[pkgsrc/trunk]: pkgsrc/biology/vsearch biology/vsearch: Update to 2.18.0

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/301e89cf4cff
branches:  trunk
changeset: 771370:301e89cf4cff
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Fri Dec 17 19:20:44 2021 +0000

description:
biology/vsearch: Update to 2.18.0

Add powerpc64 support
Numerous fixes and enhancements since 2.13

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

diffstat:

 biology/vsearch/Makefile                      |   8 +++++---
 biology/vsearch/PLIST                         |   2 +-
 biology/vsearch/distinfo                      |  13 ++++++-------
 biology/vsearch/patch-src_Makefile.am         |  22 ++++++++++++++++++++++
 biology/vsearch/patches/patch-configure.ac    |   8 ++++----
 biology/vsearch/patches/patch-man_Makefile.am |  13 -------------
 biology/vsearch/patches/patch-src_Makefile.am |   8 ++++----
 7 files changed, 42 insertions(+), 32 deletions(-)

diffs (143 lines):

diff -r 84c12aeb24c1 -r 301e89cf4cff biology/vsearch/Makefile
--- a/biology/vsearch/Makefile  Fri Dec 17 19:13:57 2021 +0000
+++ b/biology/vsearch/Makefile  Fri Dec 17 19:20:44 2021 +0000
@@ -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 @@
 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 -r 84c12aeb24c1 -r 301e89cf4cff biology/vsearch/PLIST
--- a/biology/vsearch/PLIST     Fri Dec 17 19:13:57 2021 +0000
+++ b/biology/vsearch/PLIST     Fri Dec 17 19:20:44 2021 +0000
@@ -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 -r 84c12aeb24c1 -r 301e89cf4cff biology/vsearch/distinfo
--- a/biology/vsearch/distinfo  Fri Dec 17 19:13:57 2021 +0000
+++ b/biology/vsearch/distinfo  Fri Dec 17 19:20:44 2021 +0000
@@ -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 -r 84c12aeb24c1 -r 301e89cf4cff biology/vsearch/patch-src_Makefile.am
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/vsearch/patch-src_Makefile.am     Fri Dec 17 19:20:44 2021 +0000
@@ -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 = $(top_builddir)/bin/vsearch
+ 
+ if TARGET_PPC
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8
++AM_CXXFLAGS=-Wall -Wsign-compare
+ else
+ if TARGET_AARCH64
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=armv8-a+simd -mtune=generic
++AM_CXXFLAGS=-Wall -Wsign-compare
+ else
+-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -march=x86-64 -mtune=generic
++AM_CXXFLAGS=-Wall -Wsign-compare
+ endif
+ endif
+ 
diff -r 84c12aeb24c1 -r 301e89cf4cff biology/vsearch/patches/patch-configure.ac
--- a/biology/vsearch/patches/patch-configure.ac        Fri Dec 17 19:13:57 2021 +0000
+++ b/biology/vsearch/patches/patch-configure.ac        Fri Dec 17 19:20:44 2021 +0000
@@ -1,15 +1,15 @@
-$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 -r 84c12aeb24c1 -r 301e89cf4cff biology/vsearch/patches/patch-man_Makefile.am
--- a/biology/vsearch/patches/patch-man_Makefile.am     Fri Dec 17 19:13:57 2021 +0000
+++ /dev/null   Thu Jan 01 00:00:00 1970 +0000
@@ -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 -r 84c12aeb24c1 -r 301e89cf4cff biology/vsearch/patches/patch-src_Makefile.am
--- a/biology/vsearch/patches/patch-src_Makefile.am     Fri Dec 17 19:13:57 2021 +0000
+++ b/biology/vsearch/patches/patch-src_Makefile.am     Fri Dec 17 19:20:44 2021 +0000
@@ -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