fix new warnings and escape apply namespace

- `std::apply` is part of C++17 and the compiler wants to use it because
of ADL. Thus it is now necessary to escape it as `::apply`.
- remove some `using namespace std` remaining in the sources.
- fix simple warnings.

edo/application/cmaes/main.cpp

@@ -84,7 +84,7 @@ int main(int ac, char** av)
     eoPop< RealVec >& pop = do_make_pop(parser, state, *init);
 
     // (2) First evaluation before starting the research algorithm
-    apply(eval, pop);
+    ::apply(eval, pop);
 
     // Prepare bounder class to set bounds of sampling.
     // This is used by edoSampler.

edo/application/eda/main.cpp

@@ -87,7 +87,7 @@ int main(int ac, char** av)
     eoPop< EOT >& pop = do_make_pop(parser, state, *init);
 
     // (2) First evaluation before starting the research algorithm
-    apply(eval, pop);
+    ::apply(eval, pop);
 
     // Prepare bounder class to set bounds of sampling.
     // This is used by edoSampler.

edo/src/edoDistribReset.h

@@ -52,7 +52,7 @@ class edoDistribReset : public eoAlgoReset<typename D::EOType>
             _distrib(distrib)
         { }
 
-        virtual void operator()( eoPop<EOType>& pop )
+        virtual void operator()( eoPop<EOType>& /*pop*/ )
         {
             if(_has_dim) {
                 _distrib.reset(_dim);

eo/doc/eo.doxyfile.cmake

@@ -1339,7 +1339,7 @@ HIDE_UNDOC_RELATIONS   = YES
 # toolkit from AT&T and Lucent Bell Labs. The other options in this section
 # have no effect if this option is set to NO (the default)
 
-HAVE_DOT               = NO
+HAVE_DOT               = YES
 
 # By default doxygen will write a font called FreeSans.ttf to the output
 # directory and reference it in all dot files that doxygen generates. This

eo/src/eoInitializer.h

@@ -105,10 +105,10 @@ public:
     virtual void operator() ()
     {
         eoPop<POT> empty_pop;
-        apply(proc, pop);
+        ::apply(proc, pop);
         procPara(empty_pop, pop);
-        apply < POT > (initVelo, pop);
+        ::apply < POT > (initVelo, pop);
-        apply < POT > (initBest, pop);
+        ::apply < POT > (initBest, pop);
         topology.setup(pop);
     }
 

eo/src/eoTopology.h

@@ -80,7 +80,7 @@ public:
     /**
      * Prints the neighborhoods contained in the topology.
      */
-    virtual void printOn() = 0;
+    // virtual void printOn() = 0; // Already defined in eoPop
 };
 
 

eo/src/utils/eoFileMonitor.cpp

@@ -12,7 +12,7 @@
 #include "eoParam.h"
 #include "../eoExceptions.h"
 
-using namespace std;
+// using namespace std;
 
 void eoFileMonitor::printHeader(std::ostream& os)
 {
@@ -33,7 +33,7 @@ void eoFileMonitor::printHeader(std::ostream& os)
 void eoFileMonitor::printHeader()
 {
     // create file
-    ofstream os(filename.c_str());
+    std::ofstream os(filename.c_str());
 
     if (!os)
     {
@@ -46,11 +46,11 @@ void eoFileMonitor::printHeader()
 
 eoMonitor& eoFileMonitor::operator()(void)
 {
-    ofstream os(filename.c_str(),
+    std::ofstream os(filename.c_str(),
         overwrite ?
-            ios_base::out|ios_base::trunc // truncate
+            std::ios_base::out|std::ios_base::trunc // truncate
             :
-            ios_base::out|ios_base::app   // append
+            std::ios_base::out|std::ios_base::app   // append
         );
 
     if (!os)

eo/src/utils/eoIntBounds.cpp

@@ -81,7 +81,7 @@ eoIntBounds* eoGeneralIntBounds::getBoundsFromString(std::string _value)
         }
 
