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/hgc/mafClick.c src/hg/hgc/mafClick.c
index 85c7551bfc4..fb20647e4dd 100644
--- src/hg/hgc/mafClick.c
+++ src/hg/hgc/mafClick.c
@@ -489,31 +489,31 @@
 	    }
 	}
     genePredFree(&gp);
     }
 sqlFreeResult(&sr);
 sqlDisconnect(&conn);
 }
 
 static void capMafOnTrack(struct mafAli *maf, char *track, boolean onlyCds)
 /* Capitalize parts of maf that correspond to exons according
  * to given gene prediction track.  */
 {
 char dbOnly[64];
 char *chrom;
 struct mafComp *mc = maf->components;
-strncpy(dbOnly, mc->src, sizeof(dbOnly));
+safecpy(dbOnly, sizeof(dbOnly), mc->src);
 chrom = chopPrefix(dbOnly);
 capAliTextOnTrack(maf, dbOnly, chrom, track, onlyCds);
 }
 #endif
 
 static struct mafAli *mafOrAxtLoadInRegion2(struct sqlConnection *conn,struct sqlConnection *conn2,
                                             struct trackDb *tdb, char *chrom, int start, int end,
                                             char *axtOtherDb, char *file)
 {
 if (axtOtherDb != NULL)
     {
     struct hash *qSizeHash = hChromSizeHash(axtOtherDb);
     struct mafAli *mafList = axtLoadAsMafInRegion(conn, tdb->table,
             chrom, start, end, database, axtOtherDb, hChromSize(database, chrom), qSizeHash);
     hashFree(&qSizeHash);