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/hg/geneBounds/motifSig/motifSig.c src/hg/geneBounds/motifSig/motifSig.c
index 81e31754398..3370c6075d2 100644
--- src/hg/geneBounds/motifSig/motifSig.c
+++ src/hg/geneBounds/motifSig/motifSig.c
@@ -58,31 +58,31 @@
 char *words[maxMotifSize+1];
 int wordCount;
 int i,j;
 int colCount = 0;
 
 /* Get first line and parse it. */
 ZeroVar(m);
 if (!lineFileNext(lf, &line, NULL))
     return FALSE;
 wordCount = chopLine(line, words);
 if (wordCount < 6 || !sameString(words[1], "@"))
     errAbort("Bad line %d of %s", lf->lineIx, lf->fileName);
 m->score = atof(words[0]);
 m->pos = atof(words[2]);
 m->posSd = atof(words[4]);
-strncpy(m->consensus, words[5], sizeof(m->consensus));
+safecpy(m->consensus, sizeof(m->consensus), words[5]);
 
 /* Get next lines with columns. */
 for (i=0; i<4; ++i)
     {
     if (!lineFileNext(lf, &line, NULL))
         errAbort("Unexpected end of file in %s", lf->fileName);
     wordCount = chopLine(line, words);
     if (i == 0)
         m->size = colCount = wordCount - 1;
     else
         lineFileExpectWords(lf, colCount+1, wordCount);
     for (j=0; j<colCount; ++j)
         m->profile[i][j] = atof(words[j+1]);
     }
 return TRUE;