Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/i/iqtree/iqtree_2.0.7+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/iqtree-2.0.7+dfsg-1yl67jw8g/iqtree_2.0.7+dfsg-1_amd64.buildinfo Get source package info: iqtree=2.0.7+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/iqtree/2.0.7+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12 base-passwd=3.5.52 bash=5.1-6 binutils=2.37.50.20220106-2 binutils-common=2.37.50.20220106-2 binutils-x86-64-linux-gnu=2.37.50.20220106-2 bsdextrautils=2.37.2-6 bsdutils=1:2.37.2-6 build-essential=12.9 bzip2=1.0.8-5 chrpath=0.16-2+b1 cmake=3.22.1-1+b1 cmake-data=3.22.1-1 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-14 dash=0.5.11+git20210903+057cd650a4ed-3 debconf=1.5.79 debhelper=13.6 debianutils=5.5-1 dh-autoreconf=20 dh-elpa-helper=2.0.10 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 emacsen-common=3.0.4 file=1:5.41-2 findutils=4.8.0-1 g++=4:11.2.0-2 g++-11=11.2.0-14 gcc=4:11.2.0-2 gcc-11=11.2.0-14 gcc-11-base=11.2.0-14 gettext=0.21-4 gettext-base=0.21-4 gfortran-11=11.2.0-14 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 help2man=1.48.5 hostname=3.23 ibverbs-providers=38.0-1 init-system-helpers=1.61 intltool-debian=0.35.0+20060710.5 libacl1=2.3.1-1 libarchive-zip-perl=1.68-1 libarchive13=3.5.2-1 libasan6=11.2.0-14 libatomic1=11.2.0-14 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libbinutils=2.37.50.20220106-2 libblkid1=2.37.2-6 libboost-dev=1.74.0.3 libboost1.74-dev=1.74.0-14 libbrotli1=1.0.9-2+b3 libbsd0=0.11.3-1 libbz2-1.0=1.0.8-5 libc-bin=2.33-3 libc-dev-bin=2.33-3 libc6=2.33-3 libc6-dev=2.33-3 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcbor0.8=0.8.0-2 libcc1-0=11.2.0-14 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1 libcrypt1=1:4.4.27-1 libctf-nobfd0=2.37.50.20220106-2 libctf0=2.37.50.20220106-2 libcurl3-gnutls=7.81.0-1 libcurl4=7.81.0-1 libdb5.3=5.3.28+dfsg1-0.8 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdpkg-perl=1.21.1 libedit2=3.1-20210910-1 libeigen3-dev=3.4.0-2 libelf1=0.186-1 libevent-2.1-7=2.1.12-stable-1 libevent-core-2.1-7=2.1.12-stable-1 libevent-dev=2.1.12-stable-1 libevent-extra-2.1-7=2.1.12-stable-1 libevent-openssl-2.1-7=2.1.12-stable-1 libevent-pthreads-2.1-7=2.1.12-stable-1 libexpat1=2.4.3-1 libfabric1=1.11.0-3 libffi8=3.4.2-4 libfido2-1=1.10.0-1 libfile-stripnondeterminism-perl=1.13.0-1 libgcc-11-dev=11.2.0-14 libgcc-s1=11.2.0-14 libgcrypt20=1.9.4-5 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgfortran-11-dev=11.2.0-14 libgfortran5=11.2.0-14 libglib2.0-0=2.70.2-1 libgmp-dev=2:6.2.1+dfsg-3 libgmp10=2:6.2.1+dfsg-3 libgmpxx4ldbl=2:6.2.1+dfsg-3 libgnutls30=3.7.2-5 libgomp1=11.2.0-14 libgpg-error0=1.43-3 libgssapi-krb5-2=1.18.3-7 libhogweed6=3.7.3-1 libhwloc-dev=2.7.0-1 libhwloc-plugins=2.7.0-1 libhwloc15=2.7.0-1 libibverbs-dev=38.0-1 libibverbs1=38.0-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libisl23=0.24-2 libitm1=11.2.0-14 libjs-jquery=3.5.1+dfsg+~3.5.5-8 libjs-jquery-ui=1.13.0+dfsg-1 libjsoncpp25=1.9.5-2 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libldap-2.4-2=2.4.59+dfsg-1 liblocale-gettext-perl=1.07-4+b1 liblsan0=11.2.0-14 libltdl-dev=2.4.6-15 libltdl7=2.4.6-15 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmd0=1.0.4-1 libmount1=2.37.2-6 libmpc3=1.2.1-1 libmpfr6=4.1.0-3 libncurses6=6.3-2 libncursesw6=6.3-2 libnettle8=3.7.3-1 libnghttp2-14=1.43.0-1 libnl-3-200=3.4.0-1+b1 libnl-3-dev=3.4.0-1+b1 libnl-route-3-200=3.4.0-1+b1 libnl-route-3-dev=3.4.0-1+b1 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnuma-dev=2.0.14-3 libnuma1=2.0.14-3 libopenmpi-dev=4.1.2-1 libopenmpi3=4.1.2-1 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libpciaccess0=0.16-3 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libperl5.32=5.32.1-6 libpipeline1=1.5.5-1 libpmix-dev=4.1.1~rc6-1 libpmix2=4.1.1~rc6-1 libprocps8=2:3.3.17-6 libpsl5=0.21.0-1.2 libpsm-infinipath1=3.3+20.604758e7-6.1 libpsm2-2=11.2.185-1 libquadmath0=11.2.0-14 librdmacm1=38.0-1 librhash0=1.4.2-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2=2.1.27+dfsg2-3 libsasl2-modules-db=2.1.27+dfsg2-3 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsemanage-common=3.3-1 libsemanage2=3.3-1+b1 libsepol2=3.3-1 libsigsegv2=2.13-1 libsmartcols1=2.37.2-6 libsprng2=2.0a-13 libsprng2-dev=2.0a-13 libssh2-1=1.10.0-2 libssl1.1=1.1.1m-1 libstdc++-11-dev=11.2.0-14 libstdc++6=11.2.0-14 libsub-override-perl=0.09-2 libsystemd0=250.3-1 libtasn1-6=4.18.0-4 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtsan0=11.2.0-14 libubsan1=11.2.0-14 libuchardet0=0.0.7-1 libucx0=1.12.0-1 libudev1=250.3-1 libunistring2=0.9.10-6 libuuid1=2.37.2-6 libuv1=1.43.0-1 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libxau6=1:1.0.9-1 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxml2=2.9.12+dfsg-5+b1 libxnvctrl0=470.94-1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.15-1 login=1:4.8.1-2 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-4 mawk=1.3.4.20200120-2 mpi-default-dev=1.14 ncurses-base=6.3-2 ncurses-bin=6.3-2 ocl-icd-libopencl1=2.2.14-3 openmpi-bin=4.1.2-1 openmpi-common=4.1.2-1 openssh-client=1:8.7p1-4 passwd=1:4.8.1-2 patch=2.7.6-7 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 pkg-config=0.29.2-1 po-debconf=1.0.21+nmu1 procps=2:3.3.17-6 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 time=1.9-0.1 util-linux=2.37.2-6 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 zlib1g-dev=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220124T035008Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220124T035008Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220323T151417Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220119T212311Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d iqtree=2.0.7+dfsg-1 && mkdir -p /build/iqtree-DJ09C4 && dpkg-source --no-check -x /*.dsc /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg && chown -R builduser:builduser /build/iqtree-DJ09C4" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1642763121" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/iqtree-DJ09C4 /tmp/iqtree-2.0.7+dfsg-1yl67jw8g bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220119T212311Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.PlnC2I7Aej as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.PlnC2I7Aej Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.2-6). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 136 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220119T212311Z unstable/main amd64 libfakeroot amd64 1.27-1 [48.5 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220119T212311Z unstable/main amd64 fakeroot amd64 1.27-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 136 kB in 0s (971 kB/s) Selecting previously unselected package libfakeroot:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4681 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.27-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.27-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.27-1_amd64.deb ... Unpacking fakeroot (1.27-1) ... Setting up libfakeroot:amd64 (1.27-1) ... Setting up fakeroot (1.27-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-3) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220124T035008Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220124T035008Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220323T151417Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20220119T212311Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.PlnC2I7Aej Get:1 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm InRelease [129 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220323T151417Z unstable InRelease [165 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20220119T212311Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main Sources [11.8 MB] Get:5 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main amd64 Packages [11.2 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20220323T151417Z unstable/main amd64 Packages Err:6 http://snapshot.notset.fr/archive/debian/20220323T151417Z unstable/main amd64 Packages 404 Not Found [IP: 10.13.0.253 80] Ign:6 http://snapshot.notset.fr/archive/debian/20220323T151417Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20220323T151417Z unstable/main amd64 Packages [12.3 MB] Fetched 35.5 MB in 29s (1220 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.PlnC2I7Aej I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d iqtree=2.0.7+dfsg-1 && mkdir -p /build/iqtree-DJ09C4 && dpkg-source --no-check -x /*.dsc /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg && chown -R builduser:builduser /build/iqtree-DJ09C4"' exec /tmp/mmdebstrap.PlnC2I7Aej Reading package lists... NOTICE: 'iqtree' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/iqtree.git Please use: git clone https://salsa.debian.org/med-team/iqtree.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1604 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main iqtree 2.0.7+dfsg-1 (dsc) [2236 B] Get:2 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main iqtree 2.0.7+dfsg-1 (tar) [1582 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220124T035008Z bookworm/main iqtree 2.0.7+dfsg-1 (diff) [20.0 kB] Fetched 1604 kB in 1s (1234 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'iqtree_2.0.7+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting iqtree in /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg dpkg-source: info: unpacking iqtree_2.0.7+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree_2.0.7+dfsg-1.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1642763121" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.PlnC2I7Aej dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 2.0.7+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' dh_auto_clean -Bbuild.omp dh_auto_clean -Bbuild.serial dh_auto_clean -Bbuild.mpi dh override_dh_auto_clean make[1]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' dh_auto_configure -Bbuild.omp -- -DIQTREE_FLAGS="omp" cd build.omp && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") IQ-TREE flags : omp Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -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 - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/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_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp dh_auto_configure -Bbuild.serial -- -DIQTREE_FLAGS="" cd build.serial && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") IQ-TREE flags : Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -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 - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/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_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial dh_auto_configure -Bbuild.mpi -- -DIQTREE_FLAGS="mpi" cd build.mpi && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 11.2.0 -- The CXX compiler identification is GNU 11.