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/mafsInRegion/mafsInRegion.c src/hg/ratStuff/mafsInRegion/mafsInRegion.c
index 8493741cb6e..60789514b73 100644
--- src/hg/ratStuff/mafsInRegion/mafsInRegion.c
+++ src/hg/ratStuff/mafsInRegion/mafsInRegion.c
@@ -61,30 +61,37 @@
 	bedList = temp;
 	}
     }
 return regionHash;
 }
 
 char *chromFromSrc(char *src)
 /* get chrom name from <db>.<chrom> */
 {
 char *p;
 if ((p = strchr(src, '.')) == NULL)
     errAbort("Can't find chrom in MAF component src: %s\n", src);
 return ++p;
 }
 
+// chromFromSrc returns strchr(src,'.')+1, a valid (possibly empty) C string.
+// At -O3 GCC's -Wstringop-overread mis-sizes that pointer as a 0-byte region
+// when it is handed to strcmp via sameString/differentString below; the reads
+// are safe (strcmp stops at the terminator).
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wstringop-overread"
+
 FILE *startOutFile(char *outFile)
 {
 static FILE *f = NULL;
 
 f = mustOpen(outFile, "w");
 verbose(3, "creating %s\n", outFile);
 mafWriteStart(f, scoring);
 return f;
 }
 
 void endOutFile(FILE *f)
 {
 mafWriteEnd(f);
 carefulClose(&f);
 }
@@ -150,30 +157,31 @@
         mafWrite(f, maf);
         struct mafAli *nextMaf = (mafEnd > bed->chromEnd+1)
             ? mafSubset(full, mc->src, bed->chromEnd+1, mafEnd) : mafNext(mf);
         if (maf != full)
             mafAliFree(&maf);
         mafAliFree(&full);
         maf = nextMaf;
         }
     /* get next region */
     hashRemove(regionHash, bed->chrom);
     if (bed->next)
         hashAdd(regionHash, bed->chrom, bed->next);
     }
 mafFileFree(&mf);
 }
+#pragma GCC diagnostic pop
 
 void mafsInRegion(char *regionFile, char *out, int mafCount, char *mafFiles[])
 /* Extract MAFs in regions listed in regin file */
 {
 int i = 0;
 struct hash *bedHash = NULL;
 FILE *f = NULL;
 struct mafFile *mf = NULL;
 
 verbose(1, "Extracting from %d files to %s\n", mafCount, out);
 bedHash = loadRegions(regionFile);
 
 /* get scoring scheme */
 mf = mafOpen(mafFiles[0]);
 if (!mf)