From nobody Sat Feb 25 15:03:04 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4PP949036Tz3tGjd for ; Sat, 25 Feb 2023 15:03:05 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4PP94855Hfz3Fct for ; Sat, 25 Feb 2023 15:03:04 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1677337384; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=dFgn+Xn3NeKSH77qmB7Y5OdtprfJXAxmaR92ZMYEsm4=; b=kz/SUTDhWcYPAPWzjjgdNQwKcnxYTOLcKkZ6nfuynHPOLYjNpAGpUM3wbI683ZlOnBINsD 4NGYq/UgwqmOpAusmbAuqnVBsGCmV7tsAzW92R83JMk4ohJNsNLqz9XdCdQo2Yd2SVNhdz AuTREAZsjF9S1HoeqnOIUHDnxL9/16ode8EX3DsMsivi7biJM7qOmbIZ0mz8IcRBrzaOXY AC4Ehw9tkcIWJt+o13lVrEyKU3e19iRksHEVMd1xhHQJfPZmyB4GDz6Nww3TsHpEgMUQiw 9dIXoo3Kyp2XwTw59EihaL1PPP1fytL4kCCrl1fC9d63lhhufKIWSzUXLGPBxQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1677337384; a=rsa-sha256; cv=none; b=TqprlIfm6AZQZq/QuQH8rkxzsRiJO7T7862GnYxqm6qLZ4w+COlxFN7lmNcFZJFoLyOpXc dN00Wf1H6cOg2buEjY6iET68JxVy4sG6eAapIl4rFrS+pLXuTofIryiAMCqiB936UvOlCI /g2BL7cQZ20utQtR+KWuENrL/PQegfcRnC1SHJd7Cp2P4WK47JOAKwfbvDC8UkoUaa7ISq Wt4oK0u2B+BAVeQe6XQRW8kFsI9Pk5/L4DBi2tw+GVW61TEli/jIQe8xeTkMcL0+pRxkKX 88HI8fuHXulc/eFUWvcLVfWitntqkqD0ZLMsA4nzugb/qL1DNnyxg6NS7+cm9A== Received: from ampere2.nyi.freebsd.org (ampere2.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:24]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4PP94848dQz17cm for ; Sat, 25 Feb 2023 15:03:04 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere2.nyi.freebsd.org (localhost [127.0.0.1]) by ampere2.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 31PF34kg059796 for ; Sat, 25 Feb 2023 15:03:04 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere2.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 31PF34Gi059795; Sat, 25 Feb 2023 15:03:04 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 25 Feb 2023 15:03:04 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202302251503.31PF34Gi059795@ampere2.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - main-arm64-default][science/ghmm] Failed for ghmm-0.9.r3_2 in build X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: ports@FreeBSD.org Log URL: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/p1b4f77b589d3_s357492c995/logs/ghmm-0.9.r3_2.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p1b4f77b589d3_s357492c995 Log: =>> Building science/ghmm build started at Sat Feb 25 15:01:56 UTC 2023 port directory: /usr/ports/science/ghmm package name: ghmm-0.9.r3_2 building for: FreeBSD main-arm64-default-job-05 14.0-CURRENT FreeBSD 14.0-CURRENT 1400081 arm64 maintained by: ports@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1400081 Job Id: 05 !!! Jail is newer than host. (Jail: 1400081, Host: 1400073) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400081 UNAME_v=FreeBSD 14.0-CURRENT 1400081 UNAME_r=14.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --without-python --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/science/ghmm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/ghmm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/ghmm/work/.cache HOME=/wrkdirs/usr/ports/science/ghmm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/ghmm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/ghmm/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.71 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/science/ghmm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/ghmm/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/ghmm/work/.cache HOME=/wrkdirs/usr/ports/science/ghmm/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/ghmm/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/ghmm/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.71 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT=" install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" GTK4_VERSION="4.0.0" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/ghmm" EXAMPLESDIR="share/examples/ghmm" DATADIR="share/ghmm" WWWDIR="www/ghmm" ETCDIR="etc/ghmm" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ghmm DOCSDIR=/usr/local/share/doc/ghmm EXAMPLESDIR=/usr/local/share/examples/ghmm WWWDIR=/usr/local/www/ghmm ETCDIR=/usr/local/etc/ghmm --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400081 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> NOTICE: The ghmm port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> ghmm-0.9.r3_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [main-arm64-default-job-05] Installing pkg-1.19.1_1... [main-arm64-default-job-05] Extracting pkg-1.19.1_1: .......... done ===> ghmm-0.9.r3_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ghmm-0.9.r3_2 =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The ghmm port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by ghmm-0.9.r3_2 for building =========================================================================== =================================================== --- sreestimate.lo --- mv -f .deps/sreestimate.Tpo .deps/sreestimate.Plo --- sdfoba.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdfoba.lo -MD -MP -MF .deps/sdfoba.Tpo -c -o sdfoba.lo sdfoba.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdfoba.lo -MD -MP -MF .deps/sdfoba.Tpo -c sdfoba.c -fPIC -DPIC -o .libs/sdfoba.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdfoba.lo -MD -MP -MF .deps/sdfoba.Tpo -c sdfoba.c -o sdfoba.o >/dev/null 2>&1 --- sdmodel.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdmodel.lo -MD -MP -MF .deps/sdmodel.Tpo -c sdmodel.c -o sdmodel.o >/dev/null 2>&1 --- sdfoba.lo --- mv -f .deps/sdfoba.Tpo .deps/sdfoba.Plo --- sdviterbi.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdviterbi.lo -MD -MP -MF .deps/sdviterbi.Tpo -c -o sdviterbi.lo sdviterbi.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdviterbi.lo -MD -MP -MF .deps/sdviterbi.Tpo -c sdviterbi.c -fPIC -DPIC -o .libs/sdviterbi.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sdviterbi.lo -MD -MP -MF .deps/sdviterbi.Tpo -c sdviterbi.c -o sdviterbi.o >/dev/null 2>&1 --- sdmodel.lo --- mv -f .deps/sdmodel.Tpo .deps/sdmodel.Plo --- pmodel.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pmodel.lo -MD -MP -MF .deps/pmodel.Tpo -c -o pmodel.lo pmodel.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pmodel.lo -MD -MP -MF .deps/pmodel.Tpo -c pmodel.c -fPIC -DPIC -o .libs/pmodel.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pmodel.lo -MD -MP -MF .deps/pmodel.Tpo -c pmodel.c -o pmodel.o >/dev/null 2>&1 --- sdviterbi.lo --- mv -f .deps/sdviterbi.Tpo .deps/sdviterbi.Plo --- pviterbi.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi.lo -MD -MP -MF .deps/pviterbi.Tpo -c -o pviterbi.lo pviterbi.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi.lo -MD -MP -MF .deps/pviterbi.Tpo -c pviterbi.c -fPIC -DPIC -o .libs/pviterbi.o --- pmodel.lo --- mv -f .deps/pmodel.Tpo .deps/pmodel.Plo --- pviterbi_propagate.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi_propagate.lo -MD -MP -MF .deps/pviterbi_propagate.Tpo -c -o pviterbi_propagate.lo pviterbi_propagate.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi_propagate.lo -MD -MP -MF .deps/pviterbi_propagate.Tpo -c pviterbi_propagate.c -fPIC -DPIC -o .libs/pviterbi_propagate.o --- pviterbi.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi.lo -MD -MP -MF .deps/pviterbi.Tpo -c pviterbi.c -o pviterbi.o >/dev/null 2>&1 --- pviterbi_propagate.lo --- libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT pviterbi_propagate.lo -MD -MP -MF .deps/pviterbi_propagate.Tpo -c pviterbi_propagate.c -o pviterbi_propagate.o >/dev/null 2>&1 --- pviterbi.lo --- mv -f .deps/pviterbi.Tpo .deps/pviterbi.Plo --- fbgibbs.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT fbgibbs.lo -MD -MP -MF .deps/fbgibbs.Tpo -c -o fbgibbs.lo fbgibbs.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT fbgibbs.lo -MD -MP -MF .deps/fbgibbs.Tpo -c fbgibbs.c -fPIC -DPIC -o .libs/fbgibbs.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT fbgibbs.lo -MD -MP -MF .deps/fbgibbs.Tpo -c fbgibbs.c -o fbgibbs.o >/dev/null 2>&1 --- pviterbi_propagate.lo --- mv -f .deps/pviterbi_propagate.Tpo .deps/pviterbi_propagate.Plo --- cfbgibbs.lo --- /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cfbgibbs.lo -MD -MP -MF .deps/cfbgibbs.Tpo -c -o cfbgibbs.lo cfbgibbs.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cfbgibbs.lo -MD -MP -MF .deps/cfbgibbs.Tpo -c cfbgibbs.c -fPIC -DPIC -o .libs/cfbgibbs.o cfbgibbs.c:33:1: warning: '/*' within block comment [-Wcomment] /* computes tupleSize and preposition ^ --- fbgibbs.lo --- mv -f .deps/fbgibbs.Tpo .deps/fbgibbs.Plo --- cfbgibbs.lo --- 1 warning generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cfbgibbs.lo -MD -MP -MF .deps/cfbgibbs.Tpo -c cfbgibbs.c -o cfbgibbs.o >/dev/null 2>&1 mv -f .deps/cfbgibbs.Tpo .deps/cfbgibbs.Plo --- libghmm.la --- /bin/sh ../libtool --tag=CC --mode=link cc -DDTD_LOC=\"/usr/local/share/ghmm/ghmm.dtd.1.0\" -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -version-info 1:0:0 -fstack-protector-strong -o libghmm.la -rpath /usr/local/lib rng.lo randvar.lo matrixop.lo gauss_tail.lo mes.lo ghmm_internals.lo mprintf.lo vector.lo matrix.lo scanner.lo linkedlist.lo sequence.lo psequence.lo xmlreader.lo xmlwriter.lo model.lo foba.lo viterbi.lo reestimate.lo gradescent.lo kbest.lo discrime.lo modelutil.lo cluster.lo root_finder.lo smodel.lo sfoba.lo sviterbi.lo sreestimate.lo scluster.lo sgenerate.lo smixturehmm.lo smap_classify.lo sdmodel.lo sdfoba.lo sdviterbi.lo pmodel.lo pviterbi.lo pviterbi_propagate.lo fbgibbs.lo cfbgibbs.lo -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 libtool: link: cc -shared -fPIC -DPIC .libs/rng.o .libs/randvar.o .libs/matrixop.o .libs/gauss_tail.o .libs/mes.o .libs/ghmm_internals.o .libs/mprintf.o .libs/vector.o .libs/matrix.o .libs/scanner.o .libs/linkedlist.o .libs/sequence.o .libs/psequence.o .libs/xmlreader.o .libs/xmlwriter.o .libs/model.o .libs/foba.o .libs/viterbi.o .libs/reestimate.o .libs/gradescent.o .libs/kbest.o .libs/discrime.o .libs/modelutil.o .libs/cluster.o .libs/root_finder.o .libs/smodel.o .libs/sfoba.o .libs/sviterbi.o .libs/sreestimate.o .libs/scluster.o .libs/sgenerate.o .libs/smixturehmm.o .libs/smap_classify.o .libs/sdmodel.o .libs/sdfoba.o .libs/sdviterbi.o .libs/pmodel.o .libs/pviterbi.o .libs/pviterbi_propagate.o .libs/fbgibbs.o .libs/cfbgibbs.o -lm -lpthread -L/usr/local/lib -lxml2 -O2 -fstack-protector-strong -fstack-protector-strong -Wl,-soname -Wl,libghmm.so.1 -o .libs/libghmm.so.1.0.0 libtool: link: (cd ".libs" && rm -f "libghmm.so.1" && ln -s "libghmm.so.1.0.0" "libghmm.so.1") libtool: link: (cd ".libs" && rm -f "libghmm.so" && ln -s "libghmm.so.1.0.0" "libghmm.so") libtool: link: ar cr .libs/libghmm.a rng.o randvar.o matrixop.o gauss_tail.o mes.o ghmm_internals.o mprintf.o vector.o matrix.o scanner.o linkedlist.o sequence.o psequence.o xmlreader.o xmlwriter.o model.o foba.o viterbi.o reestimate.o gradescent.o kbest.o discrime.o modelutil.o cluster.o root_finder.o smodel.o sfoba.o sviterbi.o sreestimate.o scluster.o sgenerate.o smixturehmm.o smap_classify.o sdmodel.o sdfoba.o sdviterbi.o pmodel.o pviterbi.o pviterbi_propagate.o fbgibbs.o cfbgibbs.o libtool: link: ranlib .libs/libghmm.a libtool: link: ( cd ".libs" && rm -f "libghmm.la" && ln -s "../libghmm.la" "libghmm.la" ) Making all in tools --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in . --- probdist.o --- --- cluster.o --- --- probdist.