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/nci60/stanToBedAndExpRecs.c src/hg/nci60/stanToBedAndExpRecs.c
index ddd3f1b3352..1e774aa1352 100644
--- src/hg/nci60/stanToBedAndExpRecs.c
+++ src/hg/nci60/stanToBedAndExpRecs.c
@@ -58,31 +58,31 @@
 
 /* A tiny bit of error checking on the psl. */
 if (psl->qStart >= psl->qEnd || psl->qEnd > psl->qSize 
     || psl->tStart >= psl->tEnd || psl->tEnd > psl->tSize)
     {
     errAbort("mangled psl format for %s", psl->qName);
     }
 
 /* Allocate bed and fill in from psl. */
 AllocVar(bed);
 bed->chrom = cloneString(psl->tName);
 bed->chromStart = bed->thickStart =  chromStart = psl->tStart;
 bed->chromEnd = bed->thickEnd = psl->tEnd;
 bed->score = 1000 - 2*pslCalcMilliBad(psl, TRUE);
 if (bed->score < 0) bed->score = 0;
-strncpy(bed->strand,  psl->strand, sizeof(bed->strand));
+safecpy(bed->strand, sizeof(bed->strand), psl->strand);
 bed->blockCount = blockCount = psl->blockCount;
 bed->blockSizes = (int *)cloneMem(psl->blockSizes,(sizeof(int)*psl->blockCount));
 bed->chromStarts = chromStarts = (int *)cloneMem(psl->tStarts, (sizeof(int)*psl->blockCount));
 bed->name = cloneString(psl->qName);
 
 /* Switch minus target strand to plus strand. */
 if (psl->strand[1] == '-')
     {
     int chromSize = psl->tSize;
     reverseInts(bed->blockSizes, blockCount);
     reverseInts(chromStarts, blockCount);
     for (i=0; i<blockCount; ++i)
 	chromStarts[i] = chromSize - chromStarts[i];
     }