[package - main-amd64-default][science/ghmm] Failed for ghmm-0.9.r3_2 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Wed, 08 Mar 2023 02:47:19 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: ports@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/peacac0805609_s08e66b7a37/logs/ghmm-0.9.r3_2.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=peacac0805609_s08e66b7a37
Log:
=>> Building science/ghmm
build started at Wed Mar 8 02:46:49 UTC 2023
port directory: /usr/ports/science/ghmm
package name: ghmm-0.9.r3_2
building for: FreeBSD main-amd64-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400081 amd64
maintained by: ports@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400081
Job Id: 10
!!! Jail is newer than host. (Jail: 1400081, Host: 1400073) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1400081
UNAME_v=FreeBSD 14.0-CURRENT 1400081
UNAME_r=14.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-23-ga7f8d188
MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=main-amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
ports@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--without-python --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/science/ghmm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/ghmm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/ghmm/work/.cache HOME=/wrkdirs/usr/ports/science/ghmm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/ghmm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/ghmm/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.71 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/science/ghmm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/ghmm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/ghmm/work/.cache HOME=/wrkdirs/usr/ports/science/ghmm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/ghmm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/ghmm/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.71 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -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"
--End MAKE_ENV--
--PLIST_SUB--
GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/ghmm" EXAMPLESDIR="share/examples/ghmm" DATADIR="share/ghmm" WWWDIR="www/ghmm" ETCDIR="etc/ghmm"
--End PLIST_SUB--
--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---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_53255a77=yes
CC_OUTPUT_921dbbb2_911cfe02=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
CC_OUTPUT_921dbbb2_af59ad06=yes
CC_OUTPUT_921dbbb2_a15f3fcf=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=amd64
OPSYS=FreeBSD
_OSRELEASE=14.0-CURRENT
OSREL=14.0
OSVERSION=1400081
PYTHONBASE=/usr/local
HAVE_COMPAT_IA32_KERN=YES
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 33554432
stack size (kbytes, -s) 524288
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 1024
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===> NOTICE:
The ghmm 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://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> License GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> ghmm-0.9.r3_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-amd64-default-job-10] Installing pkg-1.19.1_1...
[main-amd64-default-job-10] Extracting pkg-1.19.1_1: .......... done
===> ghmm-0.9.r3_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of ghmm-0.9.r3_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> NOTICE:
The ghmm 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://docs.freebsd.org/en/articles/contributing/#ports-contributing
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by ghmm-0.9.r3_2 for building
===========================================================================
<snip>
mv -f .deps/sreestimate.Tpo .deps/sreestimate.Plo
--- sdfoba.lo ---
