5 files changed, 342 insertions, 0 deletions

diff --git a/biology/adun/files/patch-AdunLinkedList.m b/biology/adun/files/patch-AdunLinkedList.m
new file mode 100644
index 000000000000..165fbbf6fcb0
--- /dev/null
+++ b/biology/adun/files/patch-AdunLinkedList.m
@@ -0,0 +1,14 @@
+--- Kernel/AdunKernel/Framework/AdunLinkedList.m.orig	Tue Jun 13 12:16:44 2006
++++ Kernel/AdunKernel/Framework/AdunLinkedList.m	Sun Nov  5 13:34:01 2006
+@@ -109,7 +109,11 @@
+ 	NSDebugLLog(@"AdListMemoryManagement", @"Creating New Block - There are now %d blocks", block_no);
+ 	//On 64 bit machines we should align on a 64 bit boundary
+ 
++#ifndef __FreeBSD__
+ 	posix_memalign((void**)&listPointer, 32, BLOCKSIZE*sizeof(ListElement));
++#else
++	listPointer = malloc(BLOCKSIZE*sizeof(ListElement));
++#endif
+ 	blocks[block_no-1] = listPointer;
+ 
+ 	return blocks[block_no-1];
diff --git a/biology/adun/files/patch-AdunMemoryManager.h b/biology/adun/files/patch-AdunMemoryManager.h
new file mode 100644
index 000000000000..e88031346f82
--- /dev/null
+++ b/biology/adun/files/patch-AdunMemoryManager.h
@@ -0,0 +1,22 @@
+--- Kernel/AdunKernel/Headers/AdunKernel/AdunMemoryManager.h.orig	Tue Jun 13 12:16:44 2006
++++ Kernel/AdunKernel/Headers/AdunKernel/AdunMemoryManager.h	Sun Nov  5 13:16:58 2006
+@@ -24,7 +24,9 @@
+ #define _ADUNIOMANAGER_
+ 
+ #include <stdlib.h>
++#ifndef __FreeBSD__
+ #include <malloc.h>
++#endif
+ #include "Base/InterTable.h"
+ #include "AdunKernel/AdunDefinitions.h"
+ #include "AdunKernel/AdunObject.h"
+@@ -38,7 +40,9 @@
+ 
+ @interface AdMemoryManager: AdObject 
+ {
++#ifndef __FreeBSD__
+ 	struct mallinfo mem_struct;
++#endif
+ 	BOOL MEMORY_STATS;
+ }
+ 
diff --git a/biology/adun/files/patch-AdunMemoryManager.m b/biology/adun/files/patch-AdunMemoryManager.m
new file mode 100644
index 000000000000..c1d7235482b7
--- /dev/null
+++ b/biology/adun/files/patch-AdunMemoryManager.m
@@ -0,0 +1,266 @@
+--- Kernel/AdunKernel/Framework/AdunMemoryManager.m.orig	Tue Jun 13 12:16:44 2006
++++ Kernel/AdunKernel/Framework/AdunMemoryManager.m	Sun Nov  5 13:15:25 2006
+@@ -68,6 +68,7 @@
+ 	NSError* error;
+ 	NSMutableDictionary* errorDict;
+ 
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -77,6 +78,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ 	//The return value of malloc(0) is implementation dependant
+ 	//It can return NULL in which case it is indistinguisable from
+@@ -133,6 +135,7 @@
+ 	
+ 	memset(array, 0, size);
+ 	
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -143,6 +146,7 @@
+ 			mem_struct.fordblks); 
+ 		fflush(stderr);
+ 	}
++#endif
+ 
+ 
+ 	return array;
+@@ -154,6 +158,7 @@
+ 	double *array;
+ 	AdMatrix *matrix;
+ 
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -163,6 +168,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ 	matrix = (AdMatrix*)malloc(sizeof(AdMatrix));
+ 	matrix->no_rows = no_rows;
+@@ -172,6 +178,7 @@
+ 	for(i=0, j=0; i < no_rows; i++, j = j + no_columns)
+ 			matrix->matrix[i] = array + j;
+ 
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -181,6 +188,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON,
+ 		 	mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ 	return matrix;
+ }
+@@ -191,6 +199,7 @@
+ 	int *array;
+ 	IntMatrix *matrix;
+ 
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -200,6 +209,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ 	matrix = (IntMatrix*)malloc(sizeof(IntMatrix));
+ 	matrix->no_rows = no_rows;
+@@ -209,6 +219,7 @@
+ 	for(i=0, j=0; i < no_rows; i++, j = j + no_columns)
+ 			matrix->matrix[i] = array + j;
+ 
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -220,6 +231,7 @@
+ 	}
+ 
+ 	return matrix;
++#endif
+ }
+ 
+ - (InterTable*) allocateInterTableWithRows: (int) no_rows withColumns: (int) no_columns
+@@ -228,6 +240,7 @@
+ 	double *array;
+ 	InterTable *table;
+ 	