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") IQ-TREE flags : mpi Target OS : Unix Compiler : GNU Compiler (gcc) -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") Target binary : 64-bit OpenMP : Yes MPI : Yes Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-z,relro -Wl,-z,now -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 - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/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_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' dh_auto_build -Bbuild.omp cd build.omp && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -B/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/CMakeFiles /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/sprng /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lbfgsb /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/lbfgsb /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/gsl /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make 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'/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 1%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 1%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o [ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp [ 2%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/bitset_index.c [ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o [ 2%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/alignment.c [ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/lcg64.c [ 3%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/hashmap.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 4%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/makeseed.c [ 4%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/io.c [ 4%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/memory.c [ 5%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/sort.c [ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/multinomial.cpp [ 6%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/store.c [ 6%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree.c [ 6%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/pow_int.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c [ 8%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/gauss.cpp [ 8%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/checkid.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro ‘rax_posix_memalign’ 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 9%] Linking C static library libsprng.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/sprng && /usr/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 [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o /usr/bin/ranlib libsprng.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 9%] Built target sprng make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/vectorclass /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 10%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 10%] Linking CXX static library libvectorclass.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake [ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 10%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/nclextra /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 11%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp [ 12%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp [ 12%] Linking CXX static library libgsl.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/gsl && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 12%] Built target gsl make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 12%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/eigen.c [ 12%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro ‘rax_posix_memalign’ 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro ‘rax_posix_memalign’ 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro ‘rax_posix_memalign’ 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro ‘rax_posix_memalign’ 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 13%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c: In function ‘main_booster’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ [ 13%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c [ 14%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c [ 14%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/prng.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro ‘rax_posix_memalign’ 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro ‘rax_posix_memalign’ 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 15%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/stats.c [ 15%] Linking CXX static library liblbfgsb.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/lbfgsb && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 15%] Built target lbfgsb make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 15%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/avxLikelihood.c [ 15%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 15%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hardware.c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hash.c [ 17%] Linking C static library libbooster.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/booster && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 17%] Built target booster make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 17%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 17%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/lexer.c [ 18%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/eigen_sym.c [ 19%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c [ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro ‘rax_posix_memalign’ 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro ‘rax_posix_memalign’ 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp [ 19%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/random.c [ 20%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/weisslambda.c [ 20%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c [ 20%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest.c [ 21%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp [ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/models.c [ 22%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/models.c:53: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp [ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp [ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp [ 25%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp [ 25%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp [ 25%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp [ 26%] Linking C static library libpllavx.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 26%] Built target pllavx make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 26%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp [ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp [ 26%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp [ 27%] Linking CXX static library libwhtest.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/whtest && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 27%] Built target whtest [ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp [ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp [ 29%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp [ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp [ 30%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newick.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 31%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro ‘rax_posix_memalign’ 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro ‘rax_posix_memalign’ 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro ‘rax_posix_memalign’ 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro ‘rax_posix_memalign’ 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp [ 31%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/gzstream.cpp [ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp [ 31%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp [ 32%] Linking CXX static library libnclextra.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/nclextra && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 32%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 33%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 33%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp [ 33%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/greedy.cpp [ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp [ 34%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/stoprule.cpp [ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp [ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp [ 35%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp [ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp [ 35%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/genericParallelization.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 36%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/optimizeModel.c [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp [ 39%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp [ 39%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/parsePartition.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 39%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp [ 39%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/queue.c [ 40%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/randomTree.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 40%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/recom.c [ 40%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp [ 40%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp [ 42%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 42%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/searchAlgo.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 43%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/tools.cpp [ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp [ 44%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/ssort.c [ 45%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp [ 46%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/stack.c [ 46%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/topologies.c [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 47%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/trash.