Date: Sat, 30 Aug 2014 15:34:57 GMT From: pkg-fallout@FreeBSD.org To: h2+fbsdports@fsfe.org Cc: pkg-fallout@FreeBSD.org Subject: [package - head-i386-default-ssp][biology/ugene] Failed for ugene-1.13.1 in build Message-ID: <201408301534.s7UFYvcd096816@beefy4.isc.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: h2+fbsdports@fsfe.org Last committer: bapt@FreeBSD.org Ident: $FreeBSD: head/biology/ugene/Makefile 364067 2014-08-04 23:06:21Z bapt $ Log URL: http://beefy4.isc.freebsd.org/data/head-i386-default-ssp/2014-08-30_02h25m58s/logs/ugene-1.13.1.log Build URL: http://beefy4.isc.freebsd.org/build.html?mastername=head-i386-default-ssp&build=2014-08-30_02h25m58s Log: ====>> Building biology/ugene build started at Sat Aug 30 14:33:24 UTC 2014 port directory: /usr/ports/biology/ugene building for: FreeBSD pkg.FreeBSD.org 11.0-CURRENT FreeBSD 11.0-CURRENT r269897 i386 maintained by: h2+fbsdports@fsfe.org Makefile ident: $FreeBSD: head/biology/ugene/Makefile 364067 2014-08-04 23:06:21Z bapt $ Poudriere version: 3.1-pre Host OSVERSION: 1100027 Jail OSVERSION: 1100028 !!! Jail is newer than host. (Jail: 1100028, Host: 1100027) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- UNAME_m=i386 UNAME_p=i386 OSVERSION=1100028 UNAME_v=FreeBSD 11.0-CURRENT r269897 UNAME_r=11.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM=screen MASTERMNT=/usr/local/poudriere/data/.m/head-i386-default-ssp/ref PKG_EXT=txz FORCE_PACKAGE=yes PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNG=1 PKGNAME=ugene-1.13.1 PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f PKG_ADD=/usr/local/sbin/pkg-static add OLDPWD=/root PWD=/usr/local/poudriere/data/.m/head-i386-default-ssp/ref/.p/pool MASTERNAME=head-i386-default-ssp USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=/.p/pkg-static version PKG_BIN=/usr/local/sbin/pkg-static ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for ugene-1.13.1: DOCS=on: Install official UGENE documentation (PDF) ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --with-qt-includes=/usr/local/include/qt4 --with-qt-libraries=/usr/local/lib/qt4 --with-extra-includes=/usr/local/include --with-extra-libs=/usr/local/lib --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ugene/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ugene/work HOME=/wrkdirs/usr/ports/biology/ugene/work TMPDIR="/tmp" QTDIR="/usr/local" QMAKE="/usr/local/bin/qmake-qt4" MOC="/usr/local/bin/moc-qt4" RCC="/usr/local/bin/rcc" UIC="/usr/local/bin/uic-qt4" QMAKESPEC="/usr/local/share/qt4/mkspecs/freebsd-$(ccver="$(c++ --version)"; case "$ccver" in *clang*) echo clang ;; *) echo g++ ;; esac)" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ugene/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ugene/work HOME=/wrkdirs/usr/ports/biology/ugene/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh PATH=/usr/local/libexec/ccache:/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin CCACHE_DIR="/root/.ccache" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ugene/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ugene/work HOME=/wrkdirs/usr/ports/biology/ugene/work TMPDIR="/tmp" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ugene/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ugene/work HOME=/wrkdirs/usr/ports/biology/ugene/work TMPDIR="/tmp" NO_PIE=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11" MANPREFIX="/usr/local" PATH=/usr/local/libexec/ccache:/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin CCACHE_DIR="/root/.ccache" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --PLIST_SUB-- NOX64="" OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" DOCSDIR="share/ugene/manuals" EXAMPLESDIR="share/examples/ugene" DATADIR="share/ugene" WWWDIR="www/ugene" ETCDIR="etc/ugene" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ugene DOCSDIR=/usr/local/share/ugene/manuals EXAMPLESDIR=/usr/local/share/examples/ugene WWWDIR=/usr/local/www/ugene ETCDIR=/usr/local/etc/ugene --End SUB_LIST-- ---Begin make.conf--- ARCH=i386 MACHINE=i386 MACHINE_ARCH=i386 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs ARCH=i386 MACHINE=i386 