From owner-freebsd-pkg-fallout@FreeBSD.ORG Wed Sep 25 05:01:25 2013 Return-Path: Delivered-To: pkg-fallout@FreeBSD.org Received: from mx1.freebsd.org (mx1.freebsd.org [8.8.178.115]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by hub.freebsd.org (Postfix) with ESMTP id 734B3D16 for ; Wed, 25 Sep 2013 05:01:25 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy1.isc.freebsd.org (beefy1.isc.freebsd.org [IPv6:2001:4f8:3:ffe0:4072:0:16:38]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by mx1.freebsd.org (Postfix) with ESMTPS id 4EF2026D1 for ; Wed, 25 Sep 2013 05:01:25 +0000 (UTC) Received: from beefy1.isc.freebsd.org (localhost [127.0.0.1]) by beefy1.isc.freebsd.org (8.14.7/8.14.7) with ESMTP id r8P51P45019337 for ; Wed, 25 Sep 2013 05:01:25 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy1.isc.freebsd.org (8.14.7/8.14.7/Submit) id r8P51PlK019300; Wed, 25 Sep 2013 05:01:25 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 25 Sep 2013 05:01:25 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201309250501.r8P51PlK019300@beefy1.isc.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [REL - 83i386-default][biology/jalview] Failed for jalview-2.07_2 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.14 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 25 Sep 2013 05:01:25 -0000 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: ports@FreeBSD.org Last committer: bapt@FreeBSD.org Ident: $FreeBSD: head/biology/jalview/Makefile 327709 2013-09-20 15:55:44Z bapt $ Log URL: http://beefy1.isc.freebsd.org/bulk/83i386-default/2013-09-25_01h04m56s/logs/jalview-2.07_2.log Build URL: http://beefy1.isc.freebsd.org/bulk/83i386-default/2013-09-25_01h04m56s Log: ====>> Building biology/jalview build started at Wed Sep 25 05:01:00 UTC 2013 port directory: /usr/ports/biology/jalview building for: FreeBSD 83i386-default-job-10 8.3-RELEASE FreeBSD 8.3-RELEASE i386 maintained by: ports@FreeBSD.org Makefile ident: $FreeBSD: head/biology/jalview/Makefile 327709 2013-09-20 15:55:44Z bapt $ Poudriere version: 3.1-pre ---Begin Environment--- UNAME_m=i386 UNAME_p=i386 OSVERSION=803000 UNAME_v=FreeBSD 8.3-RELEASE UNAME_r=8.3-RELEASE FTP_PASSIVE_MODE=YES BLOCKSIZE=K MAIL=/var/mail/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin STATUS=1 MASTERMNT=/usr/local/poudriere/data/build/83i386-default/ref PKG_EXT=txz tpid=91341 POUDRIERE_BUILD_TYPE=bulk NBPARALLEL=24 PKGNG=1 PKGNAME=jalview-2.07_2 PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f PKG_ADD=/usr/local/sbin/pkg-static add PWD=/root MASTERNAME=83i386-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=/poudriere/pkg-static version ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- TMPDIR="/tmp" JAVA_HOME=/usr/local/openjdk6 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="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" 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-- --SUB_LIST-- JAVASHAREDIR="/usr/local/share/java" JAVAJARDIR="/usr/local/share/java/classes" JAVALIBDIR="/usr/local/share/java/classes" JAVA_VERSION="1.6+" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/java/jalview DOCSDIR=/usr/local/share/doc/jalview EXAMPLESDIR=/usr/local/share/examples/jalview WWWDIR=/usr/local/www/jalview ETCDIR=/usr/local/etc/jalview --End SUB_LIST-- ---Begin make.conf--- ARCH=i386 MACHINE=i386 MACHINE_ARCH=i386 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### WITH_PKGNG=yes NO_RESTRICTED=yes DISABLE_MAKE_JOBS=yes ---End make.conf--- ===> Cleaning for jalview-2.07_2 =================================================== =========================================================================== =================================================== ===> jalview-2.07_2 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-1.1.4_5.txz Installing pkg-1.1.4_5... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of jalview-2.07_2 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by jalview-2.07_2 for building =========================================================================== =================================================== ===> Fetching all distfiles required by jalview-2.07_2 for building => SHA256 Checksum OK for jalview_2_07.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by jalview-2.07_2 for building ===> Extracting for jalview-2.07_2 => SHA256 Checksum OK for jalview_2_07.