=> Building biology/pbbam Started : Thursday, 30 AUG 2018 at 10:54:56 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-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 -------------------------------------------------- PKG_CONFIG=pkgconf XDG_DATA_HOME=/construction/biology/pbbam XDG_CONFIG_HOME=/construction/biology/pbbam HOME=/construction/biology/pbbam TMPDIR="/tmp" PATH=/construction/biology/pbbam/.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/pbbam XDG_CONFIG_HOME=/construction/biology/pbbam HOME=/construction/biology/pbbam TMPDIR="/tmp" PATH=/construction/biology/pbbam/.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/pbbam/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/pbbam" EXAMPLESDIR="share/examples/pbbam" DATADIR="share/pbbam" WWWDIR="www/pbbam" ETCDIR="etc/pbbam" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/pbbam DOCSDIR=/usr/local/share/doc/pbbam EXAMPLESDIR=/usr/local/share/examples/pbbam WWWDIR=/usr/local/www/pbbam ETCDIR=/usr/local/etc/pbbam -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem 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=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> pbbam-g20180416 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 ===> pbbam-g20180416 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of pbbam-g20180416 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by pbbam-g20180416 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by pbbam-g20180416 for building => SHA256 Checksum OK for PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by pbbam-g20180416 for building ===> Extracting for pbbam-g20180416 => SHA256 Checksum OK for PacificBiosciences-pbbam-g20180416-c6b8113adb5104948879e9ff69f739121f12a09f_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for pbbam-g20180416 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> pbbam-g20180416 depends on package: boost-libs>=1.60.0 - 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. ===> pbbam-g20180416 depends on package: boost-libs>=1.60.0 - found ===> Returning to build of pbbam-g20180416 ===> pbbam-g20180416 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 *************************************************************************** ===> pbbam-g20180416 depends on file: /usr/local/bin/cmake - found ===> Returning to build of pbbam-g20180416 ===> pbbam-g20180416 depends on package: pkgconf>=1.3.0_1 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> pbbam-g20180416 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.6.txz Installing htslib-1.6... Extracting htslib-1.6: .......... done ===> pbbam-g20180416 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of pbbam-g20180416 ===> pbbam-g20180416 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for pbbam-g20180416 ===> Performing in-source build /bin/mkdir -p /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f -- 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 -- Performing Test HAS_NO_SIGN_COMPARE -- Performing Test HAS_NO_SIGN_COMPARE - Success -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- Boost version: 1.67.0 -- Found PkgConfig: pkgconf (found version "1.4.2") -- Checking for module 'zlib' -- Found zlib, version 1.2.8 -- Performing Test HAS_NO_UNUSED_PRIVATE_FIELD -- Performing Test HAS_NO_UNUSED_PRIVATE_FIELD - Success -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- 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 PacBioBAM_build_docs -- Build files have been written to: /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for pbbam-g20180416 /usr/local/bin/cmake -H/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f -B/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/CMakeFiles /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- src/CMakeFiles/pbbam.dir/all --- /usr/bin/make -f src/CMakeFiles/pbbam.dir/build.make src/CMakeFiles/pbbam.dir/depend --- src/CMakeFiles/pbbam.dir/depend --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/CMakeFiles/pbbam.dir/DependInfo.cmake Scanning dependencies of target pbbam /usr/bin/make -f