Symbol(s) not found for architecture x86_64 - Cmake - Mac sierra - c++

Question

Recently I have started a new project in C++. The problem is, when I try to compile it I get a linking error. I spent the whole day today trying to debug it, but I did not really find a good solution anywhere. If someone could help with it it would be amazing. I am using a Mac Sierra.
parsing/methylation.h
#ifndef EPIRL_METHYLATION_H
#define EPIRL_METHYLATION_H
#include <stdio.h>
#include <iostream>
#include <fstream>
#include <vector>
#include <sstream>
using namespace std;
namespace methylation {
struct MethLine {
string chr;
int coord;
char strand;
int methylated;
int un_methylated;
string context;
string tag;
};
string calculateMethylationByContext(
MethLine m_input[], int length,
int window_start, int window_end, int threshold);
void calculateMethylation(
const istream &methylation_stream,
const istream &coordinate_stream,
const ostream &output_stream
);
}
#endif //EPIRL_METHYLATION_H
parsing/methylation.cpp
#include "methylation.h"
namespace methylation {
string calculateMethylationByContext(
MethLine m_input[], int length,
int window_start, int window_end, int threshold) {
// rest of the code ...
}
}
main.cpp
#include <iostream>
#include <fstream>
#include "parsing/methylation.h"
using namespace std;
int main(int argc, char **argv) {
if (argc != 4) {
cout << "Invalid number of arguments..." << endl;
return 1;
}
char *methylation_file = argv[1];
char *coordinate_file = argv[2];
char *output_file = argv[3];
ifstream methylation_file_stream(methylation_file, ios::binary);
ifstream coordinate_file_stream(coordinate_file, ios::binary);
ofstream output_file_stream(output_file, ios::binary);
methylation::calculateMethylation(methylation_file_stream,
coordinate_file_stream, output_file_stream);
methylation_file_stream.close();
coordinate_file_stream.close();
output_file_stream.close();
return 0;
}
I use CLion for my coding. When I try to build it, my cmake command works fine, but when I then click 'make' I get the following error:
Undefined symbols for architecture x86_64:
"methylation::calculateMethylation(std::__1::basic_istream<char, std::__1::char_traits<char> > const&, std::__1::basic_istream<char, std::__1::char_traits<char> > const&, std::__1::basic_ostream<char, std::__1::char_traits<char> > const&)", referenced from:
_main 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)
make[3]: *** [src] Error 1
make[2]: *** [CMakeFiles/src.dir/all] Error 2
make[1]: *** [CMakeFiles/src.dir/rule] Error 2
make: *** [src] Error 2
my CMakeLists.txt file looks like the following:
cmake_minimum_required(VERSION 3.6)
project(src)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
set(SOURCE_FILES
parsing/methylation.cpp
parsing/methylation.h
main.cpp)
add_executable(src ${SOURCE_FILES})
When I run the cmake command, my output is this:
-- The C compiler identification is AppleClang 8.0.0.8000042
-- The CXX compiler identification is AppleClang 8.0.0.8000042
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done
-- Generating done
-- Build files have been written to: /Users/sztankatt/Documents/University/PartIII/Project/epiRL/src

Answer 1

Your CMakeLists.txt is fine.
As #thomas-matthews #tsyvarev #nos pointed out in their comments, your example code is missing the definition/implementation of methylation::calculateMethylation(). What you're seeing is the expected failure with Apple/clang in this situation.
❯ make
[ 33%] Building CXX object CMakeFiles/src.dir/parsing/methylation.cpp.o
/Users/nega/foo/parsing/methylation.cpp:8:5: warning: control reaches end of non-void function [-Wreturn-type]
}
^
1 warning generated.
[ 66%] Building CXX object CMakeFiles/src.dir/main.cpp.o
[100%] Linking CXX executable src
Undefined symbols for architecture x86_64:
"methylation::calculateMethylation(std::__1::basic_istream<char, std::__1::char_traits<char> > const&, std::__1::basic_istream<char, std::__1::char_traits<char> > const&, std::__1::basic_ostream<char, std::__1::char_traits<char> > const&)", referenced from:
_main 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)
make[2]: *** [src] Error 1
make[1]: *** [CMakeFiles/src.dir/all] Error 2
make: *** [all] Error 2
Adding a dummy implementation, or commenting out the call in your main.cpp, will allow make to complete successfully.
Assuming you have a correct implementation
Let's assume you do have an implementation of methylation::calculateMethylation() in your code (maybe in another file). The fist step in debugging build errors in CMake generated Makefiles is to run with the make variable VERBOSE set to a true value, ie: make VERBOSE=1.
❯ make VERBOSE=1
/usr/local/Cellar/cmake/3.7.0/bin/cmake -H/Users/nega/foo -B/Users/nega/foo/build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/Cellar/cmake/3.7.0/bin/cmake -E cmake_progress_start /Users/nega/foo/build/CMakeFiles /Users/nega/foo/build/CMakeFiles/progress.marks
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/Makefile2 all
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/src.dir/build.make CMakeFiles/src.dir/depend
cd /Users/nega/foo/build && /usr/local/Cellar/cmake/3.7.0/bin/cmake -E cmake_depends "Unix Makefiles" /Users/nega/foo /Users/nega/foo /Users/nega/foo/build /Users/nega/foo/build /Users/nega/foo/build/CMakeFiles/src.dir/DependInfo.cmake --color=
/Applications/Xcode.app/Contents/Developer/usr/bin/make -f CMakeFiles/src.dir/build.make CMakeFiles/src.dir/build
[ 33%] Building CXX object CMakeFiles/src.dir/parsing/methylation.cpp.o
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=gnu++11 -o CMakeFiles/src.dir/parsing/methylation.cpp.o -c /Users/nega/foo/parsing/methylation.cpp
/Users/nega/foo/parsing/methylation.cpp:8:5: warning: control reaches end of non-void function [-Wreturn-type]
}
^
1 warning generated.
[ 66%] Building CXX object CMakeFiles/src.dir/main.cpp.o
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -std=gnu++11 -o CMakeFiles/src.dir/main.cpp.o -c /Users/nega/foo/main.cpp
[100%] Linking CXX executable src
/usr/local/Cellar/cmake/3.7.0/bin/cmake -E cmake_link_script CMakeFiles/src.dir/link.txt --verbose=1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/c++ -Wl,-search_paths_first -Wl,-headerpad_max_install_names CMakeFiles/src.dir/parsing/methylation.cpp.o CMakeFiles/src.dir/main.cpp.o -o src
Undefined symbols for architecture x86_64:
"methylation::calculateMethylation(std::__1::basic_istream<char, std::__1::char_traits<char> > const&, std::__1::basic_istream<char, std::__1::char_traits<char> > const&, std::__1::basic_ostream<char, std::__1::char_traits<char> > const&)", referenced from:
_main 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)
make[2]: *** [src] Error 1
make[1]: *** [CMakeFiles/src.dir/all] Error 2
make: *** [all] Error 2
Now you can look at the link step and see if you're missing items; maybe a library, or an object file. If so, now you know to go back and add it to your CMakeLists.txt
Summary
The first step in debugging unexpected build failures with CMake generated Makefiles is to run:
❯ make VERBOSE=1
This will give you insight into what CMake is doing behind the scenes.

Answer 2

Double check which compiler is automatically detected by CMAKE.
Can you post, what CMAKE tells you when you initially run CMAKE?
This may be a hint for your problem, too