Problems Reinstalling Root on MacBook After OS Upgrade

[James_Bowen]

All,

I installed Root on my 2023 MacBook about 13 months ago using Homebrew, and it worked fine. However, I believe Root was broken when my MacBook upgraded to OS Sequoia 15.5. I tried reinstalling it with both Homebrew and MacPorts, and both times I got segmentation violations when I tried to open root. This is what happens:

*Jamess-MacBook-Pro:~ jamesbowen$ root -l*
*warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk'*
*C system headers (glibc/Xcode/Windows SDK) must be installed.*
*fatal error: module map file 'module.modulemap' not found*
*Module Darwin not found.*
*Module std not found.*
*<<< cling interactive line includer >>>: fatal error: module file '/private/tmp/root-20250525-17868-r9txow/root-6.36.00/builddir/lib/Darwin.pcm' not found: module file not found*
*<<< cling interactive line includer >>>: note: imported by module '_Builtin_intrinsics' in '/usr/local/Cellar/root/6.36.00/lib/root/_Builtin_intrinsics.pcm'*
*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 ROOTDataFrame*
*Failed to load module XMLParser*
*Failed to load module SpectrumPainter*
*Failed to load module RooFitHS3*
*Failed to load module Core*
*Failed to load module SPlot*
*Failed to load module TreePlayer*
*Failed to load module Gpad*
*Failed to load module Foam*
*Failed to load module ROOTBrowserv7*
*Failed to load module Physics*
*Failed to load module ROOTBrowsable*
*Failed to load module RCsg*
*Failed to load module _Builtin_intrinsics*
*Failed to load module Rint*
*Failed to load module Minuit2*
*Failed to load module Thread*
*Failed to load module Imt*
*Failed to load module PyMVA*
*Failed to load module Graf3d*
*Failed to load module FFTW*
*Failed to load module Quadp*
*Failed to load module RooFitMore*
*Failed to load module Hbook*
*Failed to load module Postscript*
*Failed to load module ROOTGraphicsPrimitives*
*Failed to load module Genetic*
*Failed to load module ROOT_Rtypes*
*Failed to load module RSQLite*
*Failed to load module GCocoa*
*Failed to load module RIO*
*Failed to load module HistFactory*
*Failed to load module FITSIO*
*Failed to load module ROOTGeomViewer*
*Failed to load module MathCore*
*Failed to load module Fumili*
*Failed to load module FitPanel*
*Failed to load module RHTTP*
*Failed to load module Smatrix*
*Failed to load module ROOT_Foundation_Stage1_NoRTTI*
*Failed to load module Spectrum*
*Failed to load module ROOTFitPanelv7*
*Failed to load module ASImageGui*
*Failed to load module Geom*
*Failed to load module Graf*
*Failed to load module MultiProc*
*Failed to load module Net*
*Failed to load module Gviz3d*
*Failed to load module Eve*
*Failed to load module Minuit*
*Failed to load module WebGui6*
*Failed to load module TMVAUtils*
*Failed to load module RooStats*
*Failed to load module ROOTGpadv7*
*Failed to load module GeomPainter*
*Failed to load module GuiHtml*
*Failed to load module RMySQL*
*Failed to load module ROOTEve*
*Failed to load module Cling_Runtime_Extra*
*Failed to load module RDAVIX*
*Failed to load module ROOTTPython*
*Failed to load module HistPainter*
*Failed to load module XMLIO*
*Failed to load module MLP*
*Failed to load module Ged*
*Failed to load module GuiBld*
*Failed to load module TMVA*
*Failed to load module TMVAGui*
*Failed to load module RooFitCodegen*
*Failed to load module ROOTWebDisplay*
*Failed to load module NetxNG*
*Failed to load module RHTTPSniff*
*Failed to load module RooFitXRooFit*
*Failed to load module RGL*
*Failed to load module Tree*
*Failed to load module SQLIO*
*Failed to load module ROOTNTuple*
*Failed to load module ROOTTMVASofie*
*Failed to load module ROOTVecOps*
*Failed to load module RootAuth*
*Failed to load module EG*
*Failed to load module Gui*
*Failed to load module ASImage*
*Failed to load module ROOT_Config*
*Failed to load module RooFitJSONInterface*
*Failed to load module Matrix*
*Failed to load module Recorder*
*Failed to load module Gdml*
*Failed to load module ROOT_Foundation_C*
*Failed to load module ROOTTreeViewer*
*Failed to load module MathMore*
*Failed to load module GenVector*
*Failed to load module Cling_Runtime*
*Failed to load module RooFitCore*
*Failed to load module RooFit*
*Failed to load module Hist*
*Failed to load module ROOTNTupleUtil*
*Failed to load module TreeViewer*

* *** Break *** segmentation violation*
*[/usr/lib/system/libsystem_platform.dylib] _sigtramp (no debug info)*
*[<unknown binary>] (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCling.so] ROOT::TMetaUtils::TNormalizedCtxtImpl::TNormalizedCtxtImpl(cling::LookupHelper const&) (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCling.so] ROOT::TMetaUtils::TNormalizedCtxt::TNormalizedCtxt(cling::LookupHelper const&) (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCling.so] TCling::TCling(char const*, char const*, char const* const*, void*) (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCling.so] CreateInterpreter (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCore.so] TROOT::InitInterpreter() (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCore.so] ROOT::Internal::GetROOT2() (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCore.so] TApplication::TApplication(char const*, int*, char**, void*, int) (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libRint.so] TRint::TRint(char const*, int*, char**, void*, int, bool, bool) (no debug info)*
*[/usr/local/Cellar/root/6.36.00/bin/root.exe] main (no debug info)*
*[/usr/lib/dyld] start (no debug info)*
*Jamess-MacBook-Pro:~ jamesbowen$* 

Does anyone here know how I can fix this?

James Bowen

[Danilo]

Hi James,

Sorry to read ROOT installation via Brew did not work out of the box for you.

It looks some sort of misconfiguration is affecting your system.
Are you sure you properly removed all remnants of previous installations and installed the most recent Apple SDK?

Cheers,
Danilo

[James_Bowen]

Hi Danilo,

Thank you for your reply. To be honest, I am actually not sure that I properly removed all of the remnants of previous installations and installed the most recent Apple SDK. I don’t recall the Root installation instructions saying anything regarding that. What all does that entail?

Sincerely,

James

[pcanal]

You seem to have ROOT installed both in:

‘/private/tmp/root-20250525-17868-r9txow/root-6.36.00/

and

/usr/local/Cellar/root/6.36.00

You would need to delete/remove/hide the one that is older/obsolete.

[James_Bowen]

Thanks pcanal. I will give it a try, and let you know how it goes.

R/James

[James_Bowen]

pcanal,

I made sure that Root was deleted from both of the directories listed above. I then reinstalled it using Homebrew. This time, when I try to start Root, it goes into an apparently permanent wait. I type root or root -l in the terminal, and the next line is blank as if waiting for a result, but after several minutes nothing happens. Does this problem sound familiar?

Sincerely,

James

[StephanH]

Hi @James_Bowen,

that’s a new one for me. Could you try to use XCode → Developer Tools → Instruments to see what it’s doing?

[James_Bowen]

StephanH,

Thank you for your reply. What in particular should I look for in Instruments?

Also, after taking an indefinitely long period last night, I am still getting the same error above that I first posted.

Sincerely,

James

[StephanH]

@James_Bowen

Thank you for your reply. What in particular should I look for in Instruments?

It might help to know what functions are running, so instruments might be able to tell us that (provided there are debug symbols in the libraries). But from the discussion above, it looks to be an issue in finding the precompiled modules. I’ll ask a colleague about it.

[devajith]

@James_Bowen

warning: no such sysroot directory: ‘/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk’

It does seem like something is wrong with your installation (remnants from your previous installation still looking for MacOSX14.sdk)

Could you perhaps try:

source /usr/local/Cellar/root/6.36.00/bin/thisroot.sh

or whichever directory your new installation points you to?

[James_Bowen]

Thank you. I look forward to seeing what you find out.

