Author: yavor-guest
Date: 2014-05-30 18:29:16 +0000 (Fri, 30 May 2014)
New Revision: 17020

Added:
   trunk/packages/adun.app/trunk/debian/patches/gcc-warnings.patch
Modified:
   trunk/packages/adun.app/trunk/debian/changelog
   trunk/packages/adun.app/trunk/debian/patches/series
Log:
gcc-warnings.patch: New, adapt to the new GNUstep API
and fix some important warnings (Closes: #749733).


Modified: trunk/packages/adun.app/trunk/debian/changelog
===================================================================
--- trunk/packages/adun.app/trunk/debian/changelog      2014-05-29 13:26:50 UTC 
(rev 17019)
+++ trunk/packages/adun.app/trunk/debian/changelog      2014-05-30 18:29:16 UTC 
(rev 17020)
@@ -1,3 +1,11 @@
+adun.app (0.81-7) UNRELEASED; urgency=low
+
+  * debian/patches/gcc-warnings.patch: New, adapt to the new GNUstep API
+    and fix some important warnings (Closes: #749733).
+  * debian/patches/series: Update.
+
+ -- Yavor Doganov <[email protected]>  Fri, 30 May 2014 21:27:17 +0300
+
 adun.app (0.81-6) unstable; urgency=low
 
   [ Charles Plessy ]

Added: trunk/packages/adun.app/trunk/debian/patches/gcc-warnings.patch
===================================================================
--- trunk/packages/adun.app/trunk/debian/patches/gcc-warnings.patch             
                (rev 0)
+++ trunk/packages/adun.app/trunk/debian/patches/gcc-warnings.patch     
2014-05-30 18:29:16 UTC (rev 17020)
@@ -0,0 +1,592 @@
+Description: Adapt to the new GNUstep API and fix few gcc warnings.
+ Fixes the following warnings, most of them due to changes of
+ data types in recent gnustep-base.  NSNotFound is 64-bit as of
+ -base/1.24, so use the right data type when comparing.
+ .
+ comparison is always true/false due to limited range of data type
+ passing argument N of 'foo' from incompatible pointer type
+ array subscript is above array bounds
+ comparison between pointer and integer
+ comparison between signed and unsigned integer expressions
+ overflow in implicit constant conversion
+ 'dataSet' is used uninitialized in this function
+ assignment makes integer from pointer without a cast
+Author: Yavor Doganov <[email protected]>
+Bug-Debian: http://bugs.debian.org/749733
+Forwarded: no
+Last-Update: 2014-05-30
+---
+
+--- adun.app-0.81.orig/Kernel/AdunKernel/CoreAdditions/AdunTrajectory.m
++++ adun.app-0.81/Kernel/AdunKernel/CoreAdditions/AdunTrajectory.m
+@@ -209,7 +209,7 @@
+ - (BOOL) compareCheckpointsForSystem: (id) aSystem inTrajectory: 
(AdTrajectory*) aTrajectory toSystem: (id) ourSystem range: (NSRange) range
+ {
+       BOOL retval = NO;
+-      int i;
++      NSUInteger i;
+       AdMatrix* matrixOne, *matrixTwo;
+       
+       if(NSMaxRange(range) > [self numberTrajectoryCheckpoints]) 
+--- adun.app-0.81.orig/Kernel/AdunKernel/CoreAdditions/AdunTemplateProcessor.m
++++ adun.app-0.81/Kernel/AdunKernel/CoreAdditions/AdunTemplateProcessor.m
+@@ -341,7 +341,7 @@
+       }
+       
+       allKeys = [NSMutableArray array];
+-      if(![testTemplate objectForKey: @"externalObjects"] == nil)
++      if([testTemplate objectForKey: @"externalObjects"] != nil)
+               [allKeys addObjectsFromArray: [[testTemplate objectForKey: 
@"externalObjects"] allKeys]];
+ 
+       [allKeys addObjectsFromArray: [[testTemplate objectForKey: 
@"objectTemplates"] allKeys]];
+--- 
adun.app-0.81.orig/Kernel/AdunKernel/CoreAdditions/AdunFileSystemSimulationStorage.m
++++ 
adun.app-0.81/Kernel/AdunKernel/CoreAdditions/AdunFileSystemSimulationStorage.m
+@@ -181,7 +181,7 @@
+ + (void) initialize
+ {
+       [[NSUserDefaults standardUserDefaults] registerDefaults:
+-              [NSDictionary dictionaryWithObject: [NSNumber numberWithInt: 
