Date: Sat, 07 May 2016 16:25:41 +0000 From: bugzilla-noreply@freebsd.org To: freebsd-ports-bugs@FreeBSD.org Subject: [Bug 209366] biology/ugene: Fix build with libc++ 3.8.0 Message-ID: <bug-209366-13@https.bugs.freebsd.org/bugzilla/>
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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 <stddef.h> ^ 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.=
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