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 47%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/treeIO.c [ 47%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 48%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp [ 48%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:16, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:588:7: note: in expansion of macro ‘rax_posix_memalign’ 588 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:589:7: note: in expansion of macro ‘rax_posix_memalign’ 589 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:591:7: note: in expansion of macro ‘rax_posix_memalign’ 591 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:609:15: note: in expansion of macro ‘rax_posix_memalign’ 609 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:613:15: note: in expansion of macro ‘rax_posix_memalign’ 613 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:679:7: note: in expansion of macro ‘rax_posix_memalign’ 679 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:686:7: note: in expansion of macro ‘rax_posix_memalign’ 686 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:716:7: note: in expansion of macro ‘rax_posix_memalign’ 716 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:736:7: note: in expansion of macro ‘rax_posix_memalign’ 736 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro ‘rax_posix_memalign’ 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp [ 49%] Linking C static library libpll.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pll && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 49%] Built target pll [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp [ 50%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp [ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp [ 51%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp [ 52%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp [ 54%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp [ 54%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp [ 54%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp [ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp [ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp [ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pruning.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/pllnni.cpp [ 56%] Linking CXX static library libterraphast.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terraphast && /usr/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 [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp /usr/bin/ranlib libterraphast.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 57%] Built target terraphast [ 57%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/split.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/splitgraph.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o [ 59%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/splitset.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o [ 60%] Linking CXX static library libncl.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/ncl && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 60%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 60%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/checkpoint.cpp [ 61%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/ecopd.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/graph.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pdtree.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/alignment.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp [ 63%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp [ 63%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp [ 64%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp [ 64%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp [ 64%] Linking CXX static library libutils.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/utils && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 65%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp [ 65%] Built target utils [ 66%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp [ 67%] Linking CXX static library libyaml-cpp.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/yaml-cpp && /usr/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 make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 67%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 67%] Built target yaml-cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelbin.cpp make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/phylo-yaml /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 68%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/maalignment.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelbin.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignment.cpp [ 69%] Linking CXX static library libpda.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/pda && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 69%] Built target pda [ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp [ 70%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 70%] Built target kernelsse make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/main /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 71%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/main.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ [ 72%] Linking CXX static library libphyloYAML.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/phylo-yaml && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 72%] Built target phyloYAML [ 72%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp [ 73%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelset.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelsubst.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodel.cpp [ 76%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/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 In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelset.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 76%] Built target kernelfma [ 76%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rategamma.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rategammainvar.cpp [ 78%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(PML::SeqType)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function ‘double CandidateModel::getScore(ModelTestCriterion)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp [ 80%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 80%] Built target kernelavx [ 80%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/treetesting.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratekategory.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratefree.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelcodon.cpp [ 82%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/timetree.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelunrest.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelcodon.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelunrest.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.cpp [ 85%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp [ 85%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ [ 85%] Linking CXX static library libalignment.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/alignment && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 85%] Built target alignment [ 86%] Linking CXX static library libmain.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/main && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 86%] Built target main [ 87%] Linking CXX static library libmodel.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/model && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/constrainttree.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/candidateset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/iqtree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/memslot.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/mexttree.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/matree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/node.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/ncbitree.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylonode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/quartet.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/supernode.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function ‘std::string getASCName(ASCType)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/tinatree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/parstree.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/discordance.cpp [ 98%] Linking CXX static library libtree.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/tree && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terrace /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terrace /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terrace/CMakeFiles/terrace.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terrace/terrace.cpp [ 99%] Linking CXX static library libterrace.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/terrace && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/CMakeFiles/iqtree2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [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/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lib: 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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' [100%] Built target iqtree2 make[3]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.omp' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.serial cd build.serial && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -B/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/CMakeFiles /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/sprng /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lbfgsb /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/lbfgsb /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/gsl /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 1%] 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/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build [ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build [ 2%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/bitset_index.c [ 2%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/alignment.c make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 2%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp [ 2%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/lcg64.c make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp [ 4%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/makeseed.c [ 5%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c [ 5%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/hashmap.c [ 5%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/memory.c [ 6%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/store.c [ 6%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/io.c [ 7%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/sort.c [ 7%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree.c [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/multinomial.