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/ameme/ameme.c src/ameme/ameme.c
index 0a1f68268cc..df9249e4f5c 100644
--- src/ameme/ameme.c
+++ src/ameme/ameme.c
@@ -280,31 +280,31 @@
 return list;
 }
 
 struct seqList *readSeqMaybeMakeFrame(char *faFileName, int nullModel)
 /* Load in an FA file.  If nullModel is coding figure out frame for each
  * sequence. */
 {
 struct seqList *seqList, *seqEl;
 seqList = readSeqList(faFileName);
 if (seqList == NULL)
     errAbort("No sequences in %s\n", faFileName);
 if (nullModel == nmCoding)
     {
     char codFileName[512];
     struct codonBias *cb;
-    snprintf(codFileName, sizeof(codFileName), "%s%s", amemeDir(), "ce.cod");
+    safef(codFileName, sizeof(codFileName), "%s%s", amemeDir(), "ce.cod");
     cb = codonLoadBias(codFileName);
     for (seqEl = seqList; seqEl != NULL; seqEl = seqEl->next)
         {
         struct dnaSeq *seq = seqEl->seq;
         seqEl->frame = codonFindFrame(seq->dna, seq->size, cb);
         }
     freeMem(cb);
     }
 return seqList;
 }
 
 int totalSeqSize(struct seqList *list)
 /* How long is total sequence? */
 {
 struct seqList *el;
@@ -2473,31 +2473,31 @@
 }
 
 void loadAndColorProfiles(char *profFileName, struct seqList *seqList, int seqSize, boolean considerRc)
 /* Display profile in color on sequences. */
 {
 struct profile *profList = loadProfiles(profFileName);
 if (profList != NULL)
     colorProfiles(profList, seqList, seqSize, considerRc);
 freeProfileList(&profList);
 }
 
 void makePremadeBgPathName(char *fileName, char *retPathName, int retPathSize)
 /* Make path name for background file out of just file name. */
 {
 char *dir = amemeDir();
-sprintf(retPathName, "%s%s", dir, fileName);
+safef(retPathName, retPathSize, "%s%s", dir, fileName);
 }
 
 static double randScale;    /* Scales rand() result to 0.0 to 1.0 */
 
 double normRand()
 /* Return a random number between 0 and 1 */
 {
 return rand() * randScale;
 }
 
 void initRandom()
 /* Initialize random number generator */
 {
 /* Set up random number generator with seed depending on time and host. */
 unsigned seed = (unsigned)time(NULL);