vsearch: Upgrade to 2.13.3

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed May 8 19:58:45 2019 -0500
Changeset:	d352c68cb3f2e4e720de932c467352dc96964cc3

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

Log Message:
vsearch: Upgrade to 2.13.3

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d352c68cb3f2e4e720de932c467352dc96964cc3

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

diffstat:
 vsearch/Makefile                    |  7 ++---
 vsearch/distinfo                    | 11 ++++----
 vsearch/patches/patch-src_city.cc   | 18 ++++++-------
 vsearch/patches/patch-src_vsearch.h | 54 +++++++++++++++++++++++++++++++++++++
 4 files changed, 71 insertions(+), 19 deletions(-)

diffs:
diff --git a/vsearch/Makefile b/vsearch/Makefile
index a65f84f22b..399c0ccd6b 100644
--- a/vsearch/Makefile
+++ b/vsearch/Makefile
@@ -5,11 +5,10 @@
 #              Fri May 20 17:39:48 CDT 2016               #
 ###########################################################
 
-DISTNAME=	vsearch-${PORTVERSION}
+DISTNAME=	vsearch-2.13.3
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=torognes/}
-GITHUB_PROJECT=	vsearch
-GITHUB_TAG=	v${PORTVERSION}
+GITHUB_TAG=	v${PKGVERSION_NOREV}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	https://github.com/torognes/vsearch
@@ -21,8 +20,6 @@ USE_TOOLS+=		autoconf automake autoreconf gmake
 GNU_CONFIGURE=		yes
 CONFIGURE_ARGS+=	--disable-pdfman
 
-PORTVERSION=	2.4.2
-
 pre-configure:
 	cd ${WRKSRC} && autoreconf -fi
 
diff --git a/vsearch/distinfo b/vsearch/distinfo
index 096364eb18..2aa3b0e67a 100644
--- a/vsearch/distinfo
+++ b/vsearch/distinfo
@@ -1,7 +1,8 @@
 $NetBSD$
 
-SHA1 (vsearch-2.4.2.tar.gz) = b11c32391da4c1b2476b8e13915be619e099613b
-RMD160 (vsearch-2.4.2.tar.gz) = 0f4b6ef5911a9e84dd664f93a5e5fd757be82da4
-SHA512 (vsearch-2.4.2.tar.gz) = e4652a9df664f2ba519364c880716c753045976084b9ba2c1aad1c46c967172bbb78537f9110a49c1719c5b7274f854c918fb123aa52fed866c1a04c52751554
-Size (vsearch-2.4.2.tar.gz) = 201460 bytes
-SHA1 (patch-src_city.cc) = bfe1c8cf6da32aef6f45dc47da1adb8197711090
+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 (patch-src_city.cc) = 3a5bcbca0a0c733a32a9d152189de10df3cb515f
+SHA1 (patch-src_vsearch.h) = 35318f5a3da82fa5ea3846be5c0f6617a8b6408a
diff --git a/vsearch/patches/patch-src_city.cc b/vsearch/patches/patch-src_city.cc
index 06085bfefc..a379a802bc 100644
--- a/vsearch/patches/patch-src_city.cc
+++ b/vsearch/patches/patch-src_city.cc
@@ -1,20 +1,20 @@
 $NetBSD$
 
-# Handle non-standardized swap macros
+# Portability
 
---- src/city.cc.orig	2016-01-25 19:23:36 UTC
+--- src/city.cc.orig	2019-04-30 11:57:32 UTC
 +++ src/city.cc
-@@ -69,6 +69,13 @@ static uint32 UNALIGNED_LOAD32(const cha
- #define bswap_64(x) bswap64(x)
- #endif
+@@ -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)
 +
-+#include <sys/endian.h>
-+
- #else
+ #elif defined(__NetBSD__)
  
- #include <byteswap.h>
+ #include <sys/types.h>
diff --git a/vsearch/patches/patch-src_vsearch.h b/vsearch/patches/patch-src_vsearch.h
new file mode 100644
index 0000000000..ca3c2df67d
--- /dev/null
+++ b/vsearch/patches/patch-src_vsearch.h
@@ -0,0 +1,54 @@
+$NetBSD$
+
+# Portability
+
+--- src/vsearch.h.orig	2019-04-30 11:57:32 UTC
++++ src/vsearch.h
+@@ -138,10 +138,8 @@
+ #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>
+@@ -149,20 +147,28 @@
+ #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 <sys/resource.h>
+ #include <byteswap.h>
+ 
+-#endif
++#elif defined(__FreeBSD__)
+ 
++#define PROG_OS "freebsd"
++#include <sys/sysinfo.h>
+ #include <sys/resource.h>
++
++#define bswap_16(x) bswap16(x)
++#define bswap_32(x) bswap32(x)
++#define bswap_64(x) bswap64(x)
++
++#else
++
++#define PROG_OS "unknown"
++#include <sys/sysinfo.h>
++#include <byteswap.h>
+ 
+ #endif
+