From nobody Sat Jul 08 03:50:04 2023 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 4QybrF0WTbz4lKsR; Sat, 8 Jul 2023 03:50:05 +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 4QybrD73tNz4Kwx; Sat, 8 Jul 2023 03:50:04 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1688788205; 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=9V5hrxRoYLeFZCoHBkkC9mDBbCljfksxtT+a/L3193U=; b=d9aPTSRM2fn7m6SwFqJSoqNKBWat1v4WomVko2AcCOQ1rIN5T80jPbWhu8E4jR3j0vnf7I BCy5T+c+s+MK5xEeXjJvbUAa0ewmmpO08mVUJWq/D4ZH51AcO0aB8Obajb5rzjEiMri105 YuCmiczfUGU5uSR+2mD6uUfc79j2h5UzVCICWYNdaFctnRbfbNOK9Ni7+mpeUu4nRHMYtG /A2W485xNBl4GTsityGPcbg7vr3IYYtR27/lkvtvfGqblO/6ipeTbMhIdcwhRCeFp+OWMR TspJ5SHZ3wO+rPQj7sgvbo90cA5FvkqzGbnn/cqzLDtmrM8RJ6rr9IU0t8cPnQ== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1688788205; 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=9V5hrxRoYLeFZCoHBkkC9mDBbCljfksxtT+a/L3193U=; b=SICLWmLDeAsMOnGWsYKnHMWn4XUlOijD9pG+CWgXoTSZy4IVqQs2G/JsKbQvg+pa+3XhpJ WF/+mHF5ofDLA+3LeOiITF5Sw7+JSyN6f/hUlnUsWqrJu8iz9pguFLwVTeVACDYiLNJk/u B06EO7Ir4PhynCsTycfgt2kHAzmV7x/B2k/HG5Bg8L/Jn0VUIrVCtihvIDgOQdnBUE4+qG BA5WNC/f4FqUiWZZXtM7CfwYwD9K5d5eTjwGzd1RWXLiDRMgZHhEIHhXDyCuJc5IGZh2TF YGGipZx6eKlplYTad1iqQc0JeitBKDTljaK8xYIXsRIwNwLcqYCaVhDNp+Ym7g== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1688788205; a=rsa-sha256; cv=none; b=T4OQJp0G1k4b9RJ1QhHFESfwH89A21uPCFnqr8wVmmZkise68ucJzXpQF2zAPwGYJu9DfM IbDDABDMCCCdryiYZDkEljBwlONp2kXyNKwHaWj80nV/EMz+k6R0+TwKrCz/qQmZ3wdpfN upzApuoulctwPMpDyftMvAM5zQTtQo1w8X+uA+L/9WCEiebPCfJQpvYZO3hiQahx17zd+F UMlNs/23T8qsKBmVY1yUrs5jdznQlL0OMoEhV8AGV8K8J/u4pF8+38iezaeRpUIbsN65vS 0EgO51jPLvF7zlSG93nSONV9jz3Aj6cpxFfd7S0apNCS5MrGGv6ViZ4pTOVdzw== 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 4QybrD63gWz15Tl; Sat, 8 Jul 2023 03:50:04 +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 3683o4s0094754; Sat, 8 Jul 2023 03:50:04 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 3683o4wc094751; Sat, 8 Jul 2023 03:50:04 GMT (envelope-from git) Date: Sat, 8 Jul 2023 03:50:04 GMT Message-Id: <202307080350.3683o4wc094751@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: 5fc301443c77 - main - biology/paml: Update to 4.10.7 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: Sender: owner-dev-commits-ports-main@freebsd.org X-BeenThere: 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: 5fc301443c77a4952c42153f12a7520f913f60a3 Auto-Submitted: auto-generated X-ThisMailContainsUnwantedMimeParts: N The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=5fc301443c77a4952c42153f12a7520f913f60a3 commit 5fc301443c77a4952c42153f12a7520f913f60a3 Author: Joseph Mingrone AuthorDate: 2023-07-08 03:44:17 +0000 Commit: Joseph Mingrone CommitDate: 2023-07-08 03:46:53 +0000 biology/paml: Update to 4.10.7 Remove -Wmemset-elt-size from CFLAGS. The warning is only applicable to gcc and is already enabled with -Wall. Changes: https://github.com/abacus-gene/paml/releases/tag/4.10.7 Sponsored by: The FreeBSD Foundation --- biology/paml/Makefile | 3 +-- biology/paml/distinfo | 6 +++--- biology/paml/files/patch-src_Makefile | 10 +++++++++ biology/paml/pkg-plist | 38 +++++++++++++++++++++++++++++++++-- 4 files changed, 50 insertions(+), 7 deletions(-) diff --git a/biology/paml/Makefile b/biology/paml/Makefile index 6a0b8081fd19..7ba18e506f72 100644 --- a/biology/paml/Makefile +++ b/biology/paml/Makefile @@ -1,6 +1,5 @@ PORTNAME= paml -DISTVERSIONPREFIX= v -DISTVERSION= 4.10.6 +DISTVERSION= 4.10.7 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org diff --git a/biology/paml/distinfo b/biology/paml/distinfo index f597c10ced71..cd64f0e34127 100644 --- a/biology/paml/distinfo +++ b/biology/paml/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1668305503 -SHA256 (abacus-gene-paml-v4.10.6_GH0.tar.gz) = d6437f04ee233209e1ded83addbfe65d1363185877a03ba7924ce81f9ebc7777 -SIZE (abacus-gene-paml-v4.10.6_GH0.tar.gz) = 3386016 +TIMESTAMP = 1688759942 +SHA256 (abacus-gene-paml-4.10.7_GH0.tar.gz) = 0f29e768b3797b69eadc6332c3d046d8727702052d56c3b729883626c0a5a4e3 +SIZE (abacus-gene-paml-4.10.7_GH0.tar.gz) = 5250841 diff --git a/biology/paml/files/patch-src_Makefile b/biology/paml/files/patch-src_Makefile new file mode 100644 index 000000000000..4a9bd7ed2da6 --- /dev/null +++ b/biology/paml/files/patch-src_Makefile @@ -0,0 +1,10 @@ +--- src/Makefile.orig 2023-07-08 03:40:50 UTC ++++ src/Makefile +@@ -1,6 +1,6 @@ CC = cc # cc, gcc, cl + 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 + diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist index aac062f86730..544b761367c3 100644 --- a/biology/paml/pkg-plist +++ b/biology/paml/pkg-plist @@ -44,9 +44,13 @@ bin/yn00 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/README.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/codeml.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/README.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.phy %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.trees @@ -126,6 +130,12 @@ bin/yn00 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtREV24.dat %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtmam.dat %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/wag.dat +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/6s-bracing.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/6s.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/MCbase-6s.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/mc.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/mcmctree-bracing.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dating-cross-bracing/mcmctree.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.nuc %%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.trees %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/README.txt @@ -165,10 +175,34 @@ bin/yn00 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.trees %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.txt %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtprim9.nuc -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-mc.trees -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-mc.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/codeml-M0.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.aln +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.tree +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata-maintree.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/5s-mc.trees +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/MCbase.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree-ml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree-ml.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree.ctl %%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/mc.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/README.txt +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/baseml-nhomo4.ctl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nhomo/baseml-nhomo5.ctl +%%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 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupblock %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupend