--- ./app_minkowski.cpp.orig	2011-01-25 08:33:15.000000000 -0700

+++ ./app_minkowski.cpp	2012-01-09 11:28:20.926240318 -0700

@@ -160,7 +160,7 @@ public:

 	    //log0 fprintf(Stderr,"4");

 	    f.insert(c);

 	    //log0 fprintf(Stderr,"5\n");

-	    static int i;

+	    //static int i;

 	    //log0 fprintf(Stderr,"inserted:%i\n",++i);

 	  }

 	log1 fprintf(Stderr,"Resolving symmetries.\n");

--- ./app_test.cpp.orig	2011-01-25 08:33:15.000000000 -0700

+++ ./app_test.cpp	2012-01-09 11:27:29.305437764 -0700

@@ -1,5 +1,7 @@

 #include <iostream>

 #include <stdlib.h>

+#include <dirent.h>

+#include <unistd.h>

 #include "parser.h"

 #include "printer.h"

 #include "polynomial.h"

@@ -193,10 +195,7 @@ public:

 		  {

 			  outputName=outputName+"New";

 		  }

-		  {

-			  string t="rm "+outputName;

-			  system(t.c_str());

-		  }

+		  unlink(outputName.c_str());

 		  string command3="cat <"+input+"|"+string(command2)+">"+outputName;

 		  cerr<<"Running command:\""<

 		  system(command3.c_str());

@@ -207,22 +206,17 @@ public:

   list<string> subFolderNames()

   {

-#define tempName "GfAnTeMpTeStS"

-	  char command[256];

-	  system("rm "tempName);

-	  sprintf(command,"ls %s>" tempName ,testSuiteFolderOption.getValue());

-	  system(command);

-

 	  list<string> ret;

-	  FILE *f=fopen(tempName,"r");

-	  assert(f);

-	  char name[256];

-	  while(fgets(name,255,f))

+	  DIR *dir = opendir(testSuiteFolderOption.getValue());

+	  struct dirent *dirent;

+

+	  assert(dir);

+	  for (struct dirent *ent = readdir(dir); ent; ent = readdir(dir))

 	  {

-		  for(int i=0;i<255 && name[i];i++)if(name[i]=='\n'){name[i]=0;}

-		  if(name[0]>='0' && name[0]<='9')ret.push_back(string(testSuiteFolderOption.getValue())+"/"+string(name));

+		  if (ent->d_name[0]>='0' && ent->d_name[0]<='9')

+			  ret.push_back(string(testSuiteFolderOption.getValue())+"/"+string(ent->d_name));

 	  }

-	  fclose(f);

+	  closedir(dir);

 	  return ret;

   }

--- ./gfanlib_vector.h.orig	2011-01-25 08:33:18.000000000 -0700

+++ ./gfanlib_vector.h	2012-01-09 11:27:29.307437580 -0700

@@ -288,6 +288,7 @@ public:

           f<<*i;

         }

         f<<")";

+        return f;

       }

   typ gcd()const

   {

--- ./app_tropicalintersection.cpp.orig	2011-01-25 08:33:15.000000000 -0700

+++ ./app_tropicalintersection.cpp	2012-01-09 11:27:29.304437850 -0700

@@ -42,6 +42,7 @@ public:

 			AsciiPrinter(Stdout)<<"The following vector is in intersection, but initial ideal contains a monomial:\n"<

 			assert(0);

 		}

+		return true;

 	}

 };

--- ./application.cpp.orig	2011-01-25 08:33:16.000000000 -0700

+++ ./application.cpp	2012-01-09 11:27:29.312437096 -0700

@@ -3,6 +3,8 @@

 #include <assert.h>

 #include <stdlib.h>

 #include <stdio.h>

+#include <limits.h>

+#include <unistd.h>

 #include <string>

 #include <list>

@@ -546,10 +548,11 @@ void Application::makeSymbolicLinks(cons

       if(all || p->includeInDefaultInstallation())

 	if(strlen(p->name())>0)

 	  {

-	    char c[1024];

-	    sprintf(c,"ln -s %s%s %s%s%s\n",path,name,path,name,p->name());

-	    fprintf(stderr,"%s",c);

-	    system(c);

+	    char c[PATH_MAX], d[PATH_MAX];

+	    snprintf(c,PATH_MAX,"%s%s",path,name);

+	    snprintf(d,PATH_MAX,"%s%s%s",path,name,p->name());

+	    fprintf(stderr,"ln -s %s %s\n",c,d);

+	    symlink(c,d);

 	  }

       p=p->next;

     }

--- ./field_rationals.cpp.orig	2011-01-25 08:33:16.000000000 -0700

+++ ./field_rationals.cpp	2012-01-09 11:27:29.300438251 -0700

@@ -326,17 +326,17 @@ const char *FieldRationalsImplementation

   return "GmpRationals";

