Compiling on linux

[benfulcher]

headnode:~/nftsim > gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36)
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

headnode:~/nftsim > make
g++  -c src/firing_response.cpp -o obj/firing_response.o
In file included from /usr/include/c++/4.8.2/random:35:0,
                 from src/random.h:13,
                 from src/timeseries.h:15,
                 from src/population.h:23,
                 from src/coupling.h:19,
                 from src/firing_response.h:19,
                 from src/firing_response.cpp:15:
/usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
 #error This file requires compiler and library support for the \
  ^
In file included from src/firing_response.h:17:0,
                 from src/firing_response.cpp:15:
src/array.h:23:9: error: expected nested-name-specifier before ‘size_type’
   using size_type = typename std::vector<T>::size_type;
         ^
src/array.h:23:9: error: using-declaration for non-member at class scope
src/array.h:23:19: error: expected ‘;’ before ‘=’ token
   using size_type = typename std::vector<T>::size_type;
                   ^
src/array.h:23:19: error: expected unqualified-id before ‘=’ token
src/array.h:30:25: error: declaration of ‘operator[]’ as non-function
   inline T* operator[]( size_type index ) const; ///< accesses underlying vector's `operator[]`.
                         ^
src/array.h:30:22: error: expected ‘;’ at end of member declaration
   inline T* operator[]( size_type index ) const; ///< accesses underlying vector's `operator[]`.
                      ^
src/array.h:30:35: error: expected ‘)’ before ‘index’
   inline T* operator[]( size_type index ) const; ///< accesses underlying vector's `operator[]`.
                                   ^
src/array.h:31:3: error: ‘size_type’ does not name a type
   size_type size() const; ///< accesses underlying vector's `size()` member.
   ^
src/array.h: In member function ‘void Array<T>::add(std::vector<T*>)’:
src/array.h:44:8: error: ‘size_type’ was not declared in this scope
   for( size_type i=0; i<t.size(); i++ ) {
        ^
src/array.h:44:18: error: expected ‘;’ before ‘i’
   for( size_type i=0; i<t.size(); i++ ) {
                  ^
src/array.h:44:23: error: ‘i’ was not declared in this scope
   for( size_type i=0; i<t.size(); i++ ) {
                       ^
src/array.h: In member function ‘virtual void Array<T>::step()’:
src/array.h:56:8: error: ‘size_type’ was not declared in this scope
   for( size_type i=0; i<m.size(); i++ ) {
        ^
src/array.h:56:18: error: expected ‘;’ before ‘i’
   for( size_type i=0; i<m.size(); i++ ) {
                  ^
src/array.h:56:23: error: ‘i’ was not declared in this scope
   for( size_type i=0; i<m.size(); i++ ) {
                       ^
src/array.h: In member function ‘virtual void Array<T>::pstep()’:
src/array.h:66:8: error: ‘size_type’ was not declared in this scope
   for( size_type i=0; i<m.size(); i++ ) {
        ^
src/array.h:66:18: error: expected ‘;’ before ‘i’
   for( size_type i=0; i<m.size(); i++ ) {
                  ^
src/array.h:66:23: error: ‘i’ was not declared in this scope
   for( size_type i=0; i<m.size(); i++ ) {
                       ^
src/array.h: At global scope:
src/array.h:72:21: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
 Array<T>::Array() = default;
                     ^
src/array.h: In destructor ‘virtual Array<T>::~Array()’:
src/array.h:76:8: error: ‘size_type’ was not declared in this scope
   for( size_type i=0; i<m.size(); i++ ) {
        ^
src/array.h:76:18: error: expected ‘;’ before ‘i’
   for( size_type i=0; i<m.size(); i++ ) {
                  ^
src/array.h:76:23: error: ‘i’ was not declared in this scope
   for( size_type i=0; i<m.size(); i++ ) {
                       ^
src/array.h: At global scope:
src/array.h:84:26: error: declaration of ‘operator[]’ as non-function
 T* Array<T>::operator[]( size_type index ) const {
                          ^
src/array.h:84:26: error: ‘size_type’ was not declared in this scope
src/array.h:89:47: error: no ‘typename Array<T>::size_type Array<T>::size() const’ member function declared in class ‘Array<T>’
 typename Array<T>::size_type Array<T>::size() const {
                                               ^
In file included from src/firing_response.h:18:0,
                 from src/firing_response.cpp:15:
src/configf.h:24:29: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Configf(const Configf&) = delete;  ///< No copy constructor allowed.
                             ^
src/configf.h:25:15: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Configf() = delete;                ///< No default constructor allowed.
               ^
src/configf.h:26:40: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Configf& operator=(const Configf&) = delete; ///< No copy assignment operator allowed.
                                        ^
