=> Building biology/iqtree Started : Sunday, 7 JUL 2019 at 04:17:58 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- ===> The following configuration options are available for iqtree-1.6.10: 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=gcc80 -------------------------------------------------- -- 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=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/iqtree/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=5.4 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=Release-5.4 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> iqtree-1.6.10 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> iqtree-1.6.10 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of iqtree-1.6.10 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by iqtree-1.6.10 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by iqtree-1.6.10 for building => SHA256 Checksum OK for Cibiv-IQ-TREE-v1.6.10_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by iqtree-1.6.10 for building ===> Extracting for iqtree-1.6.10 => SHA256 Checksum OK for Cibiv-IQ-TREE-v1.6.10_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for iqtree-1.6.10 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> iqtree-1.6.10 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.14.5.txz Installing cmake-3.14.5... `-- Installing curl-7.65.1... | `-- Installing ca_root_nss-3.44... | `-- Extracting ca_root_nss-3.44: ........ done | `-- Installing libnghttp2-1.39.1... | `-- Extracting libnghttp2-1.39.1: .......... done | `-- Installing libressl-2.9.2... | `-- Extracting libressl-2.9.2: .......... done `-- Extracting curl-7.65.1: .......... done `-- Installing expat-2.2.6_1... `-- Extracting expat-2.2.6_1: .......... done `-- Installing jsoncpp-1.8.1_6... `-- Extracting jsoncpp-1.8.1_6: .......... done `-- Installing libarchive-3.3.3,1... | `-- Installing liblz4-1.9.1,1... | `-- Extracting liblz4-1.9.1,1: .......... done | `-- Installing lzo2-2.10_1... | `-- Extracting lzo2-2.10_1: .......... done `-- Extracting libarchive-3.3.3,1: .......... done `-- Installing libuv-1.29.1... `-- Extracting libuv-1.29.1: .......... done `-- Installing ncurses-6.1.20190525... `-- Extracting ncurses-6.1.20190525: .......... done `-- Installing rhash-1.3.5... `-- Extracting rhash-1.3.5: .......... done Extracting cmake-3.14.5: .......... done Message from ca_root_nss-3.44: ********************************* 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-1.6.10 depends on file: /usr/local/bin/cmake - found ===> Returning to build of iqtree-1.6.10 ===> iqtree-1.6.10 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.3.7.txz Installing eigen-3.3.7... Extracting eigen-3.3.7: .......... done ===> iqtree-1.6.10 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of iqtree-1.6.10 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for iqtree-1.6.10 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/iqtree/.build -- The C compiler identification is GNU 8.1.0 -- The CXX compiler identification is GNU 8.1.0 -- 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/.build -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for iqtree-1.6.10 /usr/local/bin/cmake -S/construction/biology/iqtree/IQ-TREE-1.6.10 -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/pll.dir/all --- --- pll/CMakeFiles/pllavx.dir/all --- --- CMakeFiles/kernelfma.dir/all --- /usr/bin/make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend --- CMakeFiles/kernelsse.dir/all --- /usr/bin/make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend --- CMakeFiles/kernelavx.dir/all --- /usr/bin/make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.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 --- CMakeFiles/kernelsse.dir/all --- --- CMakeFiles/kernelsse.dir/depend --- --- CMakeFiles/kernelfma.dir/all --- --- CMakeFiles/kernelfma.dir/depend --- --- pll/CMakeFiles/pllavx.dir/all --- --- pll/CMakeFiles/pllavx.dir/depend --- --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelavx.dir/depend --- --- CMakeFiles/kernelsse.dir/all --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelsse.dir/DependInfo.cmake --- CMakeFiles/kernelfma.dir/all --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelfma.dir/DependInfo.cmake --- pll/CMakeFiles/pllavx.dir/all --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/pll /construction/biology/iqtree/.build /construction/biology/iqtree/.build/pll /construction/biology/iqtree/.build/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --- CMakeFiles/kernelavx.dir/all --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelavx.dir/DependInfo.cmake --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/pll /construction/biology/iqtree/.build /construction/biology/iqtree/.build/pll /construction/biology/iqtree/.build/pll/CMakeFiles/pll.dir/DependInfo.cmake --- pll/CMakeFiles/pllavx.dir/all --- Scanning dependencies of target pllavx /usr/bin/make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build --- pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o --- [ 0%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/avxLikelihood.c --- CMakeFiles/kernelsse.dir/all --- Scanning dependencies of target kernelsse /usr/bin/make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build --- pll/CMakeFiles/pll.dir/all --- Scanning dependencies of target pll /usr/bin/make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build --- CMakeFiles/kernelsse.dir/all --- --- CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o --- --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/alignment.c.o --- --- CMakeFiles/kernelsse.dir/all --- [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/phylokernelsse.cpp --- 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 -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/alignment.c --- CMakeFiles/kernelavx.dir/all --- Scanning dependencies of target kernelavx /usr/bin/make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build --- CMakeFiles/kernelfma.dir/all --- Scanning dependencies of target kernelfma /usr/bin/make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o --- --- CMakeFiles/kernelfma.dir/all --- --- CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o --- --- CMakeFiles/kernelavx.dir/all --- [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/phylotreeavx.cpp --- CMakeFiles/kernelfma.dir/all --- [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/phylokernelfma.cpp --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/alignment.c:40: /construction/biology/iqtree/IQ-TREE-1.6.10/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/bipartitionList.c.o --- [ 2%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/bipartitionList.