From 75055f8a7f540517d9f2d762238516fd44103eca Mon Sep 17 00:00:00 2001
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Date: Sat, 11 May 2019 13:42:33 +0000
Subject: [PATCH] biology/vsearch: Update to 2.13.4

FreeBSD patches incorporated into new upstream release

Reported by:    portscout
---
 biology/vsearch/Makefile                  |  2 +-
 biology/vsearch/distinfo                  |  6 +-
 biology/vsearch/files/patch-src_city.cc   | 20 -------
 biology/vsearch/files/patch-src_vsearch.h | 67 -----------------------
 4 files changed, 4 insertions(+), 91 deletions(-)
 delete mode 100644 biology/vsearch/files/patch-src_city.cc
 delete mode 100644 biology/vsearch/files/patch-src_vsearch.h

diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile
index 8c1f4c976e71..eeaaa05cfee2 100644
--- a/biology/vsearch/Makefile
+++ b/biology/vsearch/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=		vsearch
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.13.3
+DISTVERSION=		2.13.4
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo
index 584b0d4a06ae..ea8344a2be56 100644
--- a/biology/vsearch/distinfo
+++ b/biology/vsearch/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1557339663
-SHA256 (torognes-vsearch-v2.13.3_GH0.tar.gz) = e5f34ece28b76403d3ba4a673eca41178fe399c35a1023dbc87d0c0da5efaa52
-SIZE (torognes-vsearch-v2.13.3_GH0.tar.gz) = 233846
+TIMESTAMP = 1557579514
+SHA256 (torognes-vsearch-v2.13.4_GH0.tar.gz) = 35269cbb10d1d2c33fdddd47ff4a5434eda1d4445fcc816bf4c57d7fe4740709
+SIZE (torognes-vsearch-v2.13.4_GH0.tar.gz) = 234364
diff --git a/biology/vsearch/files/patch-src_city.cc b/biology/vsearch/files/patch-src_city.cc
deleted file mode 100644
index a379a802bc90..000000000000
--- a/biology/vsearch/files/patch-src_city.cc
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD$
-
-# Portability
-
---- src/city.cc.orig	2019-04-30 11:57:32 UTC
-+++ src/city.cc
-@@ -60,6 +60,13 @@ static uint32 UNALIGNED_LOAD32(const char *p) {
- #define bswap_32(x) OSSwapInt32(x)
- #define bswap_64(x) OSSwapInt64(x)
- 
-+#elif defined(__FreeBSD__)
-+
-+#include <sys/endian.h>
-+
-+#define bswap_32(x) bswap32(x)
-+#define bswap_64(x) bswap64(x)
-+
- #elif defined(__NetBSD__)
- 
- #include <sys/types.h>
diff --git a/biology/vsearch/files/patch-src_vsearch.h b/biology/vsearch/files/patch-src_vsearch.h
deleted file mode 100644
index 2e74ffff8b56..000000000000
--- a/biology/vsearch/files/patch-src_vsearch.h
+++ /dev/null
@@ -1,67 +0,0 @@
-$NetBSD$
-
-# Add FreeBSD and NetBSD support
-
---- src/vsearch.h.orig	2019-04-30 11:57:32 UTC
-+++ src/vsearch.h
-@@ -138,30 +138,50 @@
- #define bswap_32(x) _byteswap_ulong(x)
- #define bswap_64(x) _byteswap_uint64(x)
- 
--#else
-+#elif defined(__APPLE__)
- 
--#ifdef __APPLE__
--
- #define PROG_OS "macos"
- #include <sys/sysctl.h>
- #include <libkern/OSByteOrder.h>
-+#include <sys/resource.h>
- #define bswap_16(x) OSSwapInt16(x)
- #define bswap_32(x) OSSwapInt32(x)
- #define bswap_64(x) OSSwapInt64(x)
- 
--#else
-+#elif defined(__linux__)
- 
--#ifdef __linux__
- #define PROG_OS "linux"
--#else
--#define PROG_OS "unknown"
--#endif
--
- #include <sys/sysinfo.h>
- #include <byteswap.h>
-+#include <sys/resource.h>
- 
--#endif
-+#elif defined(__FreeBSD__)
- 
-+#define PROG_OS "freebsd"
-+#include <sys/sysinfo.h>
-+#include <sys/resource.h>
-+#include <sys/endian.h>
-+#define bswap_16(x) bswap16(x)
-+#define bswap_32(x) bswap32(x)
-+#define bswap_64(x) bswap64(x)
-+
-+#elif defined(__NetBSD__)
-+
-+#define PROG_OS "netbsd"
-+#include <sys/resource.h>
-+#include <sys/types.h>
-+#include <sys/bswap.h>
-+#define bswap_16(x) bswap16(x)
-+#define bswap_32(x) bswap32(x)
-+#define bswap_64(x) bswap64(x)
-+// Alters behavior, but NetBSD 7 does not have getopt_long_only()
-+#define getopt_long_only getopt_long
-+
-+#else	// Other Unix
-+
-+#define PROG_OS "unknown"
-+#include <sys/sysinfo.h>
-+#include <byteswap.h>
- #include <sys/resource.h>
- 
- #endif