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:     po...@freebsd.org
Last committer: ger...@freebsd.org
Ident:          $FreeBSD: head/biology/crux/Makefile 437439 2017-04-01 
15:23:30Z gerald $
Log URL:        
http://thunderx1.nyi.freebsd.org/data/110arm64-default/438755/logs/crux-1.2.0_7.log
Build URL:      
http://thunderx1.nyi.freebsd.org/build.html?mastername=110arm64-default&build=438755
Log:

====>> Building biology/crux
build started at Thu Apr 20 08:33:28 UTC 2017
port directory: /usr/ports/biology/crux
building for: FreeBSD 110arm64-default-job-03 11.0-RELEASE-p1 FreeBSD 
11.0-RELEASE-p1 arm64
maintained by: po...@freebsd.org
Makefile ident:      $FreeBSD: head/biology/crux/Makefile 437439 2017-04-01 
15:23:30Z gerald $
Poudriere version: 3.1.17-9-gf49c6f78
Host OSVERSION: 1100121
Jail OSVERSION: 1100122
Job Id: 03




!!! Jail is newer than host. (Jail: 1100122, Host: 1100121) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
OSVERSION=1100122
UNAME_v=FreeBSD 11.0-RELEASE-p1
UNAME_r=11.0-RELEASE-p1
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/.m/110arm64-default/ref
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=crux-1.2.0_7
OLDPWD=/
PWD=/usr/local/poudriere/data/.m/110arm64-default/ref/.p/pool
MASTERNAME=110arm64-default
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.17-9-gf49c6f78
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---

---Begin OPTIONS List---
===> The following configuration options are available for crux-1.2.0_7:
     SYS_LINALG=off: Enable system ATLAS/LAPACK
===> Use 'make config' to modify these settings
---End OPTIONS List---

--CONFIGURE_ARGS--
--datadir=/usr/local/lib  --with-python=/usr/local/bin/python2.7  --disable-mpi 
--disable-sys-linalg --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" 
FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" MAKE=gmake 
PYTHON="/usr/local/bin/python2.7" 
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/crux/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/crux/work  
HOME=/wrkdirs/usr/ports/biology/crux/work TMPDIR="/tmp" SHELL=/bin/sh 
CONFIG_SHELL=/bin/sh 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--
F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" 
FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" 
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/crux/work  
XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/crux/work  
HOME=/wrkdirs/usr/ports/biology/crux/work TMPDIR="/tmp" NO_PIE=yes 
MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES 
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="cc" CFLAGS="-O2 -pipe  
-fno-strict-aliasing -std=gnu99"  CPP="cpp" CPPFLAGS="-I/usr/local/include"  
LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5  
-L/usr/local/lib/gcc5 -B/usr/local/bin" L
 IBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing "  
MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -m 555"  
BSD_INSTALL_LIB="install  -s -m 0644"  BSD_INSTALL_SCRIPT="install  -m 555"  
BSD_INSTALL_DATA="install  -m 0644"  BSD_INSTALL_MAN="install  -m 444"
--End MAKE_ENV--

--PLIST_SUB--
PYTHON_INCLUDEDIR=include/python2.7
PYTHON_LIBDIR=lib/python2.7
PYTHON_PLATFORM=freebsd11
PYTHON_PYOEXTENSION=pyo
PYTHON_SITELIBDIR=lib/python2.7/site-packages
PYTHON_SUFFIX=27
PYTHON_VER=2.7
PYTHON_VERSION=python2.7
PYTHON2=""
PYTHON3="@comment
"
OSREL=11.0
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
DOCSDIR="share/doc/crux"
EXAMPLESDIR="share/examples/crux"
DATADIR="share/crux"
WWWDIR="www/crux"
ETCDIR="etc/crux"
--End PLIST_SUB--

