=>> Building science/ghmm build started at Wed Apr 3 19:26:44 BST 2024 port directory: /usr/ports/science/ghmm package name: ghmm-0.9.r3_2 building for: FreeBSD pkg-builder.dan.net.uk 13.2-RELEASE-p10 FreeBSD 13.2-RELEASE-p10 amd64 maintained by: bofh@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 698 Nov 6 13:35 /usr/ports/science/ghmm/Makefile Ports top last git commit: c2c35d895e Ports top unclean checkout: yes Port dir last git commit: 06df180a9e Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.99.20240122_1 Host OSVERSION: 1400097 Jail OSVERSION: 1302001 Job Id: 18 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p10 UNAME_r=13.2-RELEASE-p10 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 MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.99.20240122_1 MASTERMNT=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/18/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=13-amd64-default-dan SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/13-amd64-default-dan/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.99.20240122_1 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- bofh@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=/ccache/libexec/ccache:/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=2.72 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CCACHE_DIR="/root/.ccache" 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=/ccache/libexec/ccache:/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=2.72 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 " CCACHE_DIR="/root/.ccache" 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=13.2 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 FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### CCACHE_CPP2=1 WITH_SSP_PORTS=yes WITH_SSP=yes #WITH_LTO=yes DISABLE_LICENSES=yes LICENSES_ACCEPTED=AGPLv3 APACHE10 APACHE11 APACHE20 ART10 ARTPERL10 ART20 BSD BSD2CLAUSE BSD3CLAUSE BSD4CLAUSE BSL CC0-1.0 CDDL ClArtistic EPL GFDL GMGPL GPLv1 GPLv2 GPLv3 GPLv3RLE ISCL LGPL20 LGPL21 LGPL3 LPPL10 LPPL11 LPPL12 LPPL13 LPPL13a LPPL13b LPPL13c MIT MPL OpenSSL OFL10 OFL11 OWL PostgreSQL PHP202 PHP30 PHP301 PSFL RUBY ZLIB ZPL21 SVM-Light EULA ALASIR Microsoft-exFAT SIMIAN UDEVGAME unknown MTA COMMERCIAL teamspeak NO_LICENSES_DIALOGS=yes #### #### NO_IGNORE=yes DEFAULT_VERSIONS+=ssl=openssl mysql=8.0 imagemagick=7 samba=4.13 java=18 WITH_SETID_MODE=force PHP_ZTS=enabled OPTIONS_UNSET+=OPENJPEG OPTIONS_UNSET+=GSSAPI_BASE OPTIONS_SET+=ZTS OPTIONS_SET+=GSSAPI_NONE WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache NO_CCACHE_DEPEND=1 CCACHE_WRAPPER_PATH= /ccache/libexec/ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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) 8192 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-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ghmm-0.9.r3_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.9_1.pkg [pkg-builder.dan.net.uk] Installing pkg-1.20.9_1... [pkg-builder.dan.net.uk] Extracting pkg-1.20.9_1: .......... done ===> ghmm-0.9.r3_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ghmm-0.9.r3_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ghmm-0.9.r3_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ghmm-0.9.r3_2 for building => SHA256 Checksum OK for ghmm-0.9-rc3.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ghmm-0.9.r3_2 for building ===> Extracting for ghmm-0.9.r3_2 => SHA256 Checksum OK for ghmm-0.9-rc3.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for ghmm-0.9.r3_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ghmm-0.9.r3_2 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.1.1,1.pkg [pkg-builder.dan.net.uk] Installing pkgconf-2.1.1,1... [pkg-builder.dan.net.uk] Extracting pkgconf-2.1.1,1: .......... done ===> ghmm-0.9.r3_2 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of ghmm-0.9.r3_2 ===> ghmm-0.9.r3_2 depends on package: autoconf>=2.72 - not found ===> Installing existing package /packages/All/autoconf-2.72.pkg [pkg-builder.dan.net.uk] Installing autoconf-2.72... [pkg-builder.dan.net.uk] `-- Installing autoconf-switch-20220527... [pkg-builder.dan.net.uk] `-- Extracting autoconf-switch-20220527: ....... done [pkg-builder.dan.net.uk] `-- Installing indexinfo-0.3.1... [pkg-builder.dan.net.uk] `-- Extracting indexinfo-0.3.1: . done [pkg-builder.dan.net.uk] `-- Installing m4-1.4.19_1,1... [pkg-builder.dan.net.uk] | `-- Installing gettext-runtime-0.22.3_1... [pkg-builder.dan.net.uk] | `-- Extracting gettext-runtime-0.22.3_1: .......... done [pkg-builder.dan.net.uk] | `-- Installing libsigsegv-2.14... [pkg-builder.dan.net.uk] | `-- Extracting