=> Building biology/pbcopper Started : Wednesday, 24 JUL 2019 at 17:13:39 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.6-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.6-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/pbcopper XDG_CONFIG_HOME=/construction/biology/pbcopper HOME=/construction/biology/pbcopper TMPDIR="/tmp" PATH=/construction/biology/pbcopper/.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" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix /usr/local --mandir man --infodir share/info --buildtype release --strip _build -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/pbcopper XDG_CONFIG_HOME=/construction/biology/pbcopper HOME=/construction/biology/pbcopper TMPDIR="/tmp" PATH=/construction/biology/pbcopper/.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 DESTDIR=/construction/biology/pbcopper/stage LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 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=" " LIBS="-L/usr/local/lib" 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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- -v -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.6 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/pbcopper" EXAMPLESDIR="share/examples/pbcopper" DATADIR="share/pbcopper" WWWDIR="www/pbcopper" ETCDIR="etc/pbcopper" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pbcopper DOCSDIR=/usr/local/share/doc/pbcopper EXAMPLESDIR=/usr/local/share/examples/pbcopper WWWDIR=/usr/local/www/pbcopper ETCDIR=/usr/local/etc/pbcopper -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.6 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500601 OSVERSION=9999999 OSREL=5.6 _OSRELEASE=5.6-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> pbcopper-0.4.1_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> pbcopper-0.4.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pbcopper-0.4.1_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by pbcopper-0.4.1_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by pbcopper-0.4.1_1 for building => SHA256 Checksum OK for PacificBiosciences-pbcopper-0.4.1_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by pbcopper-0.4.1_1 for building ===> Extracting for pbcopper-0.4.1_1 => SHA256 Checksum OK for PacificBiosciences-pbcopper-0.4.1_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for pbcopper-0.4.1_1 ===> Applying ports patches for pbcopper-0.4.1_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> pbcopper-0.4.1_1 depends on executable: meson - not found ===> Installing existing package /packages/All/meson-0.51.0.txz Installing meson-0.51.0... `-- Installing ninja-1.9.0,2... | `-- Installing python36-3.6.9... | | `-- Installing expat-2.2.6_1... | | `-- Extracting expat-2.2.6_1: .......... done | | `-- Installing gettext-runtime-0.20.1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.20.1: .......... done | | `-- Installing libffi-3.2.1_3... | | `-- Extracting libffi-3.2.1_3: .......... done | | `-- Installing libressl-2.9.2... | | `-- Extracting libressl-2.9.2: .......... done | | `-- Installing ncurses-6.1.20190525... | | `-- Extracting ncurses-6.1.20190525: .......... done | | `-- Installing readline-8.0.0... | | `-- Extracting readline-8.0.0: .......... done | `-- Extracting python36-3.6.9: .......... done `-- Extracting ninja-1.9.0,2: ......... done `-- Installing py36-setuptools-41.0.1... `-- Extracting py36-setuptools-41.0.1: .......... done Extracting meson-0.51.0: .......... done Message from python36-3.6.9: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== ===> pbcopper-0.4.1_1 depends on executable: meson - found ===> Returning to build of pbcopper-0.4.1_1 ===> pbcopper-0.4.1_1 depends on executable: ninja - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> pbcopper-0.4.1_1 depends on shared library: libboost_regex.so - not found ===> Installing existing package /packages/All/boost-libs-1.70.0_2.txz Installing boost-libs-1.70.0_2... `-- Installing icu-64.2,1... `-- Extracting icu-64.2,1: .......... done Extracting boost-libs-1.70.0_2: .......... done Message from boost-libs-1.70.0_2: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> pbcopper-0.4.1_1 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Returning to build of pbcopper-0.4.1_1 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for pbcopper-0.4.1_1 The Meson build system Version: 0.51.0 Source dir: /construction/biology/pbcopper/pbcopper-0.4.1 Build dir: /construction/biology/pbcopper/pbcopper-0.4.1/_build Build type: native build Project name: pbcopper Project version: 0.4.1 Appending CXXFLAGS from environment: ' -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include ' Appending LDFLAGS from environment: ' ' Appending CPPFLAGS from environment: '-isystem /usr/local/include' C++ compiler for the build machine: c++ (gcc 8.3.0 "c++ 8.3 [DragonFly] Release/2019-02-22") Appending CXXFLAGS from environment: ' -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include ' Appending LDFLAGS from environment: ' ' Appending CPPFLAGS