src/configf.h:30:12: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   ~Configf() override;
            ^
src/configf.h: In member function ‘void Configf::param(const string&, T&, int)’:
src/configf.h:74:12: error: ‘EXIT_FAILURE’ was not declared in this scope
       exit(EXIT_FAILURE);
            ^
src/configf.h:74:24: error: there are no arguments to ‘exit’ that depend on a template parameter, so a declaration of ‘exit’ must be available [-fpermissive]
       exit(EXIT_FAILURE);
                        ^
src/configf.h:74:24: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
src/configf.h:86:10: error: ‘EXIT_FAILURE’ was not declared in this scope
     exit(EXIT_FAILURE);
          ^
src/configf.h:86:22: error: there are no arguments to ‘exit’ that depend on a template parameter, so a declaration of ‘exit’ must be available [-fpermissive]
     exit(EXIT_FAILURE);
                      ^
src/configf.h: In member function ‘void Configf::param(const string&, T&, int) [with T = std::basic_string<char>; std::string = std::basic_string<char>]’:
src/configf.h:97:12: error: ‘EXIT_FAILURE’ was not declared in this scope
       exit(EXIT_FAILURE);
            ^
src/configf.h:97:24: error: ‘exit’ was not declared in this scope
       exit(EXIT_FAILURE);
                        ^
src/configf.h:101:10: error: ‘EXIT_FAILURE’ was not declared in this scope
     exit(EXIT_FAILURE);
          ^
src/configf.h:101:22: error: ‘exit’ was not declared in this scope
     exit(EXIT_FAILURE);
                      ^
src/configf.h: In member function ‘bool Configf::optional(const string&, T&, int)’:
src/configf.h:111:12: error: ‘EXIT_FAILURE’ was not declared in this scope
       exit(EXIT_FAILURE);
            ^
src/configf.h:111:24: error: there are no arguments to ‘exit’ that depend on a template parameter, so a declaration of ‘exit’ must be available [-fpermissive]
       exit(EXIT_FAILURE);
                        ^
In file included from src/coupling.h:17:0,
                 from src/firing_response.h:19,
                 from src/firing_response.cpp:15:
src/nf.h: At global scope:
src/nf.h:24:9: error: expected nested-name-specifier before ‘size_type’
   using size_type = std::vector<double>::size_type;
         ^
src/nf.h:24:9: error: using-declaration for non-member at class scope
src/nf.h:24:19: error: expected ‘;’ before ‘=’ token
   using size_type = std::vector<double>::size_type;
                   ^
src/nf.h:24:19: error: expected unqualified-id before ‘=’ token
src/nf.h:28:17: error: expected ‘)’ before ‘nodes’
   NF( size_type nodes, double deltat, size_type index );
                 ^
src/nf.h:29:3: error: ‘size_type’ does not name a type
   size_type nodes;  ///< number of nodes in simulation
   ^
src/nf.h:31:3: error: ‘size_type’ does not name a type
   size_type index;  ///< object index within the population/connection model
   ^
src/nf.h:33:10: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   NF() = delete;  ///< No default constructor allowed.
          ^
In file included from src/population.h:20:0,
                 from src/coupling.h:19,
                 from src/firing_response.h:19,
                 from src/firing_response.cpp:15:
src/tau.h:24:3: error: ‘size_type’ does not name a type
   size_type max; ///< if tau is inhomogeneous, == biggest element
   ^
src/tau.h:25:15: error: ‘size_type’ was not declared in this scope
   std::vector<size_type> m; ///< tau values across nodes, size()==1 if homogeneous
               ^
src/tau.h:25:24: error: template argument 1 is invalid
   std::vector<size_type> m; ///< tau values across nodes, size()==1 if homogeneous
                        ^
src/tau.h:25:24: error: template argument 2 is invalid
src/tau.h:27:31: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void init( Configf& configf ) override;
                               ^
src/tau.h:29:21: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Tau(const Tau&) = delete;  // No copy constructor allowed.
                     ^
src/tau.h:31:18: error: expected ‘)’ before ‘nodes’
   Tau( size_type nodes, double deltat, size_type index );
                  ^
src/tau.h:32:8: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   ~Tau() override;
        ^
src/tau.h:33:13: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void step() override;
             ^
In file included from src/population.h:21:0,
                 from src/coupling.h:19,
                 from src/firing_response.h:19,
                 from src/firing_response.cpp:15:
src/propagator.h:29:31: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void init( Configf& configf ) override;
                               ^
src/propagator.h:36:3: error: ‘size_type’ does not name a type
   size_type longside;
   ^
src/propagator.h:40:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
   double range = 0.0;     ///< Characteristic axonal range
                  ^