       // now create the embedded eoIntBounds object
-      eoIntBounds * locBound;
+      eoIntBounds * locBound = nullptr;
       if (minBounded && maxBounded)
         {
           if (maxBound <= minBound)

eo/src/utils/eoParser.cpp

@@ -42,7 +42,7 @@ Authors:
 #include "eoLogger.h"
 
 
-using namespace std;
+// using namespace std;
 
 std::ostream& printSectionHeader(std::ostream& os, std::string section)
 {
@@ -76,8 +76,8 @@ eoParameterLoader::~eoParameterLoader()
     }
 }
 
-eoParser::eoParser ( unsigned _argc, char **_argv , string _programDescription,
+eoParser::eoParser ( unsigned _argc, char **_argv , std::string _programDescription,
-                     string /*_lFileParamName*/, char /*_shortHand*/) :
+                     std::string /*_lFileParamName*/, char /*_shortHand*/) :
     programName(_argv[0]),
     programDescription( _programDescription),
     needHelpMessage( false ),
@@ -92,11 +92,11 @@ eoParser::eoParser ( unsigned _argc, char **_argv , string _programDescription,
         if(_argv[i][0] == '@')
         { // read response file
             char *pts = _argv[i]+1; // yes a char*, sorry :-)
-            ifstream ifs (pts);
+            std::ifstream ifs (pts);
             ifs.peek(); // check if it exists
             if (!ifs)
             {
-                // string msg = string("Could not open response file: ") + pts;
+                // std::string msg = std::string("Could not open response file: ") + pts;
                 throw eoFileError(pts);
             }
             // read  - will be overwritten by command-line
@@ -105,7 +105,7 @@ eoParser::eoParser ( unsigned _argc, char **_argv , string _programDescription,
         }
     }
     // now read arguments on command-line
-    stringstream stream;
+    std::stringstream stream;
     for (i = 1; i < _argc; ++i)
     {
         stream << _argv[i] << '\n';
@@ -159,24 +159,24 @@ void eoParser::doRegisterParam(eoParam& param)
 {
     if (param.required() && !isItThere(param))
     {
-        string msg = "Required parameter: " + param.longName() + " missing";
+        std::string msg = "Required parameter: " + param.longName() + " missing";
         needHelpMessage = true;
         messages.push_back(msg);
     }
-    pair<bool, string> value = getValue(param);
+    std::pair<bool, std::string> value = getValue(param);
     if (value.first)
     {
         param.setValue(value.second);
     }
 }
 
-pair<bool, string> eoParser::getValue(eoParam& _param) const
+std::pair<bool, std::string> eoParser::getValue(eoParam& _param) const
 {
-    pair<bool, string> result(false, "");
+    std::pair<bool, std::string> result(false, "");
 
     if (_param.shortName() != 0)
     {
-        map<char, string>::const_iterator it = shortNameMap.find(_param.shortName());
+        std::map<char, std::string>::const_iterator it = shortNameMap.find(_param.shortName());
         if (it != shortNameMap.end())
         {
             result.second = it->second;
@@ -184,7 +184,7 @@ pair<bool, string> eoParser::getValue(eoParam& _param) const
             return result;
         }
     }
-    map<string, string>::const_iterator it = longNameMap.find(_param.longName());
+    std::map<std::string, std::string>::const_iterator it = longNameMap.find(_param.longName());
     if (it != longNameMap.end())
     {
         result.second = it->second;
@@ -205,21 +205,21 @@ void eoParser::updateParameters()
   }
 }
 
