Date: Sat, 07 May 2016 19:39:34 +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-209366-13-8KglWkGfRc@https.bugs.freebsd.org/bugzilla/> In-Reply-To: <bug-209366-13@https.bugs.freebsd.org/bugzilla/> References: <bug-209366-13@https.bugs.freebsd.org/bugzilla/>
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D209366 --- Comment #2 from commit-hook@freebsd.org --- A commit references this bug: Author: dim Date: Sat May 7 19:38:54 UTC 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 <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 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 Changes: head/biology/ugene/Makefile head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri head/biology/ugene/files/patch-src_ugene__globals.pri --=20 You are receiving this mail because: You are the assignee for the bug.=
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