biology/vsearch: Upgrade to 2.13.4

pkgsrc patches incorporated into upstream release

7 files changed, 10 insertions, 99 deletions

diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile
index 6ecf6920f73..51b20a1ed11 100644
--- a/biology/vsearch/Makefile
+++ b/biology/vsearch/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.1 2019/05/10 16:19:22 bacon Exp $
+# $NetBSD: Makefile,v 1.2 2019/05/11 14:27:18 bacon Exp $
 
-DISTNAME=	vsearch-2.13.3
+DISTNAME=	vsearch-2.13.4
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=torognes/}
 GITHUB_TAG=	v${PKGVERSION_NOREV}
diff --git a/biology/vsearch/PLIST b/biology/vsearch/PLIST
index 2d78ae1c55d..31dc34da072 100644
--- a/biology/vsearch/PLIST
+++ b/biology/vsearch/PLIST
@@ -1,3 +1,3 @@
-@comment $NetBSD: PLIST,v 1.1 2019/05/10 16:19:22 bacon Exp $
+@comment $NetBSD: PLIST,v 1.2 2019/05/11 14:27:18 bacon Exp $
 bin/vsearch
 man/man1/vsearch.1
diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo
index dbc5a9d3d9a..439528b673e 100644
--- a/biology/vsearch/distinfo
+++ b/biology/vsearch/distinfo
@@ -1,10 +1,8 @@
-$NetBSD: distinfo,v 1.1 2019/05/10 16:19:22 bacon Exp $
+$NetBSD: distinfo,v 1.2 2019/05/11 14:27:18 bacon Exp $
 
-SHA1 (vsearch-2.13.3.tar.gz) = 064bfbef4271c254848f18b03bed7c41a15ae2ab
-RMD160 (vsearch-2.13.3.tar.gz) = d8f00a88449fb827878b7e301f9127799ce3d43c
-SHA512 (vsearch-2.13.3.tar.gz) = a3c539d60ed6db8bdb964a1aee18e79a6b8ed397dc01d47aad873019a8f123ed8892b08536dfd5f785f8d327fee75d42b4a744f354f5c6e3bb03d0bf10f054e5
-Size (vsearch-2.13.3.tar.gz) = 233846 bytes
+SHA1 (vsearch-2.13.4.tar.gz) = adb36075cf873620aebae6ab25f33cbac002065e
+RMD160 (vsearch-2.13.4.tar.gz) = e65a908014cbab903bef81b55c9e67003bb55458
+SHA512 (vsearch-2.13.4.tar.gz) = 31cc321f96309385414f3847a4cb29a5b3e43e42870b3f41e34fa0e6b3a928b2dd306edeff896ffa6bca85ecea776b33655611fa62749e9b29e86bf1adbe7de3
+Size (vsearch-2.13.4.tar.gz) = 234364 bytes
 SHA1 (patch-configure.ac) = 536a8565514cf9b43f4f8892d1cba0444f752c5e
 SHA1 (patch-src_Makefile.am) = bcdd1bbe9f04197084825e2c3560ba27a750f124
-SHA1 (patch-src_city.cc) = 3a5bcbca0a0c733a32a9d152189de10df3cb515f
-SHA1 (patch-src_vsearch.h) = 26b8dc6ce0448e7463ee1c3ff73747ad07286543
diff --git a/biology/vsearch/patches/patch-configure.ac b/biology/vsearch/patches/patch-configure.ac
index c4176c10f26..64fbc788c12 100644
--- a/biology/vsearch/patches/patch-configure.ac
+++ b/biology/vsearch/patches/patch-configure.ac
@@ -1,4 +1,4 @@
-$NetBSD: patch-configure.ac,v 1.1 2019/05/10 16:19:22 bacon Exp $
+$NetBSD: patch-configure.ac,v 1.2 2019/05/11 14:27:18 bacon Exp $
 
 # Respect build env
 
diff --git a/biology/vsearch/patches/patch-src_Makefile.am b/biology/vsearch/patches/patch-src_Makefile.am
index 8e00fefdaf3..f68d5ed779d 100644
--- a/biology/vsearch/patches/patch-src_Makefile.am
+++ b/biology/vsearch/patches/patch-src_Makefile.am
@@ -1,4 +1,4 @@
-$NetBSD: patch-src_Makefile.am,v 1.1 2019/05/10 16:19:22 bacon Exp $
+$NetBSD: patch-src_Makefile.am,v 1.2 2019/05/11 14:27:18 bacon Exp $
 
 # Respect build env
 
diff --git a/biology/vsearch/patches/patch-src_city.cc b/biology/vsearch/patches/patch-src_city.cc
deleted file mode 100644
index 77346020c82..00000000000
--- a/biology/vsearch/patches/patch-src_city.cc
+++ /dev/null
@@ -1,20 +0,0 @@
-$NetBSD: patch-src_city.cc,v 1.1 2019/05/10 16:19:22 bacon Exp $
-
-# 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/patches/patch-src_vsearch.h b/biology/vsearch/patches/patch-src_vsearch.h
deleted file mode 100644
index 7c4343180b2..00000000000
--- a/biology/vsearch/patches/patch-src_vsearch.h
+++ /dev/null
@@ -1,67 +0,0 @@
-$NetBSD: patch-src_vsearch.h,v 1.1 2019/05/10 16:19:22 bacon Exp $
-
-# Add FreeBSD and NetBSD support
-
---- src/vsearch.h.orig	2019-04-30 11:57:32.000000000 +0000
-+++ src/vsearch.h
-@@ -138,30 +138,50 @@
- #define bswap_32(x) _byteswap_ulong(x)
- #define bswap_64(x) _byteswap_uint64(x)
- 
--#else
--
--#ifdef __APPLE__
-+#elif defined(__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 <machine/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