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/weblet/bottleneck/bottleneck.c src/weblet/bottleneck/bottleneck.c
index 4fae28579ae..b1b89cdbce3 100644
--- src/weblet/bottleneck/bottleneck.c
+++ src/weblet/bottleneck/bottleneck.c
@@ -221,30 +221,31 @@
 void queryServer(char *ip, int count, double fraction)
 /* Query bottleneck server - just for testing.
  * Main query is over ip port. */
 {
 int i;
 char sendString[256];
 safef(sendString, sizeof(sendString), "%s %f", ip, fraction);
 for (i=0; i<count; ++i)
     {
     int socket = netMustConnect(host, port);
     char buf[256], *s;
     netSendString(socket, sendString);
     s = netGetString(socket, buf);
     if (s == NULL)
         errAbort("Shut out by bottleneck server %s:%d", host, port);
+    else
         printf("%s millisecond delay recommended\n", s);
     close(socket);
     }
 }
 
 void setUser(char *ip, char *millis)
 /* Set user current delay. */
 {
 int socket = netMustConnect(host, port);
 char buf[256];
 safef(buf, sizeof(buf), "?set %s %s", ip, millis);
 netSendString(socket, buf);
 close(socket);
 }