=> Building biology/iqtree Started : Thursday, 30 AUG 2018 at 13:00:54 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for iqtree-1.6.5: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings -------------------------------------------------- -- 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=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- 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=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/iqtree/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/iqtree" EXAMPLESDIR="share/examples/iqtree" DATADIR="share/iqtree" WWWDIR="www/iqtree" ETCDIR="etc/iqtree" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> iqtree-1.6.5 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> iqtree-1.6.5 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of iqtree-1.6.5 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by iqtree-1.6.5 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by iqtree-1.6.5 for building => SHA256 Checksum OK for Cibiv-IQ-TREE-v1.6.5_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by iqtree-1.6.5 for building ===> Extracting for iqtree-1.6.5 => SHA256 Checksum OK for Cibiv-IQ-TREE-v1.6.5_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for iqtree-1.6.5 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> iqtree-1.6.5 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.11.4_1.txz Installing cmake-3.11.4_1... `-- Installing curl-7.60.0... | `-- Installing ca_root_nss-3.38... | `-- Extracting ca_root_nss-3.38: ........ done | `-- Installing krb5-1.16.1_5... | | `-- Installing gettext-runtime-0.19.8.1_1... | | `-- Installing indexinfo-0.3.1... | | `-- Extracting indexinfo-0.3.1: .... done | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done | | `-- Installing libressl-2.7.4... | | `-- Extracting libressl-2.7.4: .......... done | | `-- Installing pkgconf-1.4.2,1... | | `-- Extracting pkgconf-1.4.2,1: .......... done | | `-- Installing readline-7.0.3_1... | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | | `-- Extracting readline-7.0.3_1: .......... done | `-- Extracting krb5-1.16.1_5: .......... done | `-- Installing libnghttp2-1.32.0... | `-- Extracting libnghttp2-1.32.0: .......... done `-- Extracting curl-7.60.0: .......... done `-- Installing expat-2.2.5... `-- Extracting expat-2.2.5: .......... done `-- Installing jsoncpp-1.8.1_3... `-- Extracting jsoncpp-1.8.1_3: .......... done `-- Installing libarchive-3.3.2,1... | `-- Installing liblz4-1.8.2,1... | `-- Extracting liblz4-1.8.2,1: .......... done | `-- Installing lzo2-2.10_1... | `-- Extracting lzo2-2.10_1: .......... done `-- Extracting libarchive-3.3.2,1: .......... done `-- Installing libuv-1.21.0... `-- Extracting libuv-1.21.0: .......... done `-- Installing rhash-1.3.5... `-- Extracting rhash-1.3.5: .......... done Extracting cmake-3.11.4_1: .......... done Message from ca_root_nss-3.38: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> iqtree-1.6.5 depends on file: /usr/local/bin/cmake - found ===> Returning to build of iqtree-1.6.5 ===> iqtree-1.6.5 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.3.4.txz Installing eigen-3.3.4... Extracting eigen-3.3.4: .......... done ===> iqtree-1.6.5 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of iqtree-1.6.5 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for iqtree-1.6.5 ===> Performing in-source build /bin/mkdir -p /construction/biology/iqtree/IQ-TREE-1.6.5 -- The C compiler identification is GNU 5.4.1 -- The CXX compiler identification is GNU 5.4.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done 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 -O3 -g -ffunction-sections -fdata-sections CXX flags : -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -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 "1.2.8") Using system zlib -- Found Eigen3: /usr/local/include/eigen3 (Required is at least version "2.91.0") -- 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/IQ-TREE-1.6.5 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for iqtree-1.6.5 /usr/local/bin/cmake -H/construction/biology/iqtree/IQ-TREE-1.6.5 -B/construction/biology/iqtree/IQ-TREE-1.6.5 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/iqtree/IQ-TREE-1.6.5/CMakeFiles 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/construction/biology/iqtree/IQ-TREE-1.6.5/pll /construction/biology/iqtree/IQ-TREE-1.6.5/pll/CMakeFiles/pll.dir/DependInfo.cmake --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelavx.dir/depend --- --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/depend --- --- vectorclass/CMakeFiles/vectorclass.dir/all --- --- vectorclass/CMakeFiles/vectorclass.dir/depend --- --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/depend --- --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/depend --- --- CMakeFiles/kernelavx.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5 && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/CMakeFiles/kernelavx.dir/DependInfo.cmake --- 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gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o --- --- CMakeFiles/kernelfma.dir/all --- Scanning dependencies of target kernelfma --- pll/CMakeFiles/pll.dir/all --- Scanning dependencies of target pll --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o --- --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- --- lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o --- --- vectorclass/CMakeFiles/vectorclass.dir/all --- /usr/bin/make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build --- CMakeFiles/kernelavx.dir/all --- Scanning dependencies of target kernelavx --- CMakeFiles/kernelfma.dir/all --- /usr/bin/make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build --- pll/CMakeFiles/pllavx.dir/all --- [ 1%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o --- pll/CMakeFiles/pll.dir/all --- /usr/bin/make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build --- CMakeFiles/kernelavx.dir/all --- /usr/bin/make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build --- pll/CMakeFiles/pllavx.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/avxLikelihood.c --- vectorclass/CMakeFiles/vectorclass.dir/all --- --- vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o --- --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/eigen.c.o --- --- CMakeFiles/kernelsse.dir/all --- Scanning dependencies of target kernelsse --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/alignment.c.o --- --- gsl/CMakeFiles/gsl.dir/all --- [ 2%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o --- --- CMakeFiles/kernelsse.dir/all --- /usr/bin/make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build --- gsl/CMakeFiles/gsl.