I am trying to import a python extension coded in c++ with boost. While I experienced some problems compiling the extension using cmake, I managed to do so linked to the boost_python27 library. I then used pythons distutils to install the extension into the python framework.
However, when I try to import the module I get the following error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
ImportError: dlopen(./tools.so, 2): Library not loaded: @rpath/libboost_python.dylib
Referenced from: /Users/DaniBook/CLionProjects/Uebung1/cmake-build-debug/tools.so
Reason: image not found
I tried everything I found on the internet including reinstalling boost and recompiling using the distutils extensions etc. to get it to work. Can anybody offer some help on this and might also answer what this ominous image thats missing is?
tools.h
#ifndef UEBUNG1_TOOLS_H
#define UEBUNG1_TOOLS_H
#include <string>
#include <vector>
#include <map>
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
using namespace std;
vector<string> *product(string alphabet, int repeats);
vector<string> *product(vector<string> pools);
vector<string>* hammdist(string &pattern, int distance);
#endif //UEBUNG1_TOOLS_H
tools.cpp
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
#include "tools.h"
#include <vector>
#include <string>
#include <map>
using namespace std;
vector<string> *product(string alphabet, int repeats) {
//initializing vector
auto *results = new vector<string>();
for(auto character : alphabet) {
string tmpstr;
tmpstr = character;
results->push_back(tmpstr);
}
//cartesian product generation
for(int i = 1; i < repeats; i++) {
vector<string> tmp = *results;
results->clear();
//iterating over temporary list adding elements from pool to each contained string
for(auto &it : tmp) {
for(auto &character : alphabet) {
results->push_back(it + character);
}
}
}
return results;
}
vector<string> product(vector<string> pools) {
//initializing vector
auto *results = new vector<string>();
for(auto character : pools[0]) {
string tmpstr;
tmpstr = character;
results->push_back(tmpstr);
}
//removing the first pool container
pools.erase(pools.begin());
//cartesian product generation
for(const auto &pool : pools) {
vector<string> tmp = *results;
results->clear();
//iterating over temporary list adding elements from pool to each contained string
for(auto &it : tmp) {
for(auto character : pool) {
results->push_back(it + character);
}
}
}
return results;
}
vector<string>* hammdist(string &pattern, int distance) {
map<char, string> possibles = {
{'A', "CGT"},
{'C', "AGT"},
{'G', "ACT"},
{'T', "ACG"}
};
auto *results = new vector<string>();
vector<string> *masks = product("01", pattern.size());
for(auto &mask : *masks) {
auto *permute = new vector<string>();
auto *tmp = new vector<string>();
if(count(mask.begin(), mask.end(), '1') == distance) {
for(int i = 0; i < pattern.size(); i++) {
if(mask[i] != '1') {
string tmpstr;
tmpstr = pattern[i];
tmp->push_back(tmpstr);
}
else {
tmp->push_back(possibles[pattern[i]]);
}
}
permute = product(*tmp);
results->insert(results->end(), permute->begin(), permute->end());
}
delete permute;
delete tmp;
}
return results;
}
/*
initializing function pointers in order to tell boost that we have
overloaded functions to expose to python
*/
vector<string> *(*product1)(string, int) = &product;
vector<string> *(*product2)(vector<string> pools) = &product;
//include all functions that are used by the function to expose to the BOOST_PYTHON_MODULE call
using namespace boost::python;
BOOST_PYTHON_MODULE(tools) {
//telling boost_python that we have overloaded functions which need to be called in the respective situations
//return_value_policy<manage_new_objects> is required in order for the interface to handle the new invocation and the returned pointer
def("product", product1, return_value_policy<manage_new_object>());
def("product", product2, return_value_policy<manage_new_object>());
def("hammdist", hammdist, return_value_policy<manage_new_object>());
//vector_indexing_suite handles the wrapping of vector member functions
//enables handling vector in a pythonic way when using in python
class_<std::vector<string>>("string_vector")
.def(vector_indexing_suite<std::vector<string>>());
}
CMakeLists.txt
make_minimum_required(VERSION 3.12)
project(tools)
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_INCLUDE_CURRENT_DIR ON)
if(APPLE)
set(CMAKE_SHARED_LIBRARY_SUFFIX ".so")
endif(APPLE)
find_package(PythonLibs 2.7 REQUIRED)
include_directories(${PYTHON_INCLUDE_DIRS})
set(PROJECT_SOURCE_DIR src/)
include_directories(${PROJECT_SOURCE_DIR})
set(BOOST_ROOT "/Users/DaniBook/miniconda3/pkgs/boost-1.66.0-py27_1")
set(BOOST_LIBRARYDIR "/Users/DaniBook/miniconda3/pkgs/boost-1.66.0-27_1/lib")
find_package(Boost COMPONENTS python REQUIRED)
include_directories(${Boost_INCLUDE_DIRS})
add_library(tools SHARED src/tools.cpp src/tools.h)
target_link_libraries(tools ${Boost_LIBRARIES} ${PYTHON_LIBRARIES})
set_target_properties(tools PROPERTIES PREFIX "")
setup.py
from distutils.core import setup
setup(
name = 'tools',
version = '0.1',
py_modules = ['tools'])
