vsearch: Upgrade to 2.13.4

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat May 11 08:44:37 2019 -0500
Changeset:	ae45544fb68dc666da210858b683a32415d07af5

Modified Files:
	vsearch/Makefile
	vsearch/distinfo
Removed Files:
	vsearch/patches/patch-src_city.cc
	vsearch/patches/patch-src_vsearch.h

Log Message:
vsearch: Upgrade to 2.13.4

pkgsrc patches incorporated into new release

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=ae45544fb68dc666da210858b683a32415d07af5

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 vsearch/Makefile                    |  2 +-
 vsearch/distinfo                    | 10 +++---
 vsearch/patches/patch-src_city.cc   | 20 -----------
 vsearch/patches/patch-src_vsearch.h | 67 -------------------------------------
 4 files changed, 5 insertions(+), 94 deletions(-)

diffs:
diff --git a/vsearch/Makefile b/vsearch/Makefile
index 8a04e5f278..05181fe910 100644
--- a/vsearch/Makefile
+++ b/vsearch/Makefile
@@ -1,6 +1,6 @@
 # $NetBSD$
 
-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/vsearch/distinfo b/vsearch/distinfo
index 1a704959d4..8570cf0164 100644
--- a/vsearch/distinfo
+++ b/vsearch/distinfo
@@ -1,10 +1,8 @@
 $NetBSD$
 
-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/vsearch/patches/patch-src_city.cc b/vsearch/patches/patch-src_city.cc
deleted file mode 100644
index a379a802bc..0000000000
--- a/vsearch/patches/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/vsearch/patches/patch-src_vsearch.h b/vsearch/patches/patch-src_vsearch.h
deleted file mode 100644
index 0ee651eca7..0000000000
--- a/vsearch/patches/patch-src_vsearch.h
+++ /dev/null
@@ -1,67 +0,0 @@
-$NetBSD$
-
-# Add FreeBSD and NetBSD support
-
---- src/vsearch.h.orig	2019-04-30 11:57:32.000000000 +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