=>> Building science/ghmm build started at Thu Mar 12 12:45:43 EDT 2026 port directory: /usr/ports/science/ghmm package name: ghmm-0.9.r3_3 building for: FreeBSD pkg.DaveG.ca 14.4-RELEASE FreeBSD 14.4-RELEASE 1404000 amd64 maintained by: bofh@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 611 Jul 9 2025 /usr/ports/science/ghmm/Makefile Ports top last git commit: 26b198eb3ee3 Ports top unclean checkout: no Port dir last git commit: 3068854dd026 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1404000 Job Id: 07 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1404000 UNAME_v=FreeBSD 14.4-RELEASE 1404000 UNAME_r=14.4-RELEASE 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=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/07/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_4_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_4_x64-HEAD-ALL/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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=/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 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=2.72 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing " 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=14.4 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--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 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 #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### Misc Poudriere #### .include "/etc/make.conf.ports_env" 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) 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 pipebuf (-y) 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_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> ghmm-0.9.r3_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ghmm-0.9.r3_3 =========================================================================== =================================================== ===== 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_3 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by ghmm-0.9.r3_3 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_3 for building ===> Extracting for ghmm-0.9.r3_3 => 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_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ghmm-0.9.r3_3 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [pkg.DaveG.ca] Installing pkgconf-2.4.3,1... [pkg.DaveG.ca] Extracting pkgconf-2.4.3,1: .......... done ===> ghmm-0.9.r3_3 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of ghmm-0.9.r3_3 ===> ghmm-0.9.r3_3 depends on package: autoconf>=2.72_1 - not found ===> Installing existing package /packages/All/autoconf-2.72_1.pkg [pkg.DaveG.ca] Installing autoconf-2.72_1... [pkg.DaveG.ca] `-- Installing autoconf-switch-20220527... [pkg.DaveG.ca] `-- Extracting autoconf-switch-20220527: ....... done [pkg.DaveG.ca] `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] `-- Installing m4-1.4.20,1... [pkg.DaveG.ca] | `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] | `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] `-- Extracting m4-1.4.20,1: .......... done [pkg.DaveG.ca] `-- Installing perl5-5.42.0_1... [pkg.DaveG.ca] `-- Extracting perl5-5.42.0_1: .......... done [pkg.DaveG.ca] Extracting autoconf-2.72_1: .......... done ===> ghmm-0.9.r3_3 depends on package: autoconf>=2.72_1 - found ===> Returning to build of ghmm-0.9.r3_3 ===> ghmm-0.9.r3_3 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [pkg.DaveG.ca] Installing automake-1.18.1... [pkg.DaveG.ca] Extracting automake-1.18.1: .......... done ===> ghmm-0.9.r3_3 depends on package: automake>=1.18.1 - found ===> Returning to build of ghmm-0.9.r3_3 ===> ghmm-0.9.r3_3 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.5.4_1.pkg [pkg.DaveG.ca] Installing libtool-2.5.4_1... [pkg.DaveG.ca] Extracting libtool-2.5.4_1: .......... done ===> ghmm-0.9.r3_3 depends on executable: libtoolize - found ===> Returning to build of ghmm-0.9.r3_3 ===> ghmm-0.9.r3_3 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> ghmm-0.9.r3_3 depends on file: /usr/local/bin/ccache - found ===> Returning to build of ghmm-0.9.r3_3 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> ghmm-0.9.r3_3 depends on shared library: libxml2.so - not found ===> Installing existing package /packages/All/libxml2-2.15.2.pkg [pkg.DaveG.ca] Installing libxml2-2.15.2... [pkg.DaveG.ca] `-- Installing readline-8.3.3... [pkg.DaveG.ca] `-- Extracting readline-8.3.3: .......... done [pkg.DaveG.ca] Extracting libxml2-2.15.2: .......... done ===> ghmm-0.9.r3_3 depends on shared library: libxml2.so - found (/usr/local/lib/libxml2.so) ===> Returning to build of ghmm-0.9.r3_3 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for ghmm-0.9.r3_3 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. aclocal.m4:9889: 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 sleep supports fractional seconds... yes checking filesystem timestamp resolution... 