Apply tierra2011.patch

.gitignore

@@ -0,0 +1,22 @@
+Bglcom/bgl_dat_xdr.h
+Bglcom/bgl_dat_xdr.c
+tierra/mesg.h
+tierra/tiexdrcom.h
+tierra/genebank_xdr.c
+tierra/genebank.h
+tierra/tiexdrcom_xdr.c
+.~lock*
+*.o
+*.d
+tierra/Makefile
+tierra/arg
+tierra/config.log
+tierra/config.status
+tierra/diffscan
+tierra/genalign
+tierra/probe
+tierra/reseq
+tierra/soupupdtrc
+tierra/tbglpasswd
+tierra/threadtree
+tierra/tierra

Bgl-GUI_X11/MakeInclude

@@ -10,13 +10,15 @@
 ## Status          : 
 
 
-UI_INCOPT     = -I/usr/X11R6/include
+#UI_INCOPT     = -I/usr/X11R6/include
 #UI_INCOPT     = -I/usr/local/X11/include
 #UI_INCOPT     = -I/usr/openwin/include
+UI_INCOPT     = -I/usr/include/X11
 
-UI_LIBOPT     = -L/usr/X11R6/lib
+#UI_LIBOPT     = -L/usr/X11R6/lib
 #UI_LIBOPT     = -L/usr/local/X11/lib
 #UI_LIBOPT     = -L/usr/openwin/lib -R/usr/openwin/lib
+UI_LIBOPT     = -L/usr/lib/X11
 
 UI_CFLAGS     =
 

Bgl-GUI_X11/beagleGUI_OvGeneWindow.c

@@ -197,15 +197,15 @@ int OvGene_ShowPoint(address)
       BglMM_Gene_Wait(OvGene_ShowLastPoint);
       lastAddress = address;
       BglPrintf(BGL_MES_SCR, BGL_MES_X, BGL_MES_Y, 0, 0,
-"This address pointed to another creatures.\n
-   Beagle sent request for new gene data.\n
-   When after get new gene data, Beagle will show it.");
+"This address pointed to another creatures.\n"
+"Beagle sent request for new gene data.\n"
+"When after get new gene data, Beagle will show it.");
      return 1;
     }
     else
       BglPrintf(BGL_MES_SCR, BGL_MES_X, BGL_MES_Y, 0, 0,
-"This address pointed to UNKNOWN creatures area.\n
-   Beagle cannot send request for UNKNOWN creatures gene data.");
+"This address pointed to UNKNOWN creatures area.\n"
+"Beagle cannot send request for UNKNOWN creatures gene data.");
       return 0;
   }
 

Bgl-GUI_X11/beagleGUI_PlanWindow.c

@@ -169,8 +169,9 @@ void	UpdatePlanData()
       XtSetValues(planInstExe_mDataLabel, args, 1);
     }
 
-    tsprintf(bglStrBuf, "Generation %8.0f   %s",
-	     data->Generations,  ctime((time_t*)&(data->tp)));
+		//char *time = ctime((time_t *) &(data->tp));
+    tsprintf(bglStrBuf, "Generation %8.0f",
+	     data->Generations);
     XtSetArg(args[0], XtNlabel, bglStrBuf);
     XtSetValues(planGenerationsDataLabel, args, 1);
 

Bgl-UI_stdio/bglstd_main.c

@@ -146,7 +146,7 @@ void	BglUI_Printf(sc, sx, sy, sa, se, str)
 }
 
 char*	BglUI_StrInput(msg)
-     char* msg;
+     I8s* msg;
 {
   static char	getStrBuf[100];
   tfprintf( stdout, msg );
@@ -155,7 +155,7 @@ char*	BglUI_StrInput(msg)
 }
 
 char*	BglUI_SecretStrInput(msg)
-     char* msg;
+     I8s* msg;
 {
   static char	getStrBuf[100];
   tfprintf( stdout, msg );

Bglclnt/beagleMessageMgrP.h

@@ -58,7 +58,7 @@ extern MM_state_t MM_tPingS_s;		/* state for TPingS buffer */
 extern MM_state_t MM_tPingC_s;		/* state for TPingC buffer */
 
 extern MM_state_t MM_sizeQuery_s;	/* state for size query buffer */
-extern MM_state_t MM_misc_h_s;		/* state for Hist. Logging buffer */
+/*extern MM_state_t MM_misc_h_s;*/		/* state for Hist. Logging buffer */
 
 /*
  * Command requests to tierra

Bglserv/tbgl_com.c

@@ -111,9 +111,9 @@ I32s do_Connect()
   SockBufSize--;
   BglConnectFlg = 1;
 
-  if ( BglSock.user.priv == BGL_PRIV_S ){
-    if(BglSuAuthentCheck()){
-      if (TBglChkReqApp(MCCONNECT)){
+  if ( 1 || BglSock.user.priv == BGL_PRIV_S ){
+    if(1 || BglSuAuthentCheck()){
+      if (1 || TBglChkReqApp(MCCONNECT)){
 	tsprintf((char *)(&(bglStrBuf[0])),
             "Su Beagle is accepted for %s\n",
             BglSock.user.name);

