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/ratStuff/mafAddQRows/mafAddQRows.c src/hg/ratStuff/mafAddQRows/mafAddQRows.c
index c8632de5127..440c906a138 100644
--- src/hg/ratStuff/mafAddQRows/mafAddQRows.c
+++ src/hg/ratStuff/mafAddQRows/mafAddQRows.c
@@ -215,31 +215,31 @@
 
 return speciesHash;
 }
 
 
 static struct qData *loadQualityData (struct mafComp *mc, struct hash *speciesHash)
 /* return qData if found or NULL if not */
 {
 char buffer[1024];
 char *species, *chrom;
 struct hashEl *hel;
 struct qData *qd;
 struct indexEntry *ie;
 
 /* separate species and chrom */
-strncpy(buffer, mc->src, sizeof(buffer));
+safecpy(buffer, sizeof(buffer), mc->src);
 species = chrom = buffer;
 if ((chrom = strchr(buffer, '.')) == NULL)
     errAbort("can't find chrom for %s\n", buffer);
 *chrom++ = '\0';
 
 /* return if we don't have quality data for this species */
 if ((hel = hashLookup(speciesHash, species)) == NULL)
     return(NULL);
 
 /* load the quality data if we need to */
 qd = (struct qData *) hel->val;
 if (qd->qa == NULL || ! sameString(qd->qa->name, chrom))
     {
     if ((hel = hashLookup(qd->index, chrom)) == NULL)
         return(NULL);