From nobody Wed May 14 16:53:45 2025 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 4ZyKDT32C7z5wwMX; Wed, 14 May 2025 16:53:45 +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 "R11" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4ZyKDT2WtCz3ClN; Wed, 14 May 2025 16:53:45 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1747241625; 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=MGlEEsleR8Nogsxe19Tx0GBkox4bIkXdHuj561H7hwg=; b=Rw3zjTZtTC2sQ7adfvERpBrE+4VJ+g2B0rUFYIdSz/i11j11SBmiD4w6M4xthTItSQXYS2 qYFfmmH7fPmyi0kRWvYsDe8i0utMxpjRUUAIhMtA5VEdS5VeNnIYZ9G8gymUkIdPvCNBdE /f/UacBBDnb+2/O6MD+359ua18Dx5ogk8sQYvNlaEw9NIB2rr3US7q8LFDI82EOqHx/NQ1 DdFmjCBVsCGFiCUA+e6WSEArTcpNxic0UCRK1Cs4/UpzAOvWkOGITp7P6q/GJYv+FM6TsH RFuAHcjoqALeB/GJS9JVzWEk7QYYgLXmB1gxL0kt3y3QZvIV4TJVzNla3SlASQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1747241625; 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=MGlEEsleR8Nogsxe19Tx0GBkox4bIkXdHuj561H7hwg=; b=GZ1SbM7xnYaCJk+XoPaCZ0OwTsgBudnlN2Y/WicDwFaWku5LRozcrGvabt4NIYBRtscUTX 4a8ka4+9qo5aPk/mHL2duMbN6T1bUbNGeeL4pUy6Zv0K8g5vl0ydduFtTuC31gJkJo86z+ 55lNZK5XZfgXT/tDBzoLzEqRkuIeooM41zA52XOEeWeQbrcaIWR1fVUgg3HrHjkXrMSAsF Ul9uslcQObXITZkk+AFh60Y8TU6thETI2MsRV6SeXemw9RH5JfhltBVpwnoeimVyvjnVr8 uIvaCj4fnLeYQoqER7V+QB+NPNg3bQEbNi9yNW6qdtT8sQK+NDaDbnolcBxb+A== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1747241625; a=rsa-sha256; cv=none; b=Jj9ZIuF0RgJ3T+QevzcsqHKMt2RzxwFufB+/hxPFq3HeJBW10HS4RNPgQglC2C2aZGXJ// GTelnVa3L7BLPZBi/9l14i8+7I3NCejDO+Qo+oNcnEehuRx4ba1Ivo9ptm8HRWrZwAwUfJ 6zz4Wh4Y9PBU7OX2uXOtI7Urv9WxVaux336+q0PU5qOXY1nRdLEvq4IscoSncikK5mzLtg KDBvm4NMrQxhTpaHf6cqVsP4Alk/e2GoufqlQtU2HJICbmls3jfe4IWxV0ZHmTBdczKhgt dnFBILx/9MJ0Z0uGTE1zM83LxKm2jWVUD7ldHMA/cOXiMPjxhfA2cdNvJdG7mg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none 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 4ZyKDT26QPzh7N; Wed, 14 May 2025 16:53:45 +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 54EGrjMn040959; Wed, 14 May 2025 16:53:45 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 54EGrjvh040956; Wed, 14 May 2025 16:53:45 GMT (envelope-from git) Date: Wed, 14 May 2025 16:53:45 GMT Message-Id: <202505141653.54EGrjvh040956@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Joseph Mingrone Subject: git: 5fd436fa038a - main - biology/paml: Update to 4.10.9 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: jrm X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 5fd436fa038a51191243a93ecb8a73c7514feace Auto-Submitted: auto-generated The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=5fd436fa038a51191243a93ecb8a73c7514feace commit 5fd436fa038a51191243a93ecb8a73c7514feace Author: Joseph Mingrone AuthorDate: 2025-05-14 15:52:35 +0000 Commit: Joseph Mingrone CommitDate: 2025-05-14 15:59:29 +0000 biology/paml: Update to 4.10.9 Also patch out upstream's newly introduced hardcoded values for CC and CFLAGS. Release notes: https://github.com/abacus-gene/paml/releases/tag/v4.10.8 https://github.com/abacus-gene/paml/releases/tag/v4.10.9 Sponsored by: The FreeBSD Foundation --- biology/paml/Makefile | 3 ++- biology/paml/distinfo | 6 +++--- biology/paml/files/patch-src_Makefile | 15 ++++++++------- biology/paml/pkg-plist | 2 -- 4 files changed, 13 insertions(+), 13 deletions(-) diff --git a/biology/paml/Makefile b/biology/paml/Makefile index 7ba18e506f72..4a6375689d5e 100644 --- a/biology/paml/Makefile +++ b/biology/paml/Makefile @@ -1,5 +1,6 @@ PORTNAME= paml -DISTVERSION= 4.10.7 +DISTVERSIONPREFIX= v +DISTVERSION= 4.10.9 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/paml/distinfo b/biology/paml/distinfo index cd64f0e34127..7dd47591a370 100644 --- a/biology/paml/distinfo +++ b/biology/paml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1688759942 -SHA256 (abacus-gene-paml-4.10.7_GH0.tar.gz) = 0f29e768b3797b69eadc6332c3d046d8727702052d56c3b729883626c0a5a4e3 -SIZE (abacus-gene-paml-4.10.7_GH0.tar.gz) = 5250841 +TIMESTAMP = 1747232666 +SHA256 (abacus-gene-paml-v4.10.9_GH0.tar.gz) = 19ca9d484d729324748b9c86453e4c8f4a1fa79ad6fa3ac7cdbfaa7d0bfb8c22 +SIZE (abacus-gene-paml-v4.10.9_GH0.tar.gz) = 3920159 diff --git a/biology/paml/files/patch-src_Makefile b/biology/paml/files/patch-src_Makefile index 4a9bd7ed2da6..1fd048a0594b 100644 --- a/biology/paml/files/patch-src_Makefile +++ b/biology/paml/files/patch-src_Makefile @@ -1,10 +1,11 @@ ---- src/Makefile.orig 2023-07-08 03:40:50 UTC +--- src/Makefile.orig 2025-05-14 14:29:51 UTC +++ src/Makefile -@@ -1,6 +1,6 @@ CC = cc # cc, gcc, cl +@@ -1,6 +1,6 @@ PRGS = baseml codeml basemlg mcmctree pamp evolver yn PRGS = baseml codeml basemlg mcmctree pamp evolver yn00 chi2 - CC = cc # cc, gcc, cl --CFLAGS = -O3 -Wall -Wno-unused-result -Wmemset-elt-size -+CFLAGS = -O3 -Wall -Wno-unused-result - #CC = icc - #CFLAGS = -fast -Wall +-CC = gcc +-CFLAGS = -O3 -Wall -Wno-unused-variable -Wno-unused-result ++#CC = gcc ++#CFLAGS = -O3 -Wall -Wno-unused-variable -Wno-unused-result + + LIBS = -lm diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist index 544b761367c3..02f053d2563e 100644 --- a/biology/paml/pkg-plist +++ b/biology/paml/pkg-plist @@ -199,8 +199,6 @@ bin/yn00 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/data-MCU0.95-rep1.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo4.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/mlb-nhomo5.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/rst-nhomo4.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/rst-nhomo5.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo4.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/tree-nhomo5.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl