ROOT6 - fatal error: malformed or corrupted AST file

ROOT
1

Hi!

I was about to give ROOT6 a try using commit 5412d8d5f94b5 - but unfortunately it doesn’t work:

[code]sschmitt@dopamine:~/local/bin$ source thisroot.sh
sschmitt@dopamine:~/local/bin$ ./root -l
./root: can’t start ROOT – check that ~/local/bin/root.exe exists!
sschmitt@dopamine:~/local/bin$ ls ~/local/bin/root.exe
/afsuser/sschmitt/local/bin/root.exe
sschmitt@dopamine:~/local/bin$ ./root.exe
ERROR in cling::CIFactory::createCI():
resource directory ~/local/etc/cling/lib/clang/3.4 not found!
error: unable to read PCH file ~/local/etc/allDict.cxx.pch: 'No such file or directory’
fatal error: malformed or corrupted AST file: ‘Unable to load module “~/local/etc/allDict.cxx.pch”: module file not found’

*** Break *** segmentation violation
Error in TUnixSystem::StackTrace script ~/local/etc/gdb-backtrace.sh is missing
Segmentation fault

sschmitt@dopamine:~/local/bin$ du -h ~/local/etc/allDict.cxx.pch
27M /afsuser/sschmitt/local/etc/allDict.cxx.pch
[/code]

Anything I can do about it or is ROOT6 not mature enough for some beta tests?

Thanks,

Sebastian

2

Hi!

I found the problem. It originates from the way the directory is checked in cling/lib/Interpreter/CIFactory.cpp:

if (!llvm::sys::fs::is_directory(resource_path.str())) { llvm::errs() << "ERROR in cling::CIFactory::createCI():\n resource directory " << resource_path.str() << " not found!\n"; resource_path = ""; }

Apparently “is_directory” does not handle “~”. If I configure with absolute paths

ROOT6 does start.

Best,

Sebastian

3

Hi Sebastian,

That’s a bug, now tracked as sft.its.cern.ch/jira/browse/ROOT-5880. I have added you (or a person with identical name :slight_smile: as watcher.

Cheers, Axel.

4

Hi!

Sorry that I didn’t update my posting - I also reported the bug via JIRA yesterday:

sft.its.cern.ch/jira/browse/ROOT-5904

Can you mark one of them as duplicate of the other?

Best,

Sebastian

PS: You mean sft.its.cern.ch/jira/browse/ROOT-5907, right?

5

Hi,
I am getting a similar error on my MacOS.
Is this bug fixed?
I tried uninstalling and reinstalling couple of times but didn’t work. My xcode is running fine. I asked chat-gpt which suggest doing the following command
rm -rf /opt/homebrew/Cellar/root/6.32.04/lib/root/*.pcm
which doesn’t work either.
The whole error message on my prompt is following:

input_line_1:1:2: fatal error: malformed or corrupted AST file: 'could not find file '/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.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 '/opt/homebrew/Cellar/root/6.32.04/lib/root'
input_line_1:1:2: note: imported by module 'std' in '/opt/homebrew/Cellar/root/6.32.04/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 '/opt/homebrew/Cellar/root/6.32.04/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)
[/opt/homebrew/Cellar/root/6.32.04/lib/root/libCling.so] ROOT::TMetaUtils::TNormalizedCtxtImpl::keepTypedef(cling::LookupHelper const&, char const*, bool) (no debug info)
[/opt/homebrew/Cellar/root/6.32.04/lib/root/libCling.so] ROOT::TMetaUtils::TNormalizedCtxtImpl::TNormalizedCtxtImpl(cling::LookupHelper const&) (no debug info)
[/opt/homebrew/Cellar/root/6.32.04/lib/root/libCling.so] ROOT::TMetaUtils::TNormalizedCtxt::TNormalizedCtxt(cling::LookupHelper const&) (no debug info)
[/opt/homebrew/Cellar/root/6.32.04/lib/root/libCling.so] TCling::TCling(char const*, char const*, char const* const*, void*) (no debug info)
[/opt/homebrew/Cellar/root/6.32.04/lib/root/libCling.so] CreateInterpreter (no debug info)
[/opt/homebrew/Cellar/root/6.32.04/lib/root/libCore.so] TROOT::InitInterpreter() (no debug info)
[/opt/homebrew/Cellar/root/6.32.04/lib/root/libCore.so] ROOT::Internal::GetROOT2() (no debug info)
[/opt/homebrew/Cellar/root/6.32.04/lib/root/libCore.so] TApplication::TApplication(char const*, int*, char**, void*, int) (no debug info)
[/opt/homebrew/Cellar/root/6.32.04/lib/root/libRint.so] TRint::TRint(char const*, int*, char**, void*, int, bool, bool) (no debug info)
[/opt/homebrew/Cellar/root/6.32.04/bin/root.exe] main (no debug info)
[/usr/lib/dyld] start (no debug info)