Date: Sat, 7 May 2016 19:38:53 +0000 (UTC) From: Dimitry Andric <dim@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r414784 - in head/biology/ugene: . files Message-ID: <201605071938.u47JcrQ6023112@repo.freebsd.org>
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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@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
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