How to build RDKit 2023 on Windows w/o Conda

It looks like the build instructions for RDKit on Windows have not been updated for some time, at least they did not work for me. So I dug out the correct build process out of the Conda builds:

General instructions:

https://github.com/rdkit/rdkit/blob/master/Docs/Book/Install.md

Required to run the binaries, IF you don't have the Visual Studio C++ compiler and SDK installed:

Visual Studio 2015, 2017, 2019 and 2022 redistributable

https://learn.microsoft.com/en-us/cpp/windows/latest-supported-vc-redist?view=msvc-170

Development environment:

Windows 11 x64

Microsoft Visual Studio 2022 (Community Edition or Professional)

Windows SDK version 10.0.22000.0

Compiler MSVC 19.35.32217.1

PowerShell

Directory structure:

c:\Devel\RDBuild

boost
cairo
eigen3
freetype
RDKit
zlib

RDBASE = C:\Devel\RDBuild\RDKit

RDKit source 2023_03_1:

https://codeload.github.com/rdkit/rdkit/zip/refs/tags/Release_2023_03_1

ZLib 1.2.13:

https://github.com/kiyolee/zlib-win-build

Eigen 3.4.0:

https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.zip

Cairo 1.17.2:

https://github.com/preshing/cairo-windows/releases

Boost 1.82.0:

https://sourceforge.net/projects/boost/files/boost-binaries/

freetype 2.11.1:

https://codeload.github.com/ubawurinna/freetype-windows-binaries

CMake 3.26.3:

https://github.com/Kitware/CMake/releases/download/v3.26.3/cmake-3.26.3-windows-x86_64.msi

PostgreSQL 15.2.1:

https://get.enterprisedb.com/postgresql/postgresql-15.2-1-windows-x64-binaries.zip

Python 3.10.11:

https://www.python.org/downloads/release/python-31011/

Build commands:

1.) Prepare for DLLs and Python package:

c:/cmake/bin/cmake -DRDK_BUILD_PYTHON_WRAPPERS=ON -DBOOST_ROOT=C:/Devel/RDBuild/boost -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=OFF -DPostgreSQL_ROOT="C:\PostgreSQL\15" -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=c:/RDKit -DEIGEN3_INCLUDE_DIR=C:/Devel/RDBuild/eigen3 -DFREETYPE_INCLUDE_DIRS=c:/Devel/RDbuild/freetype/include -DFREETYPE_LIBRARY="c:/Devel/RDBuild/freetype/release dll/win64/freetype.lib" -DZLIB_INCLUDE_DIR=c:/Devel/RDBuild/zlib/include -DZLIB_LIBRARY=c:/Devel/RDBuild/zlib/libz.lib -DCAIRO_INCLUDE_DIRS=c:/Devel/RDBuild/cairo/include -DCAIRO_LIBRARIES=c:/Devel/RDBuild/cairo/lib/x64/cairo.lib -DRDK_BUILD_FREETYPE_SUPPORT=ON -DRDK_BUILD_COMPRESSED_SUPPLIERS=ON -DRDK_OPTIMIZE_POPCNT=ON -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_INSTALL_DLLS_MSVC=ON -DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_THREADSAFE_SSS=ON -G"Visual Studio 17 2022" -A x64 ..

2.) Build & install:

C:\CMake\bin\cmake --build . --config=Release --target install

3.) Prepare for static libraries and PostgreSQL extension:

