--- ncbi-tools6-6.1.20061015.orig/api/txalign.c
+++ ncbi-tools6-6.1.20061015/api/txalign.c
@@ -6284,7 +6284,7 @@
             if(seq_int1 != NULL) {
                 
                 /* This line should be checked for correctness */
-                if((line1[line_index] = BSGetByte(b_store)) == EOF)
+                if((line1[line_index] = BSGetByte(b_store)) == (Char)EOF)
                     line1[line_index] = '?';
                 
                 if(dna_strand != Seq_strand_minus)
--- ncbi-tools6-6.1.20061015.orig/api/aliread.c
+++ ncbi-tools6-6.1.20061015/api/aliread.c
@@ -383,7 +383,7 @@
   Int4    segmentLen = 0;
   Int4    segmentCount = 1;
   Boolean done = FALSE;
-  Char    ch = 0;
+  Int2    ch = 0;
 
   /* Allocate memory for the line.  More */
   /* can be added later as necessary.    */
@@ -402,12 +402,12 @@
 
       /* Process the current character */
 
-      ch = (Char) NLM_GETC (alignFilePtr);
+      ch = NLM_GETC (alignFilePtr);
 
       if (ch == '\n')
 	{
 	  done = TRUE;
-	  ch = (Char) NLM_GETC (alignFilePtr);
+	  ch = NLM_GETC (alignFilePtr);
 	  if (ch != '\r') {
 	    ungetc (ch, alignFilePtr);
 	  
--- ncbi-tools6-6.1.20061015.orig/corelib/ncbienv.c
+++ ncbi-tools6-6.1.20061015/corelib/ncbienv.c
@@ -803,6 +803,8 @@
     if (fp == NULL) {
       path[0] = '\0';
       pth = getenv ("NCBI");
+      if (pth == NULL)
+	pth = "/etc/ncbi";
       if (pth != NULL) {
         Nlm_FileBuildPath(path, pth, str + 1);
         fp = Ncbienv_FileOpen (path, "r");
--- ncbi-tools6-6.1.20061015.orig/corelib/ncbimain.c
+++ ncbi-tools6-6.1.20061015/corelib/ncbimain.c
@@ -67,6 +67,7 @@
 #pragma segment NlmSegA
 #endif
 
+extern Nlm_Int2 Nlm_Main(void) __attribute__((weak));
 
 /*****************************************************************************
 *
@@ -95,7 +96,12 @@
   /* Initialize connection library's logger, registry and lock */
   CONNECT_Init(0);
 
-  retval = Nlm_Main();
+  if (Nlm_Main) {
+    retval = Nlm_Main();
+  } else {
+    ErrPost(0, 0, "Neither main nor Nlm_Main defined by program.");
+    retval = -1;
+  }
 
   NlmThreadJoinAll();
 
--- ncbi-tools6-6.1.20061015.orig/desktop/bspview.c
+++ ncbi-tools6-6.1.20061015/desktop/bspview.c
@@ -2409,13 +2409,13 @@
     }
 #endif
 #ifdef WIN_MOTIF
-  argv [0] = "netscape";
+  argv [0] = "www-browser";
   argv [1] = url;
   argv [2] = NULL;
   child = fork();
   if(child == 0) {
-     if (execvp ("netscape", argv) == -1) {
-        Message (MSG_POST, "Unable to launch netscape");
+     if (execvp ("www-browser", argv) == -1) {
+        Message (MSG_POST, "Unable to launch browser");
         exit(-1);
     }
   }
--- ncbi-tools6-6.1.20061015.orig/desktop/ingenwin.c
+++ ncbi-tools6-6.1.20061015/desktop/ingenwin.c
@@ -3114,7 +3114,7 @@
         len++;
      }
      c = (Char)fgetc(fp);
-     if (c==EOF) {
+     if (c==(Char)EOF) {
        return NULL;
      }
   }
--- ncbi-tools6-6.1.20061015.orig/network/id1arch/idfetch.c
+++ ncbi-tools6-6.1.20061015/network/id1arch/idfetch.c
@@ -201,6 +201,7 @@
 