2 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 xargs -n works... yes checking whether UID '0' is supported by ustar format... yes checking whether GID '0' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar 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-freebsd14.4 checking host system type... amd64-portbld-freebsd14.4 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-freebsd14.4 file names to amd64-portbld-freebsd14.4 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd14.4 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... objdump 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 ranlib... ranlib checking for ar... ar checking for archiver @FILE support... no checking for strip... strip 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... freebsd14.4 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_3 --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in ghmm --- all-recursive --- Making all in . --- 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 --- --- rng.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 -Wno-error=int-conversion -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 --- randvar.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 -Wno-error=int-conversion -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 --- matrixop.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 -Wno-error=int-conversion -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 --- gauss_tail.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 -Wno-error=int-conversion -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 --- mes.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 -Wno-error=int-conversion -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 --- ghmm_internals.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 -Wno-error=int-conversion -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 --- mprintf.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 -Wno-error=int-conversion -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 --- vector.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 -Wno-error=int-conversion -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 --- matrix.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 -Wno-error=int-conversion -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 --- scanner.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 -Wno-error=int-conversion -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 --- linkedlist.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 -Wno-error=int-conversion -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 --- sequence.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 -Wno-error=int-conversion -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 --- psequence.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 -Wno-error=int-conversion -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 --- xmlreader.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 -Wno-error=int-conversion -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 --- xmlwriter.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 -Wno-error=int-conversion -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 --- model.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 -Wno-error=int-conversion -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 --- foba.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 -Wno-error=int-conversion -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 --- viterbi.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 -Wno-error=int-conversion -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 --- reestimate.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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT reestimate.lo -MD -MP -MF .deps/reestimate.Tpo -c -o reestimate.lo reestimate.c --- gradescent.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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT gradescent.lo -MD -MP -MF .deps/gradescent.Tpo -c -o gradescent.lo gradescent.c --- kbest.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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT kbest.lo -MD -MP -MF .deps/kbest.Tpo -c -o kbest.lo kbest.c --- discrime.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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT discrime.lo -MD -MP -MF .deps/discrime.Tpo -c -o discrime.lo discrime.c --- modelutil.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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT modelutil.lo -MD -MP -MF .deps/modelutil.Tpo -c -o modelutil.lo modelutil.c --- cluster.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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c -o cluster.lo cluster.c --- root_finder.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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT root_finder.lo -MD -MP -MF .deps/root_finder.Tpo -c -o root_finder.lo root_finder.c --- smodel.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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT smodel.lo -MD -MP -MF .deps/smodel.Tpo -c -o smodel.lo smodel.c --- sfoba.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 -Wno-error=int-conversion -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 --- sviterbi.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 -Wno-error=int-conversion -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 --- sreestimate.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 -Wno-error=int-conversion -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 --- scluster.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 -Wno-error=int-conversion -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 --- sgenerate.