------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/libnghttp2-1.41.0.txz Installing /packages/All/ca_root_nss-3.53.txz ===== Message from ca_root_nss-3.53: -- 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-7.70.0_1.txz Installing /packages/All/expat-2.2.8.txz Installing /packages/All/jsoncpp-1.9.2.txz Installing /packages/All/libuv-1.38.0.txz Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.2.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-6.1.20190525.txz Installing /packages/All/cmake-3.17.3.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 00:00:24 ------------------------------------------------------------------------------- -- 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 => Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://codeload.github.com/Cibiv/IQ-TREE/tar.gz/v2.0.6?dummy=/Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz fetch: https://codeload.github.com/Cibiv/IQ-TREE/tar.gz/v2.0.6?dummy=/Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz: size unknown fetch: https://codeload.github.com/Cibiv/IQ-TREE/tar.gz/v2.0.6?dummy=/Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz: size of remote file is not known Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz 0 B 0 Bps Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz 48 kB 395 kBps Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz 1824 kB 1752 kBps Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz 5142 kB 2714 kBps 02s => Fetched file size mismatch (expected 5265191, actual 5265764) => Trying next site => Attempting to fetch http://distcache.FreeBSD.org/ports-distfiles/Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz 0% of 5141 kB 0 Bps Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz 10% of 5141 kB 821 kBps Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz 61% of 5141 kB 2706 kBps Cibiv-IQ-TREE-v2.0.6_GH0.tar.gz 5141 kB 2500 kBps 02s ===> Fetching all distfiles required by iqtree-2.0.6 for building SUCCEEDED 00:00:05 ------------------------------------------------------------------------------- -- 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 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc - works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ - works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- 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 00:00:05 ------------------------------------------------------------------------------- -- 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 --- --- nclextra/CMakeFiles/nclextra.dir/all --- --- ncl/CMakeFiles/ncl.dir/all --- --- pll/CMakeFiles/pllavx.dir/all --- --- pll/CMakeFiles/pll.dir/all --- --- whtest/CMakeFiles/whtest.dir/all --- --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- --- CMakeFiles/kernelavx.dir/all --- /usr/bin/make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.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 --- nclextra/CMakeFiles/nclextra.dir/all --- /usr/bin/make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend --- ncl/CMakeFiles/ncl.dir/all --- /usr/bin/make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend --- pll/CMakeFiles/pllavx.dir/all --- /usr/bin/make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend --- pll/CMakeFiles/pll.dir/all --- /usr/bin/make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend --- whtest/CMakeFiles/whtest.dir/all --- /usr/bin/make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- /usr/bin/make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend --- CMakeFiles/kernelfma.dir/all --- /usr/bin/make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/depend --- --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelavx.dir/depend --- --- booster/CMakeFiles/booster.dir/all --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/booster /construction/biology/iqtree/.build /construction/biology/iqtree/.build/booster /construction/biology/iqtree/.build/booster/CMakeFiles/booster.dir/DependInfo.cmake --- CMakeFiles/kernelfma.dir/all --- --- CMakeFiles/kernelfma.dir/depend --- --- CMakeFiles/kernelavx.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 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelavx.dir/DependInfo.cmake --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/depend --- --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/depend --- --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/depend --- --- CMakeFiles/kernelfma.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 /construction/biology/iqtree/.build /construction/biology/iqtree/.build /construction/biology/iqtree/.build/CMakeFiles/kernelfma.dir/DependInfo.cmake --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- --- lbfgsb/CMakeFiles/lbfgsb.dir/depend --- --- ncl/CMakeFiles/ncl.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/ncl /construction/biology/iqtree/.build /construction/biology/iqtree/.build/ncl /construction/biology/iqtree/.build/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --- pll/CMakeFiles/pll.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/pll.dir/DependInfo.cmake --- nclextra/CMakeFiles/nclextra.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/nclextra /construction/biology/iqtree/.build /construction/biology/iqtree/.build/nclextra /construction/biology/iqtree/.build/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --- lbfgsb/CMakeFiles/lbfgsb.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/lbfgsb /construction/biology/iqtree/.build /construction/biology/iqtree/.build/lbfgsb /construction/biology/iqtree/.build/lbfgsb/CMakeFiles/lbfgsb.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 --- pll/CMakeFiles/pllavx.dir/all --- --- pll/CMakeFiles/pllavx.