From owner-freebsd-ports-bugs@freebsd.org Sat May 7 16:25:43 2016 Return-Path: Delivered-To: freebsd-ports-bugs@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 565A5B315C5 for ; Sat, 7 May 2016 16:25:43 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from kenobi.freebsd.org (kenobi.freebsd.org [IPv6:2001:1900:2254:206a::16:76]) (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 2D14C1224 for ; Sat, 7 May 2016 16:25:43 +0000 (UTC) (envelope-from bugzilla-noreply@freebsd.org) Received: from bugs.freebsd.org ([127.0.1.118]) by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id u47GPf7K055250 for ; Sat, 7 May 2016 16:25:43 GMT (envelope-from bugzilla-noreply@freebsd.org) From: bugzilla-noreply@freebsd.org To: freebsd-ports-bugs@FreeBSD.org Subject: [Bug 209366] biology/ugene: Fix build with libc++ 3.8.0 Date: Sat, 07 May 2016 16:25:41 +0000 X-Bugzilla-Reason: AssignedTo X-Bugzilla-Type: new X-Bugzilla-Watch-Reason: None X-Bugzilla-Product: Ports & Packages X-Bugzilla-Component: Individual Port(s) X-Bugzilla-Version: Latest X-Bugzilla-Keywords: X-Bugzilla-Severity: Affects Some People X-Bugzilla-Who: dim@FreeBSD.org X-Bugzilla-Status: New X-Bugzilla-Resolution: X-Bugzilla-Priority: --- X-Bugzilla-Assigned-To: freebsd-ports-bugs@FreeBSD.org X-Bugzilla-Flags: maintainer-feedback? X-Bugzilla-Changed-Fields: bug_id short_desc product version rep_platform op_sys bug_status bug_severity priority component assigned_to reporter cc flagtypes.name attachments.created Message-ID: Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable X-Bugzilla-URL: https://bugs.freebsd.org/bugzilla/ Auto-Submitted: auto-generated MIME-Version: 1.0 X-BeenThere: freebsd-ports-bugs@freebsd.org X-Mailman-Version: 2.1.22 Precedence: list List-Id: Ports bug reports List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 07 May 2016 16:25:43 -0000 https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D209366 Bug ID: 209366 Summary: biology/ugene: Fix build with libc++ 3.8.0 Product: Ports & Packages Version: Latest Hardware: Any OS: Any Status: New Severity: Affects Some People Priority: --- Component: Individual Port(s) Assignee: freebsd-ports-bugs@FreeBSD.org Reporter: dim@FreeBSD.org CC: h2+fbsdports@fsfe.org CC: h2+fbsdports@fsfe.org Flags: maintainer-feedback?(h2+fbsdports@fsfe.org) Created attachment 170099 --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=3D170099&action= =3Dedit Remove -isystem from compile flags to fix build under libc++ 3.8.0 During the exp-run in bug 208158, it was found that biology/ugene gives err= ors with libc++ 3.8.0 [1]: 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 director= ies. Fix it by patching up a number of .pri files to avoid using the -isystem f= lag. [1] http://package18.nyi.freebsd.org/data/headamd64PR208158-default/2016-05-01_= 10h29m48s/logs/errors/ugene-1.22.0.log --=20 You are receiving this mail because: You are the assignee for the bug.=