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/bipartitionList.c:49: /construction/biology/iqtree/IQ-TREE-1.6.10/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/pllavx.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/avxLikelihood.c:57: /construction/biology/iqtree/IQ-TREE-1.6.10/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/all --- --- pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o --- [ 2%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/evaluateGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/evaluateGenericSpecial.c:46: /construction/biology/iqtree/IQ-TREE-1.6.10/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/evaluatePartialGenericSpecial.c.o --- [ 3%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/evaluatePartialGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/evaluatePartialGenericSpecial.c:45: /construction/biology/iqtree/IQ-TREE-1.6.10/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/pllavx.dir/all --- --- pll/libpllavx.a --- [ 4%] Linking C static library libpllavx.a cd /construction/biology/iqtree/.build/pll && /usr/local/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/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 [ 4%] Built target pllavx --- ncl/CMakeFiles/ncl.dir/all --- /usr/bin/make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend --- ncl/CMakeFiles/ncl.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/ncl /construction/biology/iqtree/.build /construction/biology/iqtree/.build/ncl /construction/biology/iqtree/.build/ncl/CMakeFiles/ncl.dir/DependInfo.cmake Scanning dependencies of target ncl /usr/bin/make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build --- ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o --- [ 4%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/ncl/nxsassumptionsblock.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o --- [ 4%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/fastDNAparsimony.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/fastDNAparsimony.c:113: /construction/biology/iqtree/IQ-TREE-1.6.10/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/hardware.c.o --- [ 5%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/hardware.c --- pll/CMakeFiles/pll.dir/hash.c.o --- [ 5%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/hash.c --- pll/CMakeFiles/pll.dir/lexer.c.o --- [ 6%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/lexer.c --- pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o --- [ 7%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pll/makenewzGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/makenewzGenericSpecial.c:44: /construction/biology/iqtree/IQ-TREE-1.6.10/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/nxsblock.cpp.o --- [ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/ncl/nxsblock.cpp --- ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o --- [ 8%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/ncl/nxscharactersblock.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/models.c.o --- [ 8%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/models.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/models.c:53: /construction/biology/iqtree/IQ-TREE-1.6.10/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/newick.c.o --- [ 9%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pll/newick.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/newick.c:36: /construction/biology/iqtree/IQ-TREE-1.6.10/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 --- [ 9%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/newviewGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/newviewGenericSpecial.c:49: /construction/biology/iqtree/IQ-TREE-1.6.10/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/nxsdatablock.cpp.o --- [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/ncl/nxsdatablock.cpp --- ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o --- [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/ncl/nxsdiscretedatum.cpp --- ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o --- [ 11%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/ncl/nxsdiscretematrix.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/genericParallelization.c.o --- [ 12%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pll/genericParallelization.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/genericParallelization.c:43: /construction/biology/iqtree/IQ-TREE-1.6.10/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/nxsdistancedatum.cpp.o --- [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/ncl/nxsdistancedatum.cpp --- ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o --- [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/ncl/nxsdistancesblock.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/optimizeModel.c.o --- [ 13%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/optimizeModel.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/optimizeModel.c:47: /construction/biology/iqtree/IQ-TREE-1.6.10/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/parsePartition.c.o --- [ 14%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pll/parsePartition.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/parsePartition.c:42: /construction/biology/iqtree/IQ-TREE-1.6.10/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 --- [ 15%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pll/queue.c --- pll/CMakeFiles/pll.dir/randomTree.c.o --- [ 15%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pll/randomTree.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/randomTree.c:37: /construction/biology/iqtree/IQ-TREE-1.6.10/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 --- [ 16%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/recom.