https://launchpad.net/ubuntu/+archive/test-rebuild-20220617-kinetic/+build/24013293 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lgw01-amd64-036 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 x86_64 Buildd toolchain package versions: launchpad-buildd_215~563~ubuntu20.04.1 python3-lpbuildd_215~563~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git-build-recipe_0.3.6 git_1:2.25.1-1ubuntu3.4 dpkg-dev_1.19.7ubuntu3.2 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 22 Jun 19:11:50 ntpdate[1783]: adjust time server 10.211.37.1 offset 0.000152 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24013293 --image-type chroot /home/buildd/filecache-default/4d18961cd05542d5def75b14497015b674c37821 Creating target for build PACKAGEBUILD-24013293 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24013293 Starting target for build PACKAGEBUILD-24013293 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24013293 'deb http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic main' 'deb http://ftpmaster.internal/ubuntu kinetic main universe' Overriding sources.list in build-PACKAGEBUILD-24013293 RUN: /usr/share/launchpad-buildd/bin/in-target add-trusted-keys --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24013293 Adding trusted keys to build-PACKAGEBUILD-24013293 pub rsa1024/1E9377A2BA9EF27F 2009-10-22 [SC] Key fingerprint = 60C3 1780 3A41 BA51 845E 371A 1E93 77A2 BA9E F27F uid Launchpad Toolchain builds RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24013293 Updating target for build PACKAGEBUILD-24013293 Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic InRelease [23.8 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic InRelease [267 kB] Get:3 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 Packages [9632 B] Get:4 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main Translation-en [4132 B] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 Packages [1398 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main Translation-en [510 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/universe amd64 Packages [14.3 MB] Get:8 http://ftpmaster.internal/ubuntu kinetic/universe Translation-en [5730 kB] Fetched 22.3 MB in 6s (3690 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: libgprofng0 util-linux-extra The following packages will be upgraded: adduser apt base-files binutils binutils-common binutils-x86-64-linux-gnu bsdutils cpp-11 dpkg dpkg-dev e2fsprogs fakeroot g++-11 gcc-11 gcc-11-base gcc-12-base init init-system-helpers libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libbinutils libblkid1 libcap-ng0 libcc1-0 libcom-err2 libctf-nobfd0 libctf0 libdb5.3 libdpkg-perl libext2fs2 libfakeroot libgcc-11-dev libgcc-s1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libip4tc2 libitm1 libkeyutils1 liblsan0 liblzma5 libmount1 libncurses6 libncursesw6 libpng16-16 libquadmath0 libreadline8 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libssl3 libstdc++-11-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 login logsave lto-disabled-list mawk mount ncurses-base ncurses-bin openssl passwd pinentry-curses policyrcd-script-zg2 readline-common systemd systemd-sysv util-linux xz-utils 83 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 79.7 MB of archives. After this operation, 5304 kB of additional disk space will be used. Get:1 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf0 amd64 2.38.50.20220615-4ubuntu1 [103 kB] Get:2 http://ftpmaster.internal/ubuntu kinetic/main amd64 base-files amd64 12.2ubuntu1 [62.6 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdutils amd64 1:2.38-4ubuntu1 [80.7 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main amd64 libzstd1 amd64 1.5.2+dfsg-1 [270 kB] Get:5 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libctf-nobfd0 amd64 2.38.50.20220615-4ubuntu1 [107 kB] Get:6 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-x86-64-linux-gnu amd64 2.38.50.20220615-4ubuntu1 [2476 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 libatomic1 amd64 12.1.0-2ubuntu1 [10.4 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main amd64 libubsan1 amd64 12.1.0-2ubuntu1 [969 kB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 libquadmath0 amd64 12.1.0-2ubuntu1 [152 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblsan0 amd64 12.1.0-2ubuntu1 [1060 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main amd64 libitm1 amd64 12.1.0-2ubuntu1 [29.5 kB] Get:12 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgomp1 amd64 12.1.0-2ubuntu1 [125 kB] Get:13 http://ftpmaster.internal/ubuntu kinetic/main amd64 gcc-12-base amd64 12.1.0-2ubuntu1 [18.8 kB] Get:14 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcc-s1 amd64 12.1.0-2ubuntu1 [54.2 kB] Get:15 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcc1-0 amd64 12.1.0-2ubuntu1 [46.6 kB] Get:16 http://ftpmaster.internal/ubuntu kinetic/main amd64 libstdc++6 amd64 12.1.0-2ubuntu1 [679 kB] Get:17 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgpg-error0 amd64 1.45-2 [69.0 kB] Get:18 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgcrypt20 amd64 1.10.1-2ubuntu1 [524 kB] Get:19 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblzma5 amd64 5.2.5-2.1 [99.2 kB] Get:20 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd-sysv amd64 249.11-0ubuntu4 [10.2 kB] Get:21 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapparmor1 amd64 3.0.4-2ubuntu3 [38.0 kB] Get:22 http://ftpmaster.internal/ubuntu kinetic/main amd64 libgnutls30 amd64 3.7.6-2ubuntu1 [968 kB] Get:23 http://ftpmaster.internal/ubuntu kinetic/main amd64 libip4tc2 amd64 1.8.7-1ubuntu6 [19.7 kB] Get:24 http://ftpmaster.internal/ubuntu kinetic/main amd64 libblkid1 amd64 2.38-4ubuntu1 [103 kB] Get:25 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libbinutils amd64 2.38.50.20220615-4ubuntu1 [655 kB] Get:26 http://ftpmaster.internal/ubuntu kinetic/main amd64 libselinux1 amd64 3.4-1 [77.6 kB] Get:27 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmount1 amd64 2.38-4ubuntu1 [121 kB] Get:28 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsmartcols1 amd64 2.38-4ubuntu1 [50.8 kB] Get:29 http://ftpmaster.internal/ubuntu kinetic/main amd64 login amd64 1:4.11.1+dfsg1-2ubuntu1 [183 kB] Get:30 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux-extra amd64 2.38-4ubuntu1 [83.8 kB] Get:31 http://ftpmaster.internal/ubuntu kinetic/main amd64 util-linux amd64 2.38-4ubuntu1 [1069 kB] Get:32 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils amd64 2.38.50.20220615-4ubuntu1 [3292 B] Get:33 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 binutils-common amd64 2.38.50.20220615-4ubuntu1 [224 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 mount amd64 2.38-4ubuntu1 [114 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage-common all 3.4-1 [9828 B] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsepol2 amd64 3.4-2 [294 kB] Get:37 http://ppa.launchpadcontent.net/ubuntu-toolchain-r/binutils/ubuntu kinetic/main amd64 libgprofng0 amd64 2.38.50.20220615-4ubuntu1 [963 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsemanage2 amd64 3.4-1 [91.8 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main amd64 passwd amd64 1:4.11.1+dfsg1-2ubuntu1 [765 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/main amd64 adduser all 3.121ubuntu1 [150 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main amd64 systemd amd64 249.11-0ubuntu4 [4517 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsystemd0 amd64 249.11-0ubuntu4 [314 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 libudev1 amd64 249.11-0ubuntu4 [76.1 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main amd64 libapt-pkg6.0 amd64 2.5.0 [896 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main amd64 dpkg amd64 1.21.8ubuntu1 [1333 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-bin amd64 6.3+20220423-2 [183 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 init-system-helpers all 1.63 [38.7 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 ncurses-base all 6.3+20220423-2 [21.2 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 apt amd64 2.5.0 [1370 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main amd64 logsave amd64 1.46.5-2ubuntu2 [9914 B] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 libext2fs2 amd64 1.46.5-2ubuntu2 [205 kB] Get:52 http://ftpmaster.internal/ubuntu kinetic/main amd64 e2fsprogs amd64 1.46.5-2ubuntu2 [585 kB] Get:53 http://ftpmaster.internal/ubuntu kinetic/main amd64 init amd64 1.63 [5674 B] Get:54 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcap-ng0 amd64 0.7.9-4 [12.1 kB] Get:55 http://ftpmaster.internal/ubuntu kinetic/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.9 [717 kB] Get:56 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncurses6 amd64 6.3+20220423-2 [110 kB] Get:57 http://ftpmaster.internal/ubuntu kinetic/main amd64 libncursesw6 amd64 6.3+20220423-2 [146 kB] Get:58 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RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-24013293 amd64 kinetic -c chroot:build-PACKAGEBUILD-24013293 --arch=amd64 --dist=kinetic --nolog -A iqtree_2.0.7+dfsg-1.dsc Initiating build PACKAGEBUILD-24013293 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 x86_64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on lgw01-amd64-036.buildd +==============================================================================+ | iqtree 2.0.7+dfsg-1 (amd64) Wed, 22 Jun 2022 19:13:13 +0000 | +==============================================================================+ Package: iqtree Version: 2.0.7+dfsg-1 Source Version: 2.0.7+dfsg-1 Distribution: kinetic Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-24013293/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/iqtree-YFbkzw/resolver-Z8uoxU' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- iqtree_2.0.7+dfsg-1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/iqtree-YFbkzw/iqtree-2.0.7+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/iqtree-YFbkzw' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsprng2-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsprng2-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [424 B] Get:5 copy:/<>/apt_archive ./ Packages [506 B] Fetched 1887 B in 0s (72.0 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils chrpath cmake cmake-data cpp-12 debhelper debugedit dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz emacsen-common file gcc-12 gettext gettext-base gfortran-12 groff-base help2man ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libasan8 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0.8 libcurl3-gnutls libcurl4 libdebhelper-perl libdw1 libedit2 libeigen3-dev libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgcc-12-dev libgfortran-12-dev libgfortran5 libglib2.0-0 libgmp-dev libgmpxx4ldbl libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu71 libjs-jquery libjs-jquery-ui libjsoncpp25 libldap-2.5-0 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsprng2 libsprng2-dev libssh-4 libsub-override-perl libtool libtsan2 libuchardet0 libucx0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config po-debconf time zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build cmake-format gcc-12-locales dh-make gcc-12-multilib gcc-12-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-12-multilib gfortran-12-doc libcoarrays-dev groff lrzip libboost-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libeigen3-doc gmp-doc libgmp10-doc libmpfr-dev libhwloc-contrib-plugins libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils libsprng2-doc gcj-jdk m4-doc apparmor less www-browser opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libldap-common libcoarrays-openmpi-dev publicsuffix libsasl2-modules xauth libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils chrpath cmake cmake-data cpp-12 debhelper debugedit dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz emacsen-common file gcc-12 gettext gettext-base gfortran-12 groff-base help2man ibverbs-providers intltool-debian libarchive-zip-perl libarchive13 libasan8 libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0.8 libcurl3-gnutls libcurl4 libdebhelper-perl libdw1 libedit2 libeigen3-dev libelf1 libevent-2.1-7 libevent-core-2.1-7 libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7 libevent-pthreads-2.1-7 libexpat1 libfabric1 libfido2-1 libfile-stripnondeterminism-perl libgcc-12-dev libgfortran-12-dev libgfortran5 libglib2.0-0 libgmp-dev libgmpxx4ldbl libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu71 libjs-jquery libjs-jquery-ui libjsoncpp25 libldap-2.5-0 liblocale-gettext-perl libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libnghttp2-14 libnl-3-200 libnl-3-dev libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhash0 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsprng2 libsprng2-dev libssh-4 libsub-override-perl libtool libtsan2 libuchardet0 libucx0 libuv1 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 m4 man-db mpi-default-dev ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client pkg-config po-debconf sbuild-build-depends-main-dummy time zlib1g-dev 0 upgraded, 123 newly installed, 0 to remove and 0 not upgraded. Need to get 263 MB of archives. After this operation, 995 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [730 B] Get:2 http://ftpmaster.internal/ubuntu kinetic/main amd64 liblocale-gettext-perl amd64 1.07-4build3 [17.1 kB] Get:3 http://ftpmaster.internal/ubuntu kinetic/main amd64 libmd0 amd64 1.0.4-1build1 [23.0 kB] Get:4 http://ftpmaster.internal/ubuntu kinetic/main amd64 libbsd0 amd64 0.11.6-1 [44.5 kB] Get:5 http://ftpmaster.internal/ubuntu kinetic/main amd64 libelf1 amd64 0.187-1 [51.3 kB] Get:6 http://ftpmaster.internal/ubuntu kinetic/main amd64 libexpat1 amd64 2.4.8-1 [90.6 kB] Get:7 http://ftpmaster.internal/ubuntu kinetic/main amd64 libglib2.0-0 amd64 2.72.2-2 [1435 kB] Get:8 http://ftpmaster.internal/ubuntu kinetic/main amd64 libicu71 amd64 71.1-3 [10.6 MB] Get:9 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxml2 amd64 2.9.14+dfsg-1 [756 kB] Get:10 http://ftpmaster.internal/ubuntu kinetic/main amd64 bsdextrautils amd64 2.38-4ubuntu1 [71.1 kB] Get:11 http://ftpmaster.internal/ubuntu kinetic/main 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http://ftpmaster.internal/ubuntu kinetic/main amd64 openssh-client amd64 1:9.0p1-1 [897 kB] Get:33 http://ftpmaster.internal/ubuntu kinetic/main amd64 time amd64 1.9-0.1build2 [46.7 kB] Get:34 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsigsegv2 amd64 2.13-1ubuntu3 [14.6 kB] Get:35 http://ftpmaster.internal/ubuntu kinetic/main amd64 m4 amd64 1.4.18-5ubuntu2 [199 kB] Get:36 http://ftpmaster.internal/ubuntu kinetic/main amd64 autoconf all 2.71-2 [338 kB] Get:37 http://ftpmaster.internal/ubuntu kinetic/main amd64 autotools-dev all 20220109.1 [44.9 kB] Get:38 http://ftpmaster.internal/ubuntu kinetic/main amd64 automake all 1:1.16.5-1.3 [558 kB] Get:39 http://ftpmaster.internal/ubuntu kinetic/main amd64 autopoint all 0.21-6 [421 kB] Get:40 http://ftpmaster.internal/ubuntu kinetic/universe amd64 chrpath amd64 0.16-2 [13.2 kB] Get:41 http://ftpmaster.internal/ubuntu kinetic/main amd64 libarchive13 amd64 3.6.0-1ubuntu1 [368 kB] Get:42 http://ftpmaster.internal/ubuntu kinetic/main amd64 libbrotli1 amd64 1.0.9-2build6 [315 kB] Get:43 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-6ubuntu1 [20.5 kB] Get:44 http://ftpmaster.internal/ubuntu kinetic/main amd64 libsasl2-2 amd64 2.1.28+dfsg-6ubuntu1 [55.9 kB] Get:45 http://ftpmaster.internal/ubuntu kinetic/main amd64 libldap-2.5-0 amd64 2.5.12+dfsg-2ubuntu1 [180 kB] Get:46 http://ftpmaster.internal/ubuntu kinetic/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build4 [58.2 kB] Get:47 http://ftpmaster.internal/ubuntu kinetic/main amd64 libssh-4 amd64 0.9.6-2build1 [184 kB] Get:48 http://ftpmaster.internal/ubuntu kinetic/main amd64 libcurl4 amd64 7.83.1-2 [285 kB] Get:49 http://ftpmaster.internal/ubuntu kinetic/main amd64 libjsoncpp25 amd64 1.9.5-4 [80.3 kB] Get:50 http://ftpmaster.internal/ubuntu kinetic/main amd64 librhash0 amd64 1.4.2-1ubuntu1 [125 kB] Get:51 http://ftpmaster.internal/ubuntu kinetic/main amd64 dh-elpa-helper all 2.0.9ubuntu1 [7610 B] Get:52 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2.4.7-4 [40.3 kB] Get:101 http://ftpmaster.internal/ubuntu kinetic/main amd64 libltdl-dev amd64 2.4.7-4 [169 kB] Get:102 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnl-3-dev amd64 3.5.0-0.1 [101 kB] Get:103 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnl-route-3-dev amd64 3.5.0-0.1 [202 kB] Get:104 http://ftpmaster.internal/ubuntu kinetic/main amd64 libpciaccess0 amd64 0.16-3 [19.1 kB] Get:105 http://ftpmaster.internal/ubuntu kinetic/main amd64 libxnvctrl0 amd64 510.47.03-0ubuntu1 [11.5 kB] Get:106 http://ftpmaster.internal/ubuntu kinetic/universe amd64 ocl-icd-libopencl1 amd64 2.2.14-3 [39.1 kB] Get:107 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhwloc-plugins amd64 2.7.1-1 [15.6 kB] Get:108 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libpmix2 amd64 4.1.2-2ubuntu1 [604 kB] Get:109 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libucx0 amd64 1.13.0~rc1-1 [911 kB] Get:110 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libopenmpi3 amd64 4.1.4-1ubuntu1 [2382 kB] Get:111 http://ftpmaster.internal/ubuntu kinetic/main amd64 libnuma-dev amd64 2.0.14-3ubuntu2 [35.9 kB] Get:112 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libhwloc-dev amd64 2.7.1-1 [252 kB] Get:113 http://ftpmaster.internal/ubuntu kinetic/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu9 [164 kB] Get:114 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libpmix-dev amd64 4.1.2-2ubuntu1 [805 kB] Get:115 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libsprng2 amd64 2.0a-13 [76.4 kB] Get:116 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libsprng2-dev amd64 2.0a-13 [78.1 kB] Get:117 http://ftpmaster.internal/ubuntu kinetic/universe amd64 openmpi-common all 4.1.4-1ubuntu1 [163 kB] Get:118 http://ftpmaster.internal/ubuntu kinetic/universe amd64 openmpi-bin amd64 4.1.4-1ubuntu1 [115 kB] Get:119 http://ftpmaster.internal/ubuntu kinetic/main amd64 pkg-config amd64 0.29.2-1ubuntu3 [48.2 kB] Get:120 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libeigen3-dev all 3.4.0-2ubuntu2 [1056 kB] Get:121 http://ftpmaster.internal/ubuntu kinetic/main amd64 libibverbs-dev amd64 40.0-1 [641 kB] Get:122 http://ftpmaster.internal/ubuntu kinetic/universe amd64 libopenmpi-dev amd64 4.1.4-1ubuntu1 [865 kB] Get:123 http://ftpmaster.internal/ubuntu kinetic/universe amd64 mpi-default-dev amd64 1.14 [3698 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 263 MB in 15s (17.7 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 13495 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-4build3_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4build3) ... Selecting previously unselected package libmd0:amd64. Preparing to unpack .../001-libmd0_1.0.4-1build1_amd64.deb ... Unpacking libmd0:amd64 (1.0.4-1build1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../002-libbsd0_0.11.6-1_amd64.deb ... Unpacking libbsd0:amd64 (0.11.6-1) ... Selecting previously unselected package libelf1:amd64. Preparing to unpack .../003-libelf1_0.187-1_amd64.deb ... Unpacking libelf1:amd64 (0.187-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../004-libexpat1_2.4.8-1_amd64.deb ... Unpacking libexpat1:amd64 (2.4.8-1) ... Selecting previously unselected package libglib2.0-0:amd64. Preparing to unpack .../005-libglib2.0-0_2.72.2-2_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.72.2-2) ... 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Setting up libpsm-infinipath1 (3.3+20.604758e7-6.1) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libtsan2:amd64 (12.1.0-2ubuntu1) ... Setting up libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Setting up libfido2-1:amd64 (1.11.0-1) ... Setting up libbsd0:amd64 (0.11.6-1) ... Setting up libelf1:amd64 (0.187-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1) ... Setting up liblocale-gettext-perl (1.07-4build3) ... Setting up chrpath (0.16-2) ... Setting up libsprng2 (2.0a-13) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-5) ... Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:amd64 (0.187-1) ... Setting up libxdmcp6:amd64 (1:1.1.3-0ubuntu5) ... Setting up libevent-extra-2.1-7:amd64 (2.1.12-stable-5) ... Setting up libxcb1:amd64 (1.14-3ubuntu3) ... Setting up gettext (0.21-6) ... Setting up libgmp-dev:amd64 (2:6.2.1+dfsg-3ubuntu1) ... Setting up libtool (2.4.7-4) ... Setting up libarchive13:amd64 (3.6.0-1ubuntu1) ... Setting up libedit2:amd64 (3.1-20210910-1build1) ... Setting up libevent-openssl-2.1-7:amd64 (2.1.12-stable-5) ... Setting up m4 (1.4.18-5ubuntu2) ... Setting up libldap-2.5-0:amd64 (2.5.12+dfsg-2ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libnuma-dev:amd64 (2.0.14-3ubuntu2) ... Setting up libnl-route-3-200:amd64 (3.5.0-0.1) ... Setting up help2man (1.49.2) ... Setting up libjs-jquery-ui (1.13.1+dfsg-1) ... Setting up libgcc-12-dev:amd64 (12.1.0-2ubuntu1) ... Setting up libevent-dev (2.1.12-stable-5) ... Setting up libeigen3-dev (3.4.0-2ubuntu2) ... Setting up autoconf (2.71-2) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build2) ... Setting up libnl-3-dev:amd64 (3.5.0-0.1) ... Setting up groff-base (1.22.4-8build1) ... Setting up libsprng2-dev (2.0a-13) ... Setting up debugedit (1:5.0-4build1) ... Setting up libcurl4:amd64 (7.83.1-2) ... Setting up libx11-6:amd64 (2:1.7.5-1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libibverbs1:amd64 (40.0-1) ... Setting up ibverbs-providers:amd64 (40.0-1) ... Setting up openssh-client (1:9.0p1-1) ... update-alternatives: using /usr/bin/ssh to provide /usr/bin/rsh (rsh) in auto mode update-alternatives: using /usr/bin/slogin to provide /usr/bin/rlogin (rlogin) in auto mode update-alternatives: using /usr/bin/scp to provide /usr/bin/rcp (rcp) in auto mode Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:amd64 (2:1.3.4-1build1) ... Setting up libcurl3-gnutls:amd64 (7.83.1-2) ... Setting up libgfortran-12-dev:amd64 (12.1.0-2ubuntu1) ... Setting up man-db (2.10.2-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libxnvctrl0:amd64 (510.47.03-0ubuntu1) ... Setting up dh-autoreconf (20) ... Setting up libnl-route-3-dev:amd64 (3.5.0-0.1) ... Setting up libltdl-dev:amd64 (2.4.7-4) ... Setting up gcc-12 (12.1.0-2ubuntu1) ... Setting up cmake (3.23.2-1ubuntu1) ... Setting up libhwloc-dev:amd64 (2.7.1-1) ... Setting up librdmacm1:amd64 (40.0-1) ... Setting up libucx0:amd64 (1.13.0~rc1-1) ... Setting up debhelper (13.7.1ubuntu1) ... Setting up libibverbs-dev:amd64 (40.0-1) ... Setting up libhwloc-plugins:amd64 (2.7.1-1) ... Setting up gfortran-12 (12.1.0-2ubuntu1) ... Setting up libfabric1:amd64 (1.11.0-3) ... Setting up libpmix2:amd64 (4.1.2-2ubuntu1) ... Setting up libopenmpi3:amd64 (4.1.4-1ubuntu1) ... Setting up libpmix-dev:amd64 (4.1.2-2ubuntu1) ... Setting up openmpi-bin (4.1.4-1ubuntu1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libopenmpi-dev:amd64 (4.1.4-1ubuntu1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up mpi-default-dev (1.14) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in amd64 hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.4.0-120-generic #136-Ubuntu SMP Fri Jun 10 13:40:48 UTC 2022 amd64 (x86_64) Toolchain package versions: binutils_2.38.50.20220615-4ubuntu1 dpkg-dev_1.21.8ubuntu1 g++-11_11.3.0-3ubuntu1 gcc-11_11.3.0-3ubuntu1 gcc-12_12.1.0-2ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.3.0-3ubuntu1 libstdc++6_12.1.0-2ubuntu1 linux-libc-dev_5.15.0-27.28 Package versions: adduser_3.121ubuntu1 advancecomp_2.1-2.1ubuntu2 apt_2.5.0 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2ubuntu1 base-passwd_3.5.52build1 bash_5.1-6ubuntu1 binutils_2.38.50.20220615-4ubuntu1 binutils-common_2.38.50.20220615-4ubuntu1 binutils-x86-64-linux-gnu_2.38.50.20220615-4ubuntu1 bsdextrautils_2.38-4ubuntu1 bsdutils_1:2.38-4ubuntu1 build-essential_12.9ubuntu3 bzip2_1.0.8-5build1 ca-certificates_20211016 chrpath_0.16-2 cmake_3.23.2-1ubuntu1 cmake-data_3.23.2-1ubuntu1 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.3.0-3ubuntu1 cpp-12_12.1.0-2ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3build1 debconf_1.5.79ubuntu1 debhelper_13.7.1ubuntu1 debianutils_5.7-0.2 debugedit_1:5.0-4build1 dh-autoreconf_20 dh-elpa-helper_2.0.9ubuntu1 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu2 dpkg_1.21.8ubuntu1 dpkg-dev_1.21.8ubuntu1 dwz_0.14-1build2 e2fsprogs_1.46.5-2ubuntu2 emacsen-common_3.0.4 fakeroot_1.29-1ubuntu1 file_1:5.41-4 findutils_4.8.0-1ubuntu3 g++_4:11.2.0-1ubuntu1 g++-11_11.3.0-3ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.3.0-3ubuntu1 gcc-11-base_11.3.0-3ubuntu1 gcc-12_12.1.0-2ubuntu1 gcc-12-base_12.1.0-2ubuntu1 gettext_0.21-6 gettext-base_0.21-6 gfortran-12_12.1.0-2ubuntu1 gpg_2.2.27-3ubuntu2 gpg-agent_2.2.27-3ubuntu2 gpgconf_2.2.27-3ubuntu2 gpgv_2.2.27-3ubuntu2 grep_3.7-1build1 groff-base_1.22.4-8build1 gzip_1.10-4ubuntu4 help2man_1.49.2 hostname_3.23ubuntu2 ibverbs-providers_40.0-1 init_1.63 init-system-helpers_1.63 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapparmor1_3.0.4-2ubuntu3 libapt-pkg6.0_2.5.0 libarchive-zip-perl_1.68-1 libarchive13_3.6.0-1ubuntu1 libargon2-1_0~20171227-0.3 libasan6_11.3.0-3ubuntu1 libasan8_12.1.0-2ubuntu1 