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non port: biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
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Number of commits found: 2

Sun, 2 Sep 2018
[ 20:47 jhale ] Original commit   Revision:478818
478818 biology/ugene/Makefile
478818 biology/ugene/distinfo
478818 biology/ugene/files/patch-git_279756e4
478818 biology/ugene/files/patch-git_578c949
478818 biology/ugene/files/patch-src_corelibs_U2Private_U2Private.pro
478818 biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTKeyboardDriverLinux.cpp
478818 biology/ugene/files/patch-src_libs__3rdparty_QSpec_src_drivers_GTMouseDriverLinux.cpp
478818 biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
478818 biology/ugene/files/patch-src_plugins__3rdparty_phylip_src_phylip.h
478818 biology/ugene/files/patch-src_plugins__3rdparty_umuscle_src_MuscleWorkPool.cpp

(Only the first 10 of 17 ports in this commit are shown above. View all ports for this commit)
Update to 1.31.0

PR:		229463
Approved by:	Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer)
Sat, 7 May 2016
[ 19:38 dim ] Original commit   Revision:414784
414784 biology/ugene/Makefile
414784 biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
414784 biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
414784 biology/ugene/files/patch-src_ugene__globals.pri
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

Number of commits found: 2

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