Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/i/iqtree/iqtree_1.6.12+dfsg-1_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/iqtree-1.6.12+dfsg-1zuel4lzs/iqtree_1.6.12+dfsg-1_amd64.buildinfo Get source package info: iqtree=1.6.12+dfsg-1 Source URL: http://snapshot.notset.fr/mr/package/iqtree/1.6.12+dfsg-1/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 autoconf=2.69-11 automake=1:1.16.1-4 autopoint=0.19.8.1-10 autotools-dev=20180224.1 base-files=11 base-passwd=3.5.46 bash=5.0-5 binutils=2.33.1-4 binutils-common=2.33.1-4 binutils-x86-64-linux-gnu=2.33.1-4 bsdmainutils=11.1.2+b1 bsdutils=1:2.34-0.1 build-essential=12.8 bzip2=1.0.8-2 chrpath=0.16-2+b1 cmake=3.15.4-1 cmake-data=3.15.4-1 coreutils=8.30-3+b1 cpp=4:9.2.1-3.1 cpp-9=9.2.1-21 dash=0.5.10.2-6 debconf=1.5.73 debhelper=12.7.1 debianutils=4.9 dh-autoreconf=19 dh-strip-nondeterminism=1.6.3-1 diffutils=1:3.7-3 dpkg=1.19.7 dpkg-dev=1.19.7 dwz=0.13-4 fdisk=2.34-0.1 file=1:5.37-6 findutils=4.7.0-1 g++=4:9.2.1-3.1 g++-9=9.2.1-21 gcc=4:9.2.1-3.1 gcc-9=9.2.1-21 gcc-9-base=9.2.1-21 gettext=0.19.8.1-10 gettext-base=0.19.8.1-10 gfortran-9=9.2.1-21 grep=3.3-1 groff-base=1.22.4-3 gzip=1.9-3+b1 help2man=1.47.11 hostname=3.23 ibverbs-providers=26.0-2 init-system-helpers=1.57 intltool-debian=0.35.0+20060710.5 libacl1=2.2.53-5 libarchive-zip-perl=1.67-1 libarchive13=3.4.0-1+b1 libasan5=9.2.1-21 libatomic1=9.2.1-21 libattr1=1:2.4.48-5 libaudit-common=1:2.8.5-2 libaudit1=1:2.8.5-2+b1 libbinutils=2.33.1-4 libblkid1=2.34-0.1 libbrotli1=1.0.7-5+b1 libbsd0=0.10.0-1 libbz2-1.0=1.0.8-2 libc-bin=2.29-3 libc-dev-bin=2.29-3 libc6=2.29-3 libc6-dev=2.29-3 libcap-ng0=0.7.9-2.1+b1 libcc1-0=9.2.1-21 libcom-err2=1.45.4-1 libcroco3=0.6.13-1 libcurl4=7.67.0-2 libdb5.3=5.3.28+dfsg1-0.6 libdebconfclient0=0.250 libdebhelper-perl=12.7.1 libdpkg-perl=1.19.7 libedit2=3.1-20191025-1 libeigen3-dev=3.3.7-1 libelf1=0.176-1.1 libevent-2.1-7=2.1.11-stable-1 libevent-core-2.1-7=2.1.11-stable-1 libevent-dev=2.1.11-stable-1 libevent-extra-2.1-7=2.1.11-stable-1 libevent-openssl-2.1-7=2.1.11-stable-1 libevent-pthreads-2.1-7=2.1.11-stable-1 libexpat1=2.2.9-1 libfabric1=1.6.2-3+b1 libfdisk1=2.34-0.1 libffi6=3.2.1-9 libfile-stripnondeterminism-perl=1.6.3-1 libgcc-9-dev=9.2.1-21 libgcc1=1:9.2.1-21 libgcrypt20=1.8.5-3 libgdbm-compat4=1.18.1-5 libgdbm6=1.18.1-5 libgfortran-9-dev=9.2.1-21 libgfortran5=9.2.1-21 libglib2.0-0=2.62.3-2 libgmp-dev=2:6.1.2+dfsg-4 libgmp10=2:6.1.2+dfsg-4 libgmpxx4ldbl=2:6.1.2+dfsg-4 libgnutls30=3.6.10-5 libgomp1=9.2.1-21 libgpg-error0=1.36-7 libgssapi-krb5-2=1.17-6 libhogweed5=3.5.1+really3.5.1-2 libhwloc-dev=2.1.0+dfsg-2 libhwloc-plugins=2.1.0+dfsg-2 libhwloc15=2.1.0+dfsg-2 libibverbs-dev=26.0-2 libibverbs1=26.0-2 libicu63=63.2-2 libidn2-0=2.2.0-2 libisl22=0.22-2 libitm1=9.2.1-21 libjsoncpp1=1.7.4-3+b1 libk5crypto3=1.17-6 libkeyutils1=1.6-6 libkrb5-3=1.17-6 libkrb5support0=1.17-6 libldap-2.4-2=2.4.48+dfsg-1+b2 libldap-common=2.4.48+dfsg-1 liblocale-gettext-perl=1.07-4 liblsan0=9.2.1-21 libltdl-dev=2.4.6-11 libltdl7=2.4.6-11 liblz4-1=1.9.2-2 liblzma5=5.2.4-1+b1 libmagic-mgc=1:5.37-6 libmagic1=1:5.37-6 libmount1=2.34-0.1 libmpc3=1.1.0-1 libmpfr6=4.0.2-1 libncurses6=6.1+20191019-1 libncursesw6=6.1+20191019-1 libnettle7=3.5.1+really3.5.1-2 libnghttp2-14=1.40.0-1 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 libnuma-dev=2.0.12-1+b1 libnuma1=2.0.12-1+b1 libopenmpi-dev=4.0.2-4+b1 libopenmpi3=4.0.2-4+b1 libp11-kit0=0.23.18.1-2 libpam-modules=1.3.1-5 libpam-modules-bin=1.3.1-5 libpam-runtime=1.3.1-5 libpam0g=1.3.1-5 libpciaccess0=0.14-1 libpcre2-8-0=10.34-1 libpcre3=2:8.39-12+b1 libperl5.30=5.30.0-9 libpipeline1=1.5.1-2 libpmix2=3.1.4-1+b1 libprocps7=2:3.3.15-2+b1 libpsl5=0.20.2-2 libpsm-infinipath1=3.3+20.604758e7-6+b1 libpsm2-2=11.2.86-1 libquadmath0=9.2.1-21 librdmacm1=26.0-2 librhash0=1.3.8-1 librtmp1=2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2=2.1.27+dfsg-1 libsasl2-modules-db=2.1.27+dfsg-1 libseccomp2=2.4.2-2 libselinux1=2.9-3+b1 libsemanage-common=2.9-3 libsemanage1=2.9-3+b1 libsepol1=2.9-2+b2 libsigsegv2=2.12-2 libsmartcols1=2.34-0.1 libsprng2=2.0a-12+b1 libsprng2-dev=2.0a-12+b1 libssh2-1=1.8.0-2.1 libssl1.1=1.1.1d-2 libstdc++-9-dev=9.2.1-21 libstdc++6=9.2.1-21 libsub-override-perl=0.09-2 libsystemd0=243-9 libtasn1-6=4.15.0-2 libtinfo6=6.1+20191019-1 libtool=2.4.6-11 libtsan0=9.2.1-21 libubsan1=9.2.1-21 libuchardet0=0.0.6-3 libudev1=243-9 libunistring2=0.9.10-2 libuuid1=2.34-0.1 libuv1=1.33.1-2 libxml2=2.9.4+dfsg1-8 libzstd1=1.4.4+dfsg-1 linux-libc-dev=5.3.9-3 login=1:4.7-2 lsb-base=11.1.0 m4=1.4.18-4 make=4.2.1-1.2 man-db=2.9.0-1 mawk=1.3.3-17+b3 mpi-default-dev=1.13 ncurses-base=6.1+20191019-1 ncurses-bin=6.1+20191019-1 ocl-icd-libopencl1=2.2.12-2 openmpi-bin=4.0.2-4+b1 openmpi-common=4.0.2-4 openssh-client=1:8.1p1-1 passwd=1:4.7-2 patch=2.7.6-6 perl=5.30.0-9 perl-base=5.30.0-9 perl-modules-5.30=5.30.0-9 pkg-config=0.29-6 po-debconf=1.0.21 procps=2:3.3.15-2+b1 sed=4.7-1 sensible-utils=0.0.12+nmu1 sysvinit-utils=2.96-1 tar=1.30+dfsg-6+b1 time=1.7-25.1+b1 util-linux=2.34-0.1 xz-utils=5.2.4-1+b1 zlib1g=1:1.2.11.dfsg-1+b1 zlib1g-dev=1:1.2.11.dfsg-1+b1 --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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20191230T211841Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20191202T160249Z/ 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=1.6.12+dfsg-1 && mkdir -p /build/iqtree-X08Fx2 && dpkg-source --no-check -x /*.dsc /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg && chown -R builduser:builduser /build/iqtree-X08Fx2" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1575463977" dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/iqtree-X08Fx2 /tmp/iqtree-1.6.12+dfsg-1zuel4lzs bullseye /dev/null deb http://snapshot.notset.fr/archive/debian/20191202T160249Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: tar I: using /tmp/mmdebstrap.m7i8sQREzD 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.m7i8sQREzD Reading package lists... Building dependency tree... util-linux is already the newest version (2.34-0.1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 132 kB of archives. After this operation, 393 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20191202T160249Z unstable/main amd64 libfakeroot amd64 1.24-1 [45.7 kB] Get:2 http://snapshot.notset.fr/archive/debian/20191202T160249Z unstable/main amd64 fakeroot amd64 1.24-1 [85.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 132 kB in 0s (358 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 ... 4507 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.24-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.24-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.24-1_amd64.deb ... Unpacking fakeroot (1.24-1) ... Setting up libfakeroot:amd64 (1.24-1) ... Setting up fakeroot (1.24-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.29-3) ... 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/20210814T212851Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20210814T212851Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20191230T211841Z/ unstable main deb http://snapshot.notset.fr/archive/debian/20191202T160249Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.m7i8sQREzD Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm InRelease [81.6 kB] Get:2 http://snapshot.notset.fr/archive/debian/20191230T211841Z unstable InRelease [142 kB] Hit:3 http://snapshot.notset.fr/archive/debian/20191202T160249Z unstable InRelease Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Ign:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources Ign:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages Get:4 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main Sources [11.4 MB] Get:5 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main amd64 Packages [11.1 MB] Ign:6 http://snapshot.notset.fr/archive/debian/20191230T211841Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20191230T211841Z unstable/main amd64 Packages Ign:6 http://snapshot.notset.fr/archive/debian/20191230T211841Z unstable/main amd64 Packages Get:6 http://snapshot.notset.fr/archive/debian/20191230T211841Z unstable/main amd64 Packages [11.0 MB] Fetched 33.7 MB in 35s (956 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.m7i8sQREzD I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d iqtree=1.6.12+dfsg-1 && mkdir -p /build/iqtree-X08Fx2 && dpkg-source --no-check -x /*.dsc /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg && chown -R builduser:builduser /build/iqtree-X08Fx2"' exec /tmp/mmdebstrap.m7i8sQREzD 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 1305 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main iqtree 1.6.12+dfsg-1 (dsc) [2233 B] Get:2 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main iqtree 1.6.12+dfsg-1 (tar) [1283 kB] Get:3 http://snapshot.notset.fr/archive/debian/20210814T212851Z bookworm/main iqtree 1.6.12+dfsg-1 (diff) [19.7 kB] Fetched 1305 kB in 1s (1042 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'iqtree_1.6.12+dfsg-1.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting iqtree in /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg dpkg-source: info: unpacking iqtree_1.6.12+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree_1.6.12+dfsg-1.debian.tar.xz I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1575463977" dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.m7i8sQREzD dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 1.6.12+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg' dh_clean debian/rules build-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. -- The C compiler identification is GNU 9.2.1 -- The CXX compiler identification is GNU 9.2.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done IQ-TREE flags : 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 -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-X08Fx2/iqtree-1.6.12+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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. -- The C compiler identification is GNU 9.2.1 -- The CXX compiler identification is GNU 9.2.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done IQ-TREE flags : 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 -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-X08Fx2/iqtree-1.6.12+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_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. -- The C compiler identification is GNU 9.2.1 -- The CXX compiler identification is GNU 9.2.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done IQ-TREE flags : 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 -- Found Eigen3: /usr/include/eigen3 (Required is at least version "2.91.0") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg' debian/rules override_dh_auto_build make[1]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg' dh_auto_build -Bbuild.omp cd build.omp && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -B/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= Scanning dependencies of target gsl make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/binomial_tpe.cpp Scanning dependencies of target ncl make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build Scanning dependencies of target kernelsse make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' Scanning dependencies of target pll make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build [ 2%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o [ 3%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsassumptionsblock.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylokernelsse.cpp make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 4%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/alignment.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/alignment.c:40: /build/iqtree-X08Fx2/iqtree-1.6.12+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/multinomial.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/multinomial.cpp [ 4%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c:49: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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)); | ^~~~~~~~~~~~~~~~~~ [ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/pow_int.cpp [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c [ 6%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/gauss.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/gaussinv.cpp [ 8%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/gausspdf.cpp [ 8%] Linking CXX static library libgsl.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 8%] Built target gsl make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= Scanning dependencies of target lbfgsb make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 9%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lbfgsb/lbfgsb_new.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsblock.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/hardware.c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/hash.c [ 12%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/lexer.c [ 14%] Linking CXX static library liblbfgsb.a [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake [ 14%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxscharactersblock.cpp cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 14%] Built target lbfgsb make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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)); | ^~~~~~~~~~~~~~~~~~ Scanning dependencies of target kernelfma make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 15%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylokernelfma.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/models.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/models.c:53: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newick.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newick.c:36: /build/iqtree-X08Fx2/iqtree-1.6.12+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/newviewGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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)); | ^~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdatablock.cpp [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdiscretedatum.cpp [ 19%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/genericParallelization.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/genericParallelization.c:43: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdiscretematrix.cpp [ 20%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/optimizeModel.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/optimizeModel.c:47: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdistancedatum.cpp [ 21%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/parsePartition.