From owner-freebsd-pkg-fallout@FreeBSD.ORG Thu Jul 25 10:59:17 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 1297CE9C for ; Thu, 25 Jul 2013 10:59:17 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy2.isc.freebsd.org (unknown [IPv6:2001:4f8:3:ffe0:4072:0:16:39]) (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 E20E82098 for ; Thu, 25 Jul 2013 10:59:16 +0000 (UTC) Received: from beefy2.isc.freebsd.org (localhost [127.0.0.1]) by beefy2.isc.freebsd.org (8.14.7/8.14.7) with ESMTP id r6PAxG6w064779 for ; Thu, 25 Jul 2013 10:59:16 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy2.isc.freebsd.org (8.14.7/8.14.7/Submit) id r6PAxGpP064727 for pkg-fallout@FreeBSD.org; Thu, 25 Jul 2013 10:59:16 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 25 Jul 2013 10:59:16 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201307251059.r6PAxGpP064727@beefy2.isc.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [RELEASE - head-default] Build failed for crux-1.2.0_1 during 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: Thu, 25 Jul 2013 10:59:17 -0000 Maintainer: jasone@FreeBSD.org Last committer: jgh@FreeBSD.org Ident: $FreeBSD: head/biology/crux/Makefile 314529 2013-03-18 06:48:55Z jgh $ Log URL: http://beefy2.isc.freebsd.org/bulk/head-default/2013-07-25_07h07m51s/logs/crux-1.2.0_1.log Build URL: http://beefy2.isc.freebsd.org/bulk/head-default/2013-07-25_07h07m51s Log: ====>> Building biology/crux build started at Thu Jul 25 10:58:30 UTC 2013 port directory: /usr/ports/biology/crux building for: FreeBSD head-default-job-21 10.0-CURRENT FreeBSD 10.0-CURRENT amd64 maintained by: jasone@FreeBSD.org Makefile ident: $FreeBSD: head/biology/crux/Makefile 314529 2013-03-18 06:48:55Z jgh $ Poudriere version: 3.1-pre ---Begin Environment--- OSVERSION=1000035 UNAME_v=FreeBSD 10.0-CURRENT UNAME_r=10.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 MASTERMNT=/usr/local/poudriere/data/build/head-default/ref PKG_EXT=txz FORCE_PACKAGE=yes tpid=10085 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk NBPARALLEL=24 PKGNG=1 PKGNAME=crux-1.2.0_1 PKG_DELETE=/usr/local/sbin/pkg delete -y -f PKG_ADD=/usr/local/sbin/pkg add PWD=/root/poudriere MASTERNAME=head-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre SKIPSANITY=0 LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for crux-1.2.0_1: SYS_LINALG=off: Enable system ATLAS/LAPACK ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --with-python=/usr/local/bin/python2.7 --disable-mpi --disable-sys-linalg --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- TMPDIR="/tmp" PYTHON="/usr/local/bin/python2.7" MAKE=gmake TMPDIR="/tmp" TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh F77="gfortran46" FC="gfortran46" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc46" ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- TMPDIR="/tmp" TMPDIR="/tmp" TMPDIR="/tmp" SHELL=/bin/sh NO_LINT=YES F77="gfortran46" FC="gfortran46" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc46" ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="gcc46" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99" CPP="cpp46" CPPFLAGS="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46" CXX="g++46" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc46" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTAL L_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-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/crux DOCSDIR=/usr/local/share/doc/crux EXAMPLESDIR=/usr/local/share/examples/crux WWWDIR=/usr/local/www/crux ETCDIR=/usr/local/etc/crux --End SUB_LIST-- ---Begin make.conf--- 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 crux-1.2.0_1 =================================================== ========================================================================= =================================================== ===> crux-1.2.0_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-1.1.4_1.txz Installing pkg-1.1.4_1... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of crux-1.2.0_1 ========================================================================= =================================================== ========================================================================= =================================================== ===> Fetching all distfiles required by crux-1.2.0_1 for building ========================================================================= =================================================== ===> Fetching all distfiles required by crux-1.2.0_1 for building => SHA256 Checksum OK for crux-1.2.0.tar.bz2. ========================================================================= =================================================== ========================================================================= =================================================== ===> Fetching