Hi Charmaine,
my suggestion is to build starting from a conda environment. That will
significantly simplify your dependencies, since most packages are available
pre-built.
You can look into .azure-pipelines\vs_build_dll.yml for how to set up your
conda environment and for the cmake flags to use.
For Postgres, these are the cmake flags that I use to configure the
PostgreSQL DLL build:
-D RDK_BUILD_PGSQL=ON ^
-D RDK_PGSQL_STATIC=OFF ^
-D PostgreSQL_INCLUDE_DIR="C:/Program Files/PostgreSQL/14/include" ^
-D PostgreSQL_TYPE_INCLUDE_DIR="C:/Program
Files/PostgreSQL/14/include/server" ^
-D PostgreSQL_LIBRARY="C:/Program Files/PostgreSQL/14/lib/postgres.lib"
^
..
Note that this is to build against Postgres installed using the Windows
installer from the PostgreSQL website, not the version provided by conda.
Cheers,
p.
On Thu, Apr 14, 2022 at 11:36 AM Charmaine Siu Man Chu <
charmaine....@liverpoolchirochem.com> wrote:
> Hello,
>
>
>
> I’ve been trying to build RDKit on Windows so that I can get the RDKit
> extension in pgAdmin (Postgres) but I’ve been unsuccessful.
>
> I’ve tried to follow the instruction on
> https://www.rdkit.org/docs/Install.html to build RDKit and encountered
> several problems.
>
> Some of them I manage to resolve myself but can someone help on this?
>
>
>
> Here is what I’ve tried:
>
>
>
> To start off, I’m using the Windows 11 64-bit OS and Postgres 14 was
> installed.
>
> I then went to install the following:
>
> Python 3.10 along with numpy and Pillow
>
> Visual Studio 2022 with Visual Studio Community 2022, Visual Studio Build
> Tools 2022
>
> Cmake 3.23.0
>
> Boost_1_78_0 using the .exe installer
>
> And downloaded and extracted the rdkit-Release_2022_03_1
>
>
>
> After install the above, I ran the below in Comand Prompt
>
> cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0
> -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON
> -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14"
> -G"Visual Studio 17 2022" ..
>
> came back with error:
>
> The following variants have been tried and rejected:
>
>
>
> * boost_python310-vc143-mt-gd-x64-1_78.lib (shared, default on Windows is
>
> static, set Boost_USE_STATIC_LIBS=OFF to override)
>
>
>
> * boost_python310-vc143-mt-x64-1_78.lib (shared, default on Windows is
>
> static, set Boost_USE_STATIC_LIBS=OFF to override)
>
>
>
> I then edit the command line to
>
> cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0
> -DBoost_USE_STATIC_LIBS=OFF -DRDK_BUILD_INCHI_SUPPORT=ON
> -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON
> -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14" -G"Visual Studio 17
> 2022" ..
>
> and this time following error occured
>
> Could NOT find Eigen3 (missing: EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK)
> (Required is at least version "2.91.0")
>
> CMake Error at C:/Program
> Files/CMake/share/cmake-3.23/Modules/ExternalProject.cmake:2540 (message):
>
> error: could not find git for clone of Eigen
>
>
>
> So I went to download and extracted eigen 3.4.0 and edit the command line
> to
>
> cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/locall/boost_1_78_0
> -DBoost_USE_STATIC_LIBS=OFF -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0"
> -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON
> -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14"
> -G"Visual Studio 17 2022" ..
>
> which gave the following error
>
> CMake Error at C:/Program
> Files/CMake/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:230
> (message):
>
> Could NOT find Freetype (missing: FREETYPE_LIBRARY FREETYPE_INCLUDE_DIRS)
>
>
>
> So again I went to obtain freetype-2.12.0 and build it following the
> instructions on
> https://bobhowto.wordpress.com/2020/11/10/build-freetype-on-windows-10-using-visual-studio-2017/,
> using VS 2022 instead, and edit the command line to
>
> cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/local/boost_1_78_0
> -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON
> -DBoost_USE_STATIC_LIBS=OFF -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0"
> -DFREETYPE_INCLUDE_DIRS="C:/freetype-2.12.0/include"
> -DFREETYPE_LIBRARY="C:/freetype-2.12.0/objs/freetype.lib"
> -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\Program Files\PostgreSQL\14"
> -G"Visual Studio 17 2022" ..
