rdkit-debian

Debian packages of the RDKit C++ libraries for the rdkit-rs project. Produces .deb packages with shared libraries, headers, and pkg-config files pinned to specific RDKit releases.

Packages

Package	Contents
librdkit-rs	RDKit shared libraries (.so files)
librdkit-rs-dev	C++ headers and rdkit.pc pkg-config file

Supported Platforms

Distro	Boost	Architectures
Debian 12 (Bookworm)	1.74	amd64, arm64

We standardize on Debian Bookworm to match Quickwit's build and runtime images (rust:bookworm / debian:bookworm-slim).

Usage

Download the .deb files from the latest release and install:

# Runtime only (e.g. in a Docker image)
dpkg -i librdkit-rs_*.deb
apt-get install -f  # install missing dependencies

# For building rdkit-sys (headers + pkg-config)
dpkg -i librdkit-rs_*.deb librdkit-rs-dev_*.deb
apt-get install -f

Verify pkg-config works:

pkg-config --cflags --libs rdkit

Building a New Release

Trigger the workflow manually from the Actions tab, providing the RDKit release tag:

RDKit release tag: Release_2024_09_1

The workflow builds RDKit from source inside a debian:bookworm container for both amd64 and arm64, packages the results with nfpm, and uploads .deb artifacts.

CMake Configuration

We build RDKit with a minimal C++-only configuration:

cmake .. \
  -DCMAKE_BUILD_TYPE=Release \
  -DCMAKE_INSTALL_PREFIX=/usr \
  -DCMAKE_SKIP_RPATH=ON \
  -DRDK_BUILD_PYTHON_WRAPPERS=OFF \
  -DRDK_BUILD_JAVA_WRAPPERS=OFF \
  -DRDK_BUILD_CAIRO_SUPPORT=OFF \
  -DRDK_BUILD_PGSQL=OFF \
  -DRDK_INSTALL_INTREE=OFF \
  -DRDK_BUILD_INCHI_SUPPORT=ON \
  -DRDK_BUILD_THREADSAFE_SSS=ON \
  -DRDK_BUILD_COORDGEN_SUPPORT=OFF \
  -DRDK_BUILD_MAEPARSER_SUPPORT=OFF \
  -DRDK_BUILD_FREESASA_SUPPORT=OFF \
  -DRDK_BUILD_CPP_TESTS=OFF

Key flags:

• RDK_BUILD_THREADSAFE_SSS=ON — Critical for rdkit-rs, which uses rayon for parallel substructure search
• CMAKE_SKIP_RPATH=ON — Makes libraries relocatable for packaging
• Coordgen/maeparser/freesasa disabled — Avoids build-time downloads from GitHub and we don't wrap these in our CXX bindings

Prior Art: Debian's Official RDKit Packages

The Debian debichem team maintains official RDKit packages at salsa.debian.org/debichem-team/rdkit. They ship 6 binary packages (python3-rdkit, rdkit-doc, rdkit-data, librdkit1t64, librdkit-dev, postgresql-18-rdkit) and maintain 14 patches on top of upstream RDKit.

Why we don't use theirs:

• Debian/Ubuntu pin a single RDKit version per release (e.g. Ubuntu Jammy ships RDKit 202109). Our rdkit-sys CXX bindings are tightly coupled to specific RDKit C++ headers and we need to track upstream releases closely.
• Their packages include Python bindings, PostgreSQL cartridge, and documentation that we don't need. We only need the C++ shared libraries and headers.
• We need builds for architectures and distro versions on our timeline, not Debian's release cadence.

What we learned from their packaging:

• Disable build-time downloads. RDKit's CMake fetches dependencies at build time (coordgen, maeparser, Better Enums, RapidJSON). Debian patches these out for reproducibility. We disable the features that trigger downloads via CMake flags (-DRDK_BUILD_COORDGEN_SUPPORT=OFF, etc.) instead of maintaining patches.
• Enable thread-safe substructure search. -DRDK_BUILD_THREADSAFE_SSS=ON is critical — our Rust code runs parallel substructure searches via rayon.
• Skip RPATH. -DCMAKE_SKIP_RPATH=ON makes libraries relocatable for packaging.
• InChI linking. Depending on RDKit version, the InChI CMake variable name may need fixing (INCHI_LIBRARIES -> INCHI_LIBRARY). Test and patch if needed.