src/propagator.h:41:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
   double velocity = 0.0;  ///< Mean axonal conduction Speed
                     ^
src/propagator.h:42:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
   double gamma = 0.0;     ///< Damping coefficient
                  ^
src/propagator.h:45:18: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Propagator() = delete;                  // No default constructor allowed.
                  ^
src/propagator.h:46:35: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Propagator(const Propagator&) = delete; // No copy constructor allowed.
                                   ^
src/propagator.h:48:25: error: expected ‘)’ before ‘nodes’
   Propagator( size_type nodes, double deltat, size_type index, Population& prepop,
                         ^
src/propagator.h:50:15: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   ~Propagator() override;
               ^
src/propagator.h:51:13: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void step() override;
             ^
src/propagator.h:54:29: error: ‘size_type’ has not been declared
   inline double operator[]( size_type node ) const;
                             ^
src/propagator.h:55:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void output( Output& output ) const override;
                                 ^
src/propagator.h:58:32: error: declaration of ‘operator[]’ as non-function
 double Propagator::operator[]( size_type node ) const {
                                ^
src/propagator.h:58:32: error: ‘size_type’ was not declared in this scope
In file included from src/timeseries.h:15:0,
                 from src/population.h:23,
                 from src/coupling.h:19,
                 from src/firing_response.h:19,
                 from src/firing_response.cpp:15:
src/random.h:16:10: error: ‘uint_fast64_t’ does not name a type
   static uint_fast64_t id; // Auto-increment the ID of each Random instance to use as the default seed
          ^
src/random.h:18:3: error: ‘mt19937_64’ in namespace ‘std’ does not name a type
   std::mt19937_64 gen; ///< Generator
   ^
src/random.h:19:3: error: ‘normal_distribution’ in namespace ‘std’ does not name a type
   std::normal_distribution<double> dist; ///< Distribution
   ^
src/random.h:22:27: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Random(const Random&) = delete; // No copy constructor allowed.
                           ^
src/random.h:25:33: error: expected ‘)’ before ‘seed’
   explicit Random(uint_fast64_t seed, double mean = 0.0, double std = 1.0);
                                 ^
src/random.h:26:13: error: ‘uint_fast64_t’ has not been declared
   void init(uint_fast64_t seed, double mean, double std);
             ^
In file included from src/population.h:23:0,
                 from src/coupling.h:19,
                 from src/firing_response.h:19,
                 from src/firing_response.cpp:15:
src/timeseries.h:23:9: error: expected nested-name-specifier before ‘series_size_type’
   using series_size_type = std::vector<double>::size_type;
         ^
src/timeseries.h:23:9: error: using-declaration for non-member at class scope
src/timeseries.h:23:26: error: expected ‘;’ before ‘=’ token
   using series_size_type = std::vector<double>::size_type;
                          ^
src/timeseries.h:23:26: error: expected unqualified-id before ‘=’ token
src/timeseries.h:24:31: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void init( Configf& configf ) override;
                               ^
src/timeseries.h:27:15: error: ‘size_type’ was not declared in this scope
   std::vector<size_type> node;
               ^
src/timeseries.h:27:24: error: template argument 1 is invalid
   std::vector<size_type> node;
                        ^
src/timeseries.h:27:24: error: template argument 2 is invalid
src/timeseries.h:28:54: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
   double inf = std::numeric_limits<double>::infinity(); ///< Infinity
                                                      ^
src/timeseries.h:29:14: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
   double t = 0.0;     ///< Current time relative to stimulus onset.
              ^
src/timeseries.h:30:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
   double onset = 0.0; ///< Onset time for the stimulus.
                  ^
src/timeseries.h:31:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
   double duration = inf; ///< Duration of the stimulus.
                     ^
src/timeseries.h:33:35: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Timeseries(const Timeseries&) = delete; // No copy constructor allowed.
                                   ^
src/timeseries.h:34:18: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Timeseries() = delete;                  // No default constructor allowed.
                  ^
src/timeseries.h:36:25: error: expected ‘)’ before ‘nodes’