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/gsl/binomial_tpe.cpp --- CMakeFiles/kernelfma.dir/all --- --- CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o --- --- vectorclass/CMakeFiles/vectorclass.dir/all --- [ 3%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o --- CMakeFiles/kernelsse.dir/all --- --- CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o --- --- nclextra/CMakeFiles/nclextra.dir/all --- [ 4%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o --- vectorclass/CMakeFiles/vectorclass.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/vectorclass/instrset_detect.cpp --- ncl/CMakeFiles/ncl.dir/all --- [ 5%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o --- nclextra/CMakeFiles/nclextra.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/nclextra/mpdablock.cpp --- ncl/CMakeFiles/ncl.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/ncl/nxsassumptionsblock.cpp --- pll/CMakeFiles/pll.dir/all --- [ 6%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o --- CMakeFiles/kernelfma.dir/all --- [ 7%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o --- pll/CMakeFiles/pll.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/alignment.c --- CMakeFiles/kernelavx.dir/all --- [ 8%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/phylotreeavx.cpp --- CMakeFiles/kernelfma.dir/all --- /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/phylokernelfma.cpp --- CMakeFiles/kernelsse.dir/all --- [ 9%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o --- whtest/CMakeFiles/whtest.dir/all --- [ 10%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o --- CMakeFiles/kernelsse.dir/all --- /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/phylokernelsse.cpp --- whtest/CMakeFiles/whtest.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/whtest/eigen.c --- sprng/CMakeFiles/sprng.dir/all --- [ 11%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/sprng/lcg64.c --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- [ 11%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/lbfgsb/lbfgsb_new.cpp --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/alignment.c:40:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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); ^ --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/multinomial.cpp.o --- --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/makeseed.c.o --- [ 11%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/sprng/makeseed.c --- gsl/CMakeFiles/gsl.dir/all --- [ 11%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/gsl/multinomial.cpp --- vectorclass/CMakeFiles/vectorclass.dir/all --- --- vectorclass/libvectorclass.a --- [ 11%] Linking CXX static library libvectorclass.a cd /construction/biology/iqtree/IQ-TREE-1.6.5/vectorclass && /usr/local/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/IQ-TREE-1.6.5/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 [ 11%] Built target vectorclass --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/bipartitionList.c.o --- --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/pow_int.cpp.o --- [ 13%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o --- pll/CMakeFiles/pll.dir/all --- [ 13%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/bipartitionList.c --- gsl/CMakeFiles/gsl.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/gsl/pow_int.cpp --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/memory.c.o --- --- pll/CMakeFiles/pllavx.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/avxLikelihood.c:57:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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 --- [ 14%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/sprng/memory.c --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/gauss.cpp.o --- [ 14%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/gsl/gauss.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o --- --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/store.c.o --- --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/bipartitionList.c.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/bipartitionList.c:49:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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 --- [ 14%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/sprng/store.c --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o --- [ 14%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/evaluateGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/evaluateGenericSpecial.c:46:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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); ^ --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o --- --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o --- --- gsl/CMakeFiles/gsl.dir/all --- [ 15%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/gsl/gaussinv.cpp --- sprng/CMakeFiles/sprng.dir/all --- [ 16%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/sprng/primes-lcg64.c --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o --- --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/checkid.c.o --- [ 17%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o --- pll/CMakeFiles/pll.dir/all --- [ 18%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o --- sprng/CMakeFiles/sprng.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/sprng/checkid.c --- pll/CMakeFiles/pll.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/evaluatePartialGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/evaluatePartialGenericSpecial.c:45:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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); ^ --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o --- [ 19%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/gsl/gausspdf.cpp --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/libsprng.a --- [ 19%] Linking C static library libsprng.a cd /construction/biology/iqtree/IQ-TREE-1.6.5/sprng && /usr/local/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/libgsl.a --- --- sprng/CMakeFiles/sprng.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/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 --- gsl/CMakeFiles/gsl.dir/all --- [ 19%] Linking CXX static library libgsl.a cd /construction/biology/iqtree/IQ-TREE-1.6.5/gsl && /usr/local/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake --- sprng/CMakeFiles/sprng.dir/all --- /usr/bin/ranlib libsprng.a --- gsl/CMakeFiles/gsl.