=> Building biology/unanimity Started : Friday, 15 MAR 2019 at 13:38:35 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-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 PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/construction/biology/unanimity XDG_CONFIG_HOME=/construction/biology/unanimity HOME=/construction/biology/unanimity TMPDIR="/tmp" PATH=/construction/biology/unanimity/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/unanimity XDG_CONFIG_HOME=/construction/biology/unanimity HOME=/construction/biology/unanimity TMPDIR="/tmp" PATH=/construction/biology/unanimity/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -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/unanimity/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=dragonfly5 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/unanimity" EXAMPLESDIR="share/examples/unanimity" DATADIR="share/unanimity" WWWDIR="www/unanimity" ETCDIR="etc/unanimity" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/unanimity DOCSDIR=/usr/local/share/doc/unanimity EXAMPLESDIR=/usr/local/share/examples/unanimity WWWDIR=/usr/local/www/unanimity ETCDIR=/usr/local/etc/unanimity -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.4 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 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=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> unanimity-3.1.0_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> unanimity-3.1.0_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of unanimity-3.1.0_2 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by unanimity-3.1.0_2 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by unanimity-3.1.0_2 for building => SHA256 Checksum OK for PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by unanimity-3.1.0_2 for building ===> Extracting for unanimity-3.1.0_2 => SHA256 Checksum OK for PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for unanimity-3.1.0_2 ===> Applying ports patches for unanimity-3.1.0_2 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> unanimity-3.1.0_2 depends on package: pbseqan>=g20171002 - not found ===> Installing existing package /packages/All/pbseqan-g20171011.txz Installing pbseqan-g20171011... Extracting pbseqan-g20171011: .......... done Message from pbseqan-g20171011: ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Upstream merged into SeqAn project: Use biology/seqan. ===> unanimity-3.1.0_2 depends on package: pbseqan>=g20171002 - found ===> Returning to build of unanimity-3.1.0_2 ===> unanimity-3.1.0_2 depends on package: pbbam>=g20180416 - not found ===> Installing existing package /packages/All/pbbam-g20180416_3.txz Installing pbbam-g20180416_3... `-- Installing boost-libs-1.69.0_1... | `-- Installing icu-63.1_1,1... | `-- Extracting icu-63.1_1,1: .......... done `-- Extracting boost-libs-1.69.0_1: .......... done `-- Installing htslib-1.9... | `-- Installing curl-7.64.0_1... | | `-- Installing ca_root_nss-3.42.1... | | `-- Extracting ca_root_nss-3.42.1: ........ done | | `-- Installing krb5-1.17_1... | | `-- Installing gettext-runtime-0.19.8.1_2... | | | `-- Installing indexinfo-0.3.1... | | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done | | `-- Installing libressl-2.8.3... | | `-- Extracting libressl-2.8.3: .......... done | | `-- Installing readline-7.0.5... | | | `-- Installing ncurses-6.1.20190112... | | | `-- Extracting ncurses-6.1.20190112: .......... done | | `-- Extracting readline-7.0.5: .......... done | | `-- Extracting krb5-1.17_1: .......... done | | `-- Installing libnghttp2-1.36.0... | | `-- Extracting libnghttp2-1.36.0: .......... done | `-- Extracting curl-7.64.0_1: .......... done `-- Extracting htslib-1.9: .......... done Extracting pbbam-g20180416_3: .......... done Message from boost-libs-1.69.0_1: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Message from ca_root_nss-3.42.1: ********************************* 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 *************************************************************************** ===> unanimity-3.1.0_2 depends on package: pbbam>=g20180416 - found ===> Returning to build of unanimity-3.1.0_2 ===> unanimity-3.1.0_2 depends on package: pbcopper>=g20180413 - not found ===> Installing existing package /packages/All/pbcopper-0.4.1.txz Installing pbcopper-0.4.1... Extracting pbcopper-0.4.1: .......... done ===> unanimity-3.1.0_2 depends on package: pbcopper>=g20180413 - found ===> Returning to build of unanimity-3.1.0_2 ===> unanimity-3.1.0_2 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.13.4.txz Installing cmake-3.13.4... `-- Installing expat-2.2.6_1... `-- Extracting expat-2.2.6_1: .......... done `-- Installing jsoncpp-1.8.1_5... `-- Extracting jsoncpp-1.8.1_5: .......... done `-- Installing libarchive-3.3.3,1... | `-- Installing liblz4-1.8.3,1... | `-- Extracting liblz4-1.8.3,1: .......... done | `-- Installing lzo2-2.10_1... | `-- Extracting lzo2-2.10_1: .......... done `-- Extracting libarchive-3.3.3,1: .......... done `-- Installing libuv-1.26.0... `-- Extracting libuv-1.26.0: .......... done `-- Installing rhash-1.3.5... `-- Extracting rhash-1.3.5: .......... done Extracting cmake-3.13.4: .......... done ===> unanimity-3.1.0_2 depends on file: /usr/local/bin/cmake - found ===> Returning to build of unanimity-3.1.0_2 ===> unanimity-3.1.0_2 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-1.6.0,1.txz Installing pkgconf-1.6.0,1... Extracting pkgconf-1.6.0,1: .......... done ===> unanimity-3.1.0_2 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of unanimity-3.1.0_2 ===> unanimity-3.1.0_2 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.15.txz Installing python27-2.7.15... `-- Installing libffi-3.2.1_3... `-- Extracting libffi-3.2.1_3: .......... done Extracting python27-2.7.15: .......... done Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> unanimity-3.1.0_2 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of unanimity-3.1.0_2 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> unanimity-3.1.0_2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> unanimity-3.1.0_2 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for unanimity-3.1.0_2 ===> Performing in-source build /bin/mkdir -p /construction/biology/unanimity/unanimity-3.1.0 -- The CXX compiler identification is GNU 8.1.0 -- The C compiler identification is GNU 8.1.0 -- 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 -- Boost version: 1.69.0 -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- Found PkgConfig: pkgconf (found version "1.6.0") -- Checking for module 'zlib' -- Found zlib, version 1.2.8 -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS - Success -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_C_FLAGS_DEBUG CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS Python_ADDITIONAL_VERSIONS -- Build files have been written to: /construction/biology/unanimity/unanimity-3.1.0 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for unanimity-3.1.0_2 /usr/local/bin/cmake -S/construction/biology/unanimity/unanimity-3.1.0 -B/construction/biology/unanimity/unanimity-3.1.0 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/unanimity/unanimity-3.1.0/CMakeFiles /construction/biology/unanimity/unanimity-3.1.0/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- src/CMakeFiles/unanimity.dir/all --- --- src/CMakeFiles/cc2.dir/all --- /usr/bin/make -f src/CMakeFiles/cc2.dir/build.make src/CMakeFiles/cc2.dir/depend --- src/CMakeFiles/cc2.dir/depend --- cd /construction/biology/unanimity/unanimity-3.1.0 && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/unanimity/unanimity-3.1.0 /construction/biology/unanimity/unanimity-3.1.0/src /construction/biology/unanimity/unanimity-3.1.0 /construction/biology/unanimity/unanimity-3.1.0/src /construction/biology/unanimity/unanimity-3.1.0/src/CMakeFiles/cc2.dir/DependInfo.cmake --- src/CMakeFiles/unanimity.dir/all --- /usr/bin/make -f src/CMakeFiles/unanimity.dir/build.make src/CMakeFiles/unanimity.dir/depend --- src/CMakeFiles/unanimity.dir/depend --- cd /construction/biology/unanimity/unanimity-3.1.0 && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/unanimity/unanimity-3.1.0 /construction/biology/unanimity/unanimity-3.1.0/src /construction/biology/unanimity/unanimity-3.1.0 /construction/biology/unanimity/unanimity-3.1.0/src /construction/biology/unanimity/unanimity-3.1.0/src/CMakeFiles/unanimity.dir/DependInfo.cmake Scanning dependencies of target unanimity /usr/bin/make -f src/CMakeFiles/unanimity.dir/build.make src/CMakeFiles/unanimity.dir/build --- src/CMakeFiles/unanimity.dir/__/third-party/cpp-optparse/OptionParser.cpp.o --- --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o --- --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o --- --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o --- --- src/CMakeFiles/unanimity.dir/__/third-party/cpp-optparse/OptionParser.cpp.o --- [ 1%] Building CXX object src/CMakeFiles/unanimity.dir/__/third-party/cpp-optparse/OptionParser.