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Fri, 17 Dec 2021 19:20:44 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_163976884440020" MIME-Version: 1.0 Date: Fri, 17 Dec 2021 19:20:44 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/vsearch To: pkgsrc-changes@NetBSD.org Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20211217192044.CC05BFAEC@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_163976884440020 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Fri Dec 17 19:20:44 UTC 2021 Modified Files: pkgsrc/biology/vsearch: Makefile PLIST distinfo pkgsrc/biology/vsearch/patches: patch-configure.ac patch-src_Makefile.am Added Files: pkgsrc/biology/vsearch: patch-src_Makefile.am Removed Files: pkgsrc/biology/vsearch/patches: patch-man_Makefile.am Log Message: biology/vsearch: Update to 2.18.0 Add powerpc64 support Numerous fixes and enhancements since 2.13 Changes: https://github.com/torognes/vsearch/tags To generate a diff of this commit: cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/vsearch/Makefile cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/vsearch/PLIST cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/vsearch/distinfo cvs rdiff -u -r0 -r1.1 pkgsrc/biology/vsearch/patch-src_Makefile.am cvs rdiff -u -r1.2 -r1.3 pkgsrc/biology/vsearch/patches/patch-configure.ac \ pkgsrc/biology/vsearch/patches/patch-src_Makefile.am cvs rdiff -u -r1.1 -r0 pkgsrc/biology/vsearch/patches/patch-man_Makefile.am Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_163976884440020 Content-Disposition: inline Content-Length: 5440 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/vsearch/Makefile diff -u pkgsrc/biology/vsearch/Makefile:1.3 pkgsrc/biology/vsearch/Makefile:1.4 --- pkgsrc/biology/vsearch/Makefile:1.3 Sun Apr 25 07:51:24 2021 +++ pkgsrc/biology/vsearch/Makefile Fri Dec 17 19:20:44 2021 @@ -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 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 Index: pkgsrc/biology/vsearch/PLIST diff -u pkgsrc/biology/vsearch/PLIST:1.2 pkgsrc/biology/vsearch/PLIST:1.3 --- pkgsrc/biology/vsearch/PLIST:1.2 Sat May 11 14:27:18 2019 +++ pkgsrc/biology/vsearch/PLIST Fri Dec 17 19:20:44 2021 @@ -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 Index: pkgsrc/biology/vsearch/distinfo diff -u pkgsrc/biology/vsearch/distinfo:1.5 pkgsrc/biology/vsearch/distinfo:1.6 --- pkgsrc/biology/vsearch/distinfo:1.5 Tue Oct 26 10:03:44 2021 +++ pkgsrc/biology/vsearch/distinfo Fri Dec 17 19:20:44 2021 @@ -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 Index: pkgsrc/biology/vsearch/patches/patch-configure.ac diff -u pkgsrc/biology/vsearch/patches/patch-configure.ac:1.2 pkgsrc/biology/vsearch/patches/patch-configure.ac:1.3 --- pkgsrc/biology/vsearch/patches/patch-configure.ac:1.2 Sat May 11 14:27:18 2019 +++ pkgsrc/biology/vsearch/patches/patch-configure.ac Fri Dec 17 19:20:44 2021 @@ -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 Index: pkgsrc/biology/vsearch/patches/patch-src_Makefile.am diff -u pkgsrc/biology/vsearch/patches/patch-src_Makefile.am:1.2 pkgsrc/biology/vsearch/patches/patch-src_Makefile.am:1.3 --- pkgsrc/biology/vsearch/patches/patch-src_Makefile.am:1.2 Sat May 11 14:27:18 2019 +++ pkgsrc/biology/vsearch/patches/patch-src_Makefile.am Fri Dec 17 19:20:44 2021 @@ -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 = $(top_builddir)/bin/vsearch if TARGET_PPC --AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=power8 +-AM_CXXFLAGS=-Wall -Wsign-compare -O3 -g -mcpu=powerpc64le -maltivec +AM_CXXFLAGS=-Wall -Wsign-compare else if TARGET_AARCH64 Added files: Index: pkgsrc/biology/vsearch/patch-src_Makefile.am diff -u /dev/null pkgsrc/biology/vsearch/patch-src_Makefile.am:1.1 --- /dev/null Fri Dec 17 19:20:44 2021 +++ pkgsrc/biology/vsearch/patch-src_Makefile.am Fri Dec 17 19:20:44 2021 @@ -0,0 +1,22 @@ +$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 + --_----------=_163976884440020--