Another compile issue on Sequoia

I recently updated my Mac Pro to Sequoia and shortly after, ROOT started crashing on the open. I tried a deep reinstall from source (ROOT 6.32 latest-stable) via:

xcode-select --uninstall
xcode-select --install
brew install cmake python ninja git
brew install glew fftw openssl tbb libxml2
git clone --branch latest-stable --depth=1 https://github.com/root-project/root.git root_src
mkdir root_build root_install
cd root_build
cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src
brew install zstd
cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src -Dbuiltin_glew=ON
cmake --build . 

Unfortunately I end up with this compile crash despite several attempts/variations on the above, including cloning with older tags that I know worked for me in the past:

[ 25%] Built target LLVMDemangle
[ 25%] Building CXX object interpreter/llvm-project/llvm/lib/Support/CMakeFiles/LLVMSupport.dir/AddressRanges.cpp.o
In file included from /Users/bein/Desktop/Physics/Postdoc2/Root/root_src/interpreter/llvm-project/llvm/lib/Support/AddressRanges.cpp:9:
In file included from /Users/bein/Desktop/Physics/Postdoc2/Root/root_src/interpreter/llvm-project/llvm/include/llvm/ADT/AddressRanges.h:12:
In file included from /Users/bein/Desktop/Physics/Postdoc2/Root/root_src/interpreter/llvm-project/llvm/include/llvm/ADT/STLExtras.h:20:
In file included from /Users/bein/Desktop/Physics/Postdoc2/Root/root_src/interpreter/llvm-project/llvm/include/llvm/ADT/Hashing.h:49:
In file included from /Users/bein/Desktop/Physics/Postdoc2/Root/root_src/interpreter/llvm-project/llvm/include/llvm/Support/SwapByteOrder.h:17:
In file included from /Users/bein/Desktop/Physics/Postdoc2/Root/root_src/interpreter/llvm-project/llvm/include/llvm/ADT/bit.h:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstdint:149:5: error: <cstdint> tried including <stdint.h> but didn't find libc++'s <stdint.h> header.           This usually means that your header search paths are not configured properly.           The header search paths should contain the C++ Standard Library headers before           any C Standard Library, and you are probably using compiler flags that make that           not be the case.
  149 | #   error <cstdint> tried including <stdint.h> but didn't find libc++'s <stdint.h> header. \

Any help is greatly appreciated. My compiler is AppleClang 15.0.0 (from Xcode Command Line Tools).

Hi Sam,

Sorry to hear your brew-based setup on Sequoia did not work out of the box for ROOT.
I would start by performing the steps suggested here ROOT on macOS 15 / Xcode 16 - #8 by Danilo to make sure no remnants of previous sdks are around.
We can then discuss further steps if not successful.

Cheers,
D

Hi Danilo,

Thank you for the prompt reply. I followed the steps outlined there by @couet. I again experienced the same crash.

[ 26%] Copying /Users/bein/Desktop/Physics/Postdoc2/Root/root/etc/notebook/JsMVA/js/NetworkDesigner.min.js
[ 26%] Copying clang's clwbintrin.h...
CMake Error at /Users/bein/Desktop/Physics/Postdoc2/Root/root-build/builtins/xrootd/BUILTIN_XROOTD-prefix/src/BUILTIN_XROOTD-stamp/BUILTIN_XROOTD-build-Release.cmake:37 (message):
  Command failed: 2

   '/Library/Developer/CommandLineTools/usr/bin/make'

  See also

    /Users/bein/Desktop/Physics/Postdoc2/Root/root-build/builtins/xrootd/BUILTIN_XROOTD-prefix/src/BUILTIN_XROOTD-stamp/BUILTIN_XROOTD-build-*.log


[ 26%] Copying /Users/bein/Desktop/Physics/Postdoc2/Root/root/etc/notebook/JsMVA/js/NeuralNetwork.js
[ 26%] Copying clang's clzerointrin.h...
-- stdout output is:
...skipping to end...
s/XrdUtils.dir/XrdTls/XrdTlsSocket.cc.o

The log file pointed to there also contains the same crash I saw originally. As an additional note, the first cmake command required an extra argument -Dbuiltin_glew=ON in order not to crash.

