Regression: Linking against ROOT 6.40.04 gives dyld bus error

[2xB]

brew config AND brew doctor output OR brew gist-logs <formula> link

HOMEBREW_VERSION: 6.0.21
ORIGIN: https://github.com/Homebrew/brew
HEAD: 560147012b9678b42ef5e83b690f0895552d1366
Last commit: 28 hours ago
Branch: stable
Core tap: N/A
Core cask tap: N/A
HOMEBREW_PREFIX: /opt/homebrew
HOMEBREW_CASK_OPTS: ["--no-quarantine"]
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_INSTALL_CLEANUP: set
Homebrew Ruby: 4.0.6 => /opt/homebrew/Library/Homebrew/vendor/portable-ruby/4.0.6/bin/ruby
CPU: 3-core 64-bit dunno
Clang: 21.0.0 build 2100
Git: 2.55.0 => /opt/homebrew/bin/git
Curl: 8.7.1 => /usr/bin/curl
macOS: 26.5.2-arm64
CLT: 26.6.0.0.1781586589
Xcode: 26.6 => /Applications/Xcode_26.6.app/Contents/Developer
Metal Toolchain: 17.0 (17F109)
Rosetta 2: false
Your system is ready to brew.

Verification

• My brew doctor output says Your system is ready to brew. and am still able to reproduce my issue.
• I ran brew update and am still able to reproduce my issue.
• I have resolved all warnings from brew doctor and that did not fix my problem.
• I searched for recent similar issues at https://github.com/Homebrew/homebrew-core/issues?q=is%3Aissue and found no duplicates.
• My issue is not about a failure to build a formula from source.
• I did not use AI/LLM to create this issue, or I disclosed the tool and model used; I will answer maintainer questions myself without AI/LLM.

What were you trying to do (and why)?

We compiled https://github.com/KATRIN-Experiment/Kassiopeia against ROOT 6.40.04 and tried to run it.

What happened (include all command output)?

Also compare the log of the CI in my test fork: 2xB/Kassiopeia#40 .

That failed in a bus error and a long error message by DYLD.
Compiling our project against ROOT and executing it since updating from ROOT 6.40.02_1 to 6.40.04 results in:

