=> Building biology/pbcopper Started : Friday, 20 JUL 2018 at 16:05:38 UTC Platform: 5.3-DEVELOPMENT DragonFly v5.3.0.242.g757c0-DEVELOPMENT #30: Tue May 8 14:06:27 PDT 2018 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.2-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.2-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=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- 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=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -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" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/pbcopper/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=5.2 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-5.2 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=5.26.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500200 OSVERSION=9999999 OSREL=5.2 _OSRELEASE=5.2-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> pbcopper-g20180413 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> pbcopper-g20180413 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pbcopper-g20180413 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by pbcopper-g20180413 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by pbcopper-g20180413 for building => SHA256 Checksum OK for PacificBiosciences-pbcopper-g20180413-17ef457a0dbe1894a8d17af7ddba01a6261bf117_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by pbcopper-g20180413 for building ===> Extracting for pbcopper-g20180413 => SHA256 Checksum OK for PacificBiosciences-pbcopper-g20180413-17ef457a0dbe1894a8d17af7ddba01a6261bf117_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for pbcopper-g20180413 ===> Applying ports patches for pbcopper-g20180413 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> pbcopper-g20180413 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.11.4_1.txz Installing cmake-3.11.4_1... `-- Installing curl-7.60.0... | `-- Installing ca_root_nss-3.38... | `-- Extracting ca_root_nss-3.38: ........ done | `-- Installing krb5-1.16.1_5... | | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | | `-- Installing libressl-2.7.4... | | `-- Extracting libressl-2.7.4: .......... done | | `-- Installing pkgconf-1.4.2,1... | | `-- Extracting pkgconf-1.4.2,1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting krb5-1.16.1_5: .......... done | `-- Installing libnghttp2-1.32.0... | `-- Extracting libnghttp2-1.32.0: .......... done `-- Extracting curl-7.60.0: .......... done `-- Installing expat-2.2.5... `-- Extracting expat-2.2.5: .......... done `-- Installing jsoncpp-1.8.1_3... `-- Extracting jsoncpp-1.8.1_3: .......... done `-- Installing libarchive-3.3.2,1... | `-- Installing liblz4-1.8.2,1... | `-- Extracting liblz4-1.8.2,1: .......... done | `-- Installing lzo2-2.10_1... | `-- Extracting lzo2-2.10_1: .......... done `-- Extracting libarchive-3.3.2,1: .......... done `-- Installing libuv-1.21.0... `-- Extracting libuv-1.21.0: .......... done `-- Installing rhash-1.3.5... `-- Extracting rhash-1.3.5: .......... done Extracting cmake-3.11.4_1: .......... done Message from ca_root_nss-3.38: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> pbcopper-g20180413 depends on file: /usr/local/bin/cmake - found ===> Returning to build of pbcopper-g20180413 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> pbcopper-g20180413 depends on shared library: libboost_regex.so - not found ===> Installing existing package /packages/All/boost-libs-1.67.0_2.txz Installing boost-libs-1.67.0_2... `-- Installing icu-62.1_1,1... `-- Extracting icu-62.1_1,1: .......... done Extracting boost-libs-1.67.0_2: .......... done Message from boost-libs-1.67.0_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-g20180413 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Returning to build of pbcopper-g20180413 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for pbcopper-g20180413 ===> Performing in-source build /bin/mkdir -p /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117 -- The CXX compiler identification is GNU 5.4.1 -- The C compiler identification is GNU 5.4.1 -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS - Success -- Boost version: 1.67.0 -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) Doxygen not found. 'make doc' will not be available. Install Doxygen and re-run cmake if you would like to be able to build API documentation locally. -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_NO_BUILTIN_CHRPATH CMAKE_SHARED_LINKER_FLAGS -- Build files have been written to: /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for pbcopper-g20180413 /usr/local/bin/cmake -H/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117 -B/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/CMakeFiles /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- src/CMakeFiles/pbcopper.dir/all --- /usr/bin/make -f src/CMakeFiles/pbcopper.dir/build.make src/CMakeFiles/pbcopper.dir/depend --- src/CMakeFiles/pbcopper.dir/depend --- cd /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117 && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117 /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117 /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src/CMakeFiles/pbcopper.dir/DependInfo.cmake Scanning dependencies of target pbcopper /usr/bin/make -f src/CMakeFiles/pbcopper.dir/build.make src/CMakeFiles/pbcopper.dir/build --- src/CMakeFiles/pbcopper.dir/cli/CLI.cpp.o --- --- src/CMakeFiles/pbcopper.dir/cli/HelpPrinter.cpp.o --- --- src/CMakeFiles/pbcopper.dir/cli/Interface.cpp.o --- --- src/CMakeFiles/pbcopper.dir/cli/Option.cpp.o --- --- src/CMakeFiles/pbcopper.dir/cli/Parser.cpp.o --- --- src/CMakeFiles/pbcopper.dir/cli/CLI.cpp.o --- [ 22%] Building CXX object src/CMakeFiles/pbcopper.dir/cli/CLI.cpp.o --- src/CMakeFiles/pbcopper.dir/cli/Parser.cpp.o --- [ 16%] Building CXX object src/CMakeFiles/pbcopper.dir/cli/Parser.cpp.o --- src/CMakeFiles/pbcopper.dir/cli/HelpPrinter.cpp.o --- [ 22%] Building CXX object src/CMakeFiles/pbcopper.dir/cli/HelpPrinter.cpp.o --- src/CMakeFiles/pbcopper.dir/cli/Option.cpp.o --- [ 22%] Building CXX object src/CMakeFiles/pbcopper.dir/cli/Option.cpp.o --- src/CMakeFiles/pbcopper.dir/cli/Interface.cpp.o --- [ 27%] Building CXX object src/CMakeFiles/pbcopper.dir/cli/Interface.cpp.o --- src/CMakeFiles/pbcopper.dir/cli/CLI.cpp.o --- cd /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src && /usr/bin/c++ -isystem /usr/local/include -I/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/include -pipe -O2 -fno-strict-aliasing -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/pbcopper.dir/cli/CLI.cpp.o -c /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src/cli/CLI.cpp --- src/CMakeFiles/pbcopper.dir/cli/Option.cpp.o --- cd /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src && /usr/bin/c++ -isystem /usr/local/include -I/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/include -pipe -O2 -fno-strict-aliasing 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-I/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/include -pipe -O2 -fno-strict-aliasing -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/pbcopper.dir/cli/Parser.cpp.o -c /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src/cli/Parser.cpp --- src/CMakeFiles/pbcopper.dir/cli/Interface.cpp.o --- cd /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src && /usr/bin/c++ -isystem /usr/local/include -I/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/include -pipe -O2 -fno-strict-aliasing -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/pbcopper.dir/cli/Interface.cpp.o -c /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src/cli/Interface.cpp --- src/CMakeFiles/pbcopper.dir/cli/Results.cpp.o --- [ 33%] Building CXX object src/CMakeFiles/pbcopper.dir/cli/Results.cpp.o cd 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/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src/cli/VersionPrinter.cpp --- src/CMakeFiles/pbcopper.dir/cli/toolcontract/JsonPrinter.cpp.o --- [ 44%] Building CXX object src/CMakeFiles/pbcopper.dir/cli/toolcontract/JsonPrinter.cpp.o cd /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src && /usr/bin/c++ -isystem /usr/local/include -I/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/include -pipe -O2 -fno-strict-aliasing -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/pbcopper.dir/cli/toolcontract/JsonPrinter.cpp.o -c /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src/cli/toolcontract/JsonPrinter.cpp --- src/CMakeFiles/pbcopper.dir/cli/toolcontract/ResolvedToolContract.cpp.o --- [ 50%] Building CXX object src/CMakeFiles/pbcopper.dir/cli/toolcontract/ResolvedToolContract.cpp.o cd 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-I/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/include -pipe -O2 -fno-strict-aliasing -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/pbcopper.dir/utility/CallbackTimer.cpp.o -c /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src/utility/CallbackTimer.cpp --- src/CMakeFiles/pbcopper.dir/__/generated/utility/PbcopperVersion.cpp.o --- [ 88%] Building CXX object src/CMakeFiles/pbcopper.dir/__/generated/utility/PbcopperVersion.cpp.o cd /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src && /usr/bin/c++ -isystem /usr/local/include -I/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/include -pipe -O2 -fno-strict-aliasing -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/pbcopper.dir/__/generated/utility/PbcopperVersion.cpp.o -c 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/usr/local/bin/cmake -P CMakeFiles/pbcopper.dir/cmake_clean_target.cmake cd /construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pbcopper.dir/link.txt --verbose=1 /usr/bin/ar qc ../lib/libpbcopper.a CMakeFiles/pbcopper.dir/cli/CLI.cpp.o CMakeFiles/pbcopper.dir/cli/HelpPrinter.cpp.o CMakeFiles/pbcopper.dir/cli/Interface.cpp.o CMakeFiles/pbcopper.dir/cli/Option.cpp.o CMakeFiles/pbcopper.dir/cli/Parser.cpp.o CMakeFiles/pbcopper.dir/cli/Results.cpp.o CMakeFiles/pbcopper.dir/cli/VersionPrinter.cpp.o CMakeFiles/pbcopper.dir/cli/toolcontract/JsonPrinter.cpp.o CMakeFiles/pbcopper.dir/cli/toolcontract/ResolvedToolContract.cpp.o CMakeFiles/pbcopper.dir/data/Cigar.cpp.o CMakeFiles/pbcopper.dir/data/CigarOperation.cpp.o CMakeFiles/pbcopper.dir/data/MovieName.cpp.o CMakeFiles/pbcopper.dir/data/RSMovieName.cpp.o CMakeFiles/pbcopper.dir/logging/Logging.cpp.o CMakeFiles/pbcopper.dir/utility/CallbackTimer.cpp.o 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/construction/biology/pbcopper/pbcopper-17ef457a0dbe1894a8d17af7ddba01a6261bf117/include && /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 . /construction/biology/pbcopper/stage/usr/local/include /bin/mv /construction/biology/pbcopper/stage/usr/local/include/meson.build /construction/biology/pbcopper/stage/usr/local/include/pbcopper ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for pbcopper-g20180413 file sizes/checksums [78]: . done packing files [78]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 20 JUL 2018 at 16:06:37 UTC Duration: 00:00:58