   Timeseries( size_type nodes, double deltat, size_type index );
                         ^
src/timeseries.h:37:15: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   ~Timeseries() override;
               ^
src/timeseries.h:38:13: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void step() override;
             ^
src/timeseries.h:45:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double mean = 0.0; ///<
                   ^
src/timeseries.h:46:21: error: expected ‘)’ before ‘nodes’
     Const(size_type nodes, double deltat, size_type index) : Timeseries(nodes, deltat, index) {}
                     ^
src/timeseries.h:47:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void init( Configf& configf ) override;
                                 ^
src/timeseries.h:48:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void fire( std::vector<double>& Q ) const override;
                                         ^
src/timeseries.h:52:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double amp = 0.0;    ///< Amplitude of the pulse.
                  ^
src/timeseries.h:53:20: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double width = 0.0;  ///< Width of the pulse [s].
                    ^
src/timeseries.h:54:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double period = 0.0; ///< Time between the start of each pulse [s].
                     ^
src/timeseries.h:55:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double pulses = 0.0; ///< Maximum number of pulses.
                     ^
src/timeseries.h:56:25: error: expected ‘)’ before ‘nodes’
     PulseRect(size_type nodes, double deltat, size_type index) : Timeseries(nodes, deltat, index) {}
                         ^
src/timeseries.h:57:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void init( Configf& configf ) override;
                                 ^
src/timeseries.h:58:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void fire( std::vector<double>& Q ) const override;
                                         ^
src/timeseries.h:62:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double amp = 0.0;    ///< Amplitude of the pulse.
                  ^
src/timeseries.h:63:20: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double width = 0.0;  ///< Width of the pulse [s], wavelength of sine.
                    ^
src/timeseries.h:64:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double period = 0.0; ///< Time between the start of each pulse [s].
                     ^
src/timeseries.h:65:20: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double phase = 0.0;  ///< Phase of the sine wave in [degrees].
                    ^
src/timeseries.h:66:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double pulses = 0.0; ///< Maximum number of pulses.
                     ^
src/timeseries.h:67:25: error: expected ‘)’ before ‘nodes’
     PulseSine(size_type nodes, double deltat, size_type index) : Timeseries(nodes, deltat, index) {}
                         ^
src/timeseries.h:68:16: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     ~PulseSine() override = default;
                ^
src/timeseries.h:68:29: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
     ~PulseSine() override = default;
                             ^
src/timeseries.h:69:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void init( Configf& configf ) override;
                                 ^
src/timeseries.h:70:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void fire( std::vector<double>& Q ) const override;
                                         ^
src/timeseries.h:74:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double amp = 0.0;    ///< Amplitude of the pulse.
                  ^
src/timeseries.h:75:20: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double width = 0.0;  ///< Width of the pulse [s].
                    ^
src/timeseries.h:76:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double period = 0.0; ///< Time between the start of each pulse [s].
                     ^
src/timeseries.h:77:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double pulses = 0.0; ///< Maximum number of pulses.
                     ^
src/timeseries.h:78:20: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double sigma = 0.03125; ///< Width of transition.
                    ^
src/timeseries.h:79:28: error: expected ‘)’ before ‘nodes’
     PulseSigmoid(size_type nodes, double deltat, size_type index) : Timeseries(nodes, deltat, index) {}
                            ^
src/timeseries.h:80:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void init( Configf& configf ) override;
                                 ^
src/timeseries.h:81:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void fire( std::vector<double>& Q ) const override;
                                         ^
src/timeseries.h:83:30: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double first_pulse_mid = 0.0; ///< Mid-point of the first pulse.