libassuan0_2.5.5-3 libatomic1_12.1.0-2ubuntu1 libattr1_1:2.5.1-1build1 libaudit-common_1:3.0.7-1build1 libaudit1_1:3.0.7-1build1 libbinutils_2.38.50.20220615-4ubuntu1 libblkid1_2.38-4ubuntu1 libboost-dev_1.74.0.3ubuntu7 libboost1.74-dev_1.74.0-14ubuntu4 libbrotli1_1.0.9-2build6 libbsd0_0.11.6-1 libbz2-1.0_1.0.8-5build1 libc-bin_2.35-0ubuntu3 libc-dev-bin_2.35-0ubuntu3 libc6_2.35-0ubuntu3 libc6-dev_2.35-0ubuntu3 libcap-ng0_0.7.9-4 libcap2_1:2.44-1build3 libcbor0.8_0.8.0-2ubuntu1 libcc1-0_12.1.0-2ubuntu1 libcom-err2_1.46.5-2ubuntu2 libcrypt-dev_1:4.4.27-1 libcrypt1_1:4.4.27-1 libcryptsetup12_2:2.4.3-1ubuntu1 libctf-nobfd0_2.38.50.20220615-4ubuntu1 libctf0_2.38.50.20220615-4ubuntu1 libcurl3-gnutls_7.83.1-2 libcurl4_7.83.1-2 libdb5.3_5.3.28+dfsg1-0.9 libdebconfclient0_0.261ubuntu1 libdebhelper-perl_13.7.1ubuntu1 libdevmapper1.02.1_2:1.02.175-2.1ubuntu4 libdpkg-perl_1.21.8ubuntu1 libdw1_0.187-1 libedit2_3.1-20210910-1build1 libeigen3-dev_3.4.0-2ubuntu2 libelf1_0.187-1 libevent-2.1-7_2.1.12-stable-5 libevent-core-2.1-7_2.1.12-stable-5 libevent-dev_2.1.12-stable-5 libevent-extra-2.1-7_2.1.12-stable-5 libevent-openssl-2.1-7_2.1.12-stable-5 libevent-pthreads-2.1-7_2.1.12-stable-5 libexpat1_2.4.8-1 libext2fs2_1.46.5-2ubuntu2 libfabric1_1.11.0-3 libfakeroot_1.29-1ubuntu1 libffi8_3.4.2-4 libfido2-1_1.11.0-1 libfile-stripnondeterminism-perl_1.13.0-1 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libuchardet0_0.0.7-1build2 libucx0_1.13.0~rc1-1 libudev1_249.11-0ubuntu4 libunistring2_1.0-1 libuuid1_2.38-4ubuntu1 libuv1_1.44.1-2 libx11-6_2:1.7.5-1 libx11-data_2:1.7.5-1 libxau6_1:1.0.9-1build5 libxcb1_1.14-3ubuntu3 libxdmcp6_1:1.1.3-0ubuntu5 libxext6_2:1.3.4-1build1 libxml2_2.9.14+dfsg-1 libxnvctrl0_510.47.03-0ubuntu1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.15.0-27.28 lockfile-progs_0.1.19build1 login_1:4.11.1+dfsg1-2ubuntu1 logsave_1.46.5-2ubuntu2 lsb-base_11.1.0ubuntu4 lto-disabled-list_27 m4_1.4.18-5ubuntu2 make_4.3-4.1build1 man-db_2.10.2-1 mawk_1.3.4.20200120-3.1 mount_2.38-4ubuntu1 mpi-default-dev_1.14 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 ocl-icd-libopencl1_2.2.14-3 openmpi-bin_4.1.4-1ubuntu1 openmpi-common_4.1.4-1ubuntu1 openssh-client_1:9.0p1-1 openssl_3.0.3-5ubuntu3 optipng_0.7.7-2build1 passwd_1:4.11.1+dfsg1-2ubuntu1 patch_2.7.6-7build2 perl_5.34.0-3ubuntu1 perl-base_5.34.0-3ubuntu1 perl-modules-5.34_5.34.0-3ubuntu1 pinentry-curses_1.2.0-1ubuntu1 pkg-config_0.29.2-1ubuntu3 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3.1 procps_2:3.3.17-6ubuntu2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-0ubuntu6 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu2 sensible-utils_0.0.17 systemd_249.11-0ubuntu4 systemd-sysv_249.11-0ubuntu4 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build3 time_1.9-0.1build2 tzdata_2022a-0ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.38-4ubuntu1 util-linux-extra_2.38-4ubuntu1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-2ubuntu9 zlib1g-dev_1:1.2.11.dfsg-2ubuntu9 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: iqtree Binary: iqtree Architecture: amd64 hurd-i386 i386 kfreebsd-amd64 kfreebsd-i386 Version: 2.0.7+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille , Kevin Murray Homepage: http://www.cibiv.at/software/iqtree/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/iqtree Vcs-Git: https://salsa.debian.org/med-team/iqtree.git Testsuite: autopkgtest Testsuite-Triggers: time Build-Depends: debhelper-compat (= 13), cmake, libboost-dev, libeigen3-dev, libsprng2-dev, mpi-default-dev, zlib1g-dev, help2man, time, chrpath Package-List: iqtree deb science optional arch=amd64,hurd-i386,i386,kfreebsd-amd64,kfreebsd-i386 Checksums-Sha1: 55d95bdac2da0ae814d1823a6e3fdd40cc41fe83 1581628 iqtree_2.0.7+dfsg.orig.tar.xz f80d1bef58520f5fc6bafa50347d04056671a579 20020 iqtree_2.0.7+dfsg-1.debian.tar.xz Checksums-Sha256: 95a3a9c3b32aeb8caa63307808fed7fad68f20f877f3fe5fe751af1d49cbdb86 1581628 iqtree_2.0.7+dfsg.orig.tar.xz 704055ba4585527dacedf6b6cdf5d796c4fd20828fcd48c4d6856601b422e9d6 20020 iqtree_2.0.7+dfsg-1.debian.tar.xz Files: 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gpgv: Signature made Fri Jan 21 14:08:08 2022 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./iqtree_2.0.7+dfsg-1.dsc dpkg-source: info: extracting iqtree in /<> dpkg-source: info: unpacking iqtree_2.0.7+dfsg.orig.tar.xz dpkg-source: info: unpacking iqtree_2.0.7+dfsg-1.debian.tar.xz Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=noautodbgsym parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-24013293 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-24013293 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-24013293 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -b -rfakeroot dpkg-buildpackage: info: source package iqtree dpkg-buildpackage: info: source version 2.0.7+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean -Bbuild.omp dh_auto_clean -Bbuild.serial dh_auto_clean -Bbuild.mpi dh override_dh_auto_clean make[1]: Leaving directory '/<>' dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -Bbuild.omp -- -DIQTREE_FLAGS="omp" cd build.omp && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=omp .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") IQ-TREE flags : omp Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") Using system zlib -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success -- clang-tidy not found. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/build.omp dh_auto_configure -Bbuild.serial -- -DIQTREE_FLAGS="" cd build.serial && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS= .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") IQ-TREE flags : Target OS : Unix Compiler : GNU Compiler (gcc) Target binary : 64-bit OpenMP : Yes MPI : NONE Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") Using system zlib -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success -- clang-tidy not found. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/build.serial dh_auto_configure -Bbuild.mpi -- -DIQTREE_FLAGS="mpi" cd build.mpi && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DIQTREE_FLAGS=mpi .. CMake Deprecation Warning at CMakeLists.txt:56 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 11.3.0 -- The CXX compiler identification is GNU 11.3.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Boost: /usr/lib/x86_64-linux-gnu/cmake/Boost-1.74.0/BoostConfig.cmake (found version "1.74.0") IQ-TREE flags : mpi Target OS : Unix Compiler : GNU Compiler (gcc) -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") Target binary : 64-bit OpenMP : Yes MPI : Yes Vectorization : SSE3/AVX/AVX2 LINKER flags : -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--gc-sections -- Looking for gettimeofday -- Looking for gettimeofday - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for GlobalMemoryStatusEx -- Looking for GlobalMemoryStatusEx - not found -- Looking for strndup -- Looking for strndup - found -- Looking for strtok_r -- Looking for strtok_r - found -- Looking for backtrace -- Looking for backtrace - found -- backtrace facility detected in default set of libraries -- Found Backtrace: /usr/include -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11") Using system zlib -- Performing Test FLAG_WEXTRA -- Performing Test FLAG_WEXTRA - Success -- clang-tidy not found. -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR -- Build files have been written to: /<>/build.mpi dh override_dh_auto_configure make[1]: Leaving directory '/<>' debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -Bbuild.omp cd build.omp && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/<>/build.omp' /usr/bin/cmake -S/<> -B/<>/build.omp --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/build.omp/CMakeFiles /<>/build.omp//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.omp /<>/build.omp /<>/build.omp/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.omp /<>/build.omp /<>/build.omp/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/<>/build.omp' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/<>/build.omp' make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/terraphast /<>/build.omp /<>/build.omp/terraphast /<>/build.omp/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.omp /<>/build.omp /<>/build.omp/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Leaving directory '/<>/build.omp' make[4]: Entering directory '/<>/build.omp' [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /<>/tree/phylotreeavx.cpp make[4]: Entering directory '/<>/build.omp' make[4]: Leaving directory '/<>/build.omp' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/<>/build.omp' [ 1%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /<>/tree/phylokernelsse.cpp [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /<>/tree/phylokernelfma.cpp [ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /<>/terraphast/lib/advanced.cpp [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /<>/terraphast/lib/bigint.cpp [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /<>/terraphast/lib/bipartitions.cpp [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /<>/terraphast/lib/bitmatrix.cpp [ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /<>/terraphast/lib/clamped_uint.cpp [ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /<>/terraphast/lib/constraints.cpp [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /<>/terraphast/lib/errors.cpp [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /<>/terraphast/lib/multitree.cpp [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /<>/terraphast/lib/multitree_iterator.cpp [ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /<>/terraphast/lib/nodes.cpp [ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /<>/terraphast/lib/parser.cpp [ 6%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /<>/terraphast/lib/rooting.cpp [ 6%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /<>/terraphast/lib/simple.cpp [ 6%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /<>/terraphast/lib/subtree_extraction.cpp [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /<>/terraphast/lib/supertree_helpers.cpp [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /<>/terraphast/lib/trees.cpp [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /<>/terraphast/lib/union_find.cpp [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /<>/build.omp/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /<>/terraphast/lib/validation.cpp [ 8%] Linking CXX static library libterraphast.a cd /<>/build.omp/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /<>/build.omp/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a make[4]: Leaving directory '/<>/build.omp' [ 8%] Built target terraphast make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/pll /<>/build.omp /<>/build.omp/pll /<>/build.omp/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/<>/build.omp' [ 8%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /<>/pll/alignment.c In file included from /<>/pll/alignment.c:40: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /<>/pll/bipartitionList.c In file included from /<>/pll/bipartitionList.c:49: /<>/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 /<>/pll/bipartitionList.c:29: /<>/pll/bipartitionList.c: In function ‘insertHashRF’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ [ 10%] 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 [ 10%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /<>/pll/evaluateGenericSpecial.c make[4]: Leaving directory '/<>/build.omp' [ 10%] Built target kernelsse make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/ncl /<>/build.omp /<>/build.omp/ncl /<>/build.omp/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/<>/build.omp' [ 10%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /<>/ncl/nxsassumptionsblock.cpp In file included from /<>/pll/evaluateGenericSpecial.c:46: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 10%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /<>/pll/evaluatePartialGenericSpecial.c In file included from /<>/pll/evaluatePartialGenericSpecial.c:45: /<>/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 /<>/pll/evaluatePartialGenericSpecial.c:31: /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /<>/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 /<>/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); | ^~~~~~~~~~~~~~~~~~ /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /<>/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 /<>/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); | ^~~~~~~~~~~~~~~~~~ /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /<>/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 /<>/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); | ^~~~~~~~~~~~~~~~~~ /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /<>/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 /<>/pll/evaluatePartialGenericSpecial.c:936:3: note: in expansion of macro ‘rax_posix_memalign’ 936 | rax_posix_memalign ((void **)&lVector, PLL_BYTE_ALIGNMENT, sizeof(double) * 80 * mxtips); | ^~~~~~~~~~~~~~~~~~ [ 11%] Building C object pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /<>/pll/fastDNAparsimony.c In file included from /<>/pll/fastDNAparsimony.c:113: /<>/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 /<>/pll/fastDNAparsimony.c:29: /<>/pll/fastDNAparsimony.c: In function ‘compressDNA’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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 CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /<>/ncl/nxsblock.cpp [ 11%] Building C object pll/CMakeFiles/pll.dir/hardware.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /<>/pll/hardware.c /<>/pll/hardware.c: In function ‘pll_probe_cpu’: /<>/pll/hardware.c:93:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf (fd, "%d", &id); | ^~~~~~~~~~~~~~~~~~~~~~ [ 12%] Building C object pll/CMakeFiles/pll.dir/hash.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /<>/pll/hash.c [ 12%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /<>/pll/lexer.c [ 13%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /<>/pll/makenewzGenericSpecial.c In file included from /<>/pll/makenewzGenericSpecial.c:44: /<>/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 /<>/pll/makenewzGenericSpecial.c:29: /<>/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /<>/ncl/nxscharactersblock.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /<>/pll/models.c [ 15%] Linking CXX static library libkernelfma.a /usr/bin/cmake -P CMakeFiles/kernelfma.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/kernelfma.dir/link.txt --verbose=1 /usr/bin/ar qc libkernelfma.a CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o In file included from /<>/pll/models.c:53: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ /usr/bin/ranlib libkernelfma.a make[4]: Leaving directory '/<>/build.omp' [ 15%] Built target kernelfma make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/sprng /<>/build.omp /<>/build.omp/sprng /<>/build.omp/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/<>/build.omp' [ 15%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /<>/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /<>/sprng/lcg64.c [ 16%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /<>/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /<>/sprng/makeseed.c [ 16%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /<>/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /<>/sprng/memory.c [ 17%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /<>/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /<>/sprng/store.c [ 17%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /<>/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /<>/sprng/primes-lcg64.c [ 17%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /<>/build.omp/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /<>/sprng/checkid.c [ 18%] Linking C static library libsprng.a cd /<>/build.omp/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /<>/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.omp' [ 18%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/lbfgsb /<>/build.omp /<>/build.omp/lbfgsb /<>/build.omp/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/<>/build.omp' [ 18%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /<>/build.omp/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /<>/lbfgsb/lbfgsb_new.cpp [ 18%] 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.omp' [ 18%] Built target kernelavx make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/gsl /<>/build.omp /<>/build.omp/gsl /<>/build.omp/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/<>/build.omp' [ 19%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /<>/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /<>/gsl/binomial_tpe.cpp [ 19%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /<>/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /<>/gsl/multinomial.cpp [ 20%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /<>/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /<>/gsl/pow_int.cpp [ 20%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /<>/pll/newick.c In file included from /<>/pll/newick.c:36: /<>/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 gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /<>/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /<>/gsl/gauss.cpp [ 21%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /<>/pll/newviewGenericSpecial.c In file included from /<>/pll/newviewGenericSpecial.c:49: /<>/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 /<>/pll/newviewGenericSpecial.c:32: /<>/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /<>/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 /<>/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro ‘rax_posix_memalign’ 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro ‘rax_posix_memalign’ 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /<>/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ [ 21%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /<>/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /<>/gsl/gaussinv.cpp [ 22%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /<>/build.omp/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /<>/gsl/gausspdf.cpp [ 22%] Linking CXX static library libgsl.a cd /<>/build.omp/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /<>/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.omp' [ 22%] Built target gsl make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/booster /<>/build.omp /<>/build.omp/booster /<>/build.omp/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/<>/build.omp' [ 23%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /<>/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /<>/booster/bitset_index.c [ 23%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /<>/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /<>/booster/hashmap.c [ 23%] Linking CXX static library liblbfgsb.a cd /<>/build.omp/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /<>/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.omp' [ 23%] Built target lbfgsb make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/vectorclass /<>/build.omp /<>/build.omp/vectorclass /<>/build.omp/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/<>/build.omp' [ 24%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /<>/build.omp/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /<>/vectorclass/instrset_detect.cpp [ 24%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /<>/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /<>/booster/io.c [ 24%] Linking CXX static library libvectorclass.a cd /<>/build.omp/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /<>/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.omp' [ 24%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/nclextra /<>/build.omp /<>/build.omp/nclextra /<>/build.omp/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= [ 25%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /<>/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /<>/booster/sort.c make[4]: Leaving directory '/<>/build.omp' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/<>/build.omp' [ 26%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /<>/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /<>/nclextra/mpdablock.cpp [ 26%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /<>/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /<>/booster/tree.c [ 27%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /<>/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /<>/booster/booster.c /<>/booster/booster.c: In function ‘main_booster’: /<>/booster/booster.c:268:57: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /<>/booster/booster.c:27: /<>/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /<>/booster/booster.c:304:29: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ In file included from /<>/booster/booster.c:27: /<>/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ [ 27%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /<>/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /<>/booster/hashtables_bfields.c [ 27%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /<>/ncl/nxsdatablock.cpp [ 27%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /<>/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /<>/booster/prng.c [ 28%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /<>/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /<>/booster/stats.c [ 28%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /<>/build.omp/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /<>/booster/tree_utils.c [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /<>/ncl/nxsdiscretedatum.cpp [ 30%] Linking C static library libbooster.a cd /<>/build.omp/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /<>/build.omp/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/<>/build.omp' [ 30%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /<>/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /<>/nclextra/msetsblock.cpp [ 30%] Built target booster make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/whtest /<>/build.omp /<>/build.omp/whtest /<>/build.omp/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= [ 30%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /<>/pll/genericParallelization.c make[4]: Leaving directory '/<>/build.omp' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/<>/build.omp' [ 30%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /<>/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /<>/whtest/eigen.c In file included from /<>/pll/genericParallelization.c:43: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 31%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /<>/pll/optimizeModel.c In file included from /<>/pll/optimizeModel.c:47: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 31%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /<>/ncl/nxsdiscretematrix.cpp [ 32%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /<>/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /<>/whtest/eigen_sym.c [ 32%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /<>/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /<>/whtest/random.c [ 33%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /<>/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /<>/whtest/weisslambda.c [ 33%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /<>/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /<>/whtest/weisslambda_sub.c [ 33%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /<>/pll/parsePartition.c [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /<>/ncl/nxsdistancedatum.cpp In file included from /<>/pll/parsePartition.c:42: /<>/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); | ^~~~~~~~~~~~~~~ [ 33%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /<>/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /<>/whtest/whtest.c [ 33%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /<>/pll/queue.c [ 34%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /<>/pll/randomTree.c [ 35%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /<>/build.omp/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /<>/whtest/whtest_sub.c In file included from /<>/pll/randomTree.c:37: /<>/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); | ^~~~~~~~~~~~~~~ /<>/whtest/whtest_sub.c: In function ‘ReadData’: /<>/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 35%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /<>/pll/recom.c In file included from /<>/pll/recom.c:43: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 36%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /<>/pll/restartHashTable.c In file included from /<>/pll/restartHashTable.c:47: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 36%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /<>/pll/searchAlgo.c In file included from /<>/pll/searchAlgo.c:51: /<>/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); | ^~~~~~~~~~~~~~~ [ 37%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /<>/ncl/nxsdistancesblock.cpp [ 38%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /<>/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /<>/nclextra/msplitsblock.cpp [ 38%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /<>/build.omp/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /<>/whtest/whtest_wrapper.cpp [ 38%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /<>/pll/ssort.c [ 39%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /<>/pll/stack.c [ 39%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /<>/pll/topologies.c In file included from /<>/pll/topologies.c:48: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 40%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /<>/pll/trash.c In file included from /<>/pll/trash.c:48: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 40%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /<>/pll/treeIO.c [ 41%] Linking CXX static library libwhtest.a cd /<>/build.omp/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /<>/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 In file included from /<>/pll/treeIO.c:49: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ make[4]: Leaving directory '/<>/build.omp' [ 41%] Built target whtest make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/pll /<>/build.omp /<>/build.omp/pll /<>/build.omp/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/<>/build.omp' [ 41%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /<>/pll/avxLikelihood.c [ 41%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /<>/build.omp/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /<>/pll/utils.c In file included from /<>/pll/utils.c:70: /<>/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 /<>/pll/pllInternal.h:16, from /<>/pll/utils.c:70: /<>/pll/utils.c: In function ‘initializePartitionData’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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 * | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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 * | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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) * | ^~~~~~~~~~~~~~~~~~ In file included from /<>/pll/avxLikelihood.c:57: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /<>/ncl/nxsemptyblock.cpp [ 41%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /<>/build.omp/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /<>/nclextra/modelsblock.cpp [ 42%] Linking C static library libpll.a cd /<>/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /<>/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pll.dir/link.txt --verbose=1 /usr/bin/ar qc libpll.a CMakeFiles/pll.dir/alignment.c.o CMakeFiles/pll.dir/bipartitionList.c.o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o CMakeFiles/pll.dir/fastDNAparsimony.c.o CMakeFiles/pll.dir/hardware.c.o CMakeFiles/pll.dir/hash.c.o CMakeFiles/pll.dir/lexer.c.o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o CMakeFiles/pll.dir/models.c.o CMakeFiles/pll.dir/newick.c.o CMakeFiles/pll.dir/newviewGenericSpecial.c.o CMakeFiles/pll.dir/genericParallelization.c.o CMakeFiles/pll.dir/optimizeModel.c.o CMakeFiles/pll.dir/parsePartition.c.o CMakeFiles/pll.dir/queue.c.o CMakeFiles/pll.dir/randomTree.c.o CMakeFiles/pll.dir/recom.c.o CMakeFiles/pll.dir/restartHashTable.c.o CMakeFiles/pll.dir/searchAlgo.c.o CMakeFiles/pll.dir/ssort.c.o CMakeFiles/pll.dir/stack.c.o CMakeFiles/pll.dir/topologies.c.o CMakeFiles/pll.dir/trash.c.o CMakeFiles/pll.dir/treeIO.c.o CMakeFiles/pll.dir/utils.c.o /usr/bin/ranlib libpll.a make[4]: Leaving directory '/<>/build.omp' [ 42%] Built target pll make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/yaml-cpp /<>/build.omp /<>/build.omp/yaml-cpp /<>/build.omp/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/<>/build.omp' [ 42%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /<>/yaml-cpp/src/binary.cpp [ 43%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /<>/ncl/nxsexception.cpp [ 44%] Linking C static library libpllavx.a cd /<>/build.omp/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /<>/build.omp/pll && /usr/bin/cmake -E cmake_link_script CMakeFiles/pllavx.dir/link.txt --verbose=1 [ 45%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /<>/yaml-cpp/src/convert.cpp /usr/bin/ar qc libpllavx.a CMakeFiles/pllavx.dir/avxLikelihood.c.o /usr/bin/ranlib libpllavx.a make[4]: Leaving directory '/<>/build.omp' [ 45%] Built target pllavx make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/utils /<>/build.omp /<>/build.omp/utils /<>/build.omp/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/<>/build.omp' [ 45%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /<>/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /<>/utils/eigendecomposition.cpp [ 46%] Linking CXX static library libnclextra.a cd /<>/build.omp/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /<>/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 [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /<>/ncl/nxsreader.cpp make[4]: Leaving directory '/<>/build.omp' [ 46%] Built target nclextra [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /<>/ncl/nxssetreader.cpp [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /<>/yaml-cpp/src/directives.cpp [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /<>/yaml-cpp/src/emit.cpp [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /<>/yaml-cpp/src/emitfromevents.cpp [ 48%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /<>/ncl/nxsstring.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /<>/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /<>/utils/gzstream.cpp [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /<>/yaml-cpp/src/emitter.cpp [ 49%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /<>/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /<>/utils/optimization.cpp [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /<>/yaml-cpp/src/emitterstate.cpp [ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /<>/ncl/nxstaxablock.cpp [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /<>/ncl/nxstoken.cpp [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /<>/yaml-cpp/src/emitterutils.cpp [ 51%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /<>/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /<>/utils/stoprule.cpp [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /<>/build.omp/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /<>/ncl/nxstreesblock.cpp make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/pda /<>/build.omp /<>/build.omp/pda /<>/build.omp/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/<>/build.omp' [ 51%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /<>/pda/circularnetwork.cpp [ 51%] Linking CXX static library libncl.a cd /<>/build.omp/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /<>/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 [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /<>/yaml-cpp/src/exceptions.cpp /usr/bin/ranlib libncl.a make[4]: Leaving directory '/<>/build.omp' [ 51%] Built target ncl make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/alignment /<>/build.omp /<>/build.omp/alignment /<>/build.omp/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/<>/build.omp' [ 51%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /<>/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /<>/alignment/pattern.cpp [ 52%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /<>/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /<>/utils/tools.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /<>/yaml-cpp/src/exp.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /<>/pda/greedy.cpp [ 53%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /<>/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /<>/alignment/alignment.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /<>/yaml-cpp/src/memory.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /<>/yaml-cpp/src/node.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /<>/pda/gurobiwrapper.cpp [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /<>/yaml-cpp/src/node_data.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /<>/pda/hashsplitset.cpp [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /<>/yaml-cpp/src/nodebuilder.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /<>/pda/pdnetwork.cpp /<>/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /<>/yaml-cpp/src/nodeevents.cpp [ 57%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /<>/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /<>/utils/pllnni.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /<>/yaml-cpp/src/null.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /<>/yaml-cpp/src/ostream_wrapper.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /<>/yaml-cpp/src/parse.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /<>/yaml-cpp/src/parser.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /<>/pda/pruning.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /<>/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /<>/utils/checkpoint.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /<>/yaml-cpp/src/regex_yaml.cpp [ 59%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /<>/pda/split.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /<>/yaml-cpp/src/scanner.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /<>/pda/splitgraph.cpp [ 61%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /<>/build.omp/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /<>/utils/MPIHelper.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /<>/yaml-cpp/src/scanscalar.cpp [ 62%] Linking CXX static library libutils.a cd /<>/build.omp/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /<>/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.omp' [ 62%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/model /<>/build.omp /<>/build.omp/model /<>/build.omp/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/<>/build.omp' [ 62%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /<>/model/modelmarkov.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /<>/yaml-cpp/src/scantag.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /<>/yaml-cpp/src/scantoken.cpp In file included from /<>/model/modelmarkov.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 62%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /<>/pda/splitset.cpp [ 63%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /<>/build.omp/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /<>/pda/lpwrapper.c [ 63%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /<>/pda/ecopd.cpp /<>/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /<>/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /<>/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /<>/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ [ 64%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /<>/yaml-cpp/src/simplekey.cpp [ 64%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /<>/yaml-cpp/src/singledocparser.cpp [ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /<>/yaml-cpp/src/stream.cpp [ 65%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /<>/pda/graph.cpp [ 66%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /<>/pda/pdtree.cpp [ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /<>/build.omp/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /<>/yaml-cpp/src/tag.cpp [ 67%] Linking CXX static library libyaml-cpp.a cd /<>/build.omp/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /<>/build.omp/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" /usr/bin/ranlib libyaml-cpp.a make[4]: Leaving directory '/<>/build.omp' [ 67%] Built target yaml-cpp [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /<>/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /<>/alignment/alignmentpairwise.cpp [ 68%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /<>/pda/pdtreeset.cpp [ 68%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /<>/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /<>/alignment/maalignment.cpp [ 69%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /<>/build.omp/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /<>/pda/ecopdmtreeset.cpp [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /<>/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /<>/alignment/superalignment.cpp [ 70%] Linking CXX static library libpda.a cd /<>/build.omp/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /<>/build.omp/pda && /usr/bin/cmake -E cmake_link_script CMakeFiles/pda.dir/link.txt --verbose=1 /usr/bin/ar qc libpda.a CMakeFiles/pda.dir/circularnetwork.cpp.o CMakeFiles/pda.dir/greedy.cpp.o CMakeFiles/pda.dir/gurobiwrapper.cpp.o CMakeFiles/pda.dir/hashsplitset.cpp.o CMakeFiles/pda.dir/pdnetwork.cpp.o CMakeFiles/pda.dir/pruning.cpp.o CMakeFiles/pda.dir/split.cpp.o CMakeFiles/pda.dir/splitgraph.cpp.o CMakeFiles/pda.dir/splitset.cpp.o CMakeFiles/pda.dir/lpwrapper.c.o CMakeFiles/pda.dir/ecopd.cpp.o CMakeFiles/pda.dir/graph.cpp.o CMakeFiles/pda.dir/pdtree.cpp.o CMakeFiles/pda.dir/pdtreeset.cpp.o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o /usr/bin/ranlib libpda.a make[4]: Leaving directory '/<>/build.omp' [ 70%] Built target pda make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/phylo-yaml /<>/build.omp /<>/build.omp/phylo-yaml /<>/build.omp/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/<>/build.omp' [ 70%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /<>/build.omp/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /<>/phylo-yaml/statespace.cpp [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /<>/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /<>/alignment/superalignmentpairwise.cpp [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /<>/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /<>/alignment/superalignmentpairwiseplen.cpp [ 71%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /<>/build.omp/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /<>/alignment/superalignmentunlinked.cpp [ 72%] Linking CXX static library libphyloYAML.a cd /<>/build.omp/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /<>/build.omp/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/<>/build.omp' [ 72%] Built target phyloYAML [ 73%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /<>/model/modelbin.cpp make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/main /<>/build.omp /<>/build.omp/main /<>/build.omp/main/CMakeFiles/main.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/<>/build.omp' [ 74%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /<>/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /<>/main/main.cpp /<>/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ In file included from /<>/model/modelbin.h:23, from /<>/model/modelbin.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 74%] Linking CXX static library libalignment.a cd /<>/build.omp/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /<>/build.omp/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/<>/build.omp' [ 74%] Built target alignment [ 74%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /<>/model/modeldna.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /<>/model/modelfactory.cpp In file included from /<>/model/modeldna.h:23, from /<>/model/modeldna.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modeldna.cpp:20: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ In file included from /<>/model/modelfactory.cpp:24: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelfactory.cpp:26: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelfactory.cpp:27: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/model/modelfactory.cpp:30: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /<>/model/modelprotein.cpp In file included from /<>/model/modelprotein.h:23, from /<>/model/modelprotein.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelprotein.cpp:20: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /<>/model/modelset.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /<>/model/modelsubst.cpp In file included from /<>/model/modelset.h:23, from /<>/model/modelset.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 76%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /<>/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /<>/main/phyloanalysis.cpp /<>/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ [ 76%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /<>/model/partitionmodel.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /<>/model/partitionmodelplen.cpp In file included from /<>/model/partitionmodel.cpp:23: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phyloanalysis.cpp:37: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phyloanalysis.cpp:38: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phyloanalysis.cpp:46: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/model/partitionmodelplen.cpp:12: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /<>/model/rategamma.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /<>/model/rategammainvar.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /<>/model/rateheterogeneity.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /<>/model/rateinvar.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /<>/model/ratemeyerdiscrete.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /<>/model/ratemeyerhaeseler.cpp [ 79%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /<>/model/ratekategory.cpp [ 80%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /<>/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /<>/main/phylotesting.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /<>/model/ratefree.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /<>/model/ratefreeinvar.cpp In file included from /<>/main/phylotesting.cpp:21: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phylotesting.cpp:22: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phylotesting.cpp:31: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/main/phylotesting.cpp:34: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/model/modelmixture.h:13, from /<>/model/ratefree.cpp:13: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /<>/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(PML::SeqType)’: /<>/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /<>/main/phylotesting.cpp: In member function ‘double CandidateModel::getScore(ModelTestCriterion)’: /<>/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ [ 81%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /<>/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /<>/main/treetesting.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /<>/model/rateheterotachy.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /<>/model/rateheterotachyinvar.cpp [ 82%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /<>/build.omp/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /<>/main/timetree.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /<>/model/modelcodon.cpp In file included from /<>/model/modelcodon.h:11, from /<>/model/modelcodon.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /<>/model/modelmorphology.cpp In file included from /<>/model/modelmorphology.h:11, from /<>/model/modelmorphology.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmorphology.cpp:8: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /<>/model/modelmixture.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /<>/model/modelunrest.cpp In file included from /<>/model/modelmixture.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmixture.cpp:9: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmixture.cpp:10: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/model/modelmixture.cpp:13: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/model/modelunrest.h:11, from /<>/model/modelunrest.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /<>/model/modelliemarkov.cpp [ 85%] Linking CXX static library libmain.a cd /<>/build.omp/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /<>/build.omp/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o /usr/bin/ranlib libmain.a make[4]: Leaving directory '/<>/build.omp' [ 85%] Built target main [ 85%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /<>/model/modelpomo.cpp [ 86%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /<>/model/modelpomomixture.cpp In file included from /<>/model/modeldna.h:23, from /<>/model/modelpomo.h:4, from /<>/model/modelpomo.cpp:1: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelpomo.h:4, from /<>/model/modelpomo.cpp:1: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelliemarkov.h:11, from /<>/model/modelliemarkov.cpp:23: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modeldna.h:23, from /<>/model/modelpomo.h:4, from /<>/model/modelpomomixture.h:14, from /<>/model/modelpomomixture.cpp:9: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelpomo.h:4, from /<>/model/modelpomomixture.h:14, from /<>/model/modelpomomixture.cpp:9: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ [ 86%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /<>/build.omp/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /<>/model/modelfactorymixlen.cpp In file included from /<>/model/modelfactorymixlen.cpp:12: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 87%] Linking CXX static library libmodel.a cd /<>/build.omp/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /<>/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.omp' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tree /<>/build.omp /<>/build.omp/tree /<>/build.omp/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/<>/build.omp' [ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /<>/tree/candidateset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 88%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /<>/tree/constrainttree.cpp cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /<>/tree/matree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /<>/tree/iqtree.cpp In file included from /<>/tree/iqtree.cpp:29: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /<>/tree/memslot.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /<>/tree/mexttree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /<>/tree/mtree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /<>/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /<>/tree/ncbitree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /<>/tree/node.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /<>/tree/phylonode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /<>/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /<>/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /<>/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /<>/tree/phylosupertreeunlinked.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /<>/tree/phylotree.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /<>/tree/phylotreemixlen.cpp In file included from /<>/model/modelmixture.h:13, from /<>/tree/phylotreemixlen.cpp:12: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmixture.h:13, from /<>/tree/phylotree.cpp:34: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /<>/tree/phylotreepars.cpp /<>/tree/phylotree.cpp: In function ‘std::string getASCName(ASCType)’: /<>/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /<>/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /<>/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /<>/tree/phylotreesse.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /<>/tree/quartet.cpp In file included from /<>/tree/phylotreesse.cpp:35: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /<>/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /<>/tree/tinatree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /<>/tree/parstree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /<>/build.omp/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /<>/tree/discordance.cpp [ 98%] Linking CXX static library libtree.a cd /<>/build.omp/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /<>/build.omp/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/<>/build.omp' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/terrace /<>/build.omp /<>/build.omp/terrace /<>/build.omp/terrace/CMakeFiles/terrace.