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/recom.c:43: /construction/biology/iqtree/IQ-TREE-1.6.10/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 --- [ 16%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/restartHashTable.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/restartHashTable.c:47: /construction/biology/iqtree/IQ-TREE-1.6.10/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 --- [ 17%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/searchAlgo.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/searchAlgo.c:51: /construction/biology/iqtree/IQ-TREE-1.6.10/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 --- [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/ncl/nxsemptyblock.cpp --- ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o --- [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/ncl/nxsexception.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/ssort.c.o --- [ 18%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pll/ssort.c --- pll/CMakeFiles/pll.dir/stack.c.o --- [ 19%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pll/stack.c --- pll/CMakeFiles/pll.dir/topologies.c.o --- [ 20%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/topologies.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/topologies.c:48: /construction/biology/iqtree/IQ-TREE-1.6.10/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 --- [ 21%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/ncl/nxsreader.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/trash.c.o --- [ 21%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/trash.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/trash.c:48: /construction/biology/iqtree/IQ-TREE-1.6.10/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 --- [ 22%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/treeIO.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/treeIO.c:49: /construction/biology/iqtree/IQ-TREE-1.6.10/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 --- [ 22%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pll/utils.c In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/pll/utils.c:70: /construction/biology/iqtree/IQ-TREE-1.6.10/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/nxssetreader.cpp.o --- [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/ncl/nxssetreader.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/libpll.a --- [ 24%] 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 [ 24%] Built target pll --- nclextra/CMakeFiles/nclextra.dir/all --- /usr/bin/make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend --- nclextra/CMakeFiles/nclextra.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/nclextra /construction/biology/iqtree/.build /construction/biology/iqtree/.build/nclextra /construction/biology/iqtree/.build/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake Scanning dependencies of target nclextra /usr/bin/make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build --- nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o --- [ 25%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/nclextra/mpdablock.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o --- [ 25%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/ncl/nxsstring.cpp --- ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o --- [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/ncl/nxstaxablock.cpp --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o --- [ 27%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/nclextra/msetsblock.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o --- [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/ncl/nxstoken.cpp --- ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o --- [ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/ncl/nxstreesblock.cpp --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o --- [ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/nclextra/msplitsblock.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/libncl.a --- [ 28%] 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 [ 28%] Built target ncl --- 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-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/lbfgsb /construction/biology/iqtree/.build /construction/biology/iqtree/.build/lbfgsb /construction/biology/iqtree/.build/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake Scanning dependencies of target lbfgsb /usr/bin/make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build --- lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o --- [ 29%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /construction/biology/iqtree/.build/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/lbfgsb/lbfgsb_new.cpp --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o --- [ 30%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/nclextra/modelsblock.cpp --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- --- lbfgsb/liblbfgsb.a --- [ 30%] 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 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a [ 30%] Built target lbfgsb --- whtest/CMakeFiles/whtest.dir/all --- /usr/bin/make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend --- whtest/CMakeFiles/whtest.