src/CMakeFiles/pbbam.dir/build.make src/CMakeFiles/pbbam.dir/build --- src/CMakeFiles/pbbam.dir/Accuracy.cpp.o --- --- src/CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o --- --- src/CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o --- --- src/CMakeFiles/pbbam.dir/BamFile.cpp.o --- --- src/CMakeFiles/pbbam.dir/BamHeader.cpp.o --- --- src/CMakeFiles/pbbam.dir/BamReader.cpp.o --- --- src/CMakeFiles/pbbam.dir/BamRecord.cpp.o --- --- src/CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o --- --- src/CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o --- --- src/CMakeFiles/pbbam.dir/BamRecordTags.cpp.o --- --- src/CMakeFiles/pbbam.dir/BamTagCodec.cpp.o --- --- src/CMakeFiles/pbbam.dir/BamWriter.cpp.o --- --- src/CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o --- [ 1%] Building CXX object src/CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o --- src/CMakeFiles/pbbam.dir/Accuracy.cpp.o --- [ 2%] Building CXX object src/CMakeFiles/pbbam.dir/Accuracy.cpp.o --- src/CMakeFiles/pbbam.dir/BamHeader.cpp.o --- [ 3%] Building CXX object src/CMakeFiles/pbbam.dir/BamHeader.cpp.o --- src/CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o --- [ 4%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o --- src/CMakeFiles/pbbam.dir/BamFile.cpp.o --- [ 5%] Building CXX object src/CMakeFiles/pbbam.dir/BamFile.cpp.o --- src/CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/BaiIndexedBamReader.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/BaiIndexedBamReader.cpp --- src/CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o --- [ 6%] Building CXX object src/CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o --- src/CMakeFiles/pbbam.dir/Accuracy.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/Accuracy.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/Accuracy.cpp --- src/CMakeFiles/pbbam.dir/BamHeader.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/BamHeader.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/BamHeader.cpp --- src/CMakeFiles/pbbam.dir/BamWriter.cpp.o --- [ 7%] Building CXX object src/CMakeFiles/pbbam.dir/BamWriter.cpp.o --- src/CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/BamRecordBuilder.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/BamRecordBuilder.cpp --- src/CMakeFiles/pbbam.dir/BamFile.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/BamFile.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/BamFile.cpp --- src/CMakeFiles/pbbam.dir/BamRecordTags.cpp.o --- [ 8%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordTags.cpp.o --- src/CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o --- [ 9%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o --- src/CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/AlignmentPrinter.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/AlignmentPrinter.cpp --- src/CMakeFiles/pbbam.dir/BamWriter.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/BamWriter.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/BamWriter.cpp --- src/CMakeFiles/pbbam.dir/BamRecord.cpp.o --- [ 10%] Building CXX object src/CMakeFiles/pbbam.dir/BamRecord.cpp.o --- src/CMakeFiles/pbbam.dir/BamRecordTags.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/BamRecordTags.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/BamRecordTags.cpp --- src/CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/BamRecordImpl.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/BamRecordImpl.cpp --- src/CMakeFiles/pbbam.dir/BamTagCodec.cpp.o --- [ 11%] Building CXX object src/CMakeFiles/pbbam.dir/BamTagCodec.cpp.o --- src/CMakeFiles/pbbam.dir/BamReader.cpp.o --- [ 12%] Building CXX object src/CMakeFiles/pbbam.dir/BamReader.cpp.o --- src/CMakeFiles/pbbam.dir/BamRecord.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/BamRecord.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src/BamRecord.cpp --- src/CMakeFiles/pbbam.dir/BamTagCodec.