Merge branch 'master' into openmp

eo/CMakeLists.txt

@@ -65,6 +65,9 @@ INCLUDE(Dart OPTIONNAL)
 # now create config headers
 CONFIGURE_FILE(config.h.cmake ${CMAKE_CURRENT_BINARY_DIR}/config.h)
 
+# now create config install_symlink script file
+CONFIGURE_FILE(install_symlink.py.cmake ${CMAKE_CURRENT_BINARY_DIR}/install_symlink.py)
+
 # Set a special flag if the environment is windows (should do the same in a config.g file)
 IF (WIN32)
   ADD_DEFINITIONS(-D_WINDOWS=1)

eo/build_gcc_linux_debug

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-mkdir debug
+mkdir -p debug
 cd debug
 cmake -DCMAKE_BUILD_TYPE=Debug ..
 make

eo/build_gcc_linux_release

@@ -1,6 +1,6 @@
 #!/usr/bin/env sh
 
-mkdir release
+mkdir -p release
 cd release
 cmake ..
 make

eo/install_symlink.py.cmake

@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+
+#NAME    = "@PROJECT_NAME@"
+NAME    = "eo"
+SOURCE  = "@CMAKE_SOURCE_DIR@"
+BINARY  = "@CMAKE_BINARY_DIR@"
+PREFIX  = "/usr"
+
+DATA = {
+    'dirs': [ "%s/share/%s" % (PREFIX, NAME) ],
+    'links': [ ("%s/src" % SOURCE, "%s/include/%s" % (PREFIX, NAME)),
+               ("%s/doc" % BINARY, "%s/share/%s/doc" % (PREFIX, NAME)),
+               ("%s/%s.pc" % (BINARY, NAME), "%s/lib/pkgconfig/%s.pc" % (PREFIX, NAME)),
+               ]
+    }
+
+LIBRARIES = ["libcma.a", "libeo.a", "libeoutils.a", "libes.a", "libga.a"]
+DATA['links'] += [ ("%s/lib/%s" % (BINARY, lib), "%s/lib/%s" % (PREFIX, lib)) for lib in LIBRARIES ]
+
+import os, sys
+
+def isroot():
+    if os.getuid() != 0:
+        print '[WARNING] you have to be root'
+        return False
+    return True
+
+def uninstall():
+    for dummy, link in DATA['links']: os.remove(link)
+    for dirname in DATA['dirs']: os.rmdir(dirname)
+    print 'All symlinks have been removed.'
+
+def install():
+    for dirname in DATA['dirs']: os.mkdir(dirname)
+    for src, dst in DATA['links']: os.symlink(src, dst)
+    print 'All symlinks have been installed.'
+
+def data():
+    from pprint import pprint
+    pprint(DATA, width=200)
+
+if __name__ == '__main__':
+    if not isroot():
+        sys.exit()
+
+    if len(sys.argv) < 2:
+        print 'Usage: %s [install|uninstall|data]' % sys.argv[0]
+        sys.exit()
+
+    if sys.argv[1] == 'install': install()
+    elif sys.argv[1] == 'uninstall': uninstall()
+    elif sys.argv[1] == 'data': data()

eo/src/eoDualFitness.h

@@ -264,13 +264,13 @@ public:
 
 //    eoDualStatSwitch( eoStat<EOT,T> & stat_feasible,  eoStat<EOT,T> & stat_unfeasible, std::string sep=" "  ) :
     eoDualStatSwitch( EOSTAT & stat_feasible,  EOSTAT & stat_unfeasible, std::string sep=" "  ) :
-        _stat_feasible(stat_feasible), 
-        _stat_unfeasible(stat_unfeasible), 
-        _sep(sep),
         eoStat<EOT,std::string>(
                 "?"+sep+"?", 
                 stat_feasible.longName()+sep+stat_unfeasible.longName() 
-            )
+				),
+        _stat_feasible(stat_feasible), 
+        _stat_unfeasible(stat_unfeasible), 
+        _sep(sep)
     { }
 
     virtual void operator()( const eoPop<EOT> & pop )

eo/src/eoEvalUserTimeThrowException.h

@@ -39,7 +39,7 @@ template< class EOT >
 class eoEvalUserTimeThrowException : public eoEvalFuncCounter< EOT >
 {
 public:
-    eoEvalUserTimeThrowException( eoEvalFunc<EOT> & func, long max ) : _max(max), eoEvalFuncCounter<EOT>( func, "CPU-user") {}
+    eoEvalUserTimeThrowException( eoEvalFunc<EOT> & func, const long max ) : eoEvalFuncCounter<EOT>( func, "CPU-user"), _max(max) {}
 
     virtual void operator() ( EOT & eo )
     {
@@ -47,8 +47,9 @@ public:
 
             getrusage(RUSAGE_SELF,&_usage);
 
-            if( _usage.ru_utime.tv_sec >= _max ) {
-                throw eoMaxTimeException( _usage.ru_utime.tv_sec );
+            long current = _usage.ru_utime.tv_sec;
+            if( current >= _max ) {
+                throw eoMaxTimeException( current );
             } else {
                 func(eo);
             }
@@ -56,6 +57,6 @@ public:
     }
 
 protected:
-    long _max;
+    const long _max;
     struct rusage _usage;
 };

eo/src/eoExceptions.h

@@ -46,7 +46,7 @@ public:
     virtual const char* what() const throw()
     {
         std::ostringstream ss;
-        ss << "STOP in eoMaxTimeException: the maximum number of wallclock seconds has been reached (" << _elapsed << ").";
+        ss << "STOP in eoMaxTimeException: the maximum number of allowed seconds has been reached (" << _elapsed << ").";
         return ss.str().c_str();
     }
 

eo/src/eoMerge.h

@@ -33,6 +33,7 @@
 // EO includes
 #include <eoPop.h>     // eoPop
 #include <eoFunctor.h>  // eoMerge
+#include <utils/eoLogger.h>
 
 /**
  * eoMerge: Base class for elitist replacement algorithms. 

eo/src/eoPopEvalFunc.h

@@ -69,7 +69,8 @@ public:
   /** Do the job: simple loop over the offspring */
   void operator()(eoPop<EOT> & _parents, eoPop<EOT> & _offspring)
   {
-    apply<EOT>(eval, _offspring);
+      (void)_parents;
+      apply<EOT>(eval, _offspring);
   }
 
 private:

eo/src/eoReduce.h

@@ -34,6 +34,7 @@
 #include <eoPop.h>     // eoPop
 #include <eoFunctor.h>  // eoReduce
 #include <utils/selectors.h>
+#include <utils/eoLogger.h>
 
 /**
  * eoReduce: .reduce the new generation to the specified size

eo/src/utils/eoOStreamMonitor.h

@@ -48,6 +48,7 @@ public :
     eoOStreamMonitor( std::ostream & _out, bool _verbose=true, std::string _delim = "\t", unsigned int _width=20, char _fill=' ' ) : 
         out(_out), delim(_delim), width(_width), fill(_fill), firsttime(true) 
     {
+	(void)_verbose;
         eo::log << eo::warnings << "WARNING: the use of the verbose parameter in eoOStreamMonitor constructor is deprecated and will be removed in the next release" << std::endl;
     }