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 -Wno-error=int-conversion -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 --- smixturehmm.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 -Wno-error=int-conversion -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 --- smap_classify.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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT smap_classify.lo -MD -MP -MF .deps/smap_classify.Tpo -c -o smap_classify.lo smap_classify.c --- sdmodel.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 -Wno-error=int-conversion -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 --- 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 -Wno-error=int-conversion -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 --- 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 -Wno-error=int-conversion -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 --- 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 -Wno-error=int-conversion -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 --- 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 -Wno-error=int-conversion -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 --- 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 -Wno-error=int-conversion -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 --- 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 -Wno-error=int-conversion -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 --- 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 -Wno-error=int-conversion -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 --- mes.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- gauss_tail.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- mprintf.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- randvar.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- matrix.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- foba.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- discrime.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- vector.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- ghmm_internals.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- rng.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- xmlreader.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- smap_classify.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT smap_classify.lo -MD -MP -MF .deps/smap_classify.Tpo -c smap_classify.c -fPIC -DPIC -o .libs/smap_classify.o --- psequence.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- model.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- viterbi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- modelutil.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT modelutil.lo -MD -MP -MF .deps/modelutil.Tpo -c modelutil.c -fPIC -DPIC -o .libs/modelutil.o --- scanner.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- kbest.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT kbest.lo -MD -MP -MF .deps/kbest.Tpo -c kbest.c -fPIC -DPIC -o .libs/kbest.o --- sgenerate.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sequence.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sviterbi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- scluster.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- matrixop.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- gradescent.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT gradescent.lo -MD -MP -MF .deps/gradescent.Tpo -c gradescent.c -fPIC -DPIC -o .libs/gradescent.o --- xmlwriter.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- linkedlist.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sdfoba.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- reestimate.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT reestimate.lo -MD -MP -MF .deps/reestimate.Tpo -c reestimate.c -fPIC -DPIC -o .libs/reestimate.o --- pmodel.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- cluster.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c cluster.c -fPIC -DPIC -o .libs/cluster.o --- smodel.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- smixturehmm.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sdviterbi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sdmodel.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- root_finder.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT root_finder.lo -MD -MP -MF .deps/root_finder.Tpo -c root_finder.c -fPIC -DPIC -o .libs/root_finder.o --- sfoba.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- pviterbi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- pviterbi_propagate.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sreestimate.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- fbgibbs.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- cfbgibbs.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- cluster.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c cluster.c -o cluster.o >/dev/null 2>&1 --- scanner.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- smap_classify.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT smap_classify.lo -MD -MP -MF .deps/smap_classify.Tpo -c smap_classify.c -o smap_classify.o >/dev/null 2>&1 --- vector.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- scluster.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- ghmm_internals.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- root_finder.