------------------------------------------------------------------------------- -- Phase: Environment ------------------------------------------------------------------------------- NO_DEPENDS=1 UNAME_r=6.1 UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=unknown UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 LANG=C HOME=/root USER=root TERM=dumb SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: showconfig ------------------------------------------------------------------------------- ===> The following configuration options are available for iqtree-2.0.6_2: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/iqtree XDG_CONFIG_HOME=/construction/biology/iqtree HOME=/construction/biology/iqtree TMPDIR="/tmp" PATH=/construction/biology/iqtree/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: CONFIGURE_ARGS ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ENV ------------------------------------------------------------------------------- XDG_DATA_HOME=/construction/biology/iqtree XDG_CONFIG_HOME=/construction/biology/iqtree HOME=/construction/biology/iqtree TMPDIR="/tmp" PATH=/construction/biology/iqtree/.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" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: MAKE_ARGS ------------------------------------------------------------------------------- DESTDIR=/construction/biology/iqtree/stage SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: PLIST_SUB ------------------------------------------------------------------------------- PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=6.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/iqtree" EXAMPLESDIR="share/examples/iqtree" DATADIR="share/iqtree" WWWDIR="www/iqtree" ETCDIR="etc/iqtree" SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: SUB_LIST ------------------------------------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/iqtree DOCSDIR=/usr/local/share/doc/iqtree EXAMPLESDIR=/usr/local/share/examples/iqtree WWWDIR=/usr/local/www/iqtree ETCDIR=/usr/local/etc/iqtree SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: /etc/make.conf ------------------------------------------------------------------------------- DPORTS_BUILDER=yes DISABLE_LICENSES=yes DEFAULT_VERSIONS=ssl=openssl FORCE_PACKAGE=yes DEVELOPER=yes USE_PACKAGE_DEPENDS_ONLY=yes PORTSDIR=/xports PORT_DBDIR=/options PKG_DBDIR=/var/db/pkg PKG_CACHEDIR=/var/cache/pkg PKG_SUFX=.txz DEVELOPER=1 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=600102 OSVERSION=9999999 OSREL=6.1 _OSRELEASE=6.1-SYNTH DISTDIR=/distfiles WRKDIRPREFIX=/construction BATCH=yes PACKAGE_BUILDING=yes PKG_CREATE_VERBOSE=yes MAKE_JOBS_NUMBER=10 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libnghttp2-1.43.0.txz Installing /packages/All/ca_root_nss-3.63.txz ===== Message from ca_root_nss-3.63: -- 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. 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 Installing /packages/All/openssl-1.1.1l,1.txz Installing /packages/All/curl-7.78.0.txz Installing /packages/All/expat-2.4.1.txz Installing /packages/All/libuv-1.41.0.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/rhash-1.4.1.txz Installing /packages/All/liblz4-1.9.3,1.txz Installing /packages/All/libarchive-3.5.1,1.txz Installing /packages/All/ncurses-6.2.20210626.txz ===== Message from ncurses-6.2.20210626: -- { type: install message: < NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing Installing /packages/All/suitesparse-config-5.10.1.txz Installing /packages/All/gmp-6.2.1.txz Installing /packages/All/mpfr-4.1.0.txz Installing /packages/All/mpc-1.2.0.txz Installing /packages/All/binutils-2.33.1_5,1.txz Installing /packages/All/gcc8-8.5.0_1.txz ===== Message from gcc8-8.5.0_1: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unsupported by upstream. Use GCC 10 or newer instead.. Installing /packages/All/suitesparse-amd-2.4.6.txz Installing /packages/All/suitesparse-camd-2.4.6.txz Installing /packages/All/suitesparse-colamd-2.9.6.txz Installing /packages/All/suitesparse-ccolamd-2.9.6.txz Installing /packages/All/openblas-0.3.15,1.txz Installing /packages/All/suitesparse-cholmod-3.0.14.txz Installing /packages/All/suitesparse-umfpack-5.7.9.txz Installing /packages/All/blas-3.10.0.txz Installing /packages/All/lapack-3.10.0_1.txz Installing /packages/All/superlu-5.2.2.txz Installing /packages/All/icu-69.1,1.txz Installing /packages/All/boost-libs-1.72.0_5.txz ===== Message from boost-libs-1.72.0_5: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. Installing /packages/All/adol-c-2.7.2.txz Installing /packages/All/fftw3-3.3.9.txz Installing /packages/All/eigen-3.3.9.txz SUCCEEDED 00:00:32 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> iqtree-2.0.6_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> iqtree-2.0.6_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by iqtree-2.0.6_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> iqtree-2.0.6_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by iqtree-2.0.6_2 for building => SHA256 Checksum OK for Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> iqtree-2.0.6_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by iqtree-2.0.6_2 for building ===> Extracting for iqtree-2.0.6_2 => SHA256 Checksum OK for Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz. Extracted Memory Use: 23.54M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for iqtree-2.0.6_2 ===> Applying ports patches for iqtree-2.0.6_2 from /xports/biology/iqtree/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> iqtree-2.0.6_2 depends on file: /usr/local/bin/cmake - found ===> iqtree-2.0.6_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> iqtree-2.0.6_2 depends on shared library: libboost_filesystem.so - found (/usr/local/lib/libboost_filesystem.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> iqtree-2.0.6_2 depends on file: /usr/local/bin/cmake - found ===> iqtree-2.0.6_2 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> iqtree-2.0.6_2 depends on shared library: libboost_filesystem.so - found (/usr/local/lib/libboost_filesystem.so) ===> Configuring for iqtree-2.0.6_2 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/iqtree/.build CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/local/include (found version "1.72.0") IQ-TREE flags : Builde mode : Release Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 C flags : -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections CXX flags : -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections LINKER flags : -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - not found -- Found Backtrace: /usr/lib/libexecinfo.so -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") Using system zlib -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success -- clang-tidy not found. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /construction/biology/iqtree/.build SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for iqtree-2.0.6_2 /usr/local/bin/cmake -S/construction/biology/iqtree/IQ-TREE-2.0.6 -B/construction/biology/iqtree/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/iqtree/.build/CMakeFiles /construction/biology/iqtree/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelfma.dir/all --- --- CMakeFiles/kernelsse.dir/all --- --- pll/CMakeFiles/pllavx.dir/all --- --- pll/CMakeFiles/pll.dir/all --- --- booster/CMakeFiles/booster.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/all --- --- ncl/CMakeFiles/ncl.dir/all --- --- sprng/CMakeFiles/sprng.dir/all --- --- whtest/CMakeFiles/whtest.dir/all --- --- CMakeFiles/kernelavx.dir/all --- /usr/bin/make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend --- CMakeFiles/kernelavx.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelavx.dir/DependInfo.cmake --- CMakeFiles/kernelfma.dir/all --- /usr/bin/make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend --- CMakeFiles/kernelfma.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelfma.dir/DependInfo.cmake --- CMakeFiles/kernelsse.dir/all --- /usr/bin/make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend --- pll/CMakeFiles/pllavx.dir/all --- /usr/bin/make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend --- pll/CMakeFiles/pll.dir/all --- /usr/bin/make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend --- pll/CMakeFiles/pll.