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/hgClonePos/hgClonePos.c src/hg/makeDb/hgClonePos/hgClonePos.c
index 97bb5f6191e..2b5954548fb 100644
--- src/hg/makeDb/hgClonePos/hgClonePos.c
+++ src/hg/makeDb/hgClonePos/hgClonePos.c
@@ -167,31 +167,31 @@
 struct clonePos *clone;
 int wordCount, cloneCount;
 
 for (i=0; i<numStages; ++i)
    {
    finfFile = finfFiles[i];
    stage = stages[i];
    sprintf(pathName, "%s/%s", gsDir, finfFile);
    printf("Processing %s\n", pathName);
    lf = lineFileOpen(pathName, TRUE);
    cloneCount = 0;
    while (lineFileNext(lf, &line, NULL))
        {
        wordCount = chopLine(line, words);
        assert(wordCount == 7);
-       strncpy(cloneName, words[1], sizeof(cloneName));
+       safecpy(cloneName, sizeof(cloneName), words[1]);
        chopSuffix(cloneName);
        if ((clone = hashFindVal(cloneHash, cloneName)) == NULL)
             {
 	    if (warnsLeft > 0)
 	       {
 	       --warnsLeft;
 	       warn("%s is in %s but not in ooDir/*/*.gl", cloneName, pathName);
 	       }
 	    else if (warnsLeft == 0)
 		{
 		--warnsLeft;
 		warn("(Truncating additional warnings)");
 		}
 	    continue;
 	    }