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/src && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbam.dir/BamTagCodec.cpp.o -c 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CMakeFiles/pbbam.dir/MD5.cpp.o CMakeFiles/pbbam.dir/MemoryUtils.cpp.o CMakeFiles/pbbam.dir/PbiBuilder.cpp.o CMakeFiles/pbbam.dir/PbiFile.cpp.o CMakeFiles/pbbam.dir/PbiFilter.cpp.o CMakeFiles/pbbam.dir/PbiFilterQuery.cpp.o CMakeFiles/pbbam.dir/PbiFilterTypes.cpp.o CMakeFiles/pbbam.dir/PbiIndexedBamReader.cpp.o CMakeFiles/pbbam.dir/PbiIndexIO.cpp.o CMakeFiles/pbbam.dir/PbiRawData.cpp.o CMakeFiles/pbbam.dir/ProgramInfo.cpp.o CMakeFiles/pbbam.dir/QNameQuery.cpp.o CMakeFiles/pbbam.dir/QualityValue.cpp.o CMakeFiles/pbbam.dir/ReadAccuracyQuery.cpp.o CMakeFiles/pbbam.dir/ReadGroupInfo.cpp.o CMakeFiles/pbbam.dir/SamTagCodec.cpp.o CMakeFiles/pbbam.dir/SamWriter.cpp.o CMakeFiles/pbbam.dir/SequenceInfo.cpp.o CMakeFiles/pbbam.dir/SubreadLengthQuery.cpp.o CMakeFiles/pbbam.dir/Tag.cpp.o CMakeFiles/pbbam.dir/TagCollection.cpp.o CMakeFiles/pbbam.dir/Validator.cpp.o CMakeFiles/pbbam.dir/ValidationErrors.cpp.o CMakeFiles/pbbam.dir/ValidationException.cpp.o CMakeFiles/pbbam.dir/Version.cpp.o CMakeFiles/pbbam.dir/VirtualZmwBamRecord.cpp.o CMakeFiles/pbbam.dir/VirtualZmwCompositeReader.cpp.o CMakeFiles/pbbam.dir/VirtualZmwReader.cpp.o CMakeFiles/pbbam.dir/VirtualRegionTypeMap.cpp.o CMakeFiles/pbbam.dir/XmlReader.cpp.o CMakeFiles/pbbam.dir/XmlWriter.cpp.o CMakeFiles/pbbam.dir/WhitelistedZmwReadStitcher.cpp.o CMakeFiles/pbbam.dir/ZmwGroupQuery.cpp.o CMakeFiles/pbbam.dir/ZmwReadStitcher.cpp.o CMakeFiles/pbbam.dir/ZmwQuery.cpp.o CMakeFiles/pbbam.dir/ZmwTypeMap.cpp.o CMakeFiles/pbbam.dir/pugixml/pugixml.cpp.o /usr/bin/ranlib ../lib/libpbbam.a [ 77%] Built target pbbam --- tools/bam2sam/CMakeFiles/bam2sam.dir/all --- --- tools/pbindex/CMakeFiles/pbindex.dir/all --- --- tools/pbindexdump/CMakeFiles/pbindexdump.dir/all --- --- tools/pbmerge/CMakeFiles/pbmerge.dir/all --- --- tools/pbbamify/CMakeFiles/pbbamify.dir/all --- --- tools/bam2sam/CMakeFiles/bam2sam.dir/all --- /usr/bin/make -f tools/bam2sam/CMakeFiles/bam2sam.dir/build.make tools/bam2sam/CMakeFiles/bam2sam.dir/depend --- 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tools/bam2sam/CMakeFiles/bam2sam.dir/all --- --- tools/bam2sam/CMakeFiles/bam2sam.dir/__/common/OptionParser.cpp.o --- --- tools/bam2sam/CMakeFiles/bam2sam.dir/src/main.cpp.o --- --- tools/bam2sam/CMakeFiles/bam2sam.dir/src/Bam2Sam.cpp.o --- --- tools/pbindex/CMakeFiles/pbindex.dir/all --- --- tools/pbindex/CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o --- --- tools/pbindex/CMakeFiles/pbindex.dir/src/main.cpp.o --- --- tools/pbindex/CMakeFiles/pbindex.dir/src/PbIndex.cpp.o --- --- tools/pbindexdump/CMakeFiles/pbindexdump.dir/all --- Scanning dependencies of target pbindexdump --- tools/bam2sam/CMakeFiles/bam2sam.dir/all --- --- tools/bam2sam/CMakeFiles/bam2sam.dir/src/main.cpp.o --- [ 78%] Building CXX object tools/bam2sam/CMakeFiles/bam2sam.dir/src/main.cpp.o cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/bam2sam && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/common 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tools/pbindex/CMakeFiles/pbindex.dir/src/PbIndex.cpp.o --- tools/pbindex/CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o --- cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/pbindex && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/common -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/generated -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/common/OptionParser.cpp --- tools/pbindex/CMakeFiles/pbindex.dir/src/PbIndex.cpp.o --- cd 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/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/pbbamify && /usr/bin/c++ -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/common -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/generated -I/construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/include -I/usr/local/include/htslib -I/usr/local/include -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -pipe -O2 -fno-strict-aliasing -std=gnu++14 -o CMakeFiles/pbbamify.dir/src/QueryLookup.cpp.o -c /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/pbbamify/src/QueryLookup.cpp --- tools/bam2sam/CMakeFiles/bam2sam.dir/all --- --- bin/bam2sam --- [ 95%] Linking CXX executable ../../bin/bam2sam cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/bam2sam && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/bam2sam.