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/gbToFaRa/gbToFaRa.c src/hg/gbToFaRa/gbToFaRa.c
index b173205752c..12f8b4ea1eb 100644
--- src/hg/gbToFaRa/gbToFaRa.c
+++ src/hg/gbToFaRa/gbToFaRa.c
@@ -1379,31 +1379,31 @@
             sizeHistogram[chunkIx] += 1;
 
             if (isEst)
                 {
                 char *author = authorsField->val;
                 if (author != NULL)
                     {
                     struct authorExample *ae;
                     struct hashEl *hel;
                     if ((hel = hashLookup(estAuthorHash, author)) == NULL)
                         {
                         AllocVar(ae);
                         hel = hashAdd(estAuthorHash, author, ae);
                         ae->name = hel->name;
                         ae->count = 1;
-                        strncpy(ae->accession, accession, sizeof(ae->accession));                        
+                        safecpy(ae->accession, sizeof(ae->accession), accession);
                         slAddHead(&estAuthorList, ae);
                         }
                     else
                         {
                         ae = hel->val;
                         ae->count += 1;
                         }
                     }
                 }
             seqKey->val = NULL; /* Don't write out sequence here. */
             if (commentKey != NULL)
                 commentKey->val = NULL;  /* Don't write out comment either. */
 
             if (gByOrganism) 
                 {