from environment: '-isystem /usr/local/include' C++ compiler for the host machine: c++ (gcc 8.3.0 "c++ 8.3 [DragonFly] Release/2019-02-22") Build machine cpu family: x86_64 Build machine cpu: x86_64 Compiler for C++ supports arguments -Wduplicated-cond: YES Compiler for C++ supports arguments -Wduplicated-branches: YES Compiler for C++ supports arguments -Wlogical-op: YES Compiler for C++ supports arguments -Wrestrict: YES Compiler for C++ supports arguments -Wnull-dereference: YES Compiler for C++ supports arguments -Wuseless-cast: YES Compiler for C++ supports arguments -Wdouble-promotion: YES Compiler for C++ supports arguments -Wshadow: YES Compiler for C++ supports arguments -Wformat=1: YES Run-time dependency threads found: YES Run-time dependency Boost found: YES 1.70 Configuring PbcopperVersion.cpp using configuration Build targets in project: 3 Found ninja-1.9.0 at /usr/local/bin/ninja -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for pbcopper-0.4.1_1 [1/22] /usr/local/bin/meson --internal vcstagger ../src/utility/PbcopperGitHash.cpp.in src/utility/PbcopperGitHash.cpp 0.4.1 /construction/biology/pbcopper/pbcopper-0.4.1/src/utility @COPPER_GIT_SHA1@ '(.*)' /construction/biology/pbcopper/pbcopper-0.4.1/src/utility/git describe --always '--dirty=*' [2/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/meson-generated_.._utility_PbcopperGitHash.cpp.o' -MF 'src/25a6634@@pbcopper@sha/meson-generated_.._utility_PbcopperGitHash.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/meson-generated_.._utility_PbcopperGitHash.cpp.o' -c src/utility/PbcopperGitHash.cpp [3/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/cli_Parser.cpp.o' -MF 'src/25a6634@@pbcopper@sha/cli_Parser.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/cli_Parser.cpp.o' -c ../src/cli/Parser.cpp [4/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/cli_CLI.cpp.o' -MF 'src/25a6634@@pbcopper@sha/cli_CLI.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/cli_CLI.cpp.o' -c ../src/cli/CLI.cpp [5/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/cli_Option.cpp.o' -MF 'src/25a6634@@pbcopper@sha/cli_Option.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/cli_Option.cpp.o' -c ../src/cli/Option.cpp [6/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/cli_Interface.cpp.o' -MF 'src/25a6634@@pbcopper@sha/cli_Interface.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/cli_Interface.cpp.o' -c ../src/cli/Interface.cpp [7/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/cli_HelpPrinter.cpp.o' -MF 'src/25a6634@@pbcopper@sha/cli_HelpPrinter.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/cli_HelpPrinter.cpp.o' -c ../src/cli/HelpPrinter.cpp [8/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/cli_VersionPrinter.cpp.o' -MF 'src/25a6634@@pbcopper@sha/cli_VersionPrinter.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/cli_VersionPrinter.cpp.o' -c ../src/cli/VersionPrinter.cpp [9/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/data_Cigar.cpp.o' -MF 'src/25a6634@@pbcopper@sha/data_Cigar.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/data_Cigar.cpp.o' -c ../src/data/Cigar.cpp [10/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/data_MovieName.cpp.o' -MF 'src/25a6634@@pbcopper@sha/data_MovieName.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/data_MovieName.cpp.o' -c ../src/data/MovieName.cpp [11/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/data_CigarOperation.cpp.o' -MF 'src/25a6634@@pbcopper@sha/data_CigarOperation.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/data_CigarOperation.cpp.o' -c ../src/data/CigarOperation.cpp [12/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op 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[14/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/meson-generated_.._utility_PbcopperVersion.cpp.o' -MF 'src/25a6634@@pbcopper@sha/meson-generated_.._utility_PbcopperVersion.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/meson-generated_.._utility_PbcopperVersion.cpp.o' -c src/utility/PbcopperVersion.cpp [15/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/logging_Logging.cpp.o' -MF 'src/25a6634@@pbcopper@sha/logging_Logging.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/logging_Logging.cpp.o' -c ../src/logging/Logging.cpp [16/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/cli_toolcontract_ResolvedToolContract.cpp.o' -MF 'src/25a6634@@pbcopper@sha/cli_toolcontract_ResolvedToolContract.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/cli_toolcontract_ResolvedToolContract.cpp.o' -c ../src/cli/toolcontract/ResolvedToolContract.cpp [17/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/cli_Results.cpp.o' -MF 'src/25a6634@@pbcopper@sha/cli_Results.