From owner-svn-ports-all@freebsd.org Mon Nov 23 16:13:16 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 2878E2EF46E; Mon, 23 Nov 2020 16:13:16 +0000 (UTC) (envelope-from pkubaj@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 4CfsdR75TLz4WTQ; Mon, 23 Nov 2020 16:13:15 +0000 (UTC) (envelope-from pkubaj@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 E690174BD; Mon, 23 Nov 2020 16:13:15 +0000 (UTC) (envelope-from pkubaj@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id 0ANGDFj1061967; Mon, 23 Nov 2020 16:13:15 GMT (envelope-from pkubaj@FreeBSD.org) Received: (from pkubaj@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id 0ANGDFKS061966; Mon, 23 Nov 2020 16:13:15 GMT (envelope-from pkubaj@FreeBSD.org) Message-Id: <202011231613.0ANGDFKS061966@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: pkubaj set sender to pkubaj@FreeBSD.org using -f From: Piotr Kubaj Date: Mon, 23 Nov 2020 16:13:15 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r556113 - head/biology/tabixpp X-SVN-Group: ports-head X-SVN-Commit-Author: pkubaj X-SVN-Commit-Paths: head/biology/tabixpp X-SVN-Commit-Revision: 556113 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, 23 Nov 2020 16:13:16 -0000 Author: pkubaj Date: Mon Nov 23 16:13:15 2020 New Revision: 556113 URL: https://svnweb.freebsd.org/changeset/ports/556113 Log: biology/tabixpp: fix build on GCC architectures c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fPIC -c tabix.cpp -Ihtslib In file included from /usr/local/include/htslib/hts.h:37, from /usr/local/include/htslib/tbx.h:30, from tabix.hpp:5, from tabix.cpp:1: /usr/local/include/htslib/kstring.h: In function 'int ks_resize(kstring_t*, size_t)': /usr/local/include/htslib/kstring.h:149: error: 'SIZE_MAX' was not declared in this scope tabix.cpp: In constructor 'Tabix::Tabix(std::string&)': tabix.cpp:15: warning: 'bgzf_is_bgzf' is deprecated (declared at /usr/local/include/htslib/bgzf.h:263) tabix.cpp:15: warning: 'bgzf_is_bgzf' is deprecated (declared at /usr/local/include/htslib/bgzf.h:263) Modified: head/biology/tabixpp/Makefile Modified: head/biology/tabixpp/Makefile ============================================================================== --- head/biology/tabixpp/Makefile Mon Nov 23 15:17:26 2020 (r556112) +++ head/biology/tabixpp/Makefile Mon Nov 23 16:13:15 2020 (r556113) @@ -15,7 +15,7 @@ LICENSE_FILE= ${WRKSRC}/LICENSE LIB_DEPENDS= libhts.so:biology/htslib -USES= localbase:ldflags +USES= compiler:c11 localbase:ldflags USE_LDCONFIG= yes USE_GITHUB= yes GH_ACCOUNT= ekg