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/parsePartition.c:42: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 21%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/queue.c [ 22%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/randomTree.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/randomTree.c:37: /build/iqtree-X08Fx2/iqtree-1.6.12+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 pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/recom.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/recom.c:43: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 23%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/restartHashTable.c [ 24%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdistancesblock.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/restartHashTable.c:47: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 25%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/searchAlgo.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/searchAlgo.c:51: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 25%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/ssort.c [ 26%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/stack.c [ 26%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/topologies.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/topologies.c:48: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 27%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/trash.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/trash.c:48: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 27%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/treeIO.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/treeIO.c:49: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 28%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c [ 28%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsemptyblock.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c:70: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/pllInternal.h:16, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c:70: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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) * | ^~~~~~~~~~~~~~~~~~ [ 29%] Linking C static library libpll.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 [ 30%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsexception.cpp /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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 30%] Built target pll make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= Scanning dependencies of target kernelavx make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 31%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreeavx.cpp [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsreader.cpp [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxssetreader.cpp [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsstring.cpp [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxstaxablock.cpp [ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxstoken.cpp [ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxstreesblock.cpp [ 35%] Linking CXX static library libncl.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 35%] Built target ncl make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= Scanning dependencies of target pllavx make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 35%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/avxLikelihood.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/avxLikelihood.c:57: /build/iqtree-X08Fx2/iqtree-1.6.12+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%] Linking C static library libpllavx.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 36%] Built target pllavx make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= Scanning dependencies of target nclextra make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/mpdablock.cpp [ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/msetsblock.cpp [ 38%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/msplitsblock.cpp [ 38%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/modelsblock.cpp [ 39%] Linking CXX static library libnclextra.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 39%] Built target nclextra make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= Scanning dependencies of target whtest make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 40%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/eigen.c [ 40%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/eigen_sym.c [ 41%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/random.c [ 42%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/weisslambda.c [ 42%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/weisslambda_sub.c [ 43%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest.c [ 43%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_wrapper.cpp [ 45%] Linking CXX static library libwhtest.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 45%] Built target whtest make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= Scanning dependencies of target sprng make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 45%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/lcg64.c [ 46%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/makeseed.c [ 46%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/memory.c [ 47%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/store.c [ 48%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/primes-lcg64.c [ 48%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/checkid.c [ 49%] Linking C static library libsprng.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 49%] Built target sprng make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= Scanning dependencies of target vectorclass make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 50%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/vectorclass/instrset_detect.cpp [ 50%] Linking CXX static library libvectorclass.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 50%] Built target vectorclass make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 50%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/pattern.cpp [ 51%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/alignment.cpp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 2925 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ [ 51%] 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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 51%] Built target kernelsse make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= Scanning dependencies of target utils make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 52%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/eigendecomposition.cpp [ 52%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/gzstream.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/optimization.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/stoprule.cpp [ 54%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/tools.cpp [ 54%] 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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 54%] Built target kernelfma make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= Scanning dependencies of target pda make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 54%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/circularnetwork.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/greedy.cpp [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/alignmentpairwise.cpp [ 55%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/pllnni.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/gurobiwrapper.cpp [ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/maalignment.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/hashsplitset.cpp [ 57%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/superalignment.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pdnetwork.cpp [ 59%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/checkpoint.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/MPIHelper.cpp [ 60%] Linking CXX static library libutils.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 60%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= Scanning dependencies of target model make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 60%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pruning.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/superalignmentpairwise.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/split.cpp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 997 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1052 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1081 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1095 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ [ 62%] 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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 62%] Built target kernelavx [ 63%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelbin.cpp [ 64%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/superalignmentpairwiseplen.cpp [ 65%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/splitgraph.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelbin.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelbin.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp [ 66%] Linking CXX static library libalignment.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 66%] Built target alignment [ 66%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/splitset.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 240 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:24: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:26: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:27: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:30: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 67%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/lpwrapper.c [ 67%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/ecopd.cpp [ 67%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp [ 68%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/graph.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp:651:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 651 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 68%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pdtree.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelset.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelset.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelset.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelsubst.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/partitionmodel.cpp [ 71%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pdtreeset.cpp [ 72%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/ecopdmtreeset.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/partitionmodelplen.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rategamma.cpp [ 73%] Linking CXX static library libpda.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rategammainvar.cpp make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 74%] Built target pda [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateheterogeneity.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratemeyerhaeseler.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratekategory.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratefree.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratefreeinvar.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateheterotachy.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateheterotachyinvar.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratefree.cpp:13: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelcodon.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelunrest.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelcodon.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelcodon.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 44 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:9: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:10: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:13: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelunrest.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelunrest.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelliemarkov.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.cpp:1: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.cpp:1: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelliemarkov.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= Scanning dependencies of target tree make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/matree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/constrainttree.cpp cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/candidateset.cpp cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/iqtree.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/iqtree.cpp:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/memslot.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/mexttree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/mtreeset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/ncbitree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/node.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylonode.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylonodemixlen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylosupertree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylosupertreeplen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp:34: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] 1202 | } | ^ [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreepars.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreesse.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/quartet.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/tinatree.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/parstree.cpp [ 97%] Linking CXX static library libtree.