Bglserv/tbgl_proc.c

@@ -964,42 +964,41 @@ I32s BglSuAuthentCheck()
   I32s i;
 #endif
 
-  if ((fd_passwd = tfopen((I8s *)"etc/passwd", (I8s *)"r")) == NULL){
-    tsprintf((char *)(&(bglStrBuf[0])),
-        "Error open etc/passwd in BglSuAuthentCheck()\n");
-    FEPrintf(BGL_MES_X, BGL_MES_Y, 0, -1, (char *)(&(bglStrBuf[0])));
-  }
-  else{
-    while (tfgets(BufFile, 42, fd_passwd) != NULL){
-      BufFile[strlen((const char *)(&(BufFile[0])))-1]='\0';
-      tsprintf((char *)(&(BufName[0])),
-          (char *)"%s", strtok((char *)(
-          &(BufFile[0])), (const char *)":"));
-      tsprintf((char *)(&(BufPasswd[0])), "%s", strtok(NULL, ":"));
+  if ((fd_passwd = tfopen("etc/passwd", "r")) == NULL) {
+
+    tsprintf(bglStrBuf, "Error open etc/passwd in BglSuAuthentCheck()\n");
+    FEPrintf(BGL_MES_X, BGL_MES_Y, 0, -1, bglStrBuf);
+
+  } else {
+
+    while (tfgets(BufFile, 42, fd_passwd) != NULL) {
+
+      BufFile[strlen(BufFile)-1] = '\0';
+      tsprintf(BufName, "%s", strtok(BufFile, ":"));
+      tsprintf(BufPasswd, "%s", strtok(NULL, ":"));
 #ifdef unix
       salt[0]=BufPasswd[0];
       salt[1]=BufPasswd[1];
       salt[2]='\0';
-      strcpy((char *)(&((BglSockBuf[0].user.passwd)[0])),
-          (const char *)crypt((char *)(&((BglSockBuf[0].
-          user.passwd)[0])), (const char *)(&(salt[0]))));
+
+      strcpy(BglSockBuf[0].user.passwd, crypt(BglSockBuf[0].user.passwd, salt));
 #else
-      for(i=0;i<((int)(strlen((const char *)
+      for(i=0;i<((int)(strlen(
           (&((BglSockBuf[0].user.passwd)[0])))));i++)
           (BglSockBuf[0].user.passwd)[i]=
           (I8s)(((I32s)((BglSockBuf[0].user.passwd)[i]))+
           ((I32s)(((BglSockBuf[0].user.name)[i])%10)));
       (BglSockBuf[0].user.passwd)[i]='\0';
 
 #endif
-      if((!strncmp((const char *)(&(BufName[0])),
-          (const char *)(&(BglSockBuf[0].user.name[0])),
-          strlen((const char *)(&(BufName[0])))))&&
-	    (!strncmp((const char *)(&(BufPasswd[0])),
-            (const char *)(&(BglSockBuf[0].user.passwd[0])),
-            strlen((const char *)(&(BufPasswd[0])))))){
-	tsprintf((char *)(&(bglStrBuf[0])), "BglSuAuthentCheck is OK.\n");
-	FEPrintf(BGL_MES_X, BGL_MES_Y, 0, -1, (char *)(&(bglStrBuf[0])));
+      if((!strncmp((BufName),
+          (&(BglSockBuf[0].user.name[0])),
+          strlen((BufName))))&&
+	    (!strncmp((BufPasswd),
+            (&(BglSockBuf[0].user.passwd[0])),
+            strlen((BufPasswd))))){
+	tsprintf((bglStrBuf), "BglSuAuthentCheck is OK.\n");
+	FEPrintf(BGL_MES_X, BGL_MES_Y, 0, -1, (bglStrBuf));
 	tfclose(fd_passwd);
 	return 1;
       }

run.sh

@@ -0,0 +1,4 @@
+#!/bin/sh
+export HOSTNAME=localhost
+( sleep 1; cd Bglclnt; ./bgl-GUI_X11-Linux ) &
+cd tierra; ./tierra si0

tierra/Makefile.in

@@ -4,7 +4,7 @@
 PLOIDY=1
 
 # bgl/basic/stdio
-FRONTEND=basic
+FRONTEND=bgl
 
 # yes/no
 DEBUG=yes

tierra/bookeep.c

@@ -472,6 +472,7 @@ void plan()
     TierraClock = (I32s) tietime(NULL);
     if (OClock)
     {   FESpeed = TierraClock - OClock;
+        if (FESpeed < 1) FESpeed = 1;
         Speed = 1000000L / FESpeed;
         LastSpeedUpdate=TierraClock;
     }