svn commit: r414784 - in head/biology/ugene: . files
Dimitry Andric
dim at FreeBSD.org
Sat May 7 19:38:55 UTC 2016
Author: dim (src committer)
Date: Sat May 7 19:38:53 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
Added:
head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri (contents, props changed)
head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri (contents, props changed)
head/biology/ugene/files/patch-src_ugene__globals.pri (contents, props changed)
Modified:
head/biology/ugene/Makefile
Modified: head/biology/ugene/Makefile
==============================================================================
--- head/biology/ugene/Makefile Sat May 7 19:38:13 2016 (r414783)
+++ head/biology/ugene/Makefile Sat May 7 19:38:53 2016 (r414784)
@@ -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 \
Added: head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri Sat May 7 19:38:53 2016 (r414784)
@@ -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"
Added: head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri Sat May 7 19:38:53 2016 (r414784)
@@ -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
Added: head/biology/ugene/files/patch-src_ugene__globals.pri
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/ugene/files/patch-src_ugene__globals.pri Sat May 7 19:38:53 2016 (r414784)
@@ -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
More information about the svn-ports-head
mailing list