Thanks a lot for any help,

Sam

Hi Sam,

This seems to be an issue with your setup.
What happens if you remove the packages installed with brew install glew fftw openssl tbb libxml2 and run cmake ? What is the output of the configuration?

Cheers,
D

Hi Danilo,

I just gave it a try. Specifically I did:

536 brew uninstall --ignore-dependencies glew fftw openssl tbb libxml2
537 brew install glew fftw openssl tbb libxml2
538 cmake -DCMAKE_INSTALL_PREFIX=…/root_install …/root -Dbuiltin_glew=ON
539 make -j4

…however, that ended up with the usual cascade of errors:

[ 54%] Copying /Users/bein/Desktop/Physics/Postdoc2/Root/root/bindings/pyroot/pythonizations/python/ROOT/_pythonization/_tmva/_batchgenerator.py
[ 54%] Built target ROOTPythonizationsPySources
[ 54%] Building CXX object interpreter/llvm-project/llvm/lib/Support/CMakeFiles/LLVMSupport.dir/ABIBreak.cpp.o
[ 54%] Building CXX object interpreter/llvm-project/llvm/lib/Support/CMakeFiles/LLVMSupport.dir/AMDGPUMetadata.cpp.o
In file included from /Users/bein/Desktop/Physics/Postdoc2/Root/root/interpreter/llvm-project/llvm/lib/Support/AMDGPUMetadata.cpp:15:
In file included from /Users/bein/Desktop/Physics/Postdoc2/Root/root/interpreter/llvm-project/llvm/include/llvm/Support/AMDGPUMetadata.h:18:
In file included from /Users/bein/Desktop/Physics/Postdoc2/Root/root/interpreter/llvm-project/llvm/include/llvm/ADT/StringRef.h:12:
In file included from /Users/bein/Desktop/Physics/Postdoc2/Root/root/interpreter/llvm-project/llvm/include/llvm/ADT/DenseMapInfo.h:18:
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/v1/cstddef:46:5: error: <cstddef> tried including <stddef.h> but didn't find libc++'s <stddef.h> header.           This usually means that your header search paths are not configured properly.           T

Hi Sam,

could you try with a clean build? Do you still encounter these issues?

Hi Monica,

I just tried a clean build via:

  548  xcode-select --install
  551  git clone --branch latest-stable --depth=1 https://github.com/root-project/root.git root_src
  553  mkdir root_build root_install
  554  cd root_build
  556  cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src -Dbuiltin_glew=ON
  557  cmake --build . -- install -j4

The result was the usual crash:

[ 20%] Copying header /Users/bein/Desktop/Physics/Postdoc2/Root/root_src/roofit/roostats/inc/RooStats/UpperLimitMCSModule.h to /Users/bein/Desktop/Physics/Postdoc2/Root/root_build/include
[ 20%] Built target move_header_roofit_roostats

-- DAVIX build command succeeded.  See also /Users/bein/Desktop/Physics/Postdoc2/Root/root_build/builtins/davix/DAVIX-prefix/src/DAVIX-stamp/DAVIX-build-*.log
[ 20%] Performing install step for 'DAVIX'
-- DAVIX install command succeeded.  See also /Users/bein/Desktop/Physics/Postdoc2/Root/root_build/builtins/davix/DAVIX-prefix/src/DAVIX-stamp/DAVIX-install-*.log
[ 20%] Completed 'DAVIX'
[ 20%] Built target DAVIX
make: *** [all] Error 2

The output of that first crash log file is:

tail /Users/bein/Desktop/Physics/Postdoc2/Root/root_build/builtins/davix/DAVIX-prefix/src/DAVIX-stamp/DAVIX-build-*.log
==> /Users/bein/Desktop/Physics/Postdoc2/Root/root_build/builtins/davix/DAVIX-prefix/src/DAVIX-stamp/DAVIX-build-err.log <==
/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:218:48: note: expanded from macro ‘__deprecated_msg’
218 | #define __deprecated_msg(_msg) attribute((deprecated(_msg)))
| ^
1 warning generated.
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libdavix.a(davix_ptree.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libdavix.a(ne_ntlm.c.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libdavix.a(ne_sspi.c.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libdavix.a(davix_ptree.cpp.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libdavix.a(ne_ntlm.c.o) has no symbols
/Library/Developer/CommandLineTools/usr/bin/ranlib: file: libdavix.a(ne_sspi.c.o) has no symbols

