[Bug 209366] biology/ugene: Fix build with libc++ 3.8.0

[bugzilla-noreply at freebsd.org]

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=209366

            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 at FreeBSD.org
          Reporter: dim at FreeBSD.org
                CC: h2+fbsdports at fsfe.org
                CC: h2+fbsdports at fsfe.org
             Flags: maintainer-feedback?(h2+fbsdports at fsfe.org)

Created attachment 170099
  --> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=170099&action=edit
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

-- 
You are receiving this mail because:
You are the assignee for the bug.