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| author | Dimitry Andric <dim@FreeBSD.org> | 2016-05-07 19:38:53 +0000 |
|---|---|---|
| committer | Dimitry Andric <dim@FreeBSD.org> | 2016-05-07 19:38:53 +0000 |
| commit | 488fd1255a6b9d73ce4caee10ddc7b6864c0cdfb (patch) | |
| tree | 80deb1775b61d078368d81f05c1957ecdf7d8d90 /biology/ugene | |
| parent | aa43e0125c8d3025af96a0011ebfaa1d2ced4b1b (diff) | |
| download | ports-488fd1255a6b9d73ce4caee10ddc7b6864c0cdfb.tar.gz ports-488fd1255a6b9d73ce4caee10ddc7b6864c0cdfb.zip | |
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
Notes
Notes:
svn path=/head/; revision=414784
Diffstat (limited to 'biology/ugene')
4 files changed, 36 insertions, 0 deletions
diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index 8cd7c2e94c6f..6947d3efb962 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -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 \ diff --git a/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri b/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri new file mode 100644 index 000000000000..3951d5f87ecb --- /dev/null +++ b/biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri @@ -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" diff --git a/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri b/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri new file mode 100644 index 000000000000..9ecf2cc231fb --- /dev/null +++ b/biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri @@ -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 diff --git a/biology/ugene/files/patch-src_ugene__globals.pri b/biology/ugene/files/patch-src_ugene__globals.pri new file mode 100644 index 000000000000..6c0a38639d38 --- /dev/null +++ b/biology/ugene/files/patch-src_ugene__globals.pri @@ -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 |