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Build Notes for Debian 10 + Guix Mixed Environment

Issue

This system has both Debian 10 (glibc 2.28) and Guix (glibc 2.35) installed. When building Rust projects that use C dependencies (via bindgen/cc), the mixed glibc versions cause linker errors:

ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__pthread_barrier_wait@GLIBC_PRIVATE'
ld: /usr/lib/x86_64-linux-gnu/librt.so: undefined reference to `__libc_dlsym@GLIBC_PRIVATE'
...

This happens because:

  1. The system's librt.so.1 (from Debian glibc 2.28) depends on GLIBC_PRIVATE symbols
  2. Guix's libraries in PATH/LD_LIBRARY_PATH provide glibc 2.35 which has different GLIBC_PRIVATE symbols
  3. The symbols are incompatible → linker failure

Solution

Build with a pristine environment that excludes Guix paths:

Method 1: Use the build script (recommended)

# Build only
./scripts/build-clean.sh

# Build and install to ~/.cargo/bin
./scripts/build-clean.sh --install

Method 2: Manual build command

env -i \
  PATH="/home/erikg/.cargo/bin:/usr/local/bin:/usr/bin:/bin" \
  HOME="/home/erikg" \
  USER="$USER" \
  RUSTUP_HOME="/export/local/home/erikg/.rustup" \
  CARGO_HOME="/home/erikg/.cargo" \
  CC="/usr/bin/gcc" \
  CXX="/usr/bin/g++" \
  BINDGEN_EXTRA_CLANG_ARGS="-I/usr/lib/gcc/x86_64-linux-gnu/8/include -I/usr/local/include -I/usr/lib/gcc/x86_64-linux-gnu/8/include-fixed -I/usr/include/x86_64-linux-gnu -I/usr/include" \
  cargo build --release

Key Points

  1. Remove Guix from environment: env -i clears the environment, then we selectively add only system paths
  2. Force system GCC: CC=/usr/bin/gcc ensures we use Debian's GCC 8, not Guix's GCC 11
  3. Provide system includes: BINDGEN_EXTRA_CLANG_ARGS tells bindgen where to find system headers
  4. Keep cargo/rustup paths: Still need access to Rust toolchain

Why Not Fix Guix/Debian Conflict?

The conflict is inherent when mixing package managers with different glibc versions. Options:

  • Use only Debian packages (remove Guix)
  • Use only Guix packages (use Guix's rust/cargo)
  • Build in isolated environment (this solution)

We chose the third option as it's non-invasive and works reliably.

Related Issues

  • onecode-rs and fastga-rs both use bindgen → both affected
  • Any Rust crate with C dependencies may hit this issue
  • Standard Rust-only crates build fine without this workaround

Changes Made

  1. sweepga src/main.rs: Replaced unstable is_multiple_of() with stable % 2 == 0
  2. sweepga src/bin/alnstats.rs: Same fix for is_multiple_of()
  3. Cargo.toml: Changed onecode dependency to local path (temporary for testing)
    • Revert to git dependency before committing

Testing

./build-clean.sh
./target/release/sweepga --version  # Should print: sweepga 0.1.0