biology/vsearch: Update to 2.18.0

Add powerpc64 support
Numerous fixes and enhancements since 2.13

Changes: https://github.com/torognes/vsearch/tags

7 files changed, 42 insertions, 32 deletions

diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile
index e3d6c2249cd..343317755fa 100644
--- a/biology/vsearch/Makefile
+++ b/biology/vsearch/Makefile
@@ -1,6 +1,6 @@
-# $NetBSD: Makefile,v 1.3 2021/04/25 07:51:24 mrg Exp $
+# $NetBSD: Makefile,v 1.4 2021/12/17 19:20:44 bacon Exp $
 
-DISTNAME=	vsearch-2.13.4
+DISTNAME=	vsearch-2.18.0
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=torognes/}
 GITHUB_TAG=	v${PKGVERSION_NOREV}
@@ -11,13 +11,15 @@ COMMENT=	Versatile open-source tool for metagenomics
 LICENSE=	gnu-gpl-v3
 
 # Works on powerpc64, but only in little endian mode
-ONLY_FOR_PLATFORM=	*-*-aarch64* *-*-x86_64
+ONLY_FOR_PLATFORM=	*-*-aarch64* *-*-powerpc64 *-*-x86_64
 
 USE_LANGUAGES=		c c++
 USE_TOOLS+=		autoconf automake autoreconf gmake
 GNU_CONFIGURE=		yes
 CONFIGURE_ARGS+=	--disable-pdfman
 
+CXXFLAGS+=	-std=c++11
+
 pre-configure:
 	cd ${WRKSRC} && autoreconf -fi
 
diff --git a/biology/vsearch/PLIST b/biology/vsearch/PLIST
index 31dc34da072..d29c90e51c9 100644
--- a/biology/vsearch/PLIST
+++ b/biology/vsearch/PLIST
@@ -1,3 +1,3 @@
-@comment $NetBSD: PLIST,v 1.2 2019/05/11 14:27:18 bacon Exp $
+@comment $NetBSD: PLIST,v 1.3 2021/12/17 19:20:44 bacon Exp $
 bin/vsearch
 man/man1/vsearch.1
diff --git a/biology/vsearch/distinfo b/biology/vsearch/distinfo
index 13fa040cf50..f645b9b4c92 100644
--- a/biology/vsearch/distinfo
+++ b/biology/vsearch/distinfo
@@ -1,8 +1,7 @@
-$NetBSD: distinfo,v 1.5 2021/10/26 10:03:44 nia Exp $
+$NetBSD: distinfo,v 1.6 2021/12/17 19:20:44 bacon Exp $
 
-BLAKE2s (vsearch-2.13.4.tar.gz) = 16fd625aa53e9b9d5b062c9db71dc201c7d458dc97fe82915e37ba6ca794b706
-SHA512 (vsearch-2.13.4.tar.gz) = 31cc321f96309385414f3847a4cb29a5b3e43e42870b3f41e34fa0e6b3a928b2dd306edeff896ffa6bca85ecea776b33655611fa62749e9b29e86bf1adbe7de3
-Size (vsearch-2.13.4.tar.gz) = 234364 bytes
-SHA1 (patch-configure.ac) = 536a8565514cf9b43f4f8892d1cba0444f752c5e
-SHA1 (patch-man_Makefile.am) = e2e536f46b32eb191c2b930dcdd927a9bf11e833
-SHA1 (patch-src_Makefile.am) = bcdd1bbe9f04197084825e2c3560ba27a750f124
+BLAKE2s (vsearch-2.18.0.tar.gz) = 48ca99858b157da943eca273d4a4f25e94aa7c64ecf4c7373821c30cdfbc38c5
+SHA512 (vsearch-2.18.0.tar.gz) = 9da21685fe64743ccf43f209bdd5b586c8f7faaae9f1a204634b713d7ba8a86478f31b24bdda7820fba97318d4408c803a6b3eed1e37189907fbd5882183d781
+Size (vsearch-2.18.0.tar.gz) = 252014 bytes
+SHA1 (patch-configure.ac) = 23aa28454d5f58222b10302cbd01ceaf0e7dca3f
+SHA1 (patch-src_Makefile.am) = fb76ec48d5292aaa276a0b6105e19ccc0abb03df
diff --git a/biology/vsearch/patch-src_Makefile.am b/biology/vsearch/patch-src_Makefile.am
new file mode 100644
index 00000000000..cefbec9777b
--- /dev/null
+++ b/biology/vsearch/patch-src_Makefile.am
@@ -0,0 +1,22 @@
+$NetBSD: patch-src_Makefile.am,v 1.1 2021/12/17 19:20:44 bacon Exp $
+
+# Respect build env
+
+--- src/Makefile.am.orig	2019-04-30 11:57:32 UTC
++++ src/Makefile.am
+@@ -1,12 +1,12 @@
+ bin_PROGRAMS = $(top_builddir)/bin/vsearch
+ 
+ if TARGET_PPC
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
++AM_CXXFLAGS=-Wall -Wsign-compare
+ else
+ if TARGET_AARCH64
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=armv8-a+simd -mtune=generic
++AM_CXXFLAGS=-Wall -Wsign-compare
+ else
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic
++AM_CXXFLAGS=-Wall -Wsign-compare
+ endif
+ endif
+ 
diff --git a/biology/vsearch/patches/patch-configure.ac b/biology/vsearch/patches/patch-configure.ac
index 64fbc788c12..e8c0c865adf 100644
--- a/biology/vsearch/patches/patch-configure.ac
+++ b/biology/vsearch/patches/patch-configure.ac
@@ -1,15 +1,15 @@
-$NetBSD: patch-configure.ac,v 1.2 2019/05/11 14:27:18 bacon Exp $
+$NetBSD: patch-configure.ac,v 1.3 2021/12/17 19:20:44 bacon Exp $
 
