From bc66849a977caf6418430ffb620bad9220f1f3b8 Mon Sep 17 00:00:00 2001
From: Joseph Mingrone <jrm@FreeBSD.org>
Date: Sun, 30 Aug 2020 16:14:22 +0000
Subject: [PATCH] biology/diamond: Update to version 2.0.4

Upstream changes:
https://github.com/bbuchfink/diamond/releases/tag/v2.0.3
https://github.com/bbuchfink/diamond/releases/tag/v2.0.4

Port changes:
Remove a patch that was upstreamed:
https://github.com/bbuchfink/diamond/pull/378
---
 biology/diamond/Makefile                      |  2 +-
 biology/diamond/distinfo                      |  6 +--
 .../files/patch-src_util_system_system.cpp    | 45 -------------------
 3 files changed, 4 insertions(+), 49 deletions(-)
 delete mode 100644 biology/diamond/files/patch-src_util_system_system.cpp

diff --git a/biology/diamond/Makefile b/biology/diamond/Makefile
index 3fc27f9522a0..8308a7e5b666 100644
--- a/biology/diamond/Makefile
+++ b/biology/diamond/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=	diamond
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.0.2
+DISTVERSION=	2.0.4
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
diff --git a/biology/diamond/distinfo b/biology/diamond/distinfo
index 57ee2d88290d..78782c2c7fde 100644
--- a/biology/diamond/distinfo
+++ b/biology/diamond/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1596712682
-SHA256 (bbuchfink-diamond-v2.0.2_GH0.tar.gz) = fd22c2a1960cc1b4d02b66f87c66624c6e495de3128b73da70171fc134a508b5
-SIZE (bbuchfink-diamond-v2.0.2_GH0.tar.gz) = 1117286
+TIMESTAMP = 1598800137
+SHA256 (bbuchfink-diamond-v2.0.4_GH0.tar.gz) = 94e8fe72bdc28b83fd0f2d90c439b58b63b38263aa1a3905582ef68f614ae95d
+SIZE (bbuchfink-diamond-v2.0.4_GH0.tar.gz) = 1120470
diff --git a/biology/diamond/files/patch-src_util_system_system.cpp b/biology/diamond/files/patch-src_util_system_system.cpp
deleted file mode 100644
index 5e84a9496238..000000000000
--- a/biology/diamond/files/patch-src_util_system_system.cpp
+++ /dev/null
@@ -1,45 +0,0 @@
---- src/util/system/system.cpp.orig	2020-08-05 17:04:09 UTC
-+++ src/util/system/system.cpp
-@@ -6,14 +6,19 @@
- #include "../log_stream.h"
- 
- #ifdef _MSC_VER
--#include <windows.h>
-+  #include <windows.h>
- #else
--#include <unistd.h>
--#include <sys/stat.h>
--#ifndef __APPLE__
--#include <sys/sysinfo.h>
-+  #include <unistd.h>
-+  #include <sys/stat.h>
-+  #ifndef  __APPLE__
-+    #ifdef __FreeBSD__
-+      #include <sys/types.h>
-+      #include <sys/sysctl.h>
-+    #else
-+      #include <sys/sysinfo.h>
-+    #endif
-+  #endif
- #endif
--#endif
- 
- using std::string;
- using std::cout;
-@@ -129,6 +134,16 @@ void reset_color(bool err) {
- double total_ram() {
- #if defined(WIN32) || defined(__APPLE__)
- 	return 0.0;
-+#elif defined(__FreeBSD__)
-+	int mib[2] = { CTL_HW, HW_REALMEM };
-+	u_int namelen = sizeof(mib) / sizeof(mib[0]);
-+	uint64_t oldp;
-+	size_t oldlenp = sizeof(oldp);
-+
-+	if (sysctl(mib, namelen, &oldp, &oldlenp, NULL, 0) < 0)
-+		return 0.0;
-+	else
-+		return oldp / 1e9;
- #else
- 	struct sysinfo info;
- 	if (sysinfo(&info) != 0)