From nobody Tue Dec 3 14:55:07 2024 X-Original-To: dev-commits-ports-main@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 4Y2kGN3rpVz5gCxg; Tue, 03 Dec 2024 14:55:08 +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 "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4Y2kGN1538z4CSM; Tue, 3 Dec 2024 14:55:08 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1733237708; 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=z4/QlkGs7bjPX2q+HDidNCWP3PXgjboMqOm7EUOYZso=; b=jTii6lzp16zSGmf5l4b6yznj8q0A2dx1pxx8/eMhazdMJhAWHakE/mvpRWYjjebqms99fL 1CNoReI4INXgrcS4/kog6Fr37XDy8lCgIHl59szAcR0V+ehAy/r5+/BVLfWFsWQJVTHfAU fJnX44iIwfrR0nCDF1VznsZh2koH5JrUR0aW3EnC9yzjTjlHsbX4GIs9iU1fwgw0OPb69y E59pqjKsUi2augqriI1qQU/g8najrVAYmhhP1uwcHypLdjMlE7svtHo84Gkz0Jmy2NU1fI qDWCYpoBRIJWuF+rDSdPo6QfqI0XxiEnR0qtU3UMqAqIOrlc/mhzTOxMznqe0w== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1733237708; 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=z4/QlkGs7bjPX2q+HDidNCWP3PXgjboMqOm7EUOYZso=; b=Mj742L6WBupaoxj6dFT3v0D/yqbcxkIYLF8390OQU7NYTwhUVNy3aaejAzl4nIE5K0Vcp5 W7GM3DajIYNSgQoE+mGz07zIhHUCcPU6U+kc1uZ1OB7mLHaJyB5Ak70SX7LH1hdcsKWELZ xn5UpifazlSEYcIp6/3mPHg/TRgV10FKKGFl8HhqxqjPp7mATPt5Me0ppcEQ0TEDTRQJxh aMDrekmVsgdMgRoHGdQiN6vcW6BcicvbU1nY5QY2pifpM0hYIfY4N4P1CkhsA04lx2kflX broHgP6lKUpwGoZHRGykM7YwoZlbrZya1n72UfwjxiGbwYVMjLyUbEfapz/NQA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1733237708; a=rsa-sha256; cv=none; b=frlcayIOnDgwR7EXD1M3pSR3a7u2PPIFCpBFBXQXSItljue7BOMOp7+7U9fmPr79VkSxZH q1jVoquXAf3fpyUDqqcDOabwXSfVlEb8nHPN7nTKQliTIHxxOZTMDp6wiDm870tL8DNwZU tb2akiuxPKcZIKw06ELoW3q7xVJHXF7ip6zIUpuOkvpj6x36XT2bSI+RKiqI6W2F/wnIPa CnRchSA1crUr9/MTIelfgNFSLAkmDPgK93ALpMwxcRiwgrot8B3ZxEhrTWKSG94J17bbor EoTj8cQSI/fCX3xEpoZSBU+pt4dlf35GQJXu2v7blm4d6MT6S2zhHGuBwY1KtA== 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 4Y2kGN0ht5zS3n; Tue, 3 Dec 2024 14:55:08 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.18.1/8.18.1) with ESMTP id 4B3Et7gf084340; Tue, 3 Dec 2024 14:55:08 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 4B3Et7kQ084337; Tue, 3 Dec 2024 14:55:07 GMT (envelope-from git) Date: Tue, 3 Dec 2024 14:55:07 GMT Message-Id: <202412031455.4B3Et7kQ084337@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: 12b5c3c8f16f - main - biology/fasttree: Update to 2.1.11 List-Id: Commits to the main branch of the FreeBSD ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-main List-Help: List-Post: List-Subscribe: List-Unsubscribe: X-BeenThere: dev-commits-ports-main@freebsd.org Sender: owner-dev-commits-ports-main@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: 12b5c3c8f16f39c561373f70a554b98ae9f0dec7 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=12b5c3c8f16f39c561373f70a554b98ae9f0dec7 commit 12b5c3c8f16f39c561373f70a554b98ae9f0dec7 Author: Jason W. Bacon AuthorDate: 2024-12-03 14:52:16 +0000 Commit: Jason W. Bacon CommitDate: 2024-12-03 14:55:06 +0000 biology/fasttree: Update to 2.1.11 Add -trans option for amino acid alignments Changes: https://microbesonline.org/fasttree/ChangeLog PR: 283035 Reported by: alster@vinterdalen.se --- biology/fasttree/Makefile | 14 +++++++------- biology/fasttree/distinfo | 6 +++--- biology/fasttree/files/patch-FastTree-2.1.10.c | 4 ++-- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/biology/fasttree/Makefile b/biology/fasttree/Makefile index 560274658cd1..47ede864ea6f 100644 --- a/biology/fasttree/Makefile +++ b/biology/fasttree/Makefile @@ -1,23 +1,23 @@ PORTNAME= FastTree -DISTVERSION= 2.1.10 -PORTREVISION= 5 +DISTVERSION= 2.1.11 CATEGORIES= biology -MASTER_SITES= http://www.microbesonline.org/fasttree/ +MASTER_SITES= https://www.microbesonline.org/fasttree/ EXTRACT_SUFX= .c MAINTAINER= jwb@FreeBSD.org COMMENT= Approximately-maximum-likelihood phylogenetic trees from alignments -WWW= http://www.microbesonline.org/fasttree/ +WWW= https://www.microbesonline.org/fasttree/ LICENSE= GPLv2+ -NO_WRKSUBDIR= yes -PLIST_FILES= bin/FastTree - .if !exists(/usr/include/omp.h) USES= compiler:gcc-c++11-lib .endif +NO_WRKSUBDIR= yes + +PLIST_FILES= bin/FastTree + do-extract: @${CP} ${DISTDIR}/${DISTFILES} ${WRKSRC} @${CP} ${FILESDIR}/Makefile ${WRKSRC} diff --git a/biology/fasttree/distinfo b/biology/fasttree/distinfo index 2777da148528..2b1eecd7ac7f 100644 --- a/biology/fasttree/distinfo +++ b/biology/fasttree/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1512317739 -SHA256 (FastTree-2.1.10.c) = 54cb89fc1728a974a59eae7a7ee6309cdd3cddda9a4c55b700a71219fc6e926d -SIZE (FastTree-2.1.10.c) = 390916 +TIMESTAMP = 1732861256 +SHA256 (FastTree-2.1.11.c) = 9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f +SIZE (FastTree-2.1.11.c) = 395543 diff --git a/biology/fasttree/files/patch-FastTree-2.1.10.c b/biology/fasttree/files/patch-FastTree-2.1.10.c index 36dd31ceb877..274e2d7719af 100644 --- a/biology/fasttree/files/patch-FastTree-2.1.10.c +++ b/biology/fasttree/files/patch-FastTree-2.1.10.c @@ -1,5 +1,5 @@ ---- FastTree-2.1.10.c.orig 2017-12-04 15:09:11 UTC -+++ FastTree-2.1.10.c +--- FastTree-2.1.11.c.orig 2017-12-04 15:09:11 UTC ++++ FastTree-2.1.11.c @@ -8759,7 +8759,7 @@ double pnorm(double x) void *mymalloc(size_t sz) {