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/iqtree.dir/DependInfo.cmake --color= Scanning dependencies of target iqtree make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/main.cpp [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o [ 98%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/obsolete/parsmultistate.cpp [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/main.cpp:232:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 862 | << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:21: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:30: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:33: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(SeqType)’: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] 164 | } | ^ [100%] Linking CXX executable iqtree /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+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/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree -L/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lib -Wl,-rpath,/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree ] ; then mv build.omp/iqtree build.omp/iqtree-omp ; fi dh_auto_build -Bbuild.serial cd build.serial && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -B/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= Scanning dependencies of target gsl make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' Scanning dependencies of target kernelsse make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build Scanning dependencies of target ncl make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/binomial_tpe.cpp make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 2%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylokernelsse.cpp [ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsassumptionsblock.cpp Scanning dependencies of target pll make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 4%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/alignment.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/alignment.c:40: /build/iqtree-X08Fx2/iqtree-1.6.12+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/multinomial.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/multinomial.cpp [ 4%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c [ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/pow_int.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c:49: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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)); | ^~~~~~~~~~~~~~~~~~ [ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/gauss.cpp [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/gaussinv.cpp [ 8%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/gausspdf.cpp [ 8%] Linking CXX static library libgsl.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 8%] Built target gsl make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= Scanning dependencies of target lbfgsb make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 9%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lbfgsb/lbfgsb_new.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsblock.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/hardware.c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/hash.c [ 12%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/lexer.c [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxscharactersblock.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c [ 14%] Linking CXX static library liblbfgsb.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-X08Fx2/iqtree-1.6.12+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/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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)); | ^~~~~~~~~~~~~~~~~~ /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 14%] Built target lbfgsb make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= Scanning dependencies of target kernelfma make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 15%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylokernelfma.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/models.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/models.c:53: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newick.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newick.c:36: /build/iqtree-X08Fx2/iqtree-1.6.12+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/newviewGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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)); | ^~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdatablock.cpp [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdiscretedatum.cpp [ 19%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/genericParallelization.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/genericParallelization.c:43: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdiscretematrix.cpp [ 20%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/optimizeModel.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/optimizeModel.c:47: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdistancedatum.cpp [ 21%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/parsePartition.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/parsePartition.c:42: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 21%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/queue.c [ 22%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/randomTree.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/randomTree.c:37: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 23%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdistancesblock.cpp [ 23%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/recom.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/recom.c:43: /build/iqtree-X08Fx2/iqtree-1.6.12+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 C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/restartHashTable.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/restartHashTable.c:47: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 25%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/searchAlgo.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/searchAlgo.c:51: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 25%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/ssort.c [ 26%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/stack.c [ 26%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/topologies.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/topologies.c:48: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 27%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/trash.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/trash.c:48: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 27%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/treeIO.c [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsemptyblock.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/treeIO.c:49: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 28%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c:70: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/pllInternal.h:16, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c:70: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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) * | ^~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsexception.cpp [ 30%] Linking C static library libpll.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 30%] Built target pll make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= Scanning dependencies of target kernelavx make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 31%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreeavx.cpp [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsreader.cpp [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxssetreader.cpp [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsstring.cpp [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxstaxablock.cpp [ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxstoken.cpp [ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxstreesblock.cpp [ 35%] Linking CXX static library libncl.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 35%] Built target ncl make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= Scanning dependencies of target pllavx make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 35%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/avxLikelihood.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/avxLikelihood.c:57: /build/iqtree-X08Fx2/iqtree-1.6.12+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%] Linking C static library libpllavx.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 36%] Built target pllavx make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= Scanning dependencies of target nclextra make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/mpdablock.cpp [ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/msetsblock.cpp [ 38%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/msplitsblock.cpp [ 38%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/modelsblock.cpp [ 39%] Linking CXX static library libnclextra.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/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-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 39%] Built target nclextra make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= Scanning dependencies of target whtest make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 40%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/eigen.c [ 40%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/eigen_sym.c [ 41%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/random.c [ 42%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/weisslambda.c [ 42%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/weisslambda_sub.c [ 43%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest.c [ 43%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_wrapper.cpp [ 45%] Linking CXX static library libwhtest.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 /usr/bin/ranlib libwhtest.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 45%] Built target whtest make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= Scanning dependencies of target sprng make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 45%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/lcg64.c [ 46%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/makeseed.c [ 46%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/memory.c [ 47%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/store.c [ 48%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/primes-lcg64.c [ 48%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/checkid.c [ 49%] Linking C static library libsprng.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 /usr/bin/ranlib libsprng.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 49%] Built target sprng make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= Scanning dependencies of target vectorclass make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 50%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/vectorclass && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/vectorclass/instrset_detect.cpp [ 50%] Linking CXX static library libvectorclass.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 50%] Built target vectorclass make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 50%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/pattern.cpp [ 51%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/alignment.cpp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 2925 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ [ 51%] 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-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 51%] Built target kernelsse make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= Scanning dependencies of target utils make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 52%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/eigendecomposition.cpp [ 52%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/gzstream.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/optimization.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/stoprule.cpp [ 54%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/tools.cpp [ 54%] 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 [ 54%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/alignmentpairwise.cpp make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 54%] Built target kernelfma make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= Scanning dependencies of target pda make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 54%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/circularnetwork.cpp [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/maalignment.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/greedy.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/pllnni.cpp [ 56%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/superalignment.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/gurobiwrapper.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/hashsplitset.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/checkpoint.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pdnetwork.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/MPIHelper.cpp [ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/superalignmentpairwise.cpp [ 61%] Linking CXX static library libutils.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 61%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= Scanning dependencies of target model make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 61%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/superalignmentpairwiseplen.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pruning.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 997 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1052 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1081 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1095 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ [ 62%] Linking CXX static library libalignment.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 62%] Built target alignment [ 63%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/split.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/splitgraph.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelbin.cpp [ 65%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/splitset.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelbin.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelbin.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 66%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/cc -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/lpwrapper.c [ 66%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/ecopd.cpp [ 66%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 240 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ [ 67%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/graph.cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp [ 68%] 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 [ 68%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:24: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:26: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:27: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:30: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp:651:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 651 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 68%] Built target kernelavx [ 69%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelset.cpp [ 69%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pdtree.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelset.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelset.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 70%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pdtreeset.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelsubst.cpp [ 72%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/ecopdmtreeset.cpp [ 72%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/partitionmodel.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/partitionmodelplen.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rategamma.cpp [ 73%] Linking CXX static library libpda.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 73%] Built target pda [ 74%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rategammainvar.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateheterogeneity.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateinvar.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratemeyerdiscrete.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratemeyerhaeseler.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratekategory.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratefree.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratefreeinvar.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratefree.cpp:13: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateheterotachy.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateheterotachyinvar.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelcodon.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelcodon.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelcodon.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelunrest.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 44 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelunrest.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelunrest.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:9: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:10: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:13: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelliemarkov.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.cpp:1: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.cpp:1: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelliemarkov.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= Scanning dependencies of target tree make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o [ 86%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/iqtree.cpp cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/candidateset.cpp cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/constrainttree.cpp cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/matree.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/iqtree.cpp:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/memslot.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/mexttree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/mtreeset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/ncbitree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/node.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylonode.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylonodemixlen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylosupertree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylosupertreeplen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp:34: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] 1202 | } | ^ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreepars.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreesse.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/quartet.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/tinatree.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/parstree.cpp [ 97%] Linking CXX static library libtree.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/iqtree.dir/DependInfo.cmake --color= Scanning dependencies of target iqtree make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp [ 99%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/main.cpp /usr/bin/c++ -DIQ_TREE -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/obsolete/parsmultistate.cpp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/main.cpp:232:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 862 | << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:21: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:30: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:33: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(SeqType)’: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] 164 | } | ^ [100%] Linking CXX executable iqtree /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+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/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree -L/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lib -Wl,-rpath,/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree ] ; then mv build.omp/iqtree build.omp/iqtree-omp ; fi dh_auto_build -Bbuild.mpi cd build.mpi && make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -B/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= Scanning dependencies of target gsl make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 1%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/binomial_tpe.cpp Scanning dependencies of target kernelsse make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build Scanning dependencies of target ncl make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 2%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylokernelsse.cpp Scanning dependencies of target pll [ 3%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsassumptionsblock.cpp make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 4%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/alignment.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/alignment.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/alignment.c:40: /build/iqtree-X08Fx2/iqtree-1.6.12+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/multinomial.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/multinomial.cpp [ 4%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/bipartitionList.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c [ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/pow_int.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c:49: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/bipartitionList.c: In function ‘insertHashRF’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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)); | ^~~~~~~~~~~~~~~~~~ [ 5%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gauss.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/gauss.cpp [ 6%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluateGenericSpecial.c:46: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 7%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/gaussinv.cpp [ 8%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl/gausspdf.cpp [ 8%] Linking CXX static library libgsl.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 8%] Built target gsl make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= Scanning dependencies of target lbfgsb make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 9%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/lbfgsb && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lbfgsb/lbfgsb_new.cpp [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:45: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c:31: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsblock.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:113: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/fastDNAparsimony.c: In function ‘compressDNA’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hardware.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/hardware.c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/hardware.c: In function ‘pll_probe_cpu’: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/hash.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/hash.c [ 12%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxscharactersblock.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/lexer.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/lexer.c [ 13%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c [ 14%] Linking CXX static library liblbfgsb.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:44: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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)); | ^~~~~~~~~~~~~~~~~~ /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 14%] Built target lbfgsb make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= Scanning dependencies of target kernelfma make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 15%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylokernelfma.cpp [ 16%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/models.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/models.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/models.c:53: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 16%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newick.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newick.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newick.c:36: /build/iqtree-X08Fx2/iqtree-1.6.12+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/newviewGenericSpecial.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:49: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c:32: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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)); | ^~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdatablock.cpp [ 18%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdiscretedatum.cpp [ 19%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/genericParallelization.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/genericParallelization.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/genericParallelization.c:43: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdiscretematrix.cpp [ 20%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/optimizeModel.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/optimizeModel.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/optimizeModel.c:47: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 20%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdistancedatum.cpp [ 21%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/parsePartition.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/parsePartition.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/parsePartition.c:42: /build/iqtree-X08Fx2/iqtree-1.6.12+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 ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsdistancesblock.cpp [ 22%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/queue.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/queue.c [ 23%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/randomTree.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/randomTree.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/randomTree.c:37: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 23%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/recom.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/recom.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/recom.c:43: /build/iqtree-X08Fx2/iqtree-1.6.12+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 C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/restartHashTable.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/restartHashTable.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/restartHashTable.c:47: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 25%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/searchAlgo.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/searchAlgo.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/searchAlgo.c:51: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 25%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/ssort.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/ssort.c [ 26%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/stack.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/stack.c [ 26%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/topologies.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/topologies.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/topologies.c:48: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 27%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/trash.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/trash.c [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsemptyblock.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/trash.c:48: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 27%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/treeIO.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/treeIO.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/treeIO.c:49: /build/iqtree-X08Fx2/iqtree-1.6.12+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); | ^~~~~~~~~~~~~~~ [ 28%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pll.dir/utils.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c:70: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/pll/pllInternal.h:16, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c:70: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/utils.c: In function ‘initializePartitionData’: /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+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) * | ^~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsexception.cpp [ 30%] Linking C static library libpll.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 /usr/bin/ranlib libpll.