[REL - head-i386-default][science/ghmm] Failed for ghmm-0.7.0b in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Sep 19 01:50:18 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: clsung at FreeBSD.org
Last committer: beat at FreeBSD.org
Ident: $FreeBSD: head/science/ghmm/Makefile 300897 2012-07-14 14:29:18Z beat $
Log URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-09-19_00h27m24s/logs/ghmm-0.7.0b.log
Build URL: http://beefy1.isc.freebsd.org/bulk/head-i386-default/2013-09-19_00h27m24s
Log:
====>> Building science/ghmm
build started at Thu Sep 19 01:50:03 UTC 2013
port directory: /usr/ports/science/ghmm
building for: FreeBSD head-i386-default-job-08 10.0-CURRENT FreeBSD 10.0-CURRENT #2 r255449: Tue Sep 10 11:09:39 UTC 2013 root at beefy1.isc.freebsd.org:/usr/obj/usr/src/sys/BEEFY1 i386
maintained by: clsung at FreeBSD.org
Makefile ident: $FreeBSD: head/science/ghmm/Makefile 300897 2012-07-14 14:29:18Z beat $
Poudriere version: 3.1-pre
---Begin Environment---
UNAME_m=i386
UNAME_p=i386
OSVERSION=1000055
xUNAME_v=FreeBSD 10.0-CURRENT
UNAME_r=10.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
MASTERMNT=/usr/local/poudriere/data/build/head-i386-default/ref
PKG_EXT=txz
tpid=60552
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
NBPARALLEL=24
PKGNG=1
PKGNAME=ghmm-0.7.0b
PKG_DELETE=/usr/local/sbin/pkg delete -y -f
PKG_ADD=/usr/local/sbin/pkg add
PWD=/root
MASTERNAME=head-i386-default
USER=root
HOME=/root
POUDRIERE_VERSION=3.1-pre
SKIPSANITY=1
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
---End Environment---
---Begin OPTIONS List---
---End OPTIONS List---
--CONFIGURE_ARGS--
--prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh LIBTOOL=/usr/local/bin/libtool LIBTOOLIZE=/usr/local/bin/libtoolize LIBTOOL_LIBEXECDIR=/usr/local/libexec/libtool LIBTOOL_SHAREDIR=/usr/local/share/libtool LIBTOOL_M4=/usr/local/share/aclocal/libtool.m4 LTMAIN=/usr/local/share/libtool/config/ltmain.sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144
--End CONFIGURE_ENV--
--MAKE_ENV--
TMPDIR="/tmp" SHELL=/bin/sh NO_LINT=YES LIBTOOL=/usr/local/bin/libtool LIBTOOLIZE=/usr/local/bin/libtoolize LIBTOOL_LIBEXECDIR=/usr/local/libexec/libtool LIBTOOL_SHAREDIR=/usr/local/share/libtool LIBTOOL_M4=/usr/local/share/aclocal/libtool.m4 LTMAIN=/usr/local/share/libtool/config/ltmain.sh PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_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/ghmm
DOCSDIR=/usr/local/share/doc/ghmm
EXAMPLESDIR=/usr/local/share/examples/ghmm
WWWDIR=/usr/local/www/ghmm
ETCDIR=/usr/local/etc/ghmm
--End SUB_LIST--
---Begin make.conf---
ARCH=i386
MACHINE=i386
MACHINE_ARCH=i386
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
WITH_PKGNG=yes
NO_RESTRICTED=yes
DISABLE_MAKE_JOBS=yes
---End make.conf---
===> Cleaning for ghmm-0.7.0b
=======================<phase: check-config >============================
===========================================================================
=======================<phase: pkg-depends >============================
===> ghmm-0.7.0b 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_2.txz
Installing pkg-1.1.4_2... done
If you are upgrading from the old package format, first run:
# pkg2ng
===> Returning to build of ghmm-0.7.0b
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> Fetching all distfiles required by ghmm-0.7.0b for building
===========================================================================
=======================<phase: checksum >============================
===> Fetching all distfiles required by ghmm-0.7.0b for building
=> SHA256 Checksum OK for ghmm-0.7.0b.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> Fetching all distfiles required by ghmm-0.7.0b for building
===> Extracting for ghmm-0.7.0b
=> SHA256 Checksum OK for ghmm-0.7.0b.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for ghmm-0.7.0b
===> Applying FreeBSD patches for ghmm-0.7.0b
===========================================================================
=======================<phase: build-depends >============================
===> ghmm-0.7.0b depends on package: libtool>=2.4 - not found
===> Verifying install for libtool>=2.4 in /usr/ports/devel/libtool
===> Installing existing package /packages/All/libtool-2.4.2_1.txz
Installing libtool-2.4.2_1... done
===> Returning to build of ghmm-0.7.0b
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for ghmm-0.7.0b
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.7.0/acinclude.m4
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.7.0/aclocal.m4
===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.7.0/configure
configure: loading site script /usr/ports/Templates/config.site
checking for a BSD-compatible install... /usr/bin/install -c -o root -g wheel
checking whether build environment is sane... yes
checking for gawk... (cached) /usr/bin/awk
checking whether make sets $(MAKE)... yes
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 for style of include used by make... GNU