all distfiles required by crux-1.2.0_1 for building ===> Extracting for crux-1.2.0_1 => SHA256 Checksum OK for crux-1.2.0.tar.bz2. ========================================================================= =================================================== ========================================================================= =================================================== ===> Patching for crux-1.2.0_1 ========================================================================= =================================================== ===> crux-1.2.0_1 depends on file: /usr/local/bin/python2.7 - not found ===> Verifying install for /usr/local/bin/python2.7 in /usr/ports/lang/python27 ===> Installing existing package /packages/All/python27-2.7.5_1.txz Installing python27-2.7.5_1...Installing gettext-0.18.3...Installing libiconv-1.14_1... done done done ==== Note that some of the standard modules are provided as separate ports since they require extra dependencies: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter Install them as needed. ==== ===> Returning to build of crux-1.2.0_1 ===> crux-1.2.0_1 depends on executable: gmake - not found ===> Verifying install for gmake in /usr/ports/devel/gmake ===> Installing existing package /packages/All/gmake-3.82_1.txz Installing gmake-3.82_1... done ===> Returning to build of crux-1.2.0_1 ===> crux-1.2.0_1 depends on executable: gcc46 - not found ===> Verifying install for gcc46 in /usr/ports/lang/gcc ===> Installing existing package /packages/All/gcc-4.6.3.txz Installing gcc-4.6.3...Installing mpfr-3.1.2...Installing gmp-5.1.2... done done Installing mpc-0.9... done Installing gcc-ecj-4.5... done Installing binutils-2.23.2... done done ===> Returning to build of crux-1.2.0_1 ===> crux-1.2.0_1 depends on file: /usr/local/bin/as - found ========================================================================= =================================================== ========================================================================= =================================================== ===> Configuring for crux-1.2.0_1 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/configure configure: loading site script /usr/ports/Templates/config.site checking for gcc... gcc46 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc46 accepts -g... yes checking for gcc46 option to accept ISO C89... none needed checking how to run the C preprocessor... cpp46 checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking size of void *... 8 checking build system type... amd64-portbld-freebsd10.0 checking host system type... amd64-portbld-freebsd10.0 checking for a BSD-compatible install... /usr/bin/install -c -o root -g wheel checking for ranlib... /usr/local/bin/ranlib checking for ar... /usr/local/bin/ar checking for ld... /usr/local/bin/ld checking for test... /bin/test checking for grep... /usr/bin/grep checking for autoconf... no checking pthread.h usability... yes checking pthread.h presence... yes checking for pthread.h... yes checking for pthread_create in -lpthread... yes checking for python >= 2.5.0... 2.7.5 checking for python-config... /usr/local/bin/python2.7-config checking python site-packages path... /usr/local/lib/python2.7/site-packages checking whether byte ordering is bigendian... no checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for log in -lm... yes checking for posix_memalign... yes checking for mallopt... no checking whether we are using the GNU Fortran compiler... yes checking whether gfortran46 accepts -g... yes checking how to get verbose linking output from gfortran46... -v checking for Fortran libraries of gfortran46... -L/usr/local/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd10.0/4.6.3 -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd10.0/4.6.3/../../../../../x86_64-portbld-freebsd10.0/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd10.0/4.6.3/../../.. -lgfortran -lm -lpthread -lquadmath configure: creating ./config.status config.status: creating Makefile config.status: creating cfgoutputs.stamp config.status: creating cfg config.status: creating cydep config.status: creating cython config.status: creating lib/Crux/Cx_defs.h config.status: creating cfghdrs.stamp =============================================================================== Crux version : 1.2.0 PYTHON : /usr/local/bin/python2.7 CYTHON : /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cython FLEX : CC : gcc46 CPPFLAGS : -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT MTCPPFLAGS : -DMEXP=19937 CFLAGS : -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 MTCFLAGS : -fno-strict-aliasing FC : gfortran46 FCFLAGS : -g -O2 LDFLAGS : -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46 LIBS : -lm -lpthread FCLIBS : -L/usr/local/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd10.0/4.6.3 -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd10.0/4.6.3/../../../../../x86_64-portbld-freebsd10.0/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd10.0/4.6.3/../../.. -lgfortran -lm -lpthread -lquadmath RPATH_EXTRA : site_packages : /usr/local/lib/python2.7/site-packages PREFIX : /usr/local BINDIR : /usr/local/bin DATADIR : /usr/local/share MANDIR : /usr/local/man srcroot : abs_srcroot : /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/ objroot : abs_objroot : /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/ autogen : 0 flex : 0 debug : 0 cc-silence : 0 inlines : 1 sys-linalg : 0 mpi : 0 =============================================================================== ========================================================================= =================================================== ===> Building for crux-1.2.0_1 cp -R contrib/cython build/contrib gfortran46 -g -O2 -fPIC -c lib/BLAS/daxpy.f -o build/lib/BLAS/daxpy.o gfortran46 -g -O2 -fPIC -c lib/BLAS/dcopy.f -o build/lib/BLAS/dcopy.o gfortran46 -g -O2 -fPIC -c lib/BLAS/ddot.f -o build/lib/BLAS/ddot.o gfortran46 -g -O2 -fPIC -c lib/BLAS/dgemm.f -o build/lib/BLAS/dgemm.o gfortran46 -g -O2 -fPIC -c lib/BLAS/dgemv.f -o build/lib/BLAS/dgemv.o gfortran46 -g -O2 -fPIC -c lib/BLAS/dger.f -o build/lib/BLAS/dger.o gfortran46 -g -O2 -fPIC -c lib/BLAS/dnrm2.f -o build/lib/BLAS/dnrm2.o gfortran46 -g -O2 -fPIC -c lib/BLAS/drot.f -o build/lib/BLAS/drot.o gfortran46 -g -O2 -fPIC -c lib/BLAS/dscal.f -o build/lib/BLAS/dscal.o gfortran46 -g -O2 -fPIC -c lib/BLAS/dswap.f -o build/lib/BLAS/dswap.o gfortran46 -g -O2 -fPIC -c lib/BLAS/dtrmm.f -o build/lib/BLAS/dtrmm.o gfortran46 -g -O2 -fPIC -c lib/BLAS/dtrmv.f -o build/lib/BLAS/dtrmv.o gfortran46 -g -O2 -fPIC -c lib/BLAS/dtrsm.f -o build/lib/BLAS/dtrsm.o gfortran46 -g -O2 -fPIC -c lib/BLAS/idamax.f -o build/lib/BLAS/idamax.o gfortran46 -g -O2 -fPIC -c lib/BLAS/lsame.f -o build/lib/BLAS/lsame.o gfortran46 -g -O2 -fPIC -c lib/BLAS/xerbla.f -o build/lib/BLAS/xerbla.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgebak.f -o build/lib/LAPACK/dgebak.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgebal.f -o build/lib/LAPACK/dgebal.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgeev.f -o build/lib/LAPACK/dgeev.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgehd2.f -o build/lib/LAPACK/dgehd2.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgehrd.f -o build/lib/LAPACK/dgehrd.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgetf2.f -o build/lib/LAPACK/dgetf2.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgetrf.f -o build/lib/LAPACK/dgetrf.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgetri.f -o build/lib/LAPACK/dgetri.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dhseqr.f -o build/lib/LAPACK/dhseqr.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/disnan.f -o build/lib/LAPACK/disnan.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlabad.f -o build/lib/LAPACK/dlabad.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlacpy.f -o build/lib/LAPACK/dlacpy.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dladiv.f -o build/lib/LAPACK/dladiv.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaexc.f -o build/lib/LAPACK/dlaexc.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlahqr.f -o build/lib/LAPACK/dlahqr.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlahr2.f -o build/lib/LAPACK/dlahr2.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaisnan.f -o build/lib/LAPACK/dlaisnan.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaln2.f -o build/lib/LAPACK/dlaln2.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlamch.f -o build/lib/LAPACK/dlamch.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlange.f -o build/lib/LAPACK/dlange.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlanv2.f -o build/lib/LAPACK/dlanv2.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlapy2.f -o build/lib/LAPACK/dlapy2.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr0.f -o build/lib/LAPACK/dlaqr0.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr1.f -o build/lib/LAPACK/dlaqr1.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr2.f -o build/lib/LAPACK/dlaqr2.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr3.f -o build/lib/LAPACK/dlaqr3.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr4.f -o build/lib/LAPACK/dlaqr4.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr5.f -o build/lib/LAPACK/dlaqr5.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlarf.f -o build/lib/LAPACK/dlarf.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlarfb.f -o build/lib/LAPACK/dlarfb.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlarfg.f -o build/lib/LAPACK/dlarfg.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlarft.f -o build/lib/LAPACK/dlarft.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlarfx.f -o build/lib/LAPACK/dlarfx.