS cannot be depickled
 (github issue #1710 from greglandrum)
  - Get queries from the new cactvs SMARTS extensions to pickle correctly
 (github pull #1712 from greglandrum)
  - fix an irritating cmake problem
 (github pull #1715 from greglandrum)
  - Added dependency from Boost headers to PgSQL CMakeLists.txt
 (github pull #1717 from ptosco)
  - Updates python test runner to always use sys.executable
 (github pull #1721 from bp-kelley)
  - - make bond stereo detection in rings consistent
 (github pull #1727 from ptosco)
  - xlocale.h not needed to compile with clang
 (github issue #1728 from adalke)
 - BreakBRICSBonds() not preserving stereochemistry
 (github issue #1734 from greglandrum)
  - rdmolfiles.CanonicalRankAtoms segfaults on 0 atom molecules
 (github issue #1735 from lilleswing)
  - deprecated apply() function causes GetRDKFingerprint to fail in Python 3
 (github issue #1747 from clinntt)
  - Stop dereferencing end() iterators
 (github pull #1748 from greglandrum)
  - out of range fromAtom causes GetMorganFingerprintAsBitVect to segfault
 (github issue #1749 from adalke)
  - Generated SMARTS does not contain atomic chiral tags
 (github issue #1756 from greglandrum)
  - make the build work even if boost::serialization is disabled
 (github pull #1767 from greglandrum)
  - Fix typo in GetBoolProp documentation
 (github pull #1770 from jvansan)
  - Fingerprint segfaults with branchedPaths=False and useHs=False
 (github issue #1793 from chrishmorris)
  - Fix python linkage (primarily for conda builds)
 (github pull #1808 from greglandrum)