[REL - head-amd64-default][biology/crux] Failed for crux-1.2.0_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Fri Oct 25 07:04:44 UTC 2013
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jasone at FreeBSD.org
Last committer: bapt at FreeBSD.org
Ident: $FreeBSD: head/biology/crux/Makefile 327709 2013-09-20 15:55:44Z bapt $
Log URL: http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2013-10-24_13h53m31s/logs/crux-1.2.0_1.log
Build URL: http://beefy2.isc.freebsd.org/bulk/head-amd64-default/2013-10-24_13h53m31s
Log:
====>> Building biology/crux
build started at Fri Oct 25 07:03:59 UTC 2013
port directory: /usr/ports/biology/crux
building for: FreeBSD head-amd64-default-job-12 11.0-CURRENT FreeBSD 11.0-CURRENT r256430 amd64
maintained by: jasone at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/crux/Makefile 327709 2013-09-20 15:55:44Z bapt $
Poudriere version: 3.1-pre
---Begin Environment---
OSVERSION=1100000
UNAME_v=FreeBSD 11.0-CURRENT r256430
UNAME_r=11.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
STATUS=1
MASTERMNT=/usr/local/poudriere/data/build/head-amd64-default/ref
PKG_EXT=txz
tpid=75738
POUDRIERE_BUILD_TYPE=bulk
PKGNG=1
PKGNAME=crux-1.2.0_1
PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f
PKG_ADD=/usr/local/sbin/pkg-static add
PWD=/root
MASTERNAME=head-amd64-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
PKG_VERSION=/poudriere/pkg-static version
PKG_BIN=/usr/local/sbin/pkg-static
---End Environment---
---Begin OPTIONS List---
===> The following configuration options are available for crux-1.2.0_1:
SYS_LINALG=off: Enable system ATLAS/LAPACK
===> Use 'make config' to modify these settings
---End OPTIONS List---
--CONFIGURE_ARGS--
--with-python=/usr/local/bin/python2.7 --disable-mpi --disable-sys-linalg --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
TMPDIR="/tmp" PYTHON="/usr/local/bin/python2.7" MAKE=gmake TMPDIR="/tmp" TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh F77="gfortran46" FC="gfortran46" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc46" ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
--End CONFIGURE_ENV--
--MAKE_ENV--
TMPDIR="/tmp" TMPDIR="/tmp" TMPDIR="/tmp" SHELL=/bin/sh NO_LINT=YES F77="gfortran46" FC="gfortran46" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc46" ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="gcc46" CFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99" CPP="cpp46" CPPFLAGS="-I/usr/local/include" LDFLAGS=" -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46" CXX="g++46" CXXFLAGS="-O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc46" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTAL
L_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444"
--End MAKE_ENV--
--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/crux
DOCSDIR=/usr/local/share/doc/crux
EXAMPLESDIR=/usr/local/share/examples/crux
WWWDIR=/usr/local/www/crux
ETCDIR=/usr/local/etc/crux
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
WITH_PKGNG=yes
NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
===> Cleaning for crux-1.2.0_1
=======================<phase: check-config >============================
===========================================================================
=======================<phase: pkg-depends >============================
===> crux-1.2.0_1 depends on file: /usr/local/sbin/pkg - not found
===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg
===> Installing existing package /packages/All/pkg-1.1.4_8.txz
Installing pkg-1.1.4_8... done
If you are upgrading from the old package format, first run:
# pkg2ng
===> Returning to build of crux-1.2.0_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> Fetching all distfiles required by crux-1.2.0_1 for building
===========================================================================
=======================<phase: checksum >============================
===> Fetching all distfiles required by crux-1.2.0_1 for building
=> SHA256 Checksum OK for crux-1.2.0.tar.bz2.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> Fetching all distfiles required by crux-1.2.0_1 for building
===> Extracting for crux-1.2.0_1
=> SHA256 Checksum OK for crux-1.2.0.tar.bz2.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for crux-1.2.0_1
===========================================================================
=======================<phase: build-depends >============================
===> crux-1.2.0_1 depends on file: /usr/local/bin/python2.7 - not found
===> Verifying install for /usr/local/bin/python2.7 in /usr/ports/lang/python27
===> Installing existing package /packages/All/python27-2.7.5_3.txz
Installing python27-2.7.5_3...Installing gettext-0.18.3.1... done
done
====
Note that some of the standard modules are provided as separate
ports since they require extra dependencies:
bsddb databases/py-bsddb
gdbm databases/py-gdbm
sqlite3 databases/py-sqlite3
tkinter x11-toolkits/py-tkinter
Install them as needed.
====
===> Returning to build of crux-1.2.0_1
===> crux-1.2.0_1 depends on executable: python - not found
===> Verifying install for python in /usr/ports/lang/python
===> Installing existing package /packages/All/python-2.7_1,2.txz
Installing python-2.7_1,2...Installing python2-2_1... done
done
===> Returning to build of crux-1.2.0_1
===> crux-1.2.0_1 depends on executable: gmake - not found
===> Verifying install for gmake in /usr/ports/devel/gmake
===> Installing existing package /packages/All/gmake-3.82_1.txz
Installing gmake-3.82_1... done
===> Returning to build of crux-1.2.0_1
===> crux-1.2.0_1 depends on executable: gcc46 - not found
===> Verifying install for gcc46 in /usr/ports/lang/gcc
===> Installing existing package /packages/All/gcc-4.6.3.txz
Installing gcc-4.6.3...Installing mpfr-3.1.2...Installing gmp-5.1.3... done
done
Installing mpc-0.9... done
Installing gcc-ecj-4.5... done
Installing binutils-2.23.2... done
done
===> Returning to build of crux-1.2.0_1
===> crux-1.2.0_1 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for crux-1.2.0_1
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/configure
configure: loading site script /usr/ports/Templates/config.site
checking for gcc... gcc46
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc46 accepts -g... yes
checking for gcc46 option to accept ISO C89... none needed
checking how to run the C preprocessor... cpp46
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for ANSI C header files... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking size of void *... 8
checking build system type... amd64-portbld-freebsd11.0
checking host system type... amd64-portbld-freebsd11.0
checking for a BSD-compatible install... /usr/bin/install -c -o root -g wheel
checking for ranlib... /usr/local/bin/ranlib
checking for ar... /usr/local/bin/ar
checking for ld... /usr/local/bin/ld
checking for test... /bin/test
checking for grep... /usr/bin/grep
checking for autoconf... no
checking pthread.h usability... yes
checking pthread.h presence... yes
checking for pthread.h... yes
checking for pthread_create in -lpthread... yes
checking for python >= 2.5.0... 2.7.5
checking for python-config... /usr/local/bin/python2.7-config
checking python site-packages path... /usr/local/lib/python2.7/site-packages
checking whether byte ordering is bigendian... no
checking for stdbool.h that conforms to C99... (cached) yes
checking for _Bool... (cached) yes
checking for log in -lm... yes
checking for posix_memalign... yes
checking for mallopt... no
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran46 accepts -g... yes
checking how to get verbose linking output from gfortran46... -v
checking for Fortran libraries of gfortran46... -L/usr/local/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.3 -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.3/../../../../../x86_64-portbld-freebsd11.0/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.3/../../.. -lgfortran -lm -lpthread -lquadmath
configure: creating ./config.status
config.status: creating Makefile
config.status: creating cfgoutputs.stamp
config.status: creating cfg
config.status: creating cydep
config.status: creating cython
config.status: creating lib/Crux/Cx_defs.h
config.status: creating cfghdrs.stamp
===============================================================================
Crux version : 1.2.0
PYTHON : /usr/local/bin/python2.7
CYTHON : /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cython
FLEX :
CC : gcc46
CPPFLAGS : -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT
MTCPPFLAGS : -DMEXP=19937
CFLAGS : -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99
MTCFLAGS : -fno-strict-aliasing
FC : gfortran46
FCFLAGS : -g -O2
LDFLAGS : -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46
LIBS : -lm -lpthread
FCLIBS : -L/usr/local/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.3 -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.3/../../../../../x86_64-portbld-freebsd11.0/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.3/../../.. -lgfortran -lm -lpthread -lquadmath
RPATH_EXTRA :
site_packages : /usr/local/lib/python2.7/site-packages
PREFIX : /usr/local
BINDIR : /usr/local/bin
DATADIR : /usr/local/share
MANDIR : /usr/local/man
srcroot :
abs_srcroot : /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/
objroot :
abs_objroot : /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/
autogen : 0
flex : 0
debug : 0
cc-silence : 0
inlines : 1
sys-linalg : 0
mpi : 0
===============================================================================
===========================================================================
=======================<phase: build >============================
===> Building for crux-1.2.0_1
gmake[1]: Entering directory `/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0'
cp -R contrib/cython build/contrib
gfortran46 -g -O2 -fPIC -c lib/BLAS/daxpy.f -o build/lib/BLAS/daxpy.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/dcopy.f -o build/lib/BLAS/dcopy.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/ddot.f -o build/lib/BLAS/ddot.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/dgemm.f -o build/lib/BLAS/dgemm.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/dgemv.f -o build/lib/BLAS/dgemv.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/dger.f -o build/lib/BLAS/dger.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/dnrm2.f -o build/lib/BLAS/dnrm2.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/drot.f -o build/lib/BLAS/drot.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/dscal.f -o build/lib/BLAS/dscal.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/dswap.f -o build/lib/BLAS/dswap.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/dtrmm.f -o build/lib/BLAS/dtrmm.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/dtrmv.f -o build/lib/BLAS/dtrmv.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/dtrsm.f -o build/lib/BLAS/dtrsm.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/idamax.f -o build/lib/BLAS/idamax.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/lsame.f -o build/lib/BLAS/lsame.o
gfortran46 -g -O2 -fPIC -c lib/BLAS/xerbla.f -o build/lib/BLAS/xerbla.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgebak.f -o build/lib/LAPACK/dgebak.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgebal.f -o build/lib/LAPACK/dgebal.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgeev.f -o build/lib/LAPACK/dgeev.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgehd2.f -o build/lib/LAPACK/dgehd2.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgehrd.f -o build/lib/LAPACK/dgehrd.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgetf2.f -o build/lib/LAPACK/dgetf2.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgetrf.f -o build/lib/LAPACK/dgetrf.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dgetri.f -o build/lib/LAPACK/dgetri.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dhseqr.f -o build/lib/LAPACK/dhseqr.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/disnan.f -o build/lib/LAPACK/disnan.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlabad.f -o build/lib/LAPACK/dlabad.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlacpy.f -o build/lib/LAPACK/dlacpy.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dladiv.f -o build/lib/LAPACK/dladiv.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaexc.f -o build/lib/LAPACK/dlaexc.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlahqr.f -o build/lib/LAPACK/dlahqr.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlahr2.f -o build/lib/LAPACK/dlahr2.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaisnan.f -o build/lib/LAPACK/dlaisnan.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaln2.f -o build/lib/LAPACK/dlaln2.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlamch.f -o build/lib/LAPACK/dlamch.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlange.f -o build/lib/LAPACK/dlange.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlanv2.f -o build/lib/LAPACK/dlanv2.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlapy2.f -o build/lib/LAPACK/dlapy2.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr0.f -o build/lib/LAPACK/dlaqr0.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr1.f -o build/lib/LAPACK/dlaqr1.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr2.f -o build/lib/LAPACK/dlaqr2.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr3.f -o build/lib/LAPACK/dlaqr3.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr4.f -o build/lib/LAPACK/dlaqr4.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaqr5.f -o build/lib/LAPACK/dlaqr5.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlarf.f -o build/lib/LAPACK/dlarf.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlarfb.f -o build/lib/LAPACK/dlarfb.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlarfg.f -o build/lib/LAPACK/dlarfg.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlarft.f -o build/lib/LAPACK/dlarft.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlarfx.f -o build/lib/LAPACK/dlarfx.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlartg.f -o build/lib/LAPACK/dlartg.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlascl.f -o build/lib/LAPACK/dlascl.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaset.f -o build/lib/LAPACK/dlaset.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlassq.f -o build/lib/LAPACK/dlassq.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlaswp.f -o build/lib/LAPACK/dlaswp.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dlasy2.f -o build/lib/LAPACK/dlasy2.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dorg2r.f -o build/lib/LAPACK/dorg2r.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dorghr.f -o build/lib/LAPACK/dorghr.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dorgqr.f -o build/lib/LAPACK/dorgqr.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dorm2r.f -o build/lib/LAPACK/dorm2r.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dormhr.f -o build/lib/LAPACK/dormhr.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dormqr.f -o build/lib/LAPACK/dormqr.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dtrevc.f -o build/lib/LAPACK/dtrevc.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dtrexc.f -o build/lib/LAPACK/dtrexc.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dtrti2.f -o build/lib/LAPACK/dtrti2.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/dtrtri.f -o build/lib/LAPACK/dtrtri.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/ieeeck.f -o build/lib/LAPACK/ieeeck.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/iladlc.f -o build/lib/LAPACK/iladlc.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/iladlr.f -o build/lib/LAPACK/iladlr.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/ilaenv.f -o build/lib/LAPACK/ilaenv.o
gfortran46 -g -O2 -fPIC -c lib/LAPACK/iparmq.f -o build/lib/LAPACK/iparmq.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/Cx.c -obuild/lib/Crux/Cx.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxAmd64.c -obuild/lib/Crux/CxAmd64.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxIa32.c -obuild/lib/Crux/CxIa32.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxMat.c -obuild/lib/Crux/CxMat.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxMq.c -obuild/lib/Crux/CxMq.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxPpc.c -obuild/lib/Crux/CxPpc.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxRi.c -obuild/lib/Crux/CxRi.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/Tree/CxLik.c -obuild/lib/Crux/Tree/CxLik.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -fno-strict-aliasing -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -DMEXP=19937 -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/SFMT/SFMT.c -obuild/lib/SFMT/SFMT.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/CxNewickLexer.c -obuild/lib/Crux/CxNewickLexer.o
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -c lib/Crux/DistMatrix/CxDistMatrixLexer.c -obuild/lib/Crux/DistMatrix/CxDistMatrixLexer.o
gcc46 -shared -Wl,-rpath,/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib -Wl,-soname,libCx.so -o build/run/share/Crux/lib/libCx.so build/lib/Crux/Cx.o build/lib/Crux/CxAmd64.o build/lib/Crux/CxIa32.o build/lib/Crux/CxMat.o build/lib/Crux/CxMq.o build/lib/Crux/CxPpc.o build/lib/Crux/CxRi.o build/lib/Crux/Tree/CxLik.o build/lib/SFMT/SFMT.o build/lib/Crux/CxNewickLexer.o build/lib/Crux/DistMatrix/CxDistMatrixLexer.o build/lib/BLAS/daxpy.o build/lib/BLAS/dcopy.o build/lib/BLAS/ddot.o build/lib/BLAS/dgemm.o build/lib/BLAS/dgemv.o build/lib/BLAS/dger.o build/lib/BLAS/dnrm2.o build/lib/BLAS/drot.o build/lib/BLAS/dscal.o build/lib/BLAS/dswap.o build/lib/BLAS/dtrmm.o build/lib/BLAS/dtrmv.o build/lib/BLAS/dtrsm.o build/lib/BLAS/idamax.o build/lib/BLAS/lsame.o build/lib/BLAS/xerbla.o build/lib/LAPACK/dgebak.o build/lib/LAPACK/dgebal.o build/lib/LAPACK/dgeev.o build/lib/LAPACK/dgehd2.o build/lib/LAPACK/dgehrd.o build/lib/LAPACK/dgetf2.o build/lib/LAPACK/dgetrf.o build/l
ib/LAPACK/dgetri.o build/lib/LAPACK/dhseqr.o build/lib/LAPACK/disnan.o build/lib/LAPACK/dlabad.o build/lib/LAPACK/dlacpy.o build/lib/LAPACK/dladiv.o build/lib/LAPACK/dlaexc.o build/lib/LAPACK/dlahqr.o build/lib/LAPACK/dlahr2.o build/lib/LAPACK/dlaisnan.o build/lib/LAPACK/dlaln2.o build/lib/LAPACK/dlamch.o build/lib/LAPACK/dlange.o build/lib/LAPACK/dlanv2.o build/lib/LAPACK/dlapy2.o build/lib/LAPACK/dlaqr0.o build/lib/LAPACK/dlaqr1.o build/lib/LAPACK/dlaqr2.o build/lib/LAPACK/dlaqr3.o build/lib/LAPACK/dlaqr4.o build/lib/LAPACK/dlaqr5.o build/lib/LAPACK/dlarf.o build/lib/LAPACK/dlarfb.o build/lib/LAPACK/dlarfg.o build/lib/LAPACK/dlarft.o build/lib/LAPACK/dlarfx.o build/lib/LAPACK/dlartg.o build/lib/LAPACK/dlascl.o build/lib/LAPACK/dlaset.o build/lib/LAPACK/dlassq.o build/lib/LAPACK/dlaswp.o build/lib/LAPACK/dlasy2.o build/lib/LAPACK/dorg2r.o build/lib/LAPACK/dorghr.o build/lib/LAPACK/dorgqr.o build/lib/LAPACK/dorm2r.o build/lib/LAPACK/dormhr.o build/lib/LAPACK/dormqr.o build/lib/LAPAC
K/dtrevc.o build/lib/LAPACK/dtrexc.o build/l!
ib/LAPACK/dtrti2.o build/lib/LAPACK/dtrtri.o build/lib/LAPACK/ieeeck.o build/lib/LAPACK/iladlc.o build/lib/LAPACK/iladlr.o build/lib/LAPACK/ilaenv.o build/lib/LAPACK/iparmq.o -L/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/build/run/share/Crux/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc46 -lm -lpthread -L/usr/local/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.3 -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.3/../../../../../x86_64-portbld-freebsd11.0/lib -L/usr/local/lib/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.3/../../.. -lgfortran -lm -lpthread -lquadmath
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/CTMatrix.pyx --outfile=build/run/pkg/Crux/CTMatrix.pyx
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/CTMatrix.pxd --outfile=build/run/pkg/Crux/CTMatrix.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Character.pxd --outfile=build/run/pkg/Crux/Character.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/DistMatrix/Nj.pxd --outfile=build/run/pkg/Crux/DistMatrix/Nj.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Fasta.pxd --outfile=build/run/pkg/Crux/Fasta.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/Chain.pxd --outfile=build/run/pkg/Crux/Mc3/Chain.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/Post.pxd --outfile=build/run/pkg/Crux/Mc3/Post.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Newick.pxd --outfile=build/run/pkg/Crux/Newick.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Taxa.pxd --outfile=build/run/pkg/Crux/Taxa.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/Bipart.pxd --outfile=build/run/pkg/Crux/Tree/Bipart.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/Lik.pxd --outfile=build/run/pkg/Crux/Tree/Lik.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/Sumt.pxd --outfile=build/run/pkg/Crux/Tree/Sumt.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Parsing.pxd --outfile=build/run/pkg/Parsing.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/DistMatrix/__init__.pxd --outfile=build/run/pkg/Crux/DistMatrix/__init__.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/__init__.pxd --outfile=build/run/pkg/Crux/Mc3/__init__.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/__init__.pxd --outfile=build/run/pkg/Crux/Tree/__init__.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/__init__.pxd --outfile=build/run/pkg/Crux/__init__.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/Cx.pxd --outfile=build/run/lib/Crux/Cx.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/CxMat.pxd --outfile=build/run/lib/Crux/CxMat.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/CxMath.pxd --outfile=build/run/lib/Crux/CxMath.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/CxNewickLexer.pxd --outfile=build/run/lib/Crux/CxNewickLexer.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/CxRi.pxd --outfile=build/run/lib/Crux/CxRi.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/DistMatrix/CxDistMatrixLexer.pxd --outfile=build/run/lib/Crux/DistMatrix/CxDistMatrixLexer.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/Crux/Tree/CxLik.pxd --outfile=build/run/lib/Crux/Tree/CxLik.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/SFMT/SFMT.pxd --outfile=build/run/lib/SFMT/SFMT.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/libc.pxd --outfile=build/run/lib/libc.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=lib/libm.pxd --outfile=build/run/lib/libm.pxd
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Config.py --outfile=build/run/pkg/Crux/Config.py
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Copying.py --outfile=build/run/pkg/Crux/Copying.py
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/DistMatrix/__init__.py --outfile=build/run/pkg/Crux/DistMatrix/__init__.py
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Mc3/__init__.py --outfile=build/run/pkg/Crux/Mc3/__init__.py
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/Tree/__init__.py --outfile=build/run/pkg/Crux/Tree/__init__.py
/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cfg -r --infile=pkg/Crux/__init__.py --outfile=build/run/pkg/Crux/__init__.py
/usr/local/bin/python2.7 /wrkdirs/usr/ports/biology/crux/work/crux-1.2.0/cython --directive embedsignature=True -Ibuild/run/pkg -Ibuild/run/lib/ -Ibuild/run/lib/Crux/ -Ibuild/run/lib/Crux/DistMatrix/ -Ibuild/run/lib/Crux/Tree/ -Ibuild/run/lib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -o build/run/pkg/Crux/CTMatrix.c build/run/pkg/Crux/CTMatrix.pyx
Creating lexicon...
Done (0.04 seconds)
Pickling lexicon...
Done (0.00 seconds)
gcc46 -O2 -pipe -Wl,-rpath=/usr/local/lib/gcc46 -fno-strict-aliasing -std=gnu99 -fPIC -DPIC -I/usr/local/include -DPYREX_WITHOUT_ASSERTIONS -D_REENTRANT -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -Ilib/Crux/ -Ilib/Crux/DistMatrix/ -Ilib/Crux/Tree/ -Ilib/SFMT/ -I/usr/local/include/python2.7 -I/usr/local/include/python2.7 -fno-strict-aliasing -OPT:Olimit=0 -O2 -pipe -fno-strict-aliasing -DNDEBUG -c build/run/pkg/Crux/CTMatrix.c -obuild/run/pkg/Crux/CTMatrix.o
cc1: error: argument to '-O' should be a non-negative integer
gmake[1]: *** [build/run/pkg/Crux/CTMatrix.o] Error 1
gmake[1]: Leaving directory `/wrkdirs/usr/ports/biology/crux/work/crux-1.2.0'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/crux
===> Cleaning for crux-1.2.0_1
More information about the freebsd-pkg-fallout
mailing list