 static Boolean ProcessOneDocSum (Int4 num, Int4Ptr uids);
 static void EntrezQuery(char *query);
+static int TryGetGi(int choice, char *accession, char *name, int version);
 
 static Int4 BEGetUidsFromQuery(CharPtr query, Uint4Ptr PNTR uids,
                                Boolean is_na, Boolean count_only);
--- ncbi-tools6-6.1.20061015.orig/vibrant/netscape.c
+++ ncbi-tools6-6.1.20061015/vibrant/netscape.c
@@ -548,9 +548,8 @@
     }
 
     /* ---------- child process ------------ */
-    if (execlp("netscape", "netscape", url, NULL) < 0  &&
-        execl(NETSCAPE_PATH, NETSCAPE_PATH, url, NULL) < 0) {
-        Message(MSG_ERROR, "Failure to open URL in netscape window");
+    if (execlp("sensible-browser", "sensible-browser", url, NULL) < 0) {
+        Message(MSG_ERROR, "Failure to open URL in browser window");
         exit(1);
     }
 
--- ncbi-tools6-6.1.20061015.orig/vibrant/shim3d.c
+++ ncbi-tools6-6.1.20061015/vibrant/shim3d.c
@@ -327,7 +327,8 @@
 #include <ddvcolor.h>
 
 #if defined(_OPENGL) && defined(_PNG)
-TOGL_Data *Cn3D_GetCurrentOGLData(void); /* in cn3dxprt.c */
+/* In cn3dxprt.c; declared weak here to avoid dependency loops. */
+extern TOGL_Data *Cn3D_GetCurrentOGLData(void) __attribute__((weak));
 #endif
 
 
@@ -2711,6 +2712,9 @@
     if (OGL_Data == NULL)
         return;
 
+    if (!OGL_Data->BoundBox.set)
+        OGL_ClearBoundBox(&(OGL_Data->BoundBox));
+
     OGL_Data->MaxSize = (Nlm_FloatLo)
         fabs(OGL_Data->BoundBox.x[0] - OGL_Data->BoundBox.x[1]);
     diff = fabs(OGL_Data->BoundBox.y[0] - OGL_Data->BoundBox.y[1]);
@@ -2924,7 +2928,15 @@
     png_structp png_ptr = NULL;
     png_infop info_ptr = NULL;
     Nlm_Boolean doInterlacing = TRUE;
-    TOGL_Data *OGL_Data = (TOGL_Data *)(Cn3D_GetCurrentOGLData());
+    TOGL_Data *OGL_Data;
+    
+    if (!Cn3D_GetCurrentOGLData) {
+      Message(MSG_ERROR, "PNG output unavailable; "
+	      "please relink application with -lncbicn3d.");
+      return;
+    }
+    
+    OGL_Data = (TOGL_Data *)(Cn3D_GetCurrentOGLData());
 
 #if defined(WIN_MOTIF)
     GLint glSize;
@@ -3705,4 +3717,3 @@
     if (fblock)
         MemFree(fblock);
 }
-
--- ncbi-tools6-6.1.20061015.orig/vibrant/vibwndws.c
+++ ncbi-tools6-6.1.20061015/vibrant/vibwndws.c
@@ -6717,6 +6717,8 @@
 #endif
 }
 
+extern Nlm_Int2 Nlm_Main(void) __attribute__((weak));
+
 #ifdef WIN_MAC
 #ifdef OS_UNIX_DARWIN
 int main (int argc, char *argv[]) 
@@ -7013,7 +7015,12 @@
   /* Initialize connection library's logger, registry and lock */
   CONNECT_Init(0);
 
-  retval = Nlm_Main ();
+  if (Nlm_Main) {
+    retval = Nlm_Main();
+  } else {
+    ErrPost(0, 0, "Neither main nor Nlm_Main defined by program.");
+    retval = -1;
+  }
 
   Nlm_CleanUpWindows ();
   Nlm_CleanUpDrawingTools ();