                              ^
src/timeseries.h:84:12: error: ‘constexpr’ does not name a type
     static constexpr double pi_on_sqrt3 = 1.813799364234217836866491779801435768604278564; //M_PI / std::sqrt(3.0);
            ^
src/timeseries.h:84:12: note: C++11 ‘constexpr’ only available with -std=c++11 or -std=gnu++11
src/timeseries.h:85:5: error: ‘size_type’ does not name a type
     size_type pulse_count = 0; ///< Number of pulses, min of pulses and number of pulses that fit in duration.
     ^
src/timeseries.h:89:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double amp = 0.0;   ///< Amplitude of the sine wave.
                  ^
src/timeseries.h:90:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double freq = 0.0;  ///< Frequency of the sine wave [s^-1].
                   ^
src/timeseries.h:91:20: error: expected ‘)’ before ‘nodes’
     Sine(size_type nodes, double deltat, size_type index) : Timeseries(nodes, deltat, index) {}
                    ^
src/timeseries.h:92:11: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     ~Sine() override = default;
           ^
src/timeseries.h:92:24: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
     ~Sine() override = default;
                        ^
src/timeseries.h:93:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void init( Configf& configf ) override;
                                 ^
src/timeseries.h:94:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void fire( std::vector<double>& Q ) const override;
                                         ^
src/timeseries.h:98:5: error: ‘uint_fast64_t’ does not name a type
     uint_fast64_t seed = 0; ///<
     ^
src/timeseries.h:99:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double stddev = 0.0;    ///<
                     ^
src/timeseries.h:100:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double asd = 0.0;       ///< Amplitude spectral density.
                  ^
src/timeseries.h:101:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double mean = 0.0;      ///<
                   ^
src/timeseries.h:102:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double deltax = 0.0;    ///<
                     ^
src/timeseries.h:104:21: error: expected ‘)’ before ‘nodes’
     White(size_type nodes, double deltat, size_type index) : Timeseries(nodes, deltat, index) {}
                     ^
src/timeseries.h:105:12: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     ~White() override {
            ^
src/timeseries.h:108:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void init( Configf& configf ) override;
                                 ^
src/timeseries.h:109:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void fire( std::vector<double>& Q ) const override;
                                         ^
src/timeseries.h:113:5: error: ‘uint_fast64_t’ does not name a type
     uint_fast64_t seed = 0; ///<
     ^
src/timeseries.h:114:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double stddev = 0.0;      ///<
                     ^
src/timeseries.h:115:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double asd    = 0.0;      ///< Amplitude spectral density.
                     ^
src/timeseries.h:116:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double mean   = 0.0;      ///<
                     ^
src/timeseries.h:118:29: error: expected ‘)’ before ‘nodes’
     WhiteCoherent(size_type nodes, double deltat, size_type index) : Timeseries(nodes, deltat, index) {}
                             ^
src/timeseries.h:119:20: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     ~WhiteCoherent() override {
                    ^
src/timeseries.h:122:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void init( Configf& configf ) override;
                                 ^
src/timeseries.h:123:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void fire( std::vector<double>& Q ) const override;
                                         ^
src/timeseries.h:127:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double n20w = 0.0;  ///< Width of the negative amplitude response at around 20 ms.
                   ^
src/timeseries.h:128:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double n20h = 0.0;  ///< Height of the negative amplitude response at around 20 ms.
                   ^
src/timeseries.h:129:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double p25w = 0.0;  ///< Width of the positive amplitude response at around 25 ms.
                   ^
src/timeseries.h:130:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double p25h = 0.0;  ///< Height of the positive amplitude response at around 25 ms.
                   ^
src/timeseries.h:131:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double tmsw = 0.0;  ///< Width of the Transcranial Magnetic Stimulation(TMS).
                   ^