100]
++              [NSDictionary dictionaryWithObject: [NSNumber 
numberWithUnsignedInt: 100]
+                       forKey: @"CacheLimit"]];
+ }
+ 
+@@ -375,7 +375,7 @@
+               trajectoryInfoPath = [storagePath 
stringByAppendingPathComponent: @"trajectoryInformation.ad"];
+               energyPath = [storagePath stringByAppendingPathComponent: 
@"energy.ad"];
+               systemPath = [storagePath stringByAppendingPathComponent: 
@"system.ad"];
+-              cacheLimit = [[NSUserDefaults standardUserDefaults]
++              cacheLimit = (NSUInteger)[[NSUserDefaults standardUserDefaults]
+                               integerForKey: @"CacheLimit"];
+               
+               if(storageMode == AdSimulationStorageUpdateMode)
+--- adun.app-0.81.orig/Kernel/AdunKernel/Framework/AdunSimpleListHandler.m
++++ adun.app-0.81/Kernel/AdunKernel/Framework/AdunSimpleListHandler.m
+@@ -113,7 +113,7 @@
+       int i, j, k;
+       int incount, outcount;
+       int retVal, noAtoms;
+-      unsigned int* indexBuffer;
++      NSUInteger* indexBuffer;
+       NSIndexSet* indexSet;
+       NSRange indexRange;
+       ListElement *list_p;
+@@ -137,7 +137,7 @@
+       out_p = (ListElement*)malloc(sizeof(ListElement));
+       endin_p = AdLinkedListCreate(in_p);
+       endout_p = AdLinkedListCreate(out_p);
+-      indexBuffer = malloc(100*sizeof(int));
++      indexBuffer = malloc(100*sizeof(NSUInteger));
+       noAtoms = [interactions count]; 
+ 
+       incount = outcount = 0;
+--- adun.app-0.81.orig/Kernel/AdunKernel/Framework/AdFrameworkFunctions.m
++++ adun.app-0.81/Kernel/AdunKernel/Framework/AdFrameworkFunctions.m
+@@ -350,7 +350,7 @@
+ 
+ void AdLogMatrixRows(NSIndexSet* indexSet, AdMatrix* matrix)
+ {
+-      int index;
++      NSUInteger index;
+       
+       index = [indexSet indexGreaterThanIndex: matrix->no_rows - 1];
+       if(index != NSNotFound)
+--- adun.app-0.81.orig/Kernel/AdunKernel/Framework/AdunDataMatrix.m
++++ adun.app-0.81/Kernel/AdunKernel/Framework/AdunDataMatrix.m
+@@ -103,8 +103,9 @@
+ 
+ - (NSArray*) subarrayFromElementSelection: (NSIndexSet*) indexSet
+ {
+-      int index, i;
+-      unsigned int* buffer;
++      int i;
++      NSUInteger index;
++      NSUInteger* buffer;
+       NSMutableArray* subarray = [NSMutableArray new];
+       NSArray* arrayCopy;
+ 
+@@ -113,14 +114,14 @@
+ 
+       if(index != NSNotFound)
+       {
+-              if(index >= (int)[self count])
++              if(index >= [self count])
+                       [NSException raise: NSRangeException
+                               format: @"Index %d is out of range (%d)", 
+                               index,
+                               [self count]];
+ 
+               //FIXME: Switch to using buffer for efficency
+-              buffer = (unsigned int*)malloc([indexSet count]*sizeof(unsigned 
int));
++              buffer = malloc([indexSet count]*sizeof(NSUInteger));
+               [indexSet getIndexes: buffer 
+                           maxCount: [indexSet count]
+                       inIndexRange: NULL];
+@@ -750,7 +751,7 @@
+ 
+ - (id) valueForKey: (NSString*) key
+ {
+-      int index;
++      NSUInteger index;
+       id value;
+       
+       NSDebugLLog(@"AdDataMatrix", @"Request for key %@", key);
+@@ -848,7 +849,7 @@
+ - (id) elementAtRow: (unsigned int) row 
+       ofColumnWithHeader: (NSString*) columnHeader 
+ {
+-      int columnIndex;
++      NSUInteger columnIndex;
+ 
+       if((columnIndex = [columnHeaders indexOfObject: columnHeader]) == 
NSNotFound)
+               [NSException raise: NSInvalidArgumentException
+@@ -874,7 +875,7 @@
+ 
+ - (NSArray*) columnWithHeader: (NSString*) columnHeader