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/__/third-party/cpp-optparse/OptionParser.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse/OptionParser.cpp --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o --- [ 2%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o --- [ 4%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o --- cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/Filters.cpp --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o --- cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/ConsensusModelFactory.cpp --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o --- [ 4%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/Consensus.cpp --- src/CMakeFiles/cc2.dir/all --- Scanning dependencies of target cc2 /usr/bin/make -f src/CMakeFiles/cc2.dir/build.make src/CMakeFiles/cc2.dir/build --- src/CMakeFiles/cc2.dir/__/generated/UnanimityGitHash.cpp.o --- [ 5%] Building CXX object src/CMakeFiles/cc2.dir/__/generated/UnanimityGitHash.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/__/generated/UnanimityGitHash.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/generated/UnanimityGitHash.cpp --- src/CMakeFiles/cc2.dir/__/generated/UnanimityVersion.cpp.o --- [ 6%] Building CXX object src/CMakeFiles/cc2.dir/__/generated/UnanimityVersion.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/__/generated/UnanimityVersion.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/generated/UnanimityVersion.cpp --- src/CMakeFiles/cc2.dir/__/generated/ModelInternalInitializer.cpp.o --- [ 8%] Building CXX object src/CMakeFiles/cc2.dir/__/generated/ModelInternalInitializer.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/__/generated/ModelInternalInitializer.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/generated/ModelInternalInitializer.cpp --- src/CMakeFiles/cc2.dir/align/AffineAlignment.cpp.o --- [ 9%] Building CXX object src/CMakeFiles/cc2.dir/align/AffineAlignment.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/align/AffineAlignment.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/align/AffineAlignment.cpp In file included from /usr/local/include/boost/numeric/ublas/matrix.hpp:19, from /construction/biology/unanimity/unanimity-3.1.0/src/align/AffineAlignment.cpp:9: /usr/local/include/boost/numeric/ublas/matrix_expression.hpp: In member function 'void boost::numeric::ublas::matrix_binary::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)': /usr/local/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (it2_ != it2_end_) ^~ /usr/local/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (it2_ != it2_end_) { ^~ --- src/CMakeFiles/unanimity.dir/all --- --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/GenomicConsensus.cpp.o --- [ 10%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/GenomicConsensus.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/GenomicConsensus.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/GenomicConsensus.cpp --- src/CMakeFiles/cc2.dir/all --- --- src/CMakeFiles/cc2.dir/align/AlignConfig.cpp.o --- [ 10%] Building CXX object src/CMakeFiles/cc2.dir/align/AlignConfig.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/align/AlignConfig.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/align/AlignConfig.cpp --- src/CMakeFiles/cc2.dir/align/BandedChainAlignment.cpp.o --- [ 12%] Building CXX object src/CMakeFiles/cc2.dir/align/BandedChainAlignment.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/align/BandedChainAlignment.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/align/BandedChainAlignment.cpp --- src/CMakeFiles/unanimity.dir/all --- --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o --- [ 13%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/IPoaModel.cpp --- src/CMakeFiles/cc2.dir/all --- --- src/CMakeFiles/cc2.dir/align/LinearAlignment.cpp.o --- [ 14%] Building CXX object src/CMakeFiles/cc2.dir/align/LinearAlignment.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/align/LinearAlignment.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/align/LinearAlignment.cpp --- src/CMakeFiles/unanimity.dir/all --- --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o --- [ 16%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/Input.cpp --- src/CMakeFiles/cc2.dir/all --- In file included from /usr/local/include/boost/numeric/ublas/io.hpp:19, from /construction/biology/unanimity/unanimity-3.1.0/src/align/LinearAlignment.cpp:21: /usr/local/include/boost/numeric/ublas/matrix_expression.hpp: In member function 'void boost::numeric::ublas::matrix_binary::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)': /usr/local/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (it2_ != it2_end_) ^~ /usr/local/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (it2_ != it2_end_) { ^~ --- src/CMakeFiles/unanimity.dir/all --- --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o --- [ 17%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/Intervals.cpp --- src/CMakeFiles/cc2.dir/all --- --- src/CMakeFiles/cc2.dir/align/PairwiseAlignment.cpp.o --- [ 18%] Building CXX object src/CMakeFiles/cc2.dir/align/PairwiseAlignment.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/align/PairwiseAlignment.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/align/PairwiseAlignment.cpp --- src/CMakeFiles/unanimity.dir/all --- --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o --- [ 20%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/Output.cpp --- src/CMakeFiles/cc2.dir/all --- In file included from /usr/local/include/boost/numeric/ublas/matrix.hpp:19, from /construction/biology/unanimity/unanimity-3.1.0/src/align/PairwiseAlignment.cpp:8: /usr/local/include/boost/numeric/ublas/matrix_expression.hpp: In member function 'void boost::numeric::ublas::matrix_binary::const_iterator1::increment(boost::numeric::ublas::sparse_bidirectional_iterator_tag)': /usr/local/include/boost/numeric/ublas/matrix_expression.hpp:2224:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (it2_ != it2_end_) ^~ /usr/local/include/boost/numeric/ublas/matrix_expression.hpp:2227:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (it2_ != it2_end_) { ^~ --- src/CMakeFiles/cc2.dir/matrix/BasicDenseMatrix.cpp.o --- [ 21%] Building CXX object src/CMakeFiles/cc2.dir/matrix/BasicDenseMatrix.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/matrix/BasicDenseMatrix.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/matrix/BasicDenseMatrix.cpp --- src/CMakeFiles/cc2.dir/matrix/ScaledMatrix.cpp.o --- [ 22%] Building CXX object src/CMakeFiles/cc2.dir/matrix/ScaledMatrix.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/matrix/ScaledMatrix.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/matrix/ScaledMatrix.cpp --- src/CMakeFiles/cc2.dir/matrix/SparseMatrix.cpp.o --- [ 24%] Building CXX object src/CMakeFiles/cc2.dir/matrix/SparseMatrix.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/matrix/SparseMatrix.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/matrix/SparseMatrix.cpp --- src/CMakeFiles/cc2.dir/models/MarginalModelForm.cpp.o --- [ 25%] Building CXX object src/CMakeFiles/cc2.dir/models/MarginalModelForm.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/models/MarginalModelForm.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/models/MarginalModelForm.cpp --- src/CMakeFiles/unanimity.dir/all --- --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o --- [ 25%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/Settings.cpp --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o --- [ 27%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/Sorting.cpp --- src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o --- [ 28%] Building CXX object src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/genomicconsensus/experimental/Workflow.cpp --- src/CMakeFiles/cc2.dir/all --- --- src/CMakeFiles/cc2.dir/models/P6C4NoCov_Model.cpp.o --- [ 28%] Building CXX object src/CMakeFiles/cc2.dir/models/P6C4NoCov_Model.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/models/P6C4NoCov_Model.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/models/P6C4NoCov_Model.cpp --- src/CMakeFiles/unanimity.dir/all --- --- 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-I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -pipe -O2 -fno-strict-aliasing -o CMakeFiles/unanimity.dir/__/third-party/cssw/ssw.c.o -c /construction/biology/unanimity/unanimity-3.1.0/third-party/cssw/ssw.c --- src/CMakeFiles/unanimity.dir/ConsensusSettings.cpp.o --- [ 55%] Building CXX object src/CMakeFiles/unanimity.dir/ConsensusSettings.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/ConsensusSettings.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/ConsensusSettings.cpp --- src/CMakeFiles/unanimity.dir/LocalAlignment.cpp.o --- [ 56%] Building CXX object src/CMakeFiles/unanimity.dir/LocalAlignment.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/unanimity.dir/LocalAlignment.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/LocalAlignment.cpp --- src/CMakeFiles/cc2.dir/all --- --- src/CMakeFiles/cc2.dir/models/S_P1C1v2_Model.cpp.o --- [ 58%] Building CXX object src/CMakeFiles/cc2.dir/models/S_P1C1v2_Model.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/models/S_P1C1v2_Model.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/models/S_P1C1v2_Model.cpp --- src/CMakeFiles/cc2.dir/models/S_P2C2v5_Model.cpp.o --- [ 59%] Building CXX object src/CMakeFiles/cc2.dir/models/S_P2C2v5_Model.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/models/S_P2C2v5_Model.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/models/S_P2C2v5_Model.cpp --- src/CMakeFiles/cc2.dir/models/SnrModelForm.cpp.o --- [ 60%] Building CXX object src/CMakeFiles/cc2.dir/models/SnrModelForm.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/models/SnrModelForm.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/models/SnrModelForm.cpp --- src/CMakeFiles/unanimity.dir/all --- --- src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o --- In file included from /usr/local/include/PacBio/seqan/index.h:137, from /construction/biology/unanimity/unanimity-3.1.0/include/pacbio/ccs/SparseAlignment.h:14, from /construction/biology/unanimity/unanimity-3.1.0/src/SparsePoa.cpp:14: /usr/local/include/PacBio/seqan/index/index_dfi.h: In function 'void seqan::_storeWotdChildren(seqan::Index > >&, TSize, TSize)': /usr/local/include/PacBio/seqan/index/index_dfi.h:561:15: warning: this 'else' clause does not guard... [-Wmisleading-indentation] } else ^~~~ /usr/local/include/PacBio/seqan/index/index_dfi.h:563:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' for (TDirSize d = index.sentinelBound - index.sentinelOcc; d != index.sentinelBound; ++d) ^~~ --- src/CMakeFiles/cc2.dir/all --- --- src/CMakeFiles/cc2.dir/poa/PoaAlignmentMatrix.cpp.o --- [ 60%] Building CXX object src/CMakeFiles/cc2.dir/poa/PoaAlignmentMatrix.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra 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--- --- src/libunanimity.a --- [ 66%] Linking CXX static library libunanimity.a cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/local/bin/cmake -P CMakeFiles/unanimity.dir/cmake_clean_target.cmake cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/unanimity.dir/link.txt --verbose=1 /usr/bin/ar qc libunanimity.a CMakeFiles/unanimity.dir/__/third-party/cpp-optparse/OptionParser.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Consensus.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/ConsensusModelFactory.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Filters.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/GenomicConsensus.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o 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CMakeFiles/unanimity.dir/SparsePoa.cpp.o CMakeFiles/unanimity.dir/SubreadResultCounter.cpp.o CMakeFiles/unanimity.dir/Timer.cpp.o CMakeFiles/unanimity.dir/Utility.cpp.o CMakeFiles/unanimity.dir/__/third-party/cssw/ssw_cpp.cpp.o CMakeFiles/unanimity.dir/__/third-party/cssw/ssw.c.o CMakeFiles/unanimity.dir/ConsensusSettings.cpp.o CMakeFiles/unanimity.dir/LocalAlignment.cpp.o /usr/bin/ranlib libunanimity.a [ 66%] Built target unanimity --- src/CMakeFiles/cc2.dir/all --- --- src/CMakeFiles/cc2.dir/poa/PoaGraphTraversals.cpp.o --- [ 67%] Building CXX object src/CMakeFiles/cc2.dir/poa/PoaGraphTraversals.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/poa/PoaGraphTraversals.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/poa/PoaGraphTraversals.cpp --- src/CMakeFiles/cc2.dir/poa/RangeFinder.cpp.o --- [ 68%] Building CXX object src/CMakeFiles/cc2.dir/poa/RangeFinder.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/poa/RangeFinder.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/poa/RangeFinder.cpp --- src/CMakeFiles/cc2.dir/Coverage.cpp.o --- [ 70%] Building CXX object src/CMakeFiles/cc2.dir/Coverage.