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/pll /construction/biology/iqtree/.build /construction/biology/iqtree/.build/pll /construction/biology/iqtree/.build/pll/CMakeFiles/pll.dir/DependInfo.cmake --- booster/CMakeFiles/booster.dir/all --- /usr/bin/make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend --- booster/CMakeFiles/booster.dir/depend --- --- nclextra/CMakeFiles/nclextra.dir/all --- /usr/bin/make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend --- ncl/CMakeFiles/ncl.dir/all --- /usr/bin/make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend --- sprng/CMakeFiles/sprng.dir/all --- /usr/bin/make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend --- sprng/CMakeFiles/sprng.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/sprng /construction/biology/iqtree/.build /construction/biology/iqtree/.build/sprng /construction/biology/iqtree/.build/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --- pll/CMakeFiles/pllavx.dir/all --- --- pll/CMakeFiles/pllavx.dir/depend --- --- booster/CMakeFiles/booster.dir/all --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/booster /construction/biology/iqtree/.build /construction/biology/iqtree/.build/booster /construction/biology/iqtree/.build/booster/CMakeFiles/booster.dir/DependInfo.cmake --- whtest/CMakeFiles/whtest.dir/all --- /usr/bin/make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend --- pll/CMakeFiles/pllavx.dir/all --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/pll /construction/biology/iqtree/.build /construction/biology/iqtree/.build/pll /construction/biology/iqtree/.build/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --- CMakeFiles/kernelfma.dir/all --- /usr/bin/make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build --- pll/CMakeFiles/pll.dir/all --- /usr/bin/make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/ncl /construction/biology/iqtree/.build /construction/biology/iqtree/.build/ncl /construction/biology/iqtree/.build/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --- CMakeFiles/kernelfma.dir/all --- --- CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o --- --- CMakeFiles/kernelavx.dir/all --- /usr/bin/make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/alignment.c.o --- --- pll/CMakeFiles/pllavx.dir/all --- /usr/bin/make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build --- booster/CMakeFiles/booster.dir/all --- /usr/bin/make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o --- --- sprng/CMakeFiles/sprng.dir/all --- /usr/bin/make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build --- CMakeFiles/kernelfma.dir/all --- [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o --- pll/CMakeFiles/pllavx.dir/all --- --- pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o --- --- CMakeFiles/kernelfma.dir/all --- /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylokernelfma.cpp --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/bitset_index.c.o --- --- pll/CMakeFiles/pll.dir/all --- [ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/alignment.c --- ncl/CMakeFiles/ncl.dir/all --- /usr/bin/make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/lcg64.c.o --- --- CMakeFiles/kernelavx.dir/all --- [ 2%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreeavx.cpp --- pll/CMakeFiles/pllavx.dir/all --- [ 2%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/avxLikelihood.c --- booster/CMakeFiles/booster.dir/all --- [ 3%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/bitset_index.c --- sprng/CMakeFiles/sprng.dir/all --- [ 4%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/lcg64.c --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o --- --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/depend --- --- ncl/CMakeFiles/ncl.dir/all --- [ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o --- whtest/CMakeFiles/whtest.dir/all --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/whtest /construction/biology/iqtree/.build /construction/biology/iqtree/.build/whtest /construction/biology/iqtree/.build/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --- ncl/CMakeFiles/ncl.dir/all --- cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsassumptionsblock.cpp --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra /construction/biology/iqtree/.build /construction/biology/iqtree/.build/nclextra /construction/biology/iqtree/.build/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --- CMakeFiles/kernelsse.dir/all --- --- CMakeFiles/kernelsse.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelsse.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build --- CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o --- [ 4%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o --- whtest/CMakeFiles/whtest.dir/all --- /usr/bin/make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build --- CMakeFiles/kernelsse.dir/all --- /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylokernelsse.cpp --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/eigen.c.o --- [ 5%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/eigen.c --- nclextra/CMakeFiles/nclextra.dir/all --- /usr/bin/make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build --- nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o --- [ 5%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra/mpdablock.cpp --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/alignment.c:40: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/makeseed.c.o --- [ 5%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/makeseed.c --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/hashmap.c.o --- [ 5%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/hashmap.c --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/memory.c.o --- [ 5%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/memory.c --- sprng/CMakeFiles/sprng.dir/store.c.o --- [ 6%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/store.c --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/bipartitionList.c.o --- --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/io.c.o --- [ 6%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/io.c --- pll/CMakeFiles/pll.dir/all --- [ 7%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/bipartitionList.c --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o --- --- pll/CMakeFiles/pllavx.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/avxLikelihood.c:57: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- sprng/CMakeFiles/sprng.dir/all --- [ 7%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/primes-lcg64.c --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/sort.c.o --- [ 8%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/sort.c --- booster/CMakeFiles/booster.dir/tree.c.o --- --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/bipartitionList.c:49: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- booster/CMakeFiles/booster.dir/all --- [ 8%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/tree.c --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/checkid.c.o --- [ 9%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/checkid.c --- sprng/libsprng.a --- [ 9%] Linking C static library libsprng.a cd /construction/biology/iqtree/.build/sprng && /usr/local/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/sprng && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a [ 9%] Built target sprng --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- /usr/bin/make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend --- lbfgsb/CMakeFiles/lbfgsb.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/lbfgsb /construction/biology/iqtree/.build /construction/biology/iqtree/.build/lbfgsb /construction/biology/iqtree/.build/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake /usr/bin/make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build --- lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o --- [ 9%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /construction/biology/iqtree/.build/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/lbfgsb/lbfgsb_new.