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- send missing patch files

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OBS-URL: https://build.opensuse.org/package/show/science/gfan?expand=0&rev=6
This commit is contained in:
Corot Sebastien 2012-08-31 17:39:40 +00:00 committed by Git OBS Bridge
parent 064d365c33
commit 7d55281927
4 changed files with 575 additions and 0 deletions
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275
gfan-format.patch Normal file
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@ -0,0 +1,275 @@
--- ./genericwalk.cpp.orig 2011-01-25 08:33:16.000000000 -0700
+++ ./genericwalk.cpp 2011-04-27 13:42:52.227946066 -0600
@@ -202,7 +202,7 @@
g=newG;
nflips++;
- fprintf(Stderr,"Flip %i, new size %i\n",nflips,g.size());
+ fprintf(Stderr,"Flip %i, new size %zu\n",nflips,g.size());
}
fprintf(Stderr,"Number of flips:%i\n",nflips);
--- ./app_isgroebnerbasis.cpp.orig 2011-01-25 08:33:15.000000000 -0700
+++ ./app_isgroebnerbasis.cpp 2011-04-27 13:48:16.474949962 -0600
@@ -47,7 +47,7 @@
IntegerVectorListList sums;
IntegerVectorList polytope=minkowski(polytopes,&sums);
- fprintf(Stderr,"Number of extreme vertices in Minkowski sum: %i\n",polytope.size());
+ fprintf(Stderr,"Number of extreme vertices in Minkowski sum: %zu\n",polytope.size());
bool isGroebnerBasis=false;
int counter=0;
--- ./polyhedralfan.cpp.orig 2011-01-25 08:33:17.000000000 -0700
+++ ./polyhedralfan.cpp 2011-04-27 13:46:56.746866265 -0600
@@ -604,7 +604,7 @@
{
// log0 fprintf(Stderr,"rayComplexSymmetry - begin\n");
PolyhedralFan ret(n);
- log1 fprintf(Stderr,"Computing rays of %i cones\n",cones.size());
+ log1 fprintf(Stderr,"Computing rays of %zu cones\n",cones.size());
for(PolyhedralConeList::const_iterator i=cones.begin();i!=cones.end();i++)
{
{
@@ -812,7 +812,7 @@
SymmetryGroup localsym(n);
if(!sym)sym=&localsym;
set<IntegerVector> rays;
- log1 fprintf(Stderr,"Computing rays of %i cones\n",cones.size());
+ log1 fprintf(Stderr,"Computing rays of %zu cones\n",cones.size());
for(PolyhedralConeList::const_iterator i=cones.begin();i!=cones.end();i++)
{
{
@@ -1212,7 +1212,7 @@
static int t;
if((t&1023)==0)
{
- fprintf(Stderr,"clist size:%i\n",clist.size());
+ fprintf(Stderr,"clist size:%zu\n",clist.size());
}
t++;
}
--- ./bergman.cpp.orig 2011-01-25 08:33:16.000000000 -0700
+++ ./bergman.cpp 2011-04-27 13:45:37.266767581 -0600
@@ -149,7 +149,7 @@
if(0)
{
s=fullColoredIdeals(*g,false);
- fprintf(Stderr,"Full colored ideals computed, #=%i\n",s.size());
+ fprintf(Stderr,"Full colored ideals computed, #=%zu\n",s.size());
}
else
{
@@ -539,7 +539,7 @@
while(!active.empty())
{
log1 fprintf(Stderr,"\n-------------------------------------\n");
- log1 fprintf(Stderr,"Size of active set: %i, Completed: %i\n",active.size(),ret.cones.size());
+ log1 fprintf(Stderr,"Size of active set: %i, Completed: %zu\n",active.size(),ret.cones.size());
log1 fprintf(Stderr,"-------------------------------------\n");
AsciiPrinter p(Stderr);
--- ./symmetry.cpp.orig 2011-01-25 08:33:17.000000000 -0700