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 30%] Built target pll make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= Scanning dependencies of target kernelavx make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 31%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreeavx.cpp [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsreader.cpp [ 32%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxssetreader.cpp [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxsstring.cpp [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxstaxablock.cpp [ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxstoken.cpp [ 34%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl/nxstreesblock.cpp [ 35%] Linking CXX static library libncl.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 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-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 35%] Built target ncl make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= Scanning dependencies of target pllavx make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 35%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -D__AVX -mavx -fabi-version=0 -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/avxLikelihood.c In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll/avxLikelihood.c:57: /build/iqtree-X08Fx2/iqtree-1.6.12+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%] Linking C static library libpllavx.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 36%] Built target pllavx make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= Scanning dependencies of target nclextra make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/mpdablock.cpp [ 37%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/msetsblock.cpp [ 38%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/msplitsblock.cpp [ 38%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra/modelsblock.cpp [ 39%] Linking CXX static library libnclextra.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 /usr/bin/ranlib libnclextra.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 39%] Built target nclextra make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= Scanning dependencies of target whtest make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 40%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/eigen.c [ 40%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/eigen_sym.c [ 41%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/random.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/random.c [ 42%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/weisslambda.c [ 42%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/weisslambda_sub.c [ 43%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest.c [ 43%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c: In function ‘ReadData’: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:205:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_sub.c:221:4: warning: ignoring return value of ‘fscanf’, declared with attribute warn_unused_result [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest/whtest_wrapper.cpp [ 45%] Linking CXX static library libwhtest.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 45%] Built target whtest make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= Scanning dependencies of target sprng make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 45%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/lcg64.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/lcg64.c [ 46%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/makeseed.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/makeseed.c [ 46%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/memory.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/memory.c [ 47%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/store.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/store.c [ 48%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/primes-lcg64.c [ 48%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/sprng.dir/checkid.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng/checkid.c [ 49%] Linking C static library libsprng.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 49%] Built target sprng make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= Scanning dependencies of target vectorclass make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 50%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/vectorclass && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/vectorclass/instrset_detect.cpp [ 50%] Linking CXX static library libvectorclass.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/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-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 50%] Built target vectorclass make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= Scanning dependencies of target alignment make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 50%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/pattern.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/pattern.cpp [ 51%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignment.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/alignment.cpp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/alignment.cpp:2925:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 2925 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ [ 51%] 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-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 51%] Built target kernelsse make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= Scanning dependencies of target utils make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 52%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/eigendecomposition.cpp [ 52%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/gzstream.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/gzstream.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/optimization.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/optimization.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/stoprule.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/stoprule.cpp [ 54%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/tools.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/tools.cpp [ 54%] 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 [ 54%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/alignmentpairwise.cpp make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 54%] Built target kernelfma make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= Scanning dependencies of target pda make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 54%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/circularnetwork.cpp [ 55%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/maalignment.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/greedy.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/greedy.cpp [ 56%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/pllnni.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/pllnni.cpp [ 56%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/superalignment.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/gurobiwrapper.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/hashsplitset.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/checkpoint.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pdnetwork.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils/MPIHelper.cpp [ 61%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/superalignmentpairwise.cpp [ 61%] Linking CXX static library libutils.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/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-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 61%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= Scanning dependencies of target model make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 61%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o [ 62%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment/superalignmentpairwiseplen.cpp cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pruning.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pruning.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 63%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/split.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/split.cpp [ 63%] Linking CXX static library libalignment.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 63%] Built target alignment [ 64%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/splitgraph.cpp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:997:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 997 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1052:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1052 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1081:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1081 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.cpp:1095:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1095 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ [ 65%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelbin.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelbin.cpp [ 65%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modeldna.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelbin.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelbin.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 66%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactory.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp [ 66%] 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 In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.cpp:240:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 240 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 66%] Built target kernelavx [ 66%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelprotein.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:24: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:26: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:27: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactory.cpp:30: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 66%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/splitset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/splitset.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.cpp:651:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 651 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 67%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelset.cpp [ 68%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/cc -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/lpwrapper.c.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/lpwrapper.c [ 68%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopd.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/ecopd.cpp [ 69%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelsubst.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelsubst.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelset.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelset.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 69%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/partitionmodel.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/partitionmodelplen.cpp [ 70%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategamma.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rategamma.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rategammainvar.cpp [ 71%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateheterogeneity.cpp [ 72%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/graph.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/graph.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateinvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateinvar.cpp [ 73%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pdtree.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratemeyerdiscrete.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratemeyerhaeseler.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratekategory.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratekategory.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratefree.cpp [ 76%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/pdtreeset.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratefreeinvar.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/ratefree.cpp:13: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateheterotachy.cpp [ 79%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -D__SSE3 -msse3 -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda/ecopdmtreeset.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/rateheterotachyinvar.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelcodon.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelcodon.cpp [ 80%] Linking CXX static library libpda.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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 make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 80%] Built target pda [ 80%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelmixture.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelcodon.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelcodon.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 81%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelunrest.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelunrest.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.cpp:44:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 44 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:9: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:10: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.cpp:13: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelunrest.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelunrest.cpp:8: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 82%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelliemarkov.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomo.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.cpp:1: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.cpp:1: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:23, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomo.h:4, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.h:14, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelpomomixture.cpp:9: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/model/modelliemarkov.h:11, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelliemarkov.cpp:25: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactorymixlen.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelfactorymixlen.cpp:12: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 84%] Linking CXX static library libmodel.