Re: [Rdkit-discuss] Compiling rdkit-Release_2019_09_3 with python 3.7.5 and gnu gcc, g++ on MacOS 10.15

2020-01-20 Thread Francois Berenger 

On 21/01/2020 01:29, Zoltan Takacs wrote:

Hi,

Thanks,

I repeated the compilation procedure on an Ubuntu machine with boost
1.62.0 and everything went smashingly. This indeed seems to be some
cmake boost mismatch on my mac. I will use an older version of boost
instead.


This should do the trick; maybe you don't need to downgrade boost:

-DBoost_NO_BOOST_CMAKE=ON

The solution advised by Greg (-DBoost_NO_BOOST_CMAKE=TRUE) might have
the same effect, though I did no try it.


Best,
Zoltan

On 20 Jan 2020, at 17:25, Greg Landrum  wrote:

Hi Zoltan,

I use the system compiler (clang++) on the Mac, so I don't have direct
experience here.

One problem is likely that the cmake argument you want is
-DBoost_NO_SYSTEM_PATHS=ON
those variable names are case sensitive.

The other point is that cmake didn't officiallly support boost 1.72
until cmake v3.16.2
I'm not sure that there's a version out of cmake that directly
supports boost 1.72.
If you're using an older (but still reasonably up-to-date) version of
cmake you might also try:
-DBoost_NO_BOOST_CMAKE=TRUE

-greg

On Sat, Jan 18, 2020 at 2:10 PM Zoltan Takacs 
wrote:


Dear RDKiters,

I would like to compile RDKit from source on a macOS 10.15 computer
with gnu c/c++ compilers and a newer version of boost (1.72.0)
instead of 1.56.0.

I run cmake with the following setting:

cmake -D


PYTHON_LIBRARY=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/


-D


PYTHON_INCLUDE_DIR=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/include/python3.7m/


-D


PYTHON_EXECUTABLE=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3


-D BOOST_ROOT=/usr/local/Cellar/boost/1.72.0/
-D BOOST_NO_SYSTEM_PATHS=ON
-D CMAKE_C_COMPILER=/usr/local/bin/gcc
-D CMAKE_CXX_COMPILER=/usr/local/bin/g++ ..

This ends up throwing me loads of errors but it starts like this:

CATCH:


/Users/all/data/rdkit-Release_2019_09_3/External/catch/catch/single_include

-- Found PythonInterp:


/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3

(found version "3.7.5")
-- Found PythonLibs:


/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib

(found version "3.7.5")
-- Boost 1.56.0 found.
-- Found Boost components:
python3
PYTHON Py_ENABLE_SHARED: 0
PYTHON USING LINK LINE: -bundle -undefined dynamic_lookup -isysroot


/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk

-- Found Eigen3: /usr/local/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 - found
-- Found Threads: TRUE
CMake Warning at


/usr/local/lib/cmake/boost_serialization-1.72.0/libboost_serialization-variant-shared.cmake:64

(message):
Target Boost::serialization already has an imported location
'/usr/local/lib/libboost_serialization-mt.dylib', which will be
overwritten
with '/usr/local/lib/libboost_serialization.dylib'
Call Stack (most recent call first):



/usr/local/lib/cmake/boost_serialization-1.72.0/boost_serialization-config.cmake:57

(include)
/usr/local/lib/cmake/Boost-1.72.0/BoostConfig.cmake:120
(find_package)
/usr/local/lib/cmake/Boost-1.72.0/BoostConfig.cmake:185
(boost_find_component)



/usr/local/Cellar/cmake/3.13.2/share/cmake/Modules/FindBoost.cmake:264

(find_package)
CMakeLists.txt:361 (find_package)

It does not seem to use the specified boost libs of version 1.72.0
but it uses the 1.56.0. After this there are more error messages
thrown which are of the type:

CMake Error at Code/cmake/Modules/RDKitUtils.cmake:55 (add_library):
Target "MolStandardize_static" links to target "Boost::iostreams"
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/MolStandardize/CMakeLists.txt:4 (rdkit_library)

and then it says that the following cmake option was not used:

-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:

BOOST_NO_SYSTEM_PATHS

What are the correct settings for cmake to be able to use a newer
version of BOOST and PYTHON3?

