From nobody Wed Mar 13 13:45:46 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 4TvsGf6s3Vz5CvR4; Wed, 13 Mar 2024 13:45:46 +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 4TvsGf6HmHz55lx; Wed, 13 Mar 2024 13:45:46 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1710337546; 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=PCNG0LllzmT6gfeWb7/DwRV148oO7wyCfjWaja7phyc=; b=dI71cduHQifHXEWWsintovIYkZOtMkZvv4HynDdJzo4+p0e6ZLr+/QYbcwVj3B/NrWKFe3 L1XbSxIJUX/loCwTLtLsU8At05yIzqznwTBpFQKridhsuqUyQtBplwRvYZqyiWkQqQhwS3 FY/hKwM/LA+NipH3ENWyZ6mbAcjfwKsVXDjobNw+QAK1Wl3yDC7fZPaBYek94jRJTw3Rp0 Hkl3ZISFUFANE6pvChv6uTWn2liL/NY3vIirRRXhhiFYpvDBVbNBE0iRO+A4fqYZyS/+ev FtIEPAz7BNOHutmPgHKmKohVGCF9uwoFo5SupIawe/W8w5yVQD5sgJJR+12DsA== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1710337546; a=rsa-sha256; cv=none; b=hMPqO/gepgWw4HnKbSE/29OGbSl9Dkm7iKCRv+4xTpCYVP3smmlhV8tYIFLLG2ZPoN32ai oAO3+BNtcbkwWf7smYQwB8OScZr7tfAUzm+vUfnz46v9ATUEvUsr4nZqbPe3wxJV42w9+V TX8yzBv9NxfHMdlhYpAKKGGBt+fbrOhqrfPrzaYQfU5rVx6rU/cpwixbYY8+Ceu8RmYayc /pEpFPuxUYgis9VOQdBu4epkzp4JCCOeMlIQGDdV2HTz4CyF85533U0z2Yx1Fgq9mOnT4l B0K/CVWyk77OeOhzCIhwuHrvQ6kDT9H4VT/oFPVuygQFxxxALTSxw2UNP4PbWA== 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=1710337546; 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=PCNG0LllzmT6gfeWb7/DwRV148oO7wyCfjWaja7phyc=; b=P6Sw7Rmbdl1ybJ6UoU2hpvweTMMX4kvkEdJc0JcRrbUPyh0iv2FpXxBxJFCn+zl5dK7KMU rbX95PaoQy1fdndKn29Zl/my/ttrK8PlMK7JocEIEAHpWgoyv2Y9g1uvAUtWEw12Cb3lvS ZMBH3+rSp2eMvPDCqNiM/Aa7zBZwOBXIVondXNWOV2u3szVMQ/0e66by9Pgsf1onBUujFw 1WDRtmLzp/No5XUApGwjKLOi3e0E5Tv2hQfAOfk0CU7x5Mj5K2MiLeoTPPEuK3RucOUkUb YlnvdFopxPmX2843XGTWf22dVTj+W3/1IUUF0b9IPQ18lRtdvY4OJjJkL6AhPA== 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 4TvsGf5bJ1zlW7; Wed, 13 Mar 2024 13:45:46 +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 42DDjkZV012473; Wed, 13 Mar 2024 13:45:46 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 42DDjkRk012470; Wed, 13 Mar 2024 13:45:46 GMT (envelope-from git) Date: Wed, 13 Mar 2024 13:45:46 GMT Message-Id: <202403131345.42DDjkRk012470@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: 59bdd5ade746 - main - biology/minimap2: Update to 2.27 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: owner-dev-commits-ports-all@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: 59bdd5ade7461f7925af1ad1ae2f2a8cb90a848f Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=59bdd5ade7461f7925af1ad1ae2f2a8cb90a848f commit 59bdd5ade7461f7925af1ad1ae2f2a8cb90a848f Author: Jason W. Bacon AuthorDate: 2024-03-13 13:44:27 +0000 Commit: Jason W. Bacon CommitDate: 2024-03-13 13:44:27 +0000 biology/minimap2: Update to 2.27 Several new features and a few bug fixes 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 2ab83948882d..d403413cc324 100644 --- a/biology/minimap2/Makefile +++ b/biology/minimap2/Makefile @@ -1,7 +1,6 @@ PORTNAME= minimap2 DISTVERSIONPREFIX= v -DISTVERSION= 2.25 -PORTREVISION= 1 +DISTVERSION= 2.27 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/minimap2/distinfo b/biology/minimap2/distinfo index 7c79ce9501e2..5a1bf73dfa7d 100644 --- a/biology/minimap2/distinfo +++ b/biology/minimap2/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1682729894 -SHA256 (lh3-minimap2-v2.25_GH0.tar.gz) = 9742ff0be01e51ea7d65f70c01d1344eee6f0d7b135359e0c00aec30fb74ac38 -SIZE (lh3-minimap2-v2.25_GH0.tar.gz) = 257574 +TIMESTAMP = 1710332275 +SHA256 (lh3-minimap2-v2.27_GH0.tar.gz) = ca9ceb07e3b388858ebc2d7d91a6c74e996659402d16aa759ecedd63588b1ef7 +SIZE (lh3-minimap2-v2.27_GH0.tar.gz) = 259736 diff --git a/biology/minimap2/files/patch-Makefile.simde b/biology/minimap2/files/patch-Makefile.simde index faef217fbdab..5d5e0ccf482c 100644 --- a/biology/minimap2/files/patch-Makefile.simde +++ b/biology/minimap2/files/patch-Makefile.simde @@ -1,4 +1,4 @@ ---- Makefile.simde.orig 2023-04-25 16:44:52 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