------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for haplohseq-0.1.2_3: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- MAKE=gmake PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/construction/biology/haplohseq XDG_CONFIG_HOME=/construction/biology/haplohseq HOME=/construction/biology/haplohseq TMPDIR="/tmp" PATH=/construction/biology/haplohseq/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- STRIP=-s XDG_DATA_HOME=/construction/biology/haplohseq XDG_CONFIG_HOME=/construction/biology/haplohseq HOME=/construction/biology/haplohseq TMPDIR="/tmp" PATH=/construction/biology/haplohseq/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lpthread -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/haplohseq/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTEXAMPLES="" PYTHON_INCLUDEDIR=include/python3.7m PYTHON_LIBDIR=lib/python3.7 PYTHON_PLATFORM=dragonfly6 PYTHON_SITELIBDIR=lib/python3.7/site-packages PYTHON_SUFFIX=37 PYTHON_EXT_SUFFIX= PYTHON_VER=3.7 PYTHON_VERSION=python3.7 PYTHON2="@comment " PYTHON3="" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/haplohseq" EXAMPLESDIR="share/examples/haplohseq" DATADIR="share/haplohseq" WWWDIR="www/haplohseq" ETCDIR="etc/haplohseq" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/haplohseq DOCSDIR=/usr/local/share/doc/haplohseq EXAMPLESDIR=/usr/local/share/examples/haplohseq WWWDIR=/usr/local/www/haplohseq ETCDIR=/usr/local/etc/haplohseq SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600100 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/libffi-3.3_1.txz Installing /packages/All/expat-2.2.10.txz Installing /packages/All/ncurses-6.2.20210313_1.txz ===== Message from ncurses-6.2.20210313_1: -- { type: install message: < Creating groups. Creating group 'messagebus' with gid '556'. ===> Creating users Creating user 'messagebus' with uid '556'. Installing /packages/All/dbus-glib-0.110.txz Installing /packages/All/gdbm-1.19.txz Installing /packages/All/libevent-2.1.12.txz Installing /packages/All/gnome_subr-1.0.txz Installing /packages/All/avahi-app-0.8.txz ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. Installing /packages/All/gmp-6.2.1.txz Installing /packages/All/nettle-3.7.2_1.txz Installing /packages/All/libtasn1-4.16.0_1.txz Installing /packages/All/libunistring-0.9.10_1.txz Installing /packages/All/libidn2-2.3.0_1.txz Installing /packages/All/p11-kit-0.23.22_1.txz Installing /packages/All/tpm-emulator-0.7.4_2.txz ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. Installing /packages/All/trousers-0.3.14_3.txz ===> Creating groups. Using existing group '_tss'. ===> Creating users Using existing user '_tss'. ===== Message from trousers-0.3.14_3: -- To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Installing /packages/All/gnutls-3.6.15.txz Installing /packages/All/cups-2.3.3op2.txz ===> Creating groups. Creating group 'cups' with gid '193'. ===> Creating users Creating user 'cups' with uid '193'. Installing /packages/All/poppler-data-0.4.10.txz Installing /packages/All/ghostscript9-agpl-base-9.52_15.txz ===== Message from ghostscript9-agpl-base-9.52_15: -- This package installs a script named dvipdf that depends on dvips. If you want to use this script you need to install print/tex-dvipsk. Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/mpc-1.2.0.txz Installing /packages/All/binutils-2.33.1_4,1.txz Installing /packages/All/gcc8-8.4.0_1.txz ===== Message from gcc8-8.4.0_1: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. Installing /packages/All/libXt-1.2.1,1.txz Installing /packages/All/libXmu-1.1.3,1.txz Installing /packages/All/R-4.0.4_1.txz Installing /packages/All/R-cran-getopt-1.20.3_1.txz Installing /packages/All/R-cran-optparse-1.6.6.txz SUCCEEDED 00:01:35 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_3 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by haplohseq-0.1.2_3 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by haplohseq-0.1.2_3 for building => SHA256 Checksum OK for outpaddling-haplohseq-0.1.2_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_3 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by haplohseq-0.1.2_3 for building ===> Extracting for haplohseq-0.1.2_3 => SHA256 Checksum OK for outpaddling-haplohseq-0.1.2_GH0.tar.gz. Extracted Memory Use: 60.23M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for haplohseq-0.1.2_3 ===> Applying ports patches for haplohseq-0.1.2_3 from /xports/biology/haplohseq/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_3 depends on package: gmake>=4.3 - found ===> haplohseq-0.1.2_3 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_3 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_3 depends on package: gmake>=4.3 - found ===> haplohseq-0.1.2_3 depends on file: /usr/local/bin/python3.7 - found ===> haplohseq-0.1.2_3 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> Configuring for haplohseq-0.1.2_3 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for haplohseq-0.1.2_3 gmake[1]: Entering directory '/construction/biology/haplohseq/haplohseq-0.1.2' mkdir -p build build/bin build/obj mkdir -p build/test c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Hmm.o src/hmm/Hmm.