f952b14fca3833e9d8fef0ae8a086ad15485b552
galt
  Wed Jan 1 02:11:38 2025 -0800
fix various errors for utils compiled on Rocky 9 hgwdev-new.

diff --git src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
index 30e97c4..db34819 100644
--- src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
+++ src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
@@ -178,32 +178,32 @@
 	agpFragTabOut(&gold, goldTab);
 	}
     }
 lineFileClose(&lf);
 carefulClose(&goldTab);
 carefulClose(&gapTab);
 
 }
 
 void makeGoldAndGap(struct sqlConnection *conn, char *chromDir)
 /* Read in .agp files in chromDir and use them to create the
  * gold and gap tables for the corresponding chromosome(s). */
 {
 struct dyString *ds = dyStringNew(2048);
 struct fileInfo *fiList, *fi;
-char dir[256], chrom[128], ext[64];
-char goldName[128], gapName[128];
+char dir[PATH_LEN], chrom[FILENAME_LEN], ext[FILEEXT_LEN];
+char goldName[256], gapName[256];
 char *agpName;
 char *ptr;
 char goldFileName[128];
 char gapFileName[128];
 
 if (! noLoad)
     {
     safef(goldFileName, ArraySize(goldFileName), "%s", goldTabName);
     safef(gapFileName, ArraySize(gapFileName), "%s", gapTabName);
     }
 fiList = listDirX(chromDir, "*.agp", TRUE);
 for (fi = fiList; fi != NULL; fi = fi->next)
     {
 
     /* Get full path name of .agp file and process it
@@ -282,33 +282,33 @@
     for (i=0; i<ArraySize(row); ++i)
         fprintf(f, "\t%s", row[i]);
     fprintf(f, "\n");
     }
 carefulClose(&f);
 lineFileClose(&lf);
 }
 
 void makeGl(struct sqlConnection *conn, char *chromDir, 
 	 struct hash *cloneVerHash)
 /* Read in .gl files in chromDir and use them to create the
  * gl tables for the corresponding chromosome(s). */
 {
 struct dyString *ds = dyStringNew(2048);
 struct fileInfo *fiList, *fi;
-char dir[256], chrom[128], ext[64];
+char dir[PATH_LEN], chrom[FILENAME_LEN], ext[FILEEXT_LEN];
 char *glFileName;
-char glTable[128];
+char glTable[256];
 char *tab = "gl.tab";
 
 fiList = listDirX(chromDir, "*.gl", TRUE);
 for (fi = fiList; fi != NULL; fi = fi->next)
     {
     glFileName = fi->name;
     printf("Processing %s\n", glFileName);
 
     splitPath(glFileName, dir, chrom, ext);
     sprintf(glTable, "%s_gl", chrom);
     if ( (! noLoad) && sqlTableExists(conn, glTable))
 	{
 	dyStringClear(ds);
 	sqlDyStringPrintf(ds, "DROP table %s", glTable);
 	sqlUpdate(conn, ds->string);
@@ -339,31 +339,31 @@
 while (lineFileRow(lf, row))
     {
     strncpy(acc, row[0], sizeof(acc));
     chopSuffix(acc);
     hashAdd(cloneVerHash, acc, cloneString(row[0]));
     }
 lineFileClose(&lf);
 }
 
 void hgGoldGapGl(char *database, char *gsDir, char *ooSubDir, boolean doGl, char *oneChrom)
 /* hgGoldGapGl - Put chromosome .agp and .gl files into browser database.. */
 { 
 struct fileInfo *chrFiList, *chrFi; 
 struct sqlConnection *conn = NULL;
 char ooDir[512];
-char pathName[512];
+char pathName[1024];
 struct hash *cloneVerHash = newHash(0);
 boolean gotAny = FALSE;
 struct hash *chromDirHash = newHash(4);
 char *chromLst = optionVal("chromLst", NULL);
 
 if (! noLoad)
     conn = sqlConnect(database);
 
 verbose(2,"#\tcomplete gold, gap and .gl files produced\n");
 
 if (chromLst != NULL)
     {
     struct lineFile *clf = lineFileOpen(chromLst, TRUE);
     char *row[1];
     while (lineFileRow(clf, row))