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o --- [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/evaluateGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/evaluateGenericSpecial.c:46: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/eigen_sym.c.o --- [ 9%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/eigen_sym.c --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/booster.c.o --- [ 10%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c --- pll/CMakeFiles/pllavx.dir/all --- --- pll/libpllavx.a --- [ 11%] Linking C static library libpllavx.a cd /construction/biology/iqtree/.build/pll && /usr/local/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/random.c.o --- --- pll/CMakeFiles/pllavx.dir/all --- cd /construction/biology/iqtree/.build/pll && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 --- whtest/CMakeFiles/whtest.dir/all --- [ 11%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/random.c --- booster/CMakeFiles/booster.dir/all --- /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c: In function 'main_booster': /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); ^~~~~~~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c:27: /construction/biology/iqtree/IQ-TREE-2.0.6/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' unsigned int tell_size_of_one_tree(char* filename); ~~~~~~^~~~~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { ^~~~~~~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c:27: /construction/biology/iqtree/IQ-TREE-2.0.6/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' unsigned int tell_size_of_one_tree(char* filename); ~~~~~~^~~~~~~~ --- pll/CMakeFiles/pllavx.dir/all --- /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a [ 11%] Built target pllavx --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/weisslambda.c.o --- [ 12%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/weisslambda.c --- whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o --- [ 12%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/weisslambda_sub.c --- whtest/CMakeFiles/whtest.dir/whtest.c.o --- [ 13%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/whtest.c --- whtest/CMakeFiles/whtest.dir/whtest_sub.c.o --- [ 13%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/whtest_sub.c --- whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o --- [ 13%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/whtest_wrapper.cpp --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/hashtables_bfields.c.o --- [ 13%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/hashtables_bfields.c --- booster/CMakeFiles/booster.dir/prng.c.o --- [ 13%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/prng.c --- booster/CMakeFiles/booster.dir/stats.c.o --- [ 14%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/stats.c --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o --- [ 15%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/evaluatePartialGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/evaluatePartialGenericSpecial.c:45: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/tree_utils.c.o --- [ 15%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/tree_utils.c --- booster/libbooster.a --- [ 16%] Linking C static library libbooster.a cd /construction/biology/iqtree/.build/booster && /usr/local/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/booster && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a [ 16%] Built target booster --- gsl/CMakeFiles/gsl.dir/all --- /usr/bin/make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend --- gsl/CMakeFiles/gsl.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/gsl /construction/biology/iqtree/.build /construction/biology/iqtree/.build/gsl /construction/biology/iqtree/.build/gsl/CMakeFiles/gsl.dir/DependInfo.cmake /usr/bin/make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build --- gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o --- [ 17%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/binomial_tpe.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o --- [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsblock.cpp --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/multinomial.cpp.o --- [ 18%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/multinomial.cpp --- gsl/CMakeFiles/gsl.dir/pow_int.cpp.o --- [ 19%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/pow_int.cpp --- gsl/CMakeFiles/gsl.dir/gauss.cpp.o --- [ 19%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/gauss.cpp --- vectorclass/CMakeFiles/vectorclass.dir/all --- /usr/bin/make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend --- vectorclass/CMakeFiles/vectorclass.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/vectorclass /construction/biology/iqtree/.build /construction/biology/iqtree/.build/vectorclass /construction/biology/iqtree/.build/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake /usr/bin/make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build --- vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o --- [ 20%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /construction/biology/iqtree/.build/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/vectorclass/instrset_detect.cpp --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o --- [ 20%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/gaussinv.cpp --- vectorclass/CMakeFiles/vectorclass.dir/all --- --- vectorclass/libvectorclass.a --- [ 20%] Linking CXX static library libvectorclass.a cd /construction/biology/iqtree/.build/vectorclass && /usr/local/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/vectorclass && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a [ 20%] Built target vectorclass --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o --- [ 21%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/gausspdf.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- /usr/bin/make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend --- yaml-cpp/CMakeFiles/yaml-cpp.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp /construction/biology/iqtree/.build /construction/biology/iqtree/.build/yaml-cpp /construction/biology/iqtree/.build/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake /usr/bin/make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o --- [ 21%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/binary.cpp --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/libgsl.a --- [ 21%] Linking CXX static library libgsl.a cd /construction/biology/iqtree/.build/gsl && /usr/local/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/gsl && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 /usr/bin/ar qc libgsl.a CMakeFiles/gsl.dir/binomial_tpe.cpp.o CMakeFiles/gsl.dir/multinomial.cpp.o CMakeFiles/gsl.dir/pow_int.cpp.o CMakeFiles/gsl.dir/gauss.cpp.o CMakeFiles/gsl.dir/gaussinv.cpp.o CMakeFiles/gsl.dir/gausspdf.cpp.o /usr/bin/ranlib libgsl.a [ 21%] Built target gsl --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o --- [ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/convert.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o --- [ 22%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/fastDNAparsimony.c --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- --- lbfgsb/liblbfgsb.a --- [ 23%] Linking CXX static library liblbfgsb.a cd /construction/biology/iqtree/.build/lbfgsb && /usr/local/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/lbfgsb && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/fastDNAparsimony.c:113: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a [ 23%] Built target lbfgsb --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o --- [ 24%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra/msetsblock.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o --- [ 24%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/directives.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/hardware.c.o --- [ 24%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/hardware.c --- pll/CMakeFiles/pll.dir/hash.c.o --- [ 25%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/hash.c --- pll/CMakeFiles/pll.dir/lexer.c.o --- [ 25%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/lexer.c --- pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o --- [ 26%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/makenewzGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/makenewzGenericSpecial.c:44: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o --- [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxscharactersblock.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o --- [ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emit.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o --- [ 27%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emitfromevents.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/models.c.o --- [ 27%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/models.c --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/libwhtest.a --- [ 28%] Linking CXX static library libwhtest.a cd /construction/biology/iqtree/.build/whtest && /usr/local/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/whtest && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/models.c:53: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- whtest/CMakeFiles/whtest.dir/all --- [ 28%] Built target whtest --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o --- [ 28%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emitter.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o --- [ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emitterstate.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o --- [ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emitterutils.cpp --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o --- [ 29%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra/msplitsblock.cpp --- nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o --- [ 29%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra/modelsblock.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o --- [ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/exceptions.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o --- [ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/exp.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o --- [ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/memory.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o --- [ 31%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/node.cpp --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/libnclextra.a --- [ 32%] Linking CXX static library libnclextra.a cd /construction/biology/iqtree/.build/nclextra && /usr/local/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/nclextra && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 /usr/bin/ar qc libnclextra.a CMakeFiles/nclextra.dir/mpdablock.cpp.o CMakeFiles/nclextra.dir/msetsblock.cpp.o CMakeFiles/nclextra.dir/msplitsblock.cpp.o CMakeFiles/nclextra.dir/modelsblock.cpp.o /usr/bin/ranlib libnclextra.a [ 32%] Built target nclextra --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o --- [ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/node_data.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o --- [ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/nodebuilder.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o --- [ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/nodeevents.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o --- [ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/null.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o --- [ 34%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/ostream_wrapper.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/newick.c.o --- [ 35%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newick.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newick.c:36: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o --- [ 35%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newviewGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newviewGenericSpecial.c:49: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o --- [ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/parse.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o --- [ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/parser.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o --- [ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/regex_yaml.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o --- [ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/scanner.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o --- [ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/scanscalar.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o --- [ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/scantag.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o --- [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsdatablock.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o --- [ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/scantoken.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o --- [ 38%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/simplekey.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o --- [ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsdiscretedatum.cpp --- ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o --- [ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsdiscretematrix.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o --- [ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/singledocparser.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/genericParallelization.c.o --- [ 39%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/genericParallelization.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/genericParallelization.c:43: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o --- [ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/stream.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o --- [ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsdistancedatum.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/optimizeModel.c.o --- [ 42%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/optimizeModel.c --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o --- [ 42%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/tag.cpp --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/optimizeModel.c:47: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o --- [ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsdistancesblock.cpp --- ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o --- [ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsemptyblock.cpp --- ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o --- [ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsexception.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/parsePartition.c.o --- [ 43%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/parsePartition.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/parsePartition.c:42: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/queue.c.o --- [ 44%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/queue.c --- pll/CMakeFiles/pll.dir/randomTree.c.o --- [ 44%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/randomTree.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/randomTree.c:37: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/recom.c.o --- [ 44%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/recom.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/recom.c:43: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/restartHashTable.c.o --- [ 45%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/restartHashTable.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/restartHashTable.c:47: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/searchAlgo.c.o --- [ 45%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/searchAlgo.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/searchAlgo.c:51: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o --- [ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsreader.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/ssort.c.o --- [ 46%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/ssort.c --- pll/CMakeFiles/pll.dir/stack.c.o --- [ 46%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/stack.c --- terraphast/CMakeFiles/terraphast.dir/all --- /usr/bin/make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend --- terraphast/CMakeFiles/terraphast.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast /construction/biology/iqtree/.build /construction/biology/iqtree/.build/terraphast /construction/biology/iqtree/.build/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake /usr/bin/make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build --- terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o --- [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/advanced.