+ {
+-      int columnIndex;
++      NSUInteger columnIndex;
+ 
+       if((columnIndex = [columnHeaders indexOfObject: columnHeader]) == 
NSNotFound)
+               [NSException raise: NSInvalidArgumentException
+@@ -922,7 +923,7 @@
+ - (void) addColumnWithHeader: (NSString*) columnHeader
+               toArray: (NSMutableArray*) anArray
+ {
+-      int columnIndex;
++      NSUInteger columnIndex;
+ 
+       if((columnIndex = [columnHeaders indexOfObject: columnHeader]) == 
NSNotFound)
+               [NSException raise: NSInvalidArgumentException
+@@ -1024,7 +1025,7 @@
+ 
+ - (NSString*) dataTypeForColumnWithHeader: (NSString*) columnHeader
+ {
+-      int columnIndex;
++      NSUInteger columnIndex;
+ 
+       if((columnIndex = [columnHeaders indexOfObject: columnHeader]) == 
NSNotFound)
+               [NSException raise: NSInvalidArgumentException
+@@ -1143,8 +1144,9 @@
+ */
+ - (AdDataMatrix*) submatrixFromRowSelection: (NSIndexSet*) indexSet
+ {
+-      int index, i;
+-      unsigned int* buffer;
++      int i;
++      NSUInteger index;
++      NSUInteger* buffer;
+       NSMutableArray* rows = [NSMutableArray new];
+       AdDataMatrix* submatrix;
+ 
+@@ -1153,7 +1155,7 @@
+ 
+       if(index != NSNotFound)
+       {
+-              if(index >= (int)numberOfRows)
++              if(index >= numberOfRows)
+                       [NSException raise: NSRangeException
+                               format: @"Index %d is out of row range (%d)", 
+                               index,
+@@ -1162,7 +1164,7 @@
+               //Dont use subarrayFromElementSelection: since that
+               //will return an array containing the actual NSMutableArrays
+               //used by the object.
+-              buffer = (unsigned int*)malloc([indexSet count]*sizeof(unsigned 
int));
++              buffer = malloc([indexSet count]*sizeof(NSUInteger));
+               [indexSet getIndexes: buffer 
+                           maxCount: [indexSet count]
+                       inIndexRange: NULL];
+@@ -1191,7 +1193,7 @@
+ */
+ - (AdDataMatrix*) submatrixFromColumnSelection: (NSIndexSet*) indexSet
+ {
+-      int index;
++      NSUInteger index;
+       id row;
+       NSArray* array;
+       NSMutableArray* rows = [NSMutableArray new];
+@@ -1203,7 +1205,7 @@
+ 
+       if(index != NSNotFound)
+       {
+-              if(index >= (int)numberOfColumns)
++              if(index >= numberOfColumns)
+                       [NSException raise: NSRangeException
+                               format: @"Index %d is out of column range 
(%d)", 
+                               index,
+@@ -1263,7 +1265,7 @@
+       int i,j;
+       int matrixElements;
+       int count;
+-      unsigned int length; 
++      NSUInteger length;
+       double *matrixStore;
+       NSMutableArray* matrixRow;
+       NSNumber *element;
+@@ -1514,7 +1516,8 @@
+ 
+ - (id) initWithCoder: (NSCoder*) decoder
+ {     
+-      unsigned int length, encodedByteOrder;
++      unsigned int encodedByteOrder;
++      NSUInteger length;
+       void *bytes;
+       NSData* numericData, *stringData;
+       AdByteSwapFlag byteSwapFlag;
+@@ -1982,7 +1985,7 @@
+       ofColumnWithHeader: (NSString*) columnHeader 
+       withValue: (id) value;
+ {
+-      int columnIndex;
++      NSUInteger columnIndex;
+ 
+       if((columnIndex = [columnHeaders indexOfObject: columnHeader]) == 
NSNotFound)
+               [NSException raise: NSInvalidArgumentException
+@@ -2129,7 +2132,8 @@
+ 
+ - (void) extendMatrixWithColumnValues: (NSDictionary*) values
+ {
+-      unsigned int i, index;
++      unsigned int i;
++      NSUInteger index;
+       NSMutableArray *row;
