Module libc not found (take 3)

thrilledrelish · April 6, 2025, 1:54am

ROOT Version: 6.32.04
Built for linuxx8664gcc on Apr 05 2025, 09:35:33
From heads/master@tags/v6-32-04

Platform: Slackware64 15.0
Compiler: gcc (GCC) 11.2.0

I have an issue running ROOT I have just built with this script: link removed because the forum is ridiculously paranoid

Important bits:

PREFIX=/opt/ROOT-${VERSION}
mkdir -p build
cd build
CFLAGS="$SLKCFLAGS" \
CXXFLAGS="$SLKCFLAGS" \
cmake ../src \
  -DCMAKE_INSTALL_PREFIX=$PREFIX \
  -DCMAKE_C_FLAGS:STRING="$SLKCFLAGS" \
  -DCMAKE_CXX_FLAGS:STRING="$SLKCFLAGS" \
  -DCMAKE_CXX_STANDARD=${CXXSTD} \
  -DCMAKE_INSTALL_PYTHONDIR=lib \
  -DMAN_INSTALL_DIR=$PREFIX/man \
  -Dbuiltin_cfitsio=OFF \
  -Dbuiltin_davix=OFF \
  -Dbuiltin_fftw3=OFF \
  -Dbuiltin_gsl=OFF \
  -Dbuiltin_gtest=OFF \
  -Dbuiltin_openssl=OFF \
  -Dbuiltin_tbb=OFF \
  -Dbuiltin_vc=OFF \
  -Dbuiltin_vdt=OFF \
  -Dbuiltin_veccore=OFF \
  -Dclad=OFF \
  -Dalien=OFF \
  -Dall=OFF \
  -Darrow=OFF \
  -Dassan=OFF \
  -Dasserts=OFF \
  -Dbuiltin_freetype=OFF \
  -Dfftw3=ON \
  -Dbuiltin_glew=OFF \
  -Dbuiltin_clang=ON \
  -Dbuiltin_cling=ON \
  -Dbuiltin_llvm=ON \
  -Dbuiltin_lz4=OFF \
  -Dbuiltin_lzma=OFF \
  -Dbuiltin_nlohmannjson=ON \
  -Dbuiltin_openui5=ON \
  -Dbuiltin_pcre=OFF \
  -Dbuiltin_unuran=OFF \
  -Dbuiltin_xrootd=OFF \
  -Dbuiltin_xxhash=OFF \
  -Dbuiltin_zlib=OFF \
  -Dbuiltin_zstd=OFF \
  -Dccache=OFF \
  -Dcefweb=OFF \
  -Dclingtest=OFF \
  -Dcocoa=OFF \
  -Dcompression_default=zlib \
  -Dcoverage=OFF \
  -Dcuda=OFF \
  -Dcudnn=OFF \
  -Dcxx_modules=OFF \
  -Ddataframe=ON \
  -Ddavix=OFF \
  -Ddcache=OFF \
  -Ddev=OFF \
  -Ddistcc=OFF \
  -Dexceptions=OFF \
  -Dfail-on-missing=ON \
  -Dfcgi=OFF \
  -Dfitsio=ON \
  -Dfortran=ON \
  -Dgdml=ON \
  -Dgfal=OFF \
  -Dgminimal=OFF \
  -Dgnuinstall=OFF \
  -Dmathmore=ON \
  -Dgviz=OFF \
  -Dhttp=ON \
  -Djemalloc=OFF \
  -Dlibcxx=OFF \
  -Dmacos_native=OFF \
  -Dmemory_termination=OFF \
  -Dminimal=OFF \
  -Dmlp=ON \
  -Dmonalisa=OFF \
  -Dmpi=OFF \
  -Dmysql=OFF \
  -Dodbc=OFF \
  -Dopengl=ON \
  -Doracle=OFF \
  -Dpgsql=OFF \
  -Dpyroot=ON \
  -Dpyroot_legacy=OFF \
  -Dpythia6=OFF \
  -Dpythia6_nolink=OFF \
  -Dpythia8=OFF \
  -Dqt5web=OFF \
  -Dr=OFF \
  -Droofit=ON \
  -Droot7=ON \
  -Drootbench=OFF \
  -Droottest=OFF \
  -Drpath=OFF \
  -Druntime_cxxmodules=ON \
  -Dshadowpw=OFF \
  -Dshared=ON \
  -Dsoversion=ON \
  -Dspectrum=ON \
  -Dsqlite=OFF \
  -Dssl=ON \
  -Dtcmalloc=OFF \
  -Dtest_distrdf_pyspark=OFF \
  -Dtesting=OFF \
  -Dtmva=ON \
  -Dtmva-cpu=ON \
  -Dtmva-gpu=OFF \
  -Dtmva-pymva=ON \
  -Dtmva-rmva=OFF \
  -Dunuran=OFF \
  -During=OFF \
  -Dvc=OFF \
  -Dvdt=OFF \
  -Dveccore=OFF \
  -Dvmc=OFF \
  -Dwebgui=ON \
  -Dwin_broken_tests=OFF \
  -Dwinrtdebug=OFF \
  -Dx11=ON \
  -Dxml=ON \
  -Dxproofd=OFF \
  -Dxrootd=OFF \
  -DCMAKE_BUILD_TYPE=Release ../src
make
make install/strip DESTDIR=$PKG

When running it, I am getting Module libc not found, and std::cout does not work.