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlartg.f -o build/lib/LAPACK/dlartg.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlascl.f -o build/lib/LAPACK/dlascl.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaset.f -o build/lib/LAPACK/dlaset.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlassq.f -o build/lib/LAPACK/dlassq.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaswp.f -o build/lib/LAPACK/dlaswp.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlasy2.f -o build/lib/LAPACK/dlasy2.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dorg2r.f -o build/lib/LAPACK/dorg2r.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dorghr.f -o build/lib/LAPACK/dorghr.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dorgqr.f -o build/lib/LAPACK/dorgqr.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dorm2r.f -o build/lib/LAPACK/dorm2r.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dormhr.f -o build/lib/LAPACK/dormhr.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dormqr.f -o build/lib/LAPACK/dormqr.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dtrevc.f -o build/lib/LAPACK/dtrevc.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dtrexc.f -o build/lib/LAPACK/dtrexc.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dtrti2.f -o build/lib/LAPACK/dtrti2.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/dtrtri.f -o build/lib/LAPACK/dtrtri.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/ieeeck.f -o build/lib/LAPACK/ieeeck.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/iladlc.f -o build/lib/LAPACK/iladlc.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/iladlr.f -o build/lib/LAPACK/iladlr.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/ilaenv.f -o build/lib/LAPACK/ilaenv.o gfortran46 -g -O2 -fPIC -c lib/LAPACK/iparmq.f -o build/lib/LAPACK/iparmq.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/Cx.c -obuild/lib/Crux/Cx.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxAmd64.c -obuild/lib/Crux/CxAmd64.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxIa32.c -obuild/lib/Crux/CxIa32.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxMat.c -obuild/lib/Crux/CxMat.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxMq.c -obuild/lib/Crux/CxMq.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxPpc.c -obuild/lib/Crux/CxPpc.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxRi.c -obuild/lib/Crux/CxRi.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/Tree/CxLik.c -obuild/lib/Crux/Tree/CxLik.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -fno-strict-aliasing -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -DMEXP=19937 -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/SFMT/SFMT.c -obuild/lib/SFMT/SFMT.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxNewickLexer.c -obuild/lib/Crux/CxNewickLexer.o gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/DistMatrix/CxDistMatrixLexer.c -obuild/lib/Crux/DistMatrix/CxDistMatrixLexer.o gcc46 -shared -Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib -Wl,-soname,libCx.so -o build/run/share/Crux/lib/libCx.so build/lib/Crux/Cx.o build/lib/Crux/CxAmd64.o build/lib/Crux/CxIa32.o build/lib/Crux/CxMat.o build/lib/Crux/CxMq.o build/lib/Crux/CxPpc.o build/lib/Crux/CxRi.o build/lib/Crux/Tree/CxLik.o build/lib/SFMT/SFMT.o build/lib/Crux/CxNewickLexer.o build/lib/Crux/DistMatrix/CxDistMatrixLexer.o build/lib/BLAS/daxpy.o build/lib/BLAS/dcopy.o build/lib/BLAS/ddot.o build/lib/BLAS/dgemm.o build/lib/BLAS/dgemv.o build/lib/BLAS/dger.o build/lib/BLAS/dnrm2.o build/lib/BLAS/drot.o build/lib/BLAS/dscal.o build/lib/BLAS/dswap.o build/lib/BLAS/dtrmm.o build/lib/BLAS/dtrmv.o build/lib/BLAS/dtrsm.o build/lib/BLAS/idamax.o build/lib/BLAS/lsame.o build/lib/BLAS/xerbla.o build/lib/LAPACK/dgebak.o build/lib/LAPACK/dgebal.o build/lib/LAPACK/dgeev.o build/lib/LAPACK/dgehd2.o build/lib/LAPACK/dgehrd.o build/lib/LAPACK/dgetf2.o build/lib/LAPACK/dgetrf.o build/l ib/LAPACK/dgetri.o build/lib/LAPACK/dhseqr.o build/lib/LAPACK/disnan.o build/lib/LAPACK/dlabad.o build/lib/LAPACK/dlacpy.o build/lib/LAPACK/dladiv.o build/lib/LAPACK/dlaexc.o build/lib/LAPACK/dlahqr.o build/lib/LAPACK/dlahr2.o build/lib/LAPACK/dlaisnan.o build/lib/LAPACK/dlaln2.o build/lib/LAPACK/dlamch.o build/lib/LAPACK/dlange.o build/lib/LAPACK/dlanv2.o build/lib/LAPACK/dlapy2.o build/lib/LAPACK/dlaqr0.o build/lib/LAPACK/dlaqr1.o build/lib/LAPACK/dlaqr2.o build/lib/LAPACK/dlaqr3.o build/lib/LAPACK/dlaqr4.o build/lib/LAPACK/dlaqr5.o build/lib/LAPACK/dlarf.o build/lib/LAPACK/dlarfb.o build/lib/LAPACK/dlarfg.o build/lib/LAPACK/dlarft.o build/lib/LAPACK/dlarfx.o build/lib/LAPACK/dlartg.o build/lib/LAPACK/dlascl.o build/lib/LAPACK/dlaset.o build/lib/LAPACK/dlassq.o build/lib/LAPACK/dlaswp.o build/lib/LAPACK/dlasy2.o build/lib/LAPACK/dorg2r.o