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT root_finder.lo -MD -MP -MF .deps/root_finder.Tpo -c root_finder.c -o root_finder.o >/dev/null 2>&1 --- rng.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- gauss_tail.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- linkedlist.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- psequence.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- modelutil.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT modelutil.lo -MD -MP -MF .deps/modelutil.Tpo -c modelutil.c -o modelutil.o >/dev/null 2>&1 --- smixturehmm.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT smixturehmm.lo -MD -MP -MF .deps/smixturehmm.Tpo -c smixturehmm.c -o smixturehmm.o >/dev/null 2>&1 --- matrixop.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- pmodel.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sdfoba.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- matrix.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- viterbi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT viterbi.lo -MD -MP -MF .deps/viterbi.Tpo -c viterbi.c -o viterbi.o >/dev/null 2>&1 --- sviterbi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- scanner.lo --- mv -f .deps/scanner.Tpo .deps/scanner.Plo --- randvar.lo --- randvar.c:449:1: warning: non-void function does not return a value [-Wreturn-type] 449 | } | ^ 1 warning generated. --- mes.lo --- mes.c:148:8: warning: address of array 'mes_process' will always evaluate to 'true' [-Wpointer-bool-conversion] 148 | if (!mes_process) | ~^~~~~~~~~~~ 1 warning generated. --- randvar.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- cluster.lo --- mv -f .deps/cluster.Tpo .deps/cluster.Plo --- mes.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- smap_classify.lo --- mv -f .deps/smap_classify.Tpo .deps/smap_classify.Plo --- scluster.lo --- mv -f .deps/scluster.Tpo .deps/scluster.Plo --- mprintf.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sfoba.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- gradescent.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT gradescent.lo -MD -MP -MF .deps/gradescent.Tpo -c gradescent.c -o gradescent.o >/dev/null 2>&1 --- smixturehmm.lo --- mv -f .deps/smixturehmm.Tpo .deps/smixturehmm.Plo --- sdviterbi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- gauss_tail.lo --- mv -f .deps/gauss_tail.Tpo .deps/gauss_tail.Plo --- root_finder.lo --- mv -f .deps/root_finder.Tpo .deps/root_finder.Plo --- fbgibbs.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sgenerate.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- ghmm_internals.lo --- mv -f .deps/ghmm_internals.Tpo .deps/ghmm_internals.Plo --- rng.lo --- mv -f .deps/rng.Tpo .deps/rng.Plo --- kbest.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT kbest.lo -MD -MP -MF .deps/kbest.Tpo -c kbest.c -o kbest.o >/dev/null 2>&1 --- vector.lo --- mv -f .deps/vector.Tpo .deps/vector.Plo --- sdmodel.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- modelutil.lo --- mv -f .deps/modelutil.Tpo .deps/modelutil.Plo --- reestimate.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT reestimate.lo -MD -MP -MF .deps/reestimate.Tpo -c reestimate.c -o reestimate.o >/dev/null 2>&1 --- psequence.lo --- mv -f .deps/psequence.Tpo .deps/psequence.Plo --- linkedlist.lo --- mv -f .deps/linkedlist.Tpo .deps/linkedlist.Plo --- pviterbi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sdfoba.lo --- mv -f .deps/sdfoba.Tpo .deps/sdfoba.Plo --- pmodel.lo --- mv -f .deps/pmodel.Tpo .deps/pmodel.Plo --- sviterbi.lo --- mv -f .deps/sviterbi.Tpo .deps/sviterbi.Plo --- matrixop.lo --- mv -f .deps/matrixop.Tpo .deps/matrixop.Plo --- xmlwriter.lo --- xmlwriter.c:356:82: warning: format string is not a string literal (potentially insecure) [-Wformat-security] 356 | 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 356 | 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] 1008 | if (xmlTextWriterWriteAttribute(writer, BAD_CAST "name", w_name)) | ^~~~~~ /usr/local/include/libxml2/libxml/xmlwriter.h:221:55: note: passing argument to parameter 'content' here 221 | content); | ^ xmlwriter.c:1105:5: warning: call to undeclared function 'xmlSubstituteEntitiesDefault'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 1105 | xmlSubstituteEntitiesDefault(1); | ^ xmlwriter.c:1166:3: warning: call to undeclared function 'xmlCleanupParser'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] 1166 | xmlCleanupParser(); | ^ xmlwriter.c:1170:3: warning: 'xmlMemoryDump' is deprecated [-Wdeprecated-declarations] 1170 | xmlMemoryDump(); | ^ /usr/local/include/libxml2/libxml/xmlmemory.h:174:1: note: 'xmlMemoryDump' has been explicitly marked deprecated here 174 | XML_DEPRECATED | ^ /usr/local/include/libxml2/libxml/xmlexports.h:63:43: note: expanded from macro 'XML_DEPRECATED' 63 | #define XML_DEPRECATED __attribute__((deprecated)) | ^ 5 warnings generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- cfbgibbs.lo --- cfbgibbs.c:33:1: warning: '/*' within block comment [-Wcomment] 33 | /* computes tupleSize and preposition | ^ 1 warning generated. --- matrix.lo --- mv -f .deps/matrix.Tpo .deps/matrix.Plo --- cfbgibbs.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- pviterbi_propagate.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- viterbi.lo --- mv -f .deps/viterbi.Tpo .deps/viterbi.Plo --- smodel.