-void eoParser::readFrom(istream& is)
+void eoParser::readFrom(std::istream& is)
 {
-    string str;
+    std::string str;
     // we must avoid processing \section{xxx} if xxx is NOT "Parser"
     bool processing = true;
     while (is >> str)
     {
-        if (str.find(string("\\section{"))==0) // found section begin
+        if (str.find(std::string("\\section{"))==0) // found section begin
-            processing = (str.find(string("Parser"))<str.size());
+            processing = (str.find(std::string("Parser"))<str.size());
 
         if (processing)		// right \section (or no \section at all)
         {
             if (str[0] == '#')
             { // skip the rest of the line
-                string tempStr;
+                std::string tempStr;
                 getline(is, tempStr);
             }
             if (str[0] == '-')
@@ -233,35 +233,35 @@ void eoParser::readFrom(istream& is)
 
                 if (str[1] == '-') // two consecutive dashes
                 {
-                    string::iterator equalLocation = find(str.begin() + 2, str.end(), '=');
+                    std::string::iterator equalLocation = find(str.begin() + 2, str.end(), '=');
-                    string value;
+                    std::string value;
 
                     if (equalLocation == str.end())
-                    { //! @todo it should be the next string
+                    { //! @todo it should be the next std::string
                         value = "";
                     }
                     else
                     {
-                        value = string(equalLocation + 1, str.end());
+                        value = std::string(equalLocation + 1, str.end());
                     }
 
-                    string name(str.begin() + 2, equalLocation);
+                    std::string name(str.begin() + 2, equalLocation);
                     longNameMap[name] = value;
                 }
                 else // it should be a char
                 {
-                    string value = "1"; // flags do not need a special
+                    std::string value = "1"; // flags do not need a special
 
                     if (str.size() >= 2)
                     {
                         if (str[2] == '=')
                         {
                             if (str.size() >= 3)
-                                value = string(str.begin() + 3, str.end());
+                                value = std::string(str.begin() + 3, str.end());
                         }
                         else
                         {
-                            value = string(str.begin() + 2, str.end());
+                            value = std::string(str.begin() + 2, str.end());
                         }
                     }
 
@@ -274,7 +274,7 @@ void eoParser::readFrom(istream& is)
     updateParameters();
 }
 
-void eoParser::printOn(ostream& os) const
+void eoParser::printOn(std::ostream& os) const
 {
     typedef MultiMapType::const_iterator It;
 
@@ -299,12 +299,12 @@ void eoParser::printOn(ostream& os) const
         if (!isItThere(*param))  // comment out the ones not set by the user
           os << "# ";
 
-        string str = "--" + param->longName() + "=" + param->getValue();
+        std::string str = "--" + param->longName() + "=" + param->getValue();
 
-        os.setf(ios_base::left, ios_base::adjustfield);
+        os.setf(std::ios_base::left, std::ios_base::adjustfield);
-        os << setfill(' ') << setw(40) << str;
+        os << std::setfill(' ') << std::setw(40) << str;
 
-        os << setw(0) << " # ";
+        os << std::setw(0) << " # ";
         if (param->shortName())
             os << '-' << param->shortName() << " : ";
         os << param->description();
@@ -318,11 +318,11 @@ void eoParser::printOn(ostream& os) const
     }
 }
 
-void eoParser::printHelp(ostream& os)
+void eoParser::printHelp(std::ostream& os)
 {
     if (needHelp.value() == false && !messages.empty())
     {
-        std::copy(messages.begin(), messages.end(), ostream_iterator<string>(os, "\n"));
+        std::copy(messages.begin(), messages.end(), std::ostream_iterator<std::string>(os, "\n"));
         messages.clear();
         return;
     }
@@ -333,9 +333,9 @@ void eoParser::printHelp(ostream& os)
     // print the usage when calling the program from the command line
     os << "Usage: "<< programName<<" [Options]\n";
     // only short usage!
-    os << "Options of the form \"-f[=Value]\" or \"--Name[=value]\"" << endl;
+    os << "Options of the form \"-f[=Value]\" or \"--Name[=value]\"" << std::endl;
 
-    os << "Where:"<<endl;
+    os << "Where:"<< std::endl;
 
     typedef MultiMapType::const_iterator It;
 
