Hi, Pulled this from a larger application to isolate to the problem: -d ./tmp or -d "./tmp" doesn't go to directory string but is with the positionals: #include <stdlib.h> #include <iostream> #include <exception> #include <string> #include <cstring> #include <memory> #include <fstream> #include "boost/program_options.hpp" int main(int argc, char** argv) { try { boost::program_options::positional_options_description p; p.add("input-file", -1); std::string directory = "./"; boost::program_options::options_description visible("Allowed options"); visible.add_options() ("input-file", boost::program_options::value<std::vector<std::string>>(), "input files can be *.xml, *.pdb, *.mol2, *.mtz, *.cif, *.csv, and *.sdf. Csv and sdf formats are for NMR calculations. csv lists the atoms for which the shifts will be computed. 1st line containts the Header: \"Chain\",\"Residue ID\",\"Sequence\",\"Atom Name\",\"Unbound ppm\",\"Bound ppm\". Then atoms may be listed i.e \"A\",\"MET\",231,\"CE\",10.30,10.50. sdf file contains the ligands for a CSP calculation. ") ("directory,d", boost::program_options::value<std::string>(&directory)->implicit_value("./"), "Directory for publishing output.") ; boost::program_options::options_description all("Allowed options"); all.add(visible);//.add(hidden); boost::program_options::variables_map vm; boost::program_options::store(boost::program_options::command_line_parser(argc, argv).options(all).positional(p).run(), vm); boost::program_options::notify(vm); std::vector<std::string> fileList = vm["input-file"].as < std::vector < std::string >> (); for (unsigned int fileListIndex = 0; fileListIndex < fileList.size(); fileListIndex++) { std::cout<<" "<<fileList[fileListIndex]<<" "<<std::endl; } } catch (std::exception& e) { std::cout << e.what() << std::endl; } return 0; } Built with g++ 4.9.0 on Linux frodo.quantumbioinc.com 2.6.32-573.7.1.el6.centos.plus.x86_64 #1 SMP Wed Sep 23 03:02:55 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux g++ -fPIE -std=c++11 -I${BOOST_HOME}/include -Wl,--allow-multiple-definition -MT main.o -MMD -MP -O3 -c -o main.o main.cpp g++ -pie -Wl,--allow-multiple-definition -o main main.o -L${BOOST_HOME}/lib -lboost_program_options -lc -lm -lpthread -lz -lstdc++ -ldl -lrt And run as ./main 2-aminoethanol.pdb -d ./tmp which results in 2-aminoethanol.pdb ./tmp This code had been working with 1_57_0. Some change in the API I need to adjust for?