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter 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-I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/ModelFactory.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/ModelFactory.cpp --- src/CMakeFiles/cc2.dir/ModelFormFactory.cpp.o --- [ 79%] Building CXX object src/CMakeFiles/cc2.dir/ModelFormFactory.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/cc2.dir/ModelFormFactory.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/ModelFormFactory.cpp --- src/CMakeFiles/cc2.dir/ModelSelection.cpp.o --- [ 79%] Building CXX object src/CMakeFiles/cc2.dir/ModelSelection.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra 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-I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/gcpp.dir/main/gcpp.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/main/gcpp.cpp --- src/CMakeFiles/ccs.dir/all --- Scanning dependencies of target ccs /usr/bin/make -f src/CMakeFiles/ccs.dir/build.make src/CMakeFiles/ccs.dir/build --- src/CMakeFiles/ccs.dir/main/ccs.cpp.o --- [ 91%] Building CXX object src/CMakeFiles/ccs.dir/main/ccs.cpp.o cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/bin/c++ -I/usr/local/include/PacBio -I/construction/biology/unanimity/unanimity-3.1.0/include -I/construction/biology/unanimity/unanimity-3.1.0/generated -I/usr/local/include -I/usr/local/include/htslib -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cpp-optparse -I/usr/local/include/pbbam -I/construction/biology/unanimity/unanimity-3.1.0/third-party/cssw -I/construction/biology/unanimity/unanimity-3.1.0/src -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing -std=c++14 -o CMakeFiles/ccs.dir/main/ccs.cpp.o -c /construction/biology/unanimity/unanimity-3.1.0/src/main/ccs.cpp --- src/CMakeFiles/gcpp.dir/all --- --- gcpp --- [ 93%] Linking CXX executable ../gcpp cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gcpp.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -Wall -Wextra 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/construction/biology/unanimity/unanimity-3.1.0 /construction/biology/unanimity/unanimity-3.1.0/src /construction/biology/unanimity/unanimity-3.1.0 /construction/biology/unanimity/unanimity-3.1.0/src /construction/biology/unanimity/unanimity-3.1.0/src/CMakeFiles/ccs.dir/DependInfo.cmake /usr/bin/make -f src/CMakeFiles/ccs.dir/build.make src/CMakeFiles/ccs.dir/build [ 93%] Built target ccs /usr/bin/make -f src/CMakeFiles/arrow.dir/build.make src/CMakeFiles/arrow.dir/depend cd /construction/biology/unanimity/unanimity-3.1.0 && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/unanimity/unanimity-3.1.0 /construction/biology/unanimity/unanimity-3.1.0/src /construction/biology/unanimity/unanimity-3.1.0 /construction/biology/unanimity/unanimity-3.1.0/src /construction/biology/unanimity/unanimity-3.1.0/src/CMakeFiles/arrow.dir/DependInfo.cmake /usr/bin/make -f src/CMakeFiles/arrow.dir/build.make src/CMakeFiles/arrow.dir/build [ 95%] Built target arrow /usr/bin/make 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--verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing CMakeFiles/ccs.dir/main/ccs.cpp.o -o CMakeFiles/CMakeRelink.dir/ccs -pthread libunanimity.a libcc2.a -lz -L/usr/local/lib -lhts -L/usr/local/lib -lpbbam -L/usr/local/lib -lpbcopper /usr/bin/make -f src/CMakeFiles/arrow.dir/build.make src/CMakeFiles/arrow.dir/preinstall Linking CXX executable CMakeFiles/CMakeRelink.dir/arrow cd /construction/biology/unanimity/unanimity-3.1.0/src && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/arrow.dir/relink.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -pipe -O2 -fno-strict-aliasing CMakeFiles/arrow.dir/main/arrow.cpp.o -o CMakeFiles/CMakeRelink.dir/arrow -pthread libunanimity.a libcc2.a -lz -L/usr/local/lib -lhts -L/usr/local/lib -lpbbam -L/usr/local/lib -lpbcopper /usr/bin/make 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/construction/biology/unanimity/unanimity-3.1.0/src/libcc2.a /construction/biology/unanimity/unanimity-3.1.0/src/libunanimity.a /construction/biology/unanimity/stage/usr/local/lib ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for unanimity-3.1.0_2 file sizes/checksums [8]: . done packing files [8]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Friday, 15 MAR 2019 at 13:44:17 UTC Duration: 00:05:41