 }

-/*FieldRationals::FieldRationals():

+#if 0

+FieldRationals::FieldRationals():

   Field(new FieldRationalsImplementation())

 {

   /*  fprintf(Stderr,"Adding field rationals\n");

   next=list;

   list=this;

   */

-/*

   log2 fprintf(Stderr,"Initializing field Rationals\n");

 }

-*/

+#endif

 				//FieldRationals Q;

 Field Q(new FieldRationalsImplementation());

--- ./vektor.cpp.orig	2011-01-25 08:33:17.000000000 -0700

+++ ./vektor.cpp	2012-01-09 11:27:29.303437946 -0700

@@ -96,7 +96,7 @@ int gcdGFAN(int r, int s)

 int gcdOfVector(IntegerVector const &v)

 {

   int ret=0;

-  for(int i=0;i

+  for(int i=0;i

   if(ret<0)ret=-ret;

   assert(ret!=0);

   for(int i=0;i

--- ./gfanlib_symmetriccomplex.cpp.orig	2011-01-25 08:33:16.000000000 -0700

+++ ./gfanlib_symmetriccomplex.cpp	2012-01-09 11:27:29.311437193 -0700

@@ -215,13 +215,12 @@ bool SymmetricComplex::isMaximal(Cone co

   return true;

 }

-/*

+#if 0

 IntVector SymmetricComplex::dimensionsAtInfinity()const

 {

   /* Using a double description like method this routine computes the

      dimension of the intersection of each cone in the complex with

      the plane x_0=0 */

-/*

   IntVector ret(cones.size());

   int I=0;

@@ -240,7 +239,7 @@ IntVector SymmetricComplex::dimensionsAt

     }

   return ret;

 }

-*/

+#endif

 void SymmetricComplex::buildConeLists(bool onlyMaximal, bool compressed, std::vector<std::vector<IntVector > >*conelist/*, ZMatrix *multiplicities*/)const

 {

--- ./polymakefile.cpp.orig	2011-01-25 08:33:17.000000000 -0700

+++ ./polymakefile.cpp	2012-01-09 11:27:29.310437290 -0700

@@ -371,7 +371,7 @@ static list<int> readIntList(istream &s)

 {

   list<int> ret;

   int c=s.peek();

-  while((c>='0') && (c<='9')|| (c==' '))

+  while((c>='0' && c<='9')|| c==' ')

     {

       //      fprintf(Stderr,"?\n");

       int r;

--- ./app_fancoarsening.cpp.orig	2011-01-25 08:33:15.000000000 -0700

+++ ./app_fancoarsening.cpp	2012-01-09 11:27:29.299438352 -0700

@@ -33,12 +33,14 @@ public:

     return false;

   }

+#if 0

   IntegerVectorList inequalitiesForCone(IntegerVector const &codim1interior, IntegerVector const &newDirection)

   {

     int i=0;

   }

+#endif

   const char *helpText()

   {

--- ./gfanlib_polymakefile.cpp.orig	2011-01-25 08:33:16.000000000 -0700

+++ ./gfanlib_polymakefile.cpp	2012-01-09 11:27:29.306437673 -0700

@@ -51,7 +51,7 @@ static list<int> readIntList(istream &s)

 {

   list<int> ret;

   int c=s.peek();

-  while((c>='0') && (c<='9')|| (c==' '))

+  while((c>='0' && c<='9')|| c==' ')

     {

       //      fprintf(Stderr,"?\n");

       int r;

--- ./gfanlib_zcone.cpp.orig	2011-01-25 08:33:16.000000000 -0700

+++ ./gfanlib_zcone.cpp	2012-01-09 11:27:29.309437387 -0700

@@ -726,6 +726,7 @@ std::ostream &operator<<(std::ostream &f

   f<

   f<<"Equations:"<

   f<

+  return f;

 }

--- ./wallideal.cpp.orig	2011-01-25 08:33:17.000000000 -0700

+++ ./wallideal.cpp	2012-01-09 11:27:29.301438150 -0700

@@ -928,7 +928,7 @@ bool fastIsFacet(IntegerVectorList const

   return isFacet(normals,i);

 }

 */

- /*

+#if 0 

 bool fastIsFacet(IntegerVectorList const &normals, IntegerVectorList::const_iterator i)

 {

   int n=i->size();

@@ -963,7 +963,7 @@ bool fastIsFacet(IntegerVectorList const

 	    }

 	}

       */

-/*    int bestEntry=-1;

+      int bestEntry=-1;

       int bestCount=2000000000;

       int bestValue=0;

       for(int j=0;j

@@ -1029,7 +1029,7 @@ bool fastIsFacet(IntegerVectorList const

   //  log0 fprintf(Stderr,"LP\n");

   return isFacet(normals,i);

 }

-*/

+#endif

 IntegerVectorList fastNormals(IntegerVectorList const &inequalities)

 {