@@ -383,7 +383,7 @@ bool eoParser::userNeedsHelp(void)
       // search for unknown long names
       for (LongNameMapType::const_iterator lIt = longNameMap.begin(); lIt != longNameMap.end(); ++lIt)
         {
-          string entry = lIt->first;
+          std::string entry = lIt->first;
 
           MultiMapType::const_iterator it;
 
@@ -397,7 +397,7 @@ bool eoParser::userNeedsHelp(void)
 
           if (it == params.end())
             {
-              string msg = "Unknown parameter: --" + entry + " entered";
+              std::string msg = "Unknown parameter: --" + entry + " entered";
               needHelpMessage = true;
               messages.push_back(msg);
             }
@@ -420,15 +420,15 @@ bool eoParser::userNeedsHelp(void)
 
           if (it == params.end())
             {
-              string entryString(1, entry);
+              std::string entryString(1, entry);
-              string msg = "Unknown parameter: -" + entryString + " entered";
+              std::string msg = "Unknown parameter: -" + entryString + " entered";
               needHelpMessage = true;
               messages.push_back(msg);
             }
         } // for sIt
 
         if( needHelpMessage ) {
-            string msg = "Use -h or --help to get help about available parameters";
+            std::string msg = "Use -h or --help to get help about available parameters";
             messages.push_back( msg );
         }
 
@@ -438,13 +438,13 @@ bool eoParser::userNeedsHelp(void)
 }
 
 ///////////////// I put these here at the moment
-ostream & operator<<(ostream & _os, const eoParamParamType & _rate)
+std::ostream & operator<<(std::ostream & _os, const eoParamParamType & _rate)
 {
   _rate.printOn(_os);
   return _os;
 }
 
-istream & operator>>(istream & _is,  eoParamParamType & _rate)
+std::istream & operator>>(std::istream & _is,  eoParamParamType & _rate)
 {
   _rate.readFrom(_is);
   return _is;

eo/src/utils/eoState.cpp

@@ -14,31 +14,31 @@
 #include "../eoObject.h"
 #include "../eoPersistent.h"
 
-using namespace std;
+// using namespace std;
 
 
 
-void eoState::removeComment(string& str, string comment)
+void eoState::removeComment(std::string& str, std::string comment)
 {
-    string::size_type pos = str.find(comment);
+    std::string::size_type pos = str.find(comment);
 
-    if (pos != string::npos)
+    if (pos != std::string::npos)
     {
         str.erase(pos, str.size());
     }
 }
 
-bool eoState::is_section(const string& str, string& name)
+bool eoState::is_section(const std::string& str, std::string& name)
 {
-    string::size_type pos = str.find(_tag_section_so);
+    std::string::size_type pos = str.find(_tag_section_so);
 
-    if (pos == string::npos)
+    if (pos == std::string::npos)
         return false;
     //else
 
-    string::size_type end = str.find(_tag_section_sc);
+    std::string::size_type end = str.find(_tag_section_sc);
 
-    if (end == string::npos)
+    if (end == std::string::npos)
         return false;
     // else
 
@@ -59,9 +59,9 @@ eoState::~eoState(void)
 
 void eoState::registerObject(eoPersistent& registrant)
 {
-    string name = createObjectName(dynamic_cast<eoObject*>(&registrant));
+    std::string name = createObjectName(dynamic_cast<eoObject*>(&registrant));
 
-    pair<ObjectMap::iterator,bool> res = objectMap.insert(make_pair(name, &registrant));
+    std::pair<ObjectMap::iterator,bool> res = objectMap.insert(make_pair(name, &registrant));
 
     if (res.second == true)
     {
@@ -73,13 +73,13 @@ void eoState::registerObject(eoPersistent& registrant)
     }
 }
 
-void eoState::load(const string& _filename)
+void eoState::load(const std::string& _filename)
 {
-    ifstream is (_filename.c_str());
+    std::ifstream is (_filename.c_str());
 
     if (!is)
     {
-        // string str = "Could not open file " + _filename;
+        // std::string str = "Could not open file " + _filename;
         throw eoFileError(_filename);
     }
 