libsigsegv-2.14: ..... done [pkg-builder.dan.net.uk] `-- Extracting m4-1.4.19_1,1: .......... done [pkg-builder.dan.net.uk] `-- Installing perl5-5.36.3_1... [pkg-builder.dan.net.uk] `-- Extracting perl5-5.36.3_1: .......... done [pkg-builder.dan.net.uk] Extracting autoconf-2.72: .......... done ===== Message from libsigsegv-2.14: -- Note that the stackoverflow handling functions of this library need procfs mounted on /proc. ===> ghmm-0.9.r3_2 depends on package: autoconf>=2.72 - found ===> Returning to build of ghmm-0.9.r3_2 ===> ghmm-0.9.r3_2 depends on package: automake>=1.16.5 - not found ===> Installing existing package /packages/All/automake-1.16.5_1.pkg [pkg-builder.dan.net.uk] Installing automake-1.16.5_1... [pkg-builder.dan.net.uk] Extracting automake-1.16.5_1: .......... done ===> ghmm-0.9.r3_2 depends on package: automake>=1.16.5 - found ===> Returning to build of ghmm-0.9.r3_2 ===> ghmm-0.9.r3_2 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.4.7_2.pkg [pkg-builder.dan.net.uk] Installing libtool-2.4.7_2... [pkg-builder.dan.net.uk] Extracting libtool-2.4.7_2: .......... done ===> ghmm-0.9.r3_2 depends on executable: libtoolize - found ===> Returning to build of ghmm-0.9.r3_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ghmm-0.9.r3_2 depends on shared library: libxml2.so - not found ===> Installing existing package /packages/All/libxml2-2.11.7.pkg [pkg-builder.dan.net.uk] Installing libxml2-2.11.7... [pkg-builder.dan.net.uk] `-- Installing readline-8.2.10... [pkg-builder.dan.net.uk] `-- Extracting readline-8.2.10: .......... done [pkg-builder.dan.net.uk] Extracting libxml2-2.11.7: .......... done ===> ghmm-0.9.r3_2 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> Returning to build of ghmm-0.9.r3_2 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for ghmm-0.9.r3_2 autoreconf2.72: warning: autoconf input should be named 'configure.ac', not 'configure.in' aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.in, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:40: warning: file 'version.m4' included several times configure.in:47: warning: 'AM_CONFIG_HEADER': this macro is obsolete. configure.in:47: You should use the 'AC_CONFIG_HEADERS' macro instead. ./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from... aclocal.m4:9806: AM_CONFIG_HEADER is expanded from... configure.in:47: the top level configure.in:63: warning: The macro 'AM_PROG_LIBTOOL' is obsolete. configure.in:63: You should run autoupdate. aclocal.m4:123: AM_PROG_LIBTOOL is expanded from... configure.in:63: the top level configure.in:75: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:75: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:75: the top level configure.in:93: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:93: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:93: the top level configure.in:104: warning: The macro 'AC_LANG_C' is obsolete. configure.in:104: You should run autoupdate. ./lib/autoconf/c.m4:72: AC_LANG_C is expanded from... configure.in:104: the top level configure.in:111: warning: The macro 'AC_HEADER_STDC' is obsolete. configure.in:111: You should run autoupdate. ./lib/autoconf/headers.m4:663: AC_HEADER_STDC is expanded from... configure.in:111: the top level configure.in:117: warning: The macro 'AC_HEADER_TIME' is obsolete. configure.in:117: You should run autoupdate. ./lib/autoconf/headers.m4:702: AC_HEADER_TIME is expanded from... configure.in:117: the top level configure.in:136: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:136: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:136: the top level configure.in:135: warning: The macro 'AC_TRY_RUN' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2995: AC_TRY_RUN is expanded from... acinclude.m4:10: AM_PATH_GSL is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:135: warning: The macro 'AC_TRY_LINK' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... acinclude.m4:10: AM_PATH_GSL is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:135: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:135: warning: The macro 'AC_TRY_LINK' is obsolete. configure.in:135: You should run autoupdate. ./lib/autoconf/general.m4:2918: AC_TRY_LINK is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:135: the top level configure.in:194: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:194: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:194: the top level configure.in:207: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:207: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... configure.in:207: the top level configure.in:206: warning: The