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= Scanning dependencies of target tree make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 85%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o [ 85%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/candidateset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/candidateset.cpp cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/constrainttree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/iqtree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/iqtree.cpp [ 86%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/matree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/matree.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/iqtree.cpp:29: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 87%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/memslot.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/memslot.cpp [ 87%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mexttree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/mexttree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/mtree.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/mtreeset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/ncbitree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/node.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/node.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonode.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylonode.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylonodemixlen.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylosupertree.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylosupertreeplen.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp:34: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotree.cpp:1202:1: warning: control reaches end of non-void function [-Wreturn-type] 1202 | } | ^ [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmixture.h:13, from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreemixlen.cpp:12: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreepars.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreesse.cpp In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/phylotreesse.cpp:35: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/quartet.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/quartet.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/supernode.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/tinatree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/tinatree.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/tree.dir/parstree.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree/parstree.cpp [ 97%] Linking CXX static library libtree.a cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /build/iqtree-X08Fx2/iqtree-1.6.12+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/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/iqtree.dir/DependInfo.cmake --color= Scanning dependencies of target iqtree make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 98%] Building CXX object CMakeFiles/iqtree.dir/main/main.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/main.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/main.cpp [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phylotesting.cpp.o [ 99%] Building CXX object CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o [ 99%] Building CXX object CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp /usr/bin/c++ -DIQ_TREE -D_IQTREE_MPI -D_USE_PTHREADS -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -DUSE_EIGEN3 -D__SSE3 -msse3 -o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -c /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/obsolete/parsmultistate.cpp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:862:52: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 862 | << "." << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/main.cpp:232:58: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:35: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:36: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phyloanalysis.cpp:44: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:20: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:142:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 142 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:149:37: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 149 | virtual void readRates(string str) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:156:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 156 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmarkov.h:163:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 163 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:21: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modeldna.h:91:37: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:30: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelprotein.h:69:38: 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-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:33: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model/modelmorphology.h:78:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(SeqType)’: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/main/phylotesting.cpp:164:1: warning: control reaches end of non-void function [-Wreturn-type] 164 | } | ^ [100%] Linking CXX executable iqtree-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+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/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree-mpi -L/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lib -Wl,-rpath,/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a /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 nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree ] ; then mv build.omp/iqtree build.omp/iqtree-omp ; fi dh override_dh_auto_build make[1]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg' debian/rules override_dh_auto_test make[1]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg' # use only the first example for build time test to save time on autobuilders sed '/ myprefix/,$d' debian/Documents_source/example.sh > example.short echo 'time /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo' >> example.short time sh example.short Executing tests using /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/iqtree-omp ... + time /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy IQ-TREE multicore version 1.6.12 for Linux 64-bit built Dec 4 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: e82b8d1c7b27 (AVX, 125 GB RAM) Command: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy Seed: 994577 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Oct 13 19:35:36 2021 Kernel: AVX - 1 threads (32 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 32 cores! HINT: -nt AUTO will automatically determine the best number of threads to use. Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 17 sequences with 1998 columns, 1152 distinct patterns 1009 parsimony-informative, 303 singleton sites, 686 constant sites Gap/Ambiguity Composition p-value 1 LngfishAu 0.15% passed 6.20% 2 LngfishSA 0.00% failed 0.62% 3 LngfishAf 0.05% failed 1.60% 4 Frog 0.05% passed 58.01% 5 Turtle 0.15% passed 44.25% 6 Sphenodon 0.10% passed 59.78% 7 Lizard 0.90% passed 38.67% 8 Crocodile 0.35% failed 2.51% 9 Bird 0.00% failed 0.00% 10 Human 0.00% failed 0.85% 11 Seal 0.00% passed 68.93% 12 Cow 0.00% passed 59.11% 13 Whale 0.00% passed 97.83% 14 Mouse 0.05% failed 1.43% 15 Rat 0.00% passed 39.69% 16 Platypus 0.00% failed 3.46% 17 Opossum 0.00% failed 0.01% **** TOTAL 0.11% 8 sequences failed composition chi2 test (p-value<5%; df=3) Create initial parsimony tree by phylogenetic likelihood library (PLL)... 0.003 seconds NOTE: ModelFinder requires 6 MB RAM! ModelFinder will test 286 DNA models (sample size: 1998) ... No. Model -LnL df AIC AICc BIC 1 JC 23650.090 31 47362.181 47363.190 47535.778 2 JC+I 22582.953 32 45229.905 45230.980 45409.102 3 JC+G4 22261.254 32 44586.508 44587.583 44765.705 4 JC+I+G4 22247.807 33 44561.614 44562.756 44746.411 5 JC+R2 22284.451 33 44634.902 44636.044 44819.699 6 JC+R3 22237.152 35 44544.304 44545.588 44740.300 7 JC+R4 22237.058 37 44548.115 44549.550 44755.312 14 F81+F 23509.732 34 47087.463 47088.676 47277.860 15 F81+F+I 22401.487 35 44872.975 44874.259 45068.971 16 F81+F+G4 22037.142 35 44144.285 44145.569 44340.281 17 F81+F+I+G4 22024.011 36 44120.022 44121.381 44321.619 18 F81+F+R2 22074.203 36 44220.406 44221.764 44422.002 19 F81+F+R3 22015.103 38 44106.205 44107.718 44319.002 20 F81+F+R4 22015.031 40 44110.061 44111.737 44334.057 27 K2P 23306.003 32 46676.005 46677.080 46855.202 28 K2P+I 22218.512 33 44503.024 44504.166 44687.820 29 K2P+G4 21852.729 33 43771.457 43772.600 43956.254 30 K2P+I+G4 21838.000 34 43744.000 43745.212 43934.396 31 K2P+R2 21897.033 34 43862.067 43863.279 44052.464 32 K2P+R3 21827.620 36 43727.239 43728.598 43928.836 33 K2P+R4 21827.579 38 43731.159 43732.672 43943.955 40 HKY+F 23122.817 35 46315.634 46316.919 46511.631 41 HKY+F+I 21962.106 36 43996.212 43997.570 44197.808 42 HKY+F+G4 21498.501 36 43069.001 43070.360 43270.598 43 HKY+F+I+G4 21483.767 37 43041.534 43042.969 43248.731 44 HKY+F+R2 21586.303 37 43246.606 43248.040 43453.802 45 HKY+F+R3 21471.393 39 43020.786 43022.379 43239.182 46 HKY+F+R4 21471.360 41 43024.721 43026.481 43254.317 53 TNe 23212.914 33 46491.829 46492.971 46676.626 54 TNe+I 22133.437 34 44334.873 44336.086 44525.270 55 TNe+G4 21727.286 34 43522.572 43523.784 43712.969 56 TNe+I+G4 21717.355 35 43504.711 43505.995 43700.707 57 TNe+R2 21782.582 35 43635.164 43636.448 43831.160 58 TNe+R3 21712.362 37 43498.724 43500.159 43705.920 59 TNe+R4 21712.293 39 43502.585 43504.179 43720.981 66 TN+F 22996.000 36 46064.000 46065.359 46265.597 67 TN+F+I 21865.731 37 43805.463 43806.897 44012.659 68 TN+F+G4 21381.494 37 42836.988 42838.423 43044.184 69 TN+F+I+G4 21372.252 38 42820.504 42822.017 43033.300 70 TN+F+R2 21468.251 38 43012.502 43014.015 43225.299 71 TN+F+R3 21369.063 40 42818.126 42819.802 43042.122 72 TN+F+R4 21369.053 42 42822.106 42823.953 43057.302 79 K3P 23305.550 33 46677.101 46678.243 46861.897 80 K3P+I 22218.096 34 44504.192 44505.405 44694.589 81 K3P+G4 21852.521 34 43773.041 43774.254 43963.438 82 K3P+I+G4 21837.967 35 43745.934 43747.218 43941.931 83 K3P+R2 21896.658 35 43863.317 43864.601 44059.314 84 K3P+R3 21827.528 37 43729.057 43730.492 43936.253 85 K3P+R4 21827.427 39 43732.855 43734.448 43951.251 92 K3Pu+F 23122.378 36 46316.756 46318.114 46518.352 93 K3Pu+F+I 21961.415 37 43996.830 43998.265 44204.026 94 K3Pu+F+G4 21498.044 37 43070.087 43071.522 43277.284 95 K3Pu+F+I+G4 21483.337 38 43042.675 43044.188 43255.471 96 K3Pu+F+R2 21585.224 38 43246.449 43247.962 43459.245 97 K3Pu+F+R3 21471.104 40 43022.208 43023.885 43246.205 98 K3Pu+F+R4 21471.067 42 43026.133 43027.981 43261.329 105 TPM2+F 22822.041 36 45716.081 45717.440 45917.678 106 TPM2+F+I 21713.154 37 43500.308 43501.743 43707.504 107 TPM2+F+G4 21311.673 37 42697.345 42698.780 42904.542 108 TPM2+F+I+G4 21298.849 38 42673.698 42675.211 42886.494 109 TPM2+F+R2 21369.634 38 42815.269 42816.782 43028.065 110 TPM2+F+R3 21290.291 40 42660.582 42662.258 42884.578 111 TPM2+F+R4 21290.280 42 42664.560 42666.407 42899.756 118 TPM2u+F 22822.039 36 45716.078 45717.436 45917.674 119 TPM2u+F+I 21713.155 37 43500.310 43501.745 43707.507 120 TPM2u+F+G4 21311.689 37 42697.378 42698.813 42904.575 121 TPM2u+F+I+G4 21298.832 38 42673.665 42675.178 42886.461 122 TPM2u+F+R2 21369.633 38 42815.267 42816.780 43028.063 123 TPM2u+F+R3 21290.291 40 42660.582 42662.258 42884.578 124 TPM2u+F+R4 21290.290 42 42664.580 42666.427 42899.776 131 TPM3+F 23121.230 36 46314.459 46315.818 46516.056 132 TPM3+F+I 21961.610 37 43997.220 43998.655 44204.417 133 TPM3+F+G4 21497.751 37 43069.501 43070.936 43276.698 134 TPM3+F+I+G4 21482.992 38 43041.983 43043.496 43254.779 135 TPM3+F+R2 21586.294 38 43248.589 43250.102 43461.385 136 TPM3+F+R3 21470.760 40 43021.519 43023.195 43245.515 137 TPM3+F+R4 21470.700 42 43025.400 43027.247 43260.596 144 TPM3u+F 23121.227 36 46314.454 46315.813 46516.051 145 TPM3u+F+I 21961.610 37 43997.219 43998.654 44204.416 146 TPM3u+F+G4 21497.747 37 43069.493 43070.928 43276.689 147 TPM3u+F+I+G4 21482.990 38 43041.981 43043.494 43254.777 148 TPM3u+F+R2 21586.295 38 43248.590 43250.103 43461.386 149 TPM3u+F+R3 21470.771 40 43021.542 43023.219 43245.539 150 TPM3u+F+R4 21470.686 42 43025.372 43027.219 43260.568 157 TIMe 23212.472 34 46492.944 46494.157 46683.341 158 TIMe+I 22133.046 35 44336.091 44337.376 44532.088 159 TIMe+G4 21727.188 35 43524.377 43525.661 43720.373 160 TIMe+I+G4 21717.269 36 43506.539 43507.897 43708.135 161 TIMe+R2 21782.296 36 43636.592 43637.951 43838.189 162 TIMe+R3 21712.262 38 43500.524 43502.037 43713.320 163 TIMe+R4 21712.214 40 43504.428 43506.104 43728.424 170 TIM+F 22995.561 37 46065.122 46066.556 46272.318 171 TIM+F+I 21865.037 38 43806.074 43807.587 44018.870 172 TIM+F+G4 21381.147 38 42838.295 42839.808 43051.091 173 TIM+F+I+G4 21371.853 39 42821.707 42823.300 43040.103 174 TIM+F+R2 21467.368 39 43012.736 43014.330 43231.132 175 TIM+F+R3 21368.698 41 42819.396 42821.157 43048.992 176 TIM+F+R4 21368.665 43 42823.330 42825.266 43064.126 183 TIM2e 22744.601 34 45557.202 45558.415 45747.599 184 TIM2e+I 21720.391 35 43510.781 43512.066 43706.778 185 TIM2e+G4 21330.698 35 42731.397 42732.681 42927.393 186 TIM2e+I+G4 21317.957 36 42707.915 42709.273 42909.511 187 TIM2e+R2 21385.483 36 42842.966 42844.324 43044.562 188 TIM2e+R3 21311.772 38 42699.544 42701.057 42912.340 189 TIM2e+R4 21311.625 40 42703.251 42704.927 42927.247 196 TIM2+F 22711.070 37 45496.140 45497.574 45703.336 197 TIM2+F+I 21627.479 38 43330.958 43332.471 43543.754 198 TIM2+F+G4 21172.248 38 42420.496 42422.009 42633.292 199 TIM2+F+I+G4 21164.169 39 42406.339 42407.932 42624.735 200 TIM2+F+R2 21250.860 39 42579.719 42581.313 42798.115 201 TIM2+F+R3 21161.472 41 42404.944 42406.705 42634.540 202 TIM2+F+R4 21161.446 43 42408.893 42410.829 42649.688 209 TIM3e 23211.506 34 46491.012 46492.224 46681.409 210 TIM3e+I 22132.948 35 44335.895 44337.180 44531.892 211 TIM3e+G4 21726.608 35 43523.217 43524.501 43719.213 212 TIM3e+I+G4 21716.694 36 43505.389 43506.747 43706.985 213 TIM3e+R2 21782.533 36 43637.066 43638.425 43838.663 214 TIM3e+R3 21711.818 38 43499.636 43501.149 43712.432 215 TIM3e+R4 21711.743 40 43503.485 43505.161 43727.482 222 TIM3+F 22994.252 37 46062.504 46063.938 46269.700 223 TIM3+F+I 21865.205 38 43806.411 43807.924 44019.207 224 TIM3+F+G4 21380.441 38 42836.881 42838.394 43049.678 225 TIM3+F+I+G4 21371.201 39 42820.403 42821.996 43038.799 226 TIM3+F+R2 21468.161 39 43014.322 43015.915 43232.718 227 TIM3+F+R3 21368.552 41 42819.105 42820.865 43048.701 228 TIM3+F+R4 21368.425 43 42822.850 42824.787 43063.646 235 TVMe 