Date: Thu, 2 Mar 2017 07:26:31 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 110armv6-quarterly][biology/crux] Failed for crux-1.2.0_6 in build Message-ID: <201703020726.v227QV1A097280@beefy15.nyi.freebsd.org>
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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@FreeBSD.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: branches/2017Q1/biology/crux/Makefile 428057 2016-12-07 13:24:56Z gerald $ Log URL: http://beefy15.nyi.freebsd.org/data/110armv6-quarterly/435165/logs/crux-1.2.0_6.log Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=110armv6-quarterly&build=435165 Log: ====>> Building biology/crux build started at Thu Mar 2 07:16:57 UTC 2017 port directory: /usr/ports/biology/crux building for: FreeBSD 110armv6-quarterly-job-04 11.0-RELEASE-p8 FreeBSD 11.0-RELEASE-p8 r314125 arm maintained by: ports@FreeBSD.org Makefile ident: $FreeBSD: branches/2017Q1/biology/crux/Makefile 428057 2016-12-07 13:24:56Z gerald $ Poudriere version: 3.1.14 Host OSVERSION: 1200020 Jail OSVERSION: 1100122 Job Id: 04 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p8 r314125 UNAME_r=11.0-RELEASE-p8 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110armv6-quarterly/ref QEMU_EMULATING=1 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=crux-1.2.0_6 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110armv6-quarterly/ref/.p/pool MASTERNAME=110armv6-quarterly SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.14 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_6: 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="gfortran49" FC="gfortran49" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc49" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc49" 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="gfortran49" FC="gfortran49" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc49" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc49" 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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -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/gcc49 -L /usr/local/lib/gcc49 -B/usr/local/bin" LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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_VER=2.7 PYTHON_VERSION=python2.7 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--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} #### /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=armv6 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-p8 #### Misc Poudriere #### GID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.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 MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 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_6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.9.4_1.txz pkg-static: Warning: Major OS version upgrade detected. Running "pkg-static install -f pkg" recommended [110armv6-quarterly-job-04] Installing pkg-1.9.4_1... [110armv6-quarterly-job-04] Extracting pkg-1.9.4_1: .......... done ===> crux-1.2.0_6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of crux-1.2.0_6 =========================================================================== =======================<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 <snip> gfortran49 -Wl,-rpath=/usr/local/lib/gcc49 -fPIC -c lib/LAPACK/ilaenv.f -o build/lib/LAPACK/ilaenv.o gfortran49 -Wl,-rpath=/usr/local/lib/gcc49 -fPIC -c lib/LAPACK/iparmq.f -o build/lib/LAPACK/iparmq.o /nxb-bin/usr/bin/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 /nxb-bin/usr/bin/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 /nxb-bin/usr/bin/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 /nxb-bin/usr/bin/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 /nxb-bin/usr/bin/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 /nxb-bin/usr/bin/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 /nxb-bin/usr/bin/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 /nxb-bin/usr/bin/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 /nxb-bin/usr/bin/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 /nxb-bin/usr/bin/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 /nxb-bin/usr/bin/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 /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/gcc49 -L/usr/local/lib/gcc49 -B/usr/local/bin -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 (0.40 seconds) Pickling lexicon... Done (0.07 seconds) /nxb-bin/usr/bin/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. /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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. /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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. /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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. /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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 -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 /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/gcc49 -L/usr/local/lib/gcc49 -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/gcc49 -L/usr/local/bin -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4 -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../../../../armv6-portbld-freebsd11.0/lib -L/usr/local/lib/gcc49/gcc/armv6-portbld-freebsd11.0/4.9.4/../../.. -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/gcc49/libgfortran.so.3: Undefined symbol "__aeabi_ldivmod" 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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