From owner-svn-ports-all@freebsd.org Mon Nov 9 00:35:59 2020 Return-Path: Delivered-To: svn-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 08D2B2E3480; Mon, 9 Nov 2020 00:35:59 +0000 (UTC) (envelope-from jwb@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 "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4CTsVQ6spkz3Lc5; Mon, 9 Nov 2020 00:35:58 +0000 (UTC) (envelope-from jwb@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 DEB079B3; Mon, 9 Nov 2020 00:35:58 +0000 (UTC) (envelope-from jwb@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 0A90ZwtG085456; Mon, 9 Nov 2020 00:35:58 GMT (envelope-from jwb@FreeBSD.org) Received: (from jwb@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 0A90ZwVi085454; Mon, 9 Nov 2020 00:35:58 GMT (envelope-from jwb@FreeBSD.org) Message-Id: <202011090035.0A90ZwVi085454@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: jwb set sender to jwb@FreeBSD.org using -f From: "Jason W. Bacon" Date: Mon, 9 Nov 2020 00:35:58 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r554660 - in head/biology/vt: . files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology/vt: . files X-SVN-Commit-Revision: 554660 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: 2.1.34 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, 09 Nov 2020 00:35:59 -0000 Author: jwb Date: Mon Nov 9 00:35:58 2020 New Revision: 554660 URL: https://svnweb.freebsd.org/changeset/ports/554660 Log: biology/vt: Fix build with htslib 1.11 Reported by: fallout Added: head/biology/vt/files/patch-hts__utils.h (contents, props changed) Modified: head/biology/vt/Makefile Modified: head/biology/vt/Makefile ============================================================================== --- head/biology/vt/Makefile Sun Nov 8 23:42:10 2020 (r554659) +++ head/biology/vt/Makefile Mon Nov 9 00:35:58 2020 (r554660) @@ -2,7 +2,7 @@ PORTNAME= vt DISTVERSION= 0.57721 -PORTREVISION= 1 +PORTREVISION= 2 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -10,7 +10,7 @@ COMMENT= Discovers short variants from Next Generation LICENSE= MIT -LIB_DEPENDS= libhts.so.3:biology/htslib \ +LIB_DEPENDS= libhts.so:biology/htslib \ libsvm.so:science/libsvm \ libdeflate.so:archivers/libdeflate \ libcurl.so:ftp/curl Added: head/biology/vt/files/patch-hts__utils.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/vt/files/patch-hts__utils.h Mon Nov 9 00:35:58 2020 (r554660) @@ -0,0 +1,11 @@ +--- hts_utils.h.orig 2020-11-08 22:09:58 UTC ++++ hts_utils.h +@@ -47,7 +47,7 @@ typedef struct { + + KHASH_MAP_INIT_STR(s, faidx1_t) + +-struct __faidx_t { ++struct faidx_t { + BGZF *bgzf; + int n, m; + char **name;