Created attachment 170099 [details] 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 errors 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 directories. Fix it by patching up a number of .pri files to avoid using the -isystem flag. [1] http://package18.nyi.freebsd.org/data/headamd64PR208158-default/2016-05-01_10h29m48s/logs/errors/ugene-1.22.0.log
Sure, go ahead!
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
(In reply to Hannes Hauswedell from comment #1) Should the 1.17.0 -> 1.22.0 update be merged with this? That prior update changed a bunch and just this looks like it will conflict.
(In reply to Jason Unovitch from comment #3) Hm, I won't have any time to debug this in the next two weeks, but if you think it can feasibly be combined with an upgrade of the port, please don't hesitate :)