+       NSEnumerator* keyEnum;
+       id key;
+@@ -2175,7 +2179,7 @@
+ 
+ - (void) removeRowsWithIndexes: (NSIndexSet*) indexSet
+ {
+-      unsigned int* buffer;
++      NSUInteger* buffer;
+ 
+       if([indexSet lastIndex] == NSNotFound)
+               return;
+@@ -2189,7 +2193,7 @@
+       //maybe one day this will be implemented - only in Cocoa for now
+       //[matrix removeObjectsWithIndexes: indexSet];
+ 
+-      buffer = (unsigned int*)malloc([indexSet count]*sizeof(unsigned int));
++      buffer = malloc([indexSet count]*sizeof(NSUInteger));
+       [indexSet getIndexes: buffer 
+                       maxCount: [indexSet count]
+                       inIndexRange: NULL];
+--- adun.app-0.81.orig/Kernel/AdunKernel/Framework/AdunContainerDataSource.m
++++ adun.app-0.81/Kernel/AdunKernel/Framework/AdunContainerDataSource.m
+@@ -184,7 +184,8 @@
+ - (void) _createNonbondedPairs
+ {
+       int i, j;
+-      int currentNumberOfAtoms, currentAtom, index, offsetIndex;
++      int currentNumberOfAtoms, currentAtom, offsetIndex;
++      NSUInteger index;
+       id dataSourceNonbonded;
+       NSMutableIndexSet* indexes, *sourceIndexes, *currentInteractions;
+       NSRange indexRange;
+--- adun.app-0.81.orig/Kernel/AdunKernel/Framework/AdunHarmonicConstraintTerm.m
++++ adun.app-0.81/Kernel/AdunKernel/Framework/AdunHarmonicConstraintTerm.m
+@@ -165,7 +165,8 @@
+ 
+ - (void) evaluateForces
+ {
+-      int index, i, j;
++      int i, j;
++      NSUInteger index;
+       double forceMagnitude, rLength;
+       Vector3D difference;
+       AdMatrix* newCoordinates;
+@@ -189,7 +190,7 @@
+               //Force on the atom is towards original position
+               rLength = 1/difference.length;
+               for(j=0;j<3;j++)
+-                      forceMatrix->matrix[index][i] = 
forceMagnitude*difference.vector[i]*rLength;
++                      forceMatrix->matrix[index][j] = 
forceMagnitude*difference.vector[j]*rLength;
+               
+               energy += -1*difference.length*forceMagnitude*0.5; 
+               index = [elementIndexes indexGreaterThanIndex: index];
+@@ -198,7 +199,8 @@
+ 
+ - (void) evaluateEnergy
+ {
+-      int index, i;
++      int i;
++      NSUInteger index;
+       Vector3D difference;
+       AdMatrix* newCoordinates;
+       
+--- adun.app-0.81.orig/Kernel/AdunKernel/Framework/AdIndexSetConversions.m
++++ adun.app-0.81/Kernel/AdunKernel/Framework/AdIndexSetConversions.m
+@@ -111,7 +111,8 @@
+ - (id) initWithCoder: (NSCoder*) decoder
+ {
+       int byteSwapFlag;
+-      unsigned int i, encodedByteOrder, length;
++      unsigned int i, encodedByteOrder;
++      NSUInteger length;
+       NSRange* rangeArray, *range;
+       NSIndexSet* indexSet;
+ 
+--- adun.app-0.81.orig/Kernel/AdunKernel/Framework/AdunElementSelection.m
++++ adun.app-0.81/Kernel/AdunKernel/Framework/AdunElementSelection.m
+@@ -274,7 +274,7 @@
+                       restrictToRows: (NSIndexSet*) restrictRows
+ {
+       unsigned int i, numberRows, index;
+-      unsigned int *buffer;
++      NSUInteger *buffer;
+       NSRange matrixRange;
+       NSString *name;
+       NSArray *types, *categoryData;
+@@ -343,7 +343,7 @@
+       //Put all non selected indexes into a buffer for speed
+       numberRows = [nonSelectedRows count];
+       buffer = [[AdMemoryManager appMemoryManager] 
+-                      allocateArrayOfSize: numberRows*sizeof(int)];
++                      allocateArrayOfSize: numberRows*sizeof(NSUInteger)];
+       [nonSelectedRows getIndexes: buffer maxCount: numberRows inIndexRange: 
NULL];
+       
+       //Iterate through the string specifiers and find which of the groups 
match them.