22817.712 35 45705.425 45706.709 45901.421 236 TVMe+I 21797.850 36 43667.700 43669.058 43869.296 237 TVMe+G4 21428.286 36 42928.571 42929.930 43130.168 238 TVMe+I+G4 21413.119 37 42900.238 42901.673 43107.434 239 TVMe+R2 21479.691 37 43033.382 43034.817 43240.578 240 TVMe+R3 21406.121 39 42890.243 42891.836 43108.639 241 TVMe+R4 21406.009 41 42894.018 42895.778 43123.614 248 TVM+F 22815.643 38 45707.287 45708.800 45920.083 249 TVM+F+I 21707.713 39 43493.427 43495.020 43711.823 250 TVM+F+G4 21307.950 39 42693.901 42695.494 42912.297 251 TVM+F+I+G4 21295.083 40 42670.167 42671.843 42894.163 252 TVM+F+R2 21366.214 40 42812.428 42814.104 43036.424 253 TVM+F+R3 21286.822 42 42657.645 42659.492 42892.840 254 TVM+F+R4 21286.744 44 42661.489 42663.517 42907.885 261 SYM 22738.988 36 45549.977 45551.335 45751.573 262 SYM+I 21715.761 37 43505.521 43506.956 43712.718 263 SYM+G4 21327.259 37 42728.517 42729.952 42935.714 264 SYM+I+G4 21314.475 38 42704.950 42706.463 42917.746 265 SYM+R2 21382.507 38 42841.013 42842.526 43053.810 266 SYM+R3 21308.460 40 42696.920 42698.596 42920.916 267 SYM+R4 21308.453 42 42700.906 42702.754 42936.102 274 GTR+F 22704.654 39 45487.307 45488.901 45705.703 275 GTR+F+I 21622.109 40 43324.218 43325.894 43548.214 276 GTR+F+G4 21168.172 40 42416.343 42418.020 42640.340 277 GTR+F+I+G4 21160.196 41 42402.391 42404.152 42631.987 278 GTR+F+R2 21247.036 41 42576.071 42577.832 42805.667 279 GTR+F+R3 21157.734 43 42401.468 42403.405 42642.264 280 GTR+F+R4 21157.665 45 42405.331 42407.452 42657.326 Akaike Information Criterion: GTR+F+R3 Corrected Akaike Information Criterion: GTR+F+R3 Bayesian Information Criterion: TIM2+F+I+G4 Best-fit model: TIM2+F+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 30.297 seconds (0h:0m:30s) Wall-clock time for ModelFinder: 39.425 seconds (0h:0m:39s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.485 / LogL: -21172.273 Init pinv, alpha: 0.038, 1.000 / Estimate: 0.047, 0.538 / LogL: -21168.913 Init pinv, alpha: 0.076, 1.000 / Estimate: 0.100, 0.618 / LogL: -21165.840 Init pinv, alpha: 0.114, 1.000 / Estimate: 0.123, 0.663 / LogL: -21164.910 Init pinv, alpha: 0.153, 1.000 / Estimate: 0.156, 0.736 / LogL: -21164.117 Init pinv, alpha: 0.191, 1.000 / Estimate: 0.185, 0.813 / LogL: -21164.278 Init pinv, alpha: 0.229, 1.000 / Estimate: 0.190, 0.826 / LogL: -21164.407 Init pinv, alpha: 0.267, 1.000 / Estimate: 0.190, 0.828 / LogL: -21164.424 Init pinv, alpha: 0.305, 1.000 / Estimate: 0.190, 0.827 / LogL: -21164.417 Init pinv, alpha: 0.343, 1.000 / Estimate: 0.189, 0.823 / LogL: -21164.376 Optimal pinv,alpha: 0.156, 0.736 / LogL: -21164.117 Parameters optimization took 4.404 sec Computing ML distances based on estimated model parameters... 0.008 sec Computing BIONJ tree... 0.001 seconds Log-likelihood of BIONJ tree: -21157.759 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.537 second Computing log-likelihood of 98 initial trees ... 2.561 seconds Current best score: -21157.759 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -21157.726 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -21152.525 Iteration 10 / LogL: -21152.611 / Time: 0h:0m:9s Iteration 20 / LogL: -21152.555 / Time: 0h:0m:11s Finish initializing candidate tree set (2) Current best tree score: -21152.525 / CPU time: 6.585 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -21152.590 / Time: 0h:0m:12s (0h:0m:32s left) Iteration 40 / LogL: -21152.536 / Time: 0h:0m:15s (0h:0m:23s left) Iteration 50 / LogL: -21157.935 / Time: 0h:0m:17s (0h:0m:18s left) Iteration 60 / LogL: -21152.616 / Time: 0h:0m:19s (0h:0m:13s left) Iteration 70 / LogL: -21152.994 / Time: 0h:0m:21s (0h:0m:9s left) Iteration 80 / LogL: -21152.532 / Time: 0h:0m:23s (0h:0m:6s left) Iteration 90 / LogL: -21152.923 / Time: 0h:0m:25s (0h:0m:3s left) Iteration 100 / LogL: -21152.757 / Time: 0h:0m:27s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:27s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -21152.525 Optimal log-likelihood: -21152.523 Rate parameters: A-C: 5.58055 A-G: 7.64567 A-T: 5.58055 C-G: 1.00000 C-T: 22.62532 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.157 Gamma shape alpha: 0.736 Parameters optimization took 1 rounds (0.050 sec) BEST SCORE FOUND : -21152.523 Total tree length: 4.218 Total number of iterations: 103 CPU time used for tree search: 17.945 sec (0h:0m:17s) Wall-clock time used for tree search: 23.139 sec (0h:0m:23s) Total CPU time used: 21.409 sec (0h:0m:21s) Total wall-clock time used: 27.657 sec (0h:0m:27s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Wed Oct 13 19:36:44 2021 51.72user 0.30system 1:07.10elapsed 77%CPU (0avgtext+0avgdata 14432maxresident)k 0inputs+184outputs (0major+4124minor)pagefaults 0swaps + time /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo IQ-TREE multicore version 1.6.12 for Linux 64-bit built Dec 4 2019 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: e82b8d1c7b27 (AVX, 125 GB RAM) Command: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/iqtree-omp -s example.phy -omp 2 -redo Seed: 100908 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Oct 13 19:36:44 2021 Kernel: AVX - 2 threads (32 CPU cores detected) Reading alignment file example.phy ... Phylip format detected Alignment most likely contains DNA/RNA sequences Alignment has 17 sequences with 1998 columns, 1152 distinct patterns 1009 parsimony-informative, 303 singleton sites, 686 constant sites Gap/Ambiguity Composition p-value 1 LngfishAu 0.15% passed 6.20% 2 LngfishSA 0.00% failed 0.62% 3 LngfishAf 0.05% failed 1.60% 4 Frog 0.05% passed 58.01% 5 Turtle 0.15% passed 44.25% 6 Sphenodon 0.10% passed 59.78% 7 Lizard 0.90% passed 38.67% 8 Crocodile 0.35% failed 2.51% 9 Bird 0.00% failed 0.00% 10 Human 0.00% failed 0.85% 11 Seal 0.00% passed 68.93% 12 Cow 0.00% passed 59.11% 13 Whale 0.00% passed 97.83% 14 Mouse 0.05% failed 1.43% 15 Rat 0.00% passed 39.69% 16 Platypus 0.00% failed 3.46% 17 Opossum 0.00% failed 0.01% **** TOTAL 0.11% 8 sequences failed composition chi2 test (p-value<5%; df=3) NOTE: Restoring information from model checkpoint file example.phy.model.gz CHECKPOINT: Initial tree restored NOTE: ModelFinder requires 6 MB RAM! ModelFinder will test 286 DNA models (sample size: 1998) ... No. Model -LnL df AIC AICc BIC 1 JC 23650.090 31 47362.181 47363.190 47535.778 2 JC+I 22582.953 32 45229.905 45230.980 45409.102 3 JC+G4 22261.254 32 44586.509 44587.583 44765.705 4 JC+I+G4 22247.807 33 44561.614 44562.756 44746.411 5 JC+R2 22284.451 33 44634.902 44636.044 44819.699 6 JC+R3 22237.152 35 44544.304 44545.588 44740.300 7 JC+R4 22237.058 37 44548.115 44549.550 44755.312 14 F81+F 23509.732 34 47087.463 47088.676 47277.860 15 F81+F+I 22401.487 35 44872.975 44874.259 45068.971 16 F81+F+G4 22037.142 35 44144.285 44145.569 44340.281 17 F81+F+I+G4 22024.011 36 44120.022 44121.381 44321.619 18 F81+F+R2 22074.203 36 44220.406 44221.764 44422.002 19 F81+F+R3 22015.103 38 44106.205 44107.718 44319.002 20 F81+F+R4 22015.031 40 44110.061 44111.737 44334.057 27 K2P 23306.003 32 46676.005 46677.080 46855.202 28 K2P+I 22218.512 33 44503.024 44504.166 44687.820 29 K2P+G4 21852.729 33 43771.457 43772.600 43956.254 30 K2P+I+G4 21838.000 34 43744.000 43745.212 43934.396 31 K2P+R2 21897.033 34 43862.067 43863.279 44052.464 32 K2P+R3 21827.620 36 43727.239 43728.598 43928.836 33 K2P+R4 21827.579 38 43731.159 43732.672 43943.955 40 HKY+F 23122.817 35 46315.634 46316.919 46511.631 41 HKY+F+I 21962.106 36 43996.212 43997.570 44197.808 42 HKY+F+G4 21498.501 36 43069.001 43070.360 43270.598 43 HKY+F+I+G4 21483.767 37 43041.534 43042.969 43248.731 44 HKY+F+R2 21586.303 37 43246.606 43248.040 43453.802 45 HKY+F+R3 21471.393 39 43020.786 43022.379 43239.182 46 HKY+F+R4 21471.360 41 43024.721 43026.481 43254.317 53 TNe 23212.914 33 46491.829 46492.971 46676.626 54 TNe+I 22133.437 34 44334.873 44336.086 44525.270 55 TNe+G4 21727.286 34 43522.572 43523.784 43712.969 56 TNe+I+G4 21717.355 35 43504.711 43505.995 43700.707 57 TNe+R2 21782.582 35 43635.164 43636.448 43831.160 58 TNe+R3 21712.362 37 43498.724 43500.159 43705.920 59 TNe+R4 21712.293 39 43502.585 43504.179 43720.981 66 TN+F 22996.000 36 46064.000 46065.359 46265.597 67 TN+F+I 21865.731 37 43805.463 43806.897 44012.659 68 TN+F+G4 21381.494 37 42836.988 42838.423 43044.184 69 TN+F+I+G4 21372.252 38 42820.504 42822.017 43033.300 70 TN+F+R2 21468.251 38 43012.502 43014.015 43225.299 71 TN+F+R3 21369.063 40 42818.126 42819.802 43042.122 72 TN+F+R4 21369.053 42 42822.106 42823.953 43057.302 79 K3P 23305.550 33 46677.101 46678.243 46861.897 80 K3P+I 22218.096 34 44504.192 44505.405 44694.589 81 K3P+G4 21852.521 34 43773.041 43774.254 43963.438 82 K3P+I+G4 21837.967 35 43745.934 43747.218 43941.931 83 K3P+R2 21896.658 35 43863.317 43864.601 44059.314 84 K3P+R3 21827.528 37 43729.057 43730.492 43936.253 85 K3P+R4 21827.427 39 43732.855 43734.448 43951.251 92 K3Pu+F 23122.378 36 46316.756 46318.114 46518.352 93 K3Pu+F+I 21961.415 37 43996.830 43998.265 44204.026 94 K3Pu+F+G4 21498.044 37 43070.087 43071.522 43277.284 95 K3Pu+F+I+G4 21483.337 38 43042.675 43044.188 43255.471 96 K3Pu+F+R2 21585.224 38 43246.449 43247.962 43459.245 97 K3Pu+F+R3 21471.104 40 43022.208 43023.885 43246.205 98 K3Pu+F+R4 21471.067 42 43026.133 43027.981 43261.329 105 TPM2+F 22822.041 36 45716.082 45717.440 45917.678 106 TPM2+F+I 21713.154 37 43500.308 43501.743 43707.504 107 TPM2+F+G4 21311.673 37 42697.345 42698.780 42904.542 108 TPM2+F+I+G4 21298.849 38 42673.698 42675.211 42886.494 109 TPM2+F+R2 21369.634 38 42815.269 42816.782 43028.065 110 TPM2+F+R3 21290.291 40 42660.582 42662.258 42884.578 111 TPM2+F+R4 21290.280 42 42664.560 42666.407 42899.756 118 TPM2u+F 22822.039 36 45716.078 45717.436 45917.674 119 TPM2u+F+I 21713.155 37 43500.310 43501.745 43707.507 120 TPM2u+F+G4 21311.689 37 42697.378 42698.813 42904.575 121 TPM2u+F+I+G4 21298.832 38 42673.664 42675.178 42886.461 122 TPM2u+F+R2 21369.633 38 42815.267 42816.780 43028.063 123 TPM2u+F+R3 21290.291 40 42660.582 42662.258 42884.578 124 TPM2u+F+R4 21290.290 42 42664.580 42666.427 42899.776 131 TPM3+F 23121.230 36 46314.459 46315.818 46516.056 132 TPM3+F+I 21961.610 37 43997.220 43998.655 44204.417 133 TPM3+F+G4 21497.751 37 43069.501 43070.936 43276.698 134 TPM3+F+I+G4 21482.992 38 43041.983 43043.496 43254.779 135 TPM3+F+R2 21586.294 38 43248.589 43250.102 43461.385 136 TPM3+F+R3 21470.760 40 43021.519 43023.195 43245.515 137 TPM3+F+R4 21470.700 42 43025.400 43027.247 43260.596 144 TPM3u+F 23121.227 36 46314.454 46315.813 46516.051 145 TPM3u+F+I 21961.610 37 43997.219 43998.654 44204.416 146 TPM3u+F+G4 21497.747 37 43069.493 43070.928 43276.689 147 TPM3u+F+I+G4 21482.990 38 43041.981 43043.494 43254.777 148 TPM3u+F+R2 21586.295 38 43248.590 43250.103 43461.386 149 TPM3u+F+R3 21470.771 40 43021.543 43023.219 43245.539 150 TPM3u+F+R4 21470.686 42 43025.372 43027.219 43260.568 157 TIMe 23212.472 34 46492.944 46494.157 46683.341 158 TIMe+I 22133.046 35 44336.091 44337.376 44532.088 159 TIMe+G4 21727.188 35 43524.377 43525.661 43720.373 160 TIMe+I+G4 21717.269 36 43506.539 43507.897 43708.135 161 TIMe+R2 21782.296 36 43636.592 43637.951 43838.189 162 TIMe+R3 21712.262 38 43500.524 43502.037 43713.320 163 TIMe+R4 21712.214 40 43504.428 43506.104 43728.424 170 TIM+F 22995.561 37 46065.122 46066.556 46272.318 171 TIM+F+I 21865.037 38 43806.074 43807.587 44018.870 172 TIM+F+G4 21381.147 38 42838.295 42839.808 43051.091 173 TIM+F+I+G4 21371.853 39 42821.707 42823.300 43040.103 174 TIM+F+R2 21467.368 39 43012.736 43014.330 43231.132 175 TIM+F+R3 21368.698 41 42819.396 42821.157 43048.992 176 TIM+F+R4 21368.665 43 42823.330 42825.266 43064.126 183 TIM2e 22744.601 34 45557.202 45558.415 45747.599 184 TIM2e+I 21720.391 35 43510.781 43512.066 43706.778 185 TIM2e+G4 21330.698 35 42731.397 42732.681 42927.393 186 TIM2e+I+G4 21317.957 36 42707.915 42709.273 42909.511 187 TIM2e+R2 21385.483 36 42842.966 42844.324 43044.562 188 TIM2e+R3 21311.772 38 42699.544 42701.057 42912.340 189 TIM2e+R4 21311.625 40 42703.251 42704.927 42927.247 196 TIM2+F 22711.070 37 45496.140 45497.574 45703.336 197 TIM2+F+I 21627.479 38 43330.958 43332.471 43543.754 198 TIM2+F+G4 21172.248 38 42420.496 42422.009 42633.292 199 TIM2+F+I+G4 21164.169 39 42406.339 42407.932 42624.735 200 TIM2+F+R2 21250.860 39 42579.719 42581.313 42798.115 201 TIM2+F+R3 21161.472 41 42404.944 42406.705 42634.540 202 TIM2+F+R4 21161.446 43 42408.893 42410.829 42649.688 209 TIM3e 23211.506 34 46491.012 46492.224 46681.409 210 TIM3e+I 22132.948 35 44335.895 44337.180 44531.892 211 TIM3e+G4 21726.608 35 43523.217 43524.501 43719.213 212 TIM3e+I+G4 21716.694 36 43505.389 43506.747 43706.985 213 TIM3e+R2 21782.533 36 43637.066 43638.425 43838.663 214 TIM3e+R3 21711.818 38 43499.636 43501.149 43712.432 215 TIM3e+R4 21711.743 40 43503.485 43505.161 43727.482 222 TIM3+F 22994.252 37 46062.504 46063.938 46269.700 223 TIM3+F+I 21865.205 38 43806.411 43807.924 44019.207 224 TIM3+F+G4 21380.441 38 42836.881 42838.394 43049.678 225 TIM3+F+I+G4 21371.201 39 42820.403 42821.996 43038.799 226 TIM3+F+R2 21468.161 39 43014.322 43015.915 43232.718 227 TIM3+F+R3 21368.552 41 42819.105 42820.865 43048.701 228 TIM3+F+R4 21368.425 43 42822.850 42824.787 43063.646 235 TVMe 22817.712 35 45705.425 45706.709 45901.421 236 TVMe+I 21797.850 36 43667.700 43669.058 43869.296 237 TVMe+G4 21428.286 36 42928.571 42929.930 43130.168 238 TVMe+I+G4 21413.119 37 42900.238 42901.673 43107.434 239 TVMe+R2 21479.691 37 43033.382 43034.817 43240.578 240 TVMe+R3 21406.121 39 42890.243 42891.836 43108.639 241 TVMe+R4 21406.009 41 42894.018 42895.778 43123.614 248 TVM+F 22815.643 38 45707.287 45708.800 45920.083 249 TVM+F+I 21707.713 39 43493.427 43495.020 43711.823 250 TVM+F+G4 21307.950 39 42693.901 42695.494 42912.297 251 TVM+F+I+G4 21295.083 40 42670.167 42671.843 42894.163 252 TVM+F+R2 21366.214 40 42812.428 42814.104 43036.424 253 TVM+F+R3 21286.822 42 42657.645 42659.492 42892.840 254 TVM+F+R4 21286.744 44 42661.489 42663.517 42907.885 261 SYM 22738.988 36 45549.977 45551.335 45751.573 262 SYM+I 21715.761 37 43505.521 43506.956 43712.718 263 SYM+G4 21327.259 37 42728.517 42729.952 42935.714 264 SYM+I+G4 21314.475 38 42704.950 42706.463 42917.746 265 SYM+R2 21382.507 38 42841.013 42842.526 43053.810 266 SYM+R3 21308.460 40 42696.920 42698.596 42920.916 267 SYM+R4 21308.453 42 42700.906 42702.754 42936.102 274 GTR+F 22704.654 39 45487.307 45488.901 45705.703 275 GTR+F+I 21622.109 40 43324.218 43325.894 43548.214 276 GTR+F+G4 21168.172 40 42416.343 42418.020 42640.340 277 GTR+F+I+G4 21160.196 41 42402.391 42404.152 42631.987 278 GTR+F+R2 21247.036 41 42576.071 42577.832 42805.667 279 GTR+F+R3 21157.734 43 42401.468 42403.405 42642.264 280 GTR+F+R4 21157.665 45 42405.331 42407.452 42657.326 Akaike Information Criterion: GTR+F+R3 Corrected Akaike Information Criterion: GTR+F+R3 Bayesian Information Criterion: TIM2+F+I+G4 Best-fit model: TIM2+F+I+G4 chosen according to BIC All model information printed to example.phy.model.gz CPU time for ModelFinder: 0.067 seconds (0h:0m:0s) Wall-clock time for ModelFinder: 0.110 seconds (0h:0m:0s) NOTE: 2 MB RAM (0 GB) is required! Estimate model parameters (epsilon = 0.100) Thoroughly optimizing +I+G parameters from 10 start values... Init pinv, alpha: 0.000, 1.000 / Estimate: 0.000, 0.485 / LogL: -21172.273 Init pinv, alpha: 0.038, 1.000 / Estimate: 0.047, 0.538 / LogL: -21168.913 Init pinv, alpha: 0.076, 1.000 / Estimate: 0.100, 0.618 / LogL: -21165.840 Init pinv, alpha: 0.114, 1.000 / Estimate: 0.123, 0.663 / LogL: -21164.910 Init pinv, alpha: 0.153, 1.000 / Estimate: 0.156, 0.736 / LogL: -21164.117 Init pinv, alpha: 0.191, 1.000 / Estimate: 0.185, 0.813 / LogL: -21164.278 Init pinv, alpha: 0.229, 1.000 / Estimate: 0.190, 0.826 / LogL: -21164.407 Init pinv, alpha: 0.267, 1.000 / Estimate: 0.190, 0.828 / LogL: -21164.424 Init pinv, alpha: 0.305, 1.000 / Estimate: 0.190, 0.827 / LogL: -21164.417 Init pinv, alpha: 0.343, 1.000 / Estimate: 0.189, 0.823 / LogL: -21164.376 Optimal pinv,alpha: 0.156, 0.736 / LogL: -21164.117 Parameters optimization took 7.582 sec Computing ML distances based on estimated model parameters... 