=> Building biology/crux Started : Sunday, 8 OCT 2017 at 19:40:51 UTC Platform: 4.9-DEVELOPMENT DragonFly v4.9.0.699.g39a93-DEVELOPMENT #22: Tue Sep 19 22:06:52 PDT 2017 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.1-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.1-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for crux-1.2.0_8: SYS_LINALG=off: Enable system ATLAS/LAPACK ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" MAKE=gmake PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/construction/biology/crux XDG_CONFIG_HOME=/construction/biology/crux HOME=/construction/biology/crux TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 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=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --datadir=/usr/local/lib --with-python=/usr/local/bin/python2.7 --disable-mpi --disable-sys-linalg --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/construction/biology/crux XDG_CONFIG_HOME=/construction/biology/crux HOME=/construction/biology/crux TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 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" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing -std=gnu99" CPP="cpp" CPPFLAGS="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/crux/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/crux" EXAMPLESDIR="share/examples/crux" DATADIR="share/crux" WWWDIR="www/crux" ETCDIR="etc/crux" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500100 OSVERSION=9999999 OSREL=5.1 _OSRELEASE=5.1-SYNTH -------------------------------------------------------------------------------- -- 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_8 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz Installing pkg-1.10.1... Extracting pkg-1.10.1: .......... done ===> crux-1.2.0_8 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of crux-1.2.0_8 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: The crux port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License BSD2CLAUSE BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by crux-1.2.0_8 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: The crux port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License BSD2CLAUSE BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by crux-1.2.0_8 for building => SHA256 Checksum OK for crux-1.2.0.tar.bz2. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: The crux port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> License BSD2CLAUSE BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by crux-1.2.0_8 for building ===> Extracting for crux-1.2.0_8 => SHA256 Checksum OK for crux-1.2.0.tar.bz2. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for crux-1.2.0_8 ===> Applying ports patches for crux-1.2.0_8 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> crux-1.2.0_8 depends on executable: gfortran5 - not found ===> Installing existing package /packages/All/gcc5-5.4.0_4.txz Installing gcc5-5.4.0_4... `-- Installing binutils-2.28,1... | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.2.6... | | `-- Extracting indexinfo-0.2.6: .... done | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done `-- Extracting binutils-2.28,1: .......... done `-- Installing gmp-6.1.2... `-- Extracting gmp-6.1.2: .......... done `-- Installing mpc-1.0.3... | `-- Installing mpfr-3.1.6... | `-- Extracting mpfr-3.1.6: .......... done `-- Extracting mpc-1.0.3: ...... done Extracting gcc5-5.4.0_4: .......... done Message from gcc5-5.4.0_4: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> crux-1.2.0_8 depends on executable: gfortran5 - found ===> Returning to build of crux-1.2.0_8 ===> crux-1.2.0_8 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... Extracting gmake-4.2.1_1: .......... done ===> crux-1.2.0_8 depends on executable: gmake - found ===> Returning to build of crux-1.2.0_8 ===> crux-1.2.0_8 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.14.txz Installing python27-2.7.14... `-- Installing expat-2.2.1... `-- Extracting expat-2.2.1: .......... done `-- Installing libffi-3.2.1_1... `-- Extracting libffi-3.2.1_1: .......... done `-- Installing libressl-2.5.5... `-- Extracting libressl-2.5.5: .......... done `-- Installing ncurses-6.0_3... `-- Extracting ncurses-6.0_3: .......... done `-- Installing readline-7.0.3... `-- Extracting readline-7.0.3: .......... done Extracting python27-2.7.14: .......... done Message from ncurses-6.0_3: ===> NOTICE: The ncurses 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 Message from python27-2.7.14: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> crux-1.2.0_8 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of crux-1.2.0_8 ===> crux-1.2.0_8 depends on file: /usr/local/bin/as - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for crux-1.2.0_8 configure: loading site script /xports/Templates/config.site checking for gcc... cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking size of void *... 8 checking build system type... x86_64-portbld-dragonfly5.1 checking host system type... x86_64-portbld-dragonfly5.1 Unsupported operating system: x86_64-portbld-dragonfly5.1 checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... /usr/local/bin/ranlib checking for ar... /usr/local/bin/ar checking for ld... /usr/local/bin/ld checking for test... /bin/test checking for grep... /usr/bin/grep checking for autoconf... no checking pthread.h usability... yes checking pthread.h presence... yes checking for pthread.h... yes checking for pthread_create in -lpthread... yes checking for python >= 2.5.0... 2.7.14 checking for python-config... /usr/local/bin/python2.7-config checking python site-packages path... /usr/local/lib/python2.7/site-packages checking whether byte ordering is bigendian... no checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for log in -lm... yes checking for posix_memalign... yes checking for mallopt... no checking whether we are using the GNU Fortran compiler... yes checking whether gfortran5 accepts -g... yes checking how to get verbose linking output from gfortran5... -v checking for Fortran libraries of gfortran5... -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath configure: creating ./config.status config.status: creating Makefile config.status: creating cfgoutputs.stamp config.status: creating cfg config.status: creating cydep config.status: creating cython config.status: creating lib/Crux/Cx_defs.h config.status: creating cfghdrs.stamp =============================================================================== Crux version : 1.2.0 PYTHON : /usr/local/bin/python2.7 CYTHON : /construction/biology/crux/crux-1.2.0/cython FLEX : CC : cc CPPFLAGS : -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT MTCPPFLAGS : -DMEXP=19937 -DHAVE_SSE2=1 CFLAGS : -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse MTCFLAGS : -fno-strict-aliasing FC : gfortran5 FCFLAGS : -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse LDFLAGS : -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin LIBS : -lm -lpthread FCLIBS : -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath RPATH_EXTRA : site_packages : /usr/local/lib/python2.7/site-packages PREFIX : /usr/local BINDIR : /usr/local/bin DATADIR : /usr/local/lib MANDIR : /usr/local/man srcroot : abs_srcroot : /construction/biology/crux/crux-1.2.0/ objroot : abs_objroot : /construction/biology/crux/crux-1.2.0/ autogen : 0 flex : 0 debug : 0 cc-silence : 0 inlines : 1 sys-linalg : 0 mpi : 0 =============================================================================== -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for crux-1.2.0_8 gmake[1]: Entering directory '/construction/biology/crux/crux-1.2.0' cp -R contrib/cython build/contrib gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/daxpy.f -o build/lib/BLAS/daxpy.