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/pllavx.dir/DependInfo.cmake --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- Scanning dependencies of target lbfgsb /usr/bin/make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build --- whtest/CMakeFiles/whtest.dir/all --- --- 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 --- pll/CMakeFiles/pllavx.dir/all --- Scanning dependencies of target pllavx --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- --- lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o --- --- nclextra/CMakeFiles/nclextra.dir/all --- Scanning dependencies of target nclextra --- pll/CMakeFiles/pllavx.dir/all --- /usr/bin/make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build --- nclextra/CMakeFiles/nclextra.dir/all --- /usr/bin/make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- [ 0%] 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 --- ncl/CMakeFiles/ncl.dir/all --- Scanning dependencies of target ncl --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o --- --- ncl/CMakeFiles/ncl.dir/all --- /usr/bin/make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build --- pll/CMakeFiles/pllavx.dir/all --- --- pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o --- --- nclextra/CMakeFiles/nclextra.dir/all --- [ 0%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /construction/biology/iqtree/.build/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/nclextra/mpdablock.cpp --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o --- --- pll/CMakeFiles/pllavx.dir/all --- [ 0%] 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 --- pll/CMakeFiles/pll.dir/all --- Scanning dependencies of target pll --- CMakeFiles/kernelfma.dir/all --- Scanning dependencies of target kernelfma --- pll/CMakeFiles/pll.dir/all --- /usr/bin/make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build --- CMakeFiles/kernelfma.dir/all --- /usr/bin/make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build --- whtest/CMakeFiles/whtest.dir/all --- Scanning dependencies of target whtest --- ncl/CMakeFiles/ncl.dir/all --- [ 0%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o --- whtest/CMakeFiles/whtest.dir/all --- /usr/bin/make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build --- ncl/CMakeFiles/ncl.dir/all --- cd /construction/biology/iqtree/.build/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/ncl/nxsassumptionsblock.cpp --- booster/CMakeFiles/booster.dir/all --- Scanning dependencies of target booster --- CMakeFiles/kernelavx.dir/all --- Scanning dependencies of target kernelavx --- booster/CMakeFiles/booster.dir/all --- /usr/bin/make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build --- CMakeFiles/kernelavx.dir/all --- /usr/bin/make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build --- CMakeFiles/kernelsse.dir/all --- Scanning dependencies of target kernelsse /usr/bin/make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/alignment.c.o --- --- CMakeFiles/kernelfma.dir/all --- --- CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o --- --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/bitset_index.c.o --- --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/eigen.c.o --- --- CMakeFiles/kernelavx.dir/all --- --- CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o --- --- pll/CMakeFiles/pll.dir/all --- [ 0%] 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/kernelfma.dir/all --- [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o --- CMakeFiles/kernelsse.dir/all --- --- CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o --- --- CMakeFiles/kernelfma.dir/all --- /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylokernelfma.cpp --- CMakeFiles/kernelsse.dir/all --- [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o --- whtest/CMakeFiles/whtest.dir/all --- [ 3%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o --- booster/CMakeFiles/booster.dir/all --- [ 3%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.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 --- booster/CMakeFiles/booster.dir/all --- 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 --- whtest/CMakeFiles/whtest.dir/all --- 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 --- 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 --- 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); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/bipartitionList.c.o --- [ 5%] 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 --- 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 --- pll/CMakeFiles/pll.dir/all --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/bipartitionList.c:49: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- booster/CMakeFiles/booster.dir/all --- --- 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 --- booster/CMakeFiles/booster.dir/sort.c.o --- [ 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 --- booster/CMakeFiles/booster.dir/tree.c.o --- [ 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o --- [ 6%] 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 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); ^~~~~~~~~~~~~~~ --- 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); ^~~~~~~~~~~~~~~ --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/booster.c.o --- [ 7%] 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); ~~~~~~^~~~~~~~ --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/eigen_sym.c.o --- [ 7%] 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o --- [ 8%] 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 --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/hashtables_bfields.c.o --- --- 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); ^~~~~~~~~~~~~~~ --- booster/CMakeFiles/booster.dir/all --- [ 8%] 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/random.c.o --- [ 8%] 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 --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/prng.c.o --- [ 8%] 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 --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/weisslambda.c.o --- --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/stats.c.o --- --- whtest/CMakeFiles/whtest.dir/all --- [ 9%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o --- booster/CMakeFiles/booster.dir/all --- [ 10%] 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 --- 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 --- whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o --- [ 10%] 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 --- whtest/CMakeFiles/whtest.dir/whtest.c.o --- [ 11%] 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o --- [ 11%] 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 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); ^~~~~~~~~~~~~~~ --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/whtest_sub.c.o --- --- booster/CMakeFiles/booster.dir/all --- --- booster/CMakeFiles/booster.dir/tree_utils.c.o --- --- whtest/CMakeFiles/whtest.dir/all --- [ 11%] 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 --- booster/CMakeFiles/booster.dir/all --- [ 11%] 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 --- booster/libbooster.a --- [ 12%] Linking C static library libbooster.a cd /construction/biology/iqtree/.build/booster && /usr/local/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/booster && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a [ 12%] Built target booster --- gsl/CMakeFiles/gsl.dir/all --- /usr/bin/make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend --- gsl/CMakeFiles/gsl.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/gsl /construction/biology/iqtree/.build /construction/biology/iqtree/.build/gsl /construction/biology/iqtree/.build/gsl/CMakeFiles/gsl.dir/DependInfo.cmake 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 --- [ 13%] 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 --- gsl/CMakeFiles/gsl.dir/multinomial.cpp.o --- [ 13%] 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 --- pll/CMakeFiles/pllavx.dir/all --- --- pll/libpllavx.a --- [ 14%] 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 --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/pow_int.cpp.o --- --- pll/CMakeFiles/pllavx.dir/all --- [ 14%] Built target pllavx --- vectorclass/CMakeFiles/vectorclass.dir/all --- /usr/bin/make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend --- vectorclass/CMakeFiles/vectorclass.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/vectorclass /construction/biology/iqtree/.build /construction/biology/iqtree/.build/vectorclass /construction/biology/iqtree/.build/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --- gsl/CMakeFiles/gsl.dir/all --- [ 15%] 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 --- 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 --- vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o --- [ 16%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /construction/biology/iqtree/.build/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/vectorclass/instrset_detect.cpp --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/gauss.cpp.o --- [ 16%] 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 --- gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o --- [ 16%] 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 --- vectorclass/CMakeFiles/vectorclass.dir/all --- --- vectorclass/libvectorclass.a --- [ 16%] Linking CXX static library libvectorclass.a cd /construction/biology/iqtree/.build/vectorclass && /usr/local/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/vectorclass && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o --- --- vectorclass/CMakeFiles/vectorclass.dir/all --- /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a --- gsl/CMakeFiles/gsl.dir/all --- [ 17%] 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 --- vectorclass/CMakeFiles/vectorclass.dir/all --- [ 17%] Built target vectorclass --- sprng/CMakeFiles/sprng.dir/all --- /usr/bin/make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend --- sprng/CMakeFiles/sprng.dir/depend --- cd /construction/biology/iqtree/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /construction/biology/iqtree/IQ-TREE-2.0.6 /construction/biology/iqtree/IQ-TREE-2.0.6/sprng /construction/biology/iqtree/.build /construction/biology/iqtree/.build/sprng /construction/biology/iqtree/.build/sprng/CMakeFiles/sprng.dir/DependInfo.cmake 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 --- [ 18%] 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 --- gsl/CMakeFiles/gsl.dir/all --- --- gsl/libgsl.a --- [ 18%] 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 [ 18%] Built target gsl --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o --- [ 18%] 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 --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/makeseed.c.o --- [ 18%] 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 --- sprng/CMakeFiles/sprng.dir/memory.c.o --- [ 18%] 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 --- sprng/CMakeFiles/sprng.dir/store.c.o --- [ 19%] 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 --- lbfgsb/CMakeFiles/lbfgsb.dir/all --- --- lbfgsb/liblbfgsb.a --- [ 20%] 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 [ 20%] Built target lbfgsb --- 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 --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o --- [ 20%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- 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 --- sprng/CMakeFiles/sprng.dir/all --- 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o --- [ 20%] 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 --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/CMakeFiles/sprng.dir/checkid.c.o --- [ 21%] 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/pll.dir/all --- --- pll/CMakeFiles/pll.dir/hardware.c.o --- [ 21%] 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 --- sprng/CMakeFiles/sprng.dir/all --- --- sprng/libsprng.a --- [ 21%] 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/hash.c.o --- [ 22%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /construction/biology/iqtree/.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 --- sprng/CMakeFiles/sprng.dir/all --- [ 22%] Built target sprng --- 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 --- [ 22%] 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/lexer.c.o --- [ 22%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o --- [ 23%] 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 --- pll/CMakeFiles/pll.dir/all --- --- 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 --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o --- [ 25%] 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 --- pll/CMakeFiles/pll.dir/all --- 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); ^~~~~~~~~~~~~~~ --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o --- [ 25%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o --- [ 25%] 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 --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o --- [ 26%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o --- [ 27%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /construction/biology/iqtree/.build/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -std=gnu++11 -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/src/emitfromevents.cpp --- whtest/CMakeFiles/whtest.dir/all --- --- whtest/libwhtest.a --- [ 28%] Linking CXX static library libwhtest.a cd /construction/biology/iqtree/.build/whtest && /usr/local/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/whtest && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/whtest.dir/link.txt --verbose=1 /usr/bin/ar qc libwhtest.a CMakeFiles/whtest.dir/eigen.c.o CMakeFiles/whtest.dir/eigen_sym.c.o CMakeFiles/whtest.dir/random.c.o CMakeFiles/whtest.dir/weisslambda.c.o CMakeFiles/whtest.dir/weisslambda_sub.c.o CMakeFiles/whtest.dir/whtest.c.o CMakeFiles/whtest.dir/whtest_sub.c.o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o /usr/bin/ranlib libwhtest.a --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o --- [ 28%] 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 --- [ 28%] Built target whtest --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o --- [ 29%] 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/models.c.o --- [ 29%] 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); ^~~~~~~~~~~~~~~ --- 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/emitter.cpp.o --- [ 29%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o --- [ 30%] 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 --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o --- [ 30%] 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 --- terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o --- [ 31%] 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 --- terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o --- [ 31%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o --- [ 31%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o --- [ 31%] 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 --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o --- [ 32%] 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 --- [ 32%] 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 --- terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o --- [ 32%] 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 --- [ 33%] 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 --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o --- [ 33%] 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 --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o --- [ 33%] 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 --- terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o --- [ 34%] 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 --- terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o --- [ 34%] 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 --- --- pll/CMakeFiles/pll.dir/newick.c.o --- --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o --- [ 34%] 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 --- pll/CMakeFiles/pll.dir/all --- [ 35%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newick.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newick.c:36: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o --- [ 35%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /construction/biology/iqtree/.build/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newviewGenericSpecial.c In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/pll/newviewGenericSpecial.c:49: /construction/biology/iqtree/IQ-TREE-2.0.6/pll/pllInternal.h:150:30: warning: inline function 'bitcount_64_bit' declared but never defined extern __inline unsigned int bitcount_64_bit(uint64_t i); ^~~~~~~~~~~~~~~ --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o --- [ 36%] 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 --- terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o --- [ 36%] 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 --- terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o --- [ 36%] 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 --- terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o --- [ 37%] 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 --- nclextra/CMakeFiles/nclextra.dir/all --- --- nclextra/libnclextra.a --- [ 38%] 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 [ 38%] Built target nclextra --- terraphast/CMakeFiles/terraphast.dir/all --- --- terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o --- [ 38%] 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/exp.cpp.o --- [ 39%] 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 --- [ 39%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o --- [ 40%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o --- [ 40%] 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 --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o --- [ 40%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o --- [ 40%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o --- [ 41%] 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/genericParallelization.c.o --- [ 41%] 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/null.cpp.o --- [ 41%] 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/nxsdiscretedatum.cpp.o --- [ 42%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o --- [ 43%] 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/optimizeModel.c.o --- [ 44%] 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/libterraphast.a --- [ 45%] 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 [ 45%] Built target terraphast --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o --- [ 45%] 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 --- [ 45%] 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/nxsdiscretematrix.cpp.o --- [ 45%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o --- [ 46%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o --- [ 46%] 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/parsePartition.c.o --- [ 46%] 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 --- [ 47%] 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 --- [ 47%] 