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro ‘rax_posix_memalign’ 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/pow_int.cpp [ 8%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c [ 8%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/gauss.cpp [ 8%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/checkid.c [ 8%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp [ 9%] Linking C static library libsprng.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/sprng && /usr/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 [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 9%] Built target sprng make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/vectorclass /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= [ 10%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 11%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 11%] Linking CXX static library libgsl.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/gsl && /usr/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 [ 11%] Linking CXX static library libvectorclass.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o /usr/bin/ranlib libvectorclass.a [ 11%] Built target gsl [ 11%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro ‘rax_posix_memalign’ 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro ‘rax_posix_memalign’ 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro ‘rax_posix_memalign’ 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro ‘rax_posix_memalign’ 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 11%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/nclextra /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 12%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 12%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/eigen.c [ 13%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c: In function ‘main_booster’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ [ 13%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c [ 14%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro ‘rax_posix_memalign’ 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro ‘rax_posix_memalign’ 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ [ 14%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/prng.c [ 14%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hardware.c [ 14%] Linking CXX static library liblbfgsb.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake [ 15%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/eigen_sym.c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 [ 16%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/stats.c /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o [ 17%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hash.c /usr/bin/ranlib liblbfgsb.a [ 17%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/lexer.c make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 17%] Built target lbfgsb [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp [ 18%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp [ 19%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c [ 19%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/random.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro ‘rax_posix_memalign’ 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro ‘rax_posix_memalign’ 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 19%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 20%] Linking C static library libbooster.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake [ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/weisslambda.c cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/booster && /usr/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 [ 21%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 21%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest.c [ 21%] Built target booster make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 21%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/avxLikelihood.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 22%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 22%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/models.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/models.c:53: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 22%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp [ 23%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp [ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp [ 25%] Linking C static library libpllavx.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 25%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp [ 25%] Built target pllavx [ 25%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp [ 25%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp [ 26%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp [ 26%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp [ 27%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp [ 28%] Linking CXX static library libwhtest.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/whtest && /usr/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 [ 28%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 29%] Linking CXX static library libnclextra.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/nclextra && /usr/bin/cmake -E cmake_link_script CMakeFiles/nclextra.dir/link.txt --verbose=1 [ 29%] Built target whtest make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend /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 make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp [ 29%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newick.c [ 29%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ /usr/bin/ranlib libnclextra.a [ 30%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro ‘rax_posix_memalign’ 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro ‘rax_posix_memalign’ 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro ‘rax_posix_memalign’ 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro ‘rax_posix_memalign’ 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 30%] Built target nclextra [ 31%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp [ 32%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 32%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp [ 32%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp [ 33%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp [ 33%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp [ 33%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp [ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp [ 34%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp [ 35%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp [ 35%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/genericParallelization.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 35%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/gzstream.cpp [ 35%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp [ 36%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/optimizeModel.c [ 36%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp [ 37%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 37%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/greedy.cpp [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp [ 38%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp [ 38%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/parsePartition.c [ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp [ 40%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 40%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp [ 40%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/queue.c [ 41%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp [ 42%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/randomTree.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 42%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/recom.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 42%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/stoprule.cpp [ 43%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 43%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/searchAlgo.c [ 44%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 44%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp [ 45%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp [ 45%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/ssort.c [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp [ 46%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/stack.c [ 46%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/topologies.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp [ 48%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/trash.c [ 48%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 48%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/treeIO.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 48%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c [ 48%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:16, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:588:7: note: in expansion of macro ‘rax_posix_memalign’ 588 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:589:7: note: in expansion of macro ‘rax_posix_memalign’ 589 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:591:7: note: in expansion of macro ‘rax_posix_memalign’ 591 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:609:15: note: in expansion of macro ‘rax_posix_memalign’ 609 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:613:15: note: in expansion of macro ‘rax_posix_memalign’ 613 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:679:7: note: in expansion of macro ‘rax_posix_memalign’ 679 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:686:7: note: in expansion of macro ‘rax_posix_memalign’ 686 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:716:7: note: in expansion of macro ‘rax_posix_memalign’ 716 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:736:7: note: in expansion of macro ‘rax_posix_memalign’ 736 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro ‘rax_posix_memalign’ 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 48%] Linking CXX static library libterraphast.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terraphast && /usr/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 [ 49%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/tools.cpp /usr/bin/ranlib libterraphast.a [ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 50%] Built target terraphast [ 50%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pruning.cpp [ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp [ 51%] Linking C static library libpll.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pll && /usr/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 [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 51%] Built target pll [ 51%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/pllnni.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp [ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxstoken.cpp [ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/split.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/splitgraph.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/splitset.cpp [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp [ 55%] Linking CXX static library libncl.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/ncl && /usr/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 [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD 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/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/checkpoint.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 55%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/alignment.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp [ 58%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp [ 61%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/ecopd.cpp [ 61%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/graph.cpp [ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp [ 62%] Linking CXX static library libutils.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/utils && /usr/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 [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 62%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 62%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 63%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelbin.cpp [ 64%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/simplekey.cpp [ 64%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelbin.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 64%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp [ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp [ 66%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 66%] Built target kernelsse [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/maalignment.cpp [ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ [ 67%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp [ 68%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pdtree.cpp [ 69%] Linking CXX static library libyaml-cpp.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/yaml-cpp && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 69%] Built target yaml-cpp [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignment.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelset.cpp [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelsubst.cpp [ 71%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodel.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelset.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 71%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp [ 72%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 72%] Built target kernelfma make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/phylo-yaml /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 72%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 73%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp [ 74%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp [ 74%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/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 In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 74%] Built target kernelavx [ 75%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rategamma.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rategammainvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp [ 76%] Linking CXX static library libpda.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/pda && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 76%] Built target pda make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend [ 76%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateinvar.cpp make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/main /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 77%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/main.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratekategory.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratefree.cpp [ 79%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelcodon.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp [ 82%] Linking CXX static library libphyloYAML.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/phylo-yaml && /usr/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 [ 82%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 82%] Built target phyloYAML [ 83%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelunrest.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelcodon.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelunrest.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ [ 85%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 85%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/treetesting.cpp [ 85%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/timetree.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(PML::SeqType)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function ‘double CandidateModel::getScore(ModelTestCriterion)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ [ 85%] Linking CXX static library libalignment.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/alignment && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 85%] Built target alignment [ 86%] Linking CXX static library libmain.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/main && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 86%] Built target main [ 87%] Linking CXX static library libmodel.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/model && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/candidateset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/iqtree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/matree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/memslot.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/mexttree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/node.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/constrainttree.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/mtreeset.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/ncbitree.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylonode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function ‘std::string getASCName(ASCType)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/quartet.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/tinatree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/parstree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/discordance.cpp [ 98%] Linking CXX static library libtree.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/tree && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terrace /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terrace /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terrace/CMakeFiles/terrace.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terrace/terrace.cpp [ 99%] Linking CXX static library libterrace.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/terrace && /usr/bin/cmake -P 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'/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [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/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lib: 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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' [100%] Built target iqtree2 make[3]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.mpi cd build.mpi && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -B/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg 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'/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/sprng /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= [ 0%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsassumptionsblock.cpp [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylokernelfma.cpp make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lbfgsb /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/lbfgsb /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 0%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/lcg64.c [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylokernelsse.cpp make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreeavx.cpp [ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/advanced.cpp [ 1%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o [ 2%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/alignment.c cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/bitset_index.c [ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/binomial_tpe.cpp [ 3%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lbfgsb/lbfgsb_new.cpp [ 3%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/multinomial.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/alignment.c:40: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 4%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/pow_int.cpp [ 4%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/hashmap.c [ 5%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o [ 5%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/makeseed.c cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/io.c [ 6%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/sort.c [ 6%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree.c [ 6%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/memory.c [ 6%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/gauss.cpp [ 7%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/store.c [ 7%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/primes-lcg64.c [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/gaussinv.cpp [ 8%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c:49: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/bipartitionList.c:332:3: note: in expansion of macro ‘rax_posix_memalign’ 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 8%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c [ 8%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/sprng/checkid.c [ 9%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/gsl/gausspdf.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Linking C static library libsprng.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/sprng && /usr/bin/cmake -E cmake_link_script CMakeFiles/sprng.dir/link.txt --verbose=1 /usr/bin/ar qc libsprng.a CMakeFiles/sprng.dir/lcg64.c.o CMakeFiles/sprng.dir/makeseed.c.o CMakeFiles/sprng.dir/memory.c.o CMakeFiles/sprng.dir/store.c.o CMakeFiles/sprng.dir/primes-lcg64.c.o CMakeFiles/sprng.dir/checkid.c.o /usr/bin/ranlib libsprng.a [ 10%] Linking CXX static library libgsl.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/gsl && /usr/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 [ 10%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c [ 10%] Built target sprng make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/vectorclass /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/vectorclass /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1175:3: note: in expansion of macro ‘rax_posix_memalign’ 1175 | rax_posix_memalign ((void **) &lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 4 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1017:3: note: in expansion of macro ‘rax_posix_memalign’ 1017 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 16 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:1326:3: note: in expansion of macro ‘rax_posix_memalign’ 1326 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 20 * mxtips); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro ‘rax_posix_memalign’ 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 11%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/vectorclass/instrset_detect.cpp [ 11%] Linking CXX static library libvectorclass.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/vectorclass && /usr/bin/cmake -E cmake_link_script CMakeFiles/vectorclass.dir/link.txt --verbose=1 [ 11%] Built target gsl make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend /usr/bin/ar qc libvectorclass.a CMakeFiles/vectorclass.dir/instrset_detect.cpp.o make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/nclextra /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 12%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/mpdablock.cpp /usr/bin/ranlib libvectorclass.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 13%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c [ 13%] Built target vectorclass make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 13%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/eigen.c [ 14%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1692:7: note: in expansion of macro ‘rax_posix_memalign’ 1692 | rax_posix_memalign ((void **) &(pr->partitionData[model]->parsVect), PLL_BYTE_ALIGNMENT, (size_t)compressedEntriesPadded * states * totalNodes * sizeof(parsimonyNumber)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/fastDNAparsimony.c:1768:3: note: in expansion of macro ‘rax_posix_memalign’ 1768 | rax_posix_memalign ((void **) &(tr->parsimonyScore), PLL_BYTE_ALIGNMENT, sizeof(unsigned int) * totalNodes); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c: In function ‘main_booster’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:268:57: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:304:29: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/booster.c:27: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ [ 14%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/hashtables_bfields.c [ 14%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/prng.c [ 15%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/stats.c [ 15%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hardware.c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hardware.c:93:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/hash.c [ 16%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/lexer.c [ 17%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c [ 18%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/eigen_sym.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:2699:3: note: in expansion of macro ‘rax_posix_memalign’ 2699 | rax_posix_memalign ((void **) &d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 4 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/makenewzGenericSpecial.c:3074:3: note: in expansion of macro ‘rax_posix_memalign’ 3074 | rax_posix_memalign ((void **)&d_start, PLL_BYTE_ALIGNMENT, numberOfCategories * 20 * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ [ 18%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/random.c [ 18%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/booster/tree_utils.c [ 19%] Linking C static library libbooster.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 [ 20%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/weisslambda.c /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 [ 20%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/weisslambda_sub.c /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsblock.cpp [ 20%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest.c [ 20%] Linking CXX static library liblbfgsb.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/lbfgsb && /usr/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 booster make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend [ 21%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 21%] Built target lbfgsb make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= [ 21%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o [ 22%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/avxLikelihood.c cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/bigint.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 22%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/binary.cpp [ 22%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/msetsblock.cpp [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxscharactersblock.cpp [ 23%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/models.c [ 23%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/bipartitions.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/models.c:53: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/avxLikelihood.c:57: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 24%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/convert.cpp [ 24%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/whtest/whtest_wrapper.cpp [ 24%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/bitmatrix.cpp [ 25%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/clamped_uint.cpp [ 26%] Linking C static library libpllavx.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/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 [ 26%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/constraints.cpp [ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/directives.cpp /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 26%] Built target pllavx make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 26%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/eigendecomposition.cpp [ 26%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emit.cpp [ 27%] Linking CXX static library libwhtest.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/whtest && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/msplitsblock.cpp [ 28%] Built target whtest [ 28%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/nclextra/modelsblock.cpp [ 29%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitfromevents.cpp [ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/errors.cpp [ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/multitree.cpp [ 30%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/gzstream.cpp [ 30%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/multitree_iterator.cpp [ 30%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newick.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newick.c:36: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 30%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitter.cpp [ 31%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/optimization.cpp [ 32%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro ‘rax_posix_memalign’ 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro ‘rax_posix_memalign’ 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3730:11: note: in expansion of macro ‘rax_posix_memalign’ 3730 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/newviewGenericSpecial.c:3800:3: note: in expansion of macro ‘rax_posix_memalign’ 3800 | rax_posix_memalign ((void **)&diagptable, PLL_BYTE_ALIGNMENT, categories * states * states * sizeof (double)); | ^~~~~~~~~~~~~~~~~~ [ 33%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/nodes.cpp [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdatablock.cpp [ 34%] Linking CXX static library libnclextra.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake [ 35%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdiscretedatum.cpp [ 35%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/parser.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/nclextra && /usr/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 [ 36%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/rooting.cpp [ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterstate.cpp /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 37%] Built target nclextra make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend [ 37%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/stoprule.cpp make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 37%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/circularnetwork.cpp [ 37%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/emitterutils.cpp [ 37%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/genericParallelization.c [ 37%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/simple.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/genericParallelization.c:43: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 38%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/optimizeModel.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/optimizeModel.c:47: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 38%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/subtree_extraction.cpp [ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdiscretematrix.cpp [ 38%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/parsePartition.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/parsePartition.c:42: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 38%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/queue.c [ 39%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/supertree_helpers.cpp [ 40%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/randomTree.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/randomTree.c:37: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 40%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/recom.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/recom.c:43: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 41%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/restartHashTable.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/restartHashTable.c:47: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 41%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/greedy.cpp [ 41%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/searchAlgo.