@@ -89,14 +89,14 @@ void eoState::load(const string& _filename)
 // FIXME implement parsing and loading of other formats
 void eoState::load(std::istream& is)
 {
-    string str;
+    std::string str;
-    string name;
+    std::string name;
 
     getline(is, str);
 
     if (is.fail())
     {
-        // string str = "Error while reading stream";
+        // std::string str = "Error while reading stream";
         throw eoFileError("stream");
     }
 
@@ -104,7 +104,7 @@ void eoState::load(std::istream& is)
     { // parse section header
         if (is_section(str, name))
         {
-            string fullString;
+            std::string fullString;
             ObjectMap::iterator it = objectMap.find(name);
 
             if (it == objectMap.end())
@@ -122,7 +122,7 @@ void eoState::load(std::istream& is)
 
                 // now we have the object, get lines, remove comments etc.
 
-                string fullstring;
+                std::string fullstring;
 
                 while (getline(is, str))
                 {
@@ -134,7 +134,7 @@ void eoState::load(std::istream& is)
                     removeComment(str, getCommentString());
                     fullstring += str + "\n";
                 }
-                istringstream the_stream(fullstring);
+                std::istringstream the_stream(fullstring);
                 object->readFrom(the_stream);
             }
         }
@@ -148,13 +148,13 @@ void eoState::load(std::istream& is)
 
 }
 
-void eoState::save(const string& filename) const
+void eoState::save(const std::string& filename) const
 { // saves in order of insertion
-    ofstream os(filename.c_str());
+    std::ofstream os(filename.c_str());
 
     if (!os)
     {
-        // string msg = "Could not open file: " + filename + " for writing!";
+        // std::string msg = "Could not open file: " + filename + " for writing!";
         throw eoFileError(filename);
     }
 
@@ -163,7 +163,7 @@ void eoState::save(const string& filename) const
 
 //void eoState::save(std::ostream& os) const
 //{ // saves in order of insertion
-//    for (vector<ObjectMap::iterator>::const_iterator it = creationOrder.begin(); it != creationOrder.end(); ++it)
+//    for (std::vector<ObjectMap::iterator>::const_iterator it = creationOrder.begin(); it != creationOrder.end(); ++it)
 //    {
 //        os << "\\section{" << (*it)->first << "}\n";
 //        (*it)->second->printOn(os);
@@ -171,7 +171,7 @@ void eoState::save(const string& filename) const
 //    }
 //}
 
-void eoState::saveSection( std::ostream& os, vector<ObjectMap::iterator>::const_iterator it) const
+void eoState::saveSection( std::ostream& os, std::vector<ObjectMap::iterator>::const_iterator it) const
 {
     os << _tag_section_so << (*it)->first << _tag_section_sc;
 
@@ -190,7 +190,7 @@ void eoState::save(std::ostream& os) const
     // save the first section
     assert( creationOrder.size() > 0 );
     // saves in order of insertion
-    vector<ObjectMap::iterator>::const_iterator it = creationOrder.begin();
+    std::vector<ObjectMap::iterator>::const_iterator it = creationOrder.begin();
     saveSection(os,it);
     it++;
 
@@ -204,23 +204,23 @@ void eoState::save(std::ostream& os) const
 }
 
 
-string eoState::createObjectName(eoObject* obj)
+std::string eoState::createObjectName(eoObject* obj)
 {
     if (obj == 0)
     {
-        ostringstream os;
+        std::ostringstream os;
         os << objectMap.size();
         return os.str();
     }
     // else
 