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/whtest /construction/biology/iqtree/.build /construction/biology/iqtree/.build/whtest /construction/biology/iqtree/.build/whtest/CMakeFiles/whtest.dir/DependInfo.cmake Scanning dependencies of target whtest /usr/bin/make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build --- whtest/CMakeFiles/whtest.dir/eigen.c.o --- [ 31%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/whtest/eigen.c --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/libnclextra.a --- [ 31%] 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 [ 31%] Built target nclextra --- 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-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/sprng /construction/biology/iqtree/.build /construction/biology/iqtree/.build/sprng /construction/biology/iqtree/.build/sprng/CMakeFiles/sprng.dir/DependInfo.cmake Scanning dependencies of target sprng /usr/bin/make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build --- sprng/CMakeFiles/sprng.dir/lcg64.c.o --- [ 32%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/sprng/lcg64.c --- sprng/CMakeFiles/sprng.dir/makeseed.c.o --- [ 32%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/sprng/makeseed.c --- sprng/CMakeFiles/sprng.dir/memory.c.o --- [ 33%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/sprng/memory.c --- sprng/CMakeFiles/sprng.dir/store.c.o --- [ 33%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/sprng/store.c --- sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o --- [ 34%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/sprng/primes-lcg64.c --- sprng/CMakeFiles/sprng.dir/checkid.c.o --- [ 34%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/sprng/checkid.c --- sprng/libsprng.a --- [ 35%] 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 [ 35%] Built target sprng --- 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-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/vectorclass /construction/biology/iqtree/.build /construction/biology/iqtree/.build/vectorclass /construction/biology/iqtree/.build/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake Scanning dependencies of target vectorclass /usr/bin/make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build --- vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o --- [ 36%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /construction/biology/iqtree/.build/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/vectorclass/instrset_detect.cpp --- vectorclass/libvectorclass.a --- [ 36%] 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 [ 36%] Built target vectorclass --- 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-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/gsl /construction/biology/iqtree/.build /construction/biology/iqtree/.build/gsl /construction/biology/iqtree/.build/gsl/CMakeFiles/gsl.dir/DependInfo.cmake Scanning dependencies of target gsl /usr/bin/make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build --- gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o --- [ 37%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/gsl/binomial_tpe.cpp --- gsl/CMakeFiles/gsl.dir/multinomial.cpp.o --- [ 37%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/gsl/multinomial.cpp --- gsl/CMakeFiles/gsl.dir/pow_int.cpp.o --- [ 38%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/gsl/pow_int.cpp --- gsl/CMakeFiles/gsl.dir/gauss.cpp.o --- [ 38%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/gsl/gauss.cpp --- gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o --- [ 39%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/gsl/gaussinv.cpp --- gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o --- [ 40%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/gsl/gausspdf.cpp --- gsl/libgsl.a --- [ 40%] 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 [ 40%] Built target gsl --- 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-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/alignment /construction/biology/iqtree/.build /construction/biology/iqtree/.build/alignment /construction/biology/iqtree/.build/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 --- [ 40%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/alignment.dir/pattern.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/alignment/pattern.cpp --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/eigen_sym.c.o --- [ 41%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/whtest/eigen_sym.c --- whtest/CMakeFiles/whtest.dir/random.c.o --- [ 41%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/whtest/random.c --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/alignment.cpp.o --- [ 42%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/alignment.dir/alignment.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/alignment/alignment.cpp --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/weisslambda.c.o --- [ 43%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/whtest/weisslambda.c --- whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o --- [ 43%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/whtest/weisslambda_sub.c --- whtest/CMakeFiles/whtest.dir/whtest.c.o --- [ 44%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/whtest/whtest.c --- whtest/CMakeFiles/whtest.dir/whtest_sub.c.o --- [ 44%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/whtest/whtest_sub.c --- alignment/CMakeFiles/alignment.dir/all --- /construction/biology/iqtree/IQ-TREE-1.6.10/alignment/alignment.cpp:2925:92: 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) { ^~~~~ --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o --- [ 45%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/whtest/whtest_wrapper.cpp --- whtest/libwhtest.a --- [ 46%] 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 [ 46%] Built target whtest --- 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-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/utils /construction/biology/iqtree/.build /construction/biology/iqtree/.build/utils /construction/biology/iqtree/.build/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 --- [ 47%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/utils/eigendecomposition.cpp --- CMakeFiles/kernelsse.dir/all --- --- libkernelsse.a --- [ 48%] 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 [ 48%] Built target kernelsse --- 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-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/pda /construction/biology/iqtree/.build /construction/biology/iqtree/.build/pda /construction/biology/iqtree/.build/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 --- [ 49%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/pda/circularnetwork.