macro 'AC_TRY_COMPILE' is obsolete. configure.in:206: You should run autoupdate. ./lib/autoconf/general.m4:2845: AC_TRY_COMPILE is expanded from... lib/m4sugar/m4sh.m4:697: AS_IF is expanded from... ./lib/autoconf/general.m4:1534: AC_ARG_ENABLE is expanded from... configure.in:206: the top level configure.in:332: warning: The macro 'AC_HELP_STRING' is obsolete. configure.in:332: You should run autoupdate. ./lib/autoconf/general.m4:204: AC_HELP_STRING is expanded from... ./lib/autoconf/general.m4:1553: AC_ARG_WITH is expanded from... configure.in:332: the top level configure.in:363: warning: AC_OUTPUT should be used without arguments. configure.in:363: You should run autoupdate. autoheader2.72: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:62: installing './compile' configure.in:49: installing './missing' ghmm/Makefile.am:77: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' ghmm/Makefile.am: installing './depcomp' tests/Makefile.am:51: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') parallel-tests: installing './test-driver' tools/Makefile.am:48: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of cc... gcc3 checking build system type... amd64-portbld-freebsd13.2 checking host system type... amd64-portbld-freebsd13.2 checking how to print strings... printf checking for a sed that does not truncate output... (cached) /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 fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 524288 checking how to convert amd64-portbld-freebsd13.2 file names to amd64-portbld-freebsd13.2 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd13.2 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... no checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/time.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) 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... freebsd13.2 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 checking for gawk... (cached) /usr/bin/awk checking for doxygen... no checking for rm... /bin/rm checking for pkg-config... /usr/local/bin/pkg-config checking for expect... no checking for runtest... no configure: obsolete features disabled configure: unsupported features disabled checking for pthread_join in -lpthread... yes checking for egrep... (cached) /usr/bin/egrep checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking whether struct tm is in sys/time.h or time.h... time.h checking for sqrt in -lm... yes checking for exp in -lm... yes checking for pow in -lm... yes configure: "not using gsl" checking for cos in -lm... yes configure: "not using diagonal covariance matrix hack" configure: "not using lapack" configure: using internal Mersenne-Twister random number generator checking libxml2 version... ... ok checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating ghmm/Makefile config.status: creating ghmm/ghmmconfig.h config.status: creating tools/Makefile config.status: creating tests/Makefile config.status: creating tests/data/Makefile config.status: creating tools/ghmm-config config.status: creating ghmmwrapper/Makefile config.status: creating HMMEd/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands rm: libtoolT: No such file or directory =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for ghmm-0.9.r3_2 /usr/bin/make all-recursive Making all in ghmm Making all in . /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 rng.lo -MD -MP -MF .deps/rng.Tpo -c -o rng.lo rng.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 rng.lo -MD -MP -MF .deps/rng.Tpo -c rng.c -fPIC -DPIC -o .libs/rng.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 rng.lo -MD -MP -MF .deps/rng.Tpo -c rng.c -o rng.o >/dev/null 2>&1 mv -f .deps/rng.Tpo .deps/rng.Plo /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 randvar.lo -MD -MP -MF .deps/randvar.Tpo -c -o randvar.lo randvar.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 randvar.lo -MD -MP -MF .deps/randvar.Tpo -c randvar.c -fPIC -DPIC -o .libs/randvar.o randvar.c:449:1: warning: non-void function does not return a value [-Wreturn-type] } ^ 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 randvar.lo -MD -MP -MF .deps/randvar.Tpo -c randvar.c -o randvar.o >/dev/null 2>&1 mv -f .deps/randvar.Tpo .deps/randvar.Plo /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 matrixop.lo -MD -MP -MF .deps/matrixop.Tpo -c -o matrixop.lo matrixop.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 matrixop.lo -MD -MP -MF .deps/matrixop.Tpo -c matrixop.c -fPIC -DPIC -o .libs/matrixop.