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT probdist.o -MD -MP -MF .deps/probdist.Tpo -c -o probdist.o probdist.c --- cluster.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT cluster.o -MD -MP -MF .deps/cluster.Tpo -c -o cluster.o cluster.c mv -f .deps/cluster.Tpo .deps/cluster.Po --- scluster.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT scluster.o -MD -MP -MF .deps/scluster.Tpo -c -o scluster.o scluster.c --- probdist.o --- mv -f .deps/probdist.Tpo .deps/probdist.Po --- smix_hmm.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT smix_hmm.o -MD -MP -MF .deps/smix_hmm.Tpo -c -o smix_hmm.o smix_hmm.c --- scluster.o --- mv -f .deps/scluster.Tpo .deps/scluster.Po --- cluster --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- smix_hmm.o --- mv -f .deps/smix_hmm.Tpo .deps/smix_hmm.Po --- probdist --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- cluster --- libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o cluster cluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- probdist --- libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o probdist probdist.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- scluster --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- smix_hmm --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- scluster --- libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o scluster scluster.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 --- smix_hmm --- libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o smix_hmm smix_hmm.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 Making all in tests --- all-recursive --- Making all in data --- all-recursive --- Making all in . --- randvar_test.o --- --- root_finder_test.o --- --- randvar_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT randvar_test.o -MD -MP -MF .deps/randvar_test.Tpo -c -o randvar_test.o randvar_test.c --- root_finder_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT root_finder_test.o -MD -MP -MF .deps/root_finder_test.Tpo -c -o root_finder_test.o root_finder_test.c mv -f .deps/root_finder_test.Tpo .deps/root_finder_test.Po --- coin_toss_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT coin_toss_test.o -MD -MP -MF .deps/coin_toss_test.Tpo -c -o coin_toss_test.o coin_toss_test.c --- randvar_test.o --- mv -f .deps/randvar_test.Tpo .deps/randvar_test.Po --- two_states_three_symbols.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT two_states_three_symbols.o -MD -MP -MF .deps/two_states_three_symbols.Tpo -c -o two_states_three_symbols.o two_states_three_symbols.c --- coin_toss_test.o --- mv -f .deps/coin_toss_test.Tpo .deps/coin_toss_test.Po --- libxml-test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT libxml-test.o -MD -MP -MF .deps/libxml-test.Tpo -c -o libxml-test.o libxml-test.c --- two_states_three_symbols.o --- mv -f .deps/two_states_three_symbols.Tpo .deps/two_states_three_symbols.Po --- chmm.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT chmm.o -MD -MP -MF .deps/chmm.Tpo -c -o chmm.o chmm.c --- libxml-test.o --- mv -f .deps/libxml-test.Tpo .deps/libxml-test.Po --- chmm_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT chmm_test.o -MD -MP -MF .deps/chmm_test.Tpo -c -o chmm_test.o chmm_test.c --- chmm.o --- mv -f .deps/chmm.Tpo .deps/chmm.Po --- shmm_viterbi_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT shmm_viterbi_test.o -MD -MP -MF .deps/shmm_viterbi_test.Tpo -c -o shmm_viterbi_test.o shmm_viterbi_test.c --- chmm_test.o --- mv -f .deps/chmm_test.Tpo .deps/chmm_test.Po --- test_gsl_ran_gaussian_tail.