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/gzstream.cpp.o --- [ 49%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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 /construction/biology/iqtree/IQ-TREE-1.6.10/utils/gzstream.cpp --- utils/CMakeFiles/utils.dir/optimization.cpp.o --- [ 50%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/utils/optimization.cpp --- utils/CMakeFiles/utils.dir/stoprule.cpp.o --- [ 50%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/utils/stoprule.cpp --- CMakeFiles/kernelavx.dir/all --- --- libkernelavx.a --- [ 51%] Linking CXX static library libkernelavx.a /usr/local/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/greedy.cpp.o --- --- CMakeFiles/kernelavx.dir/all --- /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 --- pda/CMakeFiles/pda.dir/all --- [ 51%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/greedy.cpp --- CMakeFiles/kernelavx.dir/all --- /usr/bin/ranlib libkernelavx.a [ 51%] Built target kernelavx --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o --- [ 51%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/alignment.dir/alignmentpairwise.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/alignment/alignmentpairwise.cpp --- CMakeFiles/kernelfma.dir/all --- --- libkernelfma.a --- [ 52%] 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 [ 52%] Built target kernelfma --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o --- [ 53%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/gurobiwrapper.cpp --- pda/CMakeFiles/pda.dir/hashsplitset.cpp.o --- [ 54%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/hashsplitset.cpp --- pda/CMakeFiles/pda.dir/pdnetwork.cpp.o --- [ 54%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/pdnetwork.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/maalignment.cpp.o --- [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/alignment.dir/maalignment.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/alignment/maalignment.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/pruning.cpp.o --- [ 56%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/pruning.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/tools.cpp.o --- [ 57%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/utils/tools.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignment.cpp.o --- [ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd 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alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o --- [ 58%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/alignment.dir/superalignmentpairwise.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/alignment/superalignmentpairwise.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/splitgraph.cpp.o --- [ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/splitgraph.cpp --- pda/CMakeFiles/pda.dir/splitset.cpp.o --- [ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/splitset.cpp --- pda/CMakeFiles/pda.dir/lpwrapper.c.o --- [ 60%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /construction/biology/iqtree/.build/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/lpwrapper.c --- pda/CMakeFiles/pda.dir/ecopd.cpp.o --- [ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/ecopd.cpp --- pda/CMakeFiles/pda.dir/graph.cpp.o --- [ 61%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/graph.cpp --- pda/CMakeFiles/pda.dir/pdtree.cpp.o --- [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/pdtree.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o --- [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/alignment.dir/superalignmentpairwiseplen.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/alignment/superalignmentpairwiseplen.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/pdtreeset.cpp.o --- [ 63%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/pdtreeset.cpp --- pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o --- [ 64%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/pda/ecopdmtreeset.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/libalignment.a --- [ 64%] 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 /usr/bin/ranlib libalignment.a [ 64%] Built target alignment --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/pllnni.cpp.o --- [ 65%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/utils/pllnni.cpp --- utils/CMakeFiles/utils.dir/checkpoint.cpp.o --- [ 65%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/utils/checkpoint.cpp --- utils/CMakeFiles/utils.dir/MPIHelper.cpp.o --- [ 66%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/utils/MPIHelper.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/libpda.a --- [ 66%] 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 [ 66%] Built target pda --- utils/CMakeFiles/utils.dir/all --- --- utils/libutils.a --- [ 66%] 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 [ 66%] 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-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/model /construction/biology/iqtree/.build /construction/biology/iqtree/.build/model /construction/biology/iqtree/.build/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 --- --- model/CMakeFiles/model.dir/modelbin.cpp.o --- --- model/CMakeFiles/model.dir/modeldna.cpp.o --- --- model/CMakeFiles/model.dir/modelfactory.cpp.o --- --- model/CMakeFiles/model.dir/modelprotein.cpp.o --- [ 67%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o --- model/CMakeFiles/model.dir/modelmarkov.cpp.o --- [ 68%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o --- model/CMakeFiles/model.dir/modelprotein.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing 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model/CMakeFiles/model.dir/modelbin.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelbin.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelbin.cpp --- model/CMakeFiles/model.dir/modeldna.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modeldna.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modeldna.cpp --- model/CMakeFiles/model.dir/modelfactory.cpp.o --- [ 69%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelfactory.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelfactory.cpp In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelfactory.cpp:24: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- model/CMakeFiles/model.dir/modeldna.