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 matrixop.lo -MD -MP -MF .deps/matrixop.Tpo -c matrixop.c -o matrixop.o >/dev/null 2>&1 mv -f .deps/matrixop.Tpo .deps/matrixop.Plo /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 gauss_tail.lo -MD -MP -MF .deps/gauss_tail.Tpo -c -o gauss_tail.lo gauss_tail.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 gauss_tail.lo -MD -MP -MF .deps/gauss_tail.Tpo -c gauss_tail.c -fPIC -DPIC -o .libs/gauss_tail.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 gauss_tail.lo -MD -MP -MF .deps/gauss_tail.Tpo -c gauss_tail.c -o gauss_tail.o >/dev/null 2>&1 mv -f .deps/gauss_tail.Tpo .deps/gauss_tail.Plo /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 mes.lo -MD -MP -MF .deps/mes.Tpo -c -o mes.lo mes.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 mes.lo -MD -MP -MF .deps/mes.Tpo -c mes.c -fPIC -DPIC -o .libs/mes.o mes.c:148:8: warning: address of array 'mes_process' will always evaluate to 'true' [-Wpointer-bool-conversion] if (!mes_process) ~^~~~~~~~~~~ 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 mes.lo -MD -MP -MF .deps/mes.Tpo -c mes.c -o mes.o >/dev/null 2>&1 mv -f .deps/mes.Tpo .deps/mes.Plo /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 ghmm_internals.lo -MD -MP -MF .deps/ghmm_internals.Tpo -c -o ghmm_internals.lo ghmm_internals.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 ghmm_internals.lo -MD -MP -MF .deps/ghmm_internals.Tpo -c ghmm_internals.c -fPIC -DPIC -o .libs/ghmm_internals.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 ghmm_internals.lo -MD -MP -MF .deps/ghmm_internals.Tpo -c ghmm_internals.c -o ghmm_internals.o >/dev/null 2>&1 mv -f .deps/ghmm_internals.Tpo .deps/ghmm_internals.Plo /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 mprintf.lo -MD -MP -MF .deps/mprintf.Tpo -c -o mprintf.lo mprintf.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 mprintf.lo -MD -MP -MF .deps/mprintf.Tpo -c mprintf.c -fPIC -DPIC -o .libs/mprintf.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 mprintf.lo -MD -MP -MF .deps/mprintf.Tpo -c mprintf.c -o mprintf.o >/dev/null 2>&1 mv -f .deps/mprintf.Tpo .deps/mprintf.Plo /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 vector.lo -MD -MP -MF .deps/vector.Tpo -c -o vector.lo vector.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 vector.lo -MD -MP -MF .deps/vector.Tpo -c vector.c -fPIC -DPIC -o .libs/vector.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 vector.lo -MD -MP -MF .deps/vector.Tpo -c vector.c -o vector.o >/dev/null 2>&1 mv -f .deps/vector.Tpo .deps/vector.Plo /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 matrix.lo -MD -MP -MF .deps/matrix.Tpo -c -o matrix.lo matrix.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 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.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT matrix.lo -MD -MP -MF .deps/matrix.Tpo -c matrix.c -o matrix.o >/dev/null 2>&1 mv -f .deps/matrix.Tpo .deps/matrix.Plo /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 scanner.lo -MD -MP -MF .deps/scanner.Tpo -c -o scanner.lo scanner.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 scanner.lo -MD -MP -MF .deps/scanner.Tpo -c scanner.c -fPIC -DPIC -o .libs/scanner.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 scanner.lo -MD -MP -MF .deps/scanner.Tpo -c scanner.c -o scanner.o >/dev/null 2>&1 mv -f .deps/scanner.Tpo .deps/scanner.Plo /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 linkedlist.lo -MD -MP -MF .deps/linkedlist.Tpo -c -o linkedlist.lo linkedlist.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 linkedlist.lo -MD -MP -MF .deps/linkedlist.Tpo -c linkedlist.c -fPIC -DPIC -o .libs/linkedlist.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 linkedlist.lo -MD -MP -MF .deps/linkedlist.Tpo -c linkedlist.c -o linkedlist.o >/dev/null 2>&1 mv -f .deps/linkedlist.Tpo .deps/linkedlist.Plo /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 sequence.lo -MD -MP -MF .deps/sequence.Tpo -c -o sequence.lo sequence.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 sequence.lo -MD -MP -MF .deps/sequence.Tpo -c sequence.c -fPIC -DPIC -o .libs/sequence.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 sequence.lo -MD -MP -MF .deps/sequence.Tpo -c sequence.c -o sequence.o >/dev/null 2>&1 mv -f .deps/sequence.Tpo .deps/sequence.Plo /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 psequence.lo -MD -MP -MF .deps/psequence.Tpo -c -o psequence.lo psequence.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 psequence.lo -MD -MP -MF .deps/psequence.Tpo -c psequence.c -fPIC -DPIC -o .libs/psequence.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 psequence.lo -MD -MP -MF .deps/psequence.Tpo -c psequence.c -o psequence.o >/dev/null 2>&1 mv -f .deps/psequence.Tpo .deps/psequence.Plo /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 xmlreader.lo -MD -MP -MF .deps/xmlreader.Tpo -c -o xmlreader.lo xmlreader.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 xmlreader.lo -MD -MP -MF .deps/xmlreader.Tpo -c xmlreader.c -fPIC -DPIC -o .libs/xmlreader.o xmlreader.c:403:8: warning: assigning to 'char *' from 'xmlChar *' (aka 'unsigned char *') converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign] desc = xmlGetProp(cur, BAD_CAST "desc"); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xmlreader.c:1022:13: warning: assigning to 'char *' from 'xmlChar *' (aka 'unsigned char *') converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign] modelname = xmlGetProp(cur, BAD_CAST "name"); ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xmlreader.c:1291:27: warning: comparison of array 'fileDTD' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (filename != NULL && fileDTD != NULL) { ^~~~~~~ ~~~~ 3 warnings 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 xmlreader.lo -MD -MP -MF .deps/xmlreader.Tpo -c xmlreader.c -o xmlreader.o >/dev/null 2>&1 mv -f .deps/xmlreader.Tpo .deps/xmlreader.Plo /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 xmlwriter.lo -MD -MP -MF .deps/xmlwriter.Tpo -c -o xmlwriter.lo xmlwriter.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 xmlwriter.lo -MD -MP -MF .deps/xmlwriter.Tpo -c xmlwriter.c -fPIC -DPIC -o .libs/xmlwriter.o xmlwriter.c:356:82: warning: format string is not a string literal (potentially insecure) [-Wformat-security] rc = xmlTextWriterWriteFormatElement(writer, BAD_CAST "backgroundKey", f->model.d[moNo]->bp->name[bgId]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ xmlwriter.c:356:82: note: treat the string as an argument to avoid this rc = xmlTextWriterWriteFormatElement(writer, BAD_CAST "backgroundKey", f->model.d[moNo]->bp->name[bgId]); ^ "%s", xmlwriter.c:1008:62: warning: passing 'char *' to parameter of type 'const xmlChar *' (aka 'const unsigned char *') converts between pointers to integer types where one is of the unique plain 'char' type and the other is not [-Wpointer-sign] if (xmlTextWriterWriteAttribute(writer, BAD_CAST "name", w_name)) ^~~~~~ /usr/local/include/libxml2/libxml/xmlwriter.h:217:55: note: passing argument to parameter 'content' here content); ^ 2 warnings 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 xmlwriter.lo -MD -MP -MF .deps/xmlwriter.Tpo -c xmlwriter.c -o xmlwriter.o >/dev/null 2>&1 mv -f .deps/xmlwriter.Tpo .deps/xmlwriter.Plo /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 model.lo -MD -MP -MF .deps/model.Tpo -c -o model.lo model.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 model.lo -MD -MP -MF .deps/model.Tpo -c model.c -fPIC -DPIC -o .libs/model.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 model.lo -MD -MP -MF .deps/model.Tpo -c model.c -o model.o >/dev/null 2>&1 mv -f .deps/model.Tpo .deps/model.Plo /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 foba.lo -MD -MP -MF .deps/foba.Tpo -c -o foba.lo foba.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 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.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT foba.lo -MD -MP -MF .deps/foba.Tpo -c foba.c -o foba.o >/dev/null 2>&1 mv -f .deps/foba.Tpo .deps/foba.Plo /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 viterbi.lo -MD -MP -MF .deps/viterbi.Tpo -c -o viterbi.lo viterbi.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 viterbi.lo -MD -MP -MF .deps/viterbi.Tpo -c viterbi.c -fPIC -DPIC -o .libs/viterbi.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 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-fno-strict-aliasing -I/usr/local/include/libxml2 -MT discrime.lo -MD -MP -MF .deps/discrime.Tpo -c -o discrime.lo discrime.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 discrime.lo -MD -MP -MF .deps/discrime.Tpo -c discrime.c -fPIC -DPIC -o .libs/discrime.o discrime.c:1134:9: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value] if (fabs (nsum) > 1e-200 && psum < nsum) ^ discrime.c:1134:9: note: use function 'fabsl' instead if (fabs (nsum) > 1e-200 && psum < nsum) ^~~~ fabsl 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 discrime.lo -MD -MP -MF .deps/discrime.Tpo -c 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-MT smodel.lo -MD -MP -MF .deps/smodel.Tpo -c -o smodel.lo smodel.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 smodel.lo -MD -MP -MF .deps/smodel.Tpo -c smodel.c -fPIC -DPIC -o .libs/smodel.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 smodel.lo -MD -MP -MF .deps/smodel.Tpo -c smodel.c -o smodel.o >/dev/null 2>&1 mv -f .deps/smodel.Tpo .deps/smodel.Plo /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 sfoba.lo -MD -MP -MF .deps/sfoba.Tpo -c -o sfoba.lo sfoba.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 sfoba.lo -MD -MP -MF .deps/sfoba.Tpo -c sfoba.c -fPIC -DPIC -o .libs/sfoba.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 sfoba.lo -MD -MP -MF .deps/sfoba.Tpo -c sfoba.c -o sfoba.o >/dev/null 2>&1 mv -f .deps/sfoba.Tpo .deps/sfoba.Plo /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 sviterbi.lo -MD -MP -MF .deps/sviterbi.Tpo -c -o sviterbi.lo sviterbi.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 sviterbi.lo -MD -MP -MF .deps/sviterbi.Tpo -c sviterbi.c -fPIC -DPIC -o .libs/sviterbi.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 sviterbi.lo -MD -MP -MF .deps/sviterbi.Tpo -c sviterbi.c -o sviterbi.o >/dev/null 2>&1 mv -f .deps/sviterbi.Tpo .deps/sviterbi.Plo /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 sreestimate.lo -MD -MP -MF .deps/sreestimate.Tpo -c -o sreestimate.lo sreestimate.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 sreestimate.lo -MD -MP -MF .deps/sreestimate.Tpo -c sreestimate.c -fPIC -DPIC -o .libs/sreestimate.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 sreestimate.lo -MD -MP -MF .deps/sreestimate.Tpo -c sreestimate.c -o sreestimate.o >/dev/null 2>&1 mv -f .deps/sreestimate.Tpo .deps/sreestimate.Plo /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 scluster.lo -MD -MP -MF .deps/scluster.Tpo -c -o scluster.lo scluster.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 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.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT scluster.lo -MD -MP -MF .deps/scluster.Tpo -c scluster.c -o scluster.o >/dev/null 2>&1 mv -f .deps/scluster.Tpo .deps/scluster.Plo /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 sgenerate.lo -MD -MP -MF .deps/sgenerate.Tpo -c -o sgenerate.lo sgenerate.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 sgenerate.lo -MD -MP -MF .deps/sgenerate.Tpo -c sgenerate.c -fPIC -DPIC -o .libs/sgenerate.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 sgenerate.lo -MD -MP -MF .deps/sgenerate.Tpo -c sgenerate.c -o sgenerate.o >/dev/null 2>&1 mv -f .deps/sgenerate.Tpo .deps/sgenerate.Plo /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 smixturehmm.lo -MD -MP -MF .deps/smixturehmm.Tpo -c -o smixturehmm.lo smixturehmm.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 smixturehmm.lo -MD -MP -MF .deps/smixturehmm.Tpo -c smixturehmm.c -fPIC -DPIC -o .libs/smixturehmm.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 smixturehmm.lo -MD -MP -MF .deps/smixturehmm.Tpo -c 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-f .deps/smap_classify.Tpo .deps/smap_classify.Plo /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 sdmodel.lo -MD -MP -MF .deps/sdmodel.Tpo -c -o sdmodel.lo sdmodel.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 sdmodel.lo -MD -MP -MF .deps/sdmodel.Tpo -c sdmodel.c -fPIC -DPIC -o .libs/sdmodel.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 sdmodel.lo -MD -MP -MF .deps/sdmodel.Tpo -c sdmodel.c -o sdmodel.o >/dev/null 2>&1 mv -f .deps/sdmodel.Tpo .deps/sdmodel.Plo /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 mv -f .deps/sdfoba.Tpo .deps/sdfoba.Plo /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 mv -f .deps/sdviterbi.Tpo .deps/sdviterbi.Plo /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 mv -f .deps/pmodel.Tpo .deps/pmodel.Plo /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 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 mv -f .deps/pviterbi.Tpo .deps/pviterbi.Plo /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 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 mv -f .deps/pviterbi_propagate.Tpo .deps/pviterbi_propagate.Plo /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 mv -f .deps/fbgibbs.Tpo .deps/fbgibbs.Plo /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 ^ 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 /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 /usr/bin/make all-recursive Making all in . 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 mv -f .deps/probdist.Tpo .deps/probdist.Po /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 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 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 /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 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-lpthread -L/usr/local/lib -lxml2 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 mv -f .deps/smix_hmm.Tpo .deps/smix_hmm.Po /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 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 Making all in tests Making all in data Making all in . 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 mv -f .deps/randvar_test.Tpo .deps/randvar_test.Po /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 randvar_test randvar_test.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 randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 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 /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 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 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 mv -f .deps/coin_toss_test.Tpo .deps/coin_toss_test.Po /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 coin_toss_test coin_toss_test.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 coin_toss_test coin_toss_test.o 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-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 mv -f .deps/libxml-test.Tpo .deps/libxml-test.Po /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 libxml-test libxml-test.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 libxml-test libxml-test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 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 mv -f .deps/chmm.Tpo .deps/chmm.Po /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 chmm chmm.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 chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 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 mv -f .deps/chmm_test.Tpo .deps/chmm_test.Po /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 chmm_test chmm_test.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 chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 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 mv -f .deps/shmm_viterbi_test.Tpo .deps/shmm_viterbi_test.Po /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 shmm_viterbi_test shmm_viterbi_test.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 shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 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 mv -f .deps/test_gsl_ran_gaussian_tail.Tpo .deps/test_gsl_ran_gaussian_tail.Po /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 test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.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 test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 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 mv -f .deps/sequences_test.Tpo .deps/sequences_test.Po /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 sequences_test sequences_test.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 sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 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 mv -f .deps/sequences_old_format.Tpo .deps/sequences_old_format.Po /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 sequences_old_format sequences_old_format.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 sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 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 mv -f .deps/label_higher_order_test.Tpo .deps/label_higher_order_test.Po /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 label_higher_order_test label_higher_order_test.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 label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 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 mv -f .deps/read_fa.Tpo .deps/read_fa.Po /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 read_fa read_fa.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 read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 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 mcmc.c:144:3: warning: implicit declaration of function 'init_priors' is invalid in C99 [-Wimplicit-function-declaration] init_priors(mo, &pA, &pB, &pPi); ^ mcmc.c:146:15: warning: implicit declaration of function 'ghmm_dmodel_cfbgibbs' is invalid in C99 [-Wimplicit-function-declaration] int * Q = ghmm_dmodel_cfbgibbs(mo, my_output, ^ mcmc.c:146:9: warning: 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: warning: 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); ^ 4 warnings generated. mv -f .deps/mcmc.Tpo .deps/mcmc.Po /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 mcmc mcmc.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 mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for ghmm-0.9.r3_2 ===> Generating temporary packing list if test -z 'strip'; then /usr/bin/make INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/install-sh -c -s" install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/install-sh -c -s" INSTALL_STRIP_FLAG=-s install; else /usr/bin/make INSTALL_PROGRAM="/bin/sh /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/install-sh -c -s" install_sh_PROGRAM="/bin/sh /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/install-sh -c -s" INSTALL_STRIP_FLAG=-s "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; fi Making install in ghmm Making install in . /bin/mkdir -p '/wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c -s libghmm.la '/wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libghmm.so.1.0.0 /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib/libghmm.so.1.0.0 libtool: install: strip --strip-unneeded /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib/libghmm.so.1.0.0 libtool: install: (cd /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib && { ln -s -f libghmm.so.1.0.0 libghmm.so.1 || { rm -f libghmm.so.1 && ln -s libghmm.so.1.0.0 libghmm.so.1; }; }) libtool: install: (cd /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib && { ln -s -f libghmm.so.1.0.0 libghmm.so || { rm -f libghmm.so && ln -s libghmm.so.1.0.0 libghmm.so; }; }) libtool: install: /usr/bin/install -c .libs/libghmm.lai /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib/libghmm.la libtool: install: /usr/bin/install -c .libs/libghmm.a /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib/libghmm.a libtool: install: strip --strip-debug /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib/libghmm.a libtool: install: chmod 644 /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib/libghmm.a libtool: install: ranlib /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/lib/libghmm.a ranlib: warning: can't find .strtab section ranlib: warning: can't find .strtab section ranlib: warning: can't find .strtab section ranlib: warning: can't find .strtab section ranlib: warning: can't find .strtab section libtool: warning: remember to run 'libtool --finish /usr/local/lib' /bin/mkdir -p '/wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/include/ghmm' install -m 0644 ghmm.h ghmmconfig.h sequence.h psequence.h xmlreader.h xmlwriter.h model.h foba.h viterbi.h gradescent.h kbest.h discrime.h cluster.h scluster.h reestimate.h sfoba.h sviterbi.h smodel.h sdmodel.h sdfoba.h sreestimate.h sgenerate.h smixturehmm.h smap_classify.h pmodel.h pviterbi.h pviterbi_propagate.h rng.h scanner.h obsolete.h unsupported.h fbgibbs.h cfbgibbs.h '/wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/include/ghmm' Making install in tools /usr/bin/make install-recursive Making install in . /bin/mkdir -p '/wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ../libtool --mode=install /bin/sh /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/install-sh -c -s probdist cluster scluster smix_hmm '/wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/bin' libtool: install: /bin/sh /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/install-sh -c -s probdist /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/bin/probdist libtool: install: /bin/sh /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/install-sh -c -s cluster /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/bin/cluster libtool: install: /bin/sh /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/install-sh -c -s scluster /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/bin/scluster libtool: install: /bin/sh /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/install-sh -c -s smix_hmm /wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/bin/smix_hmm /bin/mkdir -p '/wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/bin' install -m 555 ghmm-config '/wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/bin' Making install in tests Making install in data Making install in . /bin/mkdir -p '/wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/share/ghmm' install -m 0644 doc/ghmm.dtd.1.0 '/wrkdirs/usr/ports/science/ghmm/work/stage/usr/local/share/ghmm' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2024-04-03T18:26:44+0000' 'PKG_NOTE_ports_top_git_hash=c2c35d895e' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=06df180a9e' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.99.20240122_1' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for ghmm-0.9.r3_2 ===> Building ghmm-0.9.r3_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for ghmm-0.9.r3_2 build of science/ghmm | ghmm-0.9.r3_2 ended at Wed Apr 3 19:27:43 BST 2024 build time: 00:00:59