-    string name = obj->className();
+    std::string name = obj->className();
     ObjectMap::const_iterator it = objectMap.find(name);
 
     unsigned count = 1;
     while (it != objectMap.end())
     {
-        ostringstream os;
+        std::ostringstream os;
         os << obj->className().c_str() << count++;
         name = os.str();
         it = objectMap.find(name);

eo/src/utils/make_help.cpp

@@ -32,7 +32,7 @@
 
 #include "eoParser.h"
 
-using namespace std;
+// using namespace std;
 
 /** Generation of the status file, and output of the help message if needed
  *
@@ -47,24 +47,24 @@ using namespace std;
 void make_help(eoParser & _parser, bool exit_after)
 {
     // name of the "status" file where all actual parameter values will be saved
-    string str_status = _parser.ProgramName() + ".status"; // default value
+    std::string str_status = _parser.ProgramName() + ".status"; // default value
-    eoValueParam<string>& statusParam = _parser.createParam(str_status, "status","Status file",'\0', "Persistence" );
+    eoValueParam<std::string>& statusParam = _parser.createParam(str_status, "status","Status file",'\0', "Persistence" );
 
     // dump status file BEFORE help, so the user gets a chance to use it:
     // it's probably the case where she/he needs it most!!!
     // Only help parameter will not be in status file - but who cares???
     if (statusParam.value() != "")
       {
-        ofstream os(statusParam.value().c_str());
+        std::ofstream os(statusParam.value().c_str());
         os << _parser;		// and you can use that file as parameter file
       }
    // do the following AFTER ALL PARAMETERS HAVE BEEN PROCESSED
    // i.e. in case you need parameters somewhere else, postpone these
     if (_parser.userNeedsHelp())
       {
-        _parser.printHelp(cout);
+        _parser.printHelp(std::cout);
-        cout << "You can use an edited copy of file " << statusParam.value()
+        std::cout << "You can use an edited copy of file " << statusParam.value()
-             << " as parameter file" << endl;
+             << " as parameter file" << std::endl;
         if(exit_after) {
             exit(0);
         }
@@ -80,7 +80,7 @@ void make_help(eoParser & _parser, bool exit_after)
  */
 bool testDirRes(std::string _dirName, bool _erase=true)
 {
-  string s = "test -d " + _dirName;
+  std::string s = "test -d " + _dirName;
   int res = system(s.c_str());
   // test for (unlikely) errors
   if ( (res==-1) || (res==127) )
@@ -91,7 +91,7 @@ bool testDirRes(std::string _dirName, bool _erase=true)
   // now make sure there is a dir without any file in it - or quit
   if (res)                    // no dir present
     {
-      s = string("mkdir ")+ _dirName;
+      s = std::string("mkdir ")+ _dirName;
       int res = system(s.c_str());
       (void)res;
       return true;
@@ -99,7 +99,7 @@ bool testDirRes(std::string _dirName, bool _erase=true)
   //  else
   if (_erase)                      // OK to erase
     {
-      s = string("/bin/rm ")+ _dirName + "/*";
+      s = std::string("/bin/rm ")+ _dirName + "/*";
       int res = system(s.c_str());
       (void)res;
       return true;

eo/test/t-eoRingTopology.cpp

@@ -33,9 +33,9 @@ int main_function(int argc, char **argv)
     eoFirstIsBestInit < Indi > localInit;
     eoPop < Indi > pop;
     pop.append (POP_SIZE, random);
-    apply(eval, pop);
+    ::apply(eval, pop);
-    apply < Indi > (veloRandom, pop);
+    ::apply < Indi > (veloRandom, pop);
-    apply < Indi > (localInit, pop);
+    ::apply < Indi > (localInit, pop);
     eoRingTopology<Indi> topology(NEIGHBORHOOD_SIZE);
     topology.setup(pop);
     std::cout<<"\n\n\nPopulation :\n\n"<<pop;

eo/test/t-forge-algo.cpp

@@ -91,7 +91,7 @@ int main(int /*argc*/, char** /*argv*/)
 
                         eoPop<EOT> pop;
                         pop.append(pop_size, init);
-                        apply(eval,pop);
+                        ::apply(eval,pop);
 