+--- adun.app-0.81.orig/Kernel/AdunKernel/Framework/AdunDataSource.m
++++ adun.app-0.81/Kernel/AdunKernel/Framework/AdunDataSource.m
+@@ -508,7 +508,7 @@
+       int i, j, count;
+       int totalRanges, totalSets;
+       int byteSwapFlag;
+-      unsigned int length;
++      NSUInteger length;
+       int* rangesPerSet, *value;
+       NSRange* totalRangeArray;
+       NSRange* rangeArray, *range;
+@@ -1212,7 +1212,7 @@
+ 
+ - (void) removeElements: (NSIndexSet*) indexSet
+ {
+-      unsigned int index;
++      NSUInteger index;
+       
+       //We do this check first since if the index set is empty
+       //the next test will raise an NSRangeException 
+--- 
adun.app-0.81.orig/Kernel/AdunKernel/Headers/AdunKernel/AdunFileSystemSimulationStorage.h
++++ 
adun.app-0.81/Kernel/AdunKernel/Headers/AdunKernel/AdunFileSystemSimulationStorage.h
+@@ -70,7 +70,7 @@
+       NSString* systemPath;
+       NSFileHandle* energyHandle;
+       NSFileHandle* trajectoryHandle;
+-      int cacheLimit;                         //Number of frames to be kept 
in the cache
++      NSUInteger cacheLimit;                  //Number of frames to be kept 
in the cache
+       int numberTrajectoryCheckpoints;        //Number of trajectory 
checkpoints in the store
+       int numberTopologyCheckpoints;          //Number of topology 
checkpoints in the store
+       NSMutableArray* dataPerCheckpoint;      //Size of each trajectory 
checkpoint
+--- adun.app-0.81.orig/UL/ULSystemViewController.m
++++ adun.app-0.81/UL/ULSystemViewController.m
+@@ -183,8 +183,8 @@
+ - (void) _setDelegateForOptions: (id) options
+ {
+       [outlineDelegate release];
+-      outlineDelegate = [[ULOutlineViewDelegate alloc]
+-                              initWithOptions: options];      
++      outlineDelegate = [(ULOutlineViewDelegate*)[ULOutlineViewDelegate alloc]
++                                                 initWithOptions: options];
+       [optionsView setDataSource: outlineDelegate];
+       [optionsView setDelegate: outlineDelegate];
+       [optionsView reloadData];
+--- adun.app-0.81.orig/UL/ULAnalyserPluginExtensions.m
++++ adun.app-0.81/UL/ULAnalyserPluginExtensions.m
+@@ -120,8 +120,9 @@
+ 
+               [currentOptions retain];
+               [outlineDelegate release];
+-              outlineDelegate  = [[ULOutlineViewDelegate alloc]
+-                                      initWithOptions: currentOptions];
++              outlineDelegate  =
++                [(ULOutlineViewDelegate*)[ULOutlineViewDelegate alloc]
++                                         initWithOptions: currentOptions];
+               [optionsView setDataSource: outlineDelegate];
+               [optionsView setDelegate: outlineDelegate];
+               [optionsView reloadData];
+@@ -131,8 +132,9 @@
+               [currentOptions release];
+               currentOptions = nil;
+               [outlineDelegate release];
+-              outlineDelegate  = [[ULOutlineViewDelegate alloc]
+-                                      initWithOptions: currentOptions];
++              outlineDelegate  =
++                [(ULOutlineViewDelegate*)[ULOutlineViewDelegate alloc]
++                                         initWithOptions: currentOptions];
+               [optionsView setDataSource: outlineDelegate];
