From owner-freebsd-pkg-fallout@FreeBSD.ORG Fri Nov 8 09:30:00 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 B1DC7BF8; Fri, 8 Nov 2013 09:30:00 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy2.isc.freebsd.org (beefy2.isc.freebsd.org [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 9EBE92BEF; Fri, 8 Nov 2013 09:30:00 +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 rA89U0Yk098583; Fri, 8 Nov 2013 09:30:00 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy2.isc.freebsd.org (8.14.7/8.14.7/Submit) id rA89U0Rj098575; Fri, 8 Nov 2013 09:30:00 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Fri, 8 Nov 2013 09:30:00 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201311080930.rA89U0Rj098575@beefy2.isc.freebsd.org> To: jasone@FreeBSD.org Subject: [REL - head-amd64-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: Fri, 08 Nov 2013 09:30:00 -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://beefy2.isc.freebsd.org/bulk/head-amd64-default/2013-11-07_15h05m07s/logs/crux-1.2.0_2.log Build URL: http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2013-11-07_15h05m07s Log: ====>> Building biology/crux build started at Fri Nov 8 09:29:15 UTC 2013 port directory: /usr/ports/biology/crux building for: FreeBSD head-amd64-default-job-04 11.0-CURRENT FreeBSD 11.0-CURRENT r256430 amd64 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--- OSVERSION=1100000 UNAME_v=FreeBSD 11.0-CURRENT r256430 UNAME_r=11.0-CURRENT 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/head-amd64-default/ref PKG_EXT=txz tpid=14876 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=head-amd64-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--- 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 *... 8 checking build system type... amd64-portbld-freebsd11.0 checking host system type... amd64-portbld-freebsd11.0 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-freebsd11.0/4.6.4 -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.4/../../../../../x86_64-portbld-freebsd11.0/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.4/../../.. -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-freebsd11.0/4.6.4 -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.4/../../../../../x86_64-portbld-freebsd11.0/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.4/../../.. -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_2 gmake[1]: Entering directory `/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0' 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-freebsd11.0/4.6.4 -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.4/../../../../../x86_64-portbld-freebsd11.0/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.4/../../.. -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 (0.05 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 -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