--- src/app_fancoarsening.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/app_fancoarsening.cpp	2017-08-08 20:44:07.874478774 -0600

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

     return false;

   }

+#if 0

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

   {

     int i=0;

   }

+#endif

   const char *helpText()

   {

--- src/app_librarytest.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/app_librarytest.cpp	2017-08-19 19:35:36.540662585 -0600

@@ -12,8 +12,8 @@

 #include "setoper.h"

 #include "cdd.h"

 #else

-#include "cdd/setoper.h"

-#include "cdd/cdd.h"

+#include "cddlib/setoper.h"

+#include "cddlib/cdd.h"

 #endif

 #include <iostream>

 #include <fstream>

--- src/application.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/application.cpp	2017-08-08 20:46:08.339136885 -0600

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

 #include <assert.h>

 #include <stdlib.h>

 #include <stdio.h>

+#include <limits.h>

+#include <unistd.h>

 #include <string>

 #include <list>

 #include <vector>

@@ -556,11 +558,11 @@ 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);

-	    int err=system(c);

-	    assert(err==0);

+	    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;

     }

--- src/app_test.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/app_test.cpp	2017-08-08 20:51:47.178175233 -0600

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

 #include <iostream>

 #include <stdlib.h>

+#include <dirent.h>

+#include <unistd.h>

 #include "parser.h"

 #include "printer.h"

 #include "polynomial.h"

@@ -491,10 +493,7 @@ int testIntegers()

 			  outputName=outputName+"New";

 		  }

 		  int err=0;

-		  {

-			  string t="rm "+outputName;

-			  /*err|=*/system(t.c_str());

-		  }

+		  unlink(outputName.c_str());

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

 		  cerr<<"Running command:\""<

 		  err|=system(command3.c_str());

@@ -508,24 +507,17 @@ int testIntegers()

   list<string> subFolderNames()

   {

-#define tempName "GfAnTeMpTeStS"

-	  char command[256];

-	  int err=system("rm " tempName);

-	  err=0;//Having err!=0 above is probably not at mistake. Rather the file did not exist.

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

-	  err|=system(command);

-	  assert(err==0);

-

 	  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;

   }

--- src/bergman.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/bergman.cpp	2017-08-19 19:03:16.158947524 -0600

@@ -327,7 +327,7 @@ log0 AsciiPrinter(Stderr).printPolynomia

       if(doesPermutationFixCone(*j))numFixed++;

     //  fprintf(Stderr,"groupSize = %i, numFixed = %i\n",groupSize,numFixed);

-    return groupSize/numFixed;

+    return (numFixed>0) ? groupSize/numFixed : 0;

   }

   void markFacet(IntegerVector const &relIntRidgeVector)

--- src/breadthfirstsearch.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/breadthfirstsearch.cpp	2017-08-19 19:04:35.078732494 -0600

@@ -260,7 +260,7 @@ public:

       }

     log2 fprintf(Stderr,"numFixed = %i\n",numFixed);

-    return groupSize/numFixed;

+    return (numFixed>0) ? groupSize/numFixed : 0;

   }

 };

--- src/bsptree.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/bsptree.cpp	2017-08-19 19:11:55.757531793 -0600

@@ -131,7 +131,8 @@ public:

               p=&(i->first);

             }

         }

-      normal=*p;

+      if (p)

+        normal=*p;

     }

     return normal;

     }

--- src/enumeration.h.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/enumeration.h	2017-08-08 20:53:14.696930681 -0600

@@ -36,7 +36,7 @@ class EnumerationFilePrinter: public Enu

   FILE *file;

  public:

   EnumerationFilePrinter();

-  ~EnumerationFilePrinter();

+  virtual ~EnumerationFilePrinter();

   void open(std::string filename);

   void open(FILE *file);

@@ -61,6 +61,7 @@ class EnumerationAlgorithm

   bool targetBasis(const PolynomialSet &groebnerBasis){bool ret=true;if(target)ret=target->basis(groebnerBasis);printProgress();return ret;}

  public:

   EnumerationAlgorithm(){target=0;progressCounter=0;}

+  virtual ~EnumerationAlgorithm(){}

   void setEnumerationTarget(EnumerationTarget *target){this->target=target;}

   virtual void enumerate(const PolynomialSet &groebnerBasis){}

 };

--- src/gfanlib_symmetry.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/gfanlib_symmetry.cpp	2017-08-19 19:02:38.303050669 -0600

@@ -423,7 +423,7 @@ int SymmetryGroup::orbitSize(ZVector con

           if(doesFix)numFixed++;

         }

     }

-  return groupSize/numFixed;

+  return (numFixed>0) ? groupSize/numFixed : 0;

 }

--- src/gfanlib_tropicalhomotopy.h.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/gfanlib_tropicalhomotopy.h	2017-08-19 20:27:59.920417245 -0600

@@ -454,7 +454,7 @@ template

 			//chioices are "relative" so no update is needed.

 			choices=parent.choices;

-			int numberToDrop=(subconfigurationIndex!=0) ? numberToDrop=k+1 : 0;

+			int numberToDrop=(subconfigurationIndex!=0) ? k+1 : 0;

 			choices[subconfigurationIndex-1].first-=numberToDrop;

 			choices[subconfigurationIndex-1].second-=numberToDrop;

--- src/gfanlib_zcone.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/gfanlib_zcone.cpp	2017-08-19 19:35:36.550662558 -0600

@@ -16,8 +16,8 @@

 #include "setoper.h"

 #include "cdd.h"

 #else

-#include "cdd/setoper.h"

-#include "cdd/cdd.h"

+#include "cddlib/setoper.h"

+#include "cddlib/cdd.h"

 #endif

 //}

@@ -52,8 +52,8 @@ namespace gfan{

 				  "dd_free_global_constants()\n"

 				  "in your deinitialisation code (only available for cddlib version>=094d).\n"

 				  "This requires the header includes:\n"

-				  "#include \"cdd/setoper.h\"\n"

-				  "#include \"cdd/cdd.h\"\n"

+				  "#include \"cddlib/setoper.h\"\n"

+				  "#include \"cddlib/cdd.h\"\n"

 				  "\n"

 				  "Alternatively, you may call gfan:initializeCddlibIfRequired() and deinitializeCddlibIfRequired()\n"

 				  "if gfanlib is the only code using cddlib. If at some point cddlib is no longer required by gfanlib\n"

--- src/lp_cdd.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/lp_cdd.cpp	2017-08-19 19:35:36.545662572 -0600

@@ -5,9 +5,9 @@

 #include "cdd.h"

 #include "cdd_f.h"

 #else

-#include "cdd/setoper.h"

-#include "cdd/cdd.h"

-#include "cdd/cdd_f.h"

+#include "cddlib/setoper.h"

+#include "cddlib/cdd.h"

+#include "cddlib/cdd_f.h"

 #endif

 //}

 #include "termorder.h"

--- src/polymakefile.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/polymakefile.cpp	2017-08-08 20:59:35.271908934 -0600

@@ -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;

--- src/symmetry.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/symmetry.cpp	2017-08-19 19:05:05.790648815 -0600

@@ -580,7 +580,7 @@ int SymmetryGroup::orbitSize(IntegerVect

           if(doesFix)numFixed++;

         }

     }

-  return groupSize/numFixed;

+  return (numFixed>0) ? groupSize/numFixed : 0;

 }

--- src/vektor.cpp.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/vektor.cpp	2017-08-08 21:00:13.911805196 -0600

@@ -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

--- src/vektor.h.orig	2017-06-20 08:47:37.000000000 -0600

+++ src/vektor.h	2017-08-19 20:37:20.222665653 -0600

@@ -72,7 +72,7 @@ public:

   template<class T> explicit Vektor(const Vektor<T>& c)

 	  :v(c.size())

 	{

-	  for(int i=0;i

+	  for(size_t i=0;i

 	}

   //--------

@@ -80,10 +80,10 @@ public:

   //--------

   typ& operator[](int n)

     {

-      if(!(n>=0 && n

+      if(!(n>=0 && (size_t)n

       return (v[n]);

     }

-  const typ& operator[](int n)const{assert(n>=0 && n

+  const typ& operator[](int n)const{assert(n>=0 && (size_t)n

   const typ& UNCHECKEDACCESS(int n)const{return (v[n]);}

   typ& UNCHECKEDACCESS(int n){return (v[n]);}

@@ -92,7 +92,7 @@ public:

   //-------------

   unsigned int size()const{return v.size();};

   void resize(int n){v.resize(n,0);};

-  void grow(int i){if(size()

+  void grow(int i){if(size()<(size_t)i)resize(i);}

   void push_back(typ a)

   {

     v.push_back(a);

@@ -109,7 +109,7 @@ public:

     {

       if(size()

       if(size()>b.size())return false;

-      for(int i=0;i

+      for(size_t i=0;i

 	{

 	  if(v[i]

 	  if(b[i]

@@ -120,10 +120,10 @@ public:

   //-----------------

   // Arithmetic fast

   //-----------------

-  typ sum()const{typ f=0;for(int i=0;i

-  Vektor& operator+=(const Vektor& q){assert(size()==q.size());for(int i=0;i

-  Vektor& operator-=(const Vektor& q){assert(size()==q.size());for(int i=0;i

-  inline friend typ dot(const Vektor& p, const Vektor& q){assert(p.size()==q.size());typ s=0;for(int i=0;i

+  typ sum()const{typ f=0;for(size_t i=0;i

+  Vektor& operator+=(const Vektor& q){assert(size()==q.size());for(size_t i=0;i

+  Vektor& operator-=(const Vektor& q){assert(size()==q.size());for(size_t i=0;i

+  inline friend typ dot(const Vektor& p, const Vektor& q){assert(p.size()==q.size());typ s=0;for(size_t i=0;i

  // inline friend int64 dotLong(const Vektor& p, const Vektor& q){assert(p.size()==q.size());int64 s=0;for(int i=0;i

   inline friend int64 dotLong(const Vektor& p, const Vektor& q)

   {

@@ -178,50 +178,50 @@ public:

       dest[*p]=*s;

   }

-  bool operator==(const Vektor & q)const{if(size()!=q.size())return false;for(int i=0;i

+  bool operator==(const Vektor & q)const{if(size()!=q.size())return false;for(size_t i=0;i

   bool operator!=(const Vektor & q)const {return !(operator==(q));}

   bool isZero() const

     {

-      int n=v.size();

-      for(int i=0;i

+      size_t n=v.size();

+      for(size_t i=0;i

       return 1;

     }

   bool isPositive() const

     {

-      int n=v.size();

-      for(int i=0;i

+      size_t n=v.size();

+      for(size_t i=0;i

       return 1;

     }

   bool isNonNegative() const

     {

-      int n=v.size();

-      for(int i=0;i

+      size_t n=v.size();

+      for(size_t i=0;i

       return 1;

     }

   int max()const

   {

     int ret=-0x7fffffff; //not completely correct, but kind of works for 64bit

-    for(int i=0;i

+    for(size_t i=0;i

     return ret;

   }

   int argMax()const

   {

 	  int iret=-1;

 	  int ret=-0x7fffffff; //not completely correct, but kind of works for 64bit

-	  for(int i=0;i

+	  for(size_t i=0;i

 	  return iret;

   }

   int min()const

   {

     int ret=0x7fffffff;

-    for(int i=0;i<v.size();i++)if(ret>v[i])ret=v[i];

+    for(size_t i=0;i<v.size();i++)if(ret>v[i])ret=v[i];

     return ret;

   }

   typ infinityNorm()const

   {

 	  typ a=0;

 	  typ b=0;

-	  for(int i=0;i

+	  for(size_t i=0;i

 		  {

 			  if(a

 			  if(b>v[i])b=v[i];

@@ -234,7 +234,7 @@ public:

 	  bool aOK=true;

 	  bool bOK=true;

-	  for(int i=0;i

+	  for(size_t i=0;i

 		  {

 			  aOK&=(v[i]

 			  bOK&=(v[i]>-k);

@@ -249,9 +249,9 @@ public:

       typ pq=dot(p,q);

       return pq*pq==pp*qq;

 */

-	  int n=p.size();

+	  size_t n=p.size();

 	  assert(n==q.size());

-	  int i;

+	  size_t i;

 	  for(i=0;i

 	  {

 		  if(p.v[i])break;

@@ -260,7 +260,7 @@ public:

 	  if(q.v[i]==0)return q.isZero();

 	  int64 a=p.v[i];

 	  int64 b=q.v[i];

-	  for(int j=0;j

+	  for(size_t j=0;j

 		  if(a*q.v[j]!=b*p.v[j])return false;

 	  return true;

     }

@@ -269,15 +269,15 @@ public:

   // Arithmetic slow

   //-----------------

   inline friend Vektor operator-(const Vektor& q){return -1*q;};

-  inline friend Vektor operator*(typ s, const Vektor& q){Vektor p=q;for(int i=0;i

-  inline friend Vektor operator/(const Vektor& q, typ s){Vektor p=q;for(int i=0;i

-  inline friend Vektor operator*(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1=p;for(int i=0;i

+  inline friend Vektor operator*(typ s, const Vektor& q){Vektor p=q;for(size_t i=0;i

+  inline friend Vektor operator/(const Vektor& q, typ s){Vektor p=q;for(size_t i=0;i

+  inline friend Vektor operator*(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1=p;for(size_t i=0;i

 //  inline friend Vektor operator+(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1=p;for(int i=0;i

-  inline friend Vektor operator+(const Vektor& p, const Vektor& q){if(p.size()!=q.size()){fprintf(stderr,"%i %i\n",p.size(),q.size());assert(p.size()==q.size());};Vektor p1=p;for(int i=0;i

-  inline friend Vektor operator-(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1=p;for(int i=0;i

-  friend Vektor max(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1=p;for(int i=0;i

-  friend Vektor min(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1=p;for(int i=0;i<p.size();i++)if(p1[i]>q[i])p1[i]=q[i];return p1;}

-  friend Vektor coordinatewiseProduct(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1(q.size());for(int i=0;i

+  inline friend Vektor operator+(const Vektor& p, const Vektor& q){if(p.size()!=q.size()){fprintf(stderr,"%i %i\n",p.size(),q.size());assert(p.size()==q.size());};Vektor p1=p;for(size_t i=0;i

+  inline friend Vektor operator-(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1=p;for(size_t i=0;i

+  friend Vektor max(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1=p;for(size_t i=0;i

+  friend Vektor min(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1=p;for(size_t i=0;i<p.size();i++)if(p1[i]>q[i])p1[i]=q[i];return p1;}

+  friend Vektor coordinatewiseProduct(const Vektor& p, const Vektor& q){assert(p.size()==q.size());Vektor p1(q.size());for(size_t i=0;i

   //------------------

   // Monomial related

@@ -285,8 +285,8 @@ public:

   int divides(const Vektor& q) const

     {

       assert(size()==q.size());

-      int n=v.size();

-      for(int i=0;i

+      size_t n=v.size();

+      for(size_t i=0;i

         {

           if(v[i]>0)if(q.v[i]

         }

@@ -295,14 +295,14 @@ public:

   inline friend bool relativelyPrime(const Vektor& p, const Vektor& q)

     {

       assert(p.size()==q.size());

-      int n=p.size();

-      for(int t=0;t<n;t++)if((p[t]>0)&&(q[t]>0)) return false;

+      size_t n=p.size();

+      for(size_t t=0;t<n;t++)if((p[t]>0)&&(q[t]>0)) return false;

       return true;

     }

   Vektor supportVector()const

     {

       Vektor r(v.size());

-      for(int i=0;i

+      for(size_t i=0;i

 	r[i]=(v[i]!=0);

       return r;

     }

@@ -313,7 +313,7 @@ public:

   Vektor subvector(int begin, int end)const

     {

       assert(begin>=0);

-      assert(end<=size());

+      assert((size_t)end<=size());

       assert(end>=begin);

       Vektor ret(end-begin);

       for(int i=0;i

@@ -331,36 +331,36 @@ public:

   {

 	  Vektor ret(subset.sum());

 	  int i=0;

-	  for(int j=0;j

+	  for(size_t j=0;j

 	  return ret;

   }

   Vektor expandedBoolean(Vektor<int> const &subset)const // Inverse of the above, except that unknown entries are set to zero.

   {

 	 Vektor ret(subset.size());

-	 int i=0;

-	 for(int j=0;j

+	 size_t i=0;

+	 for(size_t j=0;j

 		 if(subset[j])ret[j]=v[i++];

 	 return ret;

   }

   friend Vektor concatenation(Vektor const &a, Vektor const &b)

   {

     Vektor ret(a.size()+b.size());

-    for(int i=0;i

-    for(int i=0;i

+    for(size_t i=0;i

+    for(size_t i=0;i

     return ret;

   }

   Vektor expanded(int newSize, vector<int> const &positions)

   {

 	  Vektor ret(newSize);

 	  assert(positions.size()==size());

-	  for(int i=0;i

+	  for(size_t i=0;i

 	  return ret;

   }

   Vektor withIthCoordinateRemoved(int i)const

   {

 	  Vektor ret(size()-1);

 	  for(int j=0;j

-	  for(int j=i+1;j

+	  for(int j=i+1;(size_t)j

 	  return ret;

   }

   Vektor withIthCoordinateInserted(int i, const typ &a)const

@@ -368,7 +368,7 @@ public:

 	  Vektor ret(size()+1);

 	  for(int j=0;j

 	  ret[i]=a;

-	  for(int j=i;j

+	  for(int j=i;(size_t)j

 	  return ret;

   }

@@ -378,7 +378,7 @@ public:

   int indexOfLargestNonzeroEntry()const

   {

     int ret=-1;

-    for(int i=0;i

+    for(int i=0;(size_t)i

       {

 	if(v[i])ret=i;

       }

@@ -387,20 +387,20 @@ public:

   Vektor supportIndices()const

   {

     Vektor ret(0);

-    for(int i=0;i

+    for(int i=0;(size_t)i

       if(v[i]!=0)ret.push_back(i);

     return ret;

   }

   Vektor supportAsZeroOneVector()const

   {

     Vektor ret(v.size());

-    for(int i=0;i

+    for(size_t i=0;i

     return ret;

   }

   void calcsupport(void)

     {

       support=0;

-      for(int i=0;i<v.size();i++)support=(support<<1)|(((v[i]>0)==true)&1;;

+      for(size_t i=0;i<v.size();i++)support=(support<<1)|(((v[i]>0)==true)&1;;

     }

 };