Thanks,
Zoltan

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Re: [Rdkit-discuss] Compiling rdkit-Release_2019_09_3 with python 3.7.5 and gnu gcc, g++ on MacOS 10.15

2020-01-20 Thread Zoltan Takacs 
Hi,

Thanks,

I repeated the compilation procedure on an Ubuntu machine with boost 1.62.0 and 
everything went smashingly. This indeed seems to be some cmake boost mismatch 
on my mac. I will use an older version of boost instead. 

Best,
Zoltan 

On 20 Jan 2020, at 17:25, Greg Landrum  wrote:

Hi Zoltan,

I use the system compiler (clang++) on the Mac, so I don't have direct 
experience here.

One problem is likely that the cmake argument you want is 
-DBoost_NO_SYSTEM_PATHS=ON
those variable names are case sensitive.

The other point is that cmake didn't officiallly support boost 1.72 until cmake 
v3.16.2
I'm not sure that there's a version out of cmake that directly supports boost 
1.72.
If you're using an older (but still reasonably up-to-date) version of cmake you 
might also try:
-DBoost_NO_BOOST_CMAKE=TRUE

-greg


On Sat, Jan 18, 2020 at 2:10 PM Zoltan Takacs mailto:zozo...@gmail.com>> wrote:
Dear RDKiters, 

I would like to compile RDKit from source on a macOS 10.15 computer with gnu 
c/c++ compilers and a newer version of boost (1.72.0) instead of 1.56.0.  

I run cmake with the following setting:

cmake -D 
PYTHON_LIBRARY=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/
 
-D 
PYTHON_INCLUDE_DIR=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/include/python3.7m/
 
-D 
PYTHON_EXECUTABLE=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3
 
-D BOOST_ROOT=/usr/local/Cellar/boost/1.72.0/
-D BOOST_NO_SYSTEM_PATHS=ON 
-D CMAKE_C_COMPILER=/usr/local/bin/gcc 
-D CMAKE_CXX_COMPILER=/usr/local/bin/g++ ..

This ends up throwing me loads of errors but it starts like this: 

CATCH: 
/Users/all/data/rdkit-Release_2019_09_3/External/catch/catch/single_include
-- Found PythonInterp: 
/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3
 (found version "3.7.5") 
-- Found PythonLibs: 
/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib 
(found version "3.7.5") 
-- Boost 1.56.0 found.
-- Found Boost components:
   python3
PYTHON Py_ENABLE_SHARED: 0
PYTHON USING LINK LINE: -bundle -undefined dynamic_lookup -isysroot 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk
-- Found Eigen3: /usr/local/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 - found
-- Found Threads: TRUE  
CMake Warning at 
/usr/local/lib/cmake/boost_serialization-1.72.0/libboost_serialization-variant-shared.cmake:64
 (message):
  Target Boost::serialization already has an imported location
  '/usr/local/lib/libboost_serialization-mt.dylib', which will be overwritten
  with '/usr/local/lib/libboost_serialization.dylib'
Call Stack (most recent call first):
  
/usr/local/lib/cmake/boost_serialization-1.72.0/boost_serialization-config.cmake:57
 (include)
  /usr/local/lib/cmake/Boost-1.72.0/BoostConfig.cmake:120 (find_package)
  /usr/local/lib/cmake/Boost-1.72.0/BoostConfig.cmake:185 (boost_find_component)
  /usr/local/Cellar/cmake/3.13.2/share/cmake/Modules/FindBoost.cmake:264 
(find_package)
  CMakeLists.txt:361 (find_package) 


It does not seem to use the specified boost libs of version 1.72.0 but it uses 
the 1.56.0. After this there are more error messages thrown which are of the 
type:

CMake Error at Code/cmake/Modules/RDKitUtils.cmake:55 (add_library):
  Target "MolStandardize_static" links to target "Boost::iostreams" 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/MolStandardize/CMakeLists.txt:4 (rdkit_library)  

and then it says that the following cmake option was not used: 

-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

BOOST_NO_SYSTEM_PATHS

What are the correct settings for cmake to be able to use a newer version of 
BOOST and PYTHON3?

