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

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

--- Comment #2 from commit-hook at 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 at 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

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