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/libyaml-cpp.a --- --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/topologies.c.o --- [ 46%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/topologies.c --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- [ 47%] Linking CXX static library libyaml-cpp.a cd /construction/biology/iqtree/.build/yaml-cpp && /usr/local/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o --- [ 48%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxssetreader.cpp --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/topologies.c:48: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- cd /construction/biology/iqtree/.build/yaml-cpp && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a CMakeFiles/yaml-cpp.dir/src/binary.cpp.o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o CMakeFiles/yaml-cpp.dir/src/node.cpp.o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o CMakeFiles/yaml-cpp.dir/src/null.cpp.o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o /usr/bin/ranlib libyaml-cpp.a [ 48%] Built target yaml-cpp --- phylo-yaml/CMakeFiles/phyloYAML.dir/all --- /usr/bin/make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend --- phylo-yaml/CMakeFiles/phyloYAML.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/phylo-yaml /construction/biology/iqtree/.build /construction/biology/iqtree/.build/phylo-yaml /construction/biology/iqtree/.build/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/trash.c.o --- --- phylo-yaml/CMakeFiles/phyloYAML.dir/all --- /usr/bin/make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build --- phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o --- --- pll/CMakeFiles/pll.dir/all --- [ 49%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/trash.c --- phylo-yaml/CMakeFiles/phyloYAML.dir/all --- [ 50%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /construction/biology/iqtree/.build/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/phylo-yaml/statespace.cpp --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/trash.c:48: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/treeIO.c.o --- [ 50%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/treeIO.c --- pll/CMakeFiles/pll.dir/utils.c.o --- [ 51%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/utils.c --- pll/CMakeFiles/pll.dir/treeIO.c.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/treeIO.c:49: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/utils.c.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/utils.c:70: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o --- [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsstring.cpp --- ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o --- [ 52%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxstaxablock.cpp --- ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o --- [ 52%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxstoken.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/libpll.a --- [ 52%] Linking C static library libpll.a cd /construction/biology/iqtree/.build/pll && /usr/local/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/pll && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a [ 52%] Built target pll --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o --- [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/bigint.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o --- [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/bipartitions.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o --- [ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxstreesblock.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o --- [ 53%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/bitmatrix.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o --- [ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/clamped_uint.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o --- [ 54%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/constraints.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o --- [ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/errors.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o --- [ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/multitree.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o --- [ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/multitree_iterator.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o --- [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/nodes.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o --- [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/parser.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o --- [ 57%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/rooting.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o --- [ 57%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/simple.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o --- [ 58%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/subtree_extraction.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o --- [ 58%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/supertree_helpers.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/libncl.a --- [ 59%] Linking CXX static library libncl.a cd /construction/biology/iqtree/.build/ncl && /usr/local/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/ncl && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/ncl.dir/link.txt --verbose=1 /usr/bin/ar qc libncl.a CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o CMakeFiles/ncl.dir/nxsblock.cpp.o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o CMakeFiles/ncl.dir/nxsdatablock.cpp.o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o CMakeFiles/ncl.dir/nxsexception.cpp.o CMakeFiles/ncl.dir/nxsreader.cpp.o CMakeFiles/ncl.dir/nxssetreader.cpp.o CMakeFiles/ncl.dir/nxsstring.cpp.o CMakeFiles/ncl.dir/nxstaxablock.cpp.o CMakeFiles/ncl.dir/nxstoken.cpp.o CMakeFiles/ncl.dir/nxstreesblock.cpp.o /usr/bin/ranlib libncl.a [ 59%] Built target ncl --- utils/CMakeFiles/utils.dir/all --- /usr/bin/make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend --- utils/CMakeFiles/utils.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/utils /construction/biology/iqtree/.build /construction/biology/iqtree/.build/utils /construction/biology/iqtree/.build/utils/CMakeFiles/utils.dir/DependInfo.cmake /usr/bin/make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build --- utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o --- [ 59%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/eigendecomposition.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o --- [ 59%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/trees.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o --- [ 60%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/union_find.cpp --- phylo-yaml/CMakeFiles/phyloYAML.dir/all --- --- phylo-yaml/libphyloYAML.a --- [ 60%] Linking CXX static library libphyloYAML.a cd /construction/biology/iqtree/.build/phylo-yaml && /usr/local/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/phylo-yaml && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a [ 60%] Built target phyloYAML --- pda/CMakeFiles/pda.dir/all --- /usr/bin/make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend --- pda/CMakeFiles/pda.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/pda /construction/biology/iqtree/.build /construction/biology/iqtree/.build/pda /construction/biology/iqtree/.build/pda/CMakeFiles/pda.dir/DependInfo.cmake /usr/bin/make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build --- pda/CMakeFiles/pda.dir/circularnetwork.cpp.o --- [ 60%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/circularnetwork.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o --- [ 60%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/validation.