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/<>/build.omp' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /<>/build.omp/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /<>/terrace/terrace.cpp [ 99%] Linking CXX static library libterrace.a cd /<>/build.omp/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /<>/build.omp/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a make[4]: Leaving directory '/<>/build.omp' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/<>/build.omp' cd /<>/build.omp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.omp /<>/build.omp /<>/build.omp/CMakeFiles/iqtree2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.omp' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/<>/build.omp' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.omp -I/<>/terraphast/include -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /<>/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/<>/lib -Wl,-rpath,/<>/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.742’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.1531’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.440’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.1309’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.1076’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2600:92: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2309:9: warning: type ‘struct .omp_data_s.378’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2309:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2292:17: note: the first difference of corresponding definitions is field ‘all_lh’ ./tree/phylokernelnew.h:2292:17: note: a field of same name but different type is defined in another translation unit ./vectorclass/vectorf128.h:1507:7: note: type name ‘Vec2d’ should match type name ‘Vec4d’ ./vectorclass/vectorf256.h:1349:7: note: the incompatible type is defined here make[4]: Leaving directory '/<>/build.omp' [100%] Built target iqtree2 make[3]: Leaving directory '/<>/build.omp' /usr/bin/cmake -E cmake_progress_start /<>/build.omp/CMakeFiles 0 make[2]: Leaving directory '/<>/build.omp' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.serial cd build.serial && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/<>/build.serial' /usr/bin/cmake -S/<> -B/<>/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/build.serial/CMakeFiles /<>/build.serial//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.serial /<>/build.serial /<>/build.serial/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.serial /<>/build.serial /<>/build.serial/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.serial /<>/build.serial /<>/build.serial/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/terraphast /<>/build.serial /<>/build.serial/terraphast /<>/build.serial/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/<>/build.serial' make[4]: Entering directory '/<>/build.serial' make[4]: Leaving directory '/<>/build.serial' make[4]: Leaving directory '/<>/build.serial' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build make[4]: Entering directory '/<>/build.serial' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build [ 0%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /<>/tree/phylokernelfma.cpp make[4]: Entering directory '/<>/build.serial' [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /<>/tree/phylokernelsse.cpp /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /<>/tree/phylotreeavx.cpp [ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /<>/terraphast/lib/advanced.cpp [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /<>/terraphast/lib/bigint.cpp [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /<>/terraphast/lib/bipartitions.cpp [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /<>/terraphast/lib/bitmatrix.cpp [ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /<>/terraphast/lib/clamped_uint.cpp [ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /<>/terraphast/lib/constraints.cpp [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /<>/terraphast/lib/errors.cpp [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /<>/terraphast/lib/multitree.cpp [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /<>/terraphast/lib/multitree_iterator.cpp [ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /<>/terraphast/lib/nodes.cpp [ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /<>/terraphast/lib/parser.cpp [ 6%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /<>/terraphast/lib/rooting.cpp [ 6%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /<>/terraphast/lib/simple.cpp [ 6%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /<>/terraphast/lib/subtree_extraction.cpp [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /<>/terraphast/lib/supertree_helpers.cpp [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /<>/terraphast/lib/trees.cpp [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /<>/terraphast/lib/union_find.cpp [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /<>/build.serial/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /<>/terraphast/lib/validation.cpp [ 8%] Linking CXX static library libterraphast.a cd /<>/build.serial/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /<>/build.serial/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a make[4]: Leaving directory '/<>/build.serial' [ 8%] Built target terraphast make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/pll /<>/build.serial /<>/build.serial/pll /<>/build.serial/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/<>/build.serial' [ 8%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /<>/pll/alignment.c In file included from /<>/pll/alignment.c:40: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /<>/pll/bipartitionList.c In file included from /<>/pll/bipartitionList.c:49: /<>/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 /<>/pll/bipartitionList.c:29: /<>/pll/bipartitionList.c: In function ‘insertHashRF’: /<>/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 /<>/pll/bipartitionList.c:332:3: note: in expansion of macro ‘rax_posix_memalign’ 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /<>/pll/evaluateGenericSpecial.c In file included from /<>/pll/evaluateGenericSpecial.c:46: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /<>/pll/evaluatePartialGenericSpecial.c In file included from /<>/pll/evaluatePartialGenericSpecial.c:45: /<>/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 /<>/pll/evaluatePartialGenericSpecial.c:31: /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /<>/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 /<>/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); | ^~~~~~~~~~~~~~~~~~ /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /<>/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 /<>/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); | ^~~~~~~~~~~~~~~~~~ /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /<>/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 /<>/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); | ^~~~~~~~~~~~~~~~~~ /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /<>/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 /<>/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.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /<>/pll/fastDNAparsimony.c In file included from /<>/pll/fastDNAparsimony.c:113: /<>/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 /<>/pll/fastDNAparsimony.c:29: /<>/pll/fastDNAparsimony.c: In function ‘compressDNA’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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 C object pll/CMakeFiles/pll.dir/hardware.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /<>/pll/hardware.c /<>/pll/hardware.c: In function ‘pll_probe_cpu’: /<>/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.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /<>/pll/hash.c [ 11%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /<>/pll/lexer.c [ 12%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /<>/pll/makenewzGenericSpecial.c In file included from /<>/pll/makenewzGenericSpecial.c:44: /<>/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 /<>/pll/makenewzGenericSpecial.c:29: /<>/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ [ 12%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /<>/pll/models.c In file included from /<>/pll/models.c:53: /<>/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); | ^~~~~~~~~~~~~~~ [ 13%] 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.serial' [ 13%] Built target kernelsse make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/ncl /<>/build.serial /<>/build.serial/ncl /<>/build.serial/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/<>/build.serial' [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /<>/ncl/nxsassumptionsblock.cpp [ 14%] 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.serial' [ 14%] Built target kernelfma make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/sprng /<>/build.serial /<>/build.serial/sprng /<>/build.serial/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/<>/build.serial' [ 14%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /<>/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /<>/sprng/lcg64.c [ 15%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /<>/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /<>/sprng/makeseed.c [ 15%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /<>/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /<>/sprng/memory.c [ 16%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /<>/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /<>/sprng/store.c [ 16%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /<>/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /<>/sprng/primes-lcg64.c [ 16%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /<>/ncl/nxsblock.cpp [ 16%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /<>/build.serial/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /<>/sprng/checkid.c [ 17%] Linking C static library libsprng.a cd /<>/build.serial/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 17%] Built target sprng [ 17%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /<>/pll/newick.c make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/lbfgsb /<>/build.serial /<>/build.serial/lbfgsb /<>/build.serial/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/<>/build.serial' In file included from /<>/pll/newick.c:36: /<>/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 CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /<>/build.serial/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /<>/lbfgsb/lbfgsb_new.cpp [ 18%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /<>/pll/newviewGenericSpecial.c In file included from /<>/pll/newviewGenericSpecial.c:49: /<>/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 /<>/pll/newviewGenericSpecial.c:32: /<>/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /<>/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 /<>/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro ‘rax_posix_memalign’ 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro ‘rax_posix_memalign’ 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /<>/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ [ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /<>/ncl/nxscharactersblock.cpp [ 19%] Linking CXX static library liblbfgsb.a cd /<>/build.serial/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /<>/build.serial/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.serial' [ 19%] Built target lbfgsb make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/gsl /<>/build.serial /<>/build.serial/gsl /<>/build.serial/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/<>/build.serial' [ 20%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /<>/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /<>/gsl/binomial_tpe.cpp [ 20%] Building CXX object gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /<>/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /<>/gsl/multinomial.cpp [ 21%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /<>/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /<>/gsl/pow_int.cpp [ 21%] 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 [ 21%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /<>/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /<>/gsl/gauss.cpp /usr/bin/ranlib libkernelavx.a make[4]: Leaving directory '/<>/build.serial' [ 21%] Built target kernelavx make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/booster /<>/build.serial /<>/build.serial/booster /<>/build.serial/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/<>/build.serial' [ 22%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /<>/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /<>/booster/bitset_index.c [ 22%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /<>/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /<>/gsl/gaussinv.cpp [ 23%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /<>/build.serial/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /<>/gsl/gausspdf.cpp [ 23%] Building C object booster/CMakeFiles/booster.dir/hashmap.c.o cd /<>/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /<>/booster/hashmap.c [ 23%] Linking CXX static library libgsl.a cd /<>/build.serial/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 23%] Built target gsl make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/vectorclass /<>/build.serial /<>/build.serial/vectorclass /<>/build.serial/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/<>/build.serial' [ 24%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /<>/build.serial/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /<>/vectorclass/instrset_detect.cpp [ 24%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /<>/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /<>/booster/io.c [ 25%] Building C object booster/CMakeFiles/booster.dir/sort.c.o cd /<>/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /<>/booster/sort.c [ 25%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /<>/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /<>/booster/tree.c [ 25%] Linking CXX static library libvectorclass.a cd /<>/build.serial/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 25%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/nclextra /<>/build.serial /<>/build.serial/nclextra /<>/build.serial/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build make[4]: Entering directory '/<>/build.serial' [ 25%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o [ 26%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /<>/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /<>/nclextra/mpdablock.cpp cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /<>/pll/genericParallelization.c In file included from /<>/pll/genericParallelization.c:43: /<>/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/optimizeModel.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /<>/pll/optimizeModel.c In file included from /<>/pll/optimizeModel.c:47: /<>/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 booster/CMakeFiles/booster.dir/booster.c.o cd /<>/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /<>/booster/booster.c /<>/booster/booster.c: In function ‘main_booster’: /<>/booster/booster.c:268:57: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /<>/booster/booster.c:27: /<>/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /<>/booster/booster.c:304:29: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ In file included from /<>/booster/booster.c:27: /<>/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ [ 28%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /<>/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /<>/booster/hashtables_bfields.c [ 28%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /<>/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /<>/booster/prng.c [ 29%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /<>/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /<>/booster/stats.c [ 29%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /<>/build.serial/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /<>/booster/tree_utils.c [ 30%] Linking C static library libbooster.a cd /<>/build.serial/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake cd /<>/build.serial/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o /usr/bin/ranlib libbooster.a make[4]: Leaving directory '/<>/build.serial' [ 30%] Built target booster make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/whtest /<>/build.serial /<>/build.serial/whtest /<>/build.serial/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/<>/build.serial' [ 30%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /<>/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /<>/whtest/eigen.c [ 30%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /<>/pll/parsePartition.c In file included from /<>/pll/parsePartition.c:42: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 30%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /<>/pll/queue.c [ 31%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /<>/pll/randomTree.c In file included from /<>/pll/randomTree.c:37: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 31%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /<>/pll/recom.c In file included from /<>/pll/recom.c:43: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 31%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /<>/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /<>/nclextra/msetsblock.cpp [ 32%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /<>/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /<>/whtest/eigen_sym.c [ 33%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /<>/pll/restartHashTable.c In file included from /<>/pll/restartHashTable.c:47: /<>/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); | ^~~~~~~~~~~~~~~ [ 33%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /<>/ncl/nxsdatablock.cpp [ 33%] Building C object pll/CMakeFiles/pll.dir/searchAlgo.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /<>/pll/searchAlgo.c In file included from /<>/pll/searchAlgo.c:51: /<>/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); | ^~~~~~~~~~~~~~~ [ 33%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /<>/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /<>/whtest/random.c [ 34%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /<>/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /<>/whtest/weisslambda.c [ 34%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /<>/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /<>/whtest/weisslambda_sub.c [ 34%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /<>/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /<>/whtest/whtest.c [ 35%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /<>/build.serial/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /<>/whtest/whtest_sub.c [ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /<>/ncl/nxsdiscretedatum.cpp /<>/whtest/whtest_sub.c: In function ‘ReadData’: /<>/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 36%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /<>/pll/ssort.c [ 37%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /<>/pll/stack.c [ 37%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /<>/pll/topologies.c In file included from /<>/pll/topologies.c:48: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 38%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /<>/pll/trash.c [ 38%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /<>/build.serial/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /<>/whtest/whtest_wrapper.cpp [ 38%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /<>/ncl/nxsdiscretematrix.cpp In file included from /<>/pll/trash.c:48: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 38%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /<>/pll/treeIO.c In file included from /<>/pll/treeIO.c:49: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 38%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /<>/pll/utils.c In file included from /<>/pll/utils.c:70: /<>/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 /<>/pll/pllInternal.h:16, from /<>/pll/utils.c:70: /<>/pll/utils.c: In function ‘initializePartitionData’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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 * | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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 * | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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) * | ^~~~~~~~~~~~~~~~~~ [ 39%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /<>/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /<>/nclextra/msplitsblock.cpp [ 39%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /<>/ncl/nxsdistancedatum.cpp [ 40%] Linking C static library libpll.a cd /<>/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 40%] Built target pll make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/pll /<>/build.serial /<>/build.serial/pll /<>/build.serial/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/<>/build.serial' [ 40%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /<>/build.serial/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /<>/pll/avxLikelihood.c [ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /<>/ncl/nxsdistancesblock.cpp In file included from /<>/pll/avxLikelihood.c:57: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 41%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /<>/build.serial/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /<>/nclextra/modelsblock.cpp [ 42%] Linking CXX static library libwhtest.a cd /<>/build.serial/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 42%] Built target whtest make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/yaml-cpp /<>/build.serial /<>/build.serial/yaml-cpp /<>/build.serial/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/<>/build.serial' [ 42%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /<>/yaml-cpp/src/binary.cpp [ 43%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /<>/yaml-cpp/src/convert.cpp [ 44%] Linking C static library libpllavx.a cd /<>/build.serial/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 44%] Built target pllavx [ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /<>/yaml-cpp/src/directives.cpp make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/utils /<>/build.serial /<>/build.serial/utils /<>/build.serial/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/<>/build.serial' [ 44%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /<>/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /<>/utils/eigendecomposition.cpp [ 44%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /<>/ncl/nxsemptyblock.cpp [ 45%] Linking CXX static library libnclextra.a cd /<>/build.serial/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 45%] Built target nclextra [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /<>/ncl/nxsexception.cpp [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /<>/yaml-cpp/src/emit.cpp [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /<>/yaml-cpp/src/emitfromevents.cpp [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /<>/yaml-cpp/src/emitter.cpp [ 47%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /<>/ncl/nxsreader.cpp [ 47%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /<>/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /<>/utils/gzstream.cpp [ 48%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /<>/yaml-cpp/src/emitterstate.cpp [ 48%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /<>/ncl/nxssetreader.cpp [ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /<>/ncl/nxsstring.cpp [ 50%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /<>/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /<>/utils/optimization.cpp [ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /<>/ncl/nxstaxablock.cpp [ 50%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /<>/yaml-cpp/src/emitterutils.cpp [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /<>/ncl/nxstoken.cpp [ 51%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /<>/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /<>/utils/stoprule.cpp [ 51%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /<>/build.serial/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /<>/ncl/nxstreesblock.cpp make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/pda /<>/build.serial /<>/build.serial/pda /<>/build.serial/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/<>/build.serial' [ 51%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /<>/pda/circularnetwork.cpp [ 52%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /<>/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /<>/utils/tools.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /<>/yaml-cpp/src/exceptions.cpp [ 52%] Linking CXX static library libncl.a cd /<>/build.serial/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 52%] Built target ncl [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /<>/yaml-cpp/src/exp.cpp [ 53%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /<>/pda/greedy.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /<>/yaml-cpp/src/memory.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /<>/yaml-cpp/src/node.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /<>/yaml-cpp/src/node_data.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /<>/yaml-cpp/src/nodebuilder.cpp [ 55%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /<>/pda/gurobiwrapper.cpp [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /<>/yaml-cpp/src/nodeevents.cpp [ 56%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /<>/pda/hashsplitset.cpp [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /<>/yaml-cpp/src/null.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /<>/yaml-cpp/src/ostream_wrapper.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /<>/yaml-cpp/src/parse.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /<>/pda/pdnetwork.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /<>/pda/pruning.cpp [ 58%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /<>/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /<>/utils/pllnni.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /<>/pda/split.