--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 ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure.  It currently retries the same
# failed mirror and then fails rather then trying another.  It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
ARCH=aarch64
CONFIGURE_MAX_CMD_LEN=262144
OPSYS=FreeBSD
OSREL=11.0
OSVERSION=1100122
PYTHONBASE=/usr/local
UID=0
_JAVA_OS_LIST_REGEXP=native\|linux
_JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun
_JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+
_OSRELEASE=11.0-RELEASE-p1
#### Misc Poudriere ####
GID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
--Resource limits--
cpu time               (seconds, -t)  unlimited
file size           (512-blocks, -f)  unlimited
data seg size           (kbytes, -d)  1048576
stack size              (kbytes, -s)  1048576
core file size      (512-blocks, -c)  unlimited
max memory size         (kbytes, -m)  unlimited
locked memory           (kbytes, -l)  unlimited
max user processes              (-u)  89999
open files                      (-n)  1024
virtual mem size        (kbytes, -v)  unlimited
swap limit              (kbytes, -w)  unlimited
socket buffer size       (bytes, -b)  unlimited
pseudo-terminals                (-p)  unlimited
kqueues                         (-k)  unlimited
umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===>   NOTICE:

The crux port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port

===>  License BSD2CLAUSE BSD3CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   crux-1.2.0_7 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.1.txz
[110arm64-default-job-03] Installing pkg-1.10.1...
[110arm64-default-job-03] Extracting pkg-1.10.1: .......... done
===>   crux-1.2.0_7 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of crux-1.2.0_7
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>   NOTICE:

The crux port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port

===>  License BSD2CLAUSE BSD3CLAUSE accepted by the user
===> Fetching all distfiles required by crux-1.2.0_7 for building
===========================================================================
=======================<phase: checksum       >============================
===>   NOTICE:

The crux port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla
<snip>
gfortran5 -Wl,-rpath=/usr/local/lib/gcc5  -fPIC -c lib/LAPACK/ilaenv.f -o 
build/lib/LAPACK/ilaenv.o
gfortran5 -Wl,-rpath=/usr/local/lib/gcc5  -fPIC -c lib/LAPACK/iparmq.f -o 
build/lib/LAPACK/iparmq.o
cc -O2 -pipe  -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
cc -O2 -pipe  -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
cc -O2 -pipe  -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
cc -O2 -pipe  -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
cc -O2 -pipe  -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
cc -O2 -pipe  -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
cc -O2 -pipe  -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
cc -O2 -pipe  -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
cc -O2 -pipe  -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
cc -O2 -pipe  -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
cc -O2 -pipe  -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
cc -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/lib/
 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/LAPACK/d
 trevc.o build/lib/LAPACK/dtrexc.o build/lib/!
 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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -lm  -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 
-L/usr/local/bin -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/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 (0.56 seconds)
Pickling lexicon...
Done (0.03 seconds)
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/CTMatrix.c 
-obuild/run/pkg/Crux/CTMatrix.o
build/run/pkg/Crux/CTMatrix.c:5914:21: warning: equality comparison with 
extraneous parentheses [-Wparentheses-equality]
    if ((__pyx_v_aC == __pyx_v_bC)) {
         ~~~~~~~~~~~^~~~~~~~~~~~~
build/run/pkg/Crux/CTMatrix.c:5914:21: note: remove extraneous parentheses 
around the comparison to silence this warning
    if ((__pyx_v_aC == __pyx_v_bC)) {
        ~           ^            ~
build/run/pkg/Crux/CTMatrix.c:5914:21: note: use '=' to turn this equality 
comparison into an assignment
    if ((__pyx_v_aC == __pyx_v_bC)) {
                    ^~
                    =
build/run/pkg/Crux/CTMatrix.c:5967:25: warning: equality comparison with 
extraneous parentheses [-Wparentheses-equality]
      if ((__pyx_v_aPop == 1)) {
           ~~~~~~~~~~~~~^~~~
build/run/pkg/Crux/CTMatrix.c:5967:25: note: remove extraneous parentheses 
around the comparison to silence this warning
      if ((__pyx_v_aPop == 1)) {
          ~             ^   ~
build/run/pkg/Crux/CTMatrix.c:5967:25: note: use '=' to turn this equality 
comparison into an assignment
      if ((__pyx_v_aPop == 1)) {
                        ^~
                        =
2 warnings generated.
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/CTMatrix.so 
build/run/pkg/Crux/CTMatrix.o build/run/share/Crux/lib/libCx.so -lm  -lpthread 
-L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Character.pyx --outfile=build/run/pkg/Crux/Character.pyx
/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/Character.c build/run/pkg/Crux/Character.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Character.c 
-obuild/run/pkg/Crux/Character.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Character.so 
build/run/pkg/Crux/Character.o build/run/share/Crux/lib/libCx.so -lm  -lpthread 
-L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/DistMatrix/Nj.pyx 
--outfile=build/run/pkg/Crux/DistMatrix/Nj.pyx
/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/DistMatrix/Nj.c build/run/pkg/Crux/DistMatrix/Nj.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/DistMatrix/Nj.c 
-obuild/run/pkg/Crux/DistMatrix/Nj.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/DistMatrix/Nj.so 
build/run/pkg/Crux/DistMatrix/Nj.o build/run/share/Crux/lib/libCx.so -lm  
-lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Fasta.pyx --outfile=build/run/pkg/Crux/Fasta.pyx
/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/Fasta.c build/run/pkg/Crux/Fasta.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Fasta.c 
-obuild/run/pkg/Crux/Fasta.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Fasta.so 
build/run/pkg/Crux/Fasta.o build/run/share/Crux/lib/libCx.so -lm  -lpthread 
-L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Mc3/Chain.pyx --outfile=build/run/pkg/Crux/Mc3/Chain.pyx
/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/Mc3/Chain.c build/run/pkg/Crux/Mc3/Chain.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Mc3/Chain.c 
-obuild/run/pkg/Crux/Mc3/Chain.o
build/run/pkg/Crux/Mc3/Chain.c:9965:23: warning: equality comparison with 
extraneous parentheses [-Wparentheses-equality]
  if ((__pyx_v_nedges == ((2 * __pyx_v_ntaxa) - 3))) {
       ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
build/run/pkg/Crux/Mc3/Chain.c:9965:23: note: remove extraneous parentheses 
around the comparison to silence this warning
  if ((__pyx_v_nedges == ((2 * __pyx_v_ntaxa) - 3))) {
      ~               ^                           ~
build/run/pkg/Crux/Mc3/Chain.c:9965:23: note: use '=' to turn this equality 
comparison into an assignment
  if ((__pyx_v_nedges == ((2 * __pyx_v_ntaxa) - 3))) {
                      ^~
                      =
build/run/pkg/Crux/Mc3/Chain.c:11063:23: warning: equality comparison with 
extraneous parentheses [-Wparentheses-equality]
  if ((__pyx_v_nedges == __pyx_v_ntaxa)) {
       ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
build/run/pkg/Crux/Mc3/Chain.c:11063:23: note: remove extraneous parentheses 
around the comparison to silence this warning
  if ((__pyx_v_nedges == __pyx_v_ntaxa)) {
      ~               ^               ~
build/run/pkg/Crux/Mc3/Chain.c:11063:23: note: use '=' to turn this equality 
comparison into an assignment
  if ((__pyx_v_nedges == __pyx_v_ntaxa)) {
                      ^~
                      =
build/run/pkg/Crux/Mc3/Chain.c:14528:178: warning: incompatible pointer types 
passing 'int (void *, void *)' to parameter of type 'int (*)(const void *, 
const void *)' [-Wincompatible-pointer-types]
    __pyx_v_propInd = ((((uintptr_t)bsearch((&__pyx_v_u), 
__pyx_v_self->master->propsCdf, (((sizeof(__pyx_v_self->master->propsCdf)) / 
(sizeof(double))) - 1), (sizeof(double)), 
__pyx_f_4Crux_3Mc3_5Chain__propsCdfCmp)) - 
((uintptr_t)__pyx_v_self->master->propsCdf)) / (sizeof(double)));
                                                                                