MACHINE_ARCH=i386 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### WITH_PKGNG=yes #WITH_PKGNG=devel #### /usr/local/etc/poudriere.d/ssp-make.conf #### WITH_SSP_PORTS=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> ugene-1.13.1 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.3.7.txz [pkg.FreeBSD.org] Installing pkg-1.3.7... done Message for pkg-1.3.7: If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of ugene-1.13.1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by ugene-1.13.1 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by ugene-1.13.1 for building => SHA256 Checksum OK for ugene/ugene-1.13.1.tar.gz. => SHA256 Checksum OK for ugene/QueryDesigner_UserManual.pdf. => SHA256 Checksum OK for ugene/UniproUGENE_UserManual.pdf. => SHA256 Checksum OK for ugene/WorkflowDesigner_UserManual.pdf. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by ugene-1.13.1 for building ===> Extracting for ugene-1.13.1 => SHA256 Checksum OK for ugene/ugene-1.13.1.tar.gz. => SHA256 Checksum OK for ugene/QueryDesigner_UserManual.pdf. => SHA256 Checksum OK for ugene/UniproUGENE_UserManual.pdf. => SHA256 Checksum OK for ugene/WorkflowDesigner_UserManual.pdf. /bin/cp -p /portdistfiles/ugene/*.pdf /wrkdirs/usr/ports/biology/ugene/work/ugene-1.13.1/data/manuals =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for ugene-1.13.1 ===> Applying FreeBSD patches for ugene-1.13.1 =========================================================================== =======================<phase: build-depends >============================ ===> ugene-1.13.1 depends on file: /usr/local/libdata/pkgconfig/glproto.pc - not found ===> Verifying install for /usr/local/libdata/pkgconfig/glproto.pc in /usr/ports/x11/glproto ===> Installing existing package /packages/All/glproto-1.4.17.txz [pkg.FreeBSD.org] Installing glproto-1.4.17... done ===> Returning to build of ugene-1.13.1 ===> ugene-1.13.1 depends on file: /usr/local/libdata/pkgconfig/dri2proto.pc - not found ===> Verifying install for /usr/local/libdata/pkgconfig/dri2proto.pc in /usr/ports/x11/dri2proto ===> Installing existing package /packages/All/dri2proto-2.8.txz [pkg.FreeBSD.org] Installing dri2proto-2.8... done ===> Returning to build of ugene-1.13.1 ===> ugene-1.13.1 depends on file: /usr/local/libdata/pkgconfig/xtst.pc - not found ===> Verifying install for /usr/local/libdata/pkgconfig/xtst.pc in /usr/ports/x11/libXtst ===> Installing existing package /packages/All/libXtst-1.2.2_2.txz [pkg.FreeBSD.org] Installing inputproto-2.3.1... done [pkg.FreeBSD.org] Installing kbproto-1.0.6... done [pkg.FreeBSD.org] Installing xproto-7.0.26... done [pkg.FreeBSD.org] Installing libXau-1.0.8_2... done [pkg.FreeBSD.org] Installing libXdmcp-1.1.1_2... done [pkg.FreeBSD.org] Installing libpthread-stubs-0.3_5... done [pkg.FreeBSD.org] Installing libxml2-2.9.1_1... done [pkg.FreeBSD.org] Installing libxcb-1.10_2... done [pkg.FreeBSD.org] Installing libX11-1.6.2_2,1... done [pkg.FreeBSD.org] Installing xextproto-7.3.0... done [pkg.FreeBSD.org] Installing libXext-1.3.2_2,1... done [pkg.FreeBSD.org] Installing fixesproto-5.0... done [pkg.FreeBSD.org] Installing libXfixes-5.0.1_2... done [pkg.FreeBSD.org] Installing libXi-1.7.4,1... done [pkg.FreeBSD.org] Installing recordproto-1.14.2... done [pkg.FreeBSD.org] Installing libXtst-1.2.2_2... done ===> Returning to build of ugene-1.13.1 <snip> In file included from ../include/U2Core/../../corelibs/U2Core/src/globals/Log.h:29: In file included from /usr/local/include/qt4/QtCore/QTime:1: In file included from /usr/local/include/qt4/QtCore/qdatetime.h:47: In file included from /usr/local/include/qt4/QtCore/qsharedpointer.h:50: /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:435:17: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int tmp = o->strongref; ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:822:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = static_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:834:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = dynamic_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:848:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = const_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:868:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = qobject_cast<X *>(src.data()); ^~~~~~~~~ 6 warnings generated. /usr/local/bin/moc-qt4 -DUGENE_VERSION=1.13.1 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=13 -DUGENE_VER_PATCH=1 -DUGENE_X86 -DUGENE_DATA_DIR=\"/usr/local/share/ugene\" -DOPENCL_SUPPORT -DQT_DLL -DQT_FATAL_ASSERT -DNDEBUG -DQT_NO_DEBUG -DQT_WEBKIT_LIB -DQT_SCRIPT_LIB -DQT_XML_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-clang -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtNetwork -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4/QtScript -I/usr/local/include/qt4/QtWebKit -I/usr/local/include/qt4 -Isrc -I_tmp -I../include -I../corelibs/U2Private/src -I_tmp/moc/release -I/usr/local/include/qt4 -I/usr/local/include src/TestStarter.h -o _tmp/moc/release/moc_TestStarter.cpp c++ -c -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -pthread -D_THREAD_SAFE -Wall -W -DUGENE_VERSION=1.13.1 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=13 -DUGENE_VER_PATCH=1 -DUGENE_X86 -DUGENE_DATA_DIR=\"/usr/local/share/ugene\" -DOPENCL_SUPPORT -DQT_DLL -DQT_FATAL_ASSERT -DNDEBUG -DQT_NO_DEBUG -DQT_WEBKIT_LIB -DQT_SCRIPT_LIB -DQT_XML_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-clang -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtNetwork -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4/QtScript -I/usr/local/include/qt4/QtWebKit -I/usr/local/include/qt4 -Isrc -I_tmp -I../include -I../corelibs/U2Private/src -I_tmp/moc/release -I/usr/local/include/qt4 -I/usr/local/include -o _tmp/obj/release/moc_TestStarter.o _tmp/moc/release/moc_TestStarter.cpp In file included from _tmp/moc/release/moc_TestStarter.cpp:9: In file included from _tmp/moc/release/../../../src/TestStarter.h:25: In file included from ../include/U2Core/AppContext.h:1: In file included from ../include/U2Core/../../corelibs/U2Core/src/globals/AppContext.h:25: In file included from ../include/U2Core/../../corelibs/U2Core/src/globals/global.h:28: In file included from /usr/local/include/qt4/QtCore/QVariantMap:1: In file included from /usr/local/include/qt4/QtCore/qvariant.h:48: /usr/local/include/qt4/QtCore/qmetatype.h:256:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int id = qMetaTypeId<T>(); ^~~~~~~~~ In file included from _tmp/moc/release/moc_TestStarter.cpp:9: In file included from _tmp/moc/release/../../../src/TestStarter.h:26: In file included from ../include/U2Core/Task.h:1: In file included from ../include/U2Core/../../corelibs/U2Core/src/globals/Task.h:26: In file included from ../include/U2Core/Log.h:1: In file included from ../include/U2Core/../../corelibs/U2Core/src/globals/Log.h:29: In file included from /usr/local/include/qt4/QtCore/QTime:1: In file included from /usr/local/include/qt4/QtCore/qdatetime.h:47: In file included from /usr/local/include/qt4/QtCore/qsharedpointer.h:50: /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:435:17: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int tmp = o->strongref; ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:822:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = static_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:834:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = dynamic_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:848:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = const_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:868:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = qobject_cast<X *>(src.data()); ^~~~~~~~~ 6 warnings generated. c++ -fstack-protector -Wl,-O1 -lexecinfo -pthread -Wl,-rpath,/usr/local/lib/qt4 -o ../_release/ugenecl _tmp/obj/release/DumpHelpTask.o _tmp/obj/release/DumpLicenseTask.o _tmp/obj/release/DumpVersionTask.o _tmp/obj/release/ForeverTask.o _tmp/obj/release/Main.o _tmp/obj/release/TaskStatusBar.o _tmp/obj/release/TestStarter.o _tmp/obj/release/moc_DumpHelpTask.o _tmp/obj/release/moc_DumpLicenseTask.o _tmp/obj/release/moc_DumpVersionTask.o _tmp/obj/release/moc_ForeverTask.o _tmp/obj/release/moc_TaskStatusBar.o _tmp/obj/release/moc_TestStarter.o -L/usr/local/lib/qt4 -L/usr/local/lib -L../_release -lU2Core -lU2Algorithm -lU2Formats -lU2Gui -lU2Test -lU2Remote -lU2Lang -lU2Private -lugenedb -lQtWebKit -lQtScript -L/usr/local/lib/qt4 -L/usr/local/lib -lQtXml -lQtGui -lQtNetwork -lQtCore cd src/ugenem/ && /usr/bin/make -f Makefile release /usr/bin/make -f Makefile.Release /usr/local/bin/uic-qt4 src/ui/SendReportDialog.ui -o _tmp/ui/ui_SendReportDialog.h c++ -c -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -pthread -D_THREAD_SAFE -Wall -W -DUGENE_VERSION=1.13.1 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=13 -DUGENE_VER_PATCH=1 -DUGENE_X86 -DUGENE_DATA_DIR=\"/usr/local/share/ugene\" -DQT_DLL -DQT_FATAL_ASSERT -DNDEBUG -DQT_NO_DEBUG -DQT_WEBKIT_LIB -DQT_XML_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-clang -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtNetwork -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4/QtWebKit -I/usr/local/include/qt4 -Isrc -I_tmp -I_tmp/moc/release -I_tmp/ui -I/usr/local/include/qt4 -I/usr/local/include -o _tmp/obj/release/main.o src/main.cpp In file included from src/main.cpp:23: In file included from /usr/local/include/qt4/QtGui/QMessageBox:1: In file included from /usr/local/include/qt4/QtGui/qmessagebox.h:45: In file included from /usr/local/include/qt4/QtGui/qdialog.h:45: In file included from /usr/local/include/qt4/QtGui/qwidget.h:50: In file included from /usr/local/include/qt4/QtGui/qpalette.h:47: In file included from /usr/local/include/qt4/QtGui/qbrush.h:53: In file included from /usr/local/include/qt4/QtGui/qpixmap.h:49: In file included from /usr/local/include/qt4/QtCore/qsharedpointer.h:50: /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:435:17: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int tmp = o->strongref; ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:822:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = static_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:834:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = dynamic_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:848:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = const_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:868:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = qobject_cast<X *>(src.data()); ^~~~~~~~~ In file included from src/main.cpp:25: In file included from /usr/local/include/qt4/QtCore/QTextStream:1: In file included from /usr/local/include/qt4/QtCore/qtextstream.h:48: In file included from /usr/local/include/qt4/QtCore/qlocale.h:45: In file included from /usr/local/include/qt4/QtCore/qvariant.h:48: /usr/local/include/qt4/QtCore/qmetatype.h:256:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int id = qMetaTypeId<T>(); ^~~~~~~~~ 6 warnings generated. c++ -c -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -pthread -D_THREAD_SAFE -Wall -W -DUGENE_VERSION=1.13.1 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=13 -DUGENE_VER_PATCH=1 -DUGENE_X86 -DUGENE_DATA_DIR=\"/usr/local/share/ugene\" -DQT_DLL -DQT_FATAL_ASSERT -DNDEBUG -DQT_NO_DEBUG -DQT_WEBKIT_LIB -DQT_XML_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-clang -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtNetwork -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4/QtWebKit -I/usr/local/include/qt4 -Isrc -I_tmp -I_tmp/moc/release -I_tmp/ui -I/usr/local/include/qt4 -I/usr/local/include -o _tmp/obj/release/SendReportDialog.o src/SendReportDialog.cpp In file included from src/SendReportDialog.cpp:22: In file included from src/SendReportDialog.h:26: In file included from _tmp/ui/ui_SendReportDialog.h:12: In file included from /usr/local/include/qt4/QtCore/QVariant:1: In file included from /usr/local/include/qt4/QtCore/qvariant.h:48: /usr/local/include/qt4/QtCore/qmetatype.h:256:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int id = qMetaTypeId<T>(); ^~~~~~~~~ In file included from src/SendReportDialog.cpp:22: In file included from src/SendReportDialog.h:26: In file included from _tmp/ui/ui_SendReportDialog.h:13: In file included from /usr/local/include/qt4/QtGui/QAction:1: In file included from /usr/local/include/qt4/QtGui/qaction.h:47: In file included from /usr/local/include/qt4/QtGui/qwidget.h:50: In file included from /usr/local/include/qt4/QtGui/qpalette.h:47: In file included from /usr/local/include/qt4/QtGui/qbrush.h:53: In file included from /usr/local/include/qt4/QtGui/qpixmap.h:49: In file included from /usr/local/include/qt4/QtCore/qsharedpointer.h:50: /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:435:17: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int tmp = o->strongref; ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:822:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = static_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:834:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = dynamic_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:848:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = const_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:868:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = qobject_cast<X *>(src.data()); ^~~~~~~~~ 6 warnings generated. /usr/local/bin/moc-qt4 -DUGENE_VERSION=1.13.1 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=13 -DUGENE_VER_PATCH=1 -DUGENE_X86 -DUGENE_DATA_DIR=\"/usr/local/share/ugene\" -DQT_DLL -DQT_FATAL_ASSERT -DNDEBUG -DQT_NO_DEBUG -DQT_WEBKIT_LIB -DQT_XML_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-clang -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtNetwork -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4/QtWebKit -I/usr/local/include/qt4 -Isrc -I_tmp -I_tmp/moc/release -I_tmp/ui -I/usr/local/include/qt4 -I/usr/local/include src/SendReportDialog.h -o _tmp/moc/release/moc_SendReportDialog.cpp c++ -c -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -pthread -D_THREAD_SAFE -Wall -W -DUGENE_VERSION=1.13.1 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=13 -DUGENE_VER_PATCH=1 -DUGENE_X86 -DUGENE_DATA_DIR=\"/usr/local/share/ugene\" -DQT_DLL -DQT_FATAL_ASSERT -DNDEBUG -DQT_NO_DEBUG -DQT_WEBKIT_LIB -DQT_XML_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-clang -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtNetwork -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4/QtWebKit -I/usr/local/include/qt4 -Isrc -I_tmp -I_tmp/moc/release -I_tmp/ui -I/usr/local/include/qt4 -I/usr/local/include -o _tmp/obj/release/moc_SendReportDialog.o _tmp/moc/release/moc_SendReportDialog.cpp In file included from _tmp/moc/release/moc_SendReportDialog.cpp:9: In file included from _tmp/moc/release/../../../src/SendReportDialog.h:26: In file included from _tmp/ui/ui_SendReportDialog.h:12: In file included from /usr/local/include/qt4/QtCore/QVariant:1: In file included from /usr/local/include/qt4/QtCore/qvariant.h:48: /usr/local/include/qt4/QtCore/qmetatype.h:256:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int id = qMetaTypeId<T>(); ^~~~~~~~~ In file included from _tmp/moc/release/moc_SendReportDialog.cpp:9: In file included from _tmp/moc/release/../../../src/SendReportDialog.h:26: In file included from _tmp/ui/ui_SendReportDialog.h:13: In file included from /usr/local/include/qt4/QtGui/QAction:1: In file included from /usr/local/include/qt4/QtGui/qaction.h:47: In file included from /usr/local/include/qt4/QtGui/qwidget.h:50: In file included from /usr/local/include/qt4/QtGui/qpalette.h:47: In file included from /usr/local/include/qt4/QtGui/qbrush.h:53: In file included from /usr/local/include/qt4/QtGui/qpixmap.h:49: In file included from /usr/local/include/qt4/QtCore/qsharedpointer.h:50: /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:435:17: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register int tmp = o->strongref; ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:822:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = static_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:834:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = dynamic_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:848:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = const_cast<X *>(src.data()); // if you get an error in this line, the