Sincerely,

James

[James_Bowen]

@devajith

source /usr/local/Cellar/root/6.36.00/bin/thisroot.sh

devajith,

I executed that command, and it doesn’t look like anything happened:

Jamess-MacBook-Pro:~ jamesbowen$ source /usr/local/Cellar/root/6.36.00/bin/thisroot.sh
Jamess-MacBook-Pro:~ jamesbowen$

Is there anything in particular that should have happened here?

James

[ferhue]

Call then “root” after that line.

[James_Bowen]

StephanH,

Were you able to find out anything more about this?

James

[couet]

What do you get when you do:

$ source /usr/local/Cellar/root/6.36.00/bin/thisroot.sh
$ root

?

[James_Bowen]

Dear Olivier,

It crashes. Here is a copy of what happens.

**Jamess-MacBook-Pro:~ jamesbowen$ source /usr/local/Cellar/root/6.36.00/bin/thisroot.sh*
*Jamess-MacBook-Pro:~ jamesbowen$ root*
*warning: no such sysroot directory: '/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk'*
*C system headers (glibc/Xcode/Windows SDK) must be installed.*
*fatal error: module map file 'module.modulemap' not found*
*Module Darwin not found.*
*Module std not found.*
*<<< cling interactive line includer >>>: fatal error: module file '/private/tmp/root-20250525-17868-r9txow/root-6.36.00/builddir/lib/Darwin.pcm' not found: module file not found*
*<<< cling interactive line includer >>>: note: imported by module '_Builtin_intrinsics' in '/usr/local/Cellar/root/6.36.00/lib/root/_Builtin_intrinsics.pcm'*
*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 ROOTDataFrame*
*Failed to load module XMLParser*
*Failed to load module SpectrumPainter*
*Failed to load module RooFitHS3*
*Failed to load module Core*
*Failed to load module SPlot*
*Failed to load module TreePlayer*
*Failed to load module Gpad*
*Failed to load module Foam*
*Failed to load module ROOTBrowserv7*
*Failed to load module Physics*
*Failed to load module ROOTBrowsable*
*Failed to load module RCsg*
*Failed to load module _Builtin_intrinsics*
*Failed to load module Rint*
*Failed to load module Minuit2*
*Failed to load module Thread*
*Failed to load module Imt*
*Failed to load module PyMVA*
*Failed to load module Graf3d*
*Failed to load module FFTW*
*Failed to load module Quadp*
*Failed to load module RooFitMore*
*Failed to load module Hbook*
*Failed to load module Postscript*
*Failed to load module ROOTGraphicsPrimitives*
*Failed to load module Genetic*
*Failed to load module ROOT_Rtypes*
*Failed to load module RSQLite*
*Failed to load module GCocoa*
*Failed to load module RIO*
*Failed to load module HistFactory*
*Failed to load module FITSIO*
*Failed to load module ROOTGeomViewer*
*Failed to load module MathCore*
*Failed to load module Fumili*
*Failed to load module FitPanel*
*Failed to load module RHTTP*
*Failed to load module Smatrix*
*Failed to load module ROOT_Foundation_Stage1_NoRTTI*
*Failed to load module Spectrum*
*Failed to load module ROOTFitPanelv7*
*Failed to load module ASImageGui*
*Failed to load module Geom*
*Failed to load module Graf*
*Failed to load module MultiProc*
*Failed to load module Net*
*Failed to load module Gviz3d*
*Failed to load module Eve*
*Failed to load module Minuit*
*Failed to load module WebGui6*
*Failed to load module TMVAUtils*
*Failed to load module RooStats*
*Failed to load module ROOTGpadv7*
*Failed to load module GeomPainter*
*Failed to load module GuiHtml*
*Failed to load module RMySQL*
*Failed to load module ROOTEve*
*Failed to load module Cling_Runtime_Extra*
*Failed to load module RDAVIX*
*Failed to load module ROOTTPython*
*Failed to load module HistPainter*
*Failed to load module XMLIO*
*Failed to load module MLP*
*Failed to load module Ged*
*Failed to load module GuiBld*
*Failed to load module TMVA*
*Failed to load module TMVAGui*
*Failed to load module RooFitCodegen*
*Failed to load module ROOTWebDisplay*
*Failed to load module NetxNG*
*Failed to load module RHTTPSniff*
*Failed to load module RooFitXRooFit*
*Failed to load module RGL*
*Failed to load module Tree*
*Failed to load module SQLIO*
*Failed to load module ROOTNTuple*
*Failed to load module ROOTTMVASofie*
*Failed to load module ROOTVecOps*
*Failed to load module RootAuth*
*Failed to load module EG*
*Failed to load module Gui*
*Failed to load module ASImage*
*Failed to load module ROOT_Config*
*Failed to load module RooFitJSONInterface*
*Failed to load module Matrix*
*Failed to load module Recorder*
*Failed to load module Gdml*
*Failed to load module ROOT_Foundation_C*
*Failed to load module ROOTTreeViewer*
*Failed to load module MathMore*
*Failed to load module GenVector*
*Failed to load module Cling_Runtime*
*Failed to load module RooFitCore*
*Failed to load module RooFit*
*Failed to load module Hist*
*Failed to load module ROOTNTupleUtil*
*Failed to load module TreeViewer*