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/gzstream.cpp.o --- [ 60%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/gzstream.cpp --- utils/CMakeFiles/utils.dir/optimization.cpp.o --- [ 61%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/optimization.cpp --- utils/CMakeFiles/utils.dir/stoprule.cpp.o --- [ 61%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/stoprule.cpp --- utils/CMakeFiles/utils.dir/tools.cpp.o --- [ 62%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/tools.cpp --- utils/CMakeFiles/utils.dir/pllnni.cpp.o --- [ 62%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/pllnni.cpp --- utils/CMakeFiles/utils.dir/checkpoint.cpp.o --- [ 62%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/checkpoint.cpp --- utils/CMakeFiles/utils.dir/MPIHelper.cpp.o --- [ 63%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/MPIHelper.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/libterraphast.a --- [ 64%] Linking CXX static library libterraphast.a cd /construction/biology/iqtree/.build/terraphast && /usr/local/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/terraphast && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a [ 64%] Built target terraphast --- alignment/CMakeFiles/alignment.dir/all --- /usr/bin/make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend --- alignment/CMakeFiles/alignment.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/alignment /construction/biology/iqtree/.build /construction/biology/iqtree/.build/alignment /construction/biology/iqtree/.build/alignment/CMakeFiles/alignment.dir/DependInfo.cmake /usr/bin/make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build --- alignment/CMakeFiles/alignment.dir/pattern.cpp.o --- [ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/pattern.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/greedy.cpp.o --- [ 65%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/greedy.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/alignment.cpp.o --- [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/alignment.cpp --- alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o --- [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/alignmentpairwise.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o --- [ 66%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/gurobiwrapper.cpp --- pda/CMakeFiles/pda.dir/hashsplitset.cpp.o --- [ 66%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/hashsplitset.cpp --- pda/CMakeFiles/pda.dir/pdnetwork.cpp.o --- [ 67%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/pdnetwork.cpp --- pda/CMakeFiles/pda.dir/pruning.cpp.o --- [ 67%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/pruning.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/maalignment.cpp.o --- [ 67%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/maalignment.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/split.cpp.o --- [ 68%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/split.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignment.cpp.o --- [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/superalignment.cpp --- alignment/CMakeFiles/alignment.dir/alignment.cpp.o --- /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { ^~~~~ --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/splitgraph.cpp.o --- [ 69%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/splitgraph.cpp --- pda/CMakeFiles/pda.dir/splitset.cpp.o --- [ 69%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/splitset.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o --- [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/superalignmentpairwise.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/lpwrapper.c.o --- [ 70%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /construction/biology/iqtree/.build/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/lpwrapper.c --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o --- [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/superalignmentpairwiseplen.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/libutils.a --- [ 70%] Linking CXX static library libutils.a cd /construction/biology/iqtree/.build/utils && /usr/local/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/utils && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 /usr/bin/ar qc libutils.a CMakeFiles/utils.dir/eigendecomposition.cpp.o CMakeFiles/utils.dir/gzstream.cpp.o CMakeFiles/utils.dir/optimization.cpp.o CMakeFiles/utils.dir/stoprule.cpp.o CMakeFiles/utils.dir/tools.cpp.o CMakeFiles/utils.dir/pllnni.cpp.o CMakeFiles/utils.dir/checkpoint.cpp.o CMakeFiles/utils.dir/MPIHelper.cpp.o /usr/bin/ranlib libutils.a [ 70%] Built target utils --- model/CMakeFiles/model.dir/all --- /usr/bin/make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend --- model/CMakeFiles/model.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/model /construction/biology/iqtree/.build /construction/biology/iqtree/.build/model /construction/biology/iqtree/.build/model/CMakeFiles/model.dir/DependInfo.cmake /usr/bin/make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build --- model/CMakeFiles/model.dir/modelmarkov.cpp.o --- [ 71%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o --- [ 72%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/superalignmentunlinked.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/ecopd.cpp.o --- [ 72%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/ecopd.cpp --- model/CMakeFiles/model.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/graph.cpp.o --- [ 73%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/graph.cpp --- pda/CMakeFiles/pda.dir/pdtree.cpp.o --- [ 73%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/pdtree.cpp --- CMakeFiles/kernelsse.dir/all --- --- libkernelsse.a --- [ 74%] Linking CXX static library libkernelsse.a /usr/local/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/local/bin/cmake -E cmake_link_script CMakeFiles/kernelsse.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelsse.a CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/ranlib libkernelsse.a [ 74%] Built target kernelsse --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/modelbin.cpp.o --- [ 74%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelbin.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/pdtreeset.cpp.o --- [ 74%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/pdtreeset.cpp --- pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o --- [ 75%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/ecopdmtreeset.cpp --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/modelmarkov.cpp.o --- /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1403:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1458:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1487:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1504:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ --- model/CMakeFiles/model.dir/modelbin.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelbin.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelbin.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modeldna.cpp.o --- [ 75%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.cpp --- model/CMakeFiles/model.dir/modelfactory.cpp.o --- [ 76%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp --- model/CMakeFiles/model.dir/modelprotein.cpp.o --- [ 76%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp --- model/CMakeFiles/model.dir/modelset.cpp.o --- [ 77%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelset.cpp --- model/CMakeFiles/model.dir/modelsubst.cpp.o --- [ 77%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelsubst.cpp --- model/CMakeFiles/model.dir/modeldna.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ --- model/CMakeFiles/model.dir/modelprotein.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelProtein::readRates(istream &in) throw(const char*, string) { ^~~~~ --- model/CMakeFiles/model.dir/modelfactory.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:24: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:26: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:27: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:30: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- model/CMakeFiles/model.dir/partitionmodel.cpp.o --- [ 77%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/partitionmodel.cpp --- model/CMakeFiles/model.dir/partitionmodelplen.cpp.o --- [ 78%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/partitionmodelplen.cpp --- model/CMakeFiles/model.dir/modelset.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelset.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelset.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- pda/CMakeFiles/pda.dir/all --- --- pda/libpda.a --- [ 78%] Linking CXX static library libpda.a cd /construction/biology/iqtree/.build/pda && /usr/local/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/pda && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a [ 78%] Built target pda --- main/CMakeFiles/main.dir/all --- /usr/bin/make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend --- main/CMakeFiles/main.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/main /construction/biology/iqtree/.build /construction/biology/iqtree/.build/main /construction/biology/iqtree/.build/main/CMakeFiles/main.dir/DependInfo.cmake /usr/bin/make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build --- main/CMakeFiles/main.dir/main.cpp.o --- [ 78%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /construction/biology/iqtree/.build/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/main/main.cpp --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/partitionmodel.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/partitionmodel.cpp:23: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/rategamma.cpp.o --- [ 78%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rategamma.cpp --- model/CMakeFiles/model.dir/partitionmodelplen.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/partitionmodelplen.cpp:12: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/rategammainvar.cpp.o --- [ 79%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rategammainvar.cpp --- model/CMakeFiles/model.dir/rateheterogeneity.cpp.o --- [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rateheterogeneity.cpp --- model/CMakeFiles/model.dir/rateinvar.cpp.o --- [ 79%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rateinvar.cpp --- model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o --- [ 80%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratemeyerdiscrete.cpp --- model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o --- [ 80%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratemeyerhaeseler.cpp --- model/CMakeFiles/model.dir/ratekategory.cpp.o --- [ 81%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratekategory.cpp --- model/CMakeFiles/model.dir/ratefree.cpp.o --- [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratefree.cpp --- model/CMakeFiles/model.dir/ratefreeinvar.cpp.o --- [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratefreeinvar.cpp --- model/CMakeFiles/model.dir/rateheterotachy.cpp.o --- [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rateheterotachy.cpp --- model/CMakeFiles/model.dir/ratefree.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratefree.cpp:13: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/phyloanalysis.cpp.o --- [ 83%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /construction/biology/iqtree/.build/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o --- [ 83%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rateheterotachyinvar.cpp --- model/CMakeFiles/model.dir/modelcodon.cpp.o --- [ 84%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelcodon.cpp --- CMakeFiles/kernelfma.dir/all --- --- libkernelfma.a --- [ 84%] Linking CXX static library libkernelfma.a /usr/local/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/local/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/ranlib libkernelfma.a [ 84%] Built target kernelfma --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/modelmorphology.cpp.o --- [ 84%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.cpp --- model/CMakeFiles/model.dir/modelmixture.cpp.o --- [ 84%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.cpp --- model/CMakeFiles/model.dir/modelunrest.cpp.o --- [ 85%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelunrest.cpp --- model/CMakeFiles/model.dir/modelcodon.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelcodon.h:11, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelcodon.cpp:8: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelliemarkov.cpp.o --- [ 85%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelliemarkov.cpp --- model/CMakeFiles/model.dir/modelmorphology.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:11, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.cpp:8: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.cpp:8: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ --- model/CMakeFiles/model.dir/modelmixture.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.cpp:8: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.cpp:9: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.cpp:10: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.cpp:13: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- CMakeFiles/kernelavx.dir/all --- --- libkernelavx.a --- [ 85%] Linking CXX static library libkernelavx.a /usr/local/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/local/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/modelpomo.cpp.o --- [ 86%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.cpp --- CMakeFiles/kernelavx.dir/all --- [ 86%] Built target kernelavx --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- [ 86%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /construction/biology/iqtree/.build/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/modelunrest.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelunrest.h:11, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelunrest.cpp:8: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/phyloanalysis.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp:37: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp:38: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp:46: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/modelpomomixture.cpp.o --- [ 86%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.cpp --- model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o --- [ 86%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactorymixlen.cpp --- model/CMakeFiles/model.dir/modelpomo.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.cpp:1: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.cpp:1: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/libalignment.a --- [ 86%] Linking CXX static library libalignment.a cd /construction/biology/iqtree/.build/alignment && /usr/local/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/alignment && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o /usr/bin/ranlib libalignment.a --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:21: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:22: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ --- alignment/CMakeFiles/alignment.dir/all --- [ 86%] Built target alignment --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/treetesting.cpp.o --- [ 86%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /construction/biology/iqtree/.build/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/main/treetesting.cpp --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:31: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:34: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/modelliemarkov.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelliemarkov.h:11, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelliemarkov.cpp:23: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/timetree.cpp.o --- [ 87%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /construction/biology/iqtree/.build/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/main/timetree.cpp --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/modelpomomixture.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.h:14, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.cpp:9: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.h:14, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.cpp:9: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactorymixlen.cpp:12: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp: In function 'std::__cxx11::string getSeqTypeName(PML::SeqType)': /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ --- main/libmain.a --- [ 87%] Linking CXX static library libmain.a cd /construction/biology/iqtree/.build/main && /usr/local/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/main && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o /usr/bin/ranlib libmain.a [ 87%] Built target main --- model/CMakeFiles/model.dir/all --- --- model/libmodel.a --- [ 88%] Linking CXX static library libmodel.a cd /construction/biology/iqtree/.build/model && /usr/local/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/model && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a [ 88%] Built target model --- tree/CMakeFiles/tree.dir/all --- /usr/bin/make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend --- tree/CMakeFiles/tree.