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/hgGene/altSplice.c src/hg/hgGene/altSplice.c
index 6c229a32b52..85b3de57e03 100644
--- src/hg/hgGene/altSplice.c
+++ src/hg/hgGene/altSplice.c
@@ -79,32 +79,32 @@
 
 char *altGraphXMakeImage(struct altGraphX *ag)
 /* create a drawing of splicing pattern */
 {
 MgFont *font = mgSmallFont();
 int fontHeight = mgFontLineHeight(font);
 struct spaceSaver *ssList = NULL;
 struct hash *heightHash = NULL;
 int rowCount = 0;
 struct tempName gifTn;
 int pixWidth = atoi(cartUsualString(cart, "pix", DEFAULT_PIX_WIDTH ));
 int pixHeight = 0;
 struct hvGfx *hvg;
 int lineHeight = 0;
 double scale = 0;
-Color shadesOfGray[9];
-int maxShade = ArraySize(shadesOfGray)-1;
+Color shadesOfGray[10];
+int maxShade = ArraySize(shadesOfGray)-2;	// makeGrayShades also writes shadesOfGray[maxShade+1]
 
 scale = (double)pixWidth/(ag->tEnd - ag->tStart);
 lineHeight = 2 * fontHeight +1;
 altGraphXLayout(ag, ag->tStart, ag->tEnd, scale, 100, &ssList, &heightHash, &rowCount);
 hashFree(&heightHash);
 pixHeight = rowCount * lineHeight;
 makeTempName(&gifTn, "hgc", ".png");
 hvg = hvGfxOpenPng(pixWidth, pixHeight, gifTn.forCgi, FALSE);
 makeGrayShades(hvg, maxShade, shadesOfGray);
 hvGfxSetClip(hvg, 0, 0, pixWidth, pixHeight);
 altGraphXDrawPack(ag, ssList, hvg, 0, 0, pixWidth, lineHeight, lineHeight-1,
                   ag->tStart, ag->tEnd, scale,
 		  font, MG_BLACK, shadesOfGray, "Dummy", NULL);
 hvGfxUnclip(hvg);
 hvGfxClose(&hvg);