>
> and it managed to compile
>
> However, when running
>
> "C:\Program Files\Microsoft Visual
> Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" /m:4
> /p:Configuration=Release INSTALL.vcxproj
>
> Gave the following error with 47 other warnings
>
> "C:\rdkit-Release_2022_03_1\build\INSTALL.vcxproj" (default target) (1) ->
>
> "C:\rdkit-Release_2022_03_1\build\ALL_BUILD.vcxproj" (default
> target) (3) ->
>
>
> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\Deprotect\Wrap\rdDeprotect.vcxproj"
> (default target) (20) ->
>
>
> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\ChemReactions\ChemReactions.vcxproj"
> (default target) (48) ->
>
>
> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\Descriptors\Descriptors.vcxproj"
> (default target) (55) ->
>
>
> "C:\rdkit-Release_2022_03_1\build\Code\GraphMol\FileParsers\FileParsers.vcxproj"
> (default target) (56) ->
>
> (ClCompile target) ->
>
>
> C:\rdkit-Release_2022_03_1\Code\GraphMol\FileParsers\PNGParser.cpp(25,10):
> fatal error C1083: Cannot open incl
>
> ude file: 'zlib.h': No such file or directory
> [C:\rdkit-Release_2022_03_1\build\Code\GraphMol\FileParsers\FilePa
>
> rsers.vcxproj]
>
>
>
> So I went to obtain zlib 1.2.12 and build it via
>
> cmake -G"Visual Studio 17 2022" ..
>
> "C:\Program Files\Microsoft Visual
> Studio\2022\Community\MSBuild\Current\Bin\MSBuild.exe" zlib.sln
>
> copy /Y zconf.h ..
>
> and compiled the boost libraries via
>
> b2 --prefix=C:\local\boost_1_78_0 -sZLIB_SOURCE="C:/zlib-1.2.12"
> -sZLIB_INCLUDE="C:/zlib-1.2.12"
> -sZLIB_LIBPATH="C:/zlib-1.2.12/build/Release"
> -sZLIB_BINARY="C:/zlib-1.2.12/build/Release/zlib.lib" --debug-configuration
> -d0 address-model=64 link=shared install
>
> and changed the PATH in the environment variables to
> C:\local\boost_1_78_0\lib
>
> but running the build code and the INSTALL.vcxproj gave the same error
>
>
>
> As during the compilation -- Could NOT find ZLIB (missing: ZLIB_LIBRARY
> ZLIB_INCLUDE_DIR) was spotted, the command line was modified to point
> towards the zlib folder as follow
>
> cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/local/boost_1_78_0
> -DZLIB_LIBRARY="C:/zlib-1.2.12/build/Release/zlib.lib"
> -DZLIB_INCLUDE_DIR="C:/zlib-1.2.12" -DBoost_USE_STATIC_LIBS=OFF
> -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON
> -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:/Program Files/PostgreSQL/14"
> -DEIGEN3_INCLUDE_DIR="C:/eigen-3.4.0"
> -DFREETYPE_INCLUDE_DIRS="C:/freetype-2.12.0/include"
> -DFREETYPE_LIBRARY="C:/freetype-2.12.0/objs/freetype.lib" -G"Visual Studio
> 17 2022" ..
>
> This time running the INSTALL.vcxproj gave 93 warnings but no errors
>
> However, when starting up python in KNIME it gives the following error:
>
> Error while loading python type extension RDKitMolDeserializer
>
> Cause: DLL load failed while importing rdBase: The specified module could
> not be found.
>
> And when loading the rdkit extension in pgAdmin gave
>
> ERROR: could not load library "C:/Program
> Files/PostgreSQL/14/lib/rdkit.dll": The specified module could not be found.
>
>
>
> I’ve made sure I delete the rdkit build folder each time I redo the
> compilation. Where had I gone wrong?
>
>
>
> Regards,
>
> Charmaine Chu
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
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