[package - head-armv6-default][biology/crux] Failed for crux-1.2.0_5 in build

pkg-fallout at FreeBSD.org pkg-fallout at FreeBSD.org
Sat Dec 12 09:57:14 UTC 2015 

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:     ports at FreeBSD.org
Last committer: danfe at FreeBSD.org
Ident:          $FreeBSD: head/biology/crux/Makefile 395826 2015-09-02 09:23:05Z danfe $
Log URL:        http://beefy8.nyi.freebsd.org/data/head-armv6-default/p403218_s291949/logs/crux-1.2.0_5.log
Build URL:      http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p403218_s291949
Log:

====>> Building biology/crux
build started at Sat Dec 12 09:37:22 UTC 2015
port directory: /usr/ports/biology/crux
building for: FreeBSD head-armv6-default-job-07 11.0-CURRENT FreeBSD 11.0-CURRENT r291949 arm
maintained by: ports at FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/crux/Makefile 395826 2015-09-02 09:23:05Z danfe $
Poudriere version: 3.1.10
Host OSVERSION: 1100085
Jail OSVERSION: 1100091




!!! Jail is newer than host. (Jail: 1100091, Host: 1100085) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



---Begin Environment---
SHELL=/bin/csh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1100091
UNAME_v=FreeBSD 11.0-CURRENT r291949
UNAME_r=11.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=screen
QEMU_EMULATING=1
MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-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_5
OLDPWD=/
PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool
MASTERNAME=head-armv6-default
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.10
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
---End Environment---

---Begin OPTIONS List---
===> The following configuration options are available for crux-1.2.0_5:
     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="gfortran48" FC="gfortran48" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc48" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc48" 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="gfortran48" FC="gfortran48" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc48" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc48" 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 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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -mfloat-abi=softfp  -fno-strict-aliasing -std=gnu99"  CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-I/usr/local/include"  LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc48  -L/usr/local/lib/gcc48
  -B/usr/local/bin" LIBS=""  CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -mfloat-abi=softfp -fno-strict-aliasing "  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 444"  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_SITELIBDIR=lib/python2.7/site-packages
PYTHON_VERSION=python2.7
PYTHON_VER=2.7
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---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
READELF=/nxb-bin/usr/bin/readelf
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
NM=/nxb-bin/usr/bin/nm
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
AS=/nxb-bin/usr/bin/as
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
<snip>
gfortran48 -Wl,-rpath=/usr/local/lib/gcc48  -fPIC -c lib/LAPACK/iparmq.f -o build/lib/LAPACK/iparmq.o
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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
/nxb-bin/usr/bin/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/dg
 etrf.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 b
 uild/lib/LAPACK/dtrevc.o build/lib/LAPACK/dt!
 rexc.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/gcc48  -L/usr/local/lib/gcc48 -B/usr/local/bin -lm  -lpthread -L/usr/local/lib -L/usr/local/lib/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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 (0.89 seconds)
Pickling lexicon...
Done (0.15 seconds)
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -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.
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Character.c -obuild/run/pkg/Crux/Character.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/DistMatrix/Nj.c -obuild/run/pkg/Crux/DistMatrix/Nj.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Fasta.c -obuild/run/pkg/Crux/Fasta.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -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.
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Mc3/Post.c -obuild/run/pkg/Crux/Mc3/Post.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Newick.c -obuild/run/pkg/Crux/Newick.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Taxa.c -obuild/run/pkg/Crux/Taxa.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/Bipart.c -obuild/run/pkg/Crux/Tree/Bipart.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/Lik.c -obuild/run/pkg/Crux/Tree/Lik.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/Sumt.c -obuild/run/pkg/Crux/Tree/Sumt.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -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.
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/DistMatrix/__init__.c -obuild/run/pkg/Crux/DistMatrix/__init__.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -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.
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/__init__.c -obuild/run/pkg/Crux/Tree/__init__.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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
/nxb-bin/usr/bin/cc -O2 -pipe -mfloat-abi=softfp  -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 -mfloat-abi=softfp -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/__init__.c -obuild/run/pkg/Crux/__init__.o
/nxb-bin/usr/bin/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/gcc48  -L/usr/local/lib/gcc48 -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/gcc48 -L/usr/local/bin -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5 -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc48/gcc/armv6-portbld-freebsd11.0/4.8.5/../../.. -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: /usr/local/lib/gcc48/libgfortran.so.3: Undefined symbol "__aeabi_ldivmod"
Makefile:125: recipe for target 'pickles' failed
gmake[1]: *** [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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