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:     jas...@freebsd.org
Last committer: j...@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-amd64-default/2013-09-12_01h37m09s/logs/crux-1.2.0_1.log
Build URL:      
http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2013-09-12_01h37m09s
Log:

====>> Building biology/crux
build started at Thu Sep 12 14:27:44 UTC 2013
port directory: /usr/ports/biology/crux
building for: FreeBSD head-amd64-default-job-24 10.0-CURRENT FreeBSD 
10.0-CURRENT amd64
maintained by: jas...@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=1000055
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-amd64-default/ref
PKG_EXT=txz
tpid=18789
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
MASTERNAME=head-amd64-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
SKIPSANITY=1
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"  BS
 D_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
=======================<phase: check-config   >============================
===========================================================================
=======================<phase: pkg-depends    >============================
===>   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_2.txz
Installing pkg-1.1.4_2... done
If you are upgrading from the old package format, first run:

  # pkg2ng
===>   Returning to build of crux-1.2.0_1
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===> Fetching all distfiles required by crux-1.2.0_1 for building
===========================================================================
=======================<phase: checksum       >============================
===> Fetching all distfiles required by crux-1.2.0_1 for building
=> SHA256 Checksum OK for crux-1.2.0.tar.bz2.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===> 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.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for crux-1.2.0_1
===========================================================================
=======================<phase: build-depends  >============================
===>   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_3.txz
Installing python27-2.7.5_3...Installing gettext-0.18.3... 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: 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... done
 done
===>   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
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  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
===============================================================================
===========================================================================
=======================<phase: build          >============================
===>  Building for crux-1.2.0_1
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/l
 ib/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 -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_1
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