Thanks,
Zoltan







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Re: [Rdkit-discuss] Compiling rdkit-Release_2019_09_3 with python 3.7.5 and gnu gcc, g++ on MacOS 10.15

2020-01-20 Thread Greg Landrum 
Hi Zoltan,

I use the system compiler (clang++) on the Mac, so I don't have direct
experience here.

One problem is likely that the cmake argument you want is
-DBoost_NO_SYSTEM_PATHS=ON
those variable names are case sensitive.

The other point is that cmake didn't officiallly support boost 1.72 until
cmake v3.16.2
I'm not sure that there's a version out of cmake that directly supports
boost 1.72.
If you're using an older (but still reasonably up-to-date) version of cmake
you might also try:
-DBoost_NO_BOOST_CMAKE=TRUE

-greg


On Sat, Jan 18, 2020 at 2:10 PM Zoltan Takacs  wrote:

> Dear RDKiters,
>
> I would like to compile RDKit from source on a macOS 10.15 computer with
> gnu c/c++ compilers and a newer version of boost (1.72.0) instead of
> 1.56.0.
>
> I run cmake with the following setting:
>
> cmake -D
> PYTHON_LIBRARY=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/
> -D
> PYTHON_INCLUDE_DIR=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/include/python3.7m/
> -D
> PYTHON_EXECUTABLE=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3
> -D BOOST_ROOT=/usr/local/Cellar/boost/1.72.0/
> -D BOOST_NO_SYSTEM_PATHS=ON
> -D CMAKE_C_COMPILER=/usr/local/bin/gcc
> -D CMAKE_CXX_COMPILER=/usr/local/bin/g++ ..
>
> This ends up throwing me loads of errors but it starts like this:
>
> CATCH:
> /Users/all/data/rdkit-Release_2019_09_3/External/catch/catch/single_include
> -- Found PythonInterp:
> /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3
> (found version "3.7.5")
> -- Found PythonLibs:
> /usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib
> (found version "3.7.5")
> -- Boost 1.56.0 found.
> -- Found Boost components:
>python3
> PYTHON Py_ENABLE_SHARED: 0
> PYTHON USING LINK LINE: -bundle -undefined dynamic_lookup -isysroot
> /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk
> -- Found Eigen3: /usr/local/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 - found
> -- Found Threads: TRUE
> CMake Warning at
> /usr/local/lib/cmake/boost_serialization-1.72.0/libboost_serialization-variant-shared.cmake:64
> (message):
>   Target Boost::serialization already has an imported location
>   '/usr/local/lib/libboost_serialization-mt.dylib', which will be
> overwritten
>   with '/usr/local/lib/libboost_serialization.dylib'
> Call Stack (most recent call first):
>
> /usr/local/lib/cmake/boost_serialization-1.72.0/boost_serialization-config.cmake:57
> (include)
>   /usr/local/lib/cmake/Boost-1.72.0/BoostConfig.cmake:120 (find_package)
>   /usr/local/lib/cmake/Boost-1.72.0/BoostConfig.cmake:185
> (boost_find_component)
>   /usr/local/Cellar/cmake/3.13.2/share/cmake/Modules/FindBoost.cmake:264
> (find_package)
>   CMakeLists.txt:361 (find_package)
>
>
> It does not seem to use the specified boost libs of version 1.72.0 but it
> uses the 1.56.0. After this there are more error messages thrown which
> are of the type:
>
> CMake Error at Code/cmake/Modules/RDKitUtils.cmake:55 (add_library):
>   Target "MolStandardize_static" links to target "Boost::iostreams" 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/MolStandardize/CMakeLists.txt:4 (rdkit_library)
>
> and then it says that the following cmake option was not used:
>
> -- Generating done
> CMake Warning:
>   Manually-specified variables were not used by the project:
>
> BOOST_NO_SYSTEM_PATHS
>
> What are the correct settings for cmake to be able to use a newer version
> of BOOST and PYTHON3?
>
> Thanks,
> Zoltan
>
>
>
>
>
>
>
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>
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[Rdkit-discuss] Compiling rdkit-Release_2019_09_3 with python 3.7.5 and gnu gcc, g++ on MacOS 10.15

