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biology/vsearch: Update to 2.18.0

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Add powerpc64 support
Numerous fixes and enhancements since 2.13

Changes: https://github.com/torognes/vsearch/tags
This commit is contained in:
bacon 2021-12-17 19:20:44 +00:00
parent eb59e9430d
commit d47d63b4e1
7 changed files with 42 additions and 32 deletions
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8
biology/vsearch/Makefile
View file

@ -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

2
biology/vsearch/PLIST
View file

@ -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

13
biology/vsearch/distinfo
View file

@ -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

22
biology/vsearch/patch-src_Makefile.am Normal file
View file

@ -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

8
biology/vsearch/patches/patch-configure.ac
View file

@ -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

13
biology/vsearch/patches/patch-man_Makefile.am
View file

@ -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 \

8
biology/vsearch/patches/patch-src_Makefile.am
View file

@ -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