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/cli_Results.cpp.o' -c ../src/cli/Results.cpp [18/22] c++ -Isrc/25a6634@@pbcopper@sha -Isrc -I../src -Iinclude -I../include -Isrc/utility -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -fPIC -pthread -Wduplicated-cond -Wduplicated-branches -Wlogical-op -Wrestrict -Wnull-dereference -Wuseless-cast -Wdouble-promotion -Wshadow -Wformat=1 -MD -MQ 'src/25a6634@@pbcopper@sha/cli_toolcontract_JsonPrinter.cpp.o' -MF 'src/25a6634@@pbcopper@sha/cli_toolcontract_JsonPrinter.cpp.o.d' -o 'src/25a6634@@pbcopper@sha/cli_toolcontract_JsonPrinter.cpp.o' -c ../src/cli/toolcontract/JsonPrinter.cpp [19/22] c++ -o src/libpbcopper.so.0.4.1 'src/25a6634@@pbcopper@sha/meson-generated_.._utility_PbcopperGitHash.cpp.o' 'src/25a6634@@pbcopper@sha/cli_CLI.cpp.o' 'src/25a6634@@pbcopper@sha/cli_HelpPrinter.cpp.o' 'src/25a6634@@pbcopper@sha/cli_Interface.cpp.o' 'src/25a6634@@pbcopper@sha/cli_Option.cpp.o' 'src/25a6634@@pbcopper@sha/cli_Parser.cpp.o' 'src/25a6634@@pbcopper@sha/cli_Results.cpp.o' 'src/25a6634@@pbcopper@sha/cli_VersionPrinter.cpp.o' 'src/25a6634@@pbcopper@sha/cli_toolcontract_JsonPrinter.cpp.o' 'src/25a6634@@pbcopper@sha/cli_toolcontract_ResolvedToolContract.cpp.o' 'src/25a6634@@pbcopper@sha/data_Cigar.cpp.o' 'src/25a6634@@pbcopper@sha/data_CigarOperation.cpp.o' 'src/25a6634@@pbcopper@sha/data_MovieName.cpp.o' 'src/25a6634@@pbcopper@sha/data_RSMovieName.cpp.o' 'src/25a6634@@pbcopper@sha/logging_Logging.cpp.o' 'src/25a6634@@pbcopper@sha/utility_CallbackTimer.cpp.o' 'src/25a6634@@pbcopper@sha/meson-generated_.._utility_PbcopperVersion.cpp.o' -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -shared -fPIC -Wl,--start-group -Wl,-soname,libpbcopper.so.0.4.1 -Wl,--end-group -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -pthread [20/22] /usr/local/bin/meson --internal symbolextractor src/libpbcopper.so.0.4.1 'src/25a6634@@pbcopper@sha/libpbcopper.so.0.4.1.symbols' [21/22] c++ -Iexamples/cli_demo/c7429bd@@cli_demo@exe -Iexamples/cli_demo -I../examples/cli_demo -Iinclude -I../include -fdiagnostics-color=always -DNDEBUG -pipe -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wnon-virtual-dtor -Wextra -Wpedantic -std=c++11 -O3 -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -isystem /usr/local/include -pthread -MD -MQ 'examples/cli_demo/c7429bd@@cli_demo@exe/main.cpp.o' -MF 'examples/cli_demo/c7429bd@@cli_demo@exe/main.cpp.o.d' -o 'examples/cli_demo/c7429bd@@cli_demo@exe/main.cpp.o' -c ../examples/cli_demo/main.cpp [22/22] c++ -o examples/cli_demo/cli_demo 'examples/cli_demo/c7429bd@@cli_demo@exe/main.cpp.o' -Wl,--no-undefined -Wl,--as-needed -Wl,-O1 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -Wl,--start-group src/libpbcopper.so.0.4.1 -Wl,--end-group -pthread -Wl,-z,origin '-Wl,-rpath,$ORIGIN/../../src' -Wl,-rpath-link,/construction/biology/pbcopper/pbcopper-0.4.1/_build/src -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for pbcopper-0.4.1_1 ===> Generating temporary packing list [1/6] /usr/local/bin/meson --internal vcstagger ../src/utility/PbcopperGitHash.cpp.in src/utility/PbcopperGitHash.cpp 0.4.1 /construction/biology/pbcopper/pbcopper-0.4.1/src/utility @COPPER_GIT_SHA1@ '(.*)' /construction/biology/pbcopper/pbcopper-0.4.1/src/utility/git describe --always '--dirty=*' [1/2] /usr/local/bin/meson install --no-rebuild Installing src/libpbcopper.so.0.4.1 to /construction/biology/pbcopper/stage/usr/local/lib Stripping target 'src/libpbcopper.so.0.4.1' Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/PbcopperConfig.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/PbcopperMakeUnique.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/align/Seed.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/align Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/align/Seeds.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/align Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/align/internal/Seed-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/align/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/align/internal/Seeds-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/align/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/CLI.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/HelpPrinter.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/Interface.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/Option.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/OptionFlags.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/Parser.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/PositionalArg.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/Results.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/SingleDashMode.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/VersionPrinter.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/internal/Option-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/Config.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/Driver.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/InputFileType.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/JsonPrinter.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/OutputFileType.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/ResolvedToolContract.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/ResourceType.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/Task.