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/dcopy.f -o build/lib/BLAS/dcopy.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/ddot.f -o build/lib/BLAS/ddot.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/dgemm.f -o build/lib/BLAS/dgemm.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/dgemv.f -o build/lib/BLAS/dgemv.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/dger.f -o build/lib/BLAS/dger.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/dnrm2.f -o build/lib/BLAS/dnrm2.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/drot.f -o build/lib/BLAS/drot.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/dscal.f -o build/lib/BLAS/dscal.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/dswap.f -o build/lib/BLAS/dswap.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/dtrmm.f -o build/lib/BLAS/dtrmm.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/dtrmv.f -o build/lib/BLAS/dtrmv.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/dtrsm.f -o build/lib/BLAS/dtrsm.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/idamax.f -o build/lib/BLAS/idamax.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/lsame.f -o build/lib/BLAS/lsame.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/BLAS/xerbla.f -o build/lib/BLAS/xerbla.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dgebak.f -o build/lib/LAPACK/dgebak.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dgebal.f -o build/lib/LAPACK/dgebal.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dgeev.f -o build/lib/LAPACK/dgeev.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dgehd2.f -o build/lib/LAPACK/dgehd2.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dgehrd.f -o build/lib/LAPACK/dgehrd.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dgetf2.f -o build/lib/LAPACK/dgetf2.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dgetrf.f -o build/lib/LAPACK/dgetrf.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dgetri.f -o build/lib/LAPACK/dgetri.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dhseqr.f -o build/lib/LAPACK/dhseqr.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/disnan.f -o build/lib/LAPACK/disnan.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlabad.f -o build/lib/LAPACK/dlabad.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlacpy.f -o build/lib/LAPACK/dlacpy.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dladiv.f -o build/lib/LAPACK/dladiv.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaexc.f -o build/lib/LAPACK/dlaexc.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlahqr.f -o build/lib/LAPACK/dlahqr.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlahr2.f -o build/lib/LAPACK/dlahr2.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaisnan.f -o build/lib/LAPACK/dlaisnan.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaln2.f -o build/lib/LAPACK/dlaln2.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlamch.f -o build/lib/LAPACK/dlamch.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlange.f -o build/lib/LAPACK/dlange.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlanv2.f -o build/lib/LAPACK/dlanv2.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlapy2.f -o build/lib/LAPACK/dlapy2.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr0.f -o build/lib/LAPACK/dlaqr0.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr1.f -o build/lib/LAPACK/dlaqr1.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr2.f -o build/lib/LAPACK/dlaqr2.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr3.f -o build/lib/LAPACK/dlaqr3.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr4.f -o build/lib/LAPACK/dlaqr4.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaqr5.f -o build/lib/LAPACK/dlaqr5.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlarf.f -o build/lib/LAPACK/dlarf.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlarfb.f -o build/lib/LAPACK/dlarfb.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlarfg.f -o build/lib/LAPACK/dlarfg.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlarft.f -o build/lib/LAPACK/dlarft.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlarfx.f -o build/lib/LAPACK/dlarfx.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlartg.f -o build/lib/LAPACK/dlartg.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlascl.f -o build/lib/LAPACK/dlascl.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaset.f -o build/lib/LAPACK/dlaset.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlassq.f -o build/lib/LAPACK/dlassq.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlaswp.f -o build/lib/LAPACK/dlaswp.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dlasy2.f -o build/lib/LAPACK/dlasy2.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dorg2r.f -o build/lib/LAPACK/dorg2r.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dorghr.f -o build/lib/LAPACK/dorghr.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dorgqr.f -o build/lib/LAPACK/dorgqr.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dorm2r.f -o build/lib/LAPACK/dorm2r.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dormhr.f -o build/lib/LAPACK/dormhr.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dormqr.f -o build/lib/LAPACK/dormqr.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dtrevc.f -o build/lib/LAPACK/dtrevc.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dtrexc.f -o build/lib/LAPACK/dtrexc.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dtrti2.f -o build/lib/LAPACK/dtrti2.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/dtrtri.f -o build/lib/LAPACK/dtrtri.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/ieeeck.f -o build/lib/LAPACK/ieeeck.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/iladlc.f -o build/lib/LAPACK/iladlc.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/iladlr.f -o build/lib/LAPACK/iladlr.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/ilaenv.f -o build/lib/LAPACK/ilaenv.o gfortran5 -Wl,-rpath=/usr/local/lib/gcc5 -mfpmath=sse -fPIC -c lib/LAPACK/iparmq.f -o build/lib/LAPACK/iparmq.