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modeldna.h:23, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modeldna.cpp:20: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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-1.6.10/model/modeldna.cpp:20: /construction/biology/iqtree/IQ-TREE-1.6.10/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/modelfactory.cpp.o --- /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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-1.6.10/model/modelfactory.cpp:26: /construction/biology/iqtree/IQ-TREE-1.6.10/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-1.6.10/model/modelfactory.cpp:27: /construction/biology/iqtree/IQ-TREE-1.6.10/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-1.6.10/model/modelfactory.cpp:30: /construction/biology/iqtree/IQ-TREE-1.6.10/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/modeldna.cpp.o --- /construction/biology/iqtree/IQ-TREE-1.6.10/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ --- model/CMakeFiles/model.dir/modelbin.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelbin.h:23, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelbin.cpp:20: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelmarkov.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.cpp:20: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelprotein.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelprotein.h:23, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelprotein.cpp:20: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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-1.6.10/model/modelprotein.cpp:20: /construction/biology/iqtree/IQ-TREE-1.6.10/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-1.6.10/model/modelprotein.cpp:634:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelProtein::readRates(istream &in) throw(const char*, string) { ^~~~~ --- model/CMakeFiles/model.dir/modelset.cpp.o --- [ 70%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelset.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelset.cpp --- model/CMakeFiles/model.dir/modelmarkov.cpp.o --- /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ --- model/CMakeFiles/model.dir/modelset.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelset.h:23, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelset.cpp:20: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelsubst.cpp.o --- [ 70%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelsubst.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelsubst.cpp --- model/CMakeFiles/model.dir/partitionmodel.cpp.o --- [ 71%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/partitionmodel.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/partitionmodel.cpp --- model/CMakeFiles/model.dir/partitionmodelplen.cpp.o --- [ 71%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/partitionmodelplen.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/partitionmodelplen.cpp --- model/CMakeFiles/model.dir/rategamma.cpp.o --- [ 72%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/rategamma.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/rategamma.cpp --- model/CMakeFiles/model.dir/rategammainvar.cpp.o --- [ 72%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/rategammainvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/rategammainvar.cpp --- model/CMakeFiles/model.dir/rateheterogeneity.cpp.o --- [ 73%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/rateheterogeneity.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/rateheterogeneity.cpp --- model/CMakeFiles/model.dir/rateinvar.cpp.o --- [ 74%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/rateinvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/rateinvar.cpp --- model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o --- [ 74%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/ratemeyerdiscrete.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/ratemeyerdiscrete.cpp --- model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o --- [ 75%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/ratemeyerhaeseler.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/ratemeyerhaeseler.cpp --- model/CMakeFiles/model.dir/ratekategory.cpp.o --- [ 75%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/ratekategory.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/ratekategory.cpp --- model/CMakeFiles/model.dir/ratefree.cpp.o --- [ 76%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/ratefree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/ratefree.cpp In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/ratefree.cpp:13: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/ratefreeinvar.cpp.o --- [ 76%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/ratefreeinvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/ratefreeinvar.cpp --- model/CMakeFiles/model.dir/rateheterotachy.cpp.o --- [ 77%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/rateheterotachy.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/rateheterotachy.cpp --- model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o --- [ 78%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/rateheterotachyinvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/rateheterotachyinvar.cpp --- model/CMakeFiles/model.dir/modelcodon.cpp.o --- [ 78%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelcodon.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelcodon.cpp --- model/CMakeFiles/model.dir/modelmorphology.cpp.o --- [ 79%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelmorphology.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmorphology.cpp --- model/CMakeFiles/model.dir/modelmixture.cpp.o --- [ 79%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelmixture.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmixture.cpp --- model/CMakeFiles/model.dir/modelunrest.cpp.o --- [ 80%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelunrest.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelunrest.cpp --- model/CMakeFiles/model.dir/modelmorphology.