From owner-svn-ports-head@freebsd.org Sat May 7 19:38:55 2016 Return-Path: Delivered-To: svn-ports-head@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 22E75B3252D; Sat, 7 May 2016 19:38:55 +0000 (UTC) (envelope-from dim@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 mx1.freebsd.org (Postfix) with ESMTPS id EF22910EF; Sat, 7 May 2016 19:38:54 +0000 (UTC) (envelope-from dim@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id u47JcsqW023116; Sat, 7 May 2016 19:38:54 GMT (envelope-from dim@FreeBSD.org) Received: (from dim@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id u47JcrQ6023112; Sat, 7 May 2016 19:38:53 GMT (envelope-from dim@FreeBSD.org) Message-Id: <201605071938.u47JcrQ6023112@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: dim set sender to dim@FreeBSD.org using -f From: Dimitry Andric Date: Sat, 7 May 2016 19:38:53 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r414784 - in head/biology/ugene: . files X-SVN-Group: ports-head MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-head@freebsd.org X-Mailman-Version: 2.1.22 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: Sat, 07 May 2016 19:38:55 -0000 Author: dim (src committer) Date: Sat May 7 19:38:53 2016 New Revision: 414784 URL: https://svnweb.freebsd.org/changeset/ports/414784 Log: During the exp-run in bug 208158, it was found that biology/ugene gives errors with libc++ 3.8.0: In file included from src/QScoreAdapter.cpp:1: In file included from src/QScoreAdapter.h:4: In file included from ../../include/U2Core/MAlignment.h:1: In file included from ../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignment.h:25: In file included from ../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignmentInfo.h:25: In file included from /usr/local/include/qt5/QtCore/QString:1: In file included from /usr/local/include/qt5/QtCore/qstring.h:41: In file included from /usr/local/include/qt5/QtCore/qchar.h:37: In file included from /usr/local/include/qt5/QtCore/qglobal.h:39: /usr/include/c++/v1/cstddef:43:15: fatal error: 'stddef.h' file not found #include_next ^ This is because the port tries to add /usr/include as a system include directory, using -isystem, and this screws up the order of include directories. Fix it by patching up a number of .pri files to avoid using the -isystem flag. Approved by: h2+fbsdports@fsfe.org (maintainer) PR: 209366 MFH: 2016Q2 Added: head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri (contents, props changed) head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri (contents, props changed) head/biology/ugene/files/patch-src_ugene__globals.pri (contents, props changed) Modified: head/biology/ugene/Makefile Modified: head/biology/ugene/Makefile ============================================================================== --- head/biology/ugene/Makefile Sat May 7 19:38:13 2016 (r414783) +++ head/biology/ugene/Makefile Sat May 7 19:38:53 2016 (r414784) @@ -3,6 +3,7 @@ PORTNAME= ugene DISTVERSION= 1.22.0 +PORTREVISION= 1 CATEGORIES= biology science MASTER_SITES= http://ugene.unipro.ru/downloads/ DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \ Added: head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri Sat May 7 19:38:53 2016 (r414784) @@ -0,0 +1,11 @@ +--- src/libs_3rdparty/samtools/samtools.pri.orig 2016-03-31 12:21:56 UTC ++++ src/libs_3rdparty/samtools/samtools.pri +@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = '' + + TEMPLATE = lib + CONFIG +=thread debug_and_release staticlib warn_off +-INCLUDEPATH += src src/samtools ../../include /usr/include ++INCLUDEPATH += src src/samtools ../../include + win32 : INCLUDEPATH += src/samtools/win32 + DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE + win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca" Added: head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri Sat May 7 19:38:53 2016 (r414784) @@ -0,0 +1,11 @@ +--- src/plugins_3rdparty/variants/variants.pri.orig 2016-03-31 12:22:09 UTC ++++ src/plugins_3rdparty/variants/variants.pri +@@ -20,7 +20,7 @@ use_bundled_zlib() { + win32 : LIBS += -lwsock32 + + +-INCLUDEPATH += src ../../include /usr/include ++INCLUDEPATH += src ../../include + INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools + INCLUDEPATH += ../../libs_3rdparty/samtools/src + INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools Added: head/biology/ugene/files/patch-src_ugene__globals.pri ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/ugene/files/patch-src_ugene__globals.pri Sat May 7 19:38:53 2016 (r414784) @@ -0,0 +1,13 @@ +--- src/ugene_globals.pri.orig 2016-03-31 12:22:21 UTC ++++ src/ugene_globals.pri +@@ -8,8 +8,8 @@ DEFINES+=UGENE_VER_MAJOR=$${UGENE_VER_MA + DEFINES+=UGENE_VER_MINOR=$${UGENE_VER_MINOR} + DEFINES+=UGENE_VER_PATCH=$${UGENE_VER_PATCH} + +-unix : !macx : INCLUDEPATH-=/usr/include +-unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include ++#unix : !macx : INCLUDEPATH-=/usr/include ++#unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include + #unix : !macx : INCLUDEPATH =/usr/include/qt5 $$INCLUDEPATH + + # NGS package