build/lib/LAPACK/dorghr.o build/lib/LAPACK/dorgqr.o build/lib/LAPACK/dorm2r.o build/lib/LAPACK/dormhr.o build/lib/LAPACK/dormqr.o build/lib/LAPAC K/dtrevc.o build/lib/LAPACK/dtrexc.o build/l! ib/LAPACK/dtrti2.o build/lib/LAPACK/dtrtri.o build/lib/LAPACK/ieeeck.o build/lib/LAPACK/iladlc.o build/lib/LAPACK/iladlr.o build/lib/LAPACK/ilaenv.o build/lib/LAPACK/iparmq.o -L/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46 -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd10.0/4.6.3 -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd10.0/4.6.3/../../../../../x86_64-portbld-freebsd10.0/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd10.0/4.6.3/../../.. -lgfortran -lm -lpthread -lquadmath /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/CTMatrix.pyx --outfile=build/run/pkg/Crux/CTMatrix.pyx /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/CTMatrix.pxd --outfile=build/run/pkg/Crux/CTMatrix.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Character.pxd --outfile=build/run/pkg/Crux/Character.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/DistMatrix/Nj.pxd --outfile=build/run/pkg/Crux/DistMatrix/Nj.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Fasta.pxd --outfile=build/run/pkg/Crux/Fasta.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/Chain.pxd --outfile=build/run/pkg/Crux/Mc3/Chain.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/Post.pxd --outfile=build/run/pkg/Crux/Mc3/Post.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Newick.pxd --outfile=build/run/pkg/Crux/Newick.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Taxa.pxd --outfile=build/run/pkg/Crux/Taxa.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/Bipart.pxd --outfile=build/run/pkg/Crux/Tree/Bipart.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/Lik.pxd --outfile=build/run/pkg/Crux/Tree/Lik.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/Sumt.pxd --outfile=build/run/pkg/Crux/Tree/Sumt.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Parsing.pxd --outfile=build/run/pkg/Parsing.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/DistMatrix/__init__.pxd --outfile=build/run/pkg/Crux/DistMatrix/__init__.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/__init__.pxd --outfile=build/run/pkg/Crux/Mc3/__init__.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/__init__.pxd --outfile=build/run/pkg/Crux/Tree/__init__.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/__init__.pxd --outfile=build/run/pkg/Crux/__init__.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/Cx.pxd --outfile=build/run/lib/Crux/Cx.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/CxMat.pxd --outfile=build/run/lib/Crux/CxMat.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/CxMath.pxd --outfile=build/run/lib/Crux/CxMath.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/CxNewickLexer.pxd --outfile=build/run/lib/Crux/CxNewickLexer.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/CxRi.pxd --outfile=build/run/lib/Crux/CxRi.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/DistMatrix/CxDistMatrixLexer.pxd --outfile=build/run/lib/Crux/DistMatrix/CxDistMatrixLexer.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/Tree/CxLik.pxd --outfile=build/run/lib/Crux/Tree/CxLik.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/SFMT/SFMT.pxd --outfile=build/run/lib/SFMT/SFMT.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/libc.pxd --outfile=build/run/lib/libc.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/libm.pxd --outfile=build/run/lib/libm.pxd /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Config.py --outfile=build/run/pkg/Crux/Config.py /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Copying.py --outfile=build/run/pkg/Crux/Copying.py /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/DistMatrix/__init__.py --outfile=build/run/pkg/Crux/DistMatrix/__init__.py /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/__init__.py --outfile=build/run/pkg/Crux/Mc3/__init__.py /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/__init__.py --outfile=build/run/pkg/Crux/Tree/__init__.py /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/__init__.py --outfile=build/run/pkg/Crux/__init__.py /usr/local/bin/python2.7 /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/CTMatrix.c build/run/pkg/Crux/CTMatrix.pyx Creating lexicon... Done (0.05 seconds) Pickling lexicon... Done (0.00 seconds) gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -fno-strict-aliasing -OPT:Olimit=0 -O2 -pipe -fno-strict-aliasing -DNDEBUG -O2 -pipe -fno-strict-aliasing -c build/run/pkg/Crux/CTMatrix.c -obuild/run/pkg/Crux/CTMatrix.o cc1: error: argument to '-O' should be a non-negative integer gmake: *** [build/run/pkg/Crux/CTMatrix.o] Error 1 *** Error code 1 Stop. make: stopped in /usr/ports/biology/crux ===> Cleaning for crux-1.2.0_1