c:/cmake/bin/cmake -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DBOOST_ROOT=C:/Devel/RDBuild/boost -DRDK_BUILD_CAIRO_SUPPORT=ON -DRDK_BUILD_INCHI_SUPPORT=ON -DRDK_BUILD_AVALON_SUPPORT=ON -DRDK_BUILD_PGSQL=ON -DPostgreSQL_ROOT="C:\PostgreSQL\15" -DRDK_INSTALL_INTREE=OFF -DCMAKE_INSTALL_PREFIX=c:/RDKit -DEIGEN3_INCLUDE_DIR=C:/Devel/RDBuild/eigen3 -DFREETYPE_INCLUDE_DIRS=c:/Devel/RDbuild/freetype/include -DFREETYPE_LIBRARY="c:/Devel/RDBuild/freetype/release dll/win64/freetype.lib" -DZLIB_INCLUDE_DIR=c:/Devel/RDBuild/zlib/include -DZLIB_LIBRARY=c:/Devel/RDBuild/zlib/libz.lib -DCAIRO_INCLUDE_DIRS=c:/Devel/RDBuild/cairo/include -DCAIRO_LIBRARIES=c:/Devel/RDBuild/cairo/lib/x64/cairo.lib -DRDK_BUILD_FREETYPE_SUPPORT=ON -DRDK_BUILD_COMPRESSED_SUPPLIERS=ON -DRDK_OPTIMIZE_POPCNT=ON -DRDK_INSTALL_STATIC_LIBS=ON -DRDK_INSTALL_DLLS_MSVC=OFF -DCMAKE_BUILD_TYPE=Release -DRDK_BUILD_THREADSAFE_SSS=ON -G"Visual Studio 17 2022" -A x64 ..

4.) Build & install:

C:\CMake\bin\cmake --build . --config=Release --target install

Usage:

If you want to use the PostgreSQL extension, it needs rdkit.dll, which is automatically copied to the PostgreSQL /lib directory BUT also freetype.dll, and boost_serialization-vc142-mt-x64-1_82.dll. The easiest way is to copy them to the PostgreSQL /lib directory AND set the PATH, e. g. $env:PATH+=';C:\PostgreSQL\15\lib'. You also need to define RDBASE, e. g.  $env:RDBASE='c:\RDKit'. Start PostgreSQL and 'CREATE EXTENSION IF NOT EXISTS rdkit;' should work.

If you want to use the Python package, you must point PYTHONPATH to the RDKit installation directory AND for Python < 3.8 add <where the dlls live> to the PATH OR for Python >= 3.8 add the DLL path explicitly with:

os.add_dll_directory(<where the DLLs live>)

In addition to the RDKit DLLs, freetype.dll, cairo.dll, libz.dll, boost_serialization-vc142-mt-x64-1_82.dll, boost_bzip2-vc143-mt-x64-1_82.dll, boost_iostreams-vc143-mt-x64-1_82.dll, boost_python310-vc143-mt-x64-1_82.dll, and boost_zlib-vc143-mt-x64-1_82.dll must be present.

Result:

• C++ static libraries
• C++ shared libraries
• PostgreSQL extension
• Python package

Windows, keep your dirty fingers off my files!

I spent the better part of the morning figuring out why a colleague could not import a PostgreSQL dump in plain format made on Linux on his Windows machine.

According to documentation, this works like so (OS agnostic):

psql dbname < infile

However, this  gave the following error:

ERROR:  missing data for ...

However, the documentation for psql gives an alternative way to read commands from a file:

The -f switch.

 "

Read commands from the file filename, rather than standard input. This option can be repeated and combined in any order with the -c option. When either -c or -f is specified, psql does not read commands from standard input; instead it terminates after processing all the -c and -f options in sequence. Except for that, this option is largely equivalent to the meta-command \i.
If filename is - (hyphen), then standard input is read until an EOF indication or \q meta-command. This can be used to intersperse interactive input with input from files. Note however that Readline is not used in this case (much as if -n had been specified).
Using this option is subtly different from writing psql < filename. In general, both will do what you expect, but using -f enables some nice features such as error messages with line numbers. There is also a slight chance that using this option will reduce the start-up overhead. On the other hand, the variant using the shell's input redirection is (in theory) guaranteed to yield exactly the same output you would have received had you entered everything by hand.

 "


What this doesn't tell you, is that on Windows, CMD.exe apparently somehow tries to interpret the file it reads. And by doing so, it destroyed data in the dump so that COPY was unable to understand it anymore. So the last sentence of the statement above is just theory on Windows.

Long story short, with psql -f all went fine - and don't use I/O redirection with psql on Windows!