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/mouseStuff/libScan/libScan.c src/hg/mouseStuff/libScan/libScan.c
index 4ee35ef4a1f..f73d798eef2 100644
--- src/hg/mouseStuff/libScan/libScan.c
+++ src/hg/mouseStuff/libScan/libScan.c
@@ -110,37 +110,37 @@
     lib->name = cloneString(row[1]);
     }
 sqlFreeResult(&sr);
 slReverse(&libList);
 printf("Got %d libraries in %s\n", slCount(libList), database);
 
 sqlSafef(query, sizeof query, "select type,library,author,acc from mrna");
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     dotOut();
     lib = hashMustFindVal(libHash, row[1]);
     isEst = sameString(row[0], "EST");
     if (lib->estCount + lib->mrnaCount == 0)
 	{
-	strncpy(lib->sampleAcc, row[3], sizeof(lib->sampleAcc));
-	strncpy(lib->authorId, row[2], sizeof(lib->authorId));
+	safecpy(lib->sampleAcc, sizeof(lib->sampleAcc), row[3]);
+	safecpy(lib->authorId, sizeof(lib->authorId), row[2]);
 	}
     else
 	{
 	if (isEst && lib->estCount == 0)
-	    strncpy(lib->sampleAcc, row[3], sizeof(lib->sampleAcc));
+	    safecpy(lib->sampleAcc, sizeof(lib->sampleAcc), row[3]);
 	if (!sameString(lib->authorId, row[2]))
 	    {
 	    if (!lib->multiAuthor)
 		{
 		lib->multiAuthor = TRUE;
 		}
 	    }
 	}
     if (isEst)
         ++lib->estCount;
     else
         ++lib->mrnaCount;
     }
 if (dotEvery)
    printf("\n");