From 488fd1255a6b9d73ce4caee10ddc7b6864c0cdfb Mon Sep 17 00:00:00 2001 From: Dimitry Andric Date: Sat, 7 May 2016 19:38:53 +0000 Subject: [PATCH] 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 ^ 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 --- biology/ugene/Makefile | 1 + .../patch-src_libs__3rdparty_samtools_samtools.pri | 11 +++++++++++ ...atch-src_plugins__3rdparty_variants_variants.pri | 11 +++++++++++ biology/ugene/files/patch-src_ugene__globals.pri | 13 +++++++++++++ 4 files changed, 36 insertions(+) create mode 100644 biology/ugene/files/patch-src_libs__3rdparty_samtools_samtools.pri create mode 100644 biology/ugene/files/patch-src_plugins__3rdparty_variants_variants.pri create mode 100644 biology/ugene/files/patch-src_ugene__globals.pri 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