From nobody Wed Apr 10 12:29:07 2024 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4VF2FH5Mhcz5H2TB; Wed, 10 Apr 2024 12:29:07 +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 4VF2FH4fl7z4QRh; Wed, 10 Apr 2024 12:29:07 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1712752147; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=t29s2N6qM6IDz9dULchhI1Q5ecbNoT1uB9lHAjCU/5c=; b=RGzLQot7Fz76vJCuXgnafcanxm6x7sbUWQKCJa5wFPFehjxNdIVeHEmPXrPJcDykrp2dPo yMLecYDJtlUMQ1OTp062+Xnk9QP5+kqvJ3YxU0IKpxDo54pRkJFkTPLpV0fnJHJSNzltkb 81l+5FLJwfzry0SyH4WIRxaiCS8AivqYnyy1v9zsO5w8ZhovtasC0m8yQVM9cDL2LDuH+U Tqm3MkICILRyzgW7dPUgXkbxl0GEDG/dm2nyPE6ZFGRCsF/4V5feO04LmeDn1zvW6pbZAC 3ahPb+xBM/8EkCEfYY3MOk7hk1MmYEQAfjmlEQu+Sunw8n8PXgkYy8xxdHfIIA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1712752147; a=rsa-sha256; cv=none; b=O3NCbX1kyUH0NR7XzGBeiu0pEa9HeeO7ka/6THh14sfJko9G4h0CU9jrBopzLJ0BMisPuR 6QrK9wsVhRx5DxJ+0H6R80EUJXjETK4xvNsUXs9L884qpVS2Cy6qJrHRK8CbPe4FyvpFBk 3Nlx2LmCcoeHyKCooXdVD+/By0IntzeG0K3C/wwNEnwyTRdZrJnwAYfyCO3iNSfXpk05Fr +qfvaUVEbzqAoGVaXSQsvPat/WyOeCLiQnyGNflkX8J4wqawob+qff46IhRJVmnvhB/0C4 WDW+KHazJV9isxMQ3H0p3ziX485YYmOWve5vOyUm/pqJLZv+FXx4rsBDs7T5+A== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1712752147; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=t29s2N6qM6IDz9dULchhI1Q5ecbNoT1uB9lHAjCU/5c=; b=Kkl1+VsHfKVGlcxk0Uki5tnxWJ9OldMDPMPmcE0p+XzxCV9bqPzgCx65xdVgtLv0hAEaDU ARjHq6CvsHxeXxCCaQ77zODBRLZjQcR6OGtCiDRqMP8PwhfI0KAcXdeIv9zGffa58jeOz8 Kq3ZIUgFKxswhWvVKfG9cr8ElXp+mk8l0wcFT3DcqhStY9Nu+T81f8v7PWbMiFS8eVsUNH xF4H15OqyGNugewR/oulRz9DuHOvninodA5AsauLaB58HI/kvN+vORKaBbBSkgvrqkpiV9 XULgpPHs1TyyBeiWv5zmn6xWyAGAZuHGcEIVkMyZ1MGX+q9gAlpK/lBq/Rb78A== 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 4VF2FH4GGyzdY7; Wed, 10 Apr 2024 12:29:07 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 43ACT7Lc003963; Wed, 10 Apr 2024 12:29:07 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 43ACT7ZS003960; Wed, 10 Apr 2024 12:29:07 GMT (envelope-from git) Date: Wed, 10 Apr 2024 12:29:07 GMT Message-Id: <202404101229.43ACT7ZS003960@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: 8efa6a228307 - main - biology/minimap2: Update to 2.28 List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: dev-commits-ports-all+owner@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org 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: 8efa6a2283076e4e556d7796161c44b90f5b3aa8 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=8efa6a2283076e4e556d7796161c44b90f5b3aa8 commit 8efa6a2283076e4e556d7796161c44b90f5b3aa8 Author: Jason W. Bacon AuthorDate: 2024-04-10 12:28:02 +0000 Commit: Jason W. Bacon CommitDate: 2024-04-10 12:28:02 +0000 biology/minimap2: Update to 2.28 Fix --MD flag Add experimental lr:hqae Changes: https://github.com/lh3/minimap2/releases Reported by: portscout --- biology/minimap2/Makefile | 3 +-- biology/minimap2/distinfo | 6 +++--- biology/minimap2/files/patch-Makefile.simde | 6 +++--- biology/minimap2/pkg-plist | 2 +- 4 files changed, 8 insertions(+), 9 deletions(-) diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile index df9552ac6ca0..2539d53f0969 100644 --- a/biology/minimap2/Makefile +++ b/biology/minimap2/Makefile @@ -1,7 +1,6 @@ PORTNAME= minimap2 DISTVERSIONPREFIX= v -DISTVERSION= 2.27 -PORTREVISION= 1 +DISTVERSION= 2.28 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo index 5a1bf73dfa7d..24b9f3d5dc0c 100644 --- a/biology/minimap2/distinfo +++ b/biology/minimap2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1710332275 -SHA256 (lh3-minimap2-v2.27_GH0.tar.gz) = ca9ceb07e3b388858ebc2d7d91a6c74e996659402d16aa759ecedd63588b1ef7 -SIZE (lh3-minimap2-v2.27_GH0.tar.gz) = 259736 +TIMESTAMP = 1712360724 +SHA256 (lh3-minimap2-v2.28_GH0.tar.gz) = 5ea6683b4184b5c49f6dbaef2bc5b66155e405888a0790d1b21fd3c93e474278 +SIZE (lh3-minimap2-v2.28_GH0.tar.gz) = 260341 diff --git a/biology/minimap2/files/patch-Makefile.simde b/biology/minimap2/files/patch-Makefile.simde index aac7981c6b10..5d5e0ccf482c 100644 --- a/biology/minimap2/files/patch-Makefile.simde +++ b/biology/minimap2/files/patch-Makefile.simde @@ -1,4 +1,4 @@ ---- Makefile.simde.orig 2024-03-12 17:20:07 UTC +--- Makefile.simde.orig 2021-11-18 22:11:48 UTC +++ Makefile.simde @@ -1,13 +1,26 @@ -CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra @@ -21,7 +21,7 @@ LIBS= -lm -lz -lpthread +PREFIX?= /usr/local -+MAN1DIR?= ${PREFIX}/share/man/man1 ++MAN1DIR?= ${PREFIX}/man/man1 +DATADIR?= ${PREFIX}/share/minimap2 +MKDIR?= mkdir @@ -32,7 +32,7 @@ ifneq ($(arm_neon),) # if arm_neon is defined ifeq ($(aarch64),) #if aarch64 is not defined CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char -@@ -26,7 +39,7 @@ endif +@@ -26,7 +39,7 @@ ifneq ($(tsan),) LIBS+=-fsanitize=thread endif diff --git a/biology/minimap2/pkg-plist b/biology/minimap2/pkg-plist index 742d1eb1b3f7..1d11d4c99c2f 100644 --- a/biology/minimap2/pkg-plist +++ b/biology/minimap2/pkg-plist @@ -1,7 +1,7 @@ bin/minimap2 bin/minimap2-lite bin/sdust -share/man/man1/minimap2.1.gz +man/man1/minimap2.1.gz %%DATADIR%%/test/MT-human.fa %%DATADIR%%/test/MT-orang.fa %%DATADIR%%/test/q-inv.fa