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/gsl && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/gsl.dir/link.txt --verbose=1 --- sprng/CMakeFiles/sprng.dir/all --- [ 19%] Built target sprng --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/eigen_sym.c.o --- --- gsl/CMakeFiles/gsl.dir/all --- /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 --- whtest/CMakeFiles/whtest.dir/all --- [ 19%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o --- gsl/CMakeFiles/gsl.dir/all --- /usr/bin/ranlib libgsl.a --- whtest/CMakeFiles/whtest.dir/all --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/whtest/eigen_sym.c --- gsl/CMakeFiles/gsl.dir/all --- [ 19%] Built target gsl --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o --- [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/ncl/nxsblock.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o --- [ 20%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/fastDNAparsimony.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/fastDNAparsimony.c:113:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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/random.c.o --- [ 21%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/whtest/random.c --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/hardware.c.o --- [ 22%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/hardware.c --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o --- [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/ncl/nxscharactersblock.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/hash.c.o --- [ 22%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/hash.c --- pll/CMakeFiles/pll.dir/lexer.c.o --- [ 23%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/lexer.c --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/weisslambda.c.o --- [ 24%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/whtest/weisslambda.c --- whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o --- [ 24%] 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-I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/models.c --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o --- [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/ncl/nxsdatablock.cpp --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/whtest_sub.c.o --- [ 27%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/whtest/whtest_sub.c --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/models.c:53:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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 --- --- lbfgsb/liblbfgsb.a --- [ 28%] Linking CXX static library liblbfgsb.a cd /construction/biology/iqtree/IQ-TREE-1.6.5/lbfgsb && /usr/local/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/IQ-TREE-1.6.5/lbfgsb && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a [ 28%] Built target lbfgsb --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o --- [ 29%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/whtest/whtest_wrapper.cpp --- 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/IQ-TREE-1.6.5 && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/utils /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/utils /construction/biology/iqtree/IQ-TREE-1.6.5/utils/CMakeFiles/utils.dir/DependInfo.cmake Scanning dependencies of target utils /usr/bin/make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build --- utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o --- [ 30%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/utils/eigendecomposition.cpp --- pll/CMakeFiles/pllavx.dir/all --- --- pll/libpllavx.a --- [ 30%] Linking C static library libpllavx.a cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/local/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a [ 30%] Built target pllavx --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o --- [ 30%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/nclextra/msetsblock.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o --- [ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/ncl/nxsdiscretedatum.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/gzstream.cpp.o --- [ 30%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c 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CMakeFiles/pll.dir/newick.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/newick.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/newick.c:36:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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/libwhtest.a --- [ 33%] Linking CXX static library libwhtest.a cd /construction/biology/iqtree/IQ-TREE-1.6.5/whtest && /usr/local/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/IQ-TREE-1.6.5/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 [ 33%] Built target whtest --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o --- [ 33%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/newviewGenericSpecial.c --- pll/CMakeFiles/pll.dir/genericParallelization.c.o --- [ 34%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections 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pll/CMakeFiles/pll.dir/optimizeModel.c.o --- [ 37%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/optimizeModel.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/optimizeModel.c:47:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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); ^ --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/stoprule.cpp.o --- [ 37%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS 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/construction/biology/iqtree/IQ-TREE-1.6.5/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); ^ --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/tools.cpp.o --- [ 39%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/utils/tools.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/queue.c.o --- [ 40%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 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[ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/ncl/nxsdistancesblock.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/recom.c.o --- [ 42%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/recom.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/recom.c:43:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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 --- [ 42%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/restartHashTable.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/restartHashTable.c:47:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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 --- [ 43%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/searchAlgo.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/searchAlgo.c:51:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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/ssort.c.o --- [ 44%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing 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-I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/trash.c --- pll/CMakeFiles/pll.dir/topologies.c.o --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/topologies.c --- pll/CMakeFiles/pll.dir/trash.c.