* *** Break *** segmentation violation*
*[/usr/lib/system/libsystem_platform.dylib] _sigtramp (no debug info)*
*[<unknown binary>] (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCling.so] ROOT::TMetaUtils::TNormalizedCtxtImpl::TNormalizedCtxtImpl(cling::LookupHelper const&) (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCling.so] ROOT::TMetaUtils::TNormalizedCtxt::TNormalizedCtxt(cling::LookupHelper const&) (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCling.so] TCling::TCling(char const*, char const*, char const* const*, void*) (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCling.so] CreateInterpreter (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCore.so] TROOT::InitInterpreter() (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCore.so] ROOT::Internal::GetROOT2() (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libCore.so] TApplication::TApplication(char const*, int*, char**, void*, int) (no debug info)*
*[/usr/local/Cellar/root/6.36.00/lib/root/libRint.so] TRint::TRint(char const*, int*, char**, void*, int, bool, bool) (no debug info)*
*[/usr/local/Cellar/root/6.36.00/bin/root.exe] main (no debug info)*
*[/usr/lib/dyld] start (no debug info)*
*Jamess-MacBook-Pro:~ jamesbowen$ *
***

[couet]

Dear James,

The message:

Jamess-MacBook-Pro:~ jamesbowen$ source /usr/local/Cellar/root/6.36.00/bin/thisroot.sh
Jamess-MacBook-Pro:~ jamesbowen$ root
warning: no such sysroot directory: ‘/Library/Developer/CommandLineTools/SDKs/MacOSX14.sdk’

Suggests the version of the SDK on your Mac is different from the one Brew used to build it. Have you updated everything ? ie OS and Compiler ?

Does it work if you install ROOT from sources:

$ git clone https://github.com/root-project/root.git
$ mkdir build
$ cd build
$ cmake ../root
$ make -j8
$ source bin/thisroot.sh
$ root

?

[James_Bowen]

Dear Olivier,

I will give this a try and let you know how it works.

Thank you.

James

[James_Bowen]

Dear Olivier,

I tried the procedure you listed. Upon executing the “make -j8” command, the following error occurred (steps before error omitted for brevity):

