[package - head-amd64-default][biology/ugene] Failed for ugene-1.13.1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Fri Aug 29 17:47:17 UTC 2014
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 at fsfe.org
Last committer: bapt at FreeBSD.org
Ident: $FreeBSD: head/biology/ugene/Makefile 364067 2014-08-04 23:06:21Z bapt $
Log URL: http://beefy2.isc.freebsd.org/data/head-amd64-default/2014-08-29_00h36m14s/logs/ugene-1.13.1.log
Build URL: http://beefy2.isc.freebsd.org/build.html?mastername=head-amd64-default&build=2014-08-29_00h36m14s
Log:
====>> Building biology/ugene
build started at Fri Aug 29 16:51:45 UTC 2014
port directory: /usr/ports/biology/ugene
building for: FreeBSD head-amd64-default-job-16 11.0-CURRENT FreeBSD 11.0-CURRENT r270708 amd64
maintained by: h2+fbsdports at 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: 1100029
!!! Jail is newer than host. (Jail: 1100029, Host: 1100027) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
OSVERSION=1100029
UNAME_v=FreeBSD 11.0-CURRENT r270708
UNAME_r=11.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=screen
MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=ugene-1.13.1
OLDPWD=/root/poudriere
PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool
MASTERNAME=head-amd64-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
---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
--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 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing -std=c++11" MANPREFIX="/usr/local" 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="@comment
"
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---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
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
# clean-restricted ran via poudriere.conf NO_RESTRICTED
#NO_RESTRICTED=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
[head-amd64-default-job-16] 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
[head-amd64-default-job-16] 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
[head-amd64-default-job-16] 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
[head-amd64-default-job-16] Installing inputproto-2.3.1... done
[head-amd64-default-job-16] Installing kbproto-1.0.6... done
[head-amd64-default-job-16] Installing xproto-7.0.26... done
[head-amd64-default-job-16] Installing libXau-1.0.8_2... done
[head-amd64-default-job-16] Installing libXdmcp-1.1.1_2... done
[head-amd64-default-job-16] Installing libpthread-stubs-0.3_5... done
[head-amd64-default-job-16] Installing libxml2-2.9.1_1... done
[head-amd64-default-job-16] Installing libxcb-1.10_2... done
[head-amd64-default-job-16] Installing libX11-1.6.2_2,1... done
[head-amd64-default-job-16] Installing xextproto-7.3.0... done
[head-amd64-default-job-16] Installing libXext-1.3.2_2,1... done
[head-amd64-default-job-16] Installing fixesproto-5.0... done
[head-amd64-default-job-16] Installing libXfixes-5.0.1_2... done
[head-amd64-default-job-16] Installing libXi-1.7.4,1... done
[head-amd64-default-job-16] Installing recordproto-1.14.2... done
[head-amd64-default-job-16] Installing libXtst-1.2.2_2... done
===> Returning to build of ugene-1.13.1
===> ugene-1.13.1 depends on file: /usr/local/lib/qt4/libQtGui.so - not found
===> Verifying install for /usr/local/lib/qt4/libQtGui.so in /usr/ports/x11-toolkits/qt4-gui
===> Installing existing package /packages/All/qt4-gui-4.8.6_2.txz
[head-amd64-default-job-16] Installing font-util-1.3.0_1... done
[head-amd64-default-job-16] Installing encodings-1.0.4_1,1... done
[head-amd64-default-job-16] Installing expat-2.1.0_1... done
[head-amd64-default-job-16] Installing freetype2-2.5.3_2... done
[head-amd64-default-job-16] Installing fontconfig-2.11.0_3,1... done
Running fc-cache to build fontconfig cache...
/usr/local/share/fonts: skipping, no such directory
/usr/local/lib/X11/fonts: caching, new cache contents: 0 fonts, 3 dirs
/usr/local/lib/X11/fonts/encodings: caching, new cache contents: 0 fonts, 1 dirs
/usr/local/lib/X11/fonts/encodings/large: caching, new cache contents: 0 fonts, 0 dirs
/usr/local/lib/X11/fonts/local: caching, new cache contents: 0 fonts, 0 dirs
/usr/local/lib/X11/fonts/util: caching, new cache contents: 0 fonts, 0 dirs
/root/.local/share/fonts: skipping, no such directory
<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_64 -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 -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_64 -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++ -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 -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_64 -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 -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_64 -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_64 -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 -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_64 -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 -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_64 -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++ -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 -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_64 -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 -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_64 -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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