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/Cx.c -obuild/lib/Crux/Cx.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxAmd64.c -obuild/lib/Crux/CxAmd64.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxIa32.c -obuild/lib/Crux/CxIa32.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxMat.c -obuild/lib/Crux/CxMat.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxMq.c -obuild/lib/Crux/CxMq.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxPpc.c -obuild/lib/Crux/CxPpc.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxRi.c -obuild/lib/Crux/CxRi.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/Tree/CxLik.c -obuild/lib/Crux/Tree/CxLik.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -fno-strict-aliasing -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -DMEXP=19937 -DHAVE_SSE2=1 -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/SFMT/SFMT.c -obuild/lib/SFMT/SFMT.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxNewickLexer.c -obuild/lib/Crux/CxNewickLexer.o cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/DistMatrix/CxDistMatrixLexer.c -obuild/lib/Crux/DistMatrix/CxDistMatrixLexer.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -Wl,-soname,libCx.so -o build/run/share/Crux/lib/libCx.so build/lib/Crux/Cx.o build/lib/Crux/CxAmd64.o build/lib/Crux/CxIa32.o build/lib/Crux/CxMat.o build/lib/Crux/CxMq.o build/lib/Crux/CxPpc.o build/lib/Crux/CxRi.o build/lib/Crux/Tree/CxLik.o build/lib/SFMT/SFMT.o build/lib/Crux/CxNewickLexer.o build/lib/Crux/DistMatrix/CxDistMatrixLexer.o build/lib/BLAS/daxpy.o build/lib/BLAS/dcopy.o build/lib/BLAS/ddot.o build/lib/BLAS/dgemm.o build/lib/BLAS/dgemv.o build/lib/BLAS/dger.o build/lib/BLAS/dnrm2.o build/lib/BLAS/drot.o build/lib/BLAS/dscal.o build/lib/BLAS/dswap.o build/lib/BLAS/dtrmm.o build/lib/BLAS/dtrmv.o build/lib/BLAS/dtrsm.o build/lib/BLAS/idamax.o build/lib/BLAS/lsame.o build/lib/BLAS/xerbla.o build/lib/LAPACK/dgebak.o build/lib/LAPACK/dgebal.o build/lib/LAPACK/dgeev.o build/lib/LAPACK/dgehd2.o build/lib/LAPACK/dgehrd.o build/lib/LAPACK/dgetf2.o build/lib/LAPACK/dgetrf.o build/lib/LAPACK/dgetri.o build/lib/LAPACK/dhseqr.o build/lib/LAPACK/disnan.o build/lib/LAPACK/dlabad.o build/lib/LAPACK/dlacpy.o build/lib/LAPACK/dladiv.o build/lib/LAPACK/dlaexc.o build/lib/LAPACK/dlahqr.o build/lib/LAPACK/dlahr2.o build/lib/LAPACK/dlaisnan.o build/lib/LAPACK/dlaln2.o build/lib/LAPACK/dlamch.o build/lib/LAPACK/dlange.o build/lib/LAPACK/dlanv2.o build/lib/LAPACK/dlapy2.o build/lib/LAPACK/dlaqr0.o build/lib/LAPACK/dlaqr1.o build/lib/LAPACK/dlaqr2.o build/lib/LAPACK/dlaqr3.o build/lib/LAPACK/dlaqr4.o build/lib/LAPACK/dlaqr5.o build/lib/LAPACK/dlarf.o build/lib/LAPACK/dlarfb.o build/lib/LAPACK/dlarfg.o build/lib/LAPACK/dlarft.o build/lib/LAPACK/dlarfx.o build/lib/LAPACK/dlartg.o build/lib/LAPACK/dlascl.o build/lib/LAPACK/dlaset.o build/lib/LAPACK/dlassq.o build/lib/LAPACK/dlaswp.o build/lib/LAPACK/dlasy2.o build/lib/LAPACK/dorg2r.o build/lib/LAPACK/dorghr.o build/lib/LAPACK/dorgqr.o build/lib/LAPACK/dorm2r.o build/lib/LAPACK/dormhr.o build/lib/LAPACK/dormqr.o build/lib/LAPACK/dtrevc.o build/lib/LAPACK/dtrexc.o build/lib/LAPACK/dtrti2.o build/lib/LAPACK/dtrtri.o build/lib/LAPACK/ieeeck.o build/lib/LAPACK/iladlc.o build/lib/LAPACK/iladlr.o build/lib/LAPACK/ilaenv.o build/lib/LAPACK/iparmq.o -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/CTMatrix.pyx --outfile=build/run/pkg/Crux/CTMatrix.pyx /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/CTMatrix.pxd --outfile=build/run/pkg/Crux/CTMatrix.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Character.pxd --outfile=build/run/pkg/Crux/Character.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/DistMatrix/Nj.pxd --outfile=build/run/pkg/Crux/DistMatrix/Nj.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Fasta.pxd --outfile=build/run/pkg/Crux/Fasta.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/Chain.pxd --outfile=build/run/pkg/Crux/Mc3/Chain.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/Post.pxd --outfile=build/run/pkg/Crux/Mc3/Post.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Newick.pxd --outfile=build/run/pkg/Crux/Newick.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Taxa.pxd --outfile=build/run/pkg/Crux/Taxa.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/Bipart.pxd --outfile=build/run/pkg/Crux/Tree/Bipart.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/Lik.pxd --outfile=build/run/pkg/Crux/Tree/Lik.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/Sumt.pxd --outfile=build/run/pkg/Crux/Tree/Sumt.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Parsing.pxd --outfile=build/run/pkg/Parsing.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/DistMatrix/__init__.pxd --outfile=build/run/pkg/Crux/DistMatrix/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/__init__.pxd --outfile=build/run/pkg/Crux/Mc3/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/__init__.pxd --outfile=build/run/pkg/Crux/Tree/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/__init__.pxd --outfile=build/run/pkg/Crux/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=lib/Crux/Cx.pxd --outfile=build/run/lib/Crux/Cx.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=lib/Crux/CxMat.pxd --outfile=build/run/lib/Crux/CxMat.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=lib/Crux/CxMath.pxd --outfile=build/run/lib/Crux/CxMath.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=lib/Crux/CxNewickLexer.pxd --outfile=build/run/lib/Crux/CxNewickLexer.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=lib/Crux/CxRi.pxd --outfile=build/run/lib/Crux/CxRi.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=lib/Crux/DistMatrix/CxDistMatrixLexer.pxd --outfile=build/run/lib/Crux/DistMatrix/CxDistMatrixLexer.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=lib/Crux/Tree/CxLik.pxd --outfile=build/run/lib/Crux/Tree/CxLik.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=lib/SFMT/SFMT.pxd --outfile=build/run/lib/SFMT/SFMT.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=lib/libc.pxd --outfile=build/run/lib/libc.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=lib/libm.pxd --outfile=build/run/lib/libm.pxd /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Config.py --outfile=build/run/pkg/Crux/Config.py /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Copying.py --outfile=build/run/pkg/Crux/Copying.py /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/DistMatrix/__init__.py --outfile=build/run/pkg/Crux/DistMatrix/__init__.py /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/__init__.py --outfile=build/run/pkg/Crux/Mc3/__init__.py /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/__init__.py --outfile=build/run/pkg/Crux/Tree/__init__.py /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/__init__.py --outfile=build/run/pkg/Crux/__init__.py /usr/local/bin/python2.7 /construction/biology/crux/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 (0.04 seconds) Pickling lexicon... Done (0.00 seconds) cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/CTMatrix.c -obuild/run/pkg/Crux/CTMatrix.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/CTMatrix.so build/run/pkg/Crux/CTMatrix.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Character.pyx --outfile=build/run/pkg/Crux/Character.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Character.c build/run/pkg/Crux/Character.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Character.c -obuild/run/pkg/Crux/Character.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Character.so build/run/pkg/Crux/Character.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/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 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/DistMatrix/Nj.c build/run/pkg/Crux/DistMatrix/Nj.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/DistMatrix/Nj.c -obuild/run/pkg/Crux/DistMatrix/Nj.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/DistMatrix/Nj.so build/run/pkg/Crux/DistMatrix/Nj.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Fasta.pyx --outfile=build/run/pkg/Crux/Fasta.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Fasta.c build/run/pkg/Crux/Fasta.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Fasta.c -obuild/run/pkg/Crux/Fasta.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Fasta.so build/run/pkg/Crux/Fasta.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/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 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Mc3/Chain.c build/run/pkg/Crux/Mc3/Chain.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -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: In function '__pyx_f_4Crux_3Mc3_5Chain_5Chain_advance0': build/run/pkg/Crux/Mc3/Chain.c:14528:178: warning: passing argument 5 of 'bsearch' from incompatible pointer type [-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))); ^ In file included from /usr/local/include/python2.7/Python.h:42:0, from build/run/pkg/Crux/Mc3/Chain.c:4: /usr/include/stdlib.h:91:7: note: expected 'int (*)(const void *, const void *)' but argument is of type 'int (*)(void *, void *)' void *bsearch(const void *, const void *, size_t, ^ cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Mc3/Chain.so build/run/pkg/Crux/Mc3/Chain.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/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 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Mc3/Post.c build/run/pkg/Crux/Mc3/Post.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Mc3/Post.c -obuild/run/pkg/Crux/Mc3/Post.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Mc3/Post.so build/run/pkg/Crux/Mc3/Post.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Newick.pyx --outfile=build/run/pkg/Crux/Newick.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Newick.c build/run/pkg/Crux/Newick.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Newick.c -obuild/run/pkg/Crux/Newick.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Newick.so build/run/pkg/Crux/Newick.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Taxa.pyx --outfile=build/run/pkg/Crux/Taxa.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Taxa.c build/run/pkg/Crux/Taxa.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Taxa.c -obuild/run/pkg/Crux/Taxa.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Taxa.so build/run/pkg/Crux/Taxa.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/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 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Tree/Bipart.c build/run/pkg/Crux/Tree/Bipart.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/Bipart.c -obuild/run/pkg/Crux/Tree/Bipart.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Tree/Bipart.so build/run/pkg/Crux/Tree/Bipart.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/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 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Tree/Lik.c build/run/pkg/Crux/Tree/Lik.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/Lik.c -obuild/run/pkg/Crux/Tree/Lik.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Tree/Lik.so build/run/pkg/Crux/Tree/Lik.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/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 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Tree/Sumt.c build/run/pkg/Crux/Tree/Sumt.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/Sumt.c -obuild/run/pkg/Crux/Tree/Sumt.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Tree/Sumt.so build/run/pkg/Crux/Tree/Sumt.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Parsing.pyx --outfile=build/run/pkg/Parsing.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Parsing.c build/run/pkg/Parsing.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Parsing.c -obuild/run/pkg/Parsing.o cc -shared -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Parsing.so build/run/pkg/Parsing.o -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/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 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/DistMatrix/__init__.c build/run/pkg/Crux/DistMatrix/__init__.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/DistMatrix/__init__.c -obuild/run/pkg/Crux/DistMatrix/__init__.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/DistMatrix/__init__.so build/run/pkg/Crux/DistMatrix/__init__.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/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 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Mc3/__init__.c build/run/pkg/Crux/Mc3/__init__.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -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: In function '__pyx_f_4Crux_3Mc3_3Mc3_computeRcovUni': build/run/pkg/Crux/Mc3/__init__.c:13665:82: warning: passing argument 4 of 'qsort' from incompatible pointer type [-Wincompatible-pointer-types] qsort(__pyx_v_rcovScratch, (__pyx_v_past - __pyx_v_first), (sizeof(double)), __pyx_f_4Crux_3Mc3__lnLCmp); ^ In file included from /usr/local/include/python2.7/Python.h:42:0, from build/run/pkg/Crux/Mc3/__init__.c:4: /usr/include/stdlib.h:106:7: note: expected 'int (*)(const void *, const void *)' but argument is of type 'int (*)(void *, void *)' void qsort(void *, size_t, size_t, int (*)(const void *, const void *)); ^ cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Mc3/__init__.so build/run/pkg/Crux/Mc3/__init__.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/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 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/Tree/__init__.c build/run/pkg/Crux/Tree/__init__.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/Tree/__init__.c -obuild/run/pkg/Crux/Tree/__init__.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/Tree/__init__.so build/run/pkg/Crux/Tree/__init__.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/__init__.pyx --outfile=build/run/pkg/Crux/__init__.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/__init__.c build/run/pkg/Crux/__init__.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/__init__.c -obuild/run/pkg/Crux/__init__.o cc -shared -Wl,-rpath,/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/run/site-packages/Crux/__init__.so build/run/pkg/Crux/__init__.o build/run/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -r --infile=bin/MrRogers --outfile=build/run/bin/MrRogers /construction/biology/crux/crux-1.2.0/cfg -r --infile=bin/crux --outfile=build/run/bin/crux /construction/biology/crux/crux-1.2.0/cfg -r --infile=bin/redpoint --outfile=build/run/bin/redpoint /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Config.py --outfile=build/run/site-packages/Crux/Config.py /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Copying.py --outfile=build/run/site-packages/Crux/Copying.py /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/DistMatrix/__init__.py --outfile=build/run/site-packages/Crux/DistMatrix/__init__.py /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/__init__.py --outfile=build/run/site-packages/Crux/Mc3/__init__.py /construction/biology/crux/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/__init__.py --outfile=build/run/site-packages/Crux/Tree/__init__.py /construction/biology/crux/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 Crux, version: 1.2.0, threaded, PID: 322020, PRNG seed: 1284579128 Begin batch processing, 2017/10/08 19:44:15 (UTC) Input file: 'pickles.cx' End batch processing, 2017/10/08 19:44:15 (UTC) cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -Wl,-soname,libCx.so -o build/inst/share/Crux/lib/libCx.so build/lib/Crux/Cx.o build/lib/Crux/CxAmd64.o build/lib/Crux/CxIa32.o build/lib/Crux/CxMat.o build/lib/Crux/CxMq.o build/lib/Crux/CxPpc.o build/lib/Crux/CxRi.o build/lib/Crux/Tree/CxLik.o build/lib/SFMT/SFMT.o build/lib/Crux/CxNewickLexer.o build/lib/Crux/DistMatrix/CxDistMatrixLexer.o build/lib/BLAS/daxpy.o build/lib/BLAS/dcopy.o build/lib/BLAS/ddot.o build/lib/BLAS/dgemm.o build/lib/BLAS/dgemv.o build/lib/BLAS/dger.o build/lib/BLAS/dnrm2.o build/lib/BLAS/drot.o build/lib/BLAS/dscal.o build/lib/BLAS/dswap.o build/lib/BLAS/dtrmm.o build/lib/BLAS/dtrmv.o build/lib/BLAS/dtrsm.o build/lib/BLAS/idamax.o build/lib/BLAS/lsame.o build/lib/BLAS/xerbla.o build/lib/LAPACK/dgebak.o build/lib/LAPACK/dgebal.o build/lib/LAPACK/dgeev.o build/lib/LAPACK/dgehd2.o build/lib/LAPACK/dgehrd.o build/lib/LAPACK/dgetf2.o build/lib/LAPACK/dgetrf.o build/lib/LAPACK/dgetri.o build/lib/LAPACK/dhseqr.o build/lib/LAPACK/disnan.o build/lib/LAPACK/dlabad.o build/lib/LAPACK/dlacpy.o build/lib/LAPACK/dladiv.o build/lib/LAPACK/dlaexc.o build/lib/LAPACK/dlahqr.o build/lib/LAPACK/dlahr2.o build/lib/LAPACK/dlaisnan.o build/lib/LAPACK/dlaln2.o build/lib/LAPACK/dlamch.o build/lib/LAPACK/dlange.o build/lib/LAPACK/dlanv2.o build/lib/LAPACK/dlapy2.o build/lib/LAPACK/dlaqr0.o build/lib/LAPACK/dlaqr1.o build/lib/LAPACK/dlaqr2.o build/lib/LAPACK/dlaqr3.o build/lib/LAPACK/dlaqr4.o build/lib/LAPACK/dlaqr5.o build/lib/LAPACK/dlarf.o build/lib/LAPACK/dlarfb.o build/lib/LAPACK/dlarfg.o build/lib/LAPACK/dlarft.o build/lib/LAPACK/dlarfx.o build/lib/LAPACK/dlartg.o build/lib/LAPACK/dlascl.o build/lib/LAPACK/dlaset.o build/lib/LAPACK/dlassq.o build/lib/LAPACK/dlaswp.o build/lib/LAPACK/dlasy2.o build/lib/LAPACK/dorg2r.o build/lib/LAPACK/dorghr.o build/lib/LAPACK/dorgqr.o build/lib/LAPACK/dorm2r.o build/lib/LAPACK/dormhr.o build/lib/LAPACK/dormqr.o build/lib/LAPACK/dtrevc.o build/lib/LAPACK/dtrexc.o build/lib/LAPACK/dtrti2.o build/lib/LAPACK/dtrtri.o build/lib/LAPACK/ieeeck.o build/lib/LAPACK/iladlc.o build/lib/LAPACK/iladlr.o build/lib/LAPACK/ilaenv.o build/lib/LAPACK/iparmq.o -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/CTMatrix.pyx --outfile=build/inst/pkg/Crux/CTMatrix.pyx /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/CTMatrix.pxd --outfile=build/inst/pkg/Crux/CTMatrix.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Character.pxd --outfile=build/inst/pkg/Crux/Character.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/DistMatrix/Nj.pxd --outfile=build/inst/pkg/Crux/DistMatrix/Nj.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Fasta.pxd --outfile=build/inst/pkg/Crux/Fasta.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/Chain.pxd --outfile=build/inst/pkg/Crux/Mc3/Chain.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/Post.pxd --outfile=build/inst/pkg/Crux/Mc3/Post.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Newick.pxd --outfile=build/inst/pkg/Crux/Newick.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Taxa.pxd --outfile=build/inst/pkg/Crux/Taxa.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/Bipart.pxd --outfile=build/inst/pkg/Crux/Tree/Bipart.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/Lik.pxd --outfile=build/inst/pkg/Crux/Tree/Lik.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/Sumt.pxd --outfile=build/inst/pkg/Crux/Tree/Sumt.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Parsing.pxd --outfile=build/inst/pkg/Parsing.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/DistMatrix/__init__.pxd --outfile=build/inst/pkg/Crux/DistMatrix/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/__init__.pxd --outfile=build/inst/pkg/Crux/Mc3/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/__init__.pxd --outfile=build/inst/pkg/Crux/Tree/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/__init__.pxd --outfile=build/inst/pkg/Crux/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/Cx.pxd --outfile=build/inst/lib/Crux/Cx.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/CxMat.pxd --outfile=build/inst/lib/Crux/CxMat.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/CxMath.pxd --outfile=build/inst/lib/Crux/CxMath.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/CxNewickLexer.pxd --outfile=build/inst/lib/Crux/CxNewickLexer.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/CxRi.pxd --outfile=build/inst/lib/Crux/CxRi.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/DistMatrix/CxDistMatrixLexer.pxd --outfile=build/inst/lib/Crux/DistMatrix/CxDistMatrixLexer.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/Tree/CxLik.pxd --outfile=build/inst/lib/Crux/Tree/CxLik.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/SFMT/SFMT.pxd --outfile=build/inst/lib/SFMT/SFMT.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/libc.pxd --outfile=build/inst/lib/libc.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/libm.pxd --outfile=build/inst/lib/libm.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Config.py --outfile=build/inst/pkg/Crux/Config.py /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Copying.py --outfile=build/inst/pkg/Crux/Copying.py /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/DistMatrix/__init__.py --outfile=build/inst/pkg/Crux/DistMatrix/__init__.py /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/__init__.py --outfile=build/inst/pkg/Crux/Mc3/__init__.py /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/__init__.py --outfile=build/inst/pkg/Crux/Tree/__init__.py /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/__init__.py --outfile=build/inst/pkg/Crux/__init__.py /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/CTMatrix.c build/inst/pkg/Crux/CTMatrix.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/CTMatrix.c -obuild/inst/pkg/Crux/CTMatrix.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/CTMatrix.so build/inst/pkg/Crux/CTMatrix.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Character.pyx --outfile=build/inst/pkg/Crux/Character.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Character.c build/inst/pkg/Crux/Character.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Character.c -obuild/inst/pkg/Crux/Character.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Character.so build/inst/pkg/Crux/Character.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/DistMatrix/Nj.pyx --outfile=build/inst/pkg/Crux/DistMatrix/Nj.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/DistMatrix/Nj.c build/inst/pkg/Crux/DistMatrix/Nj.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/DistMatrix/Nj.c -obuild/inst/pkg/Crux/DistMatrix/Nj.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/DistMatrix/Nj.so build/inst/pkg/Crux/DistMatrix/Nj.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Fasta.pyx --outfile=build/inst/pkg/Crux/Fasta.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Fasta.c build/inst/pkg/Crux/Fasta.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Fasta.c -obuild/inst/pkg/Crux/Fasta.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Fasta.so build/inst/pkg/Crux/Fasta.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/Chain.pyx --outfile=build/inst/pkg/Crux/Mc3/Chain.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Mc3/Chain.c build/inst/pkg/Crux/Mc3/Chain.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Mc3/Chain.c -obuild/inst/pkg/Crux/Mc3/Chain.o build/inst/pkg/Crux/Mc3/Chain.c: In function '__pyx_f_4Crux_3Mc3_5Chain_5Chain_advance0': build/inst/pkg/Crux/Mc3/Chain.c:14528:178: warning: passing argument 5 of 'bsearch' from incompatible pointer type [-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))); ^ In file included from /usr/local/include/python2.7/Python.h:42:0, from build/inst/pkg/Crux/Mc3/Chain.c:4: /usr/include/stdlib.h:91:7: note: expected 'int (*)(const void *, const void *)' but argument is of type 'int (*)(void *, void *)' void *bsearch(const void *, const void *, size_t, ^ cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Mc3/Chain.so build/inst/pkg/Crux/Mc3/Chain.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/Post.pyx --outfile=build/inst/pkg/Crux/Mc3/Post.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Mc3/Post.c build/inst/pkg/Crux/Mc3/Post.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Mc3/Post.c -obuild/inst/pkg/Crux/Mc3/Post.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Mc3/Post.so build/inst/pkg/Crux/Mc3/Post.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Newick.pyx --outfile=build/inst/pkg/Crux/Newick.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Newick.c build/inst/pkg/Crux/Newick.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Newick.c -obuild/inst/pkg/Crux/Newick.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Newick.so build/inst/pkg/Crux/Newick.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Taxa.pyx --outfile=build/inst/pkg/Crux/Taxa.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Taxa.c build/inst/pkg/Crux/Taxa.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Taxa.c -obuild/inst/pkg/Crux/Taxa.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Taxa.so build/inst/pkg/Crux/Taxa.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/Bipart.pyx --outfile=build/inst/pkg/Crux/Tree/Bipart.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Tree/Bipart.c build/inst/pkg/Crux/Tree/Bipart.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Tree/Bipart.c -obuild/inst/pkg/Crux/Tree/Bipart.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Tree/Bipart.so build/inst/pkg/Crux/Tree/Bipart.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/Lik.pyx --outfile=build/inst/pkg/Crux/Tree/Lik.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Tree/Lik.c build/inst/pkg/Crux/Tree/Lik.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Tree/Lik.c -obuild/inst/pkg/Crux/Tree/Lik.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Tree/Lik.so build/inst/pkg/Crux/Tree/Lik.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/Sumt.pyx --outfile=build/inst/pkg/Crux/Tree/Sumt.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Tree/Sumt.c build/inst/pkg/Crux/Tree/Sumt.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Tree/Sumt.c -obuild/inst/pkg/Crux/Tree/Sumt.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Tree/Sumt.so build/inst/pkg/Crux/Tree/Sumt.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Parsing.pyx --outfile=build/inst/pkg/Parsing.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Parsing.c build/inst/pkg/Parsing.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Parsing.c -obuild/inst/pkg/Parsing.o cc -shared -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Parsing.so build/inst/pkg/Parsing.o -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/DistMatrix/__init__.pyx --outfile=build/inst/pkg/Crux/DistMatrix/__init__.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/DistMatrix/__init__.c build/inst/pkg/Crux/DistMatrix/__init__.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/DistMatrix/__init__.c -obuild/inst/pkg/Crux/DistMatrix/__init__.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/DistMatrix/__init__.so build/inst/pkg/Crux/DistMatrix/__init__.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/__init__.pyx --outfile=build/inst/pkg/Crux/Mc3/__init__.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Mc3/__init__.c build/inst/pkg/Crux/Mc3/__init__.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Mc3/__init__.c -obuild/inst/pkg/Crux/Mc3/__init__.o build/inst/pkg/Crux/Mc3/__init__.c: In function '__pyx_f_4Crux_3Mc3_3Mc3_computeRcovUni': build/inst/pkg/Crux/Mc3/__init__.c:13665:82: warning: passing argument 4 of 'qsort' from incompatible pointer type [-Wincompatible-pointer-types] qsort(__pyx_v_rcovScratch, (__pyx_v_past - __pyx_v_first), (sizeof(double)), __pyx_f_4Crux_3Mc3__lnLCmp); ^ In file included from /usr/local/include/python2.7/Python.h:42:0, from build/inst/pkg/Crux/Mc3/__init__.c:4: /usr/include/stdlib.h:106:7: note: expected 'int (*)(const void *, const void *)' but argument is of type 'int (*)(void *, void *)' void qsort(void *, size_t, size_t, int (*)(const void *, const void *)); ^ cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Mc3/__init__.so build/inst/pkg/Crux/Mc3/__init__.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/__init__.pyx --outfile=build/inst/pkg/Crux/Tree/__init__.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/Tree/__init__.c build/inst/pkg/Crux/Tree/__init__.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/Tree/__init__.c -obuild/inst/pkg/Crux/Tree/__init__.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/Tree/__init__.so build/inst/pkg/Crux/Tree/__init__.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/__init__.pyx --outfile=build/inst/pkg/Crux/__init__.pyx /usr/local/bin/python2.7 /construction/biology/crux/crux-1.2.0/cython --directive embedsignature=True -Ibuild/inst/pkg -Ibuild/inst/lib/ -Ibuild/inst/lib/Crux/ -Ibuild/inst/lib/Crux/DistMatrix/ -Ibuild/inst/lib/Crux/Tree/ -Ibuild/inst/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/inst/pkg/Crux/__init__.c build/inst/pkg/Crux/__init__.pyx cc -pipe -O2 -fno-strict-aliasing -std=gnu99 -msse2 -mfpmath=sse -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 -pipe -I/usr/local/include -I/usr/local/include/ncurses -O2 -fno-strict-aliasing -DNDEBUG -c build/inst/pkg/Crux/__init__.c -obuild/inst/pkg/Crux/__init__.o cc -shared -Wl,-rpath,/usr/local/lib/Crux/lib -L/construction/biology/crux/crux-1.2.0/build/inst/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -L/usr/local/lib -lpython2.7 -ldl -L/usr/local/lib -lintl -lutil -lm -Wl,--export-dynamic -o build/inst/site-packages/Crux/__init__.so build/inst/pkg/Crux/__init__.o build/inst/share/Crux/lib/libCx.so -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc5 -L/usr/local/bin -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0 -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../../../../x86_64-portbld-dragonfly5.1/lib -L/usr/local/lib/gcc5/gcc/x86_64-portbld-dragonfly5.1/5.4.0/../../.. -lgfortran -lm -lpthread -lquadmath /construction/biology/crux/crux-1.2.0/cfg -i --infile=bin/MrRogers --outfile=build/inst/bin/MrRogers /construction/biology/crux/crux-1.2.0/cfg -i --infile=bin/crux --outfile=build/inst/bin/crux /construction/biology/crux/crux-1.2.0/cfg -i --infile=bin/redpoint --outfile=build/inst/bin/redpoint /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/Cx.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Crux/Cx.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/CxMat.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Crux/CxMat.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/CxMath.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Crux/CxMath.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/CxNewickLexer.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Crux/CxNewickLexer.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/CxRi.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Crux/CxRi.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/DistMatrix/CxDistMatrixLexer.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Crux/DistMatrix/CxDistMatrixLexer.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/Crux/Tree/CxLik.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Crux/Tree/CxLik.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/SFMT/SFMT.pxd --outfile=build/inst/site-packages/Crux/include/Crux/SFMT/SFMT.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/libc.pxd --outfile=build/inst/site-packages/Crux/include/Crux/libc.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=lib/libm.pxd --outfile=build/inst/site-packages/Crux/include/Crux/libm.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/CTMatrix.pxd --outfile=build/inst/site-packages/Crux/include/Crux/CTMatrix.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Character.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Character.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/DistMatrix/Nj.pxd --outfile=build/inst/site-packages/Crux/include/Crux/DistMatrix/Nj.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Fasta.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Fasta.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/Chain.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Mc3/Chain.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/Post.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Mc3/Post.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Newick.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Newick.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Taxa.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Taxa.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/Bipart.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Tree/Bipart.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/Lik.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Tree/Lik.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/Sumt.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Tree/Sumt.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Parsing.pxd --outfile=build/inst/site-packages/Crux/include/Parsing.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/DistMatrix/__init__.pxd --outfile=build/inst/site-packages/Crux/include/Crux/DistMatrix/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/__init__.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Mc3/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/__init__.pxd --outfile=build/inst/site-packages/Crux/include/Crux/Tree/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/__init__.pxd --outfile=build/inst/site-packages/Crux/include/Crux/__init__.pxd /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Config.py --outfile=build/inst/site-packages/Crux/Config.py /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Copying.py --outfile=build/inst/site-packages/Crux/Copying.py /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/DistMatrix/__init__.py --outfile=build/inst/site-packages/Crux/DistMatrix/__init__.py /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Mc3/__init__.py --outfile=build/inst/site-packages/Crux/Mc3/__init__.py /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/Tree/__init__.py --outfile=build/inst/site-packages/Crux/Tree/__init__.py /construction/biology/crux/crux-1.2.0/cfg -i --infile=pkg/Crux/__init__.py --outfile=build/inst/site-packages/Crux/__init__.py gmake[1]: Leaving directory '/construction/biology/crux/crux-1.2.0' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> crux-1.2.0_8 depends on executable: gfortran5 - found ===> crux-1.2.0_8 depends on file: /usr/local/bin/python2.7 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for crux-1.2.0_8 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/crux/crux-1.2.0' build/run/bin/crux --verbose pickles.cx Crux, version: 1.2.0, threaded, PID: 455524, PRNG seed: 1474682205 Begin batch processing, 2017/10/08 19:47:25 (UTC) Input file: 'pickles.cx' End batch processing, 2017/10/08 19:47:25 (UTC) install -d /construction/biology/crux/stage/usr/local/bin install -m 755 build/inst/bin/MrRogers /construction/biology/crux/stage/usr/local/bin install -m 755 build/inst/bin/crux /construction/biology/crux/stage/usr/local/bin install -m 755 build/inst/bin/redpoint /construction/biology/crux/stage/usr/local/bin install -d /construction/biology/crux/stage/usr/local/lib/Crux/lib install -m 755 build/inst/share/Crux/lib/libCx.so /construction/biology/crux/stage/usr/local/lib/Crux/lib install -d /construction/biology/crux/stage/usr/local/lib/Crux/parsers install -m 644 /construction/biology/crux/crux-1.2.0/build/run/share/Crux/parsers/Fasta.log /construction/biology/crux/stage/usr/local/lib/Crux/parsers install -m 644 /construction/biology/crux/crux-1.2.0/build/run/share/Crux/parsers/Fasta.pickle /construction/biology/crux/stage/usr/local/lib/Crux/parsers install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/DistMatrix/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Mc3/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Tree/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Crux/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Crux/DistMatrix/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Crux/Tree/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/DistMatrix/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Mc3/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/SFMT/ install -d /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Tree/ install -m 755 build/inst/site-packages/Crux/include/Crux/Crux/Cx.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/Crux/CxMat.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/Crux/CxMath.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/Crux/CxNewickLexer.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/Crux/CxRi.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/Crux/DistMatrix/CxDistMatrixLexer.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Crux/DistMatrix install -m 755 build/inst/site-packages/Crux/include/Crux/Crux/Tree/CxLik.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Crux/Tree install -m 755 build/inst/site-packages/Crux/include/Crux/SFMT/SFMT.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/SFMT install -m 755 build/inst/site-packages/Crux/include/Crux/libc.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/libm.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/CTMatrix.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/Character.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/DistMatrix/Nj.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/DistMatrix install -m 755 build/inst/site-packages/Crux/include/Crux/Fasta.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/Mc3/Chain.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Mc3 install -m 755 build/inst/site-packages/Crux/include/Crux/Mc3/Post.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Mc3 install -m 755 build/inst/site-packages/Crux/include/Crux/Newick.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/Taxa.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux install -m 755 build/inst/site-packages/Crux/include/Crux/Tree/Bipart.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Tree install -m 755 build/inst/site-packages/Crux/include/Crux/Tree/Lik.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Tree install -m 755 build/inst/site-packages/Crux/include/Crux/Tree/Sumt.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Tree install -m 755 build/inst/site-packages/Crux/include/Parsing.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include install -m 755 build/inst/site-packages/Crux/include/Crux/DistMatrix/__init__.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/DistMatrix install -m 755 build/inst/site-packages/Crux/include/Crux/Mc3/__init__.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Mc3 install -m 755 build/inst/site-packages/Crux/include/Crux/Tree/__init__.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux/Tree install -m 755 build/inst/site-packages/Crux/include/Crux/__init__.pxd /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/include/Crux install -m 755 build/inst/site-packages/Crux/CTMatrix.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux install -m 755 build/inst/site-packages/Crux/Character.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux install -m 755 build/inst/site-packages/Crux/DistMatrix/Nj.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/DistMatrix install -m 755 build/inst/site-packages/Crux/Fasta.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux install -m 755 build/inst/site-packages/Crux/Mc3/Chain.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Mc3 install -m 755 build/inst/site-packages/Crux/Mc3/Post.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Mc3 install -m 755 build/inst/site-packages/Crux/Newick.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux install -m 755 build/inst/site-packages/Crux/Taxa.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux install -m 755 build/inst/site-packages/Crux/Tree/Bipart.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Tree install -m 755 build/inst/site-packages/Crux/Tree/Lik.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Tree install -m 755 build/inst/site-packages/Crux/Tree/Sumt.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Tree install -m 755 build/inst/site-packages/Parsing.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/. install -m 755 build/inst/site-packages/Crux/DistMatrix/__init__.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/DistMatrix install -m 755 build/inst/site-packages/Crux/Mc3/__init__.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Mc3 install -m 755 build/inst/site-packages/Crux/Tree/__init__.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Tree install -m 755 build/inst/site-packages/Crux/__init__.so /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux install -m 755 build/inst/site-packages/Crux/Config.py /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux install -m 755 build/inst/site-packages/Crux/Copying.py /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux install -m 755 build/inst/site-packages/Crux/DistMatrix/__init__.py /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/DistMatrix install -m 755 build/inst/site-packages/Crux/Mc3/__init__.py /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Mc3 install -m 755 build/inst/site-packages/Crux/Tree/__init__.py /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux/Tree install -m 755 build/inst/site-packages/Crux/__init__.py /construction/biology/crux/stage/usr/local/lib/python2.7/site-packages/Crux gmake[1]: Leaving directory '/construction/biology/crux/crux-1.2.0' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for crux-1.2.0_8 file sizes/checksums [58]: . done packing files [58]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 8 OCT 2017 at 19:47:33 UTC Duration: 00:06:42