From owner-dev-commits-ports-main@freebsd.org Sun Apr 11 19:18:27 2021 Return-Path: Delivered-To: dev-commits-ports-main@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id B46BF5D9020; Sun, 11 Apr 2021 19:18:27 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4FJM8z4mDlz4Tk0; Sun, 11 Apr 2021 19:18:27 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 9682D10E6; Sun, 11 Apr 2021 19:18:27 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 13BJIRPS068650; Sun, 11 Apr 2021 19:18:27 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 13BJIRKG068649; Sun, 11 Apr 2021 19:18:27 GMT (envelope-from git) Date: Sun, 11 Apr 2021 19:18:27 GMT Message-Id: <202104111918.13BJIRKG068649@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: "Jason W. Bacon" Subject: git: a2fa05009fd2 - main - biology/minimap2: Update to 2.18 MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: jwb X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: a2fa05009fd280fcf8e93f1062b554fdcca63c9a Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-main@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commits to the main branch of the FreeBSD ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 11 Apr 2021 19:18:27 -0000 The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=a2fa05009fd280fcf8e93f1062b554fdcca63c9a commit a2fa05009fd280fcf8e93f1062b554fdcca63c9a Author: Jason W. Bacon AuthorDate: 2021-04-11 19:16:28 +0000 Commit: Jason W. Bacon CommitDate: 2021-04-11 19:18:02 +0000 biology/minimap2: Update to 2.18 Numerous bug fixes and a few minor improvements Reported by: portscout --- biology/minimap2/Makefile | 2 +- biology/minimap2/distinfo | 6 +++--- biology/minimap2/files/patch-Makefile | 8 +++----- 3 files changed, 7 insertions(+), 9 deletions(-) diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile index e8570bd99479..d99da2bcc4b5 100644 --- a/biology/minimap2/Makefile +++ b/biology/minimap2/Makefile @@ -1,6 +1,6 @@ PORTNAME= minimap2 DISTVERSIONPREFIX= v -DISTVERSION= 2.17 +DISTVERSION= 2.18 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo index aa8229da44d3..69632d44a87f 100644 --- a/biology/minimap2/distinfo +++ b/biology/minimap2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1557067380 -SHA256 (lh3-minimap2-v2.17_GH0.tar.gz) = 0a3eaa3ef3d9f9e41f48199cc4aac0508366ac644fc3e8fe05e3463acd23d20b -SIZE (lh3-minimap2-v2.17_GH0.tar.gz) = 224006 +TIMESTAMP = 1618167822 +SHA256 (lh3-minimap2-v2.18_GH0.tar.gz) = efe75148342decd67e16f6a9ae14918ab9e1d67cadcfab5698b847f5b66f55e3 +SIZE (lh3-minimap2-v2.18_GH0.tar.gz) = 231187 diff --git a/biology/minimap2/files/patch-Makefile b/biology/minimap2/files/patch-Makefile index f9008ea92a76..19bf99b1325d 100644 --- a/biology/minimap2/files/patch-Makefile +++ b/biology/minimap2/files/patch-Makefile @@ -1,10 +1,8 @@ ---- Makefile.orig 2019-05-05 03:49:17 UTC +--- Makefile.orig 2019-02-28 20:49:24 UTC +++ Makefile -@@ -1,11 +1,21 @@ +@@ -1,11 +1,19 @@ -CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra -CPPFLAGS= -DHAVE_KALLOC -+# Patches using ?= and adding install target were rejected by developers -+# https://github.com/lh3/minimap2/issues/388 +CFLAGS?= -g -Wall -O2 +CFLAGS+= -Wc++-compat #-Wextra +CPPFLAGS+= -DHAVE_KALLOC @@ -24,7 +22,7 @@ ifeq ($(arm_neon),) # if arm_neon is not defined ifeq ($(sse2only),) # if sse2only is not defined OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o -@@ -84,6 +94,15 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h +@@ -84,6 +92,15 @@ ksw2_exts2_neon.o:ksw2_exts2_sse.c ksw2.h kalloc.h $(CC) -c $(CFLAGS) $(CPPFLAGS) -DKSW_SSE2_ONLY -D__SSE2__ $(INCLUDES) $< -o $@ # other non-file targets