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 --- [ 47%] 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 --- [ 48%] 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 --- [ 48%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o --- [ 49%] 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 --- pll/CMakeFiles/pll.dir/all --- 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); ^~~~~~~~~~~~~~~ --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o --- [ 49%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o --- [ 49%] 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 --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o --- [ 50%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o --- [ 51%] 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/CMakeFiles/pll.dir/ssort.c.o --- [ 52%] 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 --- [ 52%] 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 --- [ 52%] 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 --- [ 53%] 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 --- [ 53%] 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 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 --- [ 54%] 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 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/nxsdistancesblock.cpp.o --- [ 54%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o --- [ 54%] 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 --- pll/CMakeFiles/pll.dir/all --- --- pll/libpll.a --- [ 54%] 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 [ 54%] Built target pll --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o --- [ 55%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o --- [ 55%] 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 --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o --- [ 56%] 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 --- ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o --- [ 56%] 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 --- ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o --- [ 56%] 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 --- ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o --- [ 57%] 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 --- 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 --- ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o --- [ 58%] 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 --- ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o --- [ 58%] 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 --- [ 58%] 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 --- 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 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 --- [ 58%] 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 --- 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 --- [ 58%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /construction/biology/iqtree/.build/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/pda/circularnetwork.cpp --- pda/CMakeFiles/pda.dir/greedy.cpp.o --- [ 59%] 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/gurobiwrapper.cpp.o --- [ 59%] 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 --- pda/CMakeFiles/pda.dir/hashsplitset.cpp.o --- [ 59%] 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 --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/gzstream.cpp.o --- [ 59%] 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 --- ncl/CMakeFiles/ncl.dir/all --- --- ncl/libncl.a --- [ 60%] 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 [ 60%] Built target ncl --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/pdnetwork.cpp.o --- [ 61%] 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 --- pda/CMakeFiles/pda.dir/pruning.cpp.o --- [ 61%] 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 --- yaml-cpp/CMakeFiles/yaml-cpp.dir/all --- --- yaml-cpp/libyaml-cpp.a --- [ 62%] 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 [ 62%] Built target yaml-cpp --- 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 --- [ 62%] 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 --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/optimization.cpp.o --- [ 63%] 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 --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/split.cpp.o --- [ 64%] 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 --- pda/CMakeFiles/pda.dir/splitgraph.cpp.o --- [ 64%] 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 --- pda/CMakeFiles/pda.dir/splitset.cpp.o --- [ 64%] 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 --- pda/CMakeFiles/pda.dir/lpwrapper.c.o --- [ 65%] 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 --- [ 65%] 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 --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/stoprule.cpp.o --- [ 65%] 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 --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/graph.cpp.o --- [ 66%] 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 --- pda/CMakeFiles/pda.dir/pdtree.cpp.o --- [ 66%] 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 --- pda/CMakeFiles/pda.dir/pdtreeset.cpp.o --- [ 66%] 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 --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/alignment.cpp.o --- [ 66%] 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 --- pda/CMakeFiles/pda.dir/all --- --- pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o --- [ 67%] 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 --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/tools.cpp.o --- [ 68%] 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 --- utils/CMakeFiles/utils.dir/pllnni.cpp.o --- [ 68%] 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 --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o --- [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o --- 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) { ^~~~~ --- 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 --- utils/CMakeFiles/utils.dir/all --- --- utils/CMakeFiles/utils.dir/checkpoint.cpp.o --- [ 69%] 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 --- utils/CMakeFiles/utils.dir/MPIHelper.cpp.o --- [ 70%] 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 --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/maalignment.cpp.o --- [ 70%] 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 --- pda/CMakeFiles/pda.dir/all --- --- pda/libpda.a --- [ 70%] Linking CXX static library libpda.a cd /construction/biology/iqtree/.build/pda && /usr/local/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /construction/biology/iqtree/.build/pda && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a [ 70%] Built target pda --- 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 --- [ 71%] 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 --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/CMakeFiles/alignment.dir/superalignment.cpp.o --- [ 72%] 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 --- alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o --- [ 72%] 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 --- alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o --- [ 72%] 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 --- alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o --- [ 73%] 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 --- 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 --- [ 73%] 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 --- main/CMakeFiles/main.dir/phyloanalysis.cpp.o --- [ 74%] 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 --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- [ 74%] 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/phyloanalysis.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp:37: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp:38: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phyloanalysis.cpp:46: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- phylo-yaml/CMakeFiles/phyloYAML.dir/all --- --- phylo-yaml/libphyloYAML.a --- [ 74%] 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 [ 74%] Built target phyloYAML --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/treetesting.cpp.o --- [ 74%] 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 --- main/CMakeFiles/main.dir/phylotesting.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:21: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/main/phylotesting.cpp:22: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ 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); ^~~~~ --- utils/CMakeFiles/utils.dir/all --- --- utils/libutils.a --- [ 74%] 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 [ 74%] 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 --- [ 75%] 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 --- main/CMakeFiles/main.dir/all --- /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 --- 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*); ^~~~~ --- model/CMakeFiles/model.dir/modelbin.cpp.o --- [ 75%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelbin.cpp --- model/CMakeFiles/model.dir/modelmarkov.cpp.o --- /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1403:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(istream &in) throw(const char*, string) { ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1458:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readRates(string str) throw(const char*) { ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1487:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(istream &in) throw(const char*) { ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.cpp:1504:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelMarkov::readStateFreq(string str) throw(const char*) { ^~~~~ --- model/CMakeFiles/model.dir/modelbin.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelbin.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelbin.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modeldna.cpp.o --- [ 75%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.cpp --- main/CMakeFiles/main.dir/all --- --- main/CMakeFiles/main.dir/timetree.cpp.o --- [ 76%] 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 --- 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/modelfactory.cpp.o --- [ 77%] 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 --- model/CMakeFiles/model.dir/modelprotein.cpp.o --- [ 77%] 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 --- model/CMakeFiles/model.dir/modelset.cpp.o --- [ 78%] 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/modelfactory.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:24: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:26: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:27: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactory.cpp:30: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ --- model/CMakeFiles/model.dir/modelprotein.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp:20: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] void ModelProtein::readRates(istream &in) throw(const char*, string) { ^~~~~ --- model/CMakeFiles/model.dir/modelsubst.cpp.o --- [ 78%] 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 --- CMakeFiles/kernelavx.dir/all --- --- libkernelavx.a --- [ 78%] 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 [ 78%] Built target kernelavx --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/partitionmodel.cpp.o --- [ 78%] 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 --- CMakeFiles/kernelsse.dir/all --- --- libkernelsse.a --- [ 79%] 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 [ 79%] Built target kernelsse --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/partitionmodelplen.cpp.o --- [ 80%] 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 --- model/CMakeFiles/model.dir/rategamma.cpp.o --- [ 80%] 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 --- alignment/CMakeFiles/alignment.dir/all --- --- alignment/libalignment.a --- [ 80%] 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 [ 80%] Built target alignment --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/rategammainvar.cpp.o --- [ 81%] 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 --- 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/rateheterogeneity.cpp.o --- [ 81%] 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/partitionmodelplen.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/partitionmodelplen.cpp:12: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/rateinvar.cpp.o --- [ 81%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -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 --- [ 82%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratemeyerdiscrete.cpp --- model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o --- [ 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 --- [ 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 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 --- [ 83%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/ratefreeinvar.cpp --- CMakeFiles/kernelfma.dir/all --- --- libkernelfma.a --- [ 83%] 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 [ 83%] Built target kernelfma --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/rateheterotachy.cpp.o --- [ 84%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/model/rateheterotachy.cpp --- main/CMakeFiles/main.dir/all --- --- main/libmain.a --- [ 84%] 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 [ 84%] Built target main --- model/CMakeFiles/model.dir/all --- --- model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o --- [ 84%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /construction/biology/iqtree/.build/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -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/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/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/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/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/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/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/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/modelpomomixture.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:23, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.h:14, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.cpp:9: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomo.h:4, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.h:14, from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelpomomixture.cpp:9: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ --- model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelfactorymixlen.cpp:12: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- 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/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/mtree.cpp.o --- [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o --- tree/CMakeFiles/tree.dir/mexttree.cpp.o --- [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o --- tree/CMakeFiles/tree.dir/ncbitree.cpp.o --- [ 88%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o --- tree/CMakeFiles/tree.dir/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/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/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/node.cpp.o --- [ 89%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o --- tree/CMakeFiles/tree.dir/candidateset.cpp.o --- [ 89%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o --- 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/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/iqtree.cpp.o --- [ 90%] Building CXX object 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/memslot.cpp.o --- [ 91%] Building CXX object 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/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/mtreeset.cpp.o --- [ 92%] 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/matree.cpp.o --- [ 92%] 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/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/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/phylotreemixlen.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreemixlen.cpp:12: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/phylotree.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmixture.h:13, from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp:34: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/quartet.cpp.o --- [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /construction/biology/iqtree/.build/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/construction/biology/iqtree/IQ-TREE-2.0.6 -I/construction/biology/iqtree/IQ-TREE-2.0.6/yaml-cpp/include -I/construction/biology/iqtree/.build -pipe -O2 -fno-strict-aliasing -std=c++11 -fopenmp -pthread -O2 -g -ffunction-sections -fdata-sections -I/usr/local/include/eigen3 -I/usr/local/include -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /construction/biology/iqtree/IQ-TREE-2.0.6/tree/quartet.cpp --- tree/CMakeFiles/tree.dir/phylotreesse.cpp.o --- In file included from /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotreesse.cpp:35: /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:146:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(istream &in) throw(const char*, string); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:153:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readRates(string str) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:160:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(istream &in) throw(const char*); ^~~~~ /construction/biology/iqtree/IQ-TREE-2.0.6/model/modelmarkov.h:167:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] virtual void readStateFreq(string str) throw(const char*); ^~~~~ --- tree/CMakeFiles/tree.dir/phylotree.cpp.o --- /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp: In function 'std::__cxx11::string getASCName(ASCType)': /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp: In member function 'virtual int PhyloTree::getNumLhCat(SiteLoglType)': /construction/biology/iqtree/IQ-TREE-2.0.6/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] } ^ --- tree/CMakeFiles/tree.dir/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/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 00:06:30 ------------------------------------------------------------------------------- -- 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 00:00:01 ------------------------------------------------------------------------------- -- 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 00:00:17 TOTAL TIME 00:07:24