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/utils/faSplit/faSplit.c src/utils/faSplit/faSplit.c
index 3ae56be89fc..4515757be2a 100644
--- src/utils/faSplit/faSplit.c
+++ src/utils/faSplit/faSplit.c
@@ -144,31 +144,31 @@
 int fileCount = 0;
 off_t nextEnd = 0;
 off_t curPos = 0;
 FILE *f = NULL;
 int linePos = 0;
 int outLineSize = 50;
 
 
 if (!lineFileNext(lf, &line, &lineSize))
     errAbort("%s is empty", inName);
 if (line[0] == '>')
     {
     line = firstWordInLine(line+1);
     if (line == NULL)
         errAbort("Empty initial '>' line in %s", inName);
-    strncpy(seqName, line, sizeof(seqName));
+    safecpy(seqName, sizeof(seqName), line);
     }
 else
     {
     splitPath(inName, dir, seqName, NULL);
     lineFileReuse(lf);
     }
 splitPath(outRoot, NULL, outFile, NULL);
 while (lineFileNext(lf, &line, &lineSize))
     {
     if (line[0] == '>')
         {
 	if (!warnedMultipleRecords)
 	    {
 	    warnedMultipleRecords = TRUE;
 	    warn("More than one record in FA file line %d of %s",