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /<>/yaml-cpp/src/parser.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /<>/yaml-cpp/src/regex_yaml.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /<>/pda/splitgraph.cpp [ 60%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /<>/yaml-cpp/src/scanner.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /<>/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /<>/utils/checkpoint.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /<>/pda/splitset.cpp make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/alignment /<>/build.serial /<>/build.serial/alignment /<>/build.serial/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/<>/build.serial' [ 60%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /<>/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /<>/alignment/pattern.cpp [ 61%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /<>/build.serial/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /<>/pda/lpwrapper.c [ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /<>/pda/ecopd.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /<>/yaml-cpp/src/scanscalar.cpp [ 62%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /<>/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /<>/alignment/alignment.cpp [ 63%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /<>/build.serial/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /<>/utils/MPIHelper.cpp [ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /<>/yaml-cpp/src/scantag.cpp [ 63%] Linking CXX static library libutils.a cd /<>/build.serial/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 63%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/model /<>/build.serial /<>/build.serial/model /<>/build.serial/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/<>/build.serial' [ 63%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /<>/model/modelmarkov.cpp [ 63%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /<>/yaml-cpp/src/scantoken.cpp In file included from /<>/model/modelmarkov.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /<>/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ [ 63%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /<>/pda/graph.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /<>/pda/pdtree.cpp [ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /<>/yaml-cpp/src/simplekey.cpp /<>/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /<>/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /<>/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /<>/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ [ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /<>/yaml-cpp/src/singledocparser.cpp [ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /<>/pda/pdtreeset.cpp [ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /<>/yaml-cpp/src/stream.cpp [ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /<>/build.serial/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /<>/yaml-cpp/src/tag.cpp [ 67%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /<>/build.serial/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /<>/pda/ecopdmtreeset.cpp [ 68%] Linking CXX static library libyaml-cpp.a cd /<>/build.serial/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /<>/build.serial/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" /usr/bin/ranlib libyaml-cpp.a make[4]: Leaving directory '/<>/build.serial' [ 68%] Built target yaml-cpp [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /<>/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /<>/alignment/alignmentpairwise.cpp [ 69%] Linking CXX static library libpda.a cd /<>/build.serial/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 69%] Built target pda make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/phylo-yaml /<>/build.serial /<>/build.serial/phylo-yaml /<>/build.serial/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/<>/build.serial' [ 69%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /<>/build.serial/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /<>/phylo-yaml/statespace.cpp [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /<>/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /<>/alignment/maalignment.cpp [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /<>/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /<>/alignment/superalignment.cpp [ 71%] Linking CXX static library libphyloYAML.a cd /<>/build.serial/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /<>/build.serial/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/<>/build.serial' [ 71%] Built target phyloYAML make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/main /<>/build.serial /<>/build.serial/main /<>/build.serial/main/CMakeFiles/main.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/<>/build.serial' [ 72%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /<>/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /<>/main/main.cpp /<>/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ [ 72%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /<>/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /<>/alignment/superalignmentpairwise.cpp [ 72%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /<>/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /<>/alignment/superalignmentpairwiseplen.cpp [ 73%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /<>/build.serial/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /<>/alignment/superalignmentunlinked.cpp [ 73%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /<>/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /<>/main/phyloanalysis.cpp /<>/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ [ 74%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /<>/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /<>/main/phylotesting.cpp In file included from /<>/main/phyloanalysis.cpp:37: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phyloanalysis.cpp:38: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phyloanalysis.cpp:46: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 74%] Linking CXX static library libalignment.a cd /<>/build.serial/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /<>/build.serial/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o In file included from /<>/main/phylotesting.cpp:21: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phylotesting.cpp:22: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phylotesting.cpp:31: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/main/phylotesting.cpp:34: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/<>/build.serial' [ 74%] Built target alignment [ 75%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /<>/model/modelbin.cpp /<>/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(PML::SeqType)’: /<>/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /<>/main/phylotesting.cpp: In member function ‘double CandidateModel::getScore(ModelTestCriterion)’: /<>/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ In file included from /<>/model/modelbin.h:23, from /<>/model/modelbin.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /<>/model/modeldna.cpp In file included from /<>/model/modeldna.h:23, from /<>/model/modeldna.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modeldna.cpp:20: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /<>/model/modelfactory.cpp In file included from /<>/model/modelfactory.cpp:24: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelfactory.cpp:26: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelfactory.cpp:27: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/model/modelfactory.cpp:30: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 76%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /<>/model/modelprotein.cpp [ 76%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /<>/model/modelset.cpp In file included from /<>/model/modelprotein.h:23, from /<>/model/modelprotein.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelprotein.cpp:20: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 76%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /<>/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /<>/main/treetesting.cpp In file included from /<>/model/modelset.h:23, from /<>/model/modelset.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 77%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /<>/model/modelsubst.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /<>/model/partitionmodel.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /<>/model/partitionmodelplen.cpp In file included from /<>/model/partitionmodel.cpp:23: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/partitionmodelplen.cpp:12: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 78%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /<>/model/rategamma.cpp [ 78%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /<>/build.serial/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /<>/main/timetree.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /<>/model/rategammainvar.cpp [ 79%] Linking CXX static library libmain.a cd /<>/build.serial/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /<>/build.serial/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o /usr/bin/ranlib libmain.a [ 80%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /<>/model/rateheterogeneity.cpp make[4]: Leaving directory '/<>/build.serial' [ 80%] Built target main [ 80%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /<>/model/rateinvar.cpp [ 80%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /<>/model/ratemeyerdiscrete.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /<>/model/ratemeyerhaeseler.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /<>/model/ratekategory.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /<>/model/ratefree.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /<>/model/ratefreeinvar.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /<>/model/rateheterotachy.cpp In file included from /<>/model/modelmixture.h:13, from /<>/model/ratefree.cpp:13: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /<>/model/rateheterotachyinvar.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /<>/model/modelcodon.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /<>/model/modelmorphology.cpp In file included from /<>/model/modelmorphology.h:11, from /<>/model/modelmorphology.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmorphology.cpp:8: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ In file included from /<>/model/modelcodon.h:11, from /<>/model/modelcodon.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 84%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /<>/model/modelmixture.cpp [ 85%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /<>/model/modelunrest.cpp [ 85%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /<>/model/modelliemarkov.cpp In file included from /<>/model/modelmixture.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmixture.cpp:9: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmixture.cpp:10: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/model/modelmixture.cpp:13: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/model/modelunrest.h:11, from /<>/model/modelunrest.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 85%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /<>/model/modelpomo.cpp In file included from /<>/model/modelliemarkov.h:11, from /<>/model/modelliemarkov.cpp:23: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 86%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /<>/model/modelpomomixture.cpp In file included from /<>/model/modeldna.h:23, from /<>/model/modelpomo.h:4, from /<>/model/modelpomo.cpp:1: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelpomo.h:4, from /<>/model/modelpomo.cpp:1: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modeldna.h:23, from /<>/model/modelpomo.h:4, from /<>/model/modelpomomixture.h:14, from /<>/model/modelpomomixture.cpp:9: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelpomo.h:4, from /<>/model/modelpomomixture.h:14, from /<>/model/modelpomomixture.cpp:9: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ [ 86%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /<>/build.serial/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /<>/model/modelfactorymixlen.cpp In file included from /<>/model/modelfactorymixlen.cpp:12: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 87%] Linking CXX static library libmodel.a cd /<>/build.serial/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /<>/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.serial' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tree /<>/build.serial /<>/build.serial/tree /<>/build.serial/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/<>/build.serial' [ 88%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /<>/tree/iqtree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /<>/tree/constrainttree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /<>/tree/candidateset.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /<>/tree/matree.cpp In file included from /<>/tree/iqtree.cpp:29: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /<>/tree/memslot.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /<>/tree/mexttree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /<>/tree/mtree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /<>/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /<>/tree/ncbitree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /<>/tree/node.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /<>/tree/phylonode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /<>/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /<>/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /<>/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /<>/tree/phylosupertreeunlinked.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /<>/tree/phylotree.cpp In file included from /<>/model/modelmixture.h:13, from /<>/tree/phylotree.cpp:34: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /<>/tree/phylotree.cpp: In function ‘std::string getASCName(ASCType)’: /<>/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /<>/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /<>/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /<>/tree/phylotreemixlen.cpp In file included from /<>/model/modelmixture.h:13, from /<>/tree/phylotreemixlen.cpp:12: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /<>/tree/phylotreepars.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /<>/tree/phylotreesse.cpp In file included from /<>/tree/phylotreesse.cpp:35: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /<>/tree/quartet.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /<>/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /<>/tree/tinatree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /<>/tree/parstree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /<>/build.serial/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /<>/tree/discordance.cpp [ 98%] Linking CXX static library libtree.a cd /<>/build.serial/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /<>/build.serial/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/<>/build.serial' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/terrace /<>/build.serial /<>/build.serial/terrace /<>/build.serial/terrace/CMakeFiles/terrace.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/<>/build.serial' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /<>/build.serial/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /<>/terrace/terrace.cpp [ 99%] Linking CXX static library libterrace.a cd /<>/build.serial/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /<>/build.serial/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a make[4]: Leaving directory '/<>/build.serial' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/<>/build.serial' cd /<>/build.serial && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.serial /<>/build.serial /<>/build.serial/CMakeFiles/iqtree2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.serial' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/<>/build.serial' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/<>/build.serial -I/<>/terraphast/include -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /<>/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2 /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2 -L/<>/lib -Wl,-rpath,/<>/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.742’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.1531’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.440’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.1309’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.1076’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2600:92: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2309:9: warning: type ‘struct .omp_data_s.378’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2309:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2292:17: note: the first difference of corresponding definitions is field ‘all_lh’ ./tree/phylokernelnew.h:2292:17: note: a field of same name but different type is defined in another translation unit ./vectorclass/vectorf128.h:1507:7: note: type name ‘Vec2d’ should match type name ‘Vec4d’ ./vectorclass/vectorf256.h:1349:7: note: the incompatible type is defined here make[4]: Leaving directory '/<>/build.serial' [100%] Built target iqtree2 make[3]: Leaving directory '/<>/build.serial' /usr/bin/cmake -E cmake_progress_start /<>/build.serial/CMakeFiles 0 make[2]: Leaving directory '/<>/build.serial' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh_auto_build -Bbuild.mpi cd build.mpi && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/<>/build.mpi' /usr/bin/cmake -S/<> -B/<>/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /<>/build.mpi/CMakeFiles /<>/build.mpi//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[3]: Entering directory '/<>/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.mpi /<>/build.mpi /<>/build.mpi/CMakeFiles/kernelsse.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.mpi /<>/build.mpi /<>/build.mpi/CMakeFiles/kernelavx.dir/DependInfo.cmake --color= make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.mpi /<>/build.mpi /<>/build.mpi/CMakeFiles/kernelfma.dir/DependInfo.cmake --color= make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/depend make[4]: Leaving directory '/<>/build.mpi' make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/terraphast /<>/build.mpi /<>/build.mpi/terraphast /<>/build.mpi/terraphast/CMakeFiles/terraphast.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f CMakeFiles/kernelsse.dir/build.make CMakeFiles/kernelsse.dir/build make -f CMakeFiles/kernelavx.dir/build.make CMakeFiles/kernelavx.dir/build make[4]: Entering directory '/<>/build.mpi' make[4]: Entering directory '/<>/build.mpi' make[4]: Leaving directory '/<>/build.mpi' make -f CMakeFiles/kernelfma.dir/build.make CMakeFiles/kernelfma.dir/build [ 0%] Building CXX object CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -MF CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o.d -o CMakeFiles/kernelsse.dir/tree/phylokernelsse.cpp.o -c /<>/tree/phylokernelsse.cpp make[4]: Entering directory '/<>/build.mpi' make[4]: Leaving directory '/<>/build.mpi' make -f terraphast/CMakeFiles/terraphast.dir/build.make terraphast/CMakeFiles/terraphast.dir/build [ 1%] Building CXX object CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -MF CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o.d -o CMakeFiles/kernelavx.dir/tree/phylotreeavx.cpp.o -c /<>/tree/phylotreeavx.cpp make[4]: Entering directory '/<>/build.mpi' [ 1%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o [ 1%] Building CXX object CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/advanced.cpp.o -MF CMakeFiles/terraphast.dir/lib/advanced.cpp.o.d -o CMakeFiles/terraphast.dir/lib/advanced.cpp.o -c /<>/terraphast/lib/advanced.cpp /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -mfma -MD -MT CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -MF CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o.d -o CMakeFiles/kernelfma.dir/tree/phylokernelfma.cpp.o -c /<>/tree/phylokernelfma.cpp [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bigint.cpp.o -MF CMakeFiles/terraphast.dir/lib/bigint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bigint.cpp.o -c /<>/terraphast/lib/bigint.cpp [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -MF CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o -c /<>/terraphast/lib/bipartitions.cpp [ 2%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -MF CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o.d -o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o -c /<>/terraphast/lib/bitmatrix.cpp [ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -MF CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o.d -o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o -c /<>/terraphast/lib/clamped_uint.cpp [ 3%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/constraints.cpp.o -MF CMakeFiles/terraphast.dir/lib/constraints.cpp.o.d -o CMakeFiles/terraphast.dir/lib/constraints.cpp.o -c /<>/terraphast/lib/constraints.cpp [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/errors.cpp.o -MF CMakeFiles/terraphast.dir/lib/errors.cpp.o.d -o CMakeFiles/terraphast.dir/lib/errors.cpp.o -c /<>/terraphast/lib/errors.cpp [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree.cpp.o -c /<>/terraphast/lib/multitree.cpp [ 4%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -MF CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o.d -o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o -c /<>/terraphast/lib/multitree_iterator.cpp [ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/nodes.cpp.o -MF CMakeFiles/terraphast.dir/lib/nodes.cpp.o.d -o CMakeFiles/terraphast.dir/lib/nodes.cpp.o -c /<>/terraphast/lib/nodes.cpp [ 5%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/parser.cpp.o -MF CMakeFiles/terraphast.dir/lib/parser.cpp.o.d -o CMakeFiles/terraphast.dir/lib/parser.cpp.o -c /<>/terraphast/lib/parser.cpp [ 6%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/rooting.cpp.o -MF CMakeFiles/terraphast.dir/lib/rooting.cpp.o.d -o CMakeFiles/terraphast.dir/lib/rooting.cpp.o -c /<>/terraphast/lib/rooting.cpp [ 6%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/simple.cpp.o -MF CMakeFiles/terraphast.dir/lib/simple.cpp.o.d -o CMakeFiles/terraphast.dir/lib/simple.cpp.o -c /<>/terraphast/lib/simple.cpp [ 6%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -MF CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o.d -o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o -c /<>/terraphast/lib/subtree_extraction.cpp [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -MF CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o.d -o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o -c /<>/terraphast/lib/supertree_helpers.cpp [ 7%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/trees.cpp.o -MF CMakeFiles/terraphast.dir/lib/trees.cpp.o.d -o CMakeFiles/terraphast.dir/lib/trees.cpp.o -c /<>/terraphast/lib/trees.cpp [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/union_find.cpp.o -MF CMakeFiles/terraphast.dir/lib/union_find.cpp.o.d -o CMakeFiles/terraphast.dir/lib/union_find.cpp.o -c /<>/terraphast/lib/union_find.cpp [ 8%] Building CXX object terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o cd /<>/build.mpi/terraphast && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -march=native -Wall -Wextra -Wpedantic -Wconversion -Wsign-conversion -Werror -std=gnu++11 -MD -MT terraphast/CMakeFiles/terraphast.dir/lib/validation.cpp.o -MF CMakeFiles/terraphast.dir/lib/validation.cpp.o.d -o CMakeFiles/terraphast.dir/lib/validation.cpp.o -c /<>/terraphast/lib/validation.cpp [ 8%] Linking CXX static library libterraphast.a cd /<>/build.mpi/terraphast && /usr/bin/cmake -P CMakeFiles/terraphast.dir/cmake_clean_target.cmake cd /<>/build.mpi/terraphast && /usr/bin/cmake -E cmake_link_script CMakeFiles/terraphast.dir/link.txt --verbose=1 /usr/bin/ar qc libterraphast.a CMakeFiles/terraphast.dir/lib/advanced.cpp.o CMakeFiles/terraphast.dir/lib/bigint.cpp.o CMakeFiles/terraphast.dir/lib/bipartitions.cpp.o CMakeFiles/terraphast.dir/lib/bitmatrix.cpp.o CMakeFiles/terraphast.dir/lib/clamped_uint.cpp.o CMakeFiles/terraphast.dir/lib/constraints.cpp.o CMakeFiles/terraphast.dir/lib/errors.cpp.o CMakeFiles/terraphast.dir/lib/multitree.cpp.o CMakeFiles/terraphast.dir/lib/multitree_iterator.cpp.o CMakeFiles/terraphast.dir/lib/nodes.cpp.o CMakeFiles/terraphast.dir/lib/parser.cpp.o CMakeFiles/terraphast.dir/lib/rooting.cpp.o CMakeFiles/terraphast.dir/lib/simple.cpp.o CMakeFiles/terraphast.dir/lib/subtree_extraction.cpp.o CMakeFiles/terraphast.dir/lib/supertree_helpers.cpp.o CMakeFiles/terraphast.dir/lib/trees.cpp.o CMakeFiles/terraphast.dir/lib/union_find.cpp.o CMakeFiles/terraphast.dir/lib/validation.cpp.o /usr/bin/ranlib libterraphast.a make[4]: Leaving directory '/<>/build.mpi' [ 8%] Built target terraphast make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/pll /<>/build.mpi /<>/build.mpi/pll /<>/build.mpi/pll/CMakeFiles/pll.