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/tree /construction/biology/iqtree/.build /construction/biology/iqtree/.build/tree /construction/biology/iqtree/.build/tree/CMakeFiles/tree.dir/DependInfo.cmake /usr/bin/make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build --- tree/CMakeFiles/tree.dir/constrainttree.cpp.o --- --- tree/CMakeFiles/tree.dir/candidateset.cpp.o --- --- tree/CMakeFiles/tree.dir/iqtree.cpp.o --- --- tree/CMakeFiles/tree.dir/matree.cpp.o --- --- tree/CMakeFiles/tree.dir/memslot.cpp.o --- --- tree/CMakeFiles/tree.dir/mexttree.cpp.o --- --- tree/CMakeFiles/tree.dir/mtree.cpp.o --- --- tree/CMakeFiles/tree.dir/mtreeset.cpp.o --- --- tree/CMakeFiles/tree.dir/ncbitree.cpp.o --- --- tree/CMakeFiles/tree.dir/node.cpp.o --- --- tree/CMakeFiles/tree.dir/mexttree.cpp.o --- [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o --- tree/CMakeFiles/tree.dir/ncbitree.cpp.o --- [ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o --- tree/CMakeFiles/tree.dir/candidateset.cpp.o --- [ 88%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o --- tree/CMakeFiles/tree.dir/node.cpp.o --- [ 89%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o --- tree/CMakeFiles/tree.dir/candidateset.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/candidateset.cpp --- tree/CMakeFiles/tree.dir/mexttree.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/mexttree.cpp --- tree/CMakeFiles/tree.dir/ncbitree.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/ncbitree.cpp --- tree/CMakeFiles/tree.dir/node.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/node.cpp --- tree/CMakeFiles/tree.dir/iqtree.cpp.o --- [ 90%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o --- tree/CMakeFiles/tree.dir/memslot.cpp.o --- [ 91%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o --- tree/CMakeFiles/tree.dir/iqtree.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/iqtree.cpp --- tree/CMakeFiles/tree.dir/memslot.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/memslot.cpp --- tree/CMakeFiles/tree.dir/mtree.cpp.o --- [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o --- tree/CMakeFiles/tree.dir/mtreeset.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o --- tree/CMakeFiles/tree.dir/matree.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o --- tree/CMakeFiles/tree.dir/mtree.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/mtree.cpp --- tree/CMakeFiles/tree.dir/mtreeset.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/mtreeset.cpp --- tree/CMakeFiles/tree.dir/matree.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/matree.cpp --- tree/CMakeFiles/tree.dir/constrainttree.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/constrainttree.cpp --- tree/CMakeFiles/tree.dir/iqtree.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/iqtree.cpp:29: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/phylonode.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylonode.cpp --- tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylonodemixlen.cpp --- tree/CMakeFiles/tree.dir/phylosupertree.cpp.o --- [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylosupertree.cpp --- tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o --- [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylosupertreeplen.cpp --- tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o --- [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylosupertreeunlinked.cpp --- tree/CMakeFiles/tree.dir/phylotree.cpp.o --- [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp --- tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o --- [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreemixlen.cpp --- tree/CMakeFiles/tree.dir/phylotreepars.cpp.o --- [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreepars.cpp --- tree/CMakeFiles/tree.dir/phylotreesse.cpp.o --- [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreesse.cpp --- tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreemixlen.cpp:12: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/phylotree.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp:34: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/quartet.cpp.o --- [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/quartet.cpp --- tree/CMakeFiles/tree.dir/supernode.cpp.o --- [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/supernode.cpp --- tree/CMakeFiles/tree.dir/phylotreesse.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreesse.cpp:35: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/phylotree.cpp.o --- /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp: In function 'std::__cxx11::string getASCName(ASCType)': /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ --- tree/CMakeFiles/tree.dir/tinatree.cpp.o --- [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/tinatree.cpp --- tree/CMakeFiles/tree.dir/parstree.cpp.o --- [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/parstree.cpp --- tree/CMakeFiles/tree.dir/discordance.cpp.o --- [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/discordance.cpp --- tree/libtree.a --- [ 98%] Linking CXX static library libtree.a cd /construction/biology/iqtree/.build/tree && /usr/local/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/tree && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a [ 98%] Built target tree --- terrace/CMakeFiles/terrace.dir/all --- /usr/bin/make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend --- terrace/CMakeFiles/terrace.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/terrace /construction/biology/iqtree/.build /construction/biology/iqtree/.build/terrace /construction/biology/iqtree/.build/terrace/CMakeFiles/terrace.dir/DependInfo.cmake /usr/bin/make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build --- terrace/CMakeFiles/terrace.dir/terrace.cpp.o --- [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /construction/biology/iqtree/.build/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terrace/terrace.cpp --- terrace/libterrace.a --- [ 99%] Linking CXX static library libterrace.a cd /construction/biology/iqtree/.build/terrace && /usr/local/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/terrace && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a [ 99%] Built target terrace --- CMakeFiles/iqtree2.dir/all --- /usr/bin/make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend --- CMakeFiles/iqtree2.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/iqtree2.dir/DependInfo.cmake /usr/bin/make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build --- CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o --- [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/obsolete/parsmultistate.cpp --- iqtree2 --- [100%] Linking CXX executable iqtree2 /usr/local/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -rdynamic -Wl,--gc-sections CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/construction/biology/iqtree/IQ-TREE-2.0.6/lib -Wl,-z,origin,-rpath,/construction/biology/iqtree/IQ-TREE-2.0.6/lib -lexecinfo booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a strip /construction/biology/iqtree/.build/iqtree2 [100%] Built target iqtree2 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/iqtree/.build/CMakeFiles 0 SUCCEEDED 00:04:52 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for iqtree-2.0.6_2 ===> Generating temporary packing list install -s -m 555 /construction/biology/iqtree/.build/iqtree2 /construction/biology/iqtree/stage/usr/local/bin/iqtree install -m 0644 /construction/biology/iqtree/IQ-TREE-2.0.6/example/* /construction/biology/iqtree/stage/usr/local/share/examples/iqtree ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for iqtree-2.0.6_2 file sizes/checksums [5]: 0% file sizes/checksums [5]: 100% packing files [5]: 0% packing files [5]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:08 TOTAL TIME 00:05:39