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- xmlreader.lo --- 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] 403 | 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] 1022 | 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] 1291 | if (filename != NULL && fileDTD != NULL) { | ^~~~~~~ ~~~~ 3 warnings generated. --- sfoba.lo --- mv -f .deps/sfoba.Tpo .deps/sfoba.Plo --- xmlreader.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sreestimate.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sequence.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- randvar.lo --- mv -f .deps/randvar.Tpo .deps/randvar.Plo --- foba.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- sdviterbi.lo --- mv -f .deps/sdviterbi.Tpo .deps/sdviterbi.Plo --- mes.lo --- mv -f .deps/mes.Tpo .deps/mes.Plo --- mprintf.lo --- mv -f .deps/mprintf.Tpo .deps/mprintf.Plo --- gradescent.lo --- mv -f .deps/gradescent.Tpo .deps/gradescent.Plo --- sgenerate.lo --- mv -f .deps/sgenerate.Tpo .deps/sgenerate.Plo --- kbest.lo --- mv -f .deps/kbest.Tpo .deps/kbest.Plo --- fbgibbs.lo --- mv -f .deps/fbgibbs.Tpo .deps/fbgibbs.Plo --- pviterbi.lo --- mv -f .deps/pviterbi.Tpo .deps/pviterbi.Plo --- sdmodel.lo --- mv -f .deps/sdmodel.Tpo .deps/sdmodel.Plo --- model.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -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 --- reestimate.lo --- mv -f .deps/reestimate.Tpo .deps/reestimate.Plo --- xmlwriter.lo --- mv -f .deps/xmlwriter.Tpo .deps/xmlwriter.Plo --- cfbgibbs.lo --- mv -f .deps/cfbgibbs.Tpo .deps/cfbgibbs.Plo --- discrime.lo --- 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] 1134 | if (fabs (nsum) > 1e-200 && psum < nsum) | ^ discrime.c:1134:9: note: use function 'fabsl' instead 1134 | if (fabs (nsum) > 1e-200 && psum < nsum) | ^~~~ | fabsl 1 warning generated. --- pviterbi_propagate.lo --- mv -f .deps/pviterbi_propagate.Tpo .deps/pviterbi_propagate.Plo --- sreestimate.lo --- mv -f .deps/sreestimate.Tpo .deps/sreestimate.Plo --- discrime.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT discrime.lo -MD -MP -MF .deps/discrime.Tpo -c discrime.c -o discrime.o >/dev/null 2>&1 --- xmlreader.lo --- mv -f .deps/xmlreader.Tpo .deps/xmlreader.Plo --- smodel.lo --- mv -f .deps/smodel.Tpo .deps/smodel.Plo --- sequence.lo --- mv -f .deps/sequence.Tpo .deps/sequence.Plo --- foba.lo --- mv -f .deps/foba.Tpo .deps/foba.Plo --- model.lo --- mv -f .deps/model.Tpo .deps/model.Plo --- discrime.lo --- mv -f .deps/discrime.Tpo .deps/discrime.Plo --- libghmm.la --- /bin/sh ../libtool --tag=CC --mode=link cc -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -version-info 1:0:0 -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 -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 --- --- scluster.o --- --- smix_hmm.o --- --- probdist.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 -Wno-error=int-conversion -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 --- scluster.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- smix_hmm.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- cluster.o --- mv -f .deps/cluster.Tpo .deps/cluster.Po --- scluster --- --- cluster --- --- probdist.o --- mv -f .deps/probdist.Tpo .deps/probdist.Po --- smix_hmm.o --- mv -f .deps/smix_hmm.Tpo .deps/smix_hmm.Po --- probdist --- --- smix_hmm --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- probdist --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o cluster cluster.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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- probdist --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- cluster --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- smix_hmm --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o smix_hmm smix_hmm.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 --- --- coin_toss_test.o --- --- two_states_three_symbols.o --- --- libxml-test.o --- --- chmm.o --- --- chmm_test.o --- --- shmm_viterbi_test.o --- --- test_gsl_ran_gaussian_tail.o --- --- sequences_test.o --- --- sequences_old_format.o --- --- label_higher_order_test.o --- --- read_fa.o --- --- mcmc.o --- --- randvar_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 -Wno-error=int-conversion -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 --- coin_toss_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- two_states_three_symbols.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- chmm.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- test_gsl_ran_gaussian_tail.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- chmm_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- shmm_viterbi_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- sequences_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- libxml-test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- sequences_old_format.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- read_fa.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- mcmc.