f57fc11d951807e19b20b5960e735fa50eaea279
braney
  Fri Jun 12 13:10:00 2026 -0700
Fix more warnings exposed by -O3 build across hg utils and errAbort

Continuation of the -O3 cleanup: a full clean rebuild surfaced warnings in
many programs whose objects had not been recompiled before.  Most are the same
mechanical patterns as the first batch (strncpy -> safecpy/memcpy, sprintf ->
safef), plus a few that needed more thought:

- errAbort.h: mark errAbort/vaErrAbort/errnoAbort/noWarnAbort as noreturn.
They provably never return (longjmp or exit; the existing "to make compiler
happy" exit(-1) in noWarnAbort confirms the intent), and this lets GCC prune
the impossible null paths after an errAbort guard, fixing false-positive
null-deref / overread warnings in mafAddIRows, mafAddIRowsStream and
phyloPlace with no source change to those files.
- altSplice.c (hgGene): real one-element stack buffer overflow.  makeGrayShades
writes shadesOfGray[maxShade+1], but the caller declared shadesOfGray[9] with
maxShade=8.  Grow the array to [10] (maxShade stays 8); behavior unchanged.
- hgc.c bedPrintPos: ~60 callers pass a track-specific struct cast to
(struct bed *) and read only its bed-compatible leading fields.  At -O3
-Warray-bounds flags the casts because the real object is smaller than
struct bed; the reads are safe by the bed-layout convention, so suppress
-Warray-bounds around just that function.
- mafsInRegion.c: chromFromSrc returns strchr(src,'.')+1, which GCC mis-sizes
as a 0-byte region when handed to strcmp via sameString/differentString;
suppress the false-positive -Wstringop-overread around extractMafs.
- sanger22gtf.c, bottleneck.c: put the printf/fprintf in the else of the
NULL guard so -Wformat-overflow (which runs before the noreturn-based
pruning) can see the argument is non-null.

safecpy/memcpy/safef conversions: basicBed already done earlier; here
haplotypes (memcpy of the original pointer pun), gbToFaRa, motifSig,
hgClonePos, featureBits, libScan, hgGoldGapGl, hgSoftPromoter, mafClick,
mafAddQRows, hgc.c, stanToBedAndExpRecs, bedUp, faSplit, trfBig,
splitFaIntoContigs, aladdin, ameme.

A full clean tree now builds with no warnings at -O3.

refs #37761

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

diff --git src/inc/errAbort.h src/inc/errAbort.h
index ba6f81cbb92..d2d3201bfb5 100644
--- src/inc/errAbort.h
+++ src/inc/errAbort.h
@@ -1,97 +1,107 @@
 /* ErrAbort.h - our error handler. 
  *
  * This maintains two stacks - a warning message printer
  * stack, and a "abort handler" stack.
  *
  * By default the warnings will go to stderr, and
  * aborts will exit the program.  You can push a
  * function on to the appropriate stack to change
  * this behavior.  The top function on the stack
  * gets called.
  *
  * Most functions in this library will call errAbort()
  * if they run out of memory.  
  *
  * This file is copyright 2002 Jim Kent, but license is hereby
  * granted for all use - public, private or commercial. */
 
 #ifndef ERRABORT_H
 #define ERRABORT_H
 
 boolean isErrAbortInProgress();  
 /* Flag to indicate that an error abort is in progress.
  * Needed so that a warn handler can tell if it's really
  * being called because of a warning or an error. */
 
 void errAbortSetDoContentType(boolean value);
 /* change the setting of doContentType, ie. if errorAbort should print a 
  * http Content type line. */
 
 void errAbort(char *format, ...)
 /* Abort function, with optional (printf formatted) error message. */
 #if defined(__GNUC__)
 __attribute__((format(printf, 1, 2)))
+__attribute__((noreturn))
 #endif
 ;
 
-void vaErrAbort(char *format, va_list args);
+void vaErrAbort(char *format, va_list args)
 /* Abort function, with optional (vprintf formatted) error message. */
+#if defined(__GNUC__)
+__attribute__((noreturn))
+#endif
+;
 
 void errnoAbort(char *format, ...)
 /* Prints error message from UNIX errno first, then does errAbort. */
 #if defined(__GNUC__)
 __attribute__((format(printf, 1, 2)))
+__attribute__((noreturn))
 #endif
 ;
 
 typedef void (*AbortHandler)();
 /* Function that can abort. */
 
 void pushAbortHandler(AbortHandler handler);
 /* Set abort handler */
 
 void popAbortHandler();
 /* Revert to old abort handler. */
 
-void noWarnAbort();
+void noWarnAbort()
 /* Abort without message. */
+#if defined(__GNUC__)
+__attribute__((noreturn))
+#endif
+;
 
 void pushDebugAbort();
 /* Push abort handler that will invoke debugger. */
 
 void vaWarn(char *format, va_list args);
 /* Call top of warning stack to issue warning. */
 
 void warn(char *format, ...)
 /* Issue a warning message. */
 #if defined(__GNUC__)
 __attribute__((format(printf, 1, 2)))
 #endif
 ;
 
 void errnoWarn(char *format, ...)
 /* Prints error message from UNIX errno first, then does rest of warning. */
 #if defined(__GNUC__)
 __attribute__((format(printf, 1, 2)))
 #endif
 ;
 
 typedef void (*WarnHandler)(char *format, va_list args);
 /* Function that can warn. */
 
 void pushWarnHandler(WarnHandler handler);
 /* Set warning handler */
 
 void popWarnHandler();
 /* Revert to old warn handler. */
 
 void pushWarnAbort();
 /* Push handler that will abort on warnings. */
 
 void pushSilentWarnHandler();
 /* Set warning handler to be quiet.  Do a popWarnHandler to restore. */
 
 void errAbortDebugnPushPopErr();
 /*  generate stack dump if there is a error in the push/pop functions */
 
 #endif /* ERRABORT_H */