Fatal error after running "make install" when built against LLVM 9

[chrisburr]

Moved from #6385 as there are too many bot comments in that PR. cc @vgvassilev

When testing the LLVM 9 PR for conda-forge and had a few issues with external LLVM/Clang/Cling so I temporarily switched to the builtins. This works from the build directory but it then has issues once make install is ran. More details are in the comment copied at the end of this issue. I think this is an issue with root's install commands rather than the conda-recipe, but you can reproduce what I'm doing it docker by running:

git clone https://github.com/chrisburr/root-feedstock.git
cd root-feedstock
git checkout llvm90-install-error
# Adjust CPU_COUNT as required
CPU_COUNT=192 ./build-locally.py --debug --output-id '*root_base*' linux_64_numpy1.16python3.8.____cpython
# When the container launches, look at the output and run the suggested command
# which will be of the form:
cd xxxxx && source xxxxx/build_env_setup.sh
source $RECIPE_DIR/build_root-base.sh
# Anything with ROOT will now fail, e.g.
root
# Rather than waiting to build again, you can roll back to before
# "make install" was ran by running
cd ../..
rm -rf $PWD/*
cp -rp $PWD.bak/* $PWD/
cd -

The command I'm running was simply root to get the interactive prompt. The full output of trying to run 1+2 is below:

$ root -b -q -x -e 1+2
input_line_1:1:2: fatal error: module 'libc' imported by AST file '/home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/std.pcm' found in a different module map file (/home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/etc/cling/libc.modulemap) than when the importing AST file was built (/home/cburr/mambaforge/conda-bld/root_1609268594446/work/build-dir/etc/cling/libc.modulemap)
#include <new>
^
input_line_1:1:2: note: imported by module 'std' in '/home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/std.pcm'
Warning in cling::IncrementalParser::CheckABICompatibility():
 Failed to extract C++ standard library version.
'at_quick_exit' not defined
<<< cling interactive line includer >>>: fatal error: module file '/home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libc.pcm' is out of date and needs to be rebuilt
Failed to load module libc
Failed to load module std
Failed to load module _Builtin_intrinsics
Failed to load module ROOT_Foundation_C
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 ROOTBrowsable
Failed to load module Unfold
Failed to load module RHTTPSniff
Failed to load module Imt
Failed to load module HistPainter
Failed to load module PyMVA
Failed to load module RDAVIX
Failed to load module RHTTP
Failed to load module FitPanel
Failed to load module ROOTVecOps
Failed to load module ProofDraw
Failed to load module Quadp
Failed to load module ROOTNTuple
Failed to load module ROOT_Foundation_Stage1_NoRTTI
Failed to load module Genetic
Failed to load module Eve
Failed to load module GeomPainter
Failed to load module TreeViewer
Failed to load module Physics
Failed to load module EG
Failed to load module Tree
Failed to load module HistFactory
Failed to load module Spectrum
Failed to load module Matrix
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 Gpad
Failed to load module TMVAGui
Failed to load module Postscript
Failed to load module ROOTEve
Failed to load module RGL
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 X3d
Failed to load module Cling_Runtime
Failed to load module SPlot
Failed to load module EGPythia8
Failed to load module RooFit
Failed to load module RCsg
Failed to load module Rint
Failed to load module XMLParser
Failed to load module MultiProc
Failed to load module RooStats
Failed to load module GeomBuilder
Failed to load module Proof
Failed to load module FITSIO
Failed to load module Ged
Failed to load module Recorder
Failed to load module FFTW
Failed to load module GuiBld
Failed to load module ROOTWebDisplay
Failed to load module RooFitCore
Failed to load module Gui
Failed to load module SQLIO
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 GX11TTF
Failed to load module RIO
Failed to load module ProofPlayer
Failed to load module ASImage
Failed to load module libc
Failed to load module ROOT_Foundation_C
Failed to load module MathMore
Failed to load module Foam
Failed to load module RSQLite
Failed to load module SpectrumPainter
Failed to load module Minuit2
Failed to load module Core
Failed to load module MLP
Failed to load module ROOTDataFrame
Failed to load module GenVector
Failed to load module NetxNG
Failed to load module ROOTBrowserv7
Failed to load module Minuit
Failed to load module RootAuth
Failed to load module Graf3d
Failed to load module TMVA
Failed to load module ASImageGui
Failed to load module Graf
Failed to load module GX11
Failed to load module Gdml
Failed to load module ProofBench
Failed to load module Cling_Runtime_Extra
Failed to load module MathCore
Failed to load module Gviz3d
Failed to load module WebGui6
Failed to load module ROOTTPython
Failed to load module ROOTHist
Failed to load module TreePlayer
Failed to load module Gviz
Failed to load module ROOTGraphicsPrimitives
Failed to load module ROOTFitPanelv7
Failed to load module Smatrix
Failed to load module SessionViewer
Failed to load module Thread
input_line_4:1:2: error: unknown type name 'ifdef'
#ifdef complex
^
<<< cling interactive line includer >>>:1:1: error: expected unqualified-id
input_line_5:1:2: error: unknown type name 'ifdef'
#ifdef PI
^
<<< cling interactive line includer >>>:1:1: error: expected unqualified-id
input_line_6:1:2: error: unknown type name 'ifdef'
#ifdef ERROR
^
<<< cling interactive line includer >>>:1:1: error: expected unqualified-id

*** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007fad7d33546c in waitpid () from /lib64/libc.so.6
#1  0x00007fad7d2b2f62 in do_system () from /lib64/libc.so.6
#2  0x00007fad7d8ebf8f in TUnixSystem::StackTrace() () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCore.so.6.23
#3  0x00007fad7d8e8857 in TUnixSystem::DispatchSignals(ESignals) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCore.so.6.23
#4  <signal handler called>
#5  0x00007fad77e65e25 in ROOT::TMetaUtils::TNormalizedCtxtImpl::keepTypedef(cling::LookupHelper const&, char const*, bool) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCling.so
#6  0x00007fad77e6659e in ROOT::TMetaUtils::TNormalizedCtxtImpl::TNormalizedCtxtImpl(cling::LookupHelper const&) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCling.so
#7  0x00007fad77e66db3 in ROOT::TMetaUtils::TNormalizedCtxt::TNormalizedCtxt(cling::LookupHelper const&) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCling.so
#8  0x00007fad77f341df in TCling::TCling(char const*, char const*, char const* const*) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCling.so
#9  0x00007fad77f35ab2 in CreateInterpreter () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCling.so
#10 0x00007fad7d789243 in TROOT::InitInterpreter() () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCore.so.6.23
#11 0x00007fad7d789740 in ROOT::Internal::GetROOT2() () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCore.so.6.23
#12 0x00007fad7d797df6 in TApplication::TApplication(char const*, int*, char**, void*, int) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCore.so.6.23
#13 0x00007fad7dc8f49b in TRint::TRint(char const*, int*, char**, void*, int, bool) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libRint.so.6.23
#14 0x0000563c1fb240d2 in main ()
===========================================================


The lines below might hint at the cause of the crash.
You may get help by asking at the ROOT forum https://root.cern.ch/forum
Only if you are really convinced it is a bug in ROOT then please submit a
report at https://root.cern.ch/bugs Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#5  0x00007fad77e65e25 in ROOT::TMetaUtils::TNormalizedCtxtImpl::keepTypedef(cling::LookupHelper const&, char const*, bool) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCling.so
#6  0x00007fad77e6659e in ROOT::TMetaUtils::TNormalizedCtxtImpl::TNormalizedCtxtImpl(cling::LookupHelper const&) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCling.so
#7  0x00007fad77e66db3 in ROOT::TMetaUtils::TNormalizedCtxt::TNormalizedCtxt(cling::LookupHelper const&) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCling.so
#8  0x00007fad77f341df in TCling::TCling(char const*, char const*, char const* const*) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCling.so
#9  0x00007fad77f35ab2 in CreateInterpreter () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCling.so
#10 0x00007fad7d789243 in TROOT::InitInterpreter() () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCore.so.6.23
#11 0x00007fad7d789740 in ROOT::Internal::GetROOT2() () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCore.so.6.23
#12 0x00007fad7d797df6 in TApplication::TApplication(char const*, int*, char**, void*, int) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libCore.so.6.23
#13 0x00007fad7dc8f49b in TRint::TRint(char const*, int*, char**, void*, int, bool) () from /home/cburr/mambaforge/conda-bld/root_1609268594446/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/libRint.so.6.23
#14 0x0000563c1fb240d2 in main ()
===========================================================

Originally posted by @chrisburr in #6385 (comment)

[vgvassilev]

Thanks for the report. Should be fixed in the new version of the #6385