+++ ./symmetry.cpp 2011-04-27 13:43:45.571656038 -0600
@@ -300,7 +300,7 @@
l.push_back(*i);
}
P.printVectorList(l);
- fprintf(f,"Group order=%i\n",elements.size());
+ fprintf(f,"Group order=%zu\n",elements.size());
P.printString("Done printing SymmetryGroup.\n");
}
--- ./xfig.cpp.orig 2011-01-25 08:33:17.000000000 -0700
+++ ./xfig.cpp 2011-04-27 13:46:06.770948094 -0600
@@ -103,7 +103,7 @@
{
if(vertices.size())
{
- fprintf(f,"2 3 0 1 0 %i 50 0 25 0.000 0 0 -1 0 0 %i\n ",7,vertices.size()+1);
+ fprintf(f,"2 3 0 1 0 %i 50 0 25 0.000 0 0 -1 0 0 %zu\n ",7,vertices.size()+1);
for(Polygon::const_iterator i=vertices.begin();i!=vertices.end();i++)
kickPoint(*i,mode);
--- ./lp_cdd.cpp.orig 2011-01-25 08:33:16.000000000 -0700
+++ ./lp_cdd.cpp 2011-04-27 13:39:42.788631110 -0600
@@ -1287,8 +1287,8 @@
if(A->rowsize!=newLin.size()+newIn.size())
{
fprintf(stderr,"A->rowsize: %i\n",(int)A->rowsize);
- fprintf(stderr,"newLin.size(): %i\n",newLin.size());
- fprintf(stderr,"newIn.size(): %i\n",newIn.size());
+ fprintf(stderr,"newLin.size(): %zu\n",newLin.size());
+ fprintf(stderr,"newIn.size(): %zu\n",newIn.size());
dd_WriteMatrix(Stderr,A);
--- ./minkowskisum.cpp.orig 2011-01-25 08:33:16.000000000 -0700
+++ ./minkowskisum.cpp 2011-04-27 13:43:17.412392770 -0600
@@ -27,7 +27,7 @@
assert(f);
{
- fprintf(f,"%i",polytopes.size());
+ fprintf(f,"%zu",polytopes.size());
TopcomPrinter p(f);
//AsciiPrinter p(f);
--- ./xfig.h.orig 2011-01-25 08:33:19.000000000 -0700
+++ ./xfig.h 2011-04-27 13:40:09.491983874 -0600
@@ -52,7 +52,7 @@
void endDrawLine()
{
assert(p.size()>0);
- fprintf(f," %i\n",p.size());
+ fprintf(f," %zu\n",p.size());
if(arrowOrigin)
fprintf(f,"\t 2 1 1.00 60.00 120.00\n");
if(arrowTarget)
--- ./gmpallocator.cpp.orig 2011-01-25 08:33:16.000000000 -0700
+++ ./gmpallocator.cpp 2011-04-27 13:44:36.363523526 -0600
@@ -145,19 +145,19 @@
//Debug
void *myAllocateFunctionD(size_t alloc_size)
{
- fprintf(stderr,"Allocating: %i bytes.\n",alloc_size);
+ fprintf(stderr,"Allocating: %zu bytes.\n",alloc_size);
return malloc(alloc_size);
}
void *myReallocateFunctionD(void *ptr, size_t old_size, size_t new_size)
{
- fprintf(stderr,"Reallocating: %i --> %i bytes.\n",old_size,new_size);
+ fprintf(stderr,"Reallocating: %zu --> %zu bytes.\n",old_size,new_size);
return realloc(ptr,new_size);
}
void myDeallocateFunctionD(void *ptr, size_t size)
{
- fprintf(stderr,"Freeing: %i bytes.\n",size);
+ fprintf(stderr,"Freeing: %zu bytes.\n",size);
return free(ptr);
}
--- ./app_test.cpp.orig 2011-01-25 08:33:15.000000000 -0700
+++ ./app_test.cpp 2011-04-27 13:49:04.826968542 -0600
@@ -128,7 +128,7 @@
M[I]=minusOne*M[I];
}
- fprintf(Stdout,"Extreme permutations (%i):\n",extreme.size());
+ fprintf(Stdout,"Extreme permutations (%zu):\n",extreme.size());
P.printVectorList(extreme);
}
--- ./buchberger.cpp.orig 2011-01-25 08:33:16.000000000 -0700
+++ ./buchberger.cpp 2011-04-27 13:41:04.116614389 -0600
@@ -540,7 +540,7 @@
{
static int t;
t++;
- if((t&31)==0)fprintf(Stderr," spolys:%i\n",sPolynomials.size());