                         algo(pop);
 

eo/tutorial/Lesson1/FirstBitGA.cpp

@@ -38,7 +38,7 @@ double binary_value(const Indi & _indi)
 }
 // GENERAL
 //-----------------------------------------------------------------------------
-void main_function(int argc, char **argv)
+void main_function(int /*argc*/, char **/*argv*/)
 {
 // PARAMETRES
   // all parameters are hard-coded!

eo/tutorial/Lesson1/FirstRealGA.cpp

@@ -38,7 +38,7 @@ double real_value(const Indi & _indi)
 }
 // GENERAL
 //-----------------------------------------------------------------------------
-void main_function(int argc, char **argv)
+void main_function(int /*argc*/, char **/*argv*/)
 {
 // PARAMETRES
   // all parameters are hard-coded!

eo/tutorial/Lesson1/exercise1.3.cpp

@@ -39,7 +39,7 @@ double binary_value(const Indi & _indi)
 
 //-----------------------------------------------------------------------------
 
-void main_function(int argc, char **argv)
+void main_function(int /*argc*/, char **/*argv*/)
 {
   const unsigned int SEED = 42;	// seed for random number generator
   const unsigned int VEC_SIZE = 8; // Number of bits in genotypes

eo/tutorial/Lesson2/FirstRealEA.cpp

@@ -36,7 +36,7 @@ using namespace std;
 // GENERAL
 //-----------------------------------------------------------------------------
 
-void main_function(int argc, char **argv)
+void main_function(int /*argc*/, char **/*argv*/)
 {
 // PARAMETRES
   const unsigned int SEED = 42;	// seed for random number generator

eo/tutorial/Lesson2/exercise2.3.cpp

@@ -36,7 +36,7 @@ typedef eoBit<double> Indi;	// A bitstring with fitness double
 
 using namespace std;
 
-void main_function(int argc, char **argv)
+void main_function(int /*argc*/, char **/*argv*/)
 {
 // PARAMETRES
   const unsigned int SEED = 42;	// seed for random number generator

eo/tutorial/Lesson5/eoOneMaxMutation.h

@@ -44,7 +44,7 @@ public:
      * modifies the parent
      * @param _genotype The parent genotype (will be modified)
      */
-    bool operator()(GenotypeT & _genotype)
+    bool operator()(GenotypeT & /*_genotype*/)
 	{
 	    bool isModified(true);
 	    // START code for mutation of the _genotype object

eo/tutorial/Lesson5/eoOneMaxQuadCrossover.h

@@ -46,7 +46,7 @@ public:
      * @param _genotype1 The first parent
      * @param _genotype2 The second parent
      */
-    bool operator()(GenotypeT& _genotype1, GenotypeT & _genotype2)
+    bool operator()(GenotypeT& /*_genotype1*/, GenotypeT & /*_genotype2*/)
 	{
 	    bool oneAtLeastIsModified(true);
 	    // START code for crossover of _genotype1 and _genotype2 objects

eo/tutorial/Lesson5/make_op_OneMax.h

@@ -73,7 +73,7 @@
 */
 
 template <class EOT>
-eoGenOp<EOT> & do_make_op(eoParameterLoader& _parser, eoState& _state, eoInit<EOT>& _init)
+eoGenOp<EOT> & do_make_op(eoParameterLoader& _parser, eoState& _state, eoInit<EOT>& /*_init*/)
 {
   // this is a temporary version, while Maarten codes the full tree-structured
   // general operator input

eo/tutorial/Lesson6/RealPSO.cpp

@@ -12,7 +12,7 @@
 #include <eo>
 
 // Use functions from namespace std
-using namespace std;
+// using namespace std; // Do not do this, this shadows EO's `apply` function.
 