src/timeseries.h:132:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double tmsh = 0.0;  ///< Height of the Transcranial Magnetic Stimulation(TMS).
                   ^
src/timeseries.h:133:20: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double t_mns = 0.0; ///<
                    ^
src/timeseries.h:134:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double isi = 0.0;   ///< Inter-Stimulus-Interval.
                  ^
src/timeseries.h:135:19: error: expected ‘)’ before ‘nodes’
     PAS(size_type nodes, double deltat, size_type index) : Timeseries(nodes, deltat, index) {}
                   ^
src/timeseries.h:136:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void init( Configf& configf ) override;
                                 ^
src/timeseries.h:137:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void fire( std::vector<double>& Q ) const override;
                                         ^
src/timeseries.h:141:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double amp = 0.0;    ///<
                  ^
src/timeseries.h:142:20: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double width = 0.0;  ///<
                    ^
src/timeseries.h:143:21: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double bursts = 0.0; ///<
                     ^
src/timeseries.h:144:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double freq = 0.0;   ///<
                   ^
src/timeseries.h:145:31: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double oscillation_freq = 0.0; ///<
                               ^
src/timeseries.h:146:17: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double on = 0.0;    ///<
                 ^
src/timeseries.h:147:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double off = 0.0;   ///<
                  ^
src/timeseries.h:148:20: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
     double total = 0.0; ///<
                    ^
src/timeseries.h:149:21: error: expected ‘)’ before ‘nodes’
     Burst(size_type nodes, double deltat, size_type index) : Timeseries(nodes, deltat, index) {}
                     ^
src/timeseries.h:150:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void init( Configf& configf ) override;
                                 ^
src/timeseries.h:151:41: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
     void fire( std::vector<double>& Q ) const override;
                                         ^
In file included from src/coupling.h:19:0,
                 from src/firing_response.h:19,
                 from src/firing_response.cpp:15:
src/population.h:36:19: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
   double length = 0.0; ///< spatial length
                   ^
src/population.h:37:18: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
   double qinit = 0.0;  ///< initial firing rate
                  ^
src/population.h:39:31: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void init( Configf& configf ) override;
                               ^
src/population.h:42:18: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Population() = delete;                   // No default constructor allowed.
                  ^
src/population.h:43:36: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Population(const Population& ) = delete; // No copy constructor allowed.
                                    ^
src/population.h:45:25: error: expected ‘)’ before ‘nodes’
   Population( size_type nodes, double deltat, size_type index );
                         ^
src/population.h:46:15: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   ~Population() override;
               ^
src/population.h:47:13: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void step() override;
             ^
src/population.h:51:29: error: ‘size_type’ has not been declared
   inline double operator[]( size_type node ) const;
                             ^
src/population.h:56:30: error: ‘size_type’ has not been declared
   virtual void add2Dendrite( size_type index, const Propagator& prepropag,
                              ^
src/population.h:59:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void output( Output& output ) const override;
                                 ^
src/population.h:60:32: error: ‘size_type’ has not been declared
   virtual void outputDendrite( size_type index, Output& output ) const;
                                ^
In file included from src/firing_response.h:19:0,
                 from src/firing_response.cpp:15:
src/coupling.h:27:31: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void init( Configf& configf ) override;
                               ^
src/coupling.h:35:13: warning: non-static data member initializers only available with -std=c++11 or -std=gnu++11 [enabled by default]
   int pos = 0;
             ^
src/coupling.h:37:16: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Coupling() = delete;                ///< No default constructor allowed.