==> /Users/bein/Desktop/Physics/Postdoc2/Root/root_build/builtins/davix/DAVIX-prefix/src/DAVIX-stamp/DAVIX-build-out.log <==
[ 91%] Building CXX object src/CMakeFiles/libdavix_static.dir/xml/davpropxmlparser.cpp.o
[ 92%] Building CXX object src/CMakeFiles/libdavix_static.dir/xml/davxmlparser.cpp.o
[ 93%] Building CXX object src/CMakeFiles/libdavix_static.dir/xml/metalinkparser.cpp.o
[ 94%] Building CXX object src/CMakeFiles/libdavix_static.dir/xml/s3deleteparser.cpp.o
[ 95%] Building CXX object src/CMakeFiles/libdavix_static.dir/xml/S3MultiPartInitiationParser.cpp.o
[ 96%] Building CXX object src/CMakeFiles/libdavix_static.dir/xml/s3propparser.cpp.o
[ 97%] Building CXX object src/CMakeFiles/libdavix_static.dir/xml/swiftpropparser.cpp.o
[ 98%] Building CXX object src/CMakeFiles/libdavix_static.dir/davixcontext.cpp.o
[100%] Linking CXX static library libdavix.a
[100%] Built target libdavix_static

Thanks for your help,

Sam

It really looks like your setup is somehow broken. Could you please upgrade your OS and then try to rerun these steps?

# remove the current Command Line Tools
sudo rm -r /Library/Developer/CommandLineTools

# Reset xcode-select
xcode-select -r

# Then install. You will be asked to click a button 
xcode-select --install

Check for new version of the Command Line Tools and update it if needed: Go in the System Settings → General → Software Update

Then proceed with a new clean build

# Install ROOT
git clone https://github.com/root-project/root.git
mkdir root-build
cd root-build
cmake -DCMAKE_INSTALL_PREFIX=../root_install ../root_src -Dbuiltin_glew=ON
make install -j4

I also add in the loop @couet, he might give some insights about your issue…

@mdessole I agree with you it looks weird. I do not have more hints than what I said in : ROOT on macOS 15 / Xcode 16 - #8 by Danilo

Hi Monica, all,

My system software is fully up to date and I’m running Sequoia. I could try falling back from Sequoia to Sonoma…

[ 12%] Copying header /Users/bein/Desktop/Physics/Postdoc2/Root/root/core/meta/inc/TMethodArg.h to /Users/bein/Desktop/Physics/Postdoc2/Root/root-build/include
CMake Error at BUILTIN_XROOTD-stamp/BUILTIN_XROOTD-download-Release.cmake:37 (message):
  Command failed: 1

   '/usr/local/Cellar/cmake/3.30.5/bin/cmake' '-Dmake=' '-Dconfig=' '-P' '/Users/bein/Desktop/Physics/Postdoc2/Root/root-build/builtins/xrootd/BUILTIN_XROOTD-prefix/src/BUILTIN_XROOTD-stamp/BUILTIN_XROOTD-download-Release-impl.cmake'

  See also

    /Users/bein/Desktop/Physics/Postdoc2/Root/root-build/builtins/xrootd/BUILTIN_XROOTD-prefix/src/BUILTIN_XROOTD-stamp/BUILTIN_XROOTD-download-*.log

CMake Error at DAVIX-stamp/DAVIX-download-Release.cmake:49 (message):
  Command failed: 1

   '/usr/local/Cellar/cmake/3.30.5/bin/cmake' '-Dmake=' '-Dconfig=' '-P' '/Users/bein/Desktop/Physics/Postdoc2/Root/root-build/builtins/davix/DAVIX-prefix/src/DAVIX-stamp/DAVIX-download-Release-impl.cmake'

  See also

    /Users/bein/Desktop/Physics/Postdoc2/Root/root-build/builtins/davix/DAVIX-prefix/src/DAVIX-stamp/DAVIX-download-*.log

I came across what seemed like a related issue, e.g., Unable to compile brms programs with rstan or cmdstanr after updating Xcode - #10 by vciocca - brms - The Stan Forums, but the solution of removing all my files in the folder /usr/local/include/ and then doing a deep clean build gave the above issue. I’m a bit at a loss.

Thanks,

Sam

Unfortunately, I don’t know what else to suggest to install from source. Do you really need to install ROOT from source? You could download the binaries as an alternative.