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -237,6 +250,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON,
+ 			 mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ 	table = (InterTable*)malloc(sizeof(InterTable));
+ 	table->no_interactions = no_rows;
+@@ -248,6 +262,7 @@
+ 	for(i=0, j=0; i < no_rows; i++, j = j + no_columns)
+ 			table->table[i] = array + j;
+ 	
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -257,12 +272,14 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ 	return table;
+ }
+ 
+ - (void) freeArray: (void*)array
+ {	
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -272,9 +289,11 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ 	free(array);
+ 
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -284,6 +303,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ }
+ 
+ /** Do not use this method to free matrices not allocated by one of the
+@@ -297,6 +317,7 @@
+ 	free(matrix[0]); 	//frees the number array	
+ 	free(matrix);		//frees the index array	
+ 
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -306,6 +327,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ }
+ 
+@@ -313,6 +335,7 @@
+ {
+ 	//matrices are allocated as arrays
+ 	//with another array of indexes
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -322,6 +345,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ 	if(matrix->no_rows != 0)
+ 	{
+@@ -330,6 +354,7 @@
+ 	}
+ 	free(matrix);
+ 	
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -339,10 +364,12 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ }
+ 
+ - (void) freeIntMatrix: (IntMatrix*) matrix 
+ {
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -352,6 +379,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ 	if(matrix->no_rows != 0)
+ 	{
+@@ -360,6 +388,7 @@
+ 	}
+ 	free(matrix);
+ 	
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -369,6 +398,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ }
+ 
+ - (void) freeInterTable: (InterTable*) matrix  
+@@ -376,6 +406,7 @@
+ 	//matrices are allocated as arrays
+ 	//with another array of indexes
+ 	
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -385,6 +416,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ 
+ 	if(matrix->no_interactions != 0)
+ 	{
+@@ -394,6 +426,7 @@
+ 
+ 	free(matrix);
+ 	
++#ifndef __FreeBSD__
+ 	if(MEMORY_STATS==YES)
+ 	{
+ 		mem_struct = mallinfo();
+@@ -403,6 +436,7 @@
+ 			(float)mem_struct.uordblks/(float)MEM_CON, 
+ 			mem_struct.fordblks); 
+ 	}
++#endif
+ }
+ 
+ @end
diff --git a/biology/adun/files/patch-GNUmakefile b/biology/adun/files/patch-GNUmakefile
new file mode 100644
index 000000000000..e9ab0c8dc869
--- /dev/null
+++ b/biology/adun/files/patch-GNUmakefile
@@ -0,0 +1,17 @@
+--- GNUmakefile.orig	Tue Apr  4 18:23:24 2006
++++ GNUmakefile	Sun Nov  5 13:56:03 2006
+@@ -2,12 +2,12 @@
+ include $(GNUSTEP_MAKEFILES)/common.make
+ 
+ SUBPROJECTS =  Kernel/ MolTalk/ UL/ 
+-GNUSTEP_INSTALLATION_DIR=$(HOME)/GNUstep
++#GNUSTEP_INSTALLATION_DIR=$(HOME)/GNUstep
+ 
+ #Rpm
+ 
+ PACKAGE_NAME=Adun
+-PACKAGE_VERSION=0.5
++PACKAGE_VERSION=0.6
+ 
+ -include GNUmakefile.preamble
+ 
diff --git a/biology/adun/files/patch-main.m b/biology/adun/files/patch-main.m
new file mode 100644
index 000000000000..fff8726b3ebb
--- /dev/null
+++ b/biology/adun/files/patch-main.m
@@ -0,0 +1,23 @@
+--- Kernel/main.m.orig	Mon Aug  7 12:17:30 2006
++++ Kernel/main.m	Sun Nov  5 13:27:26 2006
+@@ -3,7 +3,9 @@
+ #include <stdio.h>
+ #include <float.h>
+ #include <fenv.h>
++#ifndef __FreeBSD__
+ #include <mcheck.h>
++#endif
+ #include "AdunKernel/AdunKernel.h"
+ 
+ /** \mainpage
+@@ -250,8 +252,10 @@
+ 
+ 	if([[NSUserDefaults standardUserDefaults] boolForKey: @"TraceMemory"] == YES)
+ 	{
++#ifndef __FreeBSD__
+ 		mtrace();
+ 		mcheck(NULL);
++#endif
+ 	}
+ 
+ 	logFile = [[NSUserDefaults standardUserDefaults] stringForKey: @"LogFile"];