git: 0a7946717881 - main - biology/ncbi-toolkit: Unbreak by fixing chained C comparison in tools/readdb.c

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=0a7946717881fe656f1cb1947a678ace7f26b94d

commit 0a7946717881fe656f1cb1947a678ace7f26b94d
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2026-07-11 00:57:27 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2026-07-11 01:00:13 +0000

    biology/ncbi-toolkit: Unbreak by fixing chained C comparison in tools/readdb.c
    
    Reported by:    fallout
---
 biology/ncbi-toolkit/Makefile                   |  2 +-
 biology/ncbi-toolkit/files/patch-tools_readdb.c | 16 ++++++++++++++++
 2 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile
index 5dfe289470cf..589f07a4436f 100644
--- a/biology/ncbi-toolkit/Makefile
+++ b/biology/ncbi-toolkit/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	ncbi-toolkit
 DISTVERSION=	2017.01.06	# containing BLAST v2.2.27 (? is this true)
-PORTREVISION=	9
+PORTREVISION=	10
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/old/${PORTVERSION:S/.//g}/
 DISTNAME=	ncbi
diff --git a/biology/ncbi-toolkit/files/patch-tools_readdb.c b/biology/ncbi-toolkit/files/patch-tools_readdb.c
new file mode 100644
index 000000000000..3e6b09a21b95
--- /dev/null
+++ b/biology/ncbi-toolkit/files/patch-tools_readdb.c
@@ -0,0 +1,16 @@
+-- Fix a chained comparison that modern Clang rejects with -Werror.
+-- C does not support 'a <= b <= c'; rewrite as 'a <= b && b <= c'.
+
+--- tools/readdb.c.orig	2026-07-10 18:56:47 UTC
++++ tools/readdb.c
+@@ -4893,8 +4893,8 @@ readdb_check_oid(ReadDBFILEPtr rdfp_head, Int4 oid)
+ 			if (s_SearchOidInLocalOidList(rdfp_var->oidlist, oid-rdfp_var->start) == 0) 
+                   		return TRUE;
+                 } else {
+-                	if (rdfp_var->start <= oid <= rdfp_var->stop)
+-                                return TRUE;	 
++                	if (rdfp_var->start <= oid && oid <= rdfp_var->stop)
++                                return TRUE;
+                 }
+                 rdfp_var = rdfp_var->next;
+         }