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmorphology.h:11, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmorphology.cpp:8: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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-1.6.10/model/modelmorphology.cpp:8: /construction/biology/iqtree/IQ-TREE-1.6.10/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-1.6.10/model/modelmorphology.cpp:44:46: 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-1.6.10/model/modelmixture.cpp:8: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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-1.6.10/model/modelmixture.cpp:9: /construction/biology/iqtree/IQ-TREE-1.6.10/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-1.6.10/model/modelmixture.cpp:10: /construction/biology/iqtree/IQ-TREE-1.6.10/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-1.6.10/model/modelmixture.cpp:13: /construction/biology/iqtree/IQ-TREE-1.6.10/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/modelliemarkov.cpp.o --- [ 80%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelliemarkov.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelliemarkov.cpp --- model/CMakeFiles/model.dir/modelunrest.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelunrest.h:11, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelunrest.cpp:8: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelpomo.cpp.o --- [ 81%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelpomo.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelpomo.cpp --- model/CMakeFiles/model.dir/modelpomomixture.cpp.o --- [ 82%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelpomomixture.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelpomomixture.cpp --- model/CMakeFiles/model.dir/modelcodon.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelcodon.h:11, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelcodon.cpp:8: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelpomo.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modeldna.h:23, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelpomo.cpp:1: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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-1.6.10/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelpomo.cpp:1: /construction/biology/iqtree/IQ-TREE-1.6.10/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/modelpomomixture.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modeldna.h:23, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelpomomixture.h:14, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelpomomixture.cpp:9: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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-1.6.10/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelpomomixture.h:14, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelpomomixture.cpp:9: /construction/biology/iqtree/IQ-TREE-1.6.10/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/modelliemarkov.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelliemarkov.h:11, from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelliemarkov.cpp:25: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o --- [ 82%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/modelfactorymixlen.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelfactorymixlen.cpp In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelfactorymixlen.cpp:12: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/libmodel.a --- [ 83%] 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 [ 83%] 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-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10/tree /construction/biology/iqtree/.build /construction/biology/iqtree/.build/tree /construction/biology/iqtree/.build/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 --- --- tree/CMakeFiles/tree.dir/matree.cpp.o --- --- tree/CMakeFiles/tree.dir/memslot.cpp.o --- --- tree/CMakeFiles/tree.dir/candidateset.cpp.o --- [ 83%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o --- tree/CMakeFiles/tree.dir/matree.cpp.o --- [ 83%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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 /construction/biology/iqtree/IQ-TREE-1.6.10/tree/matree.cpp --- tree/CMakeFiles/tree.dir/candidateset.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/candidateset.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/tree/candidateset.cpp --- tree/CMakeFiles/tree.dir/memslot.cpp.o --- [ 84%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/memslot.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/tree/memslot.cpp --- tree/CMakeFiles/tree.dir/constrainttree.cpp.o --- [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/constrainttree.cpp --- tree/CMakeFiles/tree.dir/iqtree.cpp.o --- [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/iqtree.cpp In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/tree/iqtree.cpp:29: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/mexttree.cpp.o --- [ 86%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/mexttree.cpp --- tree/CMakeFiles/tree.dir/mtree.cpp.o --- [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/mtree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/tree/mtree.cpp --- tree/CMakeFiles/tree.dir/mtreeset.cpp.o --- [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/mtreeset.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/tree/mtreeset.cpp --- tree/CMakeFiles/tree.dir/ncbitree.cpp.o --- [ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/ncbitree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/tree/ncbitree.cpp --- tree/CMakeFiles/tree.dir/node.cpp.o --- [ 89%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/node.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/tree/node.cpp --- tree/CMakeFiles/tree.dir/phylonode.cpp.o --- [ 89%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/phylonode.cpp --- tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o --- [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/phylonodemixlen.cpp --- tree/CMakeFiles/tree.dir/phylosupertree.cpp.o --- [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/phylosupertree.cpp --- tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o --- [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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 /construction/biology/iqtree/IQ-TREE-1.6.10/tree/phylosupertreeplen.cpp --- tree/CMakeFiles/tree.dir/phylotree.