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdfoba.lo -MD -MP -MF .deps/sdfoba.Tpo -c -o sdfoba.lo sdfoba.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdfoba.lo -MD -MP -MF .deps/sdfoba.Tpo -c sdfoba.c -fPIC -DPIC -o .libs/sdfoba.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdfoba.lo -MD -MP -MF .deps/sdfoba.Tpo -c sdfoba.c -o sdfoba.o >/dev/null 2>&1
--- sdmodel.lo ---
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdmodel.lo -MD -MP -MF .deps/sdmodel.Tpo -c sdmodel.c -o sdmodel.o >/dev/null 2>&1
--- sdfoba.lo ---
mv -f .deps/sdfoba.Tpo .deps/sdfoba.Plo
--- sdviterbi.lo ---
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdviterbi.lo -MD -MP -MF .deps/sdviterbi.Tpo -c -o sdviterbi.lo sdviterbi.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdviterbi.lo -MD -MP -MF .deps/sdviterbi.Tpo -c sdviterbi.c -fPIC -DPIC -o .libs/sdviterbi.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdviterbi.lo -MD -MP -MF .deps/sdviterbi.Tpo -c sdviterbi.c -o sdviterbi.o >/dev/null 2>&1
--- sdmodel.lo ---
mv -f .deps/sdmodel.Tpo .deps/sdmodel.Plo
--- pmodel.lo ---
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pmodel.lo -MD -MP -MF .deps/pmodel.Tpo -c -o pmodel.lo pmodel.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pmodel.lo -MD -MP -MF .deps/pmodel.Tpo -c pmodel.c -fPIC -DPIC -o .libs/pmodel.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pmodel.lo -MD -MP -MF .deps/pmodel.Tpo -c pmodel.c -o pmodel.o >/dev/null 2>&1
--- sdviterbi.lo ---
mv -f .deps/sdviterbi.Tpo .deps/sdviterbi.Plo
--- pviterbi.lo ---
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi.lo -MD -MP -MF .deps/pviterbi.Tpo -c -o pviterbi.lo pviterbi.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi.lo -MD -MP -MF .deps/pviterbi.Tpo -c pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o
--- pmodel.lo ---
mv -f .deps/pmodel.Tpo .deps/pmodel.Plo
--- pviterbi_propagate.lo ---
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi_propagate.lo -MD -MP -MF .deps/pviterbi_propagate.Tpo -c -o pviterbi_propagate.lo pviterbi_propagate.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi_propagate.lo -MD -MP -MF .deps/pviterbi_propagate.Tpo -c pviterbi_propagate.c -fPIC -DPIC -o .libs/pviterbi_propagate.o
--- pviterbi.lo ---
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi.lo -MD -MP -MF .deps/pviterbi.Tpo -c pviterbi.c -o pviterbi.o >/dev/null 2>&1
--- pviterbi_propagate.lo ---
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi_propagate.lo -MD -MP -MF .deps/pviterbi_propagate.Tpo -c pviterbi_propagate.c -o pviterbi_propagate.o >/dev/null 2>&1
--- pviterbi.lo ---
mv -f .deps/pviterbi.Tpo .deps/pviterbi.Plo
--- fbgibbs.lo ---
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT fbgibbs.lo -MD -MP -MF .deps/fbgibbs.Tpo -c -o fbgibbs.lo fbgibbs.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT fbgibbs.lo -MD -MP -MF .deps/fbgibbs.Tpo -c fbgibbs.c -fPIC -DPIC -o .libs/fbgibbs.o
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT fbgibbs.lo -MD -MP -MF .deps/fbgibbs.Tpo -c fbgibbs.c -o fbgibbs.o >/dev/null 2>&1
--- pviterbi_propagate.lo ---
mv -f .deps/pviterbi_propagate.Tpo .deps/pviterbi_propagate.Plo
--- cfbgibbs.lo ---
/bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cfbgibbs.lo -MD -MP -MF .deps/cfbgibbs.Tpo -c -o cfbgibbs.lo cfbgibbs.c
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cfbgibbs.lo -MD -MP -MF .deps/cfbgibbs.Tpo -c cfbgibbs.c -fPIC -DPIC -o .libs/cfbgibbs.o
cfbgibbs.c:33:1: warning: '/*' within block comment [-Wcomment]
/* computes tupleSize and preposition
^
--- fbgibbs.lo ---
mv -f .deps/fbgibbs.Tpo .deps/fbgibbs.Plo
--- cfbgibbs.lo ---
1 warning generated.
libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cfbgibbs.lo -MD -MP -MF .deps/cfbgibbs.Tpo -c cfbgibbs.c -o cfbgibbs.o >/dev/null 2>&1
mv -f .deps/cfbgibbs.Tpo .deps/cfbgibbs.Plo
--- libghmm.la ---
