v.1.07.5_RC4

Author: djb-rwth

INCHI-1-SRC/INCHI_API/libinchi/src/CMakeLists.txt

@@ -116,6 +116,8 @@ target_sources(libinchi PRIVATE
 	${P_BASE}/mol_fmt3.c
 	${P_BASE}/mol_fmt4.c
 	${P_BASE}/mol2atom.c
+	${P_BASE}/permutation_util.h
+	${P_BASE}/permutation_util.c
 	${P_BASE}/readinch.c
 	${P_BASE}/readinch.h
 	${P_BASE}/runichi.c

INCHI-1-SRC/INCHI_BASE/src/ichican2.c

@@ -4601,7 +4601,7 @@ int CanonGraph( INCHI_CLOCK *ic,
     {
         *nLenCt = pzb_rho->lenCt - 1;
     }
-    if (pCt && pzb_rho && (*nLenCt > 0))
+    if (pCt && pzb_rho && (*nLenCt > 0)) /* djb-rwth: GHI #164 fix */
     {
         memcpy(pCt, pzb_rho->Ctbl, *nLenCt * sizeof(pCt[0]));
     }

INCHI-1-SRC/INCHI_BASE/src/ichicano.c

@@ -2691,9 +2691,10 @@ VII. Optimize isotopic stereo descriptors (optimized)
                 inchi_free( pRankStack2[n] );
             }
         }
-        inchi_free( pRankStack2 );
     }
 
+    inchi_free(pRankStack2); /* djb-rwth: fixing coverity CID #499631 */
+
     pCS->NeighList = NULL; /* keep the pointer in pBCN->ftcn[bTaut].NeighList for further deallocation */
     qfree( nAtomNumber );
     qfree( nTempRank );

INCHI-1-SRC/INCHI_BASE/src/ichimain.h

@@ -63,11 +63,6 @@ typedef struct tagLine
 #define COMP_PREP_0_RECN  0x0008
 #define COMP_ORIG_1_MAIN  0x0010
 #define COMP_ORIG_1_RECN  0x0020
-/* Renumbering atoms stuff */
-#define PERMAXATOMS 32767
-#define BYTE(X) ((unsigned char *)(X))
-int rrand( int m );
-void shuffle( void *obj, size_t nmemb, size_t size );
 
 
 /* STRUCT_DATA */
@@ -505,7 +500,6 @@ int bIsStructChiral( PINChI2 *pINChI2[INCHI_NUM], int num_components[] );
 /* ORIG_ATOM_DATA  */
 
 int  OrigAtData_Duplicate( ORIG_ATOM_DATA *new_orig_atom, ORIG_ATOM_DATA *orig_atom );
-void OrigAtData_Permute( ORIG_ATOM_DATA *permuted, ORIG_ATOM_DATA *saved, int *numbers );
 
 int  OrigAtData_RemoveAtom(ORIG_ATOM_DATA *orig_at_data, int iatom);
 int  OrigAtData_AddSingleStereolessBond( int this_atom, int other_atom,

INCHI-1-SRC/INCHI_BASE/src/ichimak2.c

@@ -330,6 +330,7 @@ int MakeHillFormula( U_CHAR *nAtom,
     mult = 0;
     bOvfl = 0;
     nPrevAtom = (U_CHAR) -2; /*  non-existent number */
+    memset(szElement, '\0', sizeof(szElement)); /* djb-rwth: fixing coverity CID #499542 */
 
     if (num_C)
     {