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/trfBig/trfBig.c src/hg/trfBig/trfBig.c
index 80fa7addaec..57ddd6ab7f0 100644
--- src/hg/trfBig/trfBig.c
+++ src/hg/trfBig/trfBig.c
@@ -108,31 +108,31 @@
 sprintf(wild, "%s%s", fn, ext);
 if (dir[0] == 0) strcpy(dir, ".");
 
 list = listDirX(tempDir, wild, TRUE);
 for (el = list; el != NULL; el = el->next)
     {
     remove(el->name);
     verbose(1, "Removed %s\n", el->name);
     }
 slFreeList(&list);
 }
 
 void makeTrfRootName(char trfRootName[512], char *faFile)
 /* Make root name of files trf produces from faFile. */
 {
-sprintf(trfRootName, "%s.2.7.7.80.10.50.%d", faFile, maxPeriod);
+safef(trfRootName, 512, "%s.2.7.7.80.10.50.%d", faFile, maxPeriod);
 }
 
 void trfSysCall(char *faFile)
 /* Invoke trf program on file. */
 {
 // need to execute in trf directory, as tmp files go to current directory
 char faBase[FILENAME_LEN], faExt[FILENAME_LEN];
 splitPath(faFile, NULL, faBase, faExt);
 
 char command[1024];
 if (trf409_l > 0)
   safef(command, sizeof(command), "cd %s && %s %s%s 2 7 7 80 10 50 %d -m %s -l %d",
       tempDir, trfExe, faBase, faExt, maxPeriod, doBed ? "-d" : "", trf409_l);
 else
   safef(command, sizeof(command), "cd %s && %s %s%s 2 7 7 80 10 50 %d -m %s",