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/searchAlgo.c:51: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdistancedatum.cpp [ 41%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/ssort.c [ 42%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/stack.c [ 42%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/topologies.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/topologies.c:48: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 42%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/trees.cpp [ 43%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/gurobiwrapper.cpp [ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsdistancesblock.cpp [ 45%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/union_find.cpp [ 46%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/trash.c [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/exceptions.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/trash.c:48: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 46%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/treeIO.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/treeIO.c:49: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 46%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/pllInternal.h:16, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:70: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:588:7: note: in expansion of macro ‘rax_posix_memalign’ 588 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->left), PLL_BYTE_ALIGNMENT, (size_t)pl->leftLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:589:7: note: in expansion of macro ‘rax_posix_memalign’ 589 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->right), PLL_BYTE_ALIGNMENT, (size_t)pl->rightLength * (maxCategories + 1) * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:591:7: note: in expansion of macro ‘rax_posix_memalign’ 591 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV), PLL_BYTE_ALIGNMENT, (size_t)pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:597:7: note: in expansion of macro ‘rax_posix_memalign’ 597 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector), PLL_BYTE_ALIGNMENT, (size_t)pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:609:15: note: in expansion of macro ‘rax_posix_memalign’ 609 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->EV_LG4[k]), PLL_BYTE_ALIGNMENT, pl->evLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:613:15: note: in expansion of macro ‘rax_posix_memalign’ 613 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->tipVector_LG4[k]), PLL_BYTE_ALIGNMENT, pl->tipVectorLength * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:679:7: note: in expansion of macro ‘rax_posix_memalign’ 679 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->sumBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:686:7: note: in expansion of macro ‘rax_posix_memalign’ 686 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->perSiteLikelihoods), PLL_BYTE_ALIGNMENT, width * sizeof(double)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:716:7: note: in expansion of macro ‘rax_posix_memalign’ 716 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->ancestralBuffer), PLL_BYTE_ALIGNMENT, width * | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:736:7: note: in expansion of macro ‘rax_posix_memalign’ 736 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->wgt), PLL_BYTE_ALIGNMENT, width * sizeof(int)); | ^~~~~~~~~~~~~~~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/mem_alloc.h:39:32: warning: ignoring return value of ‘posix_memalign’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 39 | #define rax_posix_memalign posix_memalign /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pll/utils.c:748:11: note: in expansion of macro ‘rax_posix_memalign’ 748 | rax_posix_memalign ((void **)&(localPartitions->partitionData[model]->gapColumn),PLL_BYTE_ALIGNMENT, ((size_t)localTree->mxtips) * | ^~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsemptyblock.cpp [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/exp.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/tools.cpp [ 48%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/hashsplitset.cpp [ 48%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/validation.cpp [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/memory.cpp [ 49%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pdnetwork.cpp [ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsexception.cpp [ 51%] Linking C static library libpll.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pll && /usr/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 [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsreader.cpp /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 51%] Built target pll [ 51%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pruning.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/node.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/node_data.cpp [ 52%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxssetreader.cpp [ 53%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxsstring.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/split.cpp [ 53%] Linking CXX static library libterraphast.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terraphast && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 53%] Built target terraphast [ 54%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/splitgraph.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/nodebuilder.cpp [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/nodeevents.cpp [ 55%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxstaxablock.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/splitset.cpp [ 56%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST 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-I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/null.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/ostream_wrapper.cpp [ 58%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/lpwrapper.c [ 58%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/ecopd.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/parse.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/graph.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/pllnni.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/parser.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pdtree.cpp [ 59%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/ncl/nxstreesblock.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/regex_yaml.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scanner.cpp [ 61%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scanscalar.cpp [ 61%] Linking CXX static library libncl.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/ncl && /usr/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 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-ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/pdtreeset.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/pda/ecopdmtreeset.cpp /usr/bin/ranlib libncl.a [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scantag.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/scantoken.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 62%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/pattern.cpp [ 62%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/checkpoint.cpp [ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/singledocparser.cpp [ 63%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/alignment.cpp [ 63%] Linking CXX static library libpda.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/pda && /usr/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 [ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/alignmentpairwise.cpp [ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/stream.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 65%] Built target pda [ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/src/tag.cpp [ 66%] Linking CXX static library libkernelsse.a /usr/bin/cmake -P CMakeFiles/kernelsse.dir/cmake_clean_target.cmake /usr/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 [ 67%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/utils/MPIHelper.cpp /usr/bin/ranlib libkernelsse.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 67%] Built target kernelsse make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/main /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 68%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/main.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ [ 68%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ [ 69%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/maalignment.cpp [ 70%] Linking CXX static library libyaml-cpp.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/yaml-cpp && /usr/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 [ 71%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignment.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:37: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:38: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phyloanalysis.cpp:46: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /usr/bin/ranlib libyaml-cpp.a [ 71%] Linking CXX static library libutils.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/utils && /usr/bin/cmake -E cmake_link_script CMakeFiles/utils.dir/link.txt --verbose=1 In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:21: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:22: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /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 In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:31: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:34: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 71%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignmentpairwise.cpp /usr/bin/ranlib libutils.a [ 71%] Built target yaml-cpp [ 71%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignmentpairwiseplen.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 71%] Built target utils make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/phylo-yaml /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(PML::SeqType)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp: In member function ‘double CandidateModel::getScore(ModelTestCriterion)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ [ 71%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/phylo-yaml/statespace.cpp [ 72%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/alignment/superalignmentunlinked.cpp [ 72%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/treetesting.cpp [ 72%] Linking CXX static library libkernelavx.a /usr/bin/cmake -P CMakeFiles/kernelavx.dir/cmake_clean_target.cmake /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 72%] Built target kernelavx make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 72%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp [ 72%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/main/timetree.