                ^
src/coupling.h:38:31: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   Coupling(const Coupling&) = delete; ///< No copy constructor allowed.
                               ^
src/coupling.h:40:23: error: expected ‘)’ before ‘nodes’
   Coupling( size_type nodes, double deltat, size_type index,
                       ^
src/coupling.h:42:13: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   ~Coupling() override;
             ^
src/coupling.h:43:13: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void step() override;
             ^
src/coupling.h:45:33: warning: override controls (override/final) only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void output( Output& output ) const override;
                                 ^
src/coupling.h:47:29: error: ‘size_type’ has not been declared
   inline double operator[]( size_type node ) const;
                             ^
src/coupling.h:51:30: error: declaration of ‘operator[]’ as non-function
 double Coupling::operator[]( size_type node ) const {
                              ^
src/coupling.h:51:30: error: ‘size_type’ was not declared in this scope
In file included from src/dendrite.h:19:0,
                 from src/firing_response.h:20,
                 from src/firing_response.cpp:15:
src/de.h:18:7: error: expected nested-name-specifier before ‘vvd_size_type’
 using vvd_size_type = std::vector<std::vector<double>>::size_type;
       ^
src/de.h:18:7: error: ‘vvd_size_type’ has not been declared
src/de.h:18:21: error: expected ‘;’ before ‘=’ token
 using vvd_size_type = std::vector<std::vector<double>>::size_type;
                     ^
src/de.h:18:21: error: expected unqualified-id before ‘=’ token
src/de.h:24:16: error: ‘vvd_size_type’ has not been declared
   void extend( vvd_size_type extension ) {
                ^
src/de.h:32:10: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   DE() = delete;          ///< No default constructor allowed.
          ^
src/de.h:33:19: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   DE(const DE&) = delete; ///< No copy constructor allowed.
                   ^
src/de.h:34:31: warning: defaulted and deleted functions only available with -std=c++11 or -std=gnu++11 [enabled by default]
   void operator=(const DE&) = delete; ///< No copy assignment allowed.
                               ^
src/de.h:36:3: error: ‘vvd_size_type’ does not name a type
   vvd_size_type nodes; ///< number of nodes in the system.
   ^
src/de.h:38:3: error: ‘vvd_size_type’ does not name a type
   vvd_size_type ndim;  ///< dimension of system == y.size()
   ^
src/de.h:41:21: error: expected ‘)’ before ‘nodes’
   DE( vvd_size_type nodes, double deltat, vvd_size_type ndim )
                     ^
src/firing_response.cpp:125:1: error: expected ‘}’ at end of input
 }
 ^
In file included from src/dendrite.h:19:0,
                 from src/firing_response.h:20,
                 from src/firing_response.cpp:15:
src/de.h: In member function ‘void DE::extend(int)’:
src/de.h:25:5: error: ‘ndim’ was not declared in this scope
     ndim += extension;
     ^
src/de.h:27:10: error: ‘vvd_size_type’ was not declared in this scope
     for( vvd_size_type i=0; i<ndim; i++ ) {
          ^
src/de.h:27:24: error: expected ‘;’ before ‘i’
     for( vvd_size_type i=0; i<ndim; i++ ) {
                        ^
src/de.h:27:29: error: ‘i’ was not declared in this scope
     for( vvd_size_type i=0; i<ndim; i++ ) {
                             ^
src/de.h:28:27: error: ‘nodes’ was not declared in this scope
       variables[i].resize(nodes,0);
                           ^
src/de.h: At global scope:
src/de.h:30:3: error: expected unqualified-id at end of input
   }
   ^
make: *** [obj/firing_response.o] Error 1

[pausz]

Hi Ben,

You should try using the Makefile in the repository as it has all the appropriate flags to compile the code on Linux distributions.

The following line in the error message:

/usr/include/c++/4.8.2/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support is currently experimental, and must be enabled with the -std=c++11 or -std=gnu++11 compiler options.

means that the compiler does not know it has to use features of the C++11 standard.

From gcc 5.1.0 onward, the default standard changed from C90 to C11, thus a compiler like gcc 7.2.0 (on Artemis) would not produce errors. However for gcc 4.8.5, you need to explicitly pass the flag -std=c++11 as we do in line 33 in the Makefile.

Btw, I successfully compiled the code with gcc 4.8.5 on headnode using nftsim's makefile.

[benfulcher]

@pausz You're completely right! When I changed the flags to those in the makefile it worked no problem. I was assuming pull upstream was giving me the latest, but it's keeping the changes in my fork, which are messing things up on this particular cluster. Sorry to be annoying :( Thanks so much for your detailed help 😅