+               [optionsView setDelegate: outlineDelegate];
+               [optionsView reloadData];
+--- adun.app-0.81.orig/UL/ULPasteboard.h
++++ adun.app-0.81/UL/ULPasteboard.h
+@@ -87,7 +87,7 @@
+ 
+ @interface ULPasteboard: NSObject
+ {
+-      id pasteboardOwner;
++      id<ULPasteboardDataSource> pasteboardOwner;
+       int changeCount;
+ }
+ + (id) appPasteboard;
+--- adun.app-0.81.orig/UL/ULFramework/ULDatabaseIndex.m
++++ adun.app-0.81/UL/ULFramework/ULDatabaseIndex.m
+@@ -384,7 +384,7 @@
+ - (void) removeOutputReferenceToObjectWithId: (NSString*) identOne
+               fromObjectWithId: (NSString*) identTwo
+ {
+-      int position, i;
++      NSUInteger position, i;
+       NSString* ident;
+       NSMutableArray* outputReferences;
+       NSDictionary* reference;
+@@ -398,7 +398,7 @@
+       outputReferences = [[objectOutputReferences objectForKey: identTwo] 
+                               mutableCopy];
+ 
+-      for(position = NSNotFound, i=0; i<(int)[outputReferences count]; i++)   
++      for(position = NSNotFound, i=0; i<[outputReferences count]; i++)
+       {
+               reference = [outputReferences objectAtIndex: i];
+               ident = [reference objectForKey: @"Identification"];
+--- adun.app-0.81.orig/UL/ULFramework/ULSimpleMergerDelegate.m
++++ adun.app-0.81/UL/ULFramework/ULSimpleMergerDelegate.m
+@@ -98,12 +98,12 @@
+ 
+ - (id) _updateConfiguration
+ {     
+-      unsigned int* buffer;
++      NSUInteger* buffer;
+ 
+       //we have to remove the partial charges of the atoms that are missing
+       //unfortuantly gnustep has yet to implement removeObjectsWithIndexes: 
:-()
+ 
+-      buffer = malloc([totalMissingAtoms count]*sizeof(int));
++      buffer = malloc([totalMissingAtoms count]*sizeof(NSUInteger));
+       [totalMissingAtoms getIndexes: buffer 
+                       maxCount: [totalMissingAtoms count]
+                       inIndexRange: NULL];
+@@ -200,7 +200,7 @@
+ {
+       int i, j;
+       int oldValue, newValue;
+-      unsigned int* buffer;
++      NSUInteger* buffer;
+       id bondedAtoms, newConf;
+       
+       //synchronize the pdb atom order with the frame atom order
+@@ -209,7 +209,7 @@
+       
+       //now remove all the missing atoms from the bondedAtomList
+       
+-      buffer = malloc([totalMissingAtoms count]*sizeof(int));
++      buffer = malloc([totalMissingAtoms count]*sizeof(NSUInteger));
+       [totalMissingAtoms getIndexes: buffer 
+                       maxCount: [totalMissingAtoms count]
+                       inIndexRange: NULL];
+--- adun.app-0.81.orig/UL/ULFramework/ULSystem.m
++++ adun.app-0.81/UL/ULFramework/ULSystem.m
+@@ -176,7 +176,7 @@
+ - (NSMutableArray*) _decodeArrayOfDoublesForKey: key usingCoder: (NSCoder*) 
decoder
+ {
+       int i, numberElements;
+-      unsigned int bytesLength;
++      NSUInteger bytesLength;
+       double* bytes;
+       NSMutableArray* array;
+ 
+@@ -203,7 +203,7 @@
+ {
+       int i, j, check;
+       int numberElements, count;
+-      unsigned int length;
++      NSUInteger length;
+       int* numberBondedAtomsArray;
+       int* bondedAtomsArray;
+       NSMutableArray* bondedAtoms, *list;
+@@ -242,7 +242,7 @@
+ {
+       int i, j, count;
+       int totalRanges, totalSets;