                                                                                
                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:89:20: note: passing argument to parameter here
            size_t, int (*)(const void *, const void *));
                          ^
3 warnings generated.
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Mc3/Chain.so 
build/run/pkg/Crux/Mc3/Chain.o build/run/share/Crux/lib/libCx.so -lm  -lpthread 
-L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Mc3/Post.pyx --outfile=build/run/pkg/Crux/Mc3/Post.pyx
/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/Mc3/Post.c build/run/pkg/Crux/Mc3/Post.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Mc3/Post.c 
-obuild/run/pkg/Crux/Mc3/Post.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Mc3/Post.so 
build/run/pkg/Crux/Mc3/Post.o build/run/share/Crux/lib/libCx.so -lm  -lpthread 
-L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Newick.pyx --outfile=build/run/pkg/Crux/Newick.pyx
/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/Newick.c build/run/pkg/Crux/Newick.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Newick.c 
-obuild/run/pkg/Crux/Newick.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Newick.so 
build/run/pkg/Crux/Newick.o build/run/share/Crux/lib/libCx.so -lm  -lpthread 
-L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Taxa.pyx --outfile=build/run/pkg/Crux/Taxa.pyx
/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/Taxa.c build/run/pkg/Crux/Taxa.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Taxa.c 
-obuild/run/pkg/Crux/Taxa.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Taxa.so 
build/run/pkg/Crux/Taxa.o build/run/share/Crux/lib/libCx.so -lm  -lpthread 
-L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Tree/Bipart.pyx --outfile=build/run/pkg/Crux/Tree/Bipart.pyx
/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/Tree/Bipart.c build/run/pkg/Crux/Tree/Bipart.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/Bipart.c 
-obuild/run/pkg/Crux/Tree/Bipart.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Tree/Bipart.so 
build/run/pkg/Crux/Tree/Bipart.o build/run/share/Crux/lib/libCx.so -lm  
-lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Tree/Lik.pyx --outfile=build/run/pkg/Crux/Tree/Lik.pyx
/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/Tree/Lik.c build/run/pkg/Crux/Tree/Lik.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/Lik.c 
-obuild/run/pkg/Crux/Tree/Lik.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Tree/Lik.so 
build/run/pkg/Crux/Tree/Lik.o build/run/share/Crux/lib/libCx.so -lm  -lpthread 
-L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Tree/Sumt.pyx --outfile=build/run/pkg/Crux/Tree/Sumt.pyx
/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/Tree/Sumt.c build/run/pkg/Crux/Tree/Sumt.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/Sumt.c 
-obuild/run/pkg/Crux/Tree/Sumt.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Tree/Sumt.so 
build/run/pkg/Crux/Tree/Sumt.o build/run/share/Crux/lib/libCx.so -lm  -lpthread 
-L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Parsing.pyx 
--outfile=build/run/pkg/Parsing.pyx
/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/Parsing.c build/run/pkg/Parsing.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Parsing.c 
-obuild/run/pkg/Parsing.o
build/run/pkg/Parsing.c:34989:24: warning: equality comparison with extraneous 
parentheses [-Wparentheses-equality]
  if ((__pyx_v_pathLen == -1)) {
       ~~~~~~~~~~~~~~~~^~~~~
build/run/pkg/Parsing.c:34989:24: note: remove extraneous parentheses around 
the comparison to silence this warning
  if ((__pyx_v_pathLen == -1)) {
      ~                ^    ~
build/run/pkg/Parsing.c:34989:24: note: use '=' to turn this equality 
comparison into an assignment
  if ((__pyx_v_pathLen == -1)) {
                       ^~
                       =
1 warning generated.
cc -shared 
-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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Parsing.so 
build/run/pkg/Parsing.o -lm  -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 
-L/usr/local/bin -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/DistMatrix/__init__.pyx 
--outfile=build/run/pkg/Crux/DistMatrix/__init__.pyx
/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/DistMatrix/__init__.c 
build/run/pkg/Crux/DistMatrix/__init__.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/DistMatrix/__init__.c 
-obuild/run/pkg/Crux/DistMatrix/__init__.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/DistMatrix/__init__.so 
build/run/pkg/Crux/DistMatrix/__init__.o build/run/share/Crux/lib/libCx.so -lm  
-lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Mc3/__init__.pyx --outfile=build/run/pkg/Crux/Mc3/__init__.pyx
/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/Mc3/__init__.c build/run/pkg/Crux/Mc3/__init__.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Mc3/__init__.c 
-obuild/run/pkg/Crux/Mc3/__init__.o
build/run/pkg/Crux/Mc3/__init__.c:13665:82: warning: incompatible pointer types 
passing 'int (void *, void *)' to parameter of type 'int (*)(const void *, 
const void *)' [-Wincompatible-pointer-types]
    qsort(__pyx_v_rcovScratch, (__pyx_v_past - __pyx_v_first), 
(sizeof(double)), __pyx_f_4Crux_3Mc3__lnLCmp);
                                                                                
