From nobody Thu Nov 28 15:59:21 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 4Xzgwn6GpFz5dvBv; Thu, 28 Nov 2024 15:59:21 +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 4Xzgwn59QBz4Nkj; Thu, 28 Nov 2024 15:59:21 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1732809561; 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=64pIB2WRsKVvPU7LZWv0qIyGrQxe+/aprbA3qsDfKu8=; b=Z0DzwIHrI1nix2XXEB1H7Ed0MsWAHwqyyIlKjwEvYTWIXFi9gWAxBoxrjBLH5gmKj4+N16 AMdUbpo0XmPgceC9CMPxVGPekEsHku6Mrs4QcR3dk6oup+X7lcaHVrTXH/442sdW/fjJP9 viCSdDamIbzLdgsdclExaQkOIn/NXd/x440afrwWtw0jAaFlmHmoX7i832L6gB5JT2B5sS kpKbgD36120VgE7zkF+m0mdqsqulHu/wKV1iPYQd3w4G5AIxuUn/nNv1bmkt9yadz3jSu+ rpFBomydGZqM93eVHEk70vZiXFoRvhZ1IJnktac5q6x8qvifO3BkzaUstBhwrA== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1732809561; 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=64pIB2WRsKVvPU7LZWv0qIyGrQxe+/aprbA3qsDfKu8=; b=P7yDwCBBbzvi+z38SFxHnqFRbqtyqKu3H3w2zsHYHWFZQ64UeFgB85VmTqIQxMk16MOPCm s7c0V2eCCWjpcu6gz20s/rNnItwg4qeYV8d7RCZ4dsd79pcVQEuWRS70IqBgq7OQUXWnsq VQ02rUZKYbcSYgNx3D4EsBXD7BYoQvRTcciXKzbf+BUEyeHCaTsxxc/nZDnzTNeNRJT5MR 7ZXfANEcKXP9KjqXFBQVg8NqVcI/DPi+pBLOPzRM1nedgNsy3TZXze+6CQ5AuJ2tG6rZ6D RDwyF1u14e2NO5uBL/XpzPnlOb6Q/6WR4CTKlCRf+uFYwUV9BIaZEhw4EpCnhw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1732809561; a=rsa-sha256; cv=none; b=KWBLWCiSl8eNkj/o57BUyTKv8SR3rw72eFecxFGjvZczY4J6Dz18qbDxLKDrguBjkY7Kdv TkKpAHakjzj960Mymk8UtZgkRv8R2LF0gcmkQ33fcQoUFkUgfuvanR/yZPmgFJTaVGhksb pGD+PgQc2f0llp1C6li1HoKwxPnzPFwETrDFRAxYtR7YTIr6SfwxSv8OWZHmHTvOIq00Z6 /JlmhY1lLV0HRR8PW4DQ1762tVK8T39VTmz0E7+Mxv7srY8n1EcQ1tIQdTYJv1u/GrmFz9 EYAxCWtBj1T7RMcjtU1/JryStBuqakn8OoOl5qxf5dNn7KeERvCtOgSK4922uA== 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 4Xzgwn4bbrzlwx; Thu, 28 Nov 2024 15:59:21 +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 4ASFxLPc084657; Thu, 28 Nov 2024 15:59:21 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.18.1/8.18.1/Submit) id 4ASFxLt3084654; Thu, 28 Nov 2024 15:59:21 GMT (envelope-from git) Date: Thu, 28 Nov 2024 15:59:21 GMT Message-Id: <202411281559.4ASFxLt3084654@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: 9cb153ab3484 - main - biology/ucsc-userapps: Update to v474 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: X-BeenThere: dev-commits-ports-all@freebsd.org Sender: owner-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: 9cb153ab34840d98a13cde17c524498a70cdd7f3 Auto-Submitted: auto-generated The branch main has been updated by jwb: URL: https://cgit.FreeBSD.org/ports/commit/?id=9cb153ab34840d98a13cde17c524498a70cdd7f3 commit 9cb153ab34840d98a13cde17c524498a70cdd7f3 Author: Jason W. Bacon AuthorDate: 2024-11-28 15:57:21 +0000 Commit: Jason W. Bacon CommitDate: 2024-11-28 15:59:20 +0000 biology/ucsc-userapps: Update to v474 Several fixes and a few enhancements since v472 Changes: https://github.com/ucscGenomeBrowser/kent/releases Reported by: portscout --- biology/ucsc-userapps/Makefile | 12 ++++++------ biology/ucsc-userapps/distinfo | 6 +++--- biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c | 14 -------------- 3 files changed, 9 insertions(+), 23 deletions(-) diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile index 5d4fa1eb9df6..35f30e18f80d 100644 --- a/biology/ucsc-userapps/Makefile +++ b/biology/ucsc-userapps/Makefile @@ -1,18 +1,20 @@ PORTNAME= ucsc-userapps -DISTVERSION= 472 +DISTVERSION= 474 CATEGORIES= biology perl5 python -MASTER_SITES= http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/ +MASTER_SITES= https://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/ DISTNAME= userApps.v${DISTVERSION}.src MAINTAINER= jwb@FreeBSD.org COMMENT= Command line tools from the UCSC Genome Browser project WWW= https://hgdownload.cse.ucsc.edu/admin/exe/ -# Some tools in the source dist are non-free for commercial use. -# If they are added, the license below must be changed and packaging forbidden. +# Note: Some tools in the source dist are non-free for commercial use. +# If they are added to the install, the license below must be changed +# and packaging forbidden. LICENSE= MIT BUILD_DEPENDS= bash:shells/bash +# FIXME: Switch from mysql to mariadb LIB_DEPENDS= libmysqlclient.so:databases/mysql80-client \ libunwind.so:devel/libunwind \ libfreetype.so:print/freetype2 \ @@ -21,8 +23,6 @@ RUN_DEPENDS= bash:shells/bash USES= gmake iconv localbase:ldflags shebangfix perl5 python:3.6+ ssl tar:tgz -RESTRICTED= Redistribution is limited, see license - SHEBANG_FILES= kent/src/checkUmask.sh \ kent/src/utils/bigHeat \ kent/src/utils/chromToUcsc/chromToUcsc \ diff --git a/biology/ucsc-userapps/distinfo b/biology/ucsc-userapps/distinfo index e5f22b962d6f..ea61209e348b 100644 --- a/biology/ucsc-userapps/distinfo +++ b/biology/ucsc-userapps/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1730984296 -SHA256 (userApps.v472.src.tgz) = 26d126c51d0ba3165519b116b6461af8bfd938505f6c0871cb325a7ab82368f2 -SIZE (userApps.v472.src.tgz) = 24378966 +TIMESTAMP = 1732796640 +SHA256 (userApps.v474.src.tgz) = 87c465169b1246c3d2f56ea415461b7b2a4fb24bf5b7b95a3b590274cc7daec7 +SIZE (userApps.v474.src.tgz) = 24402279 diff --git a/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c b/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c deleted file mode 100644 index e75057e7937c..000000000000 --- a/biology/ucsc-userapps/files/patch-kent_src_hg_lib_jksql.c +++ /dev/null @@ -1,14 +0,0 @@ ---- kent/src/hg/lib/jksql.c.orig 2024-10-16 04:15:27 UTC -+++ kent/src/hg/lib/jksql.c -@@ -1128,8 +1128,9 @@ if (sp->verifyServerCert && !sameString(sp->verifyServ - // If turned on this can defeat Man-In-The-Middle attacks. - if (sp->verifyServerCert && !sameString(sp->verifyServerCert,"0")) - { -- #if !defined(MARIADB_VERSION_ID) && MYSQL_VERSION_ID >= 80000 -- mysql_options(conn, MYSQL_OPT_SSL_MODE, SSL_MODE_REQUIRED); -+ #if !defined(MARIADB_BASE_VERSION) && defined(MYSQL_VERSION_ID) && (MYSQL_VERSION_ID >= 80000) -+ int ssl_mode = SSL_MODE_REQUIRED; -+ mysql_options(conn, MYSQL_OPT_SSL_MODE, &ssl_mode); - #else - my_bool flag = TRUE; - mysql_options(conn, MYSQL_OPT_SSL_VERIFY_SERVER_CERT, &flag);