------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libnghttp2-1.41.0.txz Installing /packages/All/ca_root_nss-3.56.txz ===== Message from ca_root_nss-3.56: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/curl-7.72.0.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/libuv-1.39.0.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.21.txz Installing /packages/All/rhash-1.3.9.txz Installing /packages/All/liblz4-1.9.2_1,1.txz Installing /packages/All/lzo2-2.10_1.txz Installing /packages/All/libarchive-3.4.3,1.txz Installing /packages/All/ncurses-6.2.20200831.txz Installing /packages/All/cmake-3.18.2.txz Installing /packages/All/eigen-3.3.7.txz Installing /packages/All/icu-67.1,1.txz Installing /packages/All/boost-libs-1.72.0_2.txz ===== Message from boost-libs-1.72.0_2: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. SUCCEEDED 00:00:22 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> iqtree-2.0.6 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> iqtree-2.0.6 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by iqtree-2.0.6 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> iqtree-2.0.6 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by iqtree-2.0.6 for building => SHA256 Checksum OK for Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz. SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> iqtree-2.0.6 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by iqtree-2.0.6 for building ===> Extracting for iqtree-2.0.6 => SHA256 Checksum OK for Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz. Extracted Memory Use: 23.54M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for iqtree-2.0.6 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> iqtree-2.0.6 depends on file: /usr/local/bin/cmake - found ===> iqtree-2.0.6 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> iqtree-2.0.6 depends on shared library: libboost_filesystem.so - found (/usr/local/lib/libboost_filesystem.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> iqtree-2.0.6 depends on file: /usr/local/bin/cmake - found ===> iqtree-2.0.6 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> iqtree-2.0.6 depends on shared library: libboost_filesystem.so - found (/usr/local/lib/libboost_filesystem.so) ===> Configuring for iqtree-2.0.6 ===> Performing out-of-source build /bin/mkdir -p /construction/biology/iqtree/.build -- The C compiler identification is GNU 8.3.0 -- The CXX compiler identification is GNU 8.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/local/include (found version "1.72.0") IQ-TREE flags : Builde mode : Release Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 C flags : -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections CXX flags : -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections LINKER flags : -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - not found -- Found Backtrace: /usr/lib/libexecinfo.so -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") Using system zlib -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success -- clang-tidy not found. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /construction/biology/iqtree/.build SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for iqtree-2.0.6 /usr/local/bin/cmake -S/construction/biology/iqtree/IQ-TREE-2.0.6 -B/construction/biology/iqtree/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/iqtree/.build/CMakeFiles /construction/biology/iqtree/.build//CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelfma.dir/all --- --- CMakeFiles/kernelsse.dir/all --- --- booster/CMakeFiles/booster.dir/all --- --- ncl/CMakeFiles/ncl.dir/all --- --- pll/CMakeFiles/pllavx.dir/all --- --- pll/CMakeFiles/pll.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/all --- --- vectorclass/CMakeFiles/vectorclass.dir/all --- --- sprng/CMakeFiles/sprng.dir/all --- --- CMakeFiles/kernelavx.dir/all --- /usr/bin/make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend --- 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 --- booster/CMakeFiles/booster.dir/all --- /usr/bin/make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend --- ncl/CMakeFiles/ncl.dir/all --- /usr/bin/make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend --- pll/CMakeFiles/pll.dir/all --- /usr/bin/make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend --- nclextra/CMakeFiles/nclextra.dir/all --- /usr/bin/make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelavx.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelavx.dir/DependInfo.cmake --- CMakeFiles/kernelfma.dir/all --- --- CMakeFiles/kernelfma.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelfma.dir/DependInfo.cmake --- CMakeFiles/kernelsse.dir/all --- --- CMakeFiles/kernelsse.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelsse.dir/DependInfo.cmake --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/ncl /construction/biology/iqtree/.build /construction/biology/iqtree/.build/ncl /construction/biology/iqtree/.build/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --- 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 --- --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/booster /construction/biology/iqtree/.build /construction/biology/iqtree/.build/booster /construction/biology/iqtree/.build/booster/CMakeFiles/booster.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-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/pll /construction/biology/iqtree/.build /construction/biology/iqtree/.build/pll /construction/biology/iqtree/.build/pll/CMakeFiles/pll.dir/DependInfo.cmake --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra /construction/biology/iqtree/.build /construction/biology/iqtree/.build/nclextra /construction/biology/iqtree/.build/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --- vectorclass/CMakeFiles/vectorclass.dir/all --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/vectorclass /construction/biology/iqtree/.build /construction/biology/iqtree/.build/vectorclass /construction/biology/iqtree/.build/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --- pll/CMakeFiles/pllavx.dir/all --- /usr/bin/make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend --- sprng/CMakeFiles/sprng.dir/all --- /usr/bin/make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend --- vectorclass/CMakeFiles/vectorclass.dir/all --- Scanning dependencies of target vectorclass /usr/bin/make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build --- pll/CMakeFiles/pllavx.dir/all --- --- pll/CMakeFiles/pllavx.dir/depend --- --- booster/CMakeFiles/booster.dir/all --- Scanning dependencies of target booster --- pll/CMakeFiles/pllavx.dir/all --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/pll /construction/biology/iqtree/.build /construction/biology/iqtree/.build/pll /construction/biology/iqtree/.build/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --- booster/CMakeFiles/booster.dir/all --- /usr/bin/make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build --- nclextra/CMakeFiles/nclextra.dir/all --- Scanning dependencies of target nclextra --- vectorclass/CMakeFiles/vectorclass.dir/all --- --- vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o --- --- nclextra/CMakeFiles/nclextra.dir/all --- /usr/bin/make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/sprng /construction/biology/iqtree/.build /construction/biology/iqtree/.build/sprng /construction/biology/iqtree/.build/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/bitset_index.c.o --- --- pll/CMakeFiles/pllavx.dir/all --- Scanning dependencies of target pllavx --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o --- --- vectorclass/CMakeFiles/vectorclass.dir/all --- [ 1%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o --- pll/CMakeFiles/pllavx.dir/all --- /usr/bin/make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build --- vectorclass/CMakeFiles/vectorclass.dir/all --- cd /construction/biology/iqtree/.build/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/vectorclass/instrset_detect.cpp --- booster/CMakeFiles/booster.dir/all --- [ 2%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/booster.dir/bitset_index.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/bitset_index.c --- ncl/CMakeFiles/ncl.dir/all --- Scanning dependencies of target ncl --- pll/CMakeFiles/pllavx.dir/all --- --- pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o --- --- ncl/CMakeFiles/ncl.dir/all --- /usr/bin/make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build --- CMakeFiles/kernelsse.dir/all --- Scanning dependencies of target kernelsse --- CMakeFiles/kernelfma.dir/all --- Scanning dependencies of target kernelfma --- nclextra/CMakeFiles/nclextra.dir/all --- [ 2%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o --- CMakeFiles/kernelsse.dir/all --- /usr/bin/make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build --- nclextra/CMakeFiles/nclextra.dir/all --- cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra/mpdablock.cpp --- CMakeFiles/kernelfma.dir/all --- /usr/bin/make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build --- pll/CMakeFiles/pllavx.dir/all --- [ 2%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/avxLikelihood.c --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o --- --- CMakeFiles/kernelsse.dir/all --- --- CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o --- --- CMakeFiles/kernelfma.dir/all --- --- CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o --- --- pll/CMakeFiles/pll.dir/all --- Scanning dependencies of target pll --- ncl/CMakeFiles/ncl.dir/all --- [ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsassumptionsblock.cpp --- pll/CMakeFiles/pll.dir/all --- /usr/bin/make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build --- CMakeFiles/kernelavx.dir/all --- Scanning dependencies of target kernelavx --- CMakeFiles/kernelsse.dir/all --- [ 2%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o --- CMakeFiles/kernelfma.dir/all --- [ 3%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o --- CMakeFiles/kernelsse.dir/all --- /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylokernelsse.cpp --- CMakeFiles/kernelfma.dir/all --- /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylokernelfma.cpp --- CMakeFiles/kernelavx.dir/all --- /usr/bin/make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/alignment.c.o --- --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o --- --- pll/CMakeFiles/pll.dir/all --- [ 3%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/alignment.c --- CMakeFiles/kernelavx.dir/all --- [ 4%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreeavx.cpp --- sprng/CMakeFiles/sprng.dir/all --- 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 --- [ 5%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/lcg64.c --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/alignment.c:40: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/hashmap.c.o --- [ 5%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/booster.dir/hashmap.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/hashmap.c --- booster/CMakeFiles/booster.dir/io.c.o --- [ 5%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/booster.dir/io.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/io.c --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/makeseed.c.o --- [ 5%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/makeseed.c --- vectorclass/CMakeFiles/vectorclass.dir/all --- --- vectorclass/libvectorclass.a --- [ 5%] Linking CXX static library libvectorclass.a cd /construction/biology/iqtree/.build/vectorclass && /usr/local/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/sort.c.o --- --- vectorclass/CMakeFiles/vectorclass.dir/all --- cd /construction/biology/iqtree/.build/vectorclass && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 --- booster/CMakeFiles/booster.dir/all --- [ 6%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/booster.dir/sort.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/sort.c --- vectorclass/CMakeFiles/vectorclass.dir/all --- /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a [ 6%] Built target vectorclass --- 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-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/whtest /construction/biology/iqtree/.build /construction/biology/iqtree/.build/whtest /construction/biology/iqtree/.build/whtest/CMakeFiles/whtest.dir/DependInfo.cmake Scanning dependencies of target whtest /usr/bin/make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/tree.c.o --- --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/eigen.c.o --- --- booster/CMakeFiles/booster.dir/all --- [ 6%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/booster.dir/tree.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/tree.c --- whtest/CMakeFiles/whtest.dir/all --- [ 7%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/eigen.c --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/memory.c.o --- [ 7%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/memory.c --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/bipartitionList.c.o --- [ 8%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/bipartitionList.c --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/store.c.o --- [ 9%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/store.c --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/bipartitionList.c:49: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o --- [ 9%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/primes-lcg64.c --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o --- [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/evaluateGenericSpecial.c --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/checkid.c.o --- [ 10%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /construction/biology/iqtree/.build/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/sprng/checkid.c --- pll/CMakeFiles/pllavx.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/avxLikelihood.c:57: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/libsprng.a --- --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/evaluateGenericSpecial.c:46: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- sprng/CMakeFiles/sprng.dir/all --- [ 10%] 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 [ 10%] Built target sprng --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- /usr/bin/make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend --- lbfgsb/CMakeFiles/lbfgsb.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/lbfgsb /construction/biology/iqtree/.build /construction/biology/iqtree/.build/lbfgsb /construction/biology/iqtree/.build/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake 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 --- [ 10%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /construction/biology/iqtree/.build/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/lbfgsb/lbfgsb_new.cpp --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/booster.c.o --- [ 11%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/booster.dir/booster.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c: In function 'main_booster': /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c:268:57: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); ^~~~~~~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c:27: /construction/biology/iqtree/IQ-TREE-2.0.6/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' unsigned int tell_size_of_one_tree(char* filename); ~~~~~~^~~~~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c:304:29: warning: passing argument 1 of 'tell_size_of_one_tree' discards 'const' qualifier from pointer target type [-Wdiscarded-qualifiers] if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { ^~~~~~~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/booster/booster.c:27: /construction/biology/iqtree/IQ-TREE-2.0.6/booster/tree.h:191:42: note: expected 'char *' but argument is of type 'const char *' unsigned int tell_size_of_one_tree(char* filename); ~~~~~~^~~~~~~~ --- booster/CMakeFiles/booster.dir/hashtables_bfields.c.o --- [ 11%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/hashtables_bfields.c --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/eigen_sym.c.o --- [ 11%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/eigen_sym.c --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/prng.c.o --- [ 11%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/booster.dir/prng.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/prng.c --- booster/CMakeFiles/booster.dir/stats.c.o --- [ 12%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/booster.dir/stats.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/stats.c --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/random.c.o --- [ 12%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/random.c --- whtest/CMakeFiles/whtest.dir/weisslambda.c.o --- [ 13%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/weisslambda.c --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o --- [ 14%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/evaluatePartialGenericSpecial.c --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o --- [ 14%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/weisslambda_sub.c --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/evaluatePartialGenericSpecial.c:45: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/whtest.c.o --- [ 15%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/whtest.c --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/tree_utils.c.o --- [ 15%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /construction/biology/iqtree/.build/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/booster.dir/tree_utils.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/booster/tree_utils.c --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- --- lbfgsb/liblbfgsb.a --- [ 16%] 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 [ 16%] Built target lbfgsb --- gsl/CMakeFiles/gsl.dir/all --- /usr/bin/make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend --- gsl/CMakeFiles/gsl.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/gsl /construction/biology/iqtree/.build /construction/biology/iqtree/.build/gsl /construction/biology/iqtree/.build/gsl/CMakeFiles/gsl.dir/DependInfo.cmake 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 --- --- booster/CMakeFiles/booster.dir/all --- --- booster/libbooster.a --- [ 17%] Linking C static library libbooster.a cd /construction/biology/iqtree/.build/booster && /usr/local/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake --- gsl/CMakeFiles/gsl.dir/all --- [ 18%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/binomial_tpe.cpp --- booster/CMakeFiles/booster.dir/all --- cd /construction/biology/iqtree/.build/booster && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a [ 18%] Built target booster --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- /usr/bin/make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend --- yaml-cpp/CMakeFiles/yaml-cpp.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp /construction/biology/iqtree/.build /construction/biology/iqtree/.build/yaml-cpp /construction/biology/iqtree/.build/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake Scanning dependencies of target yaml-cpp /usr/bin/make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o --- [ 18%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/binary.cpp --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/multinomial.cpp.o --- --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/whtest_sub.c.o --- --- gsl/CMakeFiles/gsl.dir/all --- [ 18%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/multinomial.cpp --- whtest/CMakeFiles/whtest.dir/all --- [ 18%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/whtest_sub.c --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/pow_int.cpp.o --- [ 19%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/pow_int.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o --- [ 19%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/fastDNAparsimony.c --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/gauss.cpp.o --- [ 19%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/gauss.cpp --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/fastDNAparsimony.c:113: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o --- [ 19%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/gaussinv.cpp --- gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o --- [ 20%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /construction/biology/iqtree/.build/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/gsl/gausspdf.cpp --- gsl/libgsl.a --- [ 20%] 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 [ 20%] Built target gsl --- terraphast/CMakeFiles/terraphast.dir/all --- /usr/bin/make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend --- terraphast/CMakeFiles/terraphast.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast /construction/biology/iqtree/.build /construction/biology/iqtree/.build/terraphast /construction/biology/iqtree/.build/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake Scanning dependencies of target terraphast /usr/bin/make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build --- terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o --- [ 20%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/advanced.cpp --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o --- [ 20%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /construction/biology/iqtree/.build/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/whtest/whtest_wrapper.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o --- [ 21%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/convert.cpp --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o --- [ 22%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra/msetsblock.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/hardware.c.o --- [ 22%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/hardware.c --- pll/CMakeFiles/pll.dir/hash.c.o --- [ 23%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/hash.c --- pll/CMakeFiles/pll.dir/lexer.c.o --- [ 23%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/lexer.c --- pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o --- [ 24%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/makenewzGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/makenewzGenericSpecial.c:44: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pllavx.dir/all --- --- pll/libpllavx.a --- [ 25%] 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 [ 25%] Built target pllavx --- utils/CMakeFiles/utils.dir/all --- /usr/bin/make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend --- utils/CMakeFiles/utils.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/utils /construction/biology/iqtree/.build /construction/biology/iqtree/.build/utils /construction/biology/iqtree/.build/utils/CMakeFiles/utils.dir/DependInfo.cmake --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o --- [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsblock.cpp --- utils/CMakeFiles/utils.dir/all --- 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 --- [ 26%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/eigendecomposition.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o --- [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxscharactersblock.cpp --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/libwhtest.a --- [ 27%] 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 [ 27%] Built target whtest --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o --- [ 27%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra/msplitsblock.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o --- [ 27%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/directives.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/models.c.o --- [ 27%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/models.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/models.c:53: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o --- [ 27%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emit.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/gzstream.cpp.o --- [ 27%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/gzstream.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o --- [ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/bigint.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/optimization.cpp.o --- [ 29%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/optimization.cpp --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o --- [ 29%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra/modelsblock.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o --- [ 29%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/bipartitions.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o --- [ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emitfromevents.cpp --- 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 --- pda/CMakeFiles/pda.dir/all --- /usr/bin/make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend --- pda/CMakeFiles/pda.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/pda /construction/biology/iqtree/.build /construction/biology/iqtree/.build/pda /construction/biology/iqtree/.build/pda/CMakeFiles/pda.dir/DependInfo.cmake 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 --- --- pda/CMakeFiles/pda.dir/greedy.cpp.o --- --- pda/CMakeFiles/pda.dir/circularnetwork.cpp.o --- [ 32%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o --- pda/CMakeFiles/pda.dir/greedy.cpp.o --- [ 32%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/greedy.cpp --- pda/CMakeFiles/pda.dir/circularnetwork.cpp.o --- cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/circularnetwork.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/stoprule.cpp.o --- [ 32%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/stoprule.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o --- [ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/bitmatrix.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o --- [ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emitter.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o --- [ 33%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/clamped_uint.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/newick.c.o --- [ 34%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newick.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newick.c:36: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o --- [ 34%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newviewGenericSpecial.c --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o --- [ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/constraints.cpp --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newviewGenericSpecial.c:49: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o --- [ 34%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/gurobiwrapper.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o --- [ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emitterstate.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/tools.cpp.o --- [ 36%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/tools.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/hashsplitset.cpp.o --- [ 36%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/hashsplitset.cpp --- pda/CMakeFiles/pda.dir/pdnetwork.cpp.o --- [ 37%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/pdnetwork.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o --- [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/errors.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o --- [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/multitree.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o --- [ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsdatablock.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/pruning.cpp.o --- [ 38%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/pruning.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o --- [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/multitree_iterator.cpp --- terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o --- [ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/nodes.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/genericParallelization.c.o --- [ 39%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/genericParallelization.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/genericParallelization.c:43: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o --- [ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emitterutils.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o --- [ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsdiscretedatum.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/split.cpp.o --- [ 41%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/split.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/optimizeModel.c.o --- [ 42%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/optimizeModel.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/optimizeModel.c:47: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o --- [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/parser.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o --- [ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsdiscretematrix.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/splitgraph.cpp.o --- [ 42%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/splitgraph.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o --- [ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsdistancedatum.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/parsePartition.c.o --- [ 43%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/parsePartition.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/parsePartition.c:42: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/queue.c.o --- [ 44%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/queue.c --- pll/CMakeFiles/pll.dir/randomTree.c.o --- [ 44%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/randomTree.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/randomTree.c:37: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/recom.c.o --- [ 44%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/recom.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/recom.c:43: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/restartHashTable.c.o --- [ 45%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/restartHashTable.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/restartHashTable.c:47: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/searchAlgo.c.o --- [ 45%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/searchAlgo.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/searchAlgo.c:51: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o --- [ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsdistancesblock.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o --- [ 46%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/rooting.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/ssort.c.o --- [ 47%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/ssort.c --- pll/CMakeFiles/pll.dir/stack.c.o --- [ 47%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/stack.c --- pll/CMakeFiles/pll.dir/topologies.c.o --- [ 47%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/topologies.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/topologies.c:48: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/trash.c.o --- [ 48%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/trash.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/trash.c:48: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/treeIO.c.o --- [ 48%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/treeIO.c --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o --- [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/simple.cpp --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/treeIO.c:49: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/utils.c.o --- [ 49%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/utils.c --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/splitset.cpp.o --- [ 49%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/splitset.cpp --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/utils.c:70: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o --- [ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsemptyblock.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/lpwrapper.c.o --- [ 51%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /construction/biology/iqtree/.build/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/lpwrapper.c --- pda/CMakeFiles/pda.dir/ecopd.cpp.o --- [ 51%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/ecopd.cpp --- pll/CMakeFiles/pll.dir/all --- --- pll/libpll.a --- [ 51%] 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 [ 51%] Built target pll --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o --- [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/exceptions.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o --- [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsexception.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o --- [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/subtree_extraction.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o --- [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/exp.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o --- [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/memory.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o --- [ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsreader.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/graph.cpp.o --- [ 54%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/graph.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o --- [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/node.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/pdtree.cpp.o --- [ 55%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/pdtree.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o --- [ 55%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/supertree_helpers.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o --- [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/node_data.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o --- [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/nodebuilder.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o --- [ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxssetreader.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/pllnni.cpp.o --- [ 56%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/pllnni.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o --- [ 56%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/trees.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o --- [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/nodeevents.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o --- [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/null.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o --- [ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsstring.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o --- [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/ostream_wrapper.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/pdtreeset.cpp.o --- [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/pdtreeset.cpp --- pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o --- [ 59%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/ecopdmtreeset.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o --- [ 60%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/union_find.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o --- [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/parse.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o --- [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/parser.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o --- [ 61%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxstaxablock.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o --- [ 61%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /construction/biology/iqtree/.build/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/validation.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o --- [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/regex_yaml.cpp --- pda/CMakeFiles/pda.dir/all --- --- pda/libpda.a --- [ 62%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o --- [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/scanner.cpp --- pda/CMakeFiles/pda.dir/all --- /usr/bin/ranlib libpda.a [ 62%] Built target pda --- main/CMakeFiles/main.dir/all --- /usr/bin/make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend --- main/CMakeFiles/main.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/main /construction/biology/iqtree/.build /construction/biology/iqtree/.build/main /construction/biology/iqtree/.build/main/CMakeFiles/main.dir/DependInfo.cmake Scanning dependencies of target main /usr/bin/make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build --- main/CMakeFiles/main.dir/main.cpp.o --- [ 62%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /construction/biology/iqtree/.build/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/main.dir/main.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/main/main.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/checkpoint.cpp.o --- [ 62%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/checkpoint.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o --- [ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/scanscalar.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o --- [ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/scantag.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o --- [ 63%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxstoken.cpp --- ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o --- [ 63%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxstreesblock.cpp --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/libterraphast.a --- [ 64%] Linking CXX static library libterraphast.a cd /construction/biology/iqtree/.build/terraphast && /usr/local/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/terraphast && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a [ 64%] Built target terraphast --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/MPIHelper.cpp.o --- [ 65%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /construction/biology/iqtree/.build/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/utils/MPIHelper.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o --- [ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/scantoken.cpp --- utils/CMakeFiles/utils.dir/all --- --- utils/libutils.a --- [ 65%] 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 [ 65%] Built target utils --- model/CMakeFiles/model.dir/all --- /usr/bin/make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend --- model/CMakeFiles/model.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/model /construction/biology/iqtree/.build /construction/biology/iqtree/.build/model /construction/biology/iqtree/.build/model/CMakeFiles/model.dir/DependInfo.cmake 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 --- [ 66%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o --- [ 67%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/simplekey.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/libncl.a --- [ 68%] 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 [ 68%] Built target ncl --- alignment/CMakeFiles/alignment.dir/all --- /usr/bin/make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend --- alignment/CMakeFiles/alignment.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/alignment /construction/biology/iqtree/.build /construction/biology/iqtree/.build/alignment /construction/biology/iqtree/.build/alignment/CMakeFiles/alignment.dir/DependInfo.cmake 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 --- [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/pattern.cpp --- model/CMakeFiles/model.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o --- [ 68%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/singledocparser.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o --- [ 69%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/stream.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/alignment.cpp.o --- [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/alignment.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o --- [ 69%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/tag.cpp --- model/CMakeFiles/model.dir/all --- /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1403:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ --- model/CMakeFiles/model.dir/modelbin.cpp.o --- --- model/CMakeFiles/model.dir/modeldna.cpp.o --- --- model/CMakeFiles/model.dir/modelmarkov.cpp.o --- /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1458:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1487:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1504:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ --- model/CMakeFiles/model.dir/modelbin.cpp.o --- [ 69%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o --- model/CMakeFiles/model.dir/modeldna.cpp.o --- [ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o --- model/CMakeFiles/model.dir/modelbin.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelbin.cpp --- model/CMakeFiles/model.dir/modeldna.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o --- [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/alignmentpairwise.cpp --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/libyaml-cpp.a --- [ 71%] Linking CXX static library libyaml-cpp.a cd /construction/biology/iqtree/.build/yaml-cpp && /usr/local/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/yaml-cpp && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a CMakeFiles/yaml-cpp.dir/src/binary.cpp.o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o CMakeFiles/yaml-cpp.dir/src/node.cpp.o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o CMakeFiles/yaml-cpp.dir/src/null.cpp.o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o /usr/bin/ranlib libyaml-cpp.a [ 71%] Built target yaml-cpp --- phylo-yaml/CMakeFiles/phyloYAML.dir/all --- /usr/bin/make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend --- phylo-yaml/CMakeFiles/phyloYAML.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/phylo-yaml /construction/biology/iqtree/.build /construction/biology/iqtree/.build/phylo-yaml /construction/biology/iqtree/.build/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake Scanning dependencies of target phyloYAML /usr/bin/make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build --- phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o --- [ 72%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /construction/biology/iqtree/.build/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/phylo-yaml/statespace.cpp --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/phyloanalysis.cpp.o --- [ 73%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /construction/biology/iqtree/.build/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp --- model/CMakeFiles/model.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelDNA::readRates(string str) throw(const char*) { ^~~~~ --- model/CMakeFiles/model.dir/modelbin.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelbin.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelbin.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelfactory.cpp.o --- [ 74%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp --- main/CMakeFiles/main.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp:37: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp:38: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp:46: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/maalignment.cpp.o --- [ 74%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/maalignment.cpp --- model/CMakeFiles/model.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:24: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:26: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:27: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:30: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/alignment.cpp.o --- /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { ^~~~~ --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/modelprotein.cpp.o --- [ 74%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelProtein::readRates(istream &in) throw(const char*, string) { ^~~~~ --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignment.cpp.o --- [ 75%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/superalignment.cpp --- phylo-yaml/CMakeFiles/phyloYAML.dir/all --- --- phylo-yaml/libphyloYAML.a --- [ 75%] Linking CXX static library libphyloYAML.a cd /construction/biology/iqtree/.build/phylo-yaml && /usr/local/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/phylo-yaml && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a [ 75%] Built target phyloYAML --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o --- [ 75%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/superalignmentpairwise.cpp --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/modelset.cpp.o --- [ 76%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelset.cpp In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelset.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelset.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelsubst.cpp.o --- [ 76%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelsubst.cpp --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o --- [ 76%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/superalignmentpairwiseplen.cpp --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/partitionmodel.cpp.o --- [ 76%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/partitionmodel.cpp --- model/CMakeFiles/model.dir/partitionmodelplen.cpp.o --- [ 77%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/partitionmodelplen.cpp --- CMakeFiles/kernelsse.dir/all --- --- libkernelsse.a --- [ 78%] 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 [ 78%] Built target kernelsse --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o --- [ 79%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /construction/biology/iqtree/.build/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/alignment/superalignmentunlinked.cpp --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/partitionmodel.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/partitionmodel.cpp:23: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/partitionmodelplen.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/partitionmodelplen.cpp:12: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- CMakeFiles/kernelfma.dir/all --- --- libkernelfma.a --- [ 79%] 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 [ 79%] Built target kernelfma --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- --- main/CMakeFiles/main.dir/treetesting.cpp.o --- --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- [ 79%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /construction/biology/iqtree/.build/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/main.dir/phylotesting.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp --- main/CMakeFiles/main.dir/treetesting.cpp.o --- [ 79%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /construction/biology/iqtree/.build/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/main.dir/treetesting.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/main/treetesting.cpp --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/rategamma.cpp.o --- [ 79%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rategamma.cpp --- model/CMakeFiles/model.dir/rategammainvar.cpp.o --- [ 80%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rategammainvar.cpp --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:21: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- main/CMakeFiles/main.dir/timetree.cpp.o --- --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:22: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ --- main/CMakeFiles/main.dir/timetree.cpp.o --- [ 81%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /construction/biology/iqtree/.build/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/main.dir/timetree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/main/timetree.cpp --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:31: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:34: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp: In function 'std::__cxx11::string getSeqTypeName(PML::SeqType)': /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp: In member function 'double CandidateModel::getScore(ModelTestCriterion)': /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/rateheterogeneity.cpp.o --- --- model/CMakeFiles/model.dir/rateinvar.cpp.o --- --- model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o --- --- model/CMakeFiles/model.dir/rateinvar.cpp.o --- [ 82%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o --- model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o --- [ 82%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o --- model/CMakeFiles/model.dir/rateinvar.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rateinvar.cpp --- model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratemeyerdiscrete.cpp --- model/CMakeFiles/model.dir/rateheterogeneity.cpp.o --- [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rateheterogeneity.cpp --- model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o --- [ 82%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratemeyerhaeseler.cpp --- model/CMakeFiles/model.dir/ratekategory.cpp.o --- --- model/CMakeFiles/model.dir/ratefree.cpp.o --- --- model/CMakeFiles/model.dir/ratefreeinvar.cpp.o --- --- model/CMakeFiles/model.dir/ratekategory.cpp.o --- [ 83%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratekategory.cpp --- model/CMakeFiles/model.dir/ratefree.cpp.o --- [ 83%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o --- model/CMakeFiles/model.dir/ratefreeinvar.cpp.o --- [ 83%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o --- model/CMakeFiles/model.dir/ratefree.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratefree.cpp --- model/CMakeFiles/model.dir/ratefreeinvar.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratefreeinvar.cpp --- CMakeFiles/kernelavx.dir/all --- --- libkernelavx.a --- [ 83%] Linking CXX static library libkernelavx.a /usr/local/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/local/bin/cmake -E cmake_link_script CMakeFiles/kernelavx.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelavx.a CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/ranlib libkernelavx.a [ 83%] Built target kernelavx --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/rateheterotachy.cpp.o --- --- model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o --- --- model/CMakeFiles/model.dir/rateheterotachy.cpp.o --- [ 84%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o --- model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o --- [ 84%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o --- model/CMakeFiles/model.dir/rateheterotachy.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rateheterotachy.cpp --- model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o --- cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rateheterotachyinvar.cpp --- model/CMakeFiles/model.dir/modelcodon.cpp.o --- [ 85%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelcodon.cpp --- model/CMakeFiles/model.dir/ratefree.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratefree.cpp:13: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelmorphology.cpp.o --- [ 85%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.cpp --- model/CMakeFiles/model.dir/modelmixture.cpp.o --- [ 85%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.cpp --- model/CMakeFiles/model.dir/modelunrest.cpp.o --- [ 86%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelunrest.cpp --- model/CMakeFiles/model.dir/modelliemarkov.cpp.o --- [ 86%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelliemarkov.cpp --- model/CMakeFiles/model.dir/modelcodon.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelcodon.h:11, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelcodon.cpp:8: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelmorphology.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:11, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.cpp:8: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.cpp:8: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMorphology::readRates(istream &in) throw(const char*, string) { ^~~~~ --- model/CMakeFiles/model.dir/modelunrest.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelunrest.h:11, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelunrest.cpp:8: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelpomo.cpp.o --- [ 87%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.cpp --- model/CMakeFiles/model.dir/modelpomomixture.cpp.o --- [ 87%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.cpp --- model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o --- [ 87%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactorymixlen.cpp --- model/CMakeFiles/model.dir/modelmixture.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.cpp:8: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.cpp:9: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.cpp:10: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.cpp:13: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- model/CMakeFiles/model.dir/modelpomomixture.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.h:14, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.cpp:9: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.h:14, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.cpp:9: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelpomo.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.cpp:1: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.cpp:1: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelliemarkov.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelliemarkov.h:11, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelliemarkov.cpp:23: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactorymixlen.cpp:12: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- main/CMakeFiles/main.dir/all --- --- main/libmain.a --- [ 87%] Linking CXX static library libmain.a cd /construction/biology/iqtree/.build/main && /usr/local/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/main && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o /usr/bin/ranlib libmain.a [ 87%] Built target main --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/libalignment.a --- [ 87%] Linking CXX static library libalignment.a cd /construction/biology/iqtree/.build/alignment && /usr/local/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/alignment && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o /usr/bin/ranlib libalignment.a [ 87%] Built target alignment --- model/CMakeFiles/model.dir/all --- --- model/libmodel.a --- [ 88%] Linking CXX static library libmodel.a cd /construction/biology/iqtree/.build/model && /usr/local/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/model && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/model.dir/link.txt --verbose=1 /usr/bin/ar qc libmodel.a CMakeFiles/model.dir/modelmarkov.cpp.o CMakeFiles/model.dir/modelbin.cpp.o CMakeFiles/model.dir/modeldna.cpp.o CMakeFiles/model.dir/modelfactory.cpp.o CMakeFiles/model.dir/modelprotein.cpp.o CMakeFiles/model.dir/modelset.cpp.o CMakeFiles/model.dir/modelsubst.cpp.o CMakeFiles/model.dir/partitionmodel.cpp.o CMakeFiles/model.dir/partitionmodelplen.cpp.o CMakeFiles/model.dir/rategamma.cpp.o CMakeFiles/model.dir/rategammainvar.cpp.o CMakeFiles/model.dir/rateheterogeneity.cpp.o CMakeFiles/model.dir/rateinvar.cpp.o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o CMakeFiles/model.dir/ratekategory.cpp.o CMakeFiles/model.dir/ratefree.cpp.o CMakeFiles/model.dir/ratefreeinvar.cpp.o CMakeFiles/model.dir/rateheterotachy.cpp.o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o CMakeFiles/model.dir/modelcodon.cpp.o CMakeFiles/model.dir/modelmorphology.cpp.o CMakeFiles/model.dir/modelmixture.cpp.o CMakeFiles/model.dir/modelunrest.cpp.o CMakeFiles/model.dir/modelliemarkov.cpp.o CMakeFiles/model.dir/modelpomo.cpp.o CMakeFiles/model.dir/modelpomomixture.cpp.o CMakeFiles/model.dir/modelfactorymixlen.cpp.o /usr/bin/ranlib libmodel.a [ 88%] Built target model --- tree/CMakeFiles/tree.dir/all --- /usr/bin/make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend --- tree/CMakeFiles/tree.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/tree /construction/biology/iqtree/.build /construction/biology/iqtree/.build/tree /construction/biology/iqtree/.build/tree/CMakeFiles/tree.dir/DependInfo.cmake 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/mexttree.cpp.o --- --- tree/CMakeFiles/tree.dir/mtree.cpp.o --- --- tree/CMakeFiles/tree.dir/mtreeset.cpp.o --- --- tree/CMakeFiles/tree.dir/ncbitree.cpp.o --- --- tree/CMakeFiles/tree.dir/node.cpp.o --- --- tree/CMakeFiles/tree.dir/iqtree.cpp.o --- [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o --- tree/CMakeFiles/tree.dir/mtree.cpp.o --- [ 89%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o --- tree/CMakeFiles/tree.dir/candidateset.cpp.o --- [ 89%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o --- tree/CMakeFiles/tree.dir/mtree.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/mtree.cpp --- tree/CMakeFiles/tree.dir/iqtree.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/iqtree.cpp --- tree/CMakeFiles/tree.dir/candidateset.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/candidateset.cpp --- tree/CMakeFiles/tree.dir/memslot.cpp.o --- [ 90%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o --- tree/CMakeFiles/tree.dir/mexttree.cpp.o --- [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o --- tree/CMakeFiles/tree.dir/memslot.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/memslot.cpp --- tree/CMakeFiles/tree.dir/mexttree.cpp.o --- cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/mexttree.cpp --- tree/CMakeFiles/tree.dir/matree.cpp.o --- [ 90%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/matree.cpp --- tree/CMakeFiles/tree.dir/mtreeset.cpp.o --- [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/mtreeset.cpp --- tree/CMakeFiles/tree.dir/constrainttree.cpp.o --- [ 91%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/constrainttree.cpp --- tree/CMakeFiles/tree.dir/node.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/node.cpp --- tree/CMakeFiles/tree.dir/ncbitree.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/ncbitree.cpp --- tree/CMakeFiles/tree.dir/iqtree.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/iqtree.cpp:29: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/phylonode.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylonode.cpp --- tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o --- [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylonodemixlen.cpp --- tree/CMakeFiles/tree.dir/phylosupertree.cpp.o --- [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylosupertree.cpp --- tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o --- [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylosupertreeplen.cpp --- tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o --- [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylosupertreeunlinked.cpp --- tree/CMakeFiles/tree.dir/phylotree.cpp.o --- [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp --- tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o --- [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreemixlen.cpp --- tree/CMakeFiles/tree.dir/phylotreepars.cpp.o --- [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreepars.cpp --- tree/CMakeFiles/tree.dir/phylotree.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp:34: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/phylotreesse.cpp.o --- [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreesse.cpp --- tree/CMakeFiles/tree.dir/quartet.cpp.o --- [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/quartet.cpp --- tree/CMakeFiles/tree.dir/supernode.cpp.o --- [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/supernode.cpp --- tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreemixlen.cpp:12: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/phylotree.cpp.o --- /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp: In function 'std::__cxx11::string getASCName(ASCType)': /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ --- tree/CMakeFiles/tree.dir/phylotreesse.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreesse.cpp:35: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/tinatree.cpp.o --- [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/tinatree.cpp --- tree/CMakeFiles/tree.dir/parstree.cpp.o --- [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/parstree.cpp --- tree/CMakeFiles/tree.dir/discordance.cpp.o --- [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/discordance.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/discordance.cpp --- tree/libtree.a --- [ 98%] Linking CXX static library libtree.a cd /construction/biology/iqtree/.build/tree && /usr/local/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/tree && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a [ 98%] Built target tree --- terrace/CMakeFiles/terrace.dir/all --- /usr/bin/make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend --- terrace/CMakeFiles/terrace.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/terrace /construction/biology/iqtree/.build /construction/biology/iqtree/.build/terrace /construction/biology/iqtree/.build/terrace/CMakeFiles/terrace.dir/DependInfo.cmake Scanning dependencies of target terrace /usr/bin/make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build --- terrace/CMakeFiles/terrace.dir/terrace.cpp.o --- [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /construction/biology/iqtree/.build/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/terrace.dir/terrace.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/terrace/terrace.cpp --- terrace/libterrace.a --- [ 99%] Linking CXX static library libterrace.a cd /construction/biology/iqtree/.build/terrace && /usr/local/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/terrace && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a [ 99%] Built target terrace --- CMakeFiles/iqtree2.dir/all --- /usr/bin/make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend --- CMakeFiles/iqtree2.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/iqtree2.dir/DependInfo.cmake Scanning dependencies of target iqtree2 /usr/bin/make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build --- CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o --- [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/include -I/construction/biology/iqtree/IQ-TREE-2.0.6/terraphast/lib/gcc_clang -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/obsolete/parsmultistate.cpp --- iqtree2 --- [100%] Linking CXX executable iqtree2 /usr/local/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -rdynamic -Wl,--gc-sections CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/construction/biology/iqtree/IQ-TREE-2.0.6/lib -Wl,-z,origin,-rpath,/construction/biology/iqtree/IQ-TREE-2.0.6/lib -lexecinfo booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a strip /construction/biology/iqtree/.build/iqtree2 [100%] Built target iqtree2 /usr/local/bin/cmake -E cmake_progress_start /construction/biology/iqtree/.build/CMakeFiles 0 SUCCEEDED 00:05:26 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for iqtree-2.0.6 ===> Generating temporary packing list install -s -m 555 /construction/biology/iqtree/.build/iqtree2 /construction/biology/iqtree/stage/usr/local/bin/iqtree install -m 0644 /construction/biology/iqtree/IQ-TREE-2.0.6/example/* /construction/biology/iqtree/stage/usr/local/share/examples/iqtree ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for iqtree-2.0.6 file sizes/checksums [5]: 0% file sizes/checksums [5]: 100% packing files [5]: 0% packing files [5]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:09 TOTAL TIME 00:06:03