From owner-svn-ports-head@freebsd.org Fri Jun 21 11:43:11 2019 Return-Path: Delivered-To: svn-ports-head@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 F1F1C15D8002; Fri, 21 Jun 2019 11:43:10 +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) server-signature RSA-PSS (4096 bits) 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 930F88C920; Fri, 21 Jun 2019 11:43:10 +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 6E87C22C19; Fri, 21 Jun 2019 11:43:10 +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 x5LBhAG7003261; Fri, 21 Jun 2019 11:43:10 GMT (envelope-from pkubaj@FreeBSD.org) Received: (from pkubaj@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id x5LBh9of003258; Fri, 21 Jun 2019 11:43:09 GMT (envelope-from pkubaj@FreeBSD.org) Message-Id: <201906211143.x5LBh9of003258@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: pkubaj set sender to pkubaj@FreeBSD.org using -f From: Piotr Kubaj Date: Fri, 21 Jun 2019 11:43:09 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r504788 - in head/biology/abyss: . files X-SVN-Group: ports-head X-SVN-Commit-Author: pkubaj X-SVN-Commit-Paths: in head/biology/abyss: . files X-SVN-Commit-Revision: 504788 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 930F88C920 X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.96 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-0.998,0]; NEURAL_HAM_SHORT(-0.97)[-0.966,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US]; NEURAL_HAM_LONG(-1.00)[-1.000,0] X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: SVN commit messages for the ports tree for head List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Jun 2019 11:43:11 -0000 Author: pkubaj Date: Fri Jun 21 11:43:09 2019 New Revision: 504788 URL: https://svnweb.freebsd.org/changeset/ports/504788 Log: biology/abyss: fix build on big-endian architectures Use new GCC from ports on GCC architectures. Merge 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5, fixes build on GCC architectures. Also include sys/endian.h and use bswap32 and bswap64 for byte-swapping (PR at https://github.com/bcgsc/abyss/pull/287 ). PR: 238737 Approved by: yuri (maintainer), mat (mentor) Differential Revision: https://reviews.freebsd.org/D20717 Added: head/biology/abyss/files/patch-Common_city.cc (contents, props changed) Modified: head/biology/abyss/Makefile head/biology/abyss/distinfo Modified: head/biology/abyss/Makefile ============================================================================== --- head/biology/abyss/Makefile Fri Jun 21 11:30:18 2019 (r504787) +++ head/biology/abyss/Makefile Fri Jun 21 11:43:09 2019 (r504788) @@ -6,6 +6,9 @@ PORTREVISION= 2 CATEGORIES= biology MASTER_SITES= http://www.bcgsc.ca/platform/bioinfo/software/${PORTNAME}/releases/${DISTVERSION}/ +PATCH_SITES= https://github.com/bcgsc/${PORTNAME}/commit/ +PATCHFILES= 25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch:-p1 + MAINTAINER= yuri@FreeBSD.org COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler @@ -21,7 +24,7 @@ LIB_DEPENDS= libffi.so:devel/libffi \ RUN_DEPENDS= bash:shells/bash \ gmake:devel/gmake -USES= gmake iconv:wchar_t localbase:ldflags shebangfix sqlite +USES= compiler:c++11-lang gmake iconv:wchar_t localbase:ldflags shebangfix sqlite SHEBANG_FILES= bin/${PORTNAME}-* SHEBANG_LANG= make make_OLD_CMD= /usr/bin/make Modified: head/biology/abyss/distinfo ============================================================================== --- head/biology/abyss/distinfo Fri Jun 21 11:30:18 2019 (r504787) +++ head/biology/abyss/distinfo Fri Jun 21 11:43:09 2019 (r504788) @@ -1,3 +1,5 @@ -TIMESTAMP = 1551061546 +TIMESTAMP = 1561103807 SHA256 (abyss-2.1.5.tar.gz) = 65bfc8241e6ff5adf7601ae4ae93a75e3db86d6bff5d593c75aaff7f0ef41757 SIZE (abyss-2.1.5.tar.gz) = 1201318 +SHA256 (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 93ad66c42610c4fba8cfbe256a2ab689bf4a76974c3b97a9e1094863614ad934 +SIZE (25eb9d2a914fb211fdfe04fcda5593f29fd23ff5.patch) = 1701 Added: head/biology/abyss/files/patch-Common_city.cc ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/abyss/files/patch-Common_city.cc Fri Jun 21 11:43:09 2019 (r504788) @@ -0,0 +1,13 @@ +--- Common/city.cc.orig 2018-09-21 23:44:14 UTC ++++ Common/city.cc +@@ -65,6 +65,10 @@ static uint32 UNALIGNED_LOAD32(const char *p) { + #define bswap_32(x) OSSwapInt32(x) + #define bswap_64(x) OSSwapInt64(x) + ++#elif defined(__FreeBSD__) ++#include ++#define bswap_32(x) bswap32(x) ++#define bswap_64(x) bswap64(x) + #else + #include + #endif