+ if((t&31)==0)fprintf(Stderr," spolys:%zu\n",sPolynomials.size());
}
{
@@ -565,7 +565,7 @@
{
static int t;
if(((++t)&=31)==0)
- fprintf(Stderr,"gsize:%i spolys:%i\n",g->size()+1,sPolynomials.size());
+ fprintf(Stderr,"gsize:%zu spolys:%zu\n",g->size()+1,sPolynomials.size());
}
PolynomialSet::iterator j=g->end();j--;
updatePairs(sPolynomials,g,&redundantOnes,j,indexj,truncationDegree,&grading);
--- ./halfopencone.cpp.orig 2011-01-25 08:33:16.000000000 -0700
+++ ./halfopencone.cpp 2011-04-27 13:47:51.531488017 -0600
@@ -555,14 +555,14 @@
{
HalfOpenConeList surface=tropicalHyperSurface(*i);
- fprintf(Stderr,"Number of cones in current intersection:%i\n",intersection.size());
- fprintf(Stderr,"Number of cones in next surface:%i\n",surface.size());
+ fprintf(Stderr,"Number of cones in current intersection:%zu\n",intersection.size());
+ fprintf(Stderr,"Number of cones in next surface:%zu\n",surface.size());
fprintf(Stderr,"A\n");
intersection=refinement(intersection,surface);
fprintf(Stderr,"B\n");
}
- fprintf(Stderr,"%i",intersection.size());
+ fprintf(Stderr,"%zu",intersection.size());
return intersection;
}
--- ./app_normalfancleanup.cpp.orig 2011-01-25 08:33:15.000000000 -0700
+++ ./app_normalfancleanup.cpp 2011-04-27 13:51:05.227545050 -0600
@@ -71,7 +71,7 @@
FILE *f=fopen("iteraTIon","w");
if(f)
{
- fprintf(f,"%i:%i\n",a,l2.size());
+ fprintf(f,"%i:%zu\n",a,l2.size());
fclose(f);
}
}
--- ./app_secondaryfan.cpp.orig 2011-01-25 08:33:15.000000000 -0700
+++ ./app_secondaryfan.cpp 2011-04-27 13:50:21.635232740 -0600
@@ -142,7 +142,7 @@
while(1)
{
- fprintf(stdout,"Triangles in current triangulation:%i\n",a.bases.size());
+ fprintf(stdout,"Triangles in current triangulation:%zu\n",a.bases.size());
PolyhedralCone C=a.secondaryCone();
C.canonicalize();
@@ -198,7 +198,7 @@
while(1)
{
- fprintf(stdout,"Triangles in current triangulation:%i\n",a.bases.size());
+ fprintf(stdout,"Triangles in current triangulation:%zu\n",a.bases.size());
// PolyhedralCone C=a.secondaryCone();
// C.canonicalize();
@@ -214,7 +214,7 @@
{
Triangulation2 b=a;
b.flipNew(-*i);
- fprintf(stdout,"Triangles in new triangulation:%i\n",b.bases.size());
+ fprintf(stdout,"Triangles in new triangulation:%zu\n",b.bases.size());
if(b.bases.size()==abortAtSize)
{
--- ./app_intsinpolytope.cpp.orig 2011-01-25 08:33:15.000000000 -0700
+++ ./app_intsinpolytope.cpp 2011-04-27 13:49:42.202664015 -0600
@@ -104,7 +104,7 @@
}
}
- fprintf(stderr,"Sets to test: %i\n",setsToCheck.size());
+ fprintf(stderr,"Sets to test: %zu\n",setsToCheck.size());
set<set<int> > ret;
for(set<set<int> >::const_iterator i=setsToCheck.begin();i!=setsToCheck.end();i++)
@@ -118,7 +118,7 @@
if(isPartOfAZBasis(l))ret.insert(*i);
}
- fprintf(stderr,"Produced sets: %i\n",ret.size());
+ fprintf(stderr,"Produced sets: %zu\n",ret.size());
return ret;
}
--- ./app_tropicaltraverse.cpp.orig 2011-01-25 08:33:15.000000000 -0700
+++ ./app_tropicaltraverse.cpp 2011-04-27 13:48:41.939379788 -0600
@@ -156,7 +156,7 @@
BergmanFan f=bergman(coneGroebnerBasis,idealGroebnerBasis,&s);
