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Code Issues Releases Activity

During the exp-run in bug 208158, it was found that biology/ugene gives

Browse Source 
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
This commit is contained in:
Dimitry Andric 2016-05-07 19:38:53 +00:00
parent aa43e0125c
commit 488fd1255a
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=414784
4 changed files with 36 additions and 0 deletions
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1
biology/ugene/Makefile
View File

@ -3,6 +3,7 @@
PORTNAME= ugene
DISTVERSION= 1.22.0
PORTREVISION= 1
CATEGORIES= biology science
MASTER_SITES= http://ugene.unipro.ru/downloads/
DISTFILES= ${DISTNAME}${EXTRACT_SUFX} QueryDesigner_UserManual.pdf \

11
biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri Normal file
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@ -0,0 +1,11 @@
--- src/libs_3rdparty/samtools/samtools.pri.orig 2016-03-31 12:21:56 UTC
+++ src/libs_3rdparty/samtools/samtools.pri
@@ -3,7 +3,7 @@ UGENE_RELATIVE_DESTDIR = ''
TEMPLATE = lib
CONFIG +=thread debug_and_release staticlib warn_off
-INCLUDEPATH += src src/samtools ../../include /usr/include
+INCLUDEPATH += src src/samtools ../../include
win32 : INCLUDEPATH += src/samtools/win32
DEFINES+="_FILE_OFFSET_BITS=64" _LARGEFILE64_SOURCE _USE_KNETFILE
win32 : DEFINES += _USE_MATH_DEFINES "inline=__inline" "__func__=__FUNCTION__" "R_OK=4" "atoll=_atoi64" "alloca=_alloca"

11
biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri Normal file
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@ -0,0 +1,11 @@
--- src/plugins_3rdparty/variants/variants.pri.orig 2016-03-31 12:22:09 UTC
+++ src/plugins_3rdparty/variants/variants.pri
@@ -20,7 +20,7 @@ use_bundled_zlib() {
win32 : LIBS += -lwsock32
-INCLUDEPATH += src ../../include /usr/include
+INCLUDEPATH += src ../../include
INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools
INCLUDEPATH += ../../libs_3rdparty/samtools/src
INCLUDEPATH += ../../libs_3rdparty/samtools/src/samtools/bcftools

13
biology/ugene/files/patch-src_ugene__globals.pri Normal file
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@ -0,0 +1,13 @@
--- src/ugene_globals.pri.orig 2016-03-31 12:22:21 UTC
+++ src/ugene_globals.pri
@@ -8,8 +8,8 @@ DEFINES+=UGENE_VER_MAJOR=$${UGENE_VER_MA
DEFINES+=UGENE_VER_MINOR=$${UGENE_VER_MINOR}
DEFINES+=UGENE_VER_PATCH=$${UGENE_VER_PATCH}
-unix : !macx : INCLUDEPATH-=/usr/include
-unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include
+#unix : !macx : INCLUDEPATH-=/usr/include
+#unix : !macx : INCLUDEPATH+=/usr/include/qt5 /usr/include
#unix : !macx : INCLUDEPATH =/usr/include/qt5 $$INCLUDEPATH
# NGS package