2020-01-18 Thread Zoltan Takacs 
Dear RDKiters, 

I would like to compile RDKit from source on a macOS 10.15 computer with gnu 
c/c++ compilers and a newer version of boost (1.72.0) instead of 1.56.0.  

I run cmake with the following setting:

cmake -D 
PYTHON_LIBRARY=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib/
 
-D 
PYTHON_INCLUDE_DIR=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/include/python3.7m/
 
-D 
PYTHON_EXECUTABLE=/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3
 
-D BOOST_ROOT=/usr/local/Cellar/boost/1.72.0/
-D BOOST_NO_SYSTEM_PATHS=ON 
-D CMAKE_C_COMPILER=/usr/local/bin/gcc 
-D CMAKE_CXX_COMPILER=/usr/local/bin/g++ ..

This ends up throwing me loads of errors but it starts like this: 

CATCH: 
/Users/all/data/rdkit-Release_2019_09_3/External/catch/catch/single_include
-- Found PythonInterp: 
/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/bin/python3
 (found version "3.7.5") 
-- Found PythonLibs: 
/usr/local/Cellar/python/3.7.5/Frameworks/Python.framework/Versions/3.7/lib 
(found version "3.7.5") 
-- Boost 1.56.0 found.
-- Found Boost components:
   python3
PYTHON Py_ENABLE_SHARED: 0
PYTHON USING LINK LINE: -bundle -undefined dynamic_lookup -isysroot 
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk
-- Found Eigen3: /usr/local/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 - found
-- Found Threads: TRUE  
CMake Warning at 
/usr/local/lib/cmake/boost_serialization-1.72.0/libboost_serialization-variant-shared.cmake:64
 (message):
  Target Boost::serialization already has an imported location
  '/usr/local/lib/libboost_serialization-mt.dylib', which will be overwritten
  with '/usr/local/lib/libboost_serialization.dylib'
Call Stack (most recent call first):
  
/usr/local/lib/cmake/boost_serialization-1.72.0/boost_serialization-config.cmake:57
 (include)
  /usr/local/lib/cmake/Boost-1.72.0/BoostConfig.cmake:120 (find_package)
  /usr/local/lib/cmake/Boost-1.72.0/BoostConfig.cmake:185 (boost_find_component)
  /usr/local/Cellar/cmake/3.13.2/share/cmake/Modules/FindBoost.cmake:264 
(find_package)
  CMakeLists.txt:361 (find_package) 


It does not seem to use the specified boost libs of version 1.72.0 but it uses 
the 1.56.0. After this there are more error messages thrown which are of the 
type:

CMake Error at Code/cmake/Modules/RDKitUtils.cmake:55 (add_library):
  Target "MolStandardize_static" links to target "Boost::iostreams" 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/MolStandardize/CMakeLists.txt:4 (rdkit_library)  

and then it says that the following cmake option was not used: 

-- Generating done
CMake Warning:
  Manually-specified variables were not used by the project:

BOOST_NO_SYSTEM_PATHS

What are the correct settings for cmake to be able to use a newer version of 
BOOST and PYTHON3?

Thanks,
Zoltan







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