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/DataStructures.o src/hmm/DataStructures.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/MathUtil.o src/hmm/MathUtil.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/StringUtil.o src/util/StringUtil.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/InputProcessor.o src/util/InputProcessor.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/Reporter.o src/Reporter.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/FreqPhase.o src/FreqPhase.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/VcfUtil.o src/util/VcfUtil.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -c -o build/obj/HaplohSeq.o src/HaplohSeq.cpp cp -r src/test/resources build/test c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/FreqPhaseTest.o src/test/FreqPhaseTest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HaplohSeqTest.o src/test/HaplohSeqTest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/HmmTest.o src/test/HmmTest.cpp c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 -isystem/usr/local/boost_1_52_0 -c -o build/test/InputProcessorTest.o src/test/InputProcessorTest.cpp c++ -o build/bin/haplohseq -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -I./src -I./src/hmm -I./src/util -isystem/usr/local/boost_1_52_0 build/obj/Hmm.o build/obj/DataStructures.o build/obj/MathUtil.o build/obj/StringUtil.o build/obj/InputProcessor.o build/obj/Reporter.o build/obj/FreqPhase.o build/obj/VcfUtil.o build/obj/HaplohSeq.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib c++ -o build/test/HmmTest -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include build/obj/Hmm.o build/obj/DataStructures.o build/obj/MathUtil.o build/obj/StringUtil.o build/test/HmmTest.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib c++ -o build/test/FreqPhaseTest -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include build/obj/StringUtil.o build/obj/InputProcessor.o build/obj/FreqPhase.o build/test/FreqPhaseTest.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib c++ -o build/test/HaplohSeqTest -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include build/obj/Hmm.o build/obj/DataStructures.o build/obj/MathUtil.o build/obj/StringUtil.o build/obj/InputProcessor.o build/test/HaplohSeqTest.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib c++ -o build/test/InputProcessorTest -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include build/obj/Hmm.o build/obj/DataStructures.o build/obj/MathUtil.o build/obj/StringUtil.o build/obj/InputProcessor.o build/test/InputProcessorTest.o -Llib/macosx -lm -lboost_program_options -lboost_system -lboost_filesystem -lboost_thread -lpthread -L/usr/local/lib gmake[1]: Leaving directory '/construction/biology/haplohseq/haplohseq-0.1.2' SUCCEEDED 00:01:11 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> haplohseq-0.1.2_3 depends on package: R-cran-optparse>0 - found ===> haplohseq-0.1.2_3 depends on file: /usr/local/bin/python3.7 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for haplohseq-0.1.2_3 ===> haplohseq-0.1.2_3 depends on package: R-cran-optparse>0 - found ===> haplohseq-0.1.2_3 depends on file: /usr/local/bin/python3.7 - found ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/haplohseq/haplohseq-0.1.2' mkdir -p /construction/biology/haplohseq/stage/usr/local/bin install -c -s build/bin/* /construction/biology/haplohseq/stage/usr/local/bin gmake[1]: Leaving directory '/construction/biology/haplohseq/haplohseq-0.1.2' install -m 555 /construction/biology/haplohseq/haplohseq-example /construction/biology/haplohseq/stage/usr/local/bin (cd /construction/biology/haplohseq/haplohseq-0.1.2 && /bin/rm -f example/*.orig scripts/*.orig && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE "example ldmap scripts" /construction/biology/haplohseq/stage/usr/local/share/examples/haplohseq) ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for haplohseq-0.1.2_3 file sizes/checksums [8]: 0% file sizes/checksums [8]: 100% packing files [8]: 0% packing files [8]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:03:14 TOTAL TIME 00:06:08