/bin/sh ../libtool --tag=CC --mode=link cc -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -version-info 1:0:0 -fstack-protector-strong -o libghmm.la -rpath /usr/local/lib rng.lo randvar.lo matrixop.lo gauss_tail.lo mes.lo ghmm_internals.lo mprintf.lo vector.lo matrix.lo scanner.lo linkedlist.lo sequence.lo psequence.lo xmlreader.lo xmlwriter.lo model.lo foba.lo viterbi.lo reestimate.lo gradescent.lo kbest.lo discrime.lo modelutil.lo cluster.lo root_finder.lo smodel.lo sfoba.lo sviterbi.lo sreestimate.lo scluster.lo sgenerate.lo smixturehmm.lo smap_classify.lo sdmodel.lo sdfoba.lo sdviterbi.lo pmodel.lo pviterbi.lo pviterbi_propagate.lo fbgibbs.lo cfbgibbs.lo -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2
libtool: link: cc -shared -fPIC -DPIC .libs/rng.o .libs/randvar.o .libs/matrixop.o .libs/gauss_tail.o .libs/mes.o .libs/ghmm_internals.o .libs/mprintf.o .libs/vector.o .libs/matrix.o .libs/scanner.o .libs/linkedlist.o .libs/sequence.o .libs/psequence.o .libs/xmlreader.o .libs/xmlwriter.o .libs/model.o .libs/foba.o .libs/viterbi.o .libs/reestimate.o .libs/gradescent.o .libs/kbest.o .libs/discrime.o .libs/modelutil.o .libs/cluster.o .libs/root_finder.o .libs/smodel.o .libs/sfoba.o .libs/sviterbi.o .libs/sreestimate.o .libs/scluster.o .libs/sgenerate.o .libs/smixturehmm.o .libs/smap_classify.o .libs/sdmodel.o .libs/sdfoba.o .libs/sdviterbi.o .libs/pmodel.o .libs/pviterbi.o .libs/pviterbi_propagate.o .libs/fbgibbs.o .libs/cfbgibbs.o -lm -lpthread -L/usr/local/lib -lxml2 -O2 -fstack-protector-strong -fstack-protector-strong -Wl,-soname -Wl,libghmm.so.1 -o .libs/libghmm.so.1.0.0
libtool: link: (cd ".libs" && rm -f "libghmm.so.1" && ln -s "libghmm.so.1.0.0" "libghmm.so.1")
libtool: link: (cd ".libs" && rm -f "libghmm.so" && ln -s "libghmm.so.1.0.0" "libghmm.so")
libtool: link: ar cr .libs/libghmm.a rng.o randvar.o matrixop.o gauss_tail.o mes.o ghmm_internals.o mprintf.o vector.o matrix.o scanner.o linkedlist.o sequence.o psequence.o xmlreader.o xmlwriter.o model.o foba.o viterbi.o reestimate.o gradescent.o kbest.o discrime.o modelutil.o cluster.o root_finder.o smodel.o sfoba.o sviterbi.o sreestimate.o scluster.o sgenerate.o smixturehmm.o smap_classify.o sdmodel.o sdfoba.o sdviterbi.o pmodel.o pviterbi.o pviterbi_propagate.o fbgibbs.o cfbgibbs.o
libtool: link: ranlib .libs/libghmm.a
libtool: link: ( cd ".libs" && rm -f "libghmm.la" && ln -s "../libghmm.la" "libghmm.la" )
Making all in tools
--- all ---
/usr/bin/make all-recursive
--- all-recursive ---
Making all in .
--- probdist.o ---
--- cluster.o ---
--- probdist.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT probdist.o -MD -MP -MF .deps/probdist.Tpo -c -o probdist.o probdist.c
--- cluster.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cluster.o -MD -MP -MF .deps/cluster.Tpo -c -o cluster.o cluster.c
mv -f .deps/cluster.Tpo .deps/cluster.Po
--- scluster.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT scluster.o -MD -MP -MF .deps/scluster.Tpo -c -o scluster.o scluster.c
--- probdist.o ---
mv -f .deps/probdist.Tpo .deps/probdist.Po
--- smix_hmm.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT smix_hmm.o -MD -MP -MF .deps/smix_hmm.Tpo -c -o smix_hmm.o smix_hmm.c
--- scluster.o ---
mv -f .deps/scluster.Tpo .deps/scluster.Po
--- smix_hmm.o ---
mv -f .deps/smix_hmm.Tpo .deps/smix_hmm.Po
--- cluster ---
--- probdist ---
/bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2
--- cluster ---
/bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2
libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2
--- probdist ---
libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2
--- smix_hmm ---
/bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2
--- scluster ---
/bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2
--- smix_hmm ---
libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2
--- scluster ---
libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2
Making all in tests
--- all-recursive ---
Making all in data
--- all-recursive ---
Making all in .