*[ 57%] Linking CXX executable src/rootcling_stage1*
*ld: warning: ignoring file '/opt/local/lib/libzstd.dylib': found architecture 'arm64', required architecture 'x86_64'*
*[ 57%] Building CXX object core/metacling/src/CMakeFiles/MetaCling.dir/TClingValue.cxx.o*
*Undefined symbols for architecture x86_64:*
*  "_ZSTD_compress", referenced from:*
*      llvm::compression::compress(llvm::compression::Params, llvm::ArrayRef<unsigned char>, llvm::SmallVectorImpl<unsigned char>&) in libLLVMSupport.a[29](Compression.cpp.o)*
*      llvm::compression::zstd::compress(llvm::ArrayRef<unsigned char>, llvm::SmallVectorImpl<unsigned char>&, int) in libLLVMSupport.a[29](Compression.cpp.o)*
*  "_ZSTD_compressBound", referenced from:*
*      llvm::compression::compress(llvm::compression::Params, llvm::ArrayRef<unsigned char>, llvm::SmallVectorImpl<unsigned char>&) in libLLVMSupport.a[29](Compression.cpp.o)*
*      llvm::compression::zstd::compress(llvm::ArrayRef<unsigned char>, llvm::SmallVectorImpl<unsigned char>&, int) in libLLVMSupport.a[29](Compression.cpp.o)*
*  "_ZSTD_decompress", referenced from:*
*      llvm::compression::decompress(llvm::DebugCompressionType, llvm::ArrayRef<unsigned char>, unsigned char*, unsigned long) in libLLVMSupport.a[29](Compression.cpp.o)*
*      llvm::compression::zstd::decompress(llvm::ArrayRef<unsigned char>, unsigned char*, unsigned long&) in libLLVMSupport.a[29](Compression.cpp.o)*
*      llvm::compression::zstd::decompress(llvm::ArrayRef<unsigned char>, llvm::SmallVectorImpl<unsigned char>&, unsigned long) in libLLVMSupport.a[29](Compression.cpp.o)*
*  "_ZSTD_getErrorName", referenced from:*
*      llvm::compression::decompress(llvm::DebugCompressionType, llvm::ArrayRef<unsigned char>, unsigned char*, unsigned long) in libLLVMSupport.a[29](Compression.cpp.o)*
*      llvm::compression::zstd::decompress(llvm::ArrayRef<unsigned char>, unsigned char*, unsigned long&) in libLLVMSupport.a[29](Compression.cpp.o)*
*      llvm::compression::zstd::decompress(llvm::ArrayRef<unsigned char>, llvm::SmallVectorImpl<unsigned char>&, unsigned long) in libLLVMSupport.a[29](Compression.cpp.o)*
*  "_ZSTD_isError", referenced from:*
*      llvm::compression::compress(llvm::compression::Params, llvm::ArrayRef<unsigned char>, llvm::SmallVectorImpl<unsigned char>&) in libLLVMSupport.a[29](Compression.cpp.o)*
*      llvm::compression::zstd::compress(llvm::ArrayRef<unsigned char>, llvm::SmallVectorImpl<unsigned char>&, int) in libLLVMSupport.a[29](Compression.cpp.o)*
*      llvm::compression::decompress(llvm::DebugCompressionType, llvm::ArrayRef<unsigned char>, unsigned char*, unsigned long) in libLLVMSupport.a[29](Compression.cpp.o)*
*      llvm::compression::zstd::decompress(llvm::ArrayRef<unsigned char>, unsigned char*, unsigned long&) in libLLVMSupport.a[29](Compression.cpp.o)*
*      llvm::compression::zstd::decompress(llvm::ArrayRef<unsigned char>, llvm::SmallVectorImpl<unsigned char>&, unsigned long) in libLLVMSupport.a[29](Compression.cpp.o)*
*ld: symbol(s) not found for architecture x86_64*
*c++: error: linker command failed with exit code 1 (use -v to see invocation)*
*make[2]: *** [core/rootcling_stage1/src/rootcling_stage1] Error 1*
*make[1]: *** [core/rootcling_stage1/CMakeFiles/rootcling_stage1.dir/all] Error 2*
*make[1]: *** Waiting for unfinished jobs....*
*-- clad configure command succeeded.  See also /Users/jamesbowen/build/interpreter/cling/tools/plugins/clad/clad-prefix/src/clad-stamp/clad-configure-*.log*
*[ 57%] Performing build step for 'clad'*
*[ 57%] Built target MetaCling*
*-- clad build command succeeded.  See also /Users/jamesbowen/build/interpreter/cling/tools/plugins/clad/clad-prefix/src/clad-stamp/clad-build-*.log*
*[ 57%] Performing install step for 'clad'*
*-- clad install command succeeded.  See also /Users/jamesbowen/build/interpreter/cling/tools/plugins/clad/clad-prefix/src/clad-stamp/clad-install-*.log*
*[ 57%] Completed 'clad'*
*[ 57%] Built target clad*
*make: *** [all] Error 2*
*Mac:build jamesbowen$*

Do you have any recommendations?

Sincerely,

James

[couet]

Dear James,

I guess the cmake step went well ? was there some message saying zstd was missing somehow ? may be you need to install it ? I see the error comes from llvm, may be @devajith has an idea about this error.

Cheers,
Olivier