CMake unable to generate search path because of library conflict - cmake

Question

Dear Colleagues,
I'm a newcommer to LINUX and am trying to use CMake to build a Geant4 example. After the following command
$cmake ~/Geant4/geant4.10.05.p01-install/share/Geant4-10.5.1/examples/basic/B1/
I get this error message:
Cannot generate a safe runtime search path for target exampleB1 because files in some directories
may conflict with libraries in implicit directories:
runtime library [libexpat.so.1] in /usr/lib/x86_64-linux-gnu may be hidden by files in:
/home/dakar/anaconda3/lib
Some of these libraries may not be found correctly.
The warning is correct and when I run $ make -j6 I get the error message
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libSM.so： undefined reference to
‘uuid_generate#UUID_1.0’
/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libSM.so： undefined reference
to‘uuid_unparse_lower#UUID_1.0’
This problem has been encountered before and some solutions are described in detail here:
https://github.com/pism/pism/issues/356
The page the URL links to say that for Conda 4.4+ this issue shouldn't occur. I'm using Conda 4.6.14 but the page adds that if does occur: you can set the NOCONDA_PATH variable in your .bashrc (or similar) just before you add conda to your path like so:
export NOCONDA_PATH=$PATH
export PATH=$HOME/anaconda3/bin:$PATH
I tried this and my .bashrc now reads:
# >>> conda init >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$(CONDA_REPORT_ERRORS=false '/home/dakar/anaconda3/bin/conda' shell.bash hook 2> /dev/null$
if [ $? -eq 0 ]; then
\eval "$__conda_setup"
else
if [ -f "/home/dakar/anaconda3/etc/profile.d/conda.sh" ]; then
. "/home/dakar/anaconda3/etc/profile.d/conda.sh"
CONDA_CHANGEPS1=false conda activate base
else
# \export NOCONDA_PATH=$PATH
\export PATH="/home/dakar/anaconda3/bin:$PATH"
fi
fi
unset __conda_setup
# <<< conda init <<<
export CLHEP_DIR=/home/dakar/CLHEP/2.3.3.2/CLHEP-install/
export CLHEP_INCLUDE_DIR=${CLHEP_DIR}/include/
export CLHEP_LIBRARY=${CLHEP_DIR}/lib/
export LD_LIBRARY_PATH=${CLHEP_LIBRARY}:${LD_LIBRARY_PATH}
export PATH=$CLHEP_DIR/bin/:$PATH
export TOPAS_G4_DATA_DIR=~/G4Data
export LD_LIBRARY_PATH=~/topas/libexternal/:$LD_LIBRARY_PATH
#export LD_LIBRARY_PATH=~/anaconda3/lib/gcc/lib:$LD_LIBRARY_PATH
#CERN ROOT
#export ROOTSYS=/usr/local/root
#export PATH=$ROOTSYS/bin:$PATH
#export PYTHONDIR=$ROOTSYS
#export LD_LIBRARY_PATH=$ROOTSYS/lib:$PYTHONDIR/lib:$ROOTSYS/bindings/pyroot:$LD_LIBRARY_PATH
#export PYTHONPATH=$ROOTSYS/lib:$PYTHONPATH:$ROOTSYS/bindings/pyroot
source ~/Geant4/geant4.10.05.p01-install/bin/geant4.sh
#source ~/Geant4/geant4.10.05.p01-install/share/Geant4-10.5.1/geant4make/geant4make.sh
export NOCONDA_PATH=$PATH
export PATH="/home/dakar/anaconda3/bin:$PATH"
This still hasn't solved the problem. When I run echo $PATH I can still see conda directories:
$ echo $PATH
/home/dakar/anaconda3/bin:/home/dakar/Geant4/geant4.10.05.p01-install/bin:/home/dakar/CLHEP/2.3.3.2/CLHEP-install//bin/:/home/dakar/anaconda3/bin:/home/dakar/anaconda3/condabin:/usr/local/cuda-8.0/bin:/home/dakar/bin:/home/dakar/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
Does anybody have any further advice? Would uninstalling Conda itself be a solution.
Thanks for your time.
L

Answer 1

The error message suggests that you are missing libuuid in your linker invocation.
Try to add -luuid to your linker flags.
Does your build system use pkg-config? In this case you could edit /usr/lib/x86_64-linux-gnu/pkgconfig/sm.pc and add -luuid to the Libs-Section.
This looks like a bug in your Linux-Distro.