Indeed, the libc.pcm is not built:

I have uploaded the build logs:
links removed because the forum is ridiculously paranoid

When building ROOT in a clean docker container (with some libraries not present, but all the strictly required by the script installed), the issue is not present when running ROOT inside that container, but installing the package in the main system produces a crash:

input_line_1:1:2: fatal error: module file '/tmp/SBo/root-6.32.04/build/lib/libc.pcm' not found: module file not found
#include <new>
 ^
input_line_1:1:2: note: imported by module 'std' in '/opt/ROOT-6.32.04/lib/std.pcm'
Warning in cling::IncrementalParser::CheckABICompatibility():
  Failed to extract C++ standard library version.
Replaced symbol at_quick_exit cannot be found in JIT!
Module libc not found.
Failed to load module std
<<< cling interactive line includer >>>: fatal error: module file '/tmp/SBo/root-6.32.04/build/lib/libc.pcm' not found: module file not found
<<< cling interactive line includer >>>: note: imported by module '_Builtin_intrinsics' in '/opt/ROOT-6.32.04/lib/_Builtin_intrinsics.pcm'
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 RHTTPSniff
Failed to load module Imt
Failed to load module HistPainter
Failed to load module PyMVA
Failed to load module RHTTP
Failed to load module FitPanel
Failed to load module ROOTVecOps
Failed to load module Quadp
Failed to load module GeomPainter
Failed to load module ROOT_Foundation_Stage1_NoRTTI
Failed to load module Genetic
Failed to load module Eve
Failed to load module TreeViewer
Failed to load module Physics
Failed to load module ROOTNTuple
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 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 Html
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 Hbook
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 RooFitRDataFrameHelpers
Failed to load module GeomBuilder
Failed to load module FITSIO
Failed to load module Ged
Failed to load module Recorder
Failed to load module FFTW
Failed to load module ROOTWebDisplay
Failed to load module GuiBld
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 TMVAUtils
Failed to load module ROOTHistDraw
Failed to load module GX11TTF
Failed to load module RIO
Failed to load module ROOTTMVASofie
Failed to load module ASImage
Failed to load module ROOT_Foundation_C
Failed to load module MathMore
Failed to load module RooFitXRooFit
Failed to load module RooFitHS3
Failed to load module Foam
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 ROOTBrowserv7
Failed to load module Minuit
Failed to load module RootAuth
Failed to load module TMVA
Failed to load module ROOTNTupleUtil
Failed to load module ASImageGui
Failed to load module Graf
Failed to load module GX11
Failed to load module Gdml
Failed to load module ROOTTreeViewer
Failed to load module Graf3d
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 ROOTGraphicsPrimitives
Failed to load module ROOTFitPanelv7
Failed to load module Smatrix
Failed to load module ROOTGeomViewer
Failed to load module RooFitJSONInterface
Failed to load module Thread

 *** Break *** segmentation violation

The libc.pcm is present where it is expected to be (/opt/ROOT-$VERSION/lib/libc.pcm)

Moreover, just symlinking works sudo ln -s /opt/ROOT-6.32.04/lib/libc.pcm /tmp/SBo/root-6.32.04/build/lib/libc.pcm , and ROOT starts to work as expected.

The issue seems to be the same with ROOT ROOT-6.34.06, but I did more testing with 6.32.04

This issue has already been seen before twice:

link removed because the forum is ridiculously paranoid
link removed because the forum is ridiculously paranoid

devajith · April 6, 2025, 6:45pm

Hi @thrilledrelish,

Thank you for your question. I will get back to you after having a look.

Cheers,
Dev

devajith · April 7, 2025, 11:18am

Hi @thrilledrelish,

Using:

-DCMAKE_INSTALL_PREFIX=$PREFIX

and actually installing it in a separate location might be the problem:

make install/strip DESTDIR=$PKG

Cheers,
Dev

thrilledrelish · April 7, 2025, 11:31am

Hmm… well, that is a normal packaging procedure which every Linux distribution does. If some paths are rewritten during make install/strip, then this is definitely a bug with the ROOT’s build system.

devajith · April 7, 2025, 11:56am

Not sure how helpful this might be, but see this comment: Questions about ROOT6 packaging - #4 by amadio