From owner-freebsd-pkg-fallout@FreeBSD.ORG Thu Nov 7 13:01:09 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 4805E6B1; Thu, 7 Nov 2013 13:01:09 +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 32A672DB2; Thu, 7 Nov 2013 13:01:09 +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 rA7D199i048044; Thu, 7 Nov 2013 13:01:09 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy1.isc.freebsd.org (8.14.7/8.14.7/Submit) id rA7D19fr048006; Thu, 7 Nov 2013 13:01:09 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 7 Nov 2013 13:01:09 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201311071301.rA7D19fr048006@beefy1.isc.freebsd.org> To: jasone@FreeBSD.org Subject: [REL - 10i386-default][biology/crux] Failed for crux-1.2.0_2 in build Cc: pkg-fallout@FreeBSD.org 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, 07 Nov 2013 13:01:09 -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: jasone@FreeBSD.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: head/biology/crux/Makefile 331644 2013-10-26 00:52:33Z gerald $ Log URL: http://beefy1.isc.freebsd.org/bulk/10i386-default/2013-11-07_03h49m18s/logs/crux-1.2.0_2.log Build URL: http://beefy1.isc.freebsd.org/bulk/10i386-default/2013-11-07_03h49m18s Log: ====>> Building biology/crux build started at Thu Nov 7 13:00:31 UTC 2013 port directory: /usr/ports/biology/crux building for: FreeBSD 10i386-default-job-07 10.0-BETA1 FreeBSD 10.0-BETA1 r256420 i386 maintained by: jasone@FreeBSD.org Makefile ident: $FreeBSD: head/biology/crux/Makefile 331644 2013-10-26 00:52:33Z gerald $ Poudriere version: 3.1-pre ---Begin Environment--- UNAME_m=i386 UNAME_p=i386 OSVERSION=1000500 UNAME_v=FreeBSD 10.0-BETA1 r256420 UNAME_r=10.0-BETA1 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/10i386-default/ref PKG_EXT=txz tpid=74583 POUDRIERE_BUILD_TYPE=bulk PKGNG=1 PKGNAME=crux-1.2.0_2 PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f PKG_ADD=/usr/local/sbin/pkg-static add PWD=/root MASTERNAME=10i386-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=/poudriere/pkg-static version PKG_BIN=/usr/local/sbin/pkg-static ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for crux-1.2.0_2: 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--- ARCH=i386 MACHINE=i386 MACHINE_ARCH=i386 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 NO_RESTRICTED=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ===> Cleaning for crux-1.2.0_2 =================================================== =========================================================================== =================================================== ===> crux-1.2.0_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_8.txz Installing pkg-1.1.4_8... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of crux-1.2.0_2 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by crux-1.2.0_2 for building =========================================================================== =================================================== ===> Fetching all distfiles required by crux-1.2.0_2 for building => SHA256 Checksum OK for crux-1.2.0.tar.bz2. =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by crux-1.2.0_2 for building ===> Extracting for crux-1.2.0_2 => SHA256 Checksum OK for crux-1.2.0.tar.bz2. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for crux-1.2.0_2 =========================================================================== =================================================== ===> crux-1.2.0_2 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_3.txz Installing python27-2.7.5_3...Installing gettext-0.18.3.1... 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_2 ===> crux-1.2.0_2 depends on executable: python - not found ===> Verifying install for python in /usr/ports/lang/python ===> Installing existing package /packages/All/python-2.7_1,2.txz Installing python-2.7_1,2...Installing python2-2_1... done done ===> Returning to build of crux-1.2.0_2 ===> crux-1.2.0_2 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_2 ===> crux-1.2.0_2 depends on executable: gcc46 - not found ===> Verifying install for gcc46 in /usr/ports/lang/gcc ===> Installing existing package /packages/All/gcc-4.6.4.txz Installing gcc-4.6.4...Installing binutils-2.23.2... done Installing gcc-ecj-4.5... done Installing gmp-5.1.3... done Installing mpc-1.0.1...Installing mpfr-3.1.2... done done done ===> Returning to build of crux-1.2.0_2 ===> crux-1.2.0_2 depends on file: /usr/local/bin/as - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for crux-1.2.0_2 ===> 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 *... 4 checking build system type... i386-portbld-freebsd10.0 checking host system type... i386-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 cp -R contrib/cython build/contrib gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/daxpy.f -o build/lib/BLAS/daxpy.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/dcopy.f -o build/lib/BLAS/dcopy.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/ddot.f -o build/lib/BLAS/ddot.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/dgemm.f -o build/lib/BLAS/dgemm.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/dgemv.f -o build/lib/BLAS/dgemv.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/dger.f -o build/lib/BLAS/dger.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/dnrm2.f -o build/lib/BLAS/dnrm2.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/drot.f -o build/lib/BLAS/drot.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/dscal.f -o build/lib/BLAS/dscal.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/dswap.f -o build/lib/BLAS/dswap.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/dtrmm.f -o build/lib/BLAS/dtrmm.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/dtrmv.f -o build/lib/BLAS/dtrmv.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/dtrsm.f -o build/lib/BLAS/dtrsm.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/idamax.f -o build/lib/BLAS/idamax.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/lsame.f -o build/lib/BLAS/lsame.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/BLAS/xerbla.f -o build/lib/BLAS/xerbla.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dgebak.f -o build/lib/LAPACK/dgebak.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dgebal.f -o build/lib/LAPACK/dgebal.