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/TaskType.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/internal/Driver-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/internal/InputFileType-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/internal/OutputFileType-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/cli/toolcontract/internal/Task-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/cli/toolcontract/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/CCSTag.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/Cigar.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/CigarOperation.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/Interval.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/MovieName.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/Position.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/ReadName.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/RSMovieName.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/RSReadName.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/Zmw.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/internal/CigarOperation-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/internal/Interval-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/internal/MovieName-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/internal/ReadNameBase-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/internal/ReadNameBase.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/data/internal/RSMovieName-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/data/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/json/JSON.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/json Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/json/internal/json.hpp to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/json/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/logging/Logging.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/logging Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/logging/internal/Logging-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/logging/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/parallel/FireAndForget.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/parallel Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/parallel/WorkQueue.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/parallel Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/qgram/Index.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/qgram Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/qgram/IndexHit.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/qgram Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/qgram/IndexHits.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/qgram Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/qgram/internal/Hashing-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/qgram/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/qgram/internal/Index-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/qgram/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/stream/Stream.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/stream Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/CallbackTimer.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/EnumClassHash.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/FileUtils.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/MoveAppend.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/PbcopperVersion.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/SafeSubtract.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/Stopwatch.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/StringUtils.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/SystemInfo.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/Unused.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/internal/CallbackTimer-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/internal/FileUtils-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/internal/Stopwatch-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/internal/StringUtils-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/include/pbcopper/utility/internal/SystemInfo-inl.h to /construction/biology/pbcopper/stage/usr/local/include/pbcopper/utility/internal Installing /construction/biology/pbcopper/pbcopper-0.4.1/_build/meson-private/pbcopper.pc to /construction/biology/pbcopper/stage/usr/local/lib/pkgconfig /bin/sh /xports/Mk/Scripts/relative_link.sh /construction/biology/pbcopper/stage/usr/local/lib/libpbcopper.so.0.4.1 /construction/biology/pbcopper/stage/usr/local/lib/libpbcopper.so.0.4 /bin/sh /xports/Mk/Scripts/relative_link.sh /construction/biology/pbcopper/stage/usr/local/lib/libpbcopper.so.0.4.1 /construction/biology/pbcopper/stage/usr/local/lib/libpbcopper.so.0 ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for pbcopper-0.4.1_1 file sizes/checksums [81]: . done packing files [81]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 24 JUL 2019 at 17:14:43 UTC Duration: 00:01:04