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/makeDb/hgGoldGapGl/hgGoldGapGl.c src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
index db348196474..aae55b266bb 100644
--- src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
+++ src/hg/makeDb/hgGoldGapGl/hgGoldGapGl.c
@@ -326,31 +326,31 @@
 	sqlUpdate(conn, ds->string);
     }
 dyStringFree(&ds);
 }
 
 void makeCloneVerHash(char *fileName, struct hash *cloneVerHash)
 /* Make up a hash indexed by clone accession that has accession.version
  * values. */
 {
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[8];
 char acc[32];
 
 while (lineFileRow(lf, row))
     {
-    strncpy(acc, row[0], sizeof(acc));
+    safecpy(acc, sizeof(acc), row[0]);
     chopSuffix(acc);
     hashAdd(cloneVerHash, acc, cloneString(row[0]));
     }
 lineFileClose(&lf);
 }
 
 void hgGoldGapGl(char *database, char *gsDir, char *ooSubDir, boolean doGl, char *oneChrom)
 /* hgGoldGapGl - Put chromosome .agp and .gl files into browser database.. */
 { 
 struct fileInfo *chrFiList, *chrFi; 
 struct sqlConnection *conn = NULL;
 char ooDir[512];
 char pathName[1024];
 struct hash *cloneVerHash = newHash(0);
 boolean gotAny = FALSE;