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/recycleDb/bedUp/bedUp.c src/hg/recycleDb/bedUp/bedUp.c
index 0caa5f9d363..ce8dfc73dae 100644
--- src/hg/recycleDb/bedUp/bedUp.c
+++ src/hg/recycleDb/bedUp/bedUp.c
@@ -25,51 +25,51 @@
     char *chrom;	  /* Human chromosome or FPC contig */
     unsigned chromStart;  /* Start position in chromosome */
     unsigned chromEnd;	  /* End position in chromosome */
     char *name;           /* Name. */
     char **extraWords;    /* Other words in this row of database. */
     char *id;             /* Unique ID - allocated in hash. */
     struct psl *pslList;  /* Conversion psl. */
     char *oldClone;       /* Old clone this used to be at. */
     bool converted;       /* TRUE if converted to new coors. */
     };
 
 char *bedIdS(char *name, char *chrom, char *chromStart)
 /* Return unique identifier for bed treating number as string. */
 {
 static char buf[128];
-sprintf(buf, "%s.%s.%s", name, chrom, chromStart);
+safef(buf, sizeof(buf), "%s.%s.%s", name, chrom, chromStart);
 return buf;
 }
 
 char *bedId(char *name, char *chrom, int chromStart)
 /* Return unique identifier for bed. */
 {
 char num[16];
 sprintf(num, "%d", chromStart);
 return bedIdS(name, chrom, num);
 }
 
 void unpackPslName(struct lineFile *lf, char *pslName, char **retName, char **retDb, char **retChrom, int *retStart)
 /* Unpack name in convert psl file. */
 {
 static char buf[128];
 char *words[8];
 int i;
 char *e;
 
-strncpy(buf, pslName, sizeof(buf));
+safecpy(buf, sizeof(buf), pslName);
 for (i=0; i<3; ++i)
     {
     e = strrchr(buf, '.');
     if (e == NULL)
         errAbort("Expecting name.db.chrom.start line %d of %s", lf->lineIx, lf->fileName);
     *e++ = 0;
     words[i] = e;
     }
 *retDb = words[2];
 *retChrom = words[1];
 *retStart = atoi(words[0]);
 *retName = buf;
 }
 
 struct bedExt *loadTable(char *fileName, struct hash *bedHash, struct hash *chromHash, struct hash *cloneHash)