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dgeev.f -o build/lib/LAPACK/dgeev.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dgehd2.f -o build/lib/LAPACK/dgehd2.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dgehrd.f -o build/lib/LAPACK/dgehrd.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dgetf2.f -o build/lib/LAPACK/dgetf2.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dgetrf.f -o build/lib/LAPACK/dgetrf.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dgetri.f -o build/lib/LAPACK/dgetri.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dhseqr.f -o build/lib/LAPACK/dhseqr.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/disnan.f -o build/lib/LAPACK/disnan.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlabad.f -o build/lib/LAPACK/dlabad.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlacpy.f -o build/lib/LAPACK/dlacpy.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dladiv.f -o build/lib/LAPACK/dladiv.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaexc.f -o build/lib/LAPACK/dlaexc.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlahqr.f -o build/lib/LAPACK/dlahqr.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlahr2.f -o build/lib/LAPACK/dlahr2.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaisnan.f -o build/lib/LAPACK/dlaisnan.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaln2.f -o build/lib/LAPACK/dlaln2.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlamch.f -o build/lib/LAPACK/dlamch.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlange.f -o build/lib/LAPACK/dlange.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlanv2.f -o build/lib/LAPACK/dlanv2.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlapy2.f -o build/lib/LAPACK/dlapy2.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr0.f -o build/lib/LAPACK/dlaqr0.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr1.f -o build/lib/LAPACK/dlaqr1.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr2.f -o build/lib/LAPACK/dlaqr2.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr3.f -o build/lib/LAPACK/dlaqr3.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr4.f -o build/lib/LAPACK/dlaqr4.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr5.f -o build/lib/LAPACK/dlaqr5.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlarf.f -o build/lib/LAPACK/dlarf.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlarfb.f -o build/lib/LAPACK/dlarfb.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlarfg.f -o build/lib/LAPACK/dlarfg.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlarft.f -o build/lib/LAPACK/dlarft.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlarfx.f -o build/lib/LAPACK/dlarfx.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlartg.f -o build/lib/LAPACK/dlartg.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlascl.f -o build/lib/LAPACK/dlascl.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaset.f -o build/lib/LAPACK/dlaset.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlassq.f -o build/lib/LAPACK/dlassq.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlaswp.f -o build/lib/LAPACK/dlaswp.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dlasy2.f -o build/lib/LAPACK/dlasy2.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dorg2r.f -o build/lib/LAPACK/dorg2r.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dorghr.f -o build/lib/LAPACK/dorghr.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dorgqr.f -o build/lib/LAPACK/dorgqr.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dorm2r.f -o build/lib/LAPACK/dorm2r.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dormhr.f -o build/lib/LAPACK/dormhr.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dormqr.f -o build/lib/LAPACK/dormqr.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dtrevc.f -o build/lib/LAPACK/dtrevc.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dtrexc.f -o build/lib/LAPACK/dtrexc.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dtrti2.f -o build/lib/LAPACK/dtrti2.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/dtrtri.f -o build/lib/LAPACK/dtrtri.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/ieeeck.f -o build/lib/LAPACK/ieeeck.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/iladlc.f -o build/lib/LAPACK/iladlc.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/iladlr.f -o build/lib/LAPACK/iladlr.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/ilaenv.f -o build/lib/LAPACK/ilaenv.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gfortran46 -g -O2 -mfpmath=sse -fPIC -c lib/LAPACK/iparmq.f -o build/lib/LAPACK/iparmq.o f951: warning: SSE instruction set disabled, using 387 arithmetics [enabled by default] gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -msse2 -mfpmath=sse -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 -msse2 -mfpmath=sse -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 -msse2 -mfpmath=sse -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 -msse2 -mfpmath=sse -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 -msse2 -mfpmath=sse -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 -msse2 -mfpmath=sse -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 -msse2 -mfpmath=sse -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 -msse2 -mfpmath=sse -fPIC -DPIC -fno-strict-aliasing -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -DMEXP=19937 -DHAVE_SSE2=1 -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 -msse2 -mfpmath=sse -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 -msse2 -mfpmath=sse -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/i386-portbld-freebsd10.0/4.6.4 -L/usr/local/lib/gcc46/gcc/i386-portbld-freebsd10.0/4.6.4/../../../../../i386-portbld-freebsd10.0/lib -L/usr/local/lib/gcc46/gcc/i386-portbld-freebsd10.0/4.6.4/../../.. -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 (0.04 seconds) Pickling lexicon... Done (0.00 seconds) gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -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[1]: *** [build/run/pkg/Crux/CTMatrix.o] Error 1 gmake[1]: Leaving directory `/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0' *** Error code 1 Stop. make: stopped in /usr/ports/biology/crux ===> Cleaning for crux-1.2.0_2