-# Respect build env
+# Respect pkgsrc env
 
---- configure.ac.orig	2019-05-09 20:58:52 UTC
+--- configure.ac.orig	2021-08-27 10:35:25.000000000 +0000
 +++ configure.ac
 @@ -14,9 +14,6 @@ MACOSX_DEPLOYMENT_TARGET="10.9"
  
  # Set default gcc and g++ options
  
 -CFLAGS='-g'
--CXXFLAGS='-g'
+-CXXFLAGS='-g -std=c++11'
 -
  # Checks for programs.
  AC_PROG_CXX
diff --git a/biology/vsearch/patches/patch-man_Makefile.am b/biology/vsearch/patches/patch-man_Makefile.am
deleted file mode 100644
index 0944b3900b1..00000000000
--- a/biology/vsearch/patches/patch-man_Makefile.am
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-man_Makefile.am,v 1.1 2020/03/26 02:37:38 joerg Exp $
-
---- man/Makefile.am.orig	2020-03-26 00:13:21.169357410 +0000
-+++ man/Makefile.am
-@@ -8,7 +8,7 @@ doc_DATA = vsearch_manual.pdf
- 
- vsearch_manual.pdf : vsearch.1
- 	TEMP=$$(mktemp temp.XXXXXXXX) ; \
--	if [ $$(uname) == "Darwin" ] ; then \
-+	if [ $$(uname) = "Darwin" ] ; then \
- 		sed -e 's/\\-/-/g' $< | \
- 		iconv -f UTF-8 -t ISO-8859-1 > $$TEMP ; \
- 	else \
diff --git a/biology/vsearch/patches/patch-src_Makefile.am b/biology/vsearch/patches/patch-src_Makefile.am
index f68d5ed779d..5f057fd20c3 100644
--- a/biology/vsearch/patches/patch-src_Makefile.am
+++ b/biology/vsearch/patches/patch-src_Makefile.am
@@ -1,14 +1,14 @@
-$NetBSD: patch-src_Makefile.am,v 1.2 2019/05/11 14:27:18 bacon Exp $
+$NetBSD: patch-src_Makefile.am,v 1.3 2021/12/17 19:20:44 bacon Exp $
 
-# Respect build env
+# Respect pkgsrc env
 
---- src/Makefile.am.orig	2019-04-30 11:57:32 UTC
+--- src/Makefile.am.orig	2021-12-17 18:04:20.932004483 +0000
 +++ src/Makefile.am
 @@ -1,12 +1,12 @@
  bin_PROGRAMS = $(top_builddir)/bin/vsearch
  
  if TARGET_PPC
--AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=powerpc64le -maltivec
 +AM_CXXFLAGS=-Wall -Wsign-compare
  else
  if TARGET_AARCH64