 //-----------------------------------------------------------------------------
 typedef eoMinimizingFitness FitT;
@@ -33,7 +33,7 @@ FitT real_value (const Particle & _particle)
 
 
 
-void main_function(int argc, char **argv)
+void main_function(int /*argc*/, char **/*argv*/)
 {
 // PARAMETRES
  // all parameters are hard-coded!
@@ -114,9 +114,9 @@ void main_function(int argc, char **argv)
   	pop.sort();
 
   	// Print (sorted) the initial population (raw printout)
-    cout << "INITIAL POPULATION:" << endl;
+    std::cout << "INITIAL POPULATION:" << std::endl;
     for (unsigned i = 0; i < pop.size(); ++i)
-	 cout <<  "\t best fit=" <<  pop[i] <<  endl;
+	 std::cout <<  "\t best fit=" <<  pop[i] <<  std::endl;
 
 
 ///////////////
@@ -158,9 +158,9 @@ void main_function(int argc, char **argv)
 // OUTPUT
   // Print (sorted) intial population
 	 pop.sort();
-	 cout << "FINAL POPULATION:" << endl;
+     std::clog << "FINAL POPULATION:" << std::endl;
   	 for (unsigned i = 0; i < pop.size(); ++i)
-	cout <<  "\t best fit=" <<  pop[i] <<  endl;
+     std::clog <<  "\t best fit=" <<  pop[i] << std::endl;
 
 }
 
@@ -173,9 +173,9 @@ int main(int argc, char **argv)
     {
 	main_function(argc, argv);
     }
-    catch(exception& e)
+    catch(std::exception& e)
     {
-	cout << "Exception: " << e.what() << '\n';
+        std::cerr << "Exception: " << e.what() << '\n';
     }
 
     return 1;

moeo/tutorial/examples/flowshop/FlowShopBenchmarkParser.cpp

@@ -45,25 +45,25 @@ FlowShopBenchmarkParser::FlowShopBenchmarkParser(const std::string _benchmarkFil
 }
 
 
-const unsigned int FlowShopBenchmarkParser::getM()
+unsigned int FlowShopBenchmarkParser::getM()
 {
     return M;
 }
 
 
-const unsigned int FlowShopBenchmarkParser::getN()
+unsigned int FlowShopBenchmarkParser::getN()
 {
     return N;
 }
 
 
-const std::vector< std::vector<unsigned int> > FlowShopBenchmarkParser::getP()
+std::vector< std::vector<unsigned int> > FlowShopBenchmarkParser::getP()
 {
     return p;
 }
 
 
-const std::vector<unsigned int> FlowShopBenchmarkParser::getD()
+std::vector<unsigned int> FlowShopBenchmarkParser::getD()
 {
     return d;
 }

moeo/tutorial/examples/flowshop/FlowShopBenchmarkParser.h

@@ -60,25 +60,25 @@ class FlowShopBenchmarkParser
     /**
      * the number of machines
      */
-    const unsigned int getM();
+    unsigned int getM();
 
 
     /**
      * the number of jobs
      */
-    const unsigned int getN();
+    unsigned int getN();
 
 
     /**
      * the processing times
      */
-    const std::vector < std::vector < unsigned int > > getP();
+    std::vector < std::vector < unsigned int > > getP();
 
 
     /**
      * the due-dates
      */
-    const std::vector < unsigned int > getD();
+    std::vector < unsigned int > getD();
 
 
     /**

moeo/tutorial/examples/flowshop/FlowShopObjectiveVectorTraits.cpp

@@ -38,13 +38,13 @@
 #include <FlowShopObjectiveVectorTraits.h>
 
 
-bool FlowShopObjectiveVectorTraits::minimizing (int _i)
+bool FlowShopObjectiveVectorTraits::minimizing (int /*_i*/)
 {
   // minimizing both
   return true;
 }
 
-bool FlowShopObjectiveVectorTraits::maximizing (int _i)
+bool FlowShopObjectiveVectorTraits::maximizing (int /*_i*/)
 {
   // minimizing both
   return false;