Hi Monica,

I would be fine to have a binary installation, as long as it comes with pyroot support. I tried downloading this file and unpacking it:

https://root.cern/download/root_v6.32.06.macos-15.0-arm64-clang160.tar.gz

mac-1T0-252:root-build bein$ source ~/Downloads/root/bin/thisroot.sh
mac-1T0-252:root-build bein$ root -l
-bash: /Users/bein/Downloads/root/bin/root: Bad CPU type in executable.

I had actually tried this before as well - do you know the issue here?

Thanks,
Sam

What’s the output of uname -a?

What is your CTL version given by the command:

pkgutil --pkg-info=com.apple.pkg.CLTools_Executables

?
It should be:

package-id: com.apple.pkg.CLTools_Executables
version: 16.0.0.0.1.1724870825

Hi, I get:

mac-1T0-252:root-build bein$ uname -a
Darwin mac-1T0-252.local 24.0.0 Darwin Kernel Version 24.0.0: Tue Sep 24 23:36:30 PDT 2024; root:xnu-11215.1.12~1/RELEASE_X86_64 x86_64

and

mac-1T0-252:root-build bein$ pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 15.3.0.0.1.1708646388
volume: /
location: /
install-time: 1729083885

Ah, you have CLT 15 . In principle the you should get 16. When you go to: System Settings → Software update it should propose you an update of the CLT

Thank you Sam. Unfortunately, we provide binaries for amr64 CPUs only… I suggest you to give a try with brew installation!
brew install root

Note that my MacBook has also an Intel CPU. It runs Sequoia, and I can install ROOT from sources. The only difference I see with your setup is the version of the CLT.

Hi all,

Thanks for your perseverance. Here, the drama continues a bit. The command

brew install root

seemed to finish out without an issue but then when I try to run ROOT I get:

mac-1T0-252:Root bein$ . /usr/local/bin/thisroot.sh
mac-1T0-252:Root bein$ root -l 
input_line_1:1:2: fatal error: malformed or corrupted AST file: 'could not find file '/Library/Developer/CommandLineTools/SDKs/MacOSX15.0.sdk/usr/include/_types.modulemap' referenced by AST file'
#include <new>
 ^
input_line_1:1:2: note: after modifying system headers, please delete the module cache at '/usr/local/Cellar/root/6.32.06/lib/root'
input_line_1:1:2: note: imported by module 'std' in '/usr/local/Cellar/root/6.32.06/lib/root/std.pcm'
Warning in cling::IncrementalParser::CheckABICompatibility():
  Failed to extract C++ standard library version.
Warning in cling::IncrementalParser::CheckABICompatibility():
  Possible C++ standard library mismatch, compiled with _LIBCPP_ABI_VERSION '1'
  Extraction of runtime standard library version was: ''
<<< cling interactive line includer >>>: fatal error: module file '/usr/local/Cellar/root/6.32.06/lib/root/Darwin.pcm' is out of date and needs to be rebuilt
Failed to load module Darwin
Failed to load module std
Failed to load module _Builtin_intrinsics
Failed to load module ROOT_Foundation_C
Failed to load module ROOT_Config
Failed to load module ROOT_Rtypes
Failed to load module ROOT_Foundation_Stage1_NoRTTI
Failed to load module Core
Failed to load module Rint
Failed to load module RIO
Failed to load module MathCore
Failed to load module Hist
Failed to load module RHTTPSniff
Failed to load module RMySQL
Failed to load module RDAVIX
Failed to load module ROOTVecOps
Failed to load module FitPanel
Failed to load module Genetic
Failed to load module Physics
Failed to load module Tree
Failed to load module Matrix
Failed to load module Gpad
Failed to load module ROOTEve
Failed to load module RGL
Failed to load module GCocoa
Failed to load module GeomBuilder
Failed to load module Cling_Runtime
Failed to load module SPlot
Failed to load module Hbook
Failed to load module ROOT_Config
Failed to load module Rint
Failed to load module XMLParser
Failed to load module Recorder
Failed to load module GuiBld
Failed to load module ROOTWebDisplay
Failed to load module XMLIO
Failed to load module ROOT_Rtypes
Failed to load module std
Failed to load module ROOTHistDraw
Failed to load module RIO
Failed to load module MathMore
Failed to load module ROOT_Foundation_C
Failed to load module SpectrumPainter
Failed to load module Core
Failed to load module NetxNG
Failed to load module Minuit
Failed to load module TMVA
Failed to load module ROOTNTupleUtil
Failed to load module Graf
Failed to load module Gdml
Failed to load module Cling_Runtime_Extra
Failed to load module MathCore
Failed to load module WebGui6
Failed to load module ROOTTPython
Failed to load module ROOTHist
Failed to load module ROOTGeomViewer
Failed to load module ROOTFitPanelv7
Failed to load module Smatrix
Failed to load module Thread
Failed to load module Darwin
Failed to load module ROOTBrowsable
Failed to load module Imt
Failed to load module HistPainter
Failed to load module PyMVA
Failed to load module RHTTP
Failed to load module ROOT_Foundation_Stage1_NoRTTI
Failed to load module Quadp
Failed to load module ROOTNTuple
Failed to load module Eve
Failed to load module GeomPainter
Failed to load module TreeViewer
Failed to load module EG
Failed to load module HistFactory
Failed to load module Spectrum
Failed to load module Html
Failed to load module Hist
Failed to load module GuiHtml
Failed to load module _Builtin_intrinsics
Failed to load module TMVAGui
Failed to load module Postscript
Failed to load module Fumili
Failed to load module Net
Failed to load module Geom
Failed to load module RooFitMore
Failed to load module ROOTGpadv7
Failed to load module RCsg
Failed to load module RooFit
Failed to load module RooFitRDataFrameHelpers
Failed to load module MultiProc
Failed to load module RooStats
Failed to load module FITSIO
Failed to load module Ged
Failed to load module FFTW
Failed to load module RooFitCore
Failed to load module Gui
Failed to load module SQLIO
Failed to load module TMVAUtils
Failed to load module ROOTTMVASofie
Failed to load module ASImage
Failed to load module RooFitXRooFit
Failed to load module RooFitHS3
Failed to load module Foam
Failed to load module RSQLite
Failed to load module Minuit2
Failed to load module MLP
Failed to load module ROOTDataFrame
Failed to load module GenVector
Failed to load module ROOTBrowserv7
Failed to load module RootAuth
Failed to load module Graf3d
Failed to load module ASImageGui
Failed to load module ROOTTreeViewer
Failed to load module Gviz3d
Failed to load module TreePlayer
Failed to load module RooFitJSONInterface
Failed to load module ROOTGraphicsPrimitives

 *** Break *** segmentation violation
[/usr/lib/system/libsystem_platform.dylib] _sigtramp (no debug info)
[<unknown binary>] (no debug info)
[/usr/local/Cellar/root/6.32.06/lib/root/libCling.so] ROOT::TMetaUtils::TNormalizedCtxtImpl::TNormalizedCtxtImpl(cling::LookupHelper const&) (no debug info)
[/usr/local/Cellar/root/6.32.06/lib/root/libCling.so] ROOT::TMetaUtils::TNormalizedCtxt::TNormalizedCtxt(cling::LookupHelper const&) (no debug info)
[/usr/local/Cellar/root/6.32.06/lib/root/libCling.so] TCling::TCling(char const*, char const*, char const* const*, void*) (no debug info)
[/usr/local/Cellar/root/6.32.06/lib/root/libCling.so] CreateInterpreter (no debug info)
[/usr/local/Cellar/root/6.32.06/lib/root/libCore.so] TROOT::InitInterpreter() (no debug info)
[/usr/local/Cellar/root/6.32.06/lib/root/libCore.so] ROOT::Internal::GetROOT2() (no debug info)
[/usr/local/Cellar/root/6.32.06/lib/root/libCore.so] TApplication::TApplication(char const*, int*, char**, void*, int) (no debug info)
[/usr/local/Cellar/root/6.32.06/lib/root/libRint.so] TRint::TRint(char const*, int*, char**, void*, int, bool, bool) (no debug info)
[/usr/local/Cellar/root/6.32.06/bin/root.exe] main (no debug info)
[/usr/lib/dyld] start (no debug info)
mac-1T0-252:Root bein$ 

Best,
Sam

It seems you now have tha similar problem as the one described here Problem Launching ROOT - #23 by gasar8 . Some solutions are listed at the end of the thread.