From owner-svn-ports-all@freebsd.org Mon Jul 16 18:11:46 2018 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 554181033CB7; Mon, 16 Jul 2018 18:11:46 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 0A4A17C800; Mon, 16 Jul 2018 18:11:46 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id C67BF20231; Mon, 16 Jul 2018 18:11:45 +0000 (UTC) (envelope-from yuri@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id w6GIBjfZ050787; Mon, 16 Jul 2018 18:11:45 GMT (envelope-from yuri@FreeBSD.org) Received: (from yuri@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id w6GIBi8g050783; Mon, 16 Jul 2018 18:11:44 GMT (envelope-from yuri@FreeBSD.org) Message-Id: <201807161811.w6GIBi8g050783@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: yuri set sender to yuri@FreeBSD.org using -f From: Yuri Victorovich Date: Mon, 16 Jul 2018 18:11:44 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r474752 - head/biology/htslib X-SVN-Group: ports-head X-SVN-Commit-Author: yuri X-SVN-Commit-Paths: head/biology/htslib X-SVN-Commit-Revision: 474752 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.27 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Mon, 16 Jul 2018 18:11:46 -0000 Author: yuri Date: Mon Jul 16 18:11:44 2018 New Revision: 474752 URL: https://svnweb.freebsd.org/changeset/ports/474752 Log: biology/htslib: Update 1.6 -> 1.8 Port changes: * Use DISTVERSION * Add USES=localbase instead of CPPFLAGS/LDFLAGS * Move USES=ssl to CURL_USES=ssl * Update WWW PR: 228908 Approved by: maintainer's timeout (cartwright@asu.edu; 35 days) Modified: head/biology/htslib/Makefile head/biology/htslib/distinfo head/biology/htslib/pkg-descr head/biology/htslib/pkg-plist Modified: head/biology/htslib/Makefile ============================================================================== --- head/biology/htslib/Makefile Mon Jul 16 17:07:19 2018 (r474751) +++ head/biology/htslib/Makefile Mon Jul 16 18:11:44 2018 (r474752) @@ -2,7 +2,7 @@ # $FreeBSD$ PORTNAME= htslib -PORTVERSION= 1.6 +DISTVERSION= 1.8 CATEGORIES= biology devel MAINTAINER= cartwright@asu.edu @@ -14,10 +14,9 @@ LICENSE_FILE= ${WRKSRC}/LICENSE TEST_DEPENDS= bash:shells/bash +USES= autoreconf gmake localbase pathfix perl5 shebangfix USE_GITHUB= yes GH_ACCOUNT= samtools - -USES= autoreconf gmake pathfix perl5 shebangfix USE_PERL5= test USE_LDCONFIG= yes GNU_CONFIGURE= yes @@ -28,11 +27,9 @@ OPTIONS_DEFINE= CURL OPTIONS_DEFAULT= CURL CURL_DESC= Use libcurl for network file access (HTTPS and S3 support). +CURL_USES= ssl CURL_LIB_DEPENDS= libcurl.so:ftp/curl CURL_CONFIGURE_ENABLE= libcurl - -CPPFLAGS+= -I${LOCALBASE}/include -LDFLAGS+= -L${LOCALBASE}/lib PLIST_SUB= PORTVERSION="${PORTVERSION}" Modified: head/biology/htslib/distinfo ============================================================================== --- head/biology/htslib/distinfo Mon Jul 16 17:07:19 2018 (r474751) +++ head/biology/htslib/distinfo Mon Jul 16 18:11:44 2018 (r474752) @@ -1,3 +1,3 @@ -TIMESTAMP = 1508301522 -SHA256 (samtools-htslib-1.6_GH0.tar.gz) = 4215c9153c27603cbaaf542f2ec128c5e839380d6df6edd4dbf67955170740c6 -SIZE (samtools-htslib-1.6_GH0.tar.gz) = 1155672 +TIMESTAMP = 1528766078 +SHA256 (samtools-htslib-1.8_GH0.tar.gz) = ad52105c0f9ce6474c8f5d2f208b8e71982436ee1ca5225162932b08aff48b23 +SIZE (samtools-htslib-1.8_GH0.tar.gz) = 1262465 Modified: head/biology/htslib/pkg-descr ============================================================================== --- head/biology/htslib/pkg-descr Mon Jul 16 17:07:19 2018 (r474751) +++ head/biology/htslib/pkg-descr Mon Jul 16 18:11:44 2018 (r474752) @@ -2,4 +2,4 @@ HTSlib is an implementation of a unified C library for formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools. -WWW: http://www.htslib.org/ +WWW: https://www.htslib.org/ Modified: head/biology/htslib/pkg-plist ============================================================================== --- head/biology/htslib/pkg-plist Mon Jul 16 17:07:19 2018 (r474751) +++ head/biology/htslib/pkg-plist Mon Jul 16 18:11:44 2018 (r474752) @@ -32,6 +32,7 @@ lib/libhts.so lib/libhts.so.%%PORTVERSION%% lib/libhts.so.2 libdata/pkgconfig/htslib.pc +man/man1/bgzip.1.gz man/man1/htsfile.1.gz man/man1/tabix.1.gz man/man5/faidx.5.gz