--- randvar_test.o ---
--- root_finder_test.o ---
--- randvar_test.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT randvar_test.o -MD -MP -MF .deps/randvar_test.Tpo -c -o randvar_test.o randvar_test.c
--- root_finder_test.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT root_finder_test.o -MD -MP -MF .deps/root_finder_test.Tpo -c -o root_finder_test.o root_finder_test.c
mv -f .deps/root_finder_test.Tpo .deps/root_finder_test.Po
--- coin_toss_test.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT coin_toss_test.o -MD -MP -MF .deps/coin_toss_test.Tpo -c -o coin_toss_test.o coin_toss_test.c
--- randvar_test.o ---
mv -f .deps/randvar_test.Tpo .deps/randvar_test.Po
--- two_states_three_symbols.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT two_states_three_symbols.o -MD -MP -MF .deps/two_states_three_symbols.Tpo -c -o two_states_three_symbols.o two_states_three_symbols.c
--- coin_toss_test.o ---
mv -f .deps/coin_toss_test.Tpo .deps/coin_toss_test.Po
--- libxml-test.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT libxml-test.o -MD -MP -MF .deps/libxml-test.Tpo -c -o libxml-test.o libxml-test.c
--- two_states_three_symbols.o ---
mv -f .deps/two_states_three_symbols.Tpo .deps/two_states_three_symbols.Po
--- chmm.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT chmm.o -MD -MP -MF .deps/chmm.Tpo -c -o chmm.o chmm.c
--- libxml-test.o ---
mv -f .deps/libxml-test.Tpo .deps/libxml-test.Po
--- chmm_test.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT chmm_test.o -MD -MP -MF .deps/chmm_test.Tpo -c -o chmm_test.o chmm_test.c
--- chmm.o ---
mv -f .deps/chmm.Tpo .deps/chmm.Po
--- shmm_viterbi_test.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT shmm_viterbi_test.o -MD -MP -MF .deps/shmm_viterbi_test.Tpo -c -o shmm_viterbi_test.o shmm_viterbi_test.c
--- chmm_test.o ---
mv -f .deps/chmm_test.Tpo .deps/chmm_test.Po
--- test_gsl_ran_gaussian_tail.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT test_gsl_ran_gaussian_tail.o -MD -MP -MF .deps/test_gsl_ran_gaussian_tail.Tpo -c -o test_gsl_ran_gaussian_tail.o test_gsl_ran_gaussian_tail.c
--- shmm_viterbi_test.o ---
mv -f .deps/shmm_viterbi_test.Tpo .deps/shmm_viterbi_test.Po
--- sequences_test.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sequences_test.o -MD -MP -MF .deps/sequences_test.Tpo -c -o sequences_test.o sequences_test.c
--- test_gsl_ran_gaussian_tail.o ---
mv -f .deps/test_gsl_ran_gaussian_tail.Tpo .deps/test_gsl_ran_gaussian_tail.Po
--- sequences_old_format.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sequences_old_format.o -MD -MP -MF .deps/sequences_old_format.Tpo -c -o sequences_old_format.o sequences_old_format.c
--- sequences_test.o ---
mv -f .deps/sequences_test.Tpo .deps/sequences_test.Po
--- label_higher_order_test.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT label_higher_order_test.o -MD -MP -MF .deps/label_higher_order_test.Tpo -c -o label_higher_order_test.o label_higher_order_test.c
--- sequences_old_format.o ---
mv -f .deps/sequences_old_format.Tpo .deps/sequences_old_format.Po
--- read_fa.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT read_fa.o -MD -MP -MF .deps/read_fa.Tpo -c -o read_fa.o read_fa.c
--- label_higher_order_test.o ---
mv -f .deps/label_higher_order_test.Tpo .deps/label_higher_order_test.Po
--- mcmc.o ---
cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c
--- read_fa.o ---
mv -f .deps/read_fa.Tpo .deps/read_fa.Po
--- root_finder_test ---
/bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2
--- mcmc.o ---
mcmc.c:144:3: warning: call to undeclared function 'init_priors'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
init_priors(mo, &pA, &pB, &pPi);
^
mcmc.c:146:15: warning: call to undeclared function 'ghmm_dmodel_cfbgibbs'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration]
int * Q = ghmm_dmodel_cfbgibbs(mo, my_output,
^
mcmc.c:146:9: error: incompatible integer to pointer conversion initializing 'int *' with an expression of type 'int' [-Wint-conversion]
int * Q = ghmm_dmodel_cfbgibbs(mo, my_output,
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mcmc.c:148:107: error: incompatible integer to pointer conversion passing 'int' to parameter of type 'int *'; take the address with & [-Wint-conversion]
printf("viterbi prob mcmc%f \n", ghmm_dmodel_viterbi_logp(mo, my_output->seq[0], my_output->seq_len[0], Q[0]));
^~~~
&
./ghmm/viterbi.h:75:76: note: passing argument to parameter 'state_seq' here
double ghmm_dmodel_viterbi_logp (ghmm_dmodel * mo, int *o, int len, int *state_seq);
^
2 warnings and 2 errors generated.
*** [mcmc.o] Error code 1
make[4]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/tests
--- root_finder_test ---
libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2
1 error
make[4]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/tests
make[3]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/tests
make[2]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3
make[1]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/science/ghmm