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 73%] Linking CXX static library libphyloYAML.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/phylo-yaml && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 73%] Built target phyloYAML [ 74%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelbin.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelbin.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelbin.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 75%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake [ 75%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp /usr/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 [ 75%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 75%] Built target kernelfma [ 76%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelset.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelsubst.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:24: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:26: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:27: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactory.cpp:30: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodel.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelset.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelset.cpp:20: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodel.cpp:23: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rategamma.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rategammainvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateheterogeneity.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/partitionmodelplen.cpp:12: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratemeyerdiscrete.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratemeyerhaeseler.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratekategory.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratefree.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratefreeinvar.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateheterotachy.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/rateheterotachyinvar.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/ratefree.cpp:13: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelcodon.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelunrest.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelcodon.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelcodon.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 85%] Linking CXX static library libmain.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/main && /usr/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 [ 85%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.cpp /usr/bin/ranlib libmain.a make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 86%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:9: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:10: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.cpp:13: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 86%] Built target main In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelunrest.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelunrest.cpp:8: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 86%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.cpp:1: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelliemarkov.h:11, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelliemarkov.cpp:23: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:23, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomo.h:4, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.h:14, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 86%] Linking CXX static library libalignment.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/alignment && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 86%] Built target alignment [ 87%] Linking CXX static library libmodel.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/model && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/constrainttree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/mtree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/iqtree.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/candidateset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/ncbitree.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/memslot.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/matree.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/mexttree.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/mtreeset.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/node.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylonode.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/iqtree.cpp:29: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylosupertreeunlinked.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreepars.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmixture.h:13, from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp:34: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In function ‘std::string getASCName(ASCType)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/quartet.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/tinatree.cpp In file included from /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/parstree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/tree/discordance.cpp [ 98%] Linking CXX static library libtree.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/tree && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terrace /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terrace /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terrace/CMakeFiles/terrace.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terrace/terrace.cpp [ 99%] Linking CXX static library libterrace.a cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/terrace && /usr/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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' cd /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles/iqtree2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/include -I/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -pthread -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2-mpi -L/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lib -Wl,-rpath,/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib: 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 /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so 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 make[4]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' [100%] Built target iqtree2 make[3]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh override_dh_auto_build make[1]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' if [ "omp" != "omp" ] ; then dh_auto_install -Bbuild.omp; fi if [ "serial" != "omp" ] ; then dh_auto_install -Bbuild.serial; fi cd build.serial && make -j10 install DESTDIR=/build/iqtree-DJ09C4/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -B/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2 -- Set runtime path of "/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2" to "" -- Installing: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/./models.nex -- Installing: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.phy -- Installing: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.nex -- Installing: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.serial' if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi cd build.mpi && make -j10 install DESTDIR=/build/iqtree-DJ09C4/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg -B/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi -- Set runtime path of "/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi" to "" -- Up-to-date: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' dh_install find debian -name iqtree2-mpi -exec chrpath --delete \{\} \; find debian -name iqtree2-omp -exec chrpath --delete \{\} \; make[1]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' # somehow the example config is installed in /usr by cmake find debian/iqtree -name example.cf -delete dh_installexamples # remove example files in unusual dir rm -f debian/*/usr/models.nex rm -f debian/*/usr/example.[np][eh][xy] make[1]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' mkdir -p /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1/ help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood' \ --version-string="2.0.7+dfsg" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2 > /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1//iqtree2.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="2.0.7+dfsg" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-omp > /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1//iqtree2-omp.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="2.0.7+dfsg" /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/bin/iqtree2-mpi > /build/iqtree-DJ09C4/iqtree-2.0.7+dfsg/debian/iqtree/usr/share/man/man1//iqtree2-mpi.1 make[1]: Leaving directory '/build/iqtree-DJ09C4/iqtree-2.0.7+dfsg' dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'iqtree' in '../iqtree_2.0.7+dfsg-1_amd64.deb'. dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any -O../iqtree_2.0.7+dfsg-1_amd64.buildinfo dpkg-genchanges --build=any -O../iqtree_2.0.7+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: running special hook: sync-out /build/iqtree-DJ09C4 /tmp/iqtree-2.0.7+dfsg-1yl67jw8g I: cleaning package lists and apt cache... I: removing tempdir /tmp/mmdebstrap.PlnC2I7Aej... I: success in 2196.4429 seconds md5: Value of 'md5' differs for iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb md5: Size differs for iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb md5: Value of 'md5' differs for iqtree_2.0.7+dfsg-1_amd64.deb md5: Size differs for iqtree_2.0.7+dfsg-1_amd64.deb sha1: Value of 'sha1' differs for iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb sha1: Size differs for iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb sha1: Value of 'sha1' differs for iqtree_2.0.7+dfsg-1_amd64.deb sha1: Size differs for iqtree_2.0.7+dfsg-1_amd64.deb sha256: Value of 'sha256' differs for iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb sha256: Size differs for iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb sha256: Value of 'sha256' differs for iqtree_2.0.7+dfsg-1_amd64.deb sha256: Size differs for iqtree_2.0.7+dfsg-1_amd64.deb Checksums: FAIL Cannot generate diffoscope for iqtree-dbgsym_2.0.7+dfsg-1_amd64.deb: Cannot find URL: http://snapshot.notset.fr/mr/file/1451ba184be4b8f33a83f663c583368408bfe4ae98f16c434fa55d85d8c3d548/download Cannot generate diffoscope for iqtree_2.0.7+dfsg-1_amd64.deb: RetryError[]