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -pipe -O2 -fno-strict-aliasing CMakeFiles/bam2sam.dir/__/common/OptionParser.cpp.o CMakeFiles/bam2sam.dir/src/main.cpp.o CMakeFiles/bam2sam.dir/src/Bam2Sam.cpp.o -o ../../bin/bam2sam ../../lib/libpbbam.a -L/usr/local/lib -lhts -lz -pthread [ 95%] Built target bam2sam --- tools/pbindexdump/CMakeFiles/pbindexdump.dir/all --- --- bin/pbindexdump --- [ 96%] Linking CXX executable ../../bin/pbindexdump cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/pbindexdump && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pbindexdump.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -pipe -O2 -fno-strict-aliasing CMakeFiles/pbindexdump.dir/__/common/OptionParser.cpp.o CMakeFiles/pbindexdump.dir/src/CppFormatter.cpp.o CMakeFiles/pbindexdump.dir/src/JsonFormatter.cpp.o CMakeFiles/pbindexdump.dir/src/PbIndexDump.cpp.o CMakeFiles/pbindexdump.dir/src/main.cpp.o -o ../../bin/pbindexdump ../../lib/libpbbam.a -L/usr/local/lib -lhts -lz -pthread [ 96%] Built target pbindexdump --- tools/pbindex/CMakeFiles/pbindex.dir/all --- --- bin/pbindex --- [ 97%] Linking CXX executable ../../bin/pbindex cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/pbindex && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pbindex.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -pipe -O2 -fno-strict-aliasing CMakeFiles/pbindex.dir/__/common/OptionParser.cpp.o CMakeFiles/pbindex.dir/src/main.cpp.o CMakeFiles/pbindex.dir/src/PbIndex.cpp.o -o ../../bin/pbindex ../../lib/libpbbam.a -L/usr/local/lib -lhts -lz -pthread [ 97%] Built target pbindex --- tools/pbbamify/CMakeFiles/pbbamify.dir/all --- --- bin/pbbamify --- [ 98%] Linking CXX executable ../../bin/pbbamify cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/pbbamify && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pbbamify.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -pipe -O2 -fno-strict-aliasing CMakeFiles/pbbamify.dir/__/common/OptionParser.cpp.o CMakeFiles/pbbamify.dir/src/main.cpp.o CMakeFiles/pbbamify.dir/src/PbBamify.cpp.o CMakeFiles/pbbamify.dir/src/QueryLookup.cpp.o -o ../../bin/pbbamify ../../lib/libpbbam.a -L/usr/local/lib -lhts -lz -pthread [ 98%] Built target pbbamify --- tools/pbmerge/CMakeFiles/pbmerge.dir/all --- --- bin/pbmerge --- [100%] Linking CXX executable ../../bin/pbmerge cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/tools/pbmerge && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pbmerge.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -Wall -Wno-unused-local-typedefs -Wno-sign-compare -Wno-unused-private-field -pipe -O2 -fno-strict-aliasing CMakeFiles/pbmerge.dir/__/common/OptionParser.cpp.o CMakeFiles/pbmerge.dir/src/main.cpp.o -o ../../bin/pbmerge ../../lib/libpbbam.a -L/usr/local/lib -lhts -lz -pthread [100%] Built target pbmerge /usr/local/bin/cmake -E cmake_progress_start /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/CMakeFiles 0 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for pbbam-g20180416 ===> Generating temporary packing list install -s -m 555 /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/bin/* /construction/biology/pbbam/stage/usr/local/bin install -m 0644 /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/lib/* /construction/biology/pbbam/stage/usr/local/lib cd /construction/biology/pbbam/pbbam-c6b8113adb5104948879e9ff69f739121f12a09f/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/pbbam/stage/usr/local/include /bin/mv /construction/biology/pbbam/stage/usr/local/include/meson.build /construction/biology/pbbam/stage/usr/local/include/pbbam ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for pbbam-g20180416 file sizes/checksums [135]: .. done packing files [135]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 10:56:36 UTC Duration: 00:01:39