Netcdf Undefined symbols for architecture x86_64 - linker

Question

I am running into the famous while using the netcdf library
Undefined symbols for architecture x86_64:
"NcVar::get(double*, long const*) const", referenced from:
Reader<itk::Image<double, 3u> >::Read() in main.cpp.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
I have installed the library using homebrew:
$brew doctor
Your system is ready to brew.
$brew info netcdf
netcdf: stable 4.3.0
http://www.unidata.ucar.edu/software/netcdf
/usr/local/Cellar/netcdf/4.3.0 (53 files, 4.5M) *
Built from source with: --enable-cxx-compat
From: https://github.com/homebrew/homebrew-science/commits/master/netcdf.rb
==> Dependencies Required: hdf5 ✔
the library is in /usr/local/lib (where it is supposed to be). and I assume this path is in the library include path.
$ls /usr/local/lib/|grep netcdf
libnetcdf.7.dylib
libnetcdf.a
libnetcdf.dylib
libnetcdf_c++.4.dylib
libnetcdf_c++.a
libnetcdf_c++.dylib
libnetcdf_c++4.1.dylib
libnetcdf_c++4.a
libnetcdf_c++4.dylib
and my code used to link, until it didn't.
#include <iostream>
#include <exception>
#include <netcdfcpp.h>
std::string _filename="blabla.nc", _varname="variableName";
int _dim;
long* _sizeArray;
long _sizeFlat;
double* _data;
// Read netCDF
void Read()
{
// Open the file.
NcFile file( _filename.c_str(), NcFile::ReadOnly, NULL, 0, NcFile::Offset64Bits);
NcVar* var = file.get_var( _varname.c_str() );
if( var->is_valid() )
{
_sizeFlat = var->num_vals();
_sizeArray = var->edges();
/*
_dim = var->num_dims();
std::cout<< _dim<<std::endl;
for (int i=0; i<_dim; i++)
std::cout<<_sizeArray[i]<<"\t";
std::cout<<"\t"<<_sizeFlat<<std::endl;
// */
_data = new PixelType[_sizeFlat];
try
{
var->get(_data, _sizeArray);
}
catch(std::exception& a)
{
a.what();
//free mem
delete[] _data;
file.close();
_sizeArray = NULL;
var = NULL;
//quit
std::cout<<"Could not read variable :"<<_varname<<std::endl;
exit(EXIT_FAILURE);
}
//free mem
file.close();
}
else
{
//free mem
file.close();
var = NULL;
//quit
std::cout<<"Could not find variable :"<<_varname<<std::endl;
exit(EXIT_FAILURE);
}
}
int main(void)
{
Read();
return 0;
}
I know that I am using old legacy code ( http://www.unidata.ucar.edu/software/netcdf/examples/programs/ ) but the methods I am using are those I found when opening the /usr/local/include/netcdfcpp.h
I am using Cmake to compile, here is the CMakeLists.txt, if it can help
cmake_minimum_required ( VERSION 2.6 )
#set project name
set( Version_Major 3 )
set( Version_Minor 0 )
set( ProjectName supercellDetection_v${Version_Major}.${Version_Minor} )
project ( ${ProjectName} )
if( COMMAND CMAKE_POLICY )
cmake_policy( SET CMP0012 NEW )
cmake_policy( SET CMP0009 NEW )
endif()
#set output path
set( EXECUTABLE_OUTPUT_PATH /absolute/path )
#generate source files list
file(
GLOB_RECURSE
source_files
src/*pp
)
#create output executable
add_executable( ${ProjectName} ${source_files} )
#look for itk
find_package( ITK REQUIRED )
include( ${ITK_USE_FILE} )
include_directories( ${ITK_INCLUDE_DIRS} )
#try for vtk
if ( ITKVtkGlue_LOADED )
find_package( VTK REQUIRED )
include( ${VTK_USE_FILE} )
endif()
#linker settings
#target_link_libraries( ${ProjectName} ITKCommon ITKIO ITKBasicFilters ITKReview )
target_link_libraries( ${ProjectName} ${ITK_LIBRARIES} )
# compilation options
add_definitions( "-Wall -std=c++11 -g" )
################################################################
#Generate list of header files
include_directories( "/opt/X11/include/" )
include_directories( "/usr/local/include/" )
#add libraries
file(
GLOB_RECURSE
x11Lib_files
/opt/X11/lib/*.dylib
)
target_link_libraries( ${ProjectName} ${x11Lib_files} )
I do not know how to solve this linker problem. Could you please help me?