0.014 sec Computing BIONJ tree... 0.001 seconds Log-likelihood of BIONJ tree: -21157.759 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.515 second Computing log-likelihood of 98 initial trees ... 3.810 seconds Current best score: -21157.759 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -21157.726 Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 2: -21152.525 Iteration 10 / LogL: -21158.008 / Time: 0h:0m:14s Iteration 20 / LogL: -21158.405 / Time: 0h:0m:17s Finish initializing candidate tree set (2) Current best tree score: -21152.525 / CPU time: 9.418 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -21152.627 / Time: 0h:0m:20s (0h:0m:51s left) Iteration 40 / LogL: -21152.559 / Time: 0h:0m:24s (0h:0m:38s left) Iteration 50 / LogL: -21152.610 / Time: 0h:0m:28s (0h:0m:29s left) Iteration 60 / LogL: -21152.573 / Time: 0h:0m:31s (0h:0m:22s left) Iteration 70 / LogL: -21157.760 / Time: 0h:0m:34s (0h:0m:15s left) Iteration 80 / LogL: -21152.603 / Time: 0h:0m:36s (0h:0m:10s left) Iteration 90 / LogL: -21157.789 / Time: 0h:0m:39s (0h:0m:5s left) Iteration 100 / LogL: -21157.751 / Time: 0h:0m:42s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 103 ITERATIONS / Time: 0h:0m:43s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -21152.525 Optimal log-likelihood: -21152.523 Rate parameters: A-C: 5.58055 A-G: 7.64567 A-T: 5.58055 C-G: 1.00000 C-T: 22.62532 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.157 Gamma shape alpha: 0.736 Parameters optimization took 1 rounds (0.093 sec) BEST SCORE FOUND : -21152.523 Total tree length: 4.218 Total number of iterations: 103 CPU time used for tree search: 27.561 sec (0h:0m:27s) Wall-clock time used for tree search: 35.830 sec (0h:0m:35s) Total CPU time used: 33.566 sec (0h:0m:33s) Total wall-clock time used: 43.618 sec (0h:0m:43s) Analysis results written to: IQ-TREE report: example.phy.iqtree Maximum-likelihood tree: example.phy.treefile Likelihood distances: example.phy.mldist Screen log file: example.phy.log Date and Time: Wed Oct 13 19:37:27 2021 33.65user 0.58system 0:43.79elapsed 78%CPU (0avgtext+0avgdata 12252maxresident)k 0inputs+168outputs (0major+22590minor)pagefaults 0swaps + rm -rf /tmp/iqtree-test.ONsliV 85.41user 0.90system 1:50.94elapsed 77%CPU (0avgtext+0avgdata 14432maxresident)k 0inputs+432outputs (0major+28430minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg' dh_auto_install -Bbuild.omp cd build.omp && make -j4 install DESTDIR=/build/iqtree-X08Fx2/iqtree-1.6.12\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' /usr/bin/cmake -S/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -B/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build [ 4%] Built target gsl make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend [ 5%] Built target kernelsse make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build [ 15%] Built target ncl make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend [ 31%] Built target pll make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build [ 33%] Built target lbfgsb make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= [ 34%] Built target kernelfma make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build [ 35%] Built target pllavx make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend [ 36%] Built target kernelavx make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 39%] Built target nclextra make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 45%] Built target whtest make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build [ 46%] Built target vectorclass make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend [ 50%] Built target sprng make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build [ 54%] Built target alignment make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 66%] Built target pda [ 68%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'model/CMakeFiles/model.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[4]: Nothing to be done for 'tree/CMakeFiles/tree.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles/iqtree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [ 98%] Linking CXX executable iqtree /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -fdebug-prefix-map=/build/iqtree-X08Fx2/iqtree-1.6.12+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/iqtree.dir/main/main.cpp.o CMakeFiles/iqtree.dir/main/phyloanalysis.cpp.o CMakeFiles/iqtree.dir/main/phylotesting.cpp.o CMakeFiles/iqtree.dir/obsolete/parsmultistate.cpp.o -o iqtree -L/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lib -Wl,-rpath,/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lib: pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a -lm libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a nclextra/libnclextra.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/bin/iqtree -- Set runtime path of "/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/bin/iqtree" to "" -- Installing: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./models.nex -- Installing: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.phy -- Installing: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.nex -- Installing: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.omp' dh_auto_install -Bbuild.serial cd build.serial && make -j4 install DESTDIR=/build/iqtree-X08Fx2/iqtree-1.6.12\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' /usr/bin/cmake -S/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -B/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 4%] Built target gsl [ 14%] Built target ncl make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= [ 15%] Built target kernelsse make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 31%] Built target pll make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 33%] Built target lbfgsb make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build [ 34%] Built target kernelfma make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 35%] Built target kernelavx make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= [ 36%] Built target pllavx make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= [ 39%] Built target nclextra make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 40%] Built target vectorclass [ 44%] Built target sprng make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build [ 50%] Built target whtest make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build [ 54%] Built target alignment make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 59%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend [ 68%] Built target pda make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'model/CMakeFiles/model.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'tree/CMakeFiles/tree.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles/iqtree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[4]: Nothing to be done for 'CMakeFiles/iqtree.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/bin/iqtree -- Set runtime path of "/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/bin/iqtree" to "" -- Up-to-date: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.serial' dh_auto_install -Bbuild.mpi cd build.mpi && make -j4 install DESTDIR=/build/iqtree-X08Fx2/iqtree-1.6.12\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' /usr/bin/cmake -S/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg -B/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'gsl/CMakeFiles/gsl.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build [ 4%] Built target gsl make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/lbfgsb /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'ncl/CMakeFiles/ncl.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelsse.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'pll/CMakeFiles/pll.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 6%] Built target kernelsse [ 15%] Built target ncl make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'lbfgsb/CMakeFiles/lbfgsb.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= [ 31%] Built target pll make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= [ 33%] Built target lbfgsb make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/nclextra /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelfma.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/kernelavx.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'pll/CMakeFiles/pllavx.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build [ 34%] Built target kernelfma [ 36%] Built target kernelavx [ 36%] Built target pllavx make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'nclextra/CMakeFiles/nclextra.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/vectorclass /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= [ 39%] Built target nclextra make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'sprng/CMakeFiles/sprng.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'vectorclass/CMakeFiles/vectorclass.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build [ 40%] Built target vectorclass make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend [ 44%] Built target sprng make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'whtest/CMakeFiles/whtest.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build [ 50%] Built target whtest make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'alignment/CMakeFiles/alignment.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'pda/CMakeFiles/pda.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 54%] Built target alignment make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'utils/CMakeFiles/utils.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 63%] Built target pda [ 68%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'model/CMakeFiles/model.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 84%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'tree/CMakeFiles/tree.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [ 97%] Built target tree make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/depend make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' cd /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles/iqtree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make -f CMakeFiles/iqtree.dir/build.make CMakeFiles/iqtree.dir/build make[4]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[4]: Nothing to be done for 'CMakeFiles/iqtree.dir/build'. make[4]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' [100%] Built target iqtree make[3]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' /usr/bin/cmake -E cmake_progress_start /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi/CMakeFiles 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/bin/iqtree-mpi -- Set runtime path of "/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/bin/iqtree-mpi" to "" -- Up-to-date: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./models.nex -- Up-to-date: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.phy -- Up-to-date: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.nex -- Up-to-date: /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg' debian/rules override_dh_install make[1]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg' dh_install find debian -name iqtree-mpi -exec chrpath --delete \{\} \; find debian -name iqtree-omp -exec chrpath --delete \{\} \; make[1]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg' dh_installdocs -a dh_installchangelogs -a debian/rules override_dh_installexamples make[1]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+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-X08Fx2/iqtree-1.6.12+dfsg' debian/rules override_dh_installman make[1]: Entering directory '/build/iqtree-X08Fx2/iqtree-1.6.12+dfsg' mkdir -p /build/iqtree-X08Fx2/iqtree-1.6.12+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="1.6.12+dfsg" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/bin/iqtree > /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/share/man/man1//iqtree.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="1.6.12+dfsg" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/bin/iqtree-omp > /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/share/man/man1//iqtree-omp.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="1.6.12+dfsg" /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/bin/iqtree-mpi > /build/iqtree-X08Fx2/iqtree-1.6.12+dfsg/debian/iqtree/usr/share/man/man1//iqtree-mpi.1 make[1]: Leaving directory '/build/iqtree-X08Fx2/iqtree-1.6.12+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_1.6.12+dfsg-1_amd64.deb'. dpkg-deb: building package 'iqtree-dbgsym' in '../iqtree-dbgsym_1.6.12+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../iqtree_1.6.12+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-X08Fx2 /tmp/iqtree-1.6.12+dfsg-1zuel4lzs I: cleaning package lists and apt cache... I: creating tarball... I: done I: removing tempdir /tmp/mmdebstrap.m7i8sQREzD... I: success in 4626.9365 seconds md5: iqtree-dbgsym_1.6.12+dfsg-1_amd64.deb: OK md5: iqtree_1.6.12+dfsg-1_amd64.deb: OK sha1: iqtree-dbgsym_1.6.12+dfsg-1_amd64.deb: OK sha1: iqtree_1.6.12+dfsg-1_amd64.deb: OK sha256: iqtree-dbgsym_1.6.12+dfsg-1_amd64.deb: OK sha256: iqtree_1.6.12+dfsg-1_amd64.deb: OK Checksums: OK