 ^~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/stdlib.h:103:12: note: passing argument to parameter here
            int (*)(const void *, const void *));
                  ^
1 warning generated.
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Mc3/__init__.so 
build/run/pkg/Crux/Mc3/__init__.o build/run/share/Crux/lib/libCx.so -lm  
-lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Tree/__init__.pyx 
--outfile=build/run/pkg/Crux/Tree/__init__.pyx
/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/Tree/__init__.c build/run/pkg/Crux/Tree/__init__.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/__init__.c 
-obuild/run/pkg/Crux/Tree/__init__.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Tree/__init__.so 
build/run/pkg/Crux/Tree/__init__.o build/run/share/Crux/lib/libCx.so -lm  
-lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/__init__.pyx --outfile=build/run/pkg/Crux/__init__.pyx
/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/__init__.c build/run/pkg/Crux/__init__.pyx
cc -O2 -pipe  -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 -O2 -pipe 
-fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/__init__.c 
-obuild/run/pkg/Crux/__init__.o
cc -shared 
-Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib
  -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/gcc5  -L/usr/local/lib/gcc5 
-B/usr/local/bin -L/usr/local/lib -lpython2.7 -L/usr/local/lib -lintl -lutil 
-lm -Wl,--export-dynamic -o build/run/site-packages/Crux/__init__.so 
build/run/pkg/Crux/__init__.o build/run/share/Crux/lib/libCx.so -lm  -lpthread 
-L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0 
-L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../../../../aarch64-portbld-freebsd11.0/lib
 -L/usr/local/lib/gcc5/gcc/aarch64-portbld-freebsd11.0/5.4.0/../../.. 
-lgfortran -lm -lpthread
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=bin/MrRogers 
--outfile=build/run/bin/MrRogers
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=bin/crux 
--outfile=build/run/bin/crux
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=bin/redpoint 
--outfile=build/run/bin/redpoint
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Config.py --outfile=build/run/site-packages/Crux/Config.py
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/Copying.py --outfile=build/run/site-packages/Crux/Copying.py
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/DistMatrix/__init__.py 
--outfile=build/run/site-packages/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/site-packages/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/site-packages/Crux/Tree/__init__.py
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r 
--infile=pkg/Crux/__init__.py --outfile=build/run/site-packages/Crux/__init__.py
build/run/bin/crux --verbose pickles.cx
Traceback (most recent call last):
  File "build/run/bin/crux", line 10, in <module>
    import Crux
ImportError: /lib/libgcc_s.so.1: version GCC_4.5.0 required by 
/usr/local/lib/gcc5/libgfortran.so.3 not found
gmake[1]: *** [Makefile:125: pickles] 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
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