--- a/black_flag.c
+++ b/black_flag.c
@@ -82,7 +82,7 @@
 
 
 
-int handle_crash_init(void (*crash_fun)())
+int handle_crash_init(void (*crash_fun)(int))
 {
 #define HANDLE_CRASH_MAX 5
   int i,signal_type[HANDLE_CRASH_MAX]
--- a/black_flag.h
+++ b/black_flag.h
@@ -230,7 +230,7 @@
 ((INDEX)<(MINIMUM_BOUND) || (INDEX)>=(MAXIMUM_BOUND))
 
 void handle_crash(int sigcode);
-int handle_crash_init(void (*crash_fun)());
+int handle_crash_init(void (*crash_fun)(int));
 int black_flag(int bug_level,
 	       char sourcefile[],
 	       int sourceline,
--- a/default.h
+++ b/default.h
@@ -19,7 +19,6 @@
 
 typedef void *voidptr;  /* ~~e: should be moved out to generic typing header
 			   --- */
-typedef int (*funptr)();
 
 #define LOOPB(i,size) for ((i)=(size);(i)-- >0;)
 #define LOOP(i,size) for ((i)=(size);(i)-- >0;)
@@ -152,7 +151,7 @@
   else if (NULL == ((memptr)=(ATYPE *)calloc((size_t)(N),sizeof(ATYPE))))  { \
     fprintf(stderr,"%s, line %d: *** out of memory \n",__FILE__,__LINE__);                \
     fprintf(stderr,"Unable to meet request: %s[%d]\n",STRINGIFY(memptr),(N));    \
-    fprintf(stderr,"requested %d x %d bytes \n",(N),sizeof(ATYPE));   \
+    fprintf(stderr,"requested %d x %zu bytes \n",(N),sizeof(ATYPE));   \
     MALLOC_FAILURE_ACTION;                                            \
   }
 
@@ -193,7 +192,7 @@
     else { \
       fprintf(stderr,"%s, line %d: *** out of memory \n",__FILE__,__LINE__); \
       fprintf(stderr,"Unable to meet request: %s\n",STRINGIFY(memptr));  \
-      fprintf(stderr,"requested %d x %d bytes \n",(NUM),sizeof(ATYPE));   \
+      fprintf(stderr,"requested %d x %zu bytes \n",(NUM),sizeof(ATYPE));   \
       REALLOC_FAILURE_ACTION;                                             \
     } \
   }
--- a/fasta_format.c
+++ b/fasta_format.c
@@ -2,6 +2,7 @@
 #include "default.h"
 #include "seq_util.h"
 
+char *stringptr_cat_pos(stringptr *s1,const char s2[],int *pos);
 
 
 /** reads FASTA formatted sequence file, and saves the sequences to
--- a/msa_format.c
+++ b/msa_format.c
@@ -16,6 +16,11 @@
 
 #include "msa_format.h"
 
+void fuse_ring_identities(int len_x,LPOLetter_T seq_x[],
+        int len_y,LPOLetter_T seq_y[],
+        LPOLetterRef_T al_x[],
+        LPOLetterRef_T al_y[]);
+void build_seq_to_po_index(LPOSequence_T *seq);
 
 /** is `ch' an allowed residue? (a-z OR A-Z OR ? OR [ OR ]) */
 static int is_residue_char (char ch);