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/phylotree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/tree/phylotree.cpp --- tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/phylotreemixlen.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/tree/phylotreemixlen.cpp In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-1.6.10/tree/phylotreemixlen.cpp:12: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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-1.6.10/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-1.6.10/tree/phylotree.cpp:34: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /construction/biology/iqtree/IQ-TREE-1.6.10/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ --- tree/CMakeFiles/tree.dir/phylotreepars.cpp.o --- [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/phylotreepars.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/tree/phylotreepars.cpp --- tree/CMakeFiles/tree.dir/phylotreesse.cpp.o --- [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/phylotreesse.cpp In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/tree/phylotreesse.cpp:35: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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 --- [ 94%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/quartet.cpp --- tree/CMakeFiles/tree.dir/supernode.cpp.o --- [ 94%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/supernode.cpp --- tree/CMakeFiles/tree.dir/tinatree.cpp.o --- [ 95%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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-1.6.10/tree/tinatree.cpp --- tree/CMakeFiles/tree.dir/parstree.cpp.o --- [ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/parstree.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/tree/parstree.cpp --- tree/libtree.a --- [ 96%] 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/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 /usr/bin/ranlib libtree.a [ 96%] Built target tree --- CMakeFiles/iqtree.dir/all --- /usr/bin/make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend --- CMakeFiles/iqtree.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/IQ-TREE-1.6.10 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/iqtree.dir/DependInfo.cmake Scanning dependencies of target iqtree /usr/bin/make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build --- CMakeFiles/iqtree.dir/main/main.cpp.o --- --- CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o --- --- CMakeFiles/iqtree.dir/main/phylotesting.cpp.o --- --- CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o --- --- CMakeFiles/iqtree.dir/main/phylotesting.cpp.o --- [ 97%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/iqtree.dir/main/phylotesting.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/main/phylotesting.cpp --- CMakeFiles/iqtree.dir/main/main.cpp.o --- [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/iqtree.dir/main/main.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/main/main.cpp --- CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o --- [ 98%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/iqtree.dir/obsolete/parsmultistate.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/obsolete/parsmultistate.cpp --- CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o --- [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-1.6.10 -I/construction/biology/iqtree/.build -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/iqtree.dir/main/phyloanalysis.cpp.o -c /construction/biology/iqtree/IQ-TREE-1.6.10/main/phyloanalysis.cpp --- CMakeFiles/iqtree.dir/main/phylotesting.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/main/phylotesting.cpp:20: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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-1.6.10/main/phylotesting.cpp:21: /construction/biology/iqtree/IQ-TREE-1.6.10/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-1.6.10/main/phylotesting.cpp:30: /construction/biology/iqtree/IQ-TREE-1.6.10/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-1.6.10/main/phylotesting.cpp:33: /construction/biology/iqtree/IQ-TREE-1.6.10/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/iqtree.dir/main/phyloanalysis.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-1.6.10/main/phyloanalysis.cpp:35: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelmarkov.h:163:41: 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-1.6.10/main/phyloanalysis.cpp:36: /construction/biology/iqtree/IQ-TREE-1.6.10/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-1.6.10/main/phyloanalysis.cpp:44: /construction/biology/iqtree/IQ-TREE-1.6.10/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- CMakeFiles/iqtree.dir/main/phylotesting.cpp.o --- /construction/biology/iqtree/IQ-TREE-1.6.10/main/phylotesting.cpp: In function 'std::__cxx11::string getSeqTypeName(SeqType)': /construction/biology/iqtree/IQ-TREE-1.6.10/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ --- iqtree --- [ 99%] Linking CXX executable iqtree /usr/local/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O3 -g -ffunction-sections -fdata-sections -rdynamic -Wl,--gc-sections CMakeFiles/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree -L/construction/biology/iqtree/IQ-TREE-1.6.10/lib -Wl,-z,origin,-rpath,/construction/biology/iqtree/IQ-TREE-1.6.10/lib -lexecinfo 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 -lm libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a strip /construction/biology/iqtree/.build/iqtree [100%] Built target iqtree /usr/local/bin/cmake -E cmake_progress_start /construction/biology/iqtree/.build/CMakeFiles 0 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for iqtree-1.6.10 ===> Generating temporary packing list install -s -m 555 /construction/biology/iqtree/.build/iqtree /construction/biology/iqtree/stage/usr/local/bin install -m 0644 /construction/biology/iqtree/IQ-TREE-1.6.10/example/* /construction/biology/iqtree/stage/usr/local/share/examples/iqtree ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for iqtree-1.6.10 file sizes/checksums [8]: . done packing files [8]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:23:56 UTC Duration: 00:05:58