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f pll/CMakeFiles/pll.dir/build.make pll/CMakeFiles/pll.dir/build make[4]: Entering directory '/<>/build.mpi' [ 8%] Building C object pll/CMakeFiles/pll.dir/alignment.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/alignment.c.o -MF CMakeFiles/pll.dir/alignment.c.o.d -o CMakeFiles/pll.dir/alignment.c.o -c /<>/pll/alignment.c In file included from /<>/pll/alignment.c:40: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/bipartitionList.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/bipartitionList.c.o -MF CMakeFiles/pll.dir/bipartitionList.c.o.d -o CMakeFiles/pll.dir/bipartitionList.c.o -c /<>/pll/bipartitionList.c In file included from /<>/pll/bipartitionList.c:49: /<>/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 /<>/pll/bipartitionList.c:29: /<>/pll/bipartitionList.c: In function ‘insertHashRF’: /<>/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 /<>/pll/bipartitionList.c:332:3: note: in expansion of macro ‘rax_posix_memalign’ 332 | rax_posix_memalign ((void **)&(e->bitVector), PLL_BYTE_ALIGNMENT, (size_t)vectorLength * sizeof(unsigned int)); | ^~~~~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluateGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluateGenericSpecial.c.o -c /<>/pll/evaluateGenericSpecial.c In file included from /<>/pll/evaluateGenericSpecial.c:46: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 9%] Building C object pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -MF CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o.d -o CMakeFiles/pll.dir/evaluatePartialGenericSpecial.c.o -c /<>/pll/evaluatePartialGenericSpecial.c In file included from /<>/pll/evaluatePartialGenericSpecial.c:45: /<>/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 /<>/pll/evaluatePartialGenericSpecial.c:31: /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCAT’: /<>/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 /<>/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); | ^~~~~~~~~~~~~~~~~~ /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMA’: /<>/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 /<>/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); | ^~~~~~~~~~~~~~~~~~ /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRCATPROT’: /<>/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 /<>/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); | ^~~~~~~~~~~~~~~~~~ /<>/pll/evaluatePartialGenericSpecial.c: In function ‘evaluatePartialGTRGAMMAPROT’: /<>/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 /<>/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.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/fastDNAparsimony.c.o -MF CMakeFiles/pll.dir/fastDNAparsimony.c.o.d -o CMakeFiles/pll.dir/fastDNAparsimony.c.o -c /<>/pll/fastDNAparsimony.c In file included from /<>/pll/fastDNAparsimony.c:113: /<>/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 /<>/pll/fastDNAparsimony.c:29: /<>/pll/fastDNAparsimony.c: In function ‘compressDNA’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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 C object pll/CMakeFiles/pll.dir/hardware.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hardware.c.o -MF CMakeFiles/pll.dir/hardware.c.o.d -o CMakeFiles/pll.dir/hardware.c.o -c /<>/pll/hardware.c /<>/pll/hardware.c: In function ‘pll_probe_cpu’: /<>/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.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/hash.c.o -MF CMakeFiles/pll.dir/hash.c.o.d -o CMakeFiles/pll.dir/hash.c.o -c /<>/pll/hash.c [ 11%] Building C object pll/CMakeFiles/pll.dir/lexer.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/lexer.c.o -MF CMakeFiles/pll.dir/lexer.c.o.d -o CMakeFiles/pll.dir/lexer.c.o -c /<>/pll/lexer.c [ 12%] Building C object pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -MF CMakeFiles/pll.dir/makenewzGenericSpecial.c.o.d -o CMakeFiles/pll.dir/makenewzGenericSpecial.c.o -c /<>/pll/makenewzGenericSpecial.c In file included from /<>/pll/makenewzGenericSpecial.c:44: /<>/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 /<>/pll/makenewzGenericSpecial.c:29: /<>/pll/makenewzGenericSpecial.c: In function ‘coreGTRCAT’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/pll/makenewzGenericSpecial.c: In function ‘coreGTRCATPROT’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ [ 13%] 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.mpi' [ 13%] Built target kernelsse make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/ncl /<>/build.mpi /<>/build.mpi/ncl /<>/build.mpi/ncl/CMakeFiles/ncl.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f ncl/CMakeFiles/ncl.dir/build.make ncl/CMakeFiles/ncl.dir/build make[4]: Entering directory '/<>/build.mpi' [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsassumptionsblock.cpp.o -c /<>/ncl/nxsassumptionsblock.cpp [ 13%] Building C object pll/CMakeFiles/pll.dir/models.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/models.c.o -MF CMakeFiles/pll.dir/models.c.o.d -o CMakeFiles/pll.dir/models.c.o -c /<>/pll/models.c In file included from /<>/pll/models.c:53: /<>/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); | ^~~~~~~~~~~~~~~ [ 13%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsblock.cpp.o -MF CMakeFiles/ncl.dir/nxsblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsblock.cpp.o -c /<>/ncl/nxsblock.cpp [ 14%] Building CXX object ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -MF CMakeFiles/ncl.dir/nxscharactersblock.cpp.o.d -o CMakeFiles/ncl.dir/nxscharactersblock.cpp.o -c /<>/ncl/nxscharactersblock.cpp [ 14%] Building C object pll/CMakeFiles/pll.dir/newick.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newick.c.o -MF CMakeFiles/pll.dir/newick.c.o.d -o CMakeFiles/pll.dir/newick.c.o -c /<>/pll/newick.c In file included from /<>/pll/newick.c:36: /<>/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); | ^~~~~~~~~~~~~~~ [ 15%] Building C object pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/newviewGenericSpecial.c.o -MF CMakeFiles/pll.dir/newviewGenericSpecial.c.o.d -o CMakeFiles/pll.dir/newviewGenericSpecial.c.o -c /<>/pll/newviewGenericSpecial.c In file included from /<>/pll/newviewGenericSpecial.c:49: /<>/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 /<>/pll/newviewGenericSpecial.c:32: /<>/pll/newviewGenericSpecial.c: In function ‘pllNewviewIterative’: /<>/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 /<>/pll/newviewGenericSpecial.c:2763:13: note: in expansion of macro ‘rax_posix_memalign’ 2763 | rax_posix_memalign ((void **)&x3_start, PLL_BYTE_ALIGNMENT, requiredLength); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/pll/newviewGenericSpecial.c:2792:17: note: in expansion of macro ‘rax_posix_memalign’ 2792 | rax_posix_memalign ((void **)&ex3, PLL_BYTE_ALIGNMENT, requiredExpLength); | ^~~~~~~~~~~~~~~~~~ /<>/pll/newviewGenericSpecial.c: In function ‘newviewAncestralIterative’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/pll/newviewGenericSpecial.c: In function ‘pllGetCLV’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ [ 16%] 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.mpi' [ 16%] Built target kernelfma make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/sprng /<>/build.mpi /<>/build.mpi/sprng /<>/build.mpi/sprng/CMakeFiles/sprng.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f sprng/CMakeFiles/sprng.dir/build.make sprng/CMakeFiles/sprng.dir/build make[4]: Entering directory '/<>/build.mpi' [ 16%] Building C object sprng/CMakeFiles/sprng.dir/lcg64.c.o cd /<>/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/lcg64.c.o -MF CMakeFiles/sprng.dir/lcg64.c.o.d -o CMakeFiles/sprng.dir/lcg64.c.o -c /<>/sprng/lcg64.c [ 17%] Building C object sprng/CMakeFiles/sprng.dir/makeseed.c.o cd /<>/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/makeseed.c.o -MF CMakeFiles/sprng.dir/makeseed.c.o.d -o CMakeFiles/sprng.dir/makeseed.c.o -c /<>/sprng/makeseed.c [ 17%] Building C object sprng/CMakeFiles/sprng.dir/memory.c.o cd /<>/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/memory.c.o -MF CMakeFiles/sprng.dir/memory.c.o.d -o CMakeFiles/sprng.dir/memory.c.o -c /<>/sprng/memory.c [ 18%] Building C object sprng/CMakeFiles/sprng.dir/store.c.o cd /<>/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/store.c.o -MF CMakeFiles/sprng.dir/store.c.o.d -o CMakeFiles/sprng.dir/store.c.o -c /<>/sprng/store.c [ 18%] Building C object sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o cd /<>/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/primes-lcg64.c.o -MF CMakeFiles/sprng.dir/primes-lcg64.c.o.d -o CMakeFiles/sprng.dir/primes-lcg64.c.o -c /<>/sprng/primes-lcg64.c [ 18%] Building C object sprng/CMakeFiles/sprng.dir/checkid.c.o cd /<>/build.mpi/sprng && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT sprng/CMakeFiles/sprng.dir/checkid.c.o -MF CMakeFiles/sprng.dir/checkid.c.o.d -o CMakeFiles/sprng.dir/checkid.c.o -c /<>/sprng/checkid.c [ 19%] Linking C static library libsprng.a cd /<>/build.mpi/sprng && /usr/bin/cmake -P CMakeFiles/sprng.dir/cmake_clean_target.cmake cd /<>/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.mpi' [ 19%] Built target sprng make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/lbfgsb /<>/build.mpi /<>/build.mpi/lbfgsb /<>/build.mpi/lbfgsb/CMakeFiles/lbfgsb.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f lbfgsb/CMakeFiles/lbfgsb.dir/build.make lbfgsb/CMakeFiles/lbfgsb.dir/build make[4]: Entering directory '/<>/build.mpi' [ 19%] Building CXX object lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o cd /<>/build.mpi/lbfgsb && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT lbfgsb/CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -MF CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o.d -o CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o -c /<>/lbfgsb/lbfgsb_new.cpp [ 19%] 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.mpi' [ 19%] Built target kernelavx [ 19%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdatablock.cpp.o -MF CMakeFiles/ncl.dir/nxsdatablock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdatablock.cpp.o -c /<>/ncl/nxsdatablock.cpp [ 19%] Building C object pll/CMakeFiles/pll.dir/genericParallelization.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/genericParallelization.c.o -MF CMakeFiles/pll.dir/genericParallelization.c.o.d -o CMakeFiles/pll.dir/genericParallelization.c.o -c /<>/pll/genericParallelization.c In file included from /<>/pll/genericParallelization.c:43: /<>/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/nxsdiscretedatum.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretedatum.cpp.o -c /<>/ncl/nxsdiscretedatum.cpp [ 20%] Linking CXX static library liblbfgsb.a cd /<>/build.mpi/lbfgsb && /usr/bin/cmake -P CMakeFiles/lbfgsb.dir/cmake_clean_target.cmake cd /<>/build.mpi/lbfgsb && /usr/bin/cmake -E cmake_link_script CMakeFiles/lbfgsb.dir/link.txt --verbose=1 /usr/bin/ar qc liblbfgsb.a CMakeFiles/lbfgsb.dir/lbfgsb_new.cpp.o /usr/bin/ranlib liblbfgsb.a make[4]: Leaving directory '/<>/build.mpi' [ 20%] Built target lbfgsb make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/gsl /<>/build.mpi /<>/build.mpi/gsl /<>/build.mpi/gsl/CMakeFiles/gsl.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f gsl/CMakeFiles/gsl.dir/build.make gsl/CMakeFiles/gsl.dir/build make[4]: Entering directory '/<>/build.mpi' [ 21%] Building C object pll/CMakeFiles/pll.dir/optimizeModel.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/optimizeModel.c.o -MF CMakeFiles/pll.dir/optimizeModel.c.o.d -o CMakeFiles/pll.dir/optimizeModel.c.o -c /<>/pll/optimizeModel.c [ 22%] Building CXX object gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o cd /<>/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/binomial_tpe.cpp.o -MF CMakeFiles/gsl.dir/binomial_tpe.cpp.o.d -o CMakeFiles/gsl.dir/binomial_tpe.cpp.o -c /<>/gsl/binomial_tpe.cpp In file included from /<>/pll/optimizeModel.c:47: /<>/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 gsl/CMakeFiles/gsl.dir/multinomial.cpp.o cd /<>/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/multinomial.cpp.o -MF CMakeFiles/gsl.dir/multinomial.cpp.o.d -o CMakeFiles/gsl.dir/multinomial.cpp.o -c /<>/gsl/multinomial.cpp [ 22%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -MF CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o.d -o CMakeFiles/ncl.dir/nxsdiscretematrix.cpp.o -c /<>/ncl/nxsdiscretematrix.cpp [ 23%] Building CXX object gsl/CMakeFiles/gsl.dir/pow_int.cpp.o cd /<>/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/pow_int.cpp.o -MF CMakeFiles/gsl.dir/pow_int.cpp.o.d -o CMakeFiles/gsl.dir/pow_int.cpp.o -c /<>/gsl/pow_int.cpp [ 23%] Building CXX object gsl/CMakeFiles/gsl.dir/gauss.cpp.o cd /<>/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gauss.cpp.o -MF CMakeFiles/gsl.dir/gauss.cpp.o.d -o CMakeFiles/gsl.dir/gauss.cpp.o -c /<>/gsl/gauss.cpp [ 23%] Building CXX object gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o cd /<>/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gaussinv.cpp.o -MF CMakeFiles/gsl.dir/gaussinv.cpp.o.d -o CMakeFiles/gsl.dir/gaussinv.cpp.o -c /<>/gsl/gaussinv.cpp [ 24%] Building CXX object gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o cd /<>/build.mpi/gsl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT gsl/CMakeFiles/gsl.dir/gausspdf.cpp.o -MF CMakeFiles/gsl.dir/gausspdf.cpp.o.d -o CMakeFiles/gsl.dir/gausspdf.cpp.o -c /<>/gsl/gausspdf.cpp [ 24%] Linking CXX static library libgsl.a cd /<>/build.mpi/gsl && /usr/bin/cmake -P CMakeFiles/gsl.dir/cmake_clean_target.cmake [ 24%] Building C object pll/CMakeFiles/pll.dir/parsePartition.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/parsePartition.c.o -MF CMakeFiles/pll.dir/parsePartition.c.o.d -o CMakeFiles/pll.dir/parsePartition.c.o -c /<>/pll/parsePartition.c cd /<>/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.mpi' [ 24%] Built target gsl make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/booster /<>/build.mpi /<>/build.mpi/booster /<>/build.mpi/booster/CMakeFiles/booster.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f booster/CMakeFiles/booster.dir/build.make booster/CMakeFiles/booster.dir/build make[4]: Entering directory '/<>/build.mpi' [ 25%] Building C object booster/CMakeFiles/booster.dir/bitset_index.c.o cd /<>/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/bitset_index.c.o -MF CMakeFiles/booster.dir/bitset_index.c.o.d -o CMakeFiles/booster.dir/bitset_index.c.o -c /<>/booster/bitset_index.c In file included from /<>/pll/parsePartition.c:42: /<>/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 booster/CMakeFiles/booster.dir/hashmap.c.o cd /<>/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashmap.c.o -MF CMakeFiles/booster.dir/hashmap.c.o.d -o CMakeFiles/booster.dir/hashmap.c.o -c /<>/booster/hashmap.c [ 25%] Building C object pll/CMakeFiles/pll.dir/queue.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/queue.c.o -MF CMakeFiles/pll.dir/queue.c.o.d -o CMakeFiles/pll.dir/queue.c.o -c /<>/pll/queue.c [ 26%] Building C object pll/CMakeFiles/pll.dir/randomTree.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/randomTree.c.o -MF CMakeFiles/pll.dir/randomTree.c.o.d -o CMakeFiles/pll.dir/randomTree.c.o -c /<>/pll/randomTree.c In file included from /<>/pll/randomTree.c:37: /<>/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); | ^~~~~~~~~~~~~~~ [ 26%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o [ 26%] Building C object booster/CMakeFiles/booster.dir/io.c.o cd /<>/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/io.c.o -MF CMakeFiles/booster.dir/io.c.o.d -o CMakeFiles/booster.dir/io.c.o -c /<>/booster/io.c cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancedatum.cpp.o -c /<>/ncl/nxsdistancedatum.cpp [ 26%] Building C object pll/CMakeFiles/pll.dir/recom.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/recom.c.o -MF CMakeFiles/pll.dir/recom.c.o.d -o CMakeFiles/pll.dir/recom.c.o -c /<>/pll/recom.c In file included from /<>/pll/recom.c:43: /<>/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 booster/CMakeFiles/booster.dir/sort.c.o cd /<>/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/sort.c.o -MF CMakeFiles/booster.dir/sort.c.o.d -o CMakeFiles/booster.dir/sort.c.o -c /<>/booster/sort.c [ 27%] Building C object booster/CMakeFiles/booster.dir/tree.c.o cd /<>/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree.c.o -MF CMakeFiles/booster.dir/tree.c.o.d -o CMakeFiles/booster.dir/tree.c.o -c /<>/booster/tree.c [ 28%] Building C object pll/CMakeFiles/pll.dir/restartHashTable.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/restartHashTable.c.o -MF CMakeFiles/pll.dir/restartHashTable.c.o.d -o CMakeFiles/pll.dir/restartHashTable.c.o -c /<>/pll/restartHashTable.c In file included from /<>/pll/restartHashTable.c:47: /<>/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/searchAlgo.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/searchAlgo.c.o -MF CMakeFiles/pll.dir/searchAlgo.c.o.d -o CMakeFiles/pll.dir/searchAlgo.c.o -c /<>/pll/searchAlgo.c In file included from /<>/pll/searchAlgo.c:51: /<>/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); | ^~~~~~~~~~~~~~~ [ 29%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -MF CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsdistancesblock.cpp.o -c /<>/ncl/nxsdistancesblock.cpp [ 30%] Building C object booster/CMakeFiles/booster.dir/booster.c.o cd /<>/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/booster.c.o -MF CMakeFiles/booster.dir/booster.c.o.d -o CMakeFiles/booster.dir/booster.c.o -c /<>/booster/booster.c /<>/booster/booster.c: In function ‘main_booster’: /<>/booster/booster.c:268:57: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 268 | unsigned int treefilesize = 3 * tell_size_of_one_tree(input_tree); | ^~~~~~~~~~ In file included from /<>/booster/booster.c:27: /<>/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ /<>/booster/booster.c:304:29: warning: passing argument 1 of ‘tell_size_of_one_tree’ discards ‘const’ qualifier from pointer target type [-Wdiscarded-qualifiers] 304 | if (tell_size_of_one_tree(boot_trees) > treefilesize /* this value is still reachable */) { | ^~~~~~~~~~ In file included from /<>/booster/booster.c:27: /<>/booster/tree.h:191:42: note: expected ‘char *’ but argument is of type ‘const char *’ 191 | unsigned int tell_size_of_one_tree(char* filename); | ~~~~~~^~~~~~~~ [ 30%] Building C object booster/CMakeFiles/booster.dir/hashtables_bfields.c.o cd /<>/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/hashtables_bfields.c.o -MF CMakeFiles/booster.dir/hashtables_bfields.c.o.d -o CMakeFiles/booster.dir/hashtables_bfields.c.o -c /<>/booster/hashtables_bfields.c [ 30%] Building C object booster/CMakeFiles/booster.dir/prng.c.o cd /<>/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/prng.c.o -MF CMakeFiles/booster.dir/prng.c.o.d -o CMakeFiles/booster.dir/prng.c.o -c /<>/booster/prng.c [ 31%] Building C object booster/CMakeFiles/booster.dir/stats.c.o cd /<>/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/stats.c.o -MF CMakeFiles/booster.dir/stats.c.o.d -o CMakeFiles/booster.dir/stats.c.o -c /<>/booster/stats.c [ 31%] Building C object booster/CMakeFiles/booster.dir/tree_utils.c.o cd /<>/build.mpi/booster && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT booster/CMakeFiles/booster.dir/tree_utils.c.o -MF CMakeFiles/booster.dir/tree_utils.c.o.d -o CMakeFiles/booster.dir/tree_utils.c.o -c /<>/booster/tree_utils.c [ 31%] Building C object pll/CMakeFiles/pll.dir/ssort.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/ssort.c.o -MF CMakeFiles/pll.dir/ssort.c.o.d -o CMakeFiles/pll.dir/ssort.c.o -c /<>/pll/ssort.c make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/vectorclass /<>/build.mpi /<>/build.mpi/vectorclass /<>/build.mpi/vectorclass/CMakeFiles/vectorclass.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f vectorclass/CMakeFiles/vectorclass.dir/build.make vectorclass/CMakeFiles/vectorclass.dir/build make[4]: Entering directory '/<>/build.mpi' [ 32%] Building CXX object vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o cd /<>/build.mpi/vectorclass && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT vectorclass/CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -MF CMakeFiles/vectorclass.dir/instrset_detect.cpp.o.d -o CMakeFiles/vectorclass.dir/instrset_detect.cpp.o -c /<>/vectorclass/instrset_detect.cpp [ 33%] Building C object pll/CMakeFiles/pll.dir/stack.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/stack.c.o -MF CMakeFiles/pll.dir/stack.c.o.d -o CMakeFiles/pll.dir/stack.c.o -c /<>/pll/stack.c [ 33%] Linking CXX static library libvectorclass.a cd /<>/build.mpi/vectorclass && /usr/bin/cmake -P CMakeFiles/vectorclass.dir/cmake_clean_target.cmake cd /<>/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 [ 33%] Building C object pll/CMakeFiles/pll.dir/topologies.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/topologies.c.o -MF CMakeFiles/pll.dir/topologies.c.o.d -o CMakeFiles/pll.dir/topologies.c.o -c /<>/pll/topologies.c [ 34%] Linking C static library libbooster.a make[4]: Leaving directory '/<>/build.mpi' cd /<>/build.mpi/booster && /usr/bin/cmake -P CMakeFiles/booster.dir/cmake_clean_target.cmake [ 34%] Built target vectorclass make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/depend cd /<>/build.mpi/booster && /usr/bin/cmake -E cmake_link_script CMakeFiles/booster.dir/link.txt --verbose=1 make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/nclextra /<>/build.mpi /<>/build.mpi/nclextra /<>/build.mpi/nclextra/CMakeFiles/nclextra.dir/DependInfo.cmake --color= /usr/bin/ar qc libbooster.a CMakeFiles/booster.dir/bitset_index.c.o CMakeFiles/booster.dir/hashmap.c.o CMakeFiles/booster.dir/io.c.o CMakeFiles/booster.dir/sort.c.o CMakeFiles/booster.dir/tree.c.o CMakeFiles/booster.dir/booster.c.o CMakeFiles/booster.dir/hashtables_bfields.c.o CMakeFiles/booster.dir/prng.c.o CMakeFiles/booster.dir/stats.c.o CMakeFiles/booster.dir/tree_utils.c.o make[4]: Leaving directory '/<>/build.mpi' make -f nclextra/CMakeFiles/nclextra.dir/build.make nclextra/CMakeFiles/nclextra.dir/build /usr/bin/ranlib libbooster.a make[4]: Entering directory '/<>/build.mpi' make[4]: Leaving directory '/<>/build.mpi' [ 35%] Building CXX object nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o cd /<>/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/mpdablock.cpp.o -MF CMakeFiles/nclextra.dir/mpdablock.cpp.o.d -o CMakeFiles/nclextra.dir/mpdablock.cpp.o -c /<>/nclextra/mpdablock.cpp [ 35%] Built target booster make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/whtest /<>/build.mpi /<>/build.mpi/whtest /<>/build.mpi/whtest/CMakeFiles/whtest.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f whtest/CMakeFiles/whtest.dir/build.make whtest/CMakeFiles/whtest.dir/build make[4]: Entering directory '/<>/build.mpi' [ 35%] Building C object whtest/CMakeFiles/whtest.dir/eigen.c.o cd /<>/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen.c.o -MF CMakeFiles/whtest.dir/eigen.c.o.d -o CMakeFiles/whtest.dir/eigen.c.o -c /<>/whtest/eigen.c In file included from /<>/pll/topologies.c:48: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 36%] Building C object pll/CMakeFiles/pll.dir/trash.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/trash.c.o -MF CMakeFiles/pll.dir/trash.c.o.d -o CMakeFiles/pll.dir/trash.c.o -c /<>/pll/trash.c In file included from /<>/pll/trash.c:48: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 36%] Building C object pll/CMakeFiles/pll.dir/treeIO.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/treeIO.c.o -MF CMakeFiles/pll.dir/treeIO.c.o.d -o CMakeFiles/pll.dir/treeIO.c.o -c /<>/pll/treeIO.c In file included from /<>/pll/treeIO.c:49: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 36%] Building C object pll/CMakeFiles/pll.dir/utils.