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT test_gsl_ran_gaussian_tail.o -MD -MP -MF .deps/test_gsl_ran_gaussian_tail.Tpo -c -o test_gsl_ran_gaussian_tail.o test_gsl_ran_gaussian_tail.c --- shmm_viterbi_test.o --- mv -f .deps/shmm_viterbi_test.Tpo .deps/shmm_viterbi_test.Po --- sequences_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sequences_test.o -MD -MP -MF .deps/sequences_test.Tpo -c -o sequences_test.o sequences_test.c --- test_gsl_ran_gaussian_tail.o --- mv -f .deps/test_gsl_ran_gaussian_tail.Tpo .deps/test_gsl_ran_gaussian_tail.Po --- sequences_old_format.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT sequences_old_format.o -MD -MP -MF .deps/sequences_old_format.Tpo -c -o sequences_old_format.o sequences_old_format.c mv -f .deps/sequences_old_format.Tpo .deps/sequences_old_format.Po --- label_higher_order_test.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT label_higher_order_test.o -MD -MP -MF .deps/label_higher_order_test.Tpo -c -o label_higher_order_test.o label_higher_order_test.c --- sequences_test.o --- mv -f .deps/sequences_test.Tpo .deps/sequences_test.Po --- read_fa.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT read_fa.o -MD -MP -MF .deps/read_fa.Tpo -c -o read_fa.o read_fa.c --- label_higher_order_test.o --- mv -f .deps/label_higher_order_test.Tpo .deps/label_higher_order_test.Po --- mcmc.o --- cc -DHAVE_CONFIG_H -I. -I.. -I.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -MT mcmc.o -MD -MP -MF .deps/mcmc.Tpo -c -o mcmc.o mcmc.c --- read_fa.o --- mv -f .deps/read_fa.Tpo .deps/read_fa.Po --- root_finder_test --- /bin/sh ../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lm -lm -lm -lpthread -L/usr/local/lib -lxml2 --- mcmc.o --- mcmc.c:144:3: warning: call to undeclared function 'init_priors'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] init_priors(mo, &pA, &pB, &pPi); ^ mcmc.c:146:15: warning: call to undeclared function 'ghmm_dmodel_cfbgibbs'; ISO C99 and later do not support implicit function declarations [-Wimplicit-function-declaration] int * Q = ghmm_dmodel_cfbgibbs(mo, my_output, ^ mcmc.c:146:9: error: incompatible integer to pointer conversion initializing 'int *' with an expression of type 'int' [-Wint-conversion] int * Q = ghmm_dmodel_cfbgibbs(mo, my_output, ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mcmc.c:148:107: error: incompatible integer to pointer conversion passing 'int' to parameter of type 'int *'; take the address with & [-Wint-conversion] printf("viterbi prob mcmc%f \n", ghmm_dmodel_viterbi_logp(mo, my_output->seq[0], my_output->seq_len[0], Q[0])); ^~~~ & ./ghmm/viterbi.h:75:76: note: passing argument to parameter 'state_seq' here double ghmm_dmodel_viterbi_logp (ghmm_dmodel * mo, int *o, int len, int *state_seq); ^ 2 warnings and 2 errors generated. *** [mcmc.o] Error code 1 make[4]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/tests --- root_finder_test --- libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/libxml2 -fstack-protector-strong -o root_finder_test root_finder_test.o ../ghmm/.libs/libghmm.a -lm -lpthread -L/usr/local/lib -lxml2 1 error make[4]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/tests make[3]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3/tests make[2]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3 make[1]: stopped in /wrkdirs/usr/ports/science/ghmm/work/ghmm-0.9-rc3 ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/science/ghmm