cast is invalid ^~~~~~~~~ /usr/local/include/qt4/QtCore/qsharedpointer_impl.h:868:5: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register X *ptr = qobject_cast<X *>(src.data()); ^~~~~~~~~ 6 warnings generated. /usr/local/bin/rcc -name ugenem ugenem.qrc -o _tmp/rcc/qrc_ugenem.cpp c++ -c -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -pthread -D_THREAD_SAFE -Wall -W -DUGENE_VERSION=1.13.1 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=13 -DUGENE_VER_PATCH=1 -DUGENE_X86 -DUGENE_DATA_DIR=\"/usr/local/share/ugene\" -DQT_DLL -DQT_FATAL_ASSERT -DNDEBUG -DQT_NO_DEBUG -DQT_WEBKIT_LIB -DQT_XML_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-clang -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtNetwork -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4/QtWebKit -I/usr/local/include/qt4 -Isrc -I_tmp -I_tmp/moc/release -I_tmp/ui -I/usr/local/include/qt4 -I/usr/local/include -o _tmp/obj/release/qrc_ugenem.o _tmp/rcc/qrc_ugenem.cpp c++ -fstack-protector -Wl,-O1 -pthread -Wl,-rpath,/usr/local/lib/qt4 -o ../_release/ugenem _tmp/obj/release/main.o _tmp/obj/release/SendReportDialog.o _tmp/obj/release/moc_SendReportDialog.o _tmp/obj/release/qrc_ugenem.o -L/usr/local/lib/qt4 -L/usr/local/lib -lX11 -lQtWebKit -lQtXml -L/usr/local/lib/qt4 -L/usr/local/lib -lQtGui -lQtNetwork -lQtCore cd src/plugins_3rdparty/ball/ && /usr/bin/make -f Makefile release /usr/bin/make -f Makefile.Release c++ -c -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -pthread -D_THREAD_SAFE -w -fPIC -DUGENE_VERSION=1.13.1 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=13 -DUGENE_VER_PATCH=1 -DUGENE_X86 -DUGENE_DATA_DIR=\"/usr/local/share/ugene\" -DQT_DLL -DNDEBUG -DQT_NO_DEBUG -DQT_WEBKIT_LIB -DQT_SCRIPT_LIB -DQT_SVG_LIB -DQT_XML_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-clang -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtNetwork -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4/QtSvg -I/usr/local/include/qt4/QtScript -I/usr/local/include/qt4/QtWebKit -I/usr/local/include/qt4 -Isrc -I_tmp -I../../include -Isrc/include -I_tmp/moc/release -I/usr/local/include/qt4 -I/usr/local/include -o _tmp/obj/release/BallPlugin.o src/BallPlugin.cpp c++ -c -O2 -pipe -fstack-protector -fno-strict-aliasing -std=c++11 -pthread -D_THREAD_SAFE -w -fPIC -DUGENE_VERSION=1.13.1 -DUGENE_VER_MAJOR=1 -DUGENE_VER_MINOR=13 -DUGENE_VER_PATCH=1 -DUGENE_X86 -DUGENE_DATA_DIR=\"/usr/local/share/ugene\" -DQT_DLL -DNDEBUG -DQT_NO_DEBUG -DQT_WEBKIT_LIB -DQT_SCRIPT_LIB -DQT_SVG_LIB -DQT_XML_LIB -DQT_GUI_LIB -DQT_NETWORK_LIB -DQT_CORE_LIB -DQT_SHARED -I/usr/local/share/qt4/mkspecs/freebsd-clang -I. -I/usr/local/include/qt4/QtCore -I/usr/local/include/qt4/QtNetwork -I/usr/local/include/qt4/QtGui -I/usr/local/include/qt4/QtXml -I/usr/local/include/qt4/QtSvg -I/usr/local/include/qt4/QtScript -I/usr/local/include/qt4/QtWebKit -I/usr/local/include/qt4 -Isrc -I_tmp -I../../include -Isrc/include -I_tmp/moc/release -I/usr/local/include/qt4 -I/usr/local/include -o _tmp/obj/release/SES.o src/SES.cpp In file included from src/SES.cpp:24: In file included from src/include/BALL/STRUCTURE/triangulatedSES.h:11: In file included from src/include/BALL/STRUCTURE/solventExcludedSurface.h:15: In file included from src/include/BALL/STRUCTURE/SESFace.h:19: In file included from src/include/BALL/STRUCTURE/RSFace.h:19: In file included from src/include/BALL/DATATYPE/hashSet.h:15: In file included from src/include/BALL/COMMON/hash.h:15: src/include/BALL/DATATYPE/string.h:904:24: error: friend declaration specifying a default argument must be a definition friend std::istream& getline(std::istream& s, String& string, char delimiter = '\n') ^ 1 error generated. *** Error code 1 Stop. make[3]: stopped in /wrkdirs/usr/ports/biology/ugene/work/ugene-1.13.1/src/plugins_3rdparty/ball *** Error code 1 Stop. make[2]: stopped in /wrkdirs/usr/ports/biology/ugene/work/ugene-1.13.1/src/plugins_3rdparty/ball *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/ugene/work/ugene-1.13.1 *** Error code 1 Stop. make: stopped in /usr/ports/biology/ugene
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