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pll/CMakeFiles/pll.dir/utils.c.o -MF CMakeFiles/pll.dir/utils.c.o.d -o CMakeFiles/pll.dir/utils.c.o -c /<>/pll/utils.c In file included from /<>/pll/utils.c:70: /<>/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 /<>/pll/pllInternal.h:16, from /<>/pll/utils.c:70: /<>/pll/utils.c: In function ‘initializePartitionData’: /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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 * | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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 * | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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)); | ^~~~~~~~~~~~~~~~~~ /<>/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 /<>/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) * | ^~~~~~~~~~~~~~~~~~ [ 36%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -MF CMakeFiles/ncl.dir/nxsemptyblock.cpp.o.d -o CMakeFiles/ncl.dir/nxsemptyblock.cpp.o -c /<>/ncl/nxsemptyblock.cpp [ 37%] Building C object whtest/CMakeFiles/whtest.dir/eigen_sym.c.o cd /<>/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/eigen_sym.c.o -MF CMakeFiles/whtest.dir/eigen_sym.c.o.d -o CMakeFiles/whtest.dir/eigen_sym.c.o -c /<>/whtest/eigen_sym.c [ 37%] Building C object whtest/CMakeFiles/whtest.dir/random.c.o cd /<>/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/random.c.o -MF CMakeFiles/whtest.dir/random.c.o.d -o CMakeFiles/whtest.dir/random.c.o -c /<>/whtest/random.c [ 38%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda.c.o cd /<>/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda.c.o -MF CMakeFiles/whtest.dir/weisslambda.c.o.d -o CMakeFiles/whtest.dir/weisslambda.c.o -c /<>/whtest/weisslambda.c [ 38%] Building C object whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o cd /<>/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/weisslambda_sub.c.o -MF CMakeFiles/whtest.dir/weisslambda_sub.c.o.d -o CMakeFiles/whtest.dir/weisslambda_sub.c.o -c /<>/whtest/weisslambda_sub.c [ 38%] Building C object whtest/CMakeFiles/whtest.dir/whtest.c.o cd /<>/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest.c.o -MF CMakeFiles/whtest.dir/whtest.c.o.d -o CMakeFiles/whtest.dir/whtest.c.o -c /<>/whtest/whtest.c [ 39%] Building C object whtest/CMakeFiles/whtest.dir/whtest_sub.c.o cd /<>/build.mpi/whtest && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_sub.c.o -MF CMakeFiles/whtest.dir/whtest_sub.c.o.d -o CMakeFiles/whtest.dir/whtest_sub.c.o -c /<>/whtest/whtest_sub.c [ 40%] Linking C static library libpll.a cd /<>/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pll.dir/cmake_clean_target.cmake cd /<>/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 /<>/whtest/whtest_sub.c: In function ‘ReadData’: /<>/whtest/whtest_sub.c:205:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 205 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ /<>/whtest/whtest_sub.c:221:25: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 221 | fscanf ( ifp, "%c", &c ); | ^~~~~~~~~~~~~~~~~~~~~~~~ [ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsexception.cpp.o -MF CMakeFiles/ncl.dir/nxsexception.cpp.o.d -o CMakeFiles/ncl.dir/nxsexception.cpp.o -c /<>/ncl/nxsexception.cpp /usr/bin/ranlib libpll.a make[4]: Leaving directory '/<>/build.mpi' [ 41%] Built target pll make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/pll /<>/build.mpi /<>/build.mpi/pll /<>/build.mpi/pll/CMakeFiles/pllavx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f pll/CMakeFiles/pllavx.dir/build.make pll/CMakeFiles/pllavx.dir/build make[4]: Entering directory '/<>/build.mpi' [ 41%] Building C object pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o cd /<>/build.mpi/pll && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -D__AVX -mavx -fabi-version=0 -MD -MT pll/CMakeFiles/pllavx.dir/avxLikelihood.c.o -MF CMakeFiles/pllavx.dir/avxLikelihood.c.o.d -o CMakeFiles/pllavx.dir/avxLikelihood.c.o -c /<>/pll/avxLikelihood.c [ 41%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o cd /<>/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msetsblock.cpp.o -MF CMakeFiles/nclextra.dir/msetsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msetsblock.cpp.o -c /<>/nclextra/msetsblock.cpp In file included from /<>/pll/avxLikelihood.c:57: /<>/pll/pllInternal.h:150:30: warning: inline function ‘bitcount_64_bit’ declared but never defined 150 | extern __inline unsigned int bitcount_64_bit(uint64_t i); | ^~~~~~~~~~~~~~~ [ 41%] Building CXX object whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o cd /<>/build.mpi/whtest && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT whtest/CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -MF CMakeFiles/whtest.dir/whtest_wrapper.cpp.o.d -o CMakeFiles/whtest.dir/whtest_wrapper.cpp.o -c /<>/whtest/whtest_wrapper.cpp [ 41%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsreader.cpp.o -MF CMakeFiles/ncl.dir/nxsreader.cpp.o.d -o CMakeFiles/ncl.dir/nxsreader.cpp.o -c /<>/ncl/nxsreader.cpp [ 42%] Linking C static library libpllavx.a cd /<>/build.mpi/pll && /usr/bin/cmake -P CMakeFiles/pllavx.dir/cmake_clean_target.cmake cd /<>/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.mpi' [ 42%] Built target pllavx make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/yaml-cpp /<>/build.mpi /<>/build.mpi/yaml-cpp /<>/build.mpi/yaml-cpp/CMakeFiles/yaml-cpp.dir/DependInfo.cmake --color= [ 42%] Building CXX object ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxssetreader.cpp.o -MF CMakeFiles/ncl.dir/nxssetreader.cpp.o.d -o CMakeFiles/ncl.dir/nxssetreader.cpp.o -c /<>/ncl/nxssetreader.cpp make[4]: Leaving directory '/<>/build.mpi' make -f yaml-cpp/CMakeFiles/yaml-cpp.dir/build.make yaml-cpp/CMakeFiles/yaml-cpp.dir/build make[4]: Entering directory '/<>/build.mpi' [ 42%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/binary.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/binary.cpp.o -c /<>/yaml-cpp/src/binary.cpp [ 43%] Linking CXX static library libwhtest.a cd /<>/build.mpi/whtest && /usr/bin/cmake -P CMakeFiles/whtest.dir/cmake_clean_target.cmake cd /<>/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.mpi' [ 43%] Built target whtest make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/utils /<>/build.mpi /<>/build.mpi/utils /<>/build.mpi/utils/CMakeFiles/utils.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f utils/CMakeFiles/utils.dir/build.make utils/CMakeFiles/utils.dir/build make[4]: Entering directory '/<>/build.mpi' [ 43%] Building CXX object utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o cd /<>/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/eigendecomposition.cpp.o -MF CMakeFiles/utils.dir/eigendecomposition.cpp.o.d -o CMakeFiles/utils.dir/eigendecomposition.cpp.o -c /<>/utils/eigendecomposition.cpp [ 44%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/convert.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/convert.cpp.o -c /<>/yaml-cpp/src/convert.cpp [ 45%] Building CXX object nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o cd /<>/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/msplitsblock.cpp.o -MF CMakeFiles/nclextra.dir/msplitsblock.cpp.o.d -o CMakeFiles/nclextra.dir/msplitsblock.cpp.o -c /<>/nclextra/msplitsblock.cpp [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxsstring.cpp.o -MF CMakeFiles/ncl.dir/nxsstring.cpp.o.d -o CMakeFiles/ncl.dir/nxsstring.cpp.o -c /<>/ncl/nxsstring.cpp [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/directives.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/directives.cpp.o -c /<>/yaml-cpp/src/directives.cpp [ 46%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emit.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emit.cpp.o -c /<>/yaml-cpp/src/emit.cpp [ 46%] Building CXX object utils/CMakeFiles/utils.dir/gzstream.cpp.o cd /<>/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/gzstream.cpp.o -MF CMakeFiles/utils.dir/gzstream.cpp.o.d -o CMakeFiles/utils.dir/gzstream.cpp.o -c /<>/utils/gzstream.cpp [ 46%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstaxablock.cpp.o -MF CMakeFiles/ncl.dir/nxstaxablock.cpp.o.d -o CMakeFiles/ncl.dir/nxstaxablock.cpp.o -c /<>/ncl/nxstaxablock.cpp [ 46%] Building CXX object nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o cd /<>/build.mpi/nclextra && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT nclextra/CMakeFiles/nclextra.dir/modelsblock.cpp.o -MF CMakeFiles/nclextra.dir/modelsblock.cpp.o.d -o CMakeFiles/nclextra.dir/modelsblock.cpp.o -c /<>/nclextra/modelsblock.cpp [ 47%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o -c /<>/yaml-cpp/src/emitfromevents.cpp [ 48%] Building CXX object utils/CMakeFiles/utils.dir/optimization.cpp.o cd /<>/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/optimization.cpp.o -MF CMakeFiles/utils.dir/optimization.cpp.o.d -o CMakeFiles/utils.dir/optimization.cpp.o -c /<>/utils/optimization.cpp [ 49%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstoken.cpp.o -MF CMakeFiles/ncl.dir/nxstoken.cpp.o.d -o CMakeFiles/ncl.dir/nxstoken.cpp.o -c /<>/ncl/nxstoken.cpp [ 49%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o -c /<>/yaml-cpp/src/emitter.cpp [ 50%] Linking CXX static library libnclextra.a cd /<>/build.mpi/nclextra && /usr/bin/cmake -P CMakeFiles/nclextra.dir/cmake_clean_target.cmake cd /<>/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.mpi' [ 50%] Built target nclextra [ 50%] Building CXX object ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o cd /<>/build.mpi/ncl && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT ncl/CMakeFiles/ncl.dir/nxstreesblock.cpp.o -MF CMakeFiles/ncl.dir/nxstreesblock.cpp.o.d -o CMakeFiles/ncl.dir/nxstreesblock.cpp.o -c /<>/ncl/nxstreesblock.cpp [ 50%] Building CXX object utils/CMakeFiles/utils.dir/stoprule.cpp.o cd /<>/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/stoprule.cpp.o -MF CMakeFiles/utils.dir/stoprule.cpp.o.d -o CMakeFiles/utils.dir/stoprule.cpp.o -c /<>/utils/stoprule.cpp [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o -c /<>/yaml-cpp/src/emitterstate.cpp [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o -c /<>/yaml-cpp/src/emitterutils.cpp [ 51%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o -c /<>/yaml-cpp/src/exceptions.cpp [ 51%] Linking CXX static library libncl.a cd /<>/build.mpi/ncl && /usr/bin/cmake -P CMakeFiles/ncl.dir/cmake_clean_target.cmake cd /<>/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.mpi' [ 51%] Built target ncl make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/pda /<>/build.mpi /<>/build.mpi/pda /<>/build.mpi/pda/CMakeFiles/pda.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f pda/CMakeFiles/pda.dir/build.make pda/CMakeFiles/pda.dir/build make[4]: Entering directory '/<>/build.mpi' [ 51%] Building CXX object pda/CMakeFiles/pda.dir/circularnetwork.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/circularnetwork.cpp.o -MF CMakeFiles/pda.dir/circularnetwork.cpp.o.d -o CMakeFiles/pda.dir/circularnetwork.cpp.o -c /<>/pda/circularnetwork.cpp [ 52%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/exp.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/exp.cpp.o -c /<>/yaml-cpp/src/exp.cpp [ 53%] Building CXX object utils/CMakeFiles/utils.dir/tools.cpp.o cd /<>/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/tools.cpp.o -MF CMakeFiles/utils.dir/tools.cpp.o.d -o CMakeFiles/utils.dir/tools.cpp.o -c /<>/utils/tools.cpp [ 53%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/memory.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/memory.cpp.o -c /<>/yaml-cpp/src/memory.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node.cpp.o -c /<>/yaml-cpp/src/node.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o -c /<>/yaml-cpp/src/node_data.cpp [ 54%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o -c /<>/yaml-cpp/src/nodebuilder.cpp [ 54%] Building CXX object pda/CMakeFiles/pda.dir/greedy.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/greedy.cpp.o -MF CMakeFiles/pda.dir/greedy.cpp.o.d -o CMakeFiles/pda.dir/greedy.cpp.o -c /<>/pda/greedy.cpp [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o -c /<>/yaml-cpp/src/nodeevents.cpp [ 55%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/null.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/null.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/null.cpp.o -c /<>/yaml-cpp/src/null.cpp [ 56%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o -c /<>/yaml-cpp/src/ostream_wrapper.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/gurobiwrapper.cpp.o -MF CMakeFiles/pda.dir/gurobiwrapper.cpp.o.d -o CMakeFiles/pda.dir/gurobiwrapper.cpp.o -c /<>/pda/gurobiwrapper.cpp [ 57%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parse.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parse.cpp.o -c /<>/yaml-cpp/src/parse.cpp [ 57%] Building CXX object pda/CMakeFiles/pda.dir/hashsplitset.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/hashsplitset.cpp.o -MF CMakeFiles/pda.dir/hashsplitset.cpp.o.d -o CMakeFiles/pda.dir/hashsplitset.cpp.o -c /<>/pda/hashsplitset.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pdnetwork.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdnetwork.cpp.o -MF CMakeFiles/pda.dir/pdnetwork.cpp.o.d -o CMakeFiles/pda.dir/pdnetwork.cpp.o -c /<>/pda/pdnetwork.cpp [ 58%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/parser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/parser.cpp.o -c /<>/yaml-cpp/src/parser.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/pruning.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pruning.cpp.o -MF CMakeFiles/pda.dir/pruning.cpp.o.d -o CMakeFiles/pda.dir/pruning.cpp.o -c /<>/pda/pruning.cpp [ 58%] Building CXX object pda/CMakeFiles/pda.dir/split.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/split.cpp.o -MF CMakeFiles/pda.dir/split.cpp.o.d -o CMakeFiles/pda.dir/split.cpp.o -c /<>/pda/split.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o -c /<>/yaml-cpp/src/regex_yaml.cpp [ 59%] Building CXX object utils/CMakeFiles/utils.dir/pllnni.cpp.o cd /<>/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/pllnni.cpp.o -MF CMakeFiles/utils.dir/pllnni.cpp.o.d -o CMakeFiles/utils.dir/pllnni.cpp.o -c /<>/utils/pllnni.cpp [ 59%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o -c /<>/yaml-cpp/src/scanner.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitgraph.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitgraph.cpp.o -MF CMakeFiles/pda.dir/splitgraph.cpp.o.d -o CMakeFiles/pda.dir/splitgraph.cpp.o -c /<>/pda/splitgraph.cpp [ 60%] Building CXX object pda/CMakeFiles/pda.dir/splitset.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/splitset.cpp.o -MF CMakeFiles/pda.dir/splitset.cpp.o.d -o CMakeFiles/pda.dir/splitset.cpp.o -c /<>/pda/splitset.cpp [ 60%] Building CXX object utils/CMakeFiles/utils.dir/checkpoint.cpp.o cd /<>/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/checkpoint.cpp.o -MF CMakeFiles/utils.dir/checkpoint.cpp.o.d -o CMakeFiles/utils.dir/checkpoint.cpp.o -c /<>/utils/checkpoint.cpp [ 61%] Building C object pda/CMakeFiles/pda.dir/lpwrapper.c.o cd /<>/build.mpi/pda && /usr/bin/cc -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/lpwrapper.c.o -MF CMakeFiles/pda.dir/lpwrapper.c.o.d -o CMakeFiles/pda.dir/lpwrapper.c.o -c /<>/pda/lpwrapper.c [ 61%] Building CXX object pda/CMakeFiles/pda.dir/ecopd.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopd.cpp.o -MF CMakeFiles/pda.dir/ecopd.cpp.o.d -o CMakeFiles/pda.dir/ecopd.cpp.o -c /<>/pda/ecopd.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o -c /<>/yaml-cpp/src/scanscalar.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o -c /<>/yaml-cpp/src/scantag.cpp [ 62%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o -c /<>/yaml-cpp/src/scantoken.cpp [ 62%] Building CXX object pda/CMakeFiles/pda.dir/graph.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/graph.cpp.o -MF CMakeFiles/pda.dir/graph.cpp.o.d -o CMakeFiles/pda.dir/graph.cpp.o -c /<>/pda/graph.cpp [ 63%] Building CXX object utils/CMakeFiles/utils.dir/MPIHelper.cpp.o cd /<>/build.mpi/utils && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT utils/CMakeFiles/utils.dir/MPIHelper.cpp.o -MF CMakeFiles/utils.dir/MPIHelper.cpp.o.d -o CMakeFiles/utils.dir/MPIHelper.cpp.o -c /<>/utils/MPIHelper.cpp [ 64%] Building CXX object pda/CMakeFiles/pda.dir/pdtree.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtree.cpp.o -MF CMakeFiles/pda.dir/pdtree.cpp.o.d -o CMakeFiles/pda.dir/pdtree.cpp.o -c /<>/pda/pdtree.cpp [ 64%] Linking CXX static library libutils.a cd /<>/build.mpi/utils && /usr/bin/cmake -P CMakeFiles/utils.dir/cmake_clean_target.cmake cd /<>/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.mpi' [ 64%] Built target utils make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/model /<>/build.mpi /<>/build.mpi/model /<>/build.mpi/model/CMakeFiles/model.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f model/CMakeFiles/model.dir/build.make model/CMakeFiles/model.dir/build make[4]: Entering directory '/<>/build.mpi' [ 64%] Building CXX object model/CMakeFiles/model.dir/modelmarkov.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmarkov.cpp.o -MF CMakeFiles/model.dir/modelmarkov.cpp.o.d -o CMakeFiles/model.dir/modelmarkov.cpp.o -c /<>/model/modelmarkov.cpp [ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o -c /<>/yaml-cpp/src/simplekey.cpp [ 65%] Building CXX object pda/CMakeFiles/pda.dir/pdtreeset.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/pdtreeset.cpp.o -MF CMakeFiles/pda.dir/pdtreeset.cpp.o.d -o CMakeFiles/pda.dir/pdtreeset.cpp.o -c /<>/pda/pdtreeset.cpp [ 65%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o -c /<>/yaml-cpp/src/singledocparser.cpp In file included from /<>/model/modelmarkov.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/stream.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/stream.cpp.o -c /<>/yaml-cpp/src/stream.cpp [ 66%] Building CXX object yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o cd /<>/build.mpi/yaml-cpp && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -DYAML_CPP_NO_CONTRIB -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/yaml-cpp/src -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -std=gnu++11 -MD -MT yaml-cpp/CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -MF CMakeFiles/yaml-cpp.dir/src/tag.cpp.o.d -o CMakeFiles/yaml-cpp.dir/src/tag.cpp.o -c /<>/yaml-cpp/src/tag.cpp make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/alignment /<>/build.mpi /<>/build.mpi/alignment /<>/build.mpi/alignment/CMakeFiles/alignment.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f alignment/CMakeFiles/alignment.dir/build.make alignment/CMakeFiles/alignment.dir/build make[4]: Entering directory '/<>/build.mpi' [ 66%] Building CXX object alignment/CMakeFiles/alignment.dir/pattern.cpp.o cd /<>/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/pattern.cpp.o -MF CMakeFiles/alignment.dir/pattern.cpp.o.d -o CMakeFiles/alignment.dir/pattern.cpp.o -c /<>/alignment/pattern.cpp [ 67%] Linking CXX static library libyaml-cpp.a cd /<>/build.mpi/yaml-cpp && /usr/bin/cmake -P CMakeFiles/yaml-cpp.dir/cmake_clean_target.cmake cd /<>/build.mpi/yaml-cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/yaml-cpp.dir/link.txt --verbose=1 /usr/bin/ar qc libyaml-cpp.a "CMakeFiles/yaml-cpp.dir/src/binary.cpp.o" "CMakeFiles/yaml-cpp.dir/src/convert.cpp.o" "CMakeFiles/yaml-cpp.dir/src/directives.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emit.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitfromevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitter.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterstate.cpp.o" "CMakeFiles/yaml-cpp.dir/src/emitterutils.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exceptions.cpp.o" "CMakeFiles/yaml-cpp.dir/src/exp.cpp.o" "CMakeFiles/yaml-cpp.dir/src/memory.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node.cpp.o" "CMakeFiles/yaml-cpp.dir/src/node_data.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodebuilder.cpp.o" "CMakeFiles/yaml-cpp.dir/src/nodeevents.cpp.o" "CMakeFiles/yaml-cpp.dir/src/null.cpp.o" "CMakeFiles/yaml-cpp.dir/src/ostream_wrapper.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parse.cpp.o" "CMakeFiles/yaml-cpp.dir/src/parser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/regex_yaml.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanner.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scanscalar.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantag.cpp.o" "CMakeFiles/yaml-cpp.dir/src/scantoken.cpp.o" "CMakeFiles/yaml-cpp.dir/src/simplekey.cpp.o" "CMakeFiles/yaml-cpp.dir/src/singledocparser.cpp.o" "CMakeFiles/yaml-cpp.dir/src/stream.cpp.o" "CMakeFiles/yaml-cpp.dir/src/tag.cpp.o" /usr/bin/ranlib libyaml-cpp.a make[4]: Leaving directory '/<>/build.mpi' [ 67%] Built target yaml-cpp [ 68%] Building CXX object model/CMakeFiles/model.dir/modelbin.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelbin.cpp.o -MF CMakeFiles/model.dir/modelbin.cpp.o.d -o CMakeFiles/model.dir/modelbin.cpp.o -c /<>/model/modelbin.cpp [ 69%] Building CXX object pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o cd /<>/build.mpi/pda && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT pda/CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -MF CMakeFiles/pda.dir/ecopdmtreeset.cpp.o.d -o CMakeFiles/pda.dir/ecopdmtreeset.cpp.o -c /<>/pda/ecopdmtreeset.cpp [ 69%] Building CXX object alignment/CMakeFiles/alignment.dir/alignment.cpp.o cd /<>/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignment.cpp.o -MF CMakeFiles/alignment.dir/alignment.cpp.o.d -o CMakeFiles/alignment.dir/alignment.cpp.o -c /<>/alignment/alignment.cpp /<>/model/modelmarkov.cpp:1413:42: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1413 | void ModelMarkov::readRates(istream &in) throw(const char*, string) { | ^~~~~ /<>/model/modelmarkov.cpp:1468:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1468 | void ModelMarkov::readRates(string str) throw(const char*) { | ^~~~~ /<>/model/modelmarkov.cpp:1497:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1497 | void ModelMarkov::readStateFreq(istream &in) throw(const char*) { | ^~~~~ /<>/model/modelmarkov.cpp:1514:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 1514 | void ModelMarkov::readStateFreq(string str) throw(const char*) { | ^~~~~ In file included from /<>/model/modelbin.h:23, from /<>/model/modelbin.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 69%] Linking CXX static library libpda.a cd /<>/build.mpi/pda && /usr/bin/cmake -P CMakeFiles/pda.dir/cmake_clean_target.cmake cd /<>/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 [ 69%] Building CXX object model/CMakeFiles/model.dir/modeldna.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modeldna.cpp.o -MF CMakeFiles/model.dir/modeldna.cpp.o.d -o CMakeFiles/model.dir/modeldna.cpp.o -c /<>/model/modeldna.cpp /usr/bin/ranlib libpda.a make[4]: Leaving directory '/<>/build.mpi' [ 69%] Built target pda [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o cd /<>/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/alignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o -c /<>/alignment/alignmentpairwise.cpp In file included from /<>/model/modeldna.h:23, from /<>/model/modeldna.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modeldna.cpp:20: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modeldna.cpp:242:38: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 242 | void ModelDNA::readRates(string str) throw(const char*) { | ^~~~~ [ 70%] Building CXX object alignment/CMakeFiles/alignment.dir/maalignment.cpp.o cd /<>/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/maalignment.cpp.o -MF CMakeFiles/alignment.dir/maalignment.cpp.o.d -o CMakeFiles/alignment.dir/maalignment.cpp.o -c /<>/alignment/maalignment.cpp /<>/alignment/alignment.cpp:3154:92: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 3154 | void convert_range(const char *str, int &lower, int &upper, int &step_size, char* &endptr) throw (string) { | ^~~~~ [ 70%] Building CXX object model/CMakeFiles/model.dir/modelfactory.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactory.cpp.o -MF CMakeFiles/model.dir/modelfactory.cpp.o.d -o CMakeFiles/model.dir/modelfactory.cpp.o -c /<>/model/modelfactory.cpp In file included from /<>/model/modelfactory.cpp:24: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelfactory.cpp:26: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelfactory.cpp:27: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/model/modelfactory.cpp:30: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/phylo-yaml /<>/build.mpi /<>/build.mpi/phylo-yaml /<>/build.mpi/phylo-yaml/CMakeFiles/phyloYAML.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f phylo-yaml/CMakeFiles/phyloYAML.dir/build.make phylo-yaml/CMakeFiles/phyloYAML.dir/build make[4]: Entering directory '/<>/build.mpi' [ 70%] Building CXX object phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o cd /<>/build.mpi/phylo-yaml && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT phylo-yaml/CMakeFiles/phyloYAML.dir/statespace.cpp.o -MF CMakeFiles/phyloYAML.dir/statespace.cpp.o.d -o CMakeFiles/phyloYAML.dir/statespace.cpp.o -c /<>/phylo-yaml/statespace.cpp [ 71%] Linking CXX static library libphyloYAML.a cd /<>/build.mpi/phylo-yaml && /usr/bin/cmake -P CMakeFiles/phyloYAML.dir/cmake_clean_target.cmake cd /<>/build.mpi/phylo-yaml && /usr/bin/cmake -E cmake_link_script CMakeFiles/phyloYAML.dir/link.txt --verbose=1 /usr/bin/ar qc libphyloYAML.a CMakeFiles/phyloYAML.dir/statespace.cpp.o /usr/bin/ranlib libphyloYAML.a make[4]: Leaving directory '/<>/build.mpi' [ 71%] Built target phyloYAML make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/main /<>/build.mpi /<>/build.mpi/main /<>/build.mpi/main/CMakeFiles/main.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f main/CMakeFiles/main.dir/build.make main/CMakeFiles/main.dir/build make[4]: Entering directory '/<>/build.mpi' [ 72%] Building CXX object main/CMakeFiles/main.dir/main.cpp.o cd /<>/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/main.cpp.o -MF CMakeFiles/main.dir/main.cpp.o.d -o CMakeFiles/main.dir/main.cpp.o -c /<>/main/main.cpp [ 73%] Building CXX object model/CMakeFiles/model.dir/modelprotein.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelprotein.cpp.o -MF CMakeFiles/model.dir/modelprotein.cpp.o.d -o CMakeFiles/model.dir/modelprotein.cpp.o -c /<>/model/modelprotein.cpp /<>/main/main.cpp:232:64: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 232 | out << " " << 8*sizeof(void*) << "-bit" << " built " << __DATE__; | ^~~~~~~~ In file included from /<>/model/modelprotein.h:23, from /<>/model/modelprotein.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelprotein.cpp:20: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelprotein.cpp:892:43: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 892 | void ModelProtein::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 73%] Building CXX object model/CMakeFiles/model.dir/modelset.