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for jalview-2.07_2 ===> Applying FreeBSD patches for jalview-2.07_2 =========================================================================== =================================================== ===> jalview-2.07_2 depends on file: /usr/local/openjdk6/bin/java - not found ===> Verifying install for /usr/local/openjdk6/bin/java in /usr/ports/java/openjdk6 ===> Installing existing package /packages/All/openjdk6-b27_7.txz Installing openjdk6-b27_7...Installing xproto-7.0.24... done Installing xextproto-7.2.1... done Installing xbitmaps-1.1.1... done Installing renderproto-0.11.1... done Installing recordproto-1.14.2... done Installing printproto-1.0.5... done Installing libxcb-1.9.1...Installing libXdmcp-1.1.1... done Installing libXau-1.0.8... done Installing libxml2-2.8.0_2...Installing pkgconf-0.9.3... done Installing libiconv-1.14_1... done done Installing libpthread-stubs-0.3_3... done done Installing libXtst-1.2.2...Installing libXi-1.7.2,1...Installing libXfixes-5.0.1...Installing libX11-1.6.1,1...Installing kbproto-1.0.6... done done Installing fixesproto-5.0... done done Installing libXext-1.3.2,1... done Installing inputproto-2.3... done done done Installing libXrender-0.9.8... done Installing libXpm-3.5.10...Installing libSM-1.2.1,1...Installing libICE-1.0.8,1... done done Installing libXt-1.1.4,1... done done Installing libXp-1.0.2,1... done Installing open-motif-2.3.4...Installing libXmu-1.1.1,1... done Installing libXaw-1.0.11,2... done Installing libXft-2.3.1...Installing fontconfig-2.10.95,1...Installing expat-2.1.0... done Installing freetype2-2.5.0.1... 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, 1 dirs /usr/local/lib/X11/fonts/local: caching, new cache contents: 0 fonts, 0 dirs /root/.local/share/fonts: skipping, no such directory /root/.fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory /root/.cache/fontconfig: not cleaning non-existent cache directory /root/.fontconfig: not cleaning non-existent cache directory fc-cache: succeeded done done Installing png-1.5.17... done Installing jpeg-8_4... done done Installing dejavu-2.34... done Installing javavmwrapper-2.4_3... done Installing java-zoneinfo-2013.d... done mkdir: /usr/local/openjdk6/jre/lib/applet: File exists done Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/lib/X11/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. ====================================================================== This OpenJDK implementation requires fdescfs(5) mounted on /dev/fd and procfs(5) mounted on /proc. If you have not done it yet, please do the following: mount -t fdescfs fdesc /dev/fd mount -t procfs proc /proc To make it permanent, you need the following lines in /etc/fstab: fdesc /dev/fd fdescfs rw 0 0 proc /proc procfs rw 0 0 ====================================================================== ===> Returning to build of jalview-2.07_2 ===> jalview-2.07_2 depends on file: /usr/local/bin/ant - not found ===> Verifying install for /usr/local/bin/ant in /usr/ports/devel/apache-ant ===> Installing existing package /packages/All/apache-ant-1.8.4.txz Installing apache-ant-1.8.4... done ===> Returning to build of jalview-2.07_2 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for jalview-2.07_2 =========================================================================== =================================================== ===> Building for jalview-2.07_2 Buildfile: /wrkdirs/usr/ports/biology/jalview/work/jalview/build.xml init: prepare: [mkdir] Created dir: /wrkdirs/usr/ports/biology/jalview/work/jalview/classes [copy] Copying 123 files to /wrkdirs/usr/ports/biology/jalview/work/jalview/classes build: [javac] /wrkdirs/usr/ports/biology/jalview/work/jalview/build.xml:142: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 249 source files to /wrkdirs/usr/ports/biology/jalview/work/jalview/classes [javac] Note: Some input files use or override a deprecated API. [javac] Note: Recompile with -Xlint:deprecation for details. buildPropertiesFile: [properties] write property file /wrkdirs/usr/ports/biology/jalview/work/jalview/classes/.build_properties buildindices: # # A fatal error has been detected by the Java Runtime Environment: # # Internal Error (threadCritical_bsd.cpp:50), pid=10975, tid=690081344 # guarantee(ret == 0) failed: fatal error with pthread_mutex_lock() # # JRE version: 6.0_32-b27 # Java VM: OpenJDK Server VM (20.0-b12 mixed mode bsd-x86 ) # An error report file with more information is saved as: # /wrkdirs/usr/ports/biology/jalview/work/jalview/hs_err_pid10975.log # # If you would like to submit a bug report, please visit: # http://java.sun.com/webapps/bugreport/crash.jsp # *** Signal 6 Stop in /usr/ports/biology/jalview. ===> Cleaning for jalview-2.07_2