From owner-dev-commits-ports-all@freebsd.org Fri Aug 20 13:57:20 2021 Return-Path: Delivered-To: dev-commits-ports-all@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 007B8660EA4; Fri, 20 Aug 2021 13:57:19 +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 4Grjqz6SZRz3rxb; Fri, 20 Aug 2021 13:57:19 +0000 (UTC) (envelope-from git@FreeBSD.org) 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 C628D1A0DD; Fri, 20 Aug 2021 13:57:19 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.16.1/8.16.1) with ESMTP id 17KDvJAu057093; Fri, 20 Aug 2021 13:57:19 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.16.1/8.16.1/Submit) id 17KDvJGl057092; Fri, 20 Aug 2021 13:57:19 GMT (envelope-from git) Date: Fri, 20 Aug 2021 13:57:19 GMT Message-Id: <202108201357.17KDvJGl057092@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: dab99da05576 - main - biology/hyphy: Update to 2.4.32 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: dab99da055766eeb61cff4d0064b02b3d0ac69c8 Auto-Submitted: auto-generated X-BeenThere: dev-commits-ports-all@freebsd.org X-Mailman-Version: 2.1.34 Precedence: list List-Id: Commit messages for all branches of the ports repository List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 20 Aug 2021 13:57:20 -0000 The branch main has been updated by jrm: URL: https://cgit.FreeBSD.org/ports/commit/?id=dab99da055766eeb61cff4d0064b02b3d0ac69c8 commit dab99da055766eeb61cff4d0064b02b3d0ac69c8 Author: Joseph Mingrone AuthorDate: 2021-08-20 13:52:29 +0000 Commit: Joseph Mingrone CommitDate: 2021-08-20 13:56:52 +0000 biology/hyphy: Update to 2.4.32 https://github.com/veg/hyphy/releases/tag/2.5.32 Port changes: - Remove USES=ssl since it's an indirect dependency from curl - Remove patch that was upstreamed --- biology/hyphy/Makefile | 4 ++-- biology/hyphy/distinfo | 6 +++--- biology/hyphy/files/patch-CMakeLists.txt | 27 --------------------------- biology/hyphy/pkg-plist | 1 + 4 files changed, 6 insertions(+), 32 deletions(-) diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index 34850adee62a..99d7ada92851 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -1,5 +1,5 @@ PORTNAME= hyphy -DISTVERSION= 2.5.31 +DISTVERSION= 2.5.32 CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org @@ -12,7 +12,7 @@ ONLY_FOR_ARCHS= amd64 i386 LIB_DEPENDS= libcurl.so:ftp/curl -USES= cmake localbase:ldflags ssl +USES= cmake localbase:ldflags USE_GITHUB= yes GH_ACCOUNT= veg diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo index 9300d52387fe..948d3cd0569a 100644 --- a/biology/hyphy/distinfo +++ b/biology/hyphy/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1622916930 -SHA256 (veg-hyphy-2.5.31_GH0.tar.gz) = 2fa27ba3c4464ee2239570ebf6a038c6a3e216350ba8c3c22e43de0cb9c5dbd7 -SIZE (veg-hyphy-2.5.31_GH0.tar.gz) = 5342292 +TIMESTAMP = 1629465228 +SHA256 (veg-hyphy-2.5.32_GH0.tar.gz) = e47be24b3de21a7a29eec6256cba7481ac8a98437d49eb682aefa5de2f4350ce +SIZE (veg-hyphy-2.5.32_GH0.tar.gz) = 5346015 diff --git a/biology/hyphy/files/patch-CMakeLists.txt b/biology/hyphy/files/patch-CMakeLists.txt deleted file mode 100644 index 704bbe9368b6..000000000000 --- a/biology/hyphy/files/patch-CMakeLists.txt +++ /dev/null @@ -1,27 +0,0 @@ ---- CMakeLists.txt.orig 2021-06-05 18:31:25 UTC -+++ CMakeLists.txt -@@ -307,21 +307,16 @@ endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD") - #------------------------------------------------------------------------------- - find_package(CURL) - if(${CURL_FOUND}) -- #if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD") -- # set(DEFAULT_LIBRARIES " crypto curl ssl") -- #else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD") -- # set(DEFAULT_LIBRARIES "dl crypto curl ssl") -- #endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD") - message(${CURL_LIBRARIES}) -- string(APPEND DEFAULT_LIBRARIES " " ${CURL_LIBRARIES}) -+ list(APPEND DEFAULT_LIBRARIES ${CURL_LIBRARIES}) - add_definitions (-D__HYPHYCURL__) - endif(${CURL_FOUND}) - - if(NOT NOZLIB) - find_package(ZLIB 1.2.9) - if(${ZLIB_FOUND}) -- string(APPEND DEFAULT_LIBRARIES " " ${ZLIB_LIBRARIES}) -- include_directories(${ZLIB_INCLUDE_DIRS}) -+ list(APPEND DEFAULT_LIBRARIES ${ZLIB_LIBRARIES}) -+ include_directories(${ZLIB_INCLUDE_DIRS}) - add_definitions (-D__ZLIB__) - endif(${ZLIB_FOUND}) - endif(NOT NOZLIB) diff --git a/biology/hyphy/pkg-plist b/biology/hyphy/pkg-plist index e2daea3233e6..588863cbd1fd 100644 --- a/biology/hyphy/pkg-plist +++ b/biology/hyphy/pkg-plist @@ -91,6 +91,7 @@ bin/hyphy %%DATADIR%%/TemplateBatchFiles/CodonModelCompare.bf %%DATADIR%%/TemplateBatchFiles/CodonToProtein.bf %%DATADIR%%/TemplateBatchFiles/ConvertDataFile.bf +%%DATADIR%%/TemplateBatchFiles/DirectionalREL.bf %%DATADIR%%/TemplateBatchFiles/DistanceMatrix.bf %%DATADIR%%/TemplateBatchFiles/Distances/CodonTools.def %%DATADIR%%/TemplateBatchFiles/Distances/CodonTools2.def