f.computeMultiplicities();
/* log1 fprintf(Stderr,"Is simplicial: %s\n",f.isSimplicial()?"true":"false");*/
- log1 fprintf(Stderr,"Order of input symmetry group: %i\n",s.elements.size());
+ log1 fprintf(Stderr,"Order of input symmetry group: %zu\n",s.elements.size());
log1 fprintf(Stderr,"Number of maximal cones: %i\n",f.numberOfMaximalCones());
log1 fprintf(Stderr,"Modulo the homogeneity space:\n");
log1 AsciiPrinter(Stderr).printVectorList(hv);

18
gfan-permissive.patch Normal file
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@ -0,0 +1,18 @@
diff -up gfan0.5/app_main.cpp.orig gfan0.5/app_main.cpp
--- gfan0.5/app_main.cpp.orig 2012-07-05 12:10:18.377378026 -0400
+++ gfan0.5/app_main.cpp 2012-07-05 12:10:24.414378093 -0400
@@ -76,14 +76,6 @@ public:
int main()
{
- if(name1[0]==0)
- {
- debug<<"This is the Gfan program for computing Groebner fans and tropical varieties.\n"
- "Use the command \"gfan list\" to view all subcommands.\n"
- "The command \"gfan\" is deprecate for computing all Groebner bases of an ideal.\n"
- "Please use subcommand \"gfan _bases\" instead. Awaiting input. <Ctrl>-D to end.\n";
- }
-
LexicographicTermOrder myOrder;
PolynomialSet g=FileParser(Stdin).parsePolynomialSetWithRing();

33
gfan-respect-destdir.patch Normal file
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@ -0,0 +1,33 @@
--- Makefile.orig 2011-01-25 08:33:19.000000000 -0700
+++ Makefile 2011-04-25 16:07:52.441724570 -0600
@@ -308,11 +308,11 @@
all: $(MAIN)
-$(BINDIR): $(PREFIX)
- $(MKDIR) $(BINDIR)
+$(DESTDIR)$(BINDIR): $(DESTDIR)$(PREFIX)
+ $(MKDIR) $(DESTDIR)$(BINDIR)
-$(PREFIX):
- $(MKDIR) $(PREFIX)
+$(DESTDIR)$(PREFIX):
+ $(MKDIR) -p $(DESTDIR)$(PREFIX)
default: $(OBJECTS) $(ADDITIONALOBJECTS) $(EXECS)
@@ -419,11 +419,11 @@
clean:
/bin/rm -f *.o $(EXECS) $(MAIN)
-install: $(BINDIR)
- cp $(EXECS) $(BINDIR)
+install: $(DESTDIR)$(BINDIR)
+ cp $(EXECS) $(DESTDIR)$(BINDIR)
# cp $(EXECS) /usr/local/bin
# ./gfan installlinks --path $(BINDIR)/
- cd $(BINDIR) && ./gfan installlinks
+ cd $(DESTDIR)$(BINDIR) && ./gfan installlinks
library:
/bin/rm -f gfanlib/*.a
/bin/rm -f gfanlib/*.o

249
gfan-warning.patch Normal file
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@ -0,0 +1,249 @@
--- ./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:\""<<command3<<"\""<<endl;
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"<<w;
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<v.size();i++)if(ret=v[i])break;
+ for(int i=0;i<v.size();i++)if((ret=v[i]))break;
if(ret<0)ret=-ret;
assert(ret!=0);
for(int i=0;i<v.size();i++)ret=gcdGFAN(ret,v[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<<c.inequalities<<std::endl;
f<<"Equations:"<<std::endl;
f<<c.equations<<std::endl;
+ 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<n;j++)
@@ -1029,7 +1029,7 @@ bool fastIsFacet(IntegerVectorList const
// log0 fprintf(Stderr,"LP\n");
return isFacet(normals,i);
}
-*/
+#endif
IntegerVectorList fastNormals(IntegerVectorList const &inequalities)
{