+-      unsigned int length;
++      NSUInteger length;
+       int* rangesPerSet;
+       NSRange* totalRangeArray, *rangeArray;
+       NSIndexSet* set;
+--- adun.app-0.81.orig/UL/ULFramework/ULProcess.m
++++ adun.app-0.81/UL/ULFramework/ULProcess.m
+@@ -207,16 +207,11 @@
+ 
+ - (void) setControllerResults: (NSArray*) results
+ {
+-      id dataSet;
+-      
+       NSDebugLLog(@"ULProcess", 
+               @"Recieved controller data %@", results);
+-      
+-      if(dataSet != results)
+-      {
+-              [dataSets release];
+-              dataSets = [results retain];
+-      }
++
++      [dataSets release];
++      dataSets = [results retain];
+ }
+ 
+ - (void) setSimulationData: (AdSimulationData*) data
+--- adun.app-0.81.orig/MolTalk/MTPDBParser.m
++++ adun.app-0.81/MolTalk/MTPDBParser.m
+@@ -519,12 +519,12 @@
+       char buffer[90];
+       unsigned int serial,resnr;
+       char aname[5]; /* atom name */
+-      char rname[4]; /* residue name */
++      char rname[5]; /* residue name */
+       double x,y,z,occ,bfact;
+       char icode;
+       char chain;
+       char element[3]; /* element name */
+-      char segid[3]; /* segment id */
++      char segid[4]; /* segment id */
+       int chrg=0;
+ 
+ 
+@@ -712,7 +712,7 @@
+       char icode;
+       char chain;
+       char element[3]; /* element name */
+-      char segid[3]; /* segment id */
++      char segid[4]; /* segment id */
+       int chrg=0;
+       id t_residue=nil;
+       BOOL isSolvent=NO;
+--- adun.app-0.81.orig/UL/ULSystemViewController.h
++++ adun.app-0.81/UL/ULSystemViewController.h
+@@ -32,6 +32,9 @@
+ #include "ULOutlineViewDelegate.h"
+ #include "ULProgressPanel.h"
+ 
++/* Forward declaration.  */
++@class ULPropertiesPanel;
++
+ /**
+ ULSystemViewController controls the "Create System" part of the GUI.
+ It acts as a conduit between ULSystemController and the GUI transmitting
+@@ -47,7 +50,7 @@
+       id forceField;          //!< The name of the forceField to be used
+       id systemWindow;        //!< The "Create System" window
+       id mainViewController;  //!< Reference to the mainViewController 
(ViewController subclass)
+-      id metadataController;
++      ULPropertiesPanel* metadataController;
+       id systemController;    //!< A ULSystemController instance
+       id moleculePathField;   //!< The path text field
+       id progressBar;
+--- adun.app-0.81.orig/UL/ULTemplateViewController.h
++++ adun.app-0.81/UL/ULTemplateViewController.h
+@@ -48,7 +48,7 @@
+       NSMutableDictionary* sections;
+       ULOutlineViewDelegate* outlineDelegate;
+       ULMutableTemplate* simulationTemplate;
+-      id propertyViewController;
++      ULPropertiesPanel* propertyViewController;
+       //Window Elements
+       id templateWindow;
+       id componentTable;

Modified: trunk/packages/adun.app/trunk/debian/patches/series
===================================================================
--- trunk/packages/adun.app/trunk/debian/patches/series 2014-05-29 13:26:50 UTC 
(rev 17019)
+++ trunk/packages/adun.app/trunk/debian/patches/series 2014-05-30 18:29:16 UTC 
(rev 17020)
@@ -2,3 +2,4 @@
 15_link-properly.patch
 20_paths.patch
 fix-implicit-pointer.patch
+gcc-warnings.patch


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