Hi Paolo, I finally had some time to look at this again and I tried building from a conda environment. I looked at the instruction on https://github.com/rdkit/conda-rdkit and after getting a bit lost as to where the recipe for building boost is (found it through https://docs.conda.io/projects/conda-build/en/latest/user-guide/recipes/sample-recipes.html) I tried first building boost but got stuck.
Running $ conda build boost through command prompt ends up giving me this error message where the process is aborted: (%BUILD_PREFIX%) %SRC_DIR%>call bootstrap.bat Building Boost.Build engine ****** B A T C H R E C U R S I O N exceeds STACK limits ****** Recursion Count=336, Stack Usage=90 percent ****** B A T C H PROCESSING IS A B O R T E D ****** Traceback (most recent call last): File "C:\Users\candy\anaconda3\Scripts\conda-build-script.py", line 10, in <module> sys.exit(main()) File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 488, in main execute(sys.argv[1:]) File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\cli\main_build.py", line 477, in execute outputs = api.build(args.recipe, post=args.post, test_run_post=args.test_run_post, File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\api.py", line 186, in build return build_tree( File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\build.py", line 3088, in build_tree packages_from_this = build(metadata, stats, File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\build.py", line 2179, in build windows.build(m, build_file, stats=build_stats, provision_only=provision_only) File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\windows.py", line 297, in build check_call_env(cmd, cwd=m.config.work_dir, stats=stats, rewrite_stdout_env=rewrite_env) File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\utils.py", line 410, in check_call_env return _func_defaulting_env_to_os_environ('call', *popenargs, **kwargs) File "C:\Users\candy\anaconda3\lib\site-packages\conda_build\utils.py", line 390, in _func_defaulting_env_to_os_environ raise subprocess.CalledProcessError(proc.returncode, _args) subprocess.CalledProcessError: Command '['cmd.exe', '/d', '/c', 'conda_build.bat']' returned non-zero exit status 255. Any idea as to why this is happening and how to fix this? Regards, Charmaine Chu Computational Chemist [A close up of a sign Description automatically generated]charmaine....@liverpoolchirochem.com<mailto:charmaine....@liverpoolchirochem.com> [cid:image003.jpg@01D874FD.052AD270]<https://www.linkedin.com/company/liverpool-chirochem-ltd>+44 (0)151 794 2936 liverpoolchirochem.com<https://www.liverpoolchirochem.com/> This message and any files transmitted with it are the property of Liverpool ChiroChem Ltd., are confidential, and are intended solely for the use of the person or entity to whom this e-mail is addressed. If you are not one of the named recipient(s) or otherwise have reason to believe that you have received this message in error, please contact the sender and delete this message immediately from your computer. Any other use, retention, dissemination, forwarding, printing, or copying of this e-mail is strictly prohibited. From: Paolo Tosco <paolo.tosco.m...@gmail.com> Sent: 14 April 2022 18:41 To: Charmaine Siu Man Chu <charmaine....@liverpoolchirochem.com> Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Building RDKit on Windows for pgAdmin (Postgres) 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<mailto: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<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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