 *** Break *** bus error
[/usr/lib/system/libsystem_platform.dylib] _sigtramp (no debug info)
[/usr/lib/dyld] invocation function for block in dyld4::Loader::findAndRunAllInitializers(dyld4::RuntimeState&) const::$_0::operator()() const (no debug info)
[/usr/lib/dyld] invocation function for block in dyld3::MachOAnalyzer::forEachInitializer(Diagnostics&, dyld3::MachOAnalyzer::VMAddrConverter const&, void (unsigned int) block_pointer, void const*) const (no debug info)
[/usr/lib/dyld] invocation function for block in mach_o::UnsafeHeader::forEachSection(void (mach_o::UnsafeHeader::SectionInfo const&, bool&) block_pointer) const (no debug info)
[/usr/lib/dyld] mach_o::UnsafeHeader::forEachLoadCommand(void (load_command const*, bool&) block_pointer) const (no debug info)
[/usr/lib/dyld] mach_o::UnsafeHeader::forEachSection(void (mach_o::UnsafeHeader::SectionInfo const&, bool&) block_pointer) const (no debug info)
[/usr/lib/dyld] dyld3::MachOAnalyzer::forEachInitializer(Diagnostics&, dyld3::MachOAnalyzer::VMAddrConverter const&, void (unsigned int) block_pointer, void const*) const (no debug info)
[/usr/lib/dyld] dyld4::Loader::findAndRunAllInitializers(dyld4::RuntimeState&) const (no debug info)
[/usr/lib/dyld] dyld4::JustInTimeLoader::runInitializers(dyld4::RuntimeState&) const (no debug info)
[/usr/lib/dyld] dyld4::Loader::runInitializersBottomUp(dyld4::RuntimeState&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&) const (no debug info)
[/usr/lib/dyld] dyld4::Loader::runInitializersBottomUp(dyld4::RuntimeState&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&) const (no debug info)
[/usr/lib/dyld] dyld4::Loader::runInitializersBottomUp(dyld4::RuntimeState&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&) const (no debug info)
[/usr/lib/dyld] dyld4::Loader::runInitializersBottomUp(dyld4::RuntimeState&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&) const (no debug info)
[/usr/lib/dyld] dyld4::Loader::runInitializersBottomUp(dyld4::RuntimeState&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&) const (no debug info)
[/usr/lib/dyld] dyld4::Loader::runInitializersBottomUp(dyld4::RuntimeState&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&) const (no debug info)
[/usr/lib/dyld] dyld4::Loader::runInitializersBottomUp(dyld4::RuntimeState&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&) const (no debug info)
[/usr/lib/dyld] dyld4::Loader::runInitializersBottomUp(dyld4::RuntimeState&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&, lsl::Vector<AuthenticatedValue<dyld4::Loader const*>>&) const (no debug info)
[/usr/lib/dyld] dyld4::Loader::runInitializersBottomUpPlusUpwardLinks(dyld4::RuntimeState&) const::$_0::operator()() const (no debug info)
[/usr/lib/dyld] dyld4::Loader::runInitializersBottomUpPlusUpwardLinks(dyld4::RuntimeState&) const (no debug info)
[/usr/lib/dyld] dyld4::prepare(dyld4::APIs&, mach_o::UnsafeHeader const*) (no debug info)
[/usr/lib/dyld] dyld4::start(dyld4::KernelArgs*, void*, void*, unsigned long long)::$_1::operator()() const (no debug info)
[/usr/lib/dyld] start (no debug info)

What did you expect to happen?

It should just run fine as before.

Step-by-step reproduction instructions (by running brew commands)

git clone https://github.com/KATRIN-Experiment/Kassiopeia
cd Kassiopeia
brew install \
            cmake \
            coreutils \
            boost \
            fftw \
            gsl \
            hdf5 \
            libxml2 \
            log4cxx \
            open-mpi \
            root \
            sqlite \
            vtk \
            libomp
export CC=/usr/bin/clang
export CXX=/usr/bin/clang++
./setup.sh
source install/bin/kasperenv.sh
UnitTestKasper

[SMillerDev]

Can you provide a minimally reproducible example? Currently it is just as likely to be an issue in the project as it is in brew.

[2xB]

This was not too straight-forward to debug thanks to very many nested CMakeLists files in our project and my only available macOS machine being a runner that is in a location far away, but it turns out we did in fact compile part of our code with C++ 14 and ROOT made us compile part of our code with C++ 20 since an update of the Homebrew formula.

What is frustrating: Comparing the formulas for 6.40.02_1 and 6.40.04, you do not see a difference between C++ 14 and C++ 20 - it seemingly was C++ 20 both times. Because 6.40.02_1 as far as I understand was updated in place from using C++ 14 to using C++ 20:

Version of ROOT 6.40.02_1 we probably used before: e4019bb
Where the C++ version was changed: 0e88938
In-place edited version of ROOT 6.40.02_1 containing that change: deeef4d

Is bottles updating in place normal or is this a bug in BrewTestBot or some procedure on how bottles are produced? If I understand correctly that that is what happened with these three commits, I can open a new issue about that or just ignore this depending on how this is viewed from your side. After answering that, I think this issue can be closed, thank you very much for the patience on a MWE.

[SMillerDev]

Is bottles updating in place normal

Yeah, that's pretty standard. We're have the revision field, but it's only used when we need to force an update for critical packaging issues.

[2xB]

Okay, I do not understand why this would be considered a good idea especially due to issues like this harming reproducibility even if one keeps track of the exact environment. But if it is standard, then it's probably difficult to change and this means there is nothing to fix here, thank you for the responses!