checking dependency style of cc... gcc3
checking dependency style of cc... (cached) gcc3
checking how to run the C preprocessor... cpp
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking dependency style of c++... gcc3
checking dependency style of c++... (cached) gcc3
checking how to run the C++ preprocessor... c++ -E
checking for ranlib... ranlib
checking build system type... i386-portbld-freebsd10.0
checking host system type... i386-portbld-freebsd10.0
checking for a sed that does not truncate output... /usr/bin/sed
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for ld used by cc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for /usr/bin/ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -B
checking whether ln -s works... yes
checking how to recognise dependent libraries... pass_all
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 for dlfcn.h... (cached) yes
checking for g77... no
checking for f77... no
checking for xlf... no
checking for frt... no
checking for pgf77... no
checking for cf77... no
checking for fort77... no
checking for fl32... no
checking for af77... no
checking for f90... no
checking for xlf90... no
checking for pgf90... no
checking for pghpf... no
checking for epcf90... no
checking for gfortran... no
checking for g95... no
checking for f95... no
checking for fort... no
checking for xlf95... no
checking for ifort... no
checking for ifc... no
checking for efc... no
checking for pgf95... no
checking for lf95... no
checking for ftn... no
checking whether we are using the GNU Fortran 77 compiler... no
checking whether accepts -g... no
checking the maximum length of command line arguments... (cached) 262144
checking command to parse /usr/bin/nm -B output from cc object... Segmentation fault
ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... (cached) ranlib
checking for strip... strip
checking if cc static flag works... yes
checking if cc supports -fno-rtti -fno-exceptions... yes
checking for cc option to produce PIC... -fPIC
checking if cc PIC flag -fPIC works... yes
checking if cc supports -c -o file.o... yes
checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... freebsd10.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
configure: creating libtool
appending configuration tag "CXX" to libtool
checking for ld used by c++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking for c++ option to produce PIC... -fPIC
checking if c++ PIC flag -fPIC works... yes
checking if c++ supports -c -o file.o... yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... freebsd10.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
appending configuration tag "F77" to libtool
checking for gawk... (cached) /usr/bin/awk
checking for rm... /bin/rm
checking for doc++... no
checking for latex... no
checking for dvips... no
checking for expect... no
checking for runtest... no
checking whether the compiler implements namespaces... yes
checking whether the compiler supports Standard Template Library... yes
checking whether the compiler implements namespaces... (cached) yes
checking cstdio usability... yes
checking cstdio presence... yes
checking for cstdio... yes
checking cstdlib usability... yes
checking cstdlib presence... yes
checking for cstdlib... yes
checking cstring usability... yes
checking cstring presence... yes
checking for cstring... yes
checking cerrno usability... yes
checking cerrno presence... yes
checking for cerrno... yes
checking cmath usability... yes
checking cmath presence... yes
checking for cmath... yes
checking cstdarg usability... yes
checking cstdarg presence... yes
checking for cstdarg... yes
checking for xmlio-config... no
configure: WARNING: "no xml support"
checking for pthread_join in -lpthread... yes
checking for ANSI C header files... (cached) yes
checking for an ANSI C-conforming const... yes
checking for size_t... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking whether struct tm is in sys/time.h or time.h... time.h
configure: WARNING: "not using gsl"
checking for cos in -lm... yes
configure: creating ./config.status
Segmentation fault
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating ghmm/Makefile
config.status: creating tools/Makefile
config.status: creating tests/Makefile
config.status: creating tests/data/Makefile
config.status: creating doc/docu.dxx
config.status: creating tools/ghmm-config
config.status: creating VisualC/Makefile
config.status: creating VisualC/coin_toss_test/Makefile
config.status: creating VisualC/coin_toss_test_pp/Makefile
config.status: creating VisualC/ghmm/Makefile
config.status: creating VisualC/ghmmpp/Makefile
config.status: creating config.h
config.status: executing depfiles commands
===========================================================================
=======================<phase: build >============================
===> Building for ghmm-0.7.0b
/usr/bin/make all-recursive
Making all in ghmm
Making all in .
if /bin/sh /usr/local/bin/libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT foba.lo -MD -MP -MF ".deps/foba.Tpo" -c -o foba.lo foba.c; then mv -f ".deps/foba.Tpo" ".deps/foba.Plo"; else rm -f ".deps/foba.Tpo"; exit 1; fi
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT foba.lo -MD -MP -MF .deps/foba.Tpo -c foba.c -fPIC -DPIC -o .libs/foba.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT foba.lo -MD -MP -MF .deps/foba.Tpo -c foba.c -o foba.o >/dev/null 2>&1
if /bin/sh /usr/local/bin/libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT matrix.lo -MD -MP -MF ".deps/matrix.Tpo" -c -o matrix.lo matrix.c; then mv -f ".deps/matrix.Tpo" ".deps/matrix.Plo"; else rm -f ".deps/matrix.Tpo"; exit 1; fi
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.c -fPIC -DPIC -o .libs/matrix.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.c -o matrix.o >/dev/null 2>&1
if /bin/sh /usr/local/bin/libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT model.lo -MD -MP -MF ".deps/model.Tpo" -c -o model.lo model.c; then mv -f ".deps/model.Tpo" ".deps/model.Plo"; else rm -f ".deps/model.Tpo"; exit 1; fi
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT model.lo -MD -MP -MF .deps/model.Tpo -c model.c -fPIC -DPIC -o .libs/model.o
model.c:2351:23: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
if (!mo->model_type && kHasBackgroundDistributions) {
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~
model.c:2351:23: note: use '&' for a bitwise operation
if (!mo->model_type && kHasBackgroundDistributions) {
^~
&
model.c:2351:23: note: remove constant to silence this warning
if (!mo->model_type && kHasBackgroundDistributions) {
~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT model.lo -MD -MP -MF .deps/model.Tpo -c model.c -o model.o >/dev/null 2>&1
if /bin/sh /usr/local/bin/libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT modelutil.lo -MD -MP -MF ".deps/modelutil.Tpo" -c -o modelutil.lo modelutil.c; then mv -f ".deps/modelutil.Tpo" ".deps/modelutil.Plo"; else rm -f ".deps/modelutil.Tpo"; exit 1; fi
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT modelutil.lo -MD -MP -MF .deps/modelutil.Tpo -c modelutil.c -fPIC -DPIC -o .libs/modelutil.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT modelutil.lo -MD -MP -MF .deps/modelutil.Tpo -c modelutil.c -o modelutil.o >/dev/null 2>&1
if /bin/sh /usr/local/bin/libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT cluster.lo -MD -MP -MF ".deps/cluster.Tpo" -c -o cluster.lo cluster.c; then mv -f ".deps/cluster.Tpo" ".deps/cluster.Plo"; else rm -f ".deps/cluster.Tpo"; exit 1; fi
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c cluster.c -fPIC -DPIC -o .libs/cluster.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c cluster.c -o cluster.o >/dev/null 2>&1
if /bin/sh /usr/local/bin/libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT scluster.lo -MD -MP -MF ".deps/scluster.Tpo" -c -o scluster.lo scluster.c; then mv -f ".deps/scluster.Tpo" ".deps/scluster.Plo"; else rm -f ".deps/scluster.Tpo"; exit 1; fi
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT scluster.lo -MD -MP -MF .deps/scluster.Tpo -c scluster.c -fPIC -DPIC -o .libs/scluster.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT scluster.lo -MD -MP -MF .deps/scluster.Tpo -c scluster.c -o scluster.o >/dev/null 2>&1
if /bin/sh /usr/local/bin/libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT root_finder.lo -MD -MP -MF ".deps/root_finder.Tpo" -c -o root_finder.lo root_finder.c; then mv -f ".deps/root_finder.Tpo" ".deps/root_finder.Plo"; else rm -f ".deps/root_finder.Tpo"; exit 1; fi
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT root_finder.lo -MD -MP -MF .deps/root_finder.Tpo -c root_finder.c -fPIC -DPIC -o .libs/root_finder.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT root_finder.lo -MD -MP -MF .deps/root_finder.Tpo -c root_finder.c -o root_finder.o >/dev/null 2>&1
if /bin/sh /usr/local/bin/libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT reestimate.lo -MD -MP -MF ".deps/reestimate.Tpo" -c -o reestimate.lo reestimate.c; then mv -f ".deps/reestimate.Tpo" ".deps/reestimate.Plo"; else rm -f ".deps/reestimate.Tpo"; exit 1; fi
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT reestimate.lo -MD -MP -MF .deps/reestimate.Tpo -c reestimate.c -fPIC -DPIC -o .libs/reestimate.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT reestimate.lo -MD -MP -MF .deps/reestimate.Tpo -c reestimate.c -o reestimate.o >/dev/null 2>&1
if /bin/sh /usr/local/bin/libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT randvar.lo -MD -MP -MF ".deps/randvar.Tpo" -c -o randvar.lo randvar.c; then mv -f ".deps/randvar.Tpo" ".deps/randvar.Plo"; else rm -f ".deps/randvar.Tpo"; exit 1; fi
libtool: compile: cc -DHAVE_CONFIG_H -I. -I. -I.. -I.. -O2 -pipe -fno-strict-aliasing -MT randvar.lo -MD -MP -MF .deps/randvar.Tpo -c randvar.c -fPIC -DPIC -o .libs/randvar.o
randvar.c:122:21: error: use of undeclared identifier 'PHI_DATA_FILE'
char filename[] = PHI_DATA_FILE;
^
randvar.c:123:2: warning: "PHI_DATA_FILE deprecated!" [-W#warnings]
#warning "PHI_DATA_FILE deprecated!"
^
1 warning and 1 error generated.
*** Error code 1
Stop.
make[4]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.7.0/ghmm
*** Error code 1
Stop.
make[3]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.7.0/ghmm
*** Error code 1
Stop.
make[2]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.7.0
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.7.0
*** Error code 1
Stop.
make: stopped in /usr/ports/science/ghmm
===> Cleaning for ghmm-0.7.0b
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