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -Wno-error=int-conversion -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 --- test_gsl_ran_gaussian_tail.o --- mv -f .deps/test_gsl_ran_gaussian_tail.Tpo .deps/test_gsl_ran_gaussian_tail.Po --- test_gsl_ran_gaussian_tail --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -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 --- root_finder_test.o --- mv -f .deps/root_finder_test.Tpo .deps/root_finder_test.Po --- root_finder_test --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- sequences_old_format.o --- mv -f .deps/sequences_old_format.Tpo .deps/sequences_old_format.Po --- two_states_three_symbols.o --- mv -f .deps/two_states_three_symbols.Tpo .deps/two_states_three_symbols.Po --- sequences_old_format --- --- two_states_three_symbols --- --- shmm_viterbi_test.o --- mv -f .deps/shmm_viterbi_test.Tpo .deps/shmm_viterbi_test.Po --- shmm_viterbi_test --- --- sequences_old_format --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- two_states_three_symbols --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- shmm_viterbi_test --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- coin_toss_test.o --- mv -f .deps/coin_toss_test.Tpo .deps/coin_toss_test.Po --- sequences_test.o --- mv -f .deps/sequences_test.Tpo .deps/sequences_test.Po --- chmm_test.o --- mv -f .deps/chmm_test.Tpo .deps/chmm_test.Po --- coin_toss_test --- --- sequences_test --- --- chmm_test --- --- coin_toss_test --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- sequences_test --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- chmm_test --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- randvar_test.o --- mv -f .deps/randvar_test.Tpo .deps/randvar_test.Po --- randvar_test --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o randvar_test randvar_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] 144 | 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] 146 | 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] 146 | int * Q = ghmm_dmodel_cfbgibbs(mo, my_output, | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 147 | pA, pB, pPi,2, iter, 0); | ~~~~~~~~~~~~~~~~~~~~~~~ mcmc.c:148:107: warning: incompatible integer to pointer conversion passing 'int' to parameter of type 'int *'; take the address with & [-Wint-conversion] 148 | 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 75 | double ghmm_dmodel_viterbi_logp (ghmm_dmodel * mo, int *o, int len, int *state_seq); | ^ 4 warnings generated. --- chmm.o --- mv -f .deps/chmm.Tpo .deps/chmm.Po --- mcmc.o --- mv -f .deps/mcmc.Tpo .deps/mcmc.Po --- mcmc --- --- chmm --- --- mcmc --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- chmm --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- test_gsl_ran_gaussian_tail --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o test_gsl_ran_gaussian_tail test_gsl_ran_gaussian_tail.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- label_higher_order_test.o --- mv -f .deps/label_higher_order_test.Tpo .deps/label_higher_order_test.Po --- label_higher_order_test --- --- root_finder_test --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- label_higher_order_test --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- read_fa.o --- mv -f .deps/read_fa.Tpo .deps/read_fa.Po --- read_fa --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- sequences_old_format --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o sequences_old_format sequences_old_format.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- shmm_viterbi_test --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o shmm_viterbi_test shmm_viterbi_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- two_states_three_symbols --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o two_states_three_symbols two_states_three_symbols.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- sequences_test --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o sequences_test sequences_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- chmm_test --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o chmm_test chmm_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- coin_toss_test --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o coin_toss_test coin_toss_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- randvar_test --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o randvar_test randvar_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- chmm --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o chmm chmm.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- mcmc --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o mcmc mcmc.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- label_higher_order_test --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o label_higher_order_test label_higher_order_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- read_fa --- libtool: link: cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o read_fa read_fa.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- libxml-test.o --- mv -f .deps/libxml-test.Tpo .deps/libxml-test.Po --- libxml-test --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -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 -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -o libxml-test libxml-test.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_3 ===> 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=2026-03-12T16:45:43+0000' 'PKG_NOTE_ports_top_git_hash=26b198eb3ee3' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=3068854dd026' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for ghmm-0.9.r3_3 ===> Building ghmm-0.9.r3_3 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for ghmm-0.9.r3_3 build of science/ghmm | ghmm-0.9.r3_3 ended at Thu Mar 12 12:46:09 EDT 2026 build time: 00:00:27