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/trash.c:48:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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/topologies.c.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/topologies.c:48:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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 --- [ 46%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/treeIO.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/treeIO.c:49:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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 --- [ 46%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pll/utils.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.5/pll/utils.c:70:0: /construction/biology/iqtree/IQ-TREE-1.6.5/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/nxsemptyblock.cpp.o --- [ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/ncl/nxsemptyblock.cpp --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/libnclextra.a --- [ 47%] Linking CXX static library libnclextra.a cd /construction/biology/iqtree/IQ-TREE-1.6.5/nclextra && /usr/local/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/IQ-TREE-1.6.5/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 [ 47%] Built target nclextra --- 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/IQ-TREE-1.6.5 && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/pda /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/pda /construction/biology/iqtree/IQ-TREE-1.6.5/pda/CMakeFiles/pda.dir/DependInfo.cmake Scanning dependencies of target pda /usr/bin/make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build --- pda/CMakeFiles/pda.dir/circularnetwork.cpp.o --- [ 48%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/pda/circularnetwork.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/pllnni.cpp.o --- --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o --- --- utils/CMakeFiles/utils.dir/all --- [ 48%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/utils/pllnni.cpp --- ncl/CMakeFiles/ncl.dir/all --- [ 48%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp 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&& /usr/local/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/IQ-TREE-1.6.5/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 [ 61%] 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/IQ-TREE-1.6.5 && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/model /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/model /construction/biology/iqtree/IQ-TREE-1.6.5/model/CMakeFiles/model.dir/DependInfo.cmake Scanning dependencies of target model /usr/bin/make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build --- model/CMakeFiles/model.dir/modelmarkov.cpp.o --- [ 61%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/model/modelmarkov.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/pdtree.cpp.o --- [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/pda && 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/construction/biology/iqtree/IQ-TREE-1.6.5/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 [ 62%] Built target ncl --- 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/IQ-TREE-1.6.5 && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/alignment /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/alignment /construction/biology/iqtree/IQ-TREE-1.6.5/alignment/CMakeFiles/alignment.dir/DependInfo.cmake Scanning dependencies of target alignment /usr/bin/make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build --- alignment/CMakeFiles/alignment.dir/pattern.cpp.o --- [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 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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 /usr/bin/ranlib libalignment.a [ 83%] Built target alignment --- CMakeFiles/kernelsse.dir/all --- --- libkernelsse.a --- [ 84%] 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 [ 84%] Built target kernelsse --- CMakeFiles/kernelavx.dir/all --- --- libkernelavx.a --- [ 84%] 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 [ 84%] Built target kernelavx --- 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/libmodel.a --- [ 84%] Linking CXX static library libmodel.a cd /construction/biology/iqtree/IQ-TREE-1.6.5/model && /usr/local/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/IQ-TREE-1.6.5/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 [ 84%] 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/IQ-TREE-1.6.5 && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/tree /construction/biology/iqtree/IQ-TREE-1.6.5 /construction/biology/iqtree/IQ-TREE-1.6.5/tree /construction/biology/iqtree/IQ-TREE-1.6.5/tree/CMakeFiles/tree.dir/DependInfo.cmake Scanning dependencies of target tree /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 --- --- 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tree/CMakeFiles/tree.dir/constrainttree.cpp.o --- [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/constrainttree.cpp --- tree/CMakeFiles/tree.dir/matree.cpp.o --- [ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c 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/construction/biology/iqtree/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/phylonode.cpp --- tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o --- cd /construction/biology/iqtree/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/phylonodemixlen.cpp --- tree/CMakeFiles/tree.dir/iqtree.cpp.o --- [ 90%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/iqtree.cpp --- tree/CMakeFiles/tree.dir/mexttree.cpp.o --- [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/mexttree.cpp --- tree/CMakeFiles/tree.dir/phylosupertree.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/phylosupertree.cpp --- tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c 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-I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/phylotreesse.cpp --- tree/CMakeFiles/tree.dir/quartet.cpp.o --- [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/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/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/supernode.cpp --- tree/CMakeFiles/tree.dir/tinatree.cpp.o --- [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /construction/biology/iqtree/IQ-TREE-1.6.5/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.5 -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.5/tree/tinatree.cpp --- tree/libtree.a --- [ 97%] Linking CXX static library libtree.a cd /construction/biology/iqtree/IQ-TREE-1.6.5/tree && 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