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/outside/sanger22gtf/sanger22gtf.c src/hg/makeDb/outside/sanger22gtf/sanger22gtf.c
index 899c21da43b..a44916edee1 100644
--- src/hg/makeDb/outside/sanger22gtf/sanger22gtf.c
+++ src/hg/makeDb/outside/sanger22gtf/sanger22gtf.c
@@ -1,62 +1,63 @@
 /* sanger22gtf - Convert Sanger chromosome 22 annotations to gtf. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "cheapcgi.h"
 
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "sanger22gtf - Convert Sanger chromosome 22 annotations to gtf\n"
   "usage:\n"
   "   sanger22gtf in.gff out.gtf\n"
   );
 }
 
 void sanger22gtf(char *inName, char *outName)
 /* sanger22gtf - Convert Sanger chromosome 22 annotations to gtf. */
 {
 struct lineFile *lf = lineFileOpen(inName, TRUE);
 FILE *f = mustOpen(outName, "w");
 char *line, *word, *s;
 int i;
 
 while (lineFileNext(lf, &line, NULL))
     {
     /* Just pass through comments and blank lines. */
     s = skipLeadingSpaces(line);
     if (s[0] == '#' || s[0] == '0')
         {
 	fprintf(f, "%s\n", line);
 	continue;
 	}
     
     for (i=0; i<8; ++i)
         {
 	word = nextWord(&line);
 	if (word == NULL)
 	    errAbort("Expecting at least 8 words line %d of %s", lf->lineIx, lf->fileName);
+	else
 	    fprintf(f, "%s\t", word);
 	}
 
     s = skipLeadingSpaces(line);
     if (s[0] != 0)
         fprintf(f, "%s", line);
     fputc('\n', f);
     }
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 cgiSpoof(&argc, argv);
 if (argc != 3)
     usage();
 sanger22gtf(argv[1], argv[2]);
 return 0;
 }