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelset.cpp.o -MF CMakeFiles/model.dir/modelset.cpp.o.d -o CMakeFiles/model.dir/modelset.cpp.o -c /<>/model/modelset.cpp In file included from /<>/model/modelset.h:23, from /<>/model/modelset.cpp:20: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/modelsubst.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelsubst.cpp.o -MF CMakeFiles/model.dir/modelsubst.cpp.o.d -o CMakeFiles/model.dir/modelsubst.cpp.o -c /<>/model/modelsubst.cpp [ 74%] Building CXX object model/CMakeFiles/model.dir/partitionmodel.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodel.cpp.o -MF CMakeFiles/model.dir/partitionmodel.cpp.o.d -o CMakeFiles/model.dir/partitionmodel.cpp.o -c /<>/model/partitionmodel.cpp In file included from /<>/model/partitionmodel.cpp:23: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 74%] Building CXX object model/CMakeFiles/model.dir/partitionmodelplen.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/partitionmodelplen.cpp.o -MF CMakeFiles/model.dir/partitionmodelplen.cpp.o.d -o CMakeFiles/model.dir/partitionmodelplen.cpp.o -c /<>/model/partitionmodelplen.cpp [ 74%] Building CXX object main/CMakeFiles/main.dir/phyloanalysis.cpp.o cd /<>/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phyloanalysis.cpp.o -MF CMakeFiles/main.dir/phyloanalysis.cpp.o.d -o CMakeFiles/main.dir/phyloanalysis.cpp.o -c /<>/main/phyloanalysis.cpp /<>/main/phyloanalysis.cpp:927:53: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time] 927 | << iqtree_VERSION_PATCH << " built " << __DATE__ << endl | ^~~~~~~~ In file included from /<>/model/partitionmodelplen.cpp:12: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phyloanalysis.cpp:37: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phyloanalysis.cpp:38: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phyloanalysis.cpp:46: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 75%] Building CXX object model/CMakeFiles/model.dir/rategamma.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategamma.cpp.o -MF CMakeFiles/model.dir/rategamma.cpp.o.d -o CMakeFiles/model.dir/rategamma.cpp.o -c /<>/model/rategamma.cpp [ 75%] Building CXX object model/CMakeFiles/model.dir/rategammainvar.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rategammainvar.cpp.o -MF CMakeFiles/model.dir/rategammainvar.cpp.o.d -o CMakeFiles/model.dir/rategammainvar.cpp.o -c /<>/model/rategammainvar.cpp [ 76%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignment.cpp.o cd /<>/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignment.cpp.o -MF CMakeFiles/alignment.dir/superalignment.cpp.o.d -o CMakeFiles/alignment.dir/superalignment.cpp.o -c /<>/alignment/superalignment.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/rateheterogeneity.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterogeneity.cpp.o -MF CMakeFiles/model.dir/rateheterogeneity.cpp.o.d -o CMakeFiles/model.dir/rateheterogeneity.cpp.o -c /<>/model/rateheterogeneity.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/rateinvar.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateinvar.cpp.o -MF CMakeFiles/model.dir/rateinvar.cpp.o.d -o CMakeFiles/model.dir/rateinvar.cpp.o -c /<>/model/rateinvar.cpp [ 77%] Building CXX object model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -MF CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o.d -o CMakeFiles/model.dir/ratemeyerdiscrete.cpp.o -c /<>/model/ratemeyerdiscrete.cpp [ 78%] Building CXX object model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -MF CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o.d -o CMakeFiles/model.dir/ratemeyerhaeseler.cpp.o -c /<>/model/ratemeyerhaeseler.cpp [ 78%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o cd /<>/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o -c /<>/alignment/superalignmentpairwise.cpp [ 79%] Building CXX object main/CMakeFiles/main.dir/phylotesting.cpp.o cd /<>/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/phylotesting.cpp.o -MF CMakeFiles/main.dir/phylotesting.cpp.o.d -o CMakeFiles/main.dir/phylotesting.cpp.o -c /<>/main/phylotesting.cpp In file included from /<>/main/phylotesting.cpp:21: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phylotesting.cpp:22: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/main/phylotesting.cpp:31: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/main/phylotesting.cpp:34: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ [ 79%] Building CXX object model/CMakeFiles/model.dir/ratekategory.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratekategory.cpp.o -MF CMakeFiles/model.dir/ratekategory.cpp.o.d -o CMakeFiles/model.dir/ratekategory.cpp.o -c /<>/model/ratekategory.cpp [ 79%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o cd /<>/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -MF CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o -c /<>/alignment/superalignmentpairwiseplen.cpp /<>/main/phylotesting.cpp: In function ‘std::string getSeqTypeName(PML::SeqType)’: /<>/main/phylotesting.cpp:180:1: warning: control reaches end of non-void function [-Wreturn-type] 180 | } | ^ /<>/main/phylotesting.cpp: In member function ‘double CandidateModel::getScore(ModelTestCriterion)’: /<>/main/phylotesting.cpp:257:1: warning: control reaches end of non-void function [-Wreturn-type] 257 | } | ^ [ 80%] Building CXX object model/CMakeFiles/model.dir/ratefree.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefree.cpp.o -MF CMakeFiles/model.dir/ratefree.cpp.o.d -o CMakeFiles/model.dir/ratefree.cpp.o -c /<>/model/ratefree.cpp [ 81%] Building CXX object alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o cd /<>/build.mpi/alignment && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT alignment/CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -MF CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o.d -o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o -c /<>/alignment/superalignmentunlinked.cpp In file included from /<>/model/modelmixture.h:13, from /<>/model/ratefree.cpp:13: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 81%] Linking CXX static library libalignment.a cd /<>/build.mpi/alignment && /usr/bin/cmake -P CMakeFiles/alignment.dir/cmake_clean_target.cmake cd /<>/build.mpi/alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/alignment.dir/link.txt --verbose=1 /usr/bin/ar qc libalignment.a CMakeFiles/alignment.dir/pattern.cpp.o CMakeFiles/alignment.dir/alignment.cpp.o CMakeFiles/alignment.dir/alignmentpairwise.cpp.o CMakeFiles/alignment.dir/maalignment.cpp.o CMakeFiles/alignment.dir/superalignment.cpp.o CMakeFiles/alignment.dir/superalignmentpairwise.cpp.o CMakeFiles/alignment.dir/superalignmentpairwiseplen.cpp.o CMakeFiles/alignment.dir/superalignmentunlinked.cpp.o /usr/bin/ranlib libalignment.a make[4]: Leaving directory '/<>/build.mpi' [ 81%] Built target alignment [ 81%] Building CXX object main/CMakeFiles/main.dir/treetesting.cpp.o cd /<>/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/treetesting.cpp.o -MF CMakeFiles/main.dir/treetesting.cpp.o.d -o CMakeFiles/main.dir/treetesting.cpp.o -c /<>/main/treetesting.cpp [ 81%] Building CXX object model/CMakeFiles/model.dir/ratefreeinvar.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/ratefreeinvar.cpp.o -MF CMakeFiles/model.dir/ratefreeinvar.cpp.o.d -o CMakeFiles/model.dir/ratefreeinvar.cpp.o -c /<>/model/ratefreeinvar.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachy.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachy.cpp.o -MF CMakeFiles/model.dir/rateheterotachy.cpp.o.d -o CMakeFiles/model.dir/rateheterotachy.cpp.o -c /<>/model/rateheterotachy.cpp [ 82%] Building CXX object main/CMakeFiles/main.dir/timetree.cpp.o cd /<>/build.mpi/main && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT main/CMakeFiles/main.dir/timetree.cpp.o -MF CMakeFiles/main.dir/timetree.cpp.o.d -o CMakeFiles/main.dir/timetree.cpp.o -c /<>/main/timetree.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -MF CMakeFiles/model.dir/rateheterotachyinvar.cpp.o.d -o CMakeFiles/model.dir/rateheterotachyinvar.cpp.o -c /<>/model/rateheterotachyinvar.cpp [ 82%] Building CXX object model/CMakeFiles/model.dir/modelcodon.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelcodon.cpp.o -MF CMakeFiles/model.dir/modelcodon.cpp.o.d -o CMakeFiles/model.dir/modelcodon.cpp.o -c /<>/model/modelcodon.cpp [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmorphology.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmorphology.cpp.o -MF CMakeFiles/model.dir/modelmorphology.cpp.o.d -o CMakeFiles/model.dir/modelmorphology.cpp.o -c /<>/model/modelmorphology.cpp In file included from /<>/model/modelcodon.h:11, from /<>/model/modelcodon.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmorphology.h:11, from /<>/model/modelmorphology.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmorphology.cpp:8: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmorphology.cpp:45:46: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 45 | void ModelMorphology::readRates(istream &in) throw(const char*, string) { | ^~~~~ [ 83%] Building CXX object model/CMakeFiles/model.dir/modelmixture.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelmixture.cpp.o -MF CMakeFiles/model.dir/modelmixture.cpp.o.d -o CMakeFiles/model.dir/modelmixture.cpp.o -c /<>/model/modelmixture.cpp [ 84%] Building CXX object model/CMakeFiles/model.dir/modelunrest.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelunrest.cpp.o -MF CMakeFiles/model.dir/modelunrest.cpp.o.d -o CMakeFiles/model.dir/modelunrest.cpp.o -c /<>/model/modelunrest.cpp [ 85%] Linking CXX static library libmain.a cd /<>/build.mpi/main && /usr/bin/cmake -P CMakeFiles/main.dir/cmake_clean_target.cmake cd /<>/build.mpi/main && /usr/bin/cmake -E cmake_link_script CMakeFiles/main.dir/link.txt --verbose=1 /usr/bin/ar qc libmain.a CMakeFiles/main.dir/main.cpp.o CMakeFiles/main.dir/phyloanalysis.cpp.o CMakeFiles/main.dir/phylotesting.cpp.o CMakeFiles/main.dir/treetesting.cpp.o CMakeFiles/main.dir/timetree.cpp.o /usr/bin/ranlib libmain.a In file included from /<>/model/modelmixture.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmixture.cpp:9: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelmixture.cpp:10: /<>/model/modelprotein.h:69:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 69 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ In file included from /<>/model/modelmixture.cpp:13: /<>/model/modelmorphology.h:78:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 78 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ make[4]: Leaving directory '/<>/build.mpi' [ 85%] Built target main [ 85%] Building CXX object model/CMakeFiles/model.dir/modelliemarkov.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelliemarkov.cpp.o -MF CMakeFiles/model.dir/modelliemarkov.cpp.o.d -o CMakeFiles/model.dir/modelliemarkov.cpp.o -c /<>/model/modelliemarkov.cpp In file included from /<>/model/modelunrest.h:11, from /<>/model/modelunrest.cpp:8: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 85%] Building CXX object model/CMakeFiles/model.dir/modelpomo.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomo.cpp.o -MF CMakeFiles/model.dir/modelpomo.cpp.o.d -o CMakeFiles/model.dir/modelpomo.cpp.o -c /<>/model/modelpomo.cpp In file included from /<>/model/modelliemarkov.h:11, from /<>/model/modelliemarkov.cpp:23: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 86%] Building CXX object model/CMakeFiles/model.dir/modelpomomixture.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelpomomixture.cpp.o -MF CMakeFiles/model.dir/modelpomomixture.cpp.o.d -o CMakeFiles/model.dir/modelpomomixture.cpp.o -c /<>/model/modelpomomixture.cpp In file included from /<>/model/modeldna.h:23, from /<>/model/modelpomo.h:4, from /<>/model/modelpomo.cpp:1: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelpomo.h:4, from /<>/model/modelpomo.cpp:1: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modeldna.h:23, from /<>/model/modelpomo.h:4, from /<>/model/modelpomomixture.h:14, from /<>/model/modelpomomixture.cpp:9: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/model/modelpomo.h:4, from /<>/model/modelpomomixture.h:14, from /<>/model/modelpomomixture.cpp:9: /<>/model/modeldna.h:91:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 91 | virtual void readRates(string str) throw(const char*); | ^~~~~ [ 86%] Building CXX object model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o cd /<>/build.mpi/model && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT model/CMakeFiles/model.dir/modelfactorymixlen.cpp.o -MF CMakeFiles/model.dir/modelfactorymixlen.cpp.o.d -o CMakeFiles/model.dir/modelfactorymixlen.cpp.o -c /<>/model/modelfactorymixlen.cpp In file included from /<>/model/modelfactorymixlen.cpp:12: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 87%] Linking CXX static library libmodel.a cd /<>/build.mpi/model && /usr/bin/cmake -P CMakeFiles/model.dir/cmake_clean_target.cmake cd /<>/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.mpi' [ 87%] Built target model make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/tree /<>/build.mpi /<>/build.mpi/tree /<>/build.mpi/tree/CMakeFiles/tree.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f tree/CMakeFiles/tree.dir/build.make tree/CMakeFiles/tree.dir/build make[4]: Entering directory '/<>/build.mpi' [ 87%] Building CXX object tree/CMakeFiles/tree.dir/candidateset.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/candidateset.cpp.o -MF CMakeFiles/tree.dir/candidateset.cpp.o.d -o CMakeFiles/tree.dir/candidateset.cpp.o -c /<>/tree/candidateset.cpp [ 88%] Building CXX object tree/CMakeFiles/tree.dir/constrainttree.cpp.o [ 89%] Building CXX object tree/CMakeFiles/tree.dir/iqtree.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/constrainttree.cpp.o -MF CMakeFiles/tree.dir/constrainttree.cpp.o.d -o CMakeFiles/tree.dir/constrainttree.cpp.o -c /<>/tree/constrainttree.cpp cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/iqtree.cpp.o -MF CMakeFiles/tree.dir/iqtree.cpp.o.d -o CMakeFiles/tree.dir/iqtree.cpp.o -c /<>/tree/iqtree.cpp [ 89%] Building CXX object tree/CMakeFiles/tree.dir/matree.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/matree.cpp.o -MF CMakeFiles/tree.dir/matree.cpp.o.d -o CMakeFiles/tree.dir/matree.cpp.o -c /<>/tree/matree.cpp In file included from /<>/tree/iqtree.cpp:29: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 89%] Building CXX object tree/CMakeFiles/tree.dir/memslot.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/memslot.cpp.o -MF CMakeFiles/tree.dir/memslot.cpp.o.d -o CMakeFiles/tree.dir/memslot.cpp.o -c /<>/tree/memslot.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mexttree.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mexttree.cpp.o -MF CMakeFiles/tree.dir/mexttree.cpp.o.d -o CMakeFiles/tree.dir/mexttree.cpp.o -c /<>/tree/mexttree.cpp [ 90%] Building CXX object tree/CMakeFiles/tree.dir/mtree.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtree.cpp.o -MF CMakeFiles/tree.dir/mtree.cpp.o.d -o CMakeFiles/tree.dir/mtree.cpp.o -c /<>/tree/mtree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/mtreeset.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/mtreeset.cpp.o -MF CMakeFiles/tree.dir/mtreeset.cpp.o.d -o CMakeFiles/tree.dir/mtreeset.cpp.o -c /<>/tree/mtreeset.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/ncbitree.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/ncbitree.cpp.o -MF CMakeFiles/tree.dir/ncbitree.cpp.o.d -o CMakeFiles/tree.dir/ncbitree.cpp.o -c /<>/tree/ncbitree.cpp [ 91%] Building CXX object tree/CMakeFiles/tree.dir/node.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/node.cpp.o -MF CMakeFiles/tree.dir/node.cpp.o.d -o CMakeFiles/tree.dir/node.cpp.o -c /<>/tree/node.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonode.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonode.cpp.o -MF CMakeFiles/tree.dir/phylonode.cpp.o.d -o CMakeFiles/tree.dir/phylonode.cpp.o -c /<>/tree/phylonode.cpp [ 92%] Building CXX object tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylonodemixlen.cpp.o -MF CMakeFiles/tree.dir/phylonodemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylonodemixlen.cpp.o -c /<>/tree/phylonodemixlen.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertree.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertree.cpp.o -MF CMakeFiles/tree.dir/phylosupertree.cpp.o.d -o CMakeFiles/tree.dir/phylosupertree.cpp.o -c /<>/tree/phylosupertree.cpp [ 93%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeplen.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o -c /<>/tree/phylosupertreeplen.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -MF CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o.d -o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o -c /<>/tree/phylosupertreeunlinked.cpp [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotree.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotree.cpp.o -MF CMakeFiles/tree.dir/phylotree.cpp.o.d -o CMakeFiles/tree.dir/phylotree.cpp.o -c /<>/tree/phylotree.cpp In file included from /<>/model/modelmixture.h:13, from /<>/tree/phylotree.cpp:34: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ /<>/tree/phylotree.cpp: In function ‘std::string getASCName(ASCType)’: /<>/tree/phylotree.cpp:653:1: warning: control reaches end of non-void function [-Wreturn-type] 653 | } | ^ /<>/tree/phylotree.cpp: In member function ‘virtual int PhyloTree::getNumLhCat(SiteLoglType)’: /<>/tree/phylotree.cpp:1298:1: warning: control reaches end of non-void function [-Wreturn-type] 1298 | } | ^ [ 94%] Building CXX object tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreemixlen.cpp.o -MF CMakeFiles/tree.dir/phylotreemixlen.cpp.o.d -o CMakeFiles/tree.dir/phylotreemixlen.cpp.o -c /<>/tree/phylotreemixlen.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreepars.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreepars.cpp.o -MF CMakeFiles/tree.dir/phylotreepars.cpp.o.d -o CMakeFiles/tree.dir/phylotreepars.cpp.o -c /<>/tree/phylotreepars.cpp [ 95%] Building CXX object tree/CMakeFiles/tree.dir/phylotreesse.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/phylotreesse.cpp.o -MF CMakeFiles/tree.dir/phylotreesse.cpp.o.d -o CMakeFiles/tree.dir/phylotreesse.cpp.o -c /<>/tree/phylotreesse.cpp In file included from /<>/model/modelmixture.h:13, from /<>/tree/phylotreemixlen.cpp:12: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ In file included from /<>/tree/phylotreesse.cpp:35: /<>/model/modelmarkov.h:146:45: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 146 | virtual void readRates(istream &in) throw(const char*, string); | ^~~~~ /<>/model/modelmarkov.h:153:44: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 153 | virtual void readRates(string str) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:160:49: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 160 | virtual void readStateFreq(istream &in) throw(const char*); | ^~~~~ /<>/model/modelmarkov.h:167:48: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated] 167 | virtual void readStateFreq(string str) throw(const char*); | ^~~~~ [ 96%] Building CXX object tree/CMakeFiles/tree.dir/quartet.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/quartet.cpp.o -MF CMakeFiles/tree.dir/quartet.cpp.o.d -o CMakeFiles/tree.dir/quartet.cpp.o -c /<>/tree/quartet.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/supernode.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/supernode.cpp.o -MF CMakeFiles/tree.dir/supernode.cpp.o.d -o CMakeFiles/tree.dir/supernode.cpp.o -c /<>/tree/supernode.cpp [ 96%] Building CXX object tree/CMakeFiles/tree.dir/tinatree.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/tinatree.cpp.o -MF CMakeFiles/tree.dir/tinatree.cpp.o.d -o CMakeFiles/tree.dir/tinatree.cpp.o -c /<>/tree/tinatree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/parstree.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/parstree.cpp.o -MF CMakeFiles/tree.dir/parstree.cpp.o.d -o CMakeFiles/tree.dir/parstree.cpp.o -c /<>/tree/parstree.cpp [ 97%] Building CXX object tree/CMakeFiles/tree.dir/discordance.cpp.o cd /<>/build.mpi/tree && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT tree/CMakeFiles/tree.dir/discordance.cpp.o -MF CMakeFiles/tree.dir/discordance.cpp.o.d -o CMakeFiles/tree.dir/discordance.cpp.o -c /<>/tree/discordance.cpp [ 98%] Linking CXX static library libtree.a cd /<>/build.mpi/tree && /usr/bin/cmake -P CMakeFiles/tree.dir/cmake_clean_target.cmake cd /<>/build.mpi/tree && /usr/bin/cmake -E cmake_link_script CMakeFiles/tree.dir/link.txt --verbose=1 /usr/bin/ar qc libtree.a CMakeFiles/tree.dir/constrainttree.cpp.o CMakeFiles/tree.dir/candidateset.cpp.o CMakeFiles/tree.dir/iqtree.cpp.o CMakeFiles/tree.dir/matree.cpp.o CMakeFiles/tree.dir/memslot.cpp.o CMakeFiles/tree.dir/mexttree.cpp.o CMakeFiles/tree.dir/mtree.cpp.o CMakeFiles/tree.dir/mtreeset.cpp.o CMakeFiles/tree.dir/ncbitree.cpp.o CMakeFiles/tree.dir/node.cpp.o CMakeFiles/tree.dir/phylonode.cpp.o CMakeFiles/tree.dir/phylonodemixlen.cpp.o CMakeFiles/tree.dir/phylosupertree.cpp.o CMakeFiles/tree.dir/phylosupertreeplen.cpp.o CMakeFiles/tree.dir/phylosupertreeunlinked.cpp.o CMakeFiles/tree.dir/phylotree.cpp.o CMakeFiles/tree.dir/phylotreemixlen.cpp.o CMakeFiles/tree.dir/phylotreepars.cpp.o CMakeFiles/tree.dir/phylotreesse.cpp.o CMakeFiles/tree.dir/quartet.cpp.o CMakeFiles/tree.dir/supernode.cpp.o CMakeFiles/tree.dir/tinatree.cpp.o CMakeFiles/tree.dir/parstree.cpp.o CMakeFiles/tree.dir/discordance.cpp.o /usr/bin/ranlib libtree.a make[4]: Leaving directory '/<>/build.mpi' [ 98%] Built target tree make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<>/terrace /<>/build.mpi /<>/build.mpi/terrace /<>/build.mpi/terrace/CMakeFiles/terrace.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f terrace/CMakeFiles/terrace.dir/build.make terrace/CMakeFiles/terrace.dir/build make[4]: Entering directory '/<>/build.mpi' [ 98%] Building CXX object terrace/CMakeFiles/terrace.dir/terrace.cpp.o cd /<>/build.mpi/terrace && /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT terrace/CMakeFiles/terrace.dir/terrace.cpp.o -MF CMakeFiles/terrace.dir/terrace.cpp.o.d -o CMakeFiles/terrace.dir/terrace.cpp.o -c /<>/terrace/terrace.cpp [ 99%] Linking CXX static library libterrace.a cd /<>/build.mpi/terrace && /usr/bin/cmake -P CMakeFiles/terrace.dir/cmake_clean_target.cmake cd /<>/build.mpi/terrace && /usr/bin/cmake -E cmake_link_script CMakeFiles/terrace.dir/link.txt --verbose=1 /usr/bin/ar qc libterrace.a CMakeFiles/terrace.dir/terrace.cpp.o /usr/bin/ranlib libterrace.a make[4]: Leaving directory '/<>/build.mpi' [ 99%] Built target terrace make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/depend make[4]: Entering directory '/<>/build.mpi' cd /<>/build.mpi && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<> /<> /<>/build.mpi /<>/build.mpi /<>/build.mpi/CMakeFiles/iqtree2.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<>/build.mpi' make -f CMakeFiles/iqtree2.dir/build.make CMakeFiles/iqtree2.dir/build make[4]: Entering directory '/<>/build.mpi' [100%] Building CXX object CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o /usr/bin/c++ -DIQTREE_TERRAPHAST -DIQ_TREE -DUSE_BOOST -DUSE_BOOSTER -D_IQTREE_MPI -D_USE_PTHREADS -I/<> -I/<>/yaml-cpp/include -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/<>/build.mpi -I/<>/terraphast/include -I/<>/terraphast/lib/gcc_clang -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -I/usr/include/eigen3 -I/usr/include -D__SSE3 -msse3 -MD -MT CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -MF CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o.d -o CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -c /<>/obsolete/parsmultistate.cpp [100%] Linking CXX executable iqtree2-mpi /usr/bin/cmake -E cmake_link_script CMakeFiles/iqtree2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/<>=. -flto=auto -ffat-lto-objects -flto=auto -ffat-lto-objects -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fopenmp -pthread -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -rdynamic -rdynamic CMakeFiles/iqtree2.dir/obsolete/parsmultistate.cpp.o -o iqtree2-mpi -L/<>/lib -Wl,-rpath,/<>/lib:/usr/lib/x86_64-linux-gnu/openmpi/lib: booster/libbooster.a pll/libpll.a ncl/libncl.a nclextra/libnclextra.a utils/libutils.a pda/libpda.a lbfgsb/liblbfgsb.a whtest/libwhtest.a sprng/libsprng.a vectorclass/libvectorclass.a model/libmodel.a gsl/libgsl.a alignment/libalignment.a tree/libtree.a yaml-cpp/libyaml-cpp.a phylo-yaml/libphyloYAML.a main/libmain.a -lm terrace/libterrace.a libkernelsse.a /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so pll/libpllavx.a libkernelavx.a libkernelfma.a yaml-cpp/libyaml-cpp.a booster/libbooster.a pda/libpda.a nclextra/libnclextra.a whtest/libwhtest.a vectorclass/libvectorclass.a tree/libtree.a pll/libpll.a model/libmodel.a utils/libutils.a lbfgsb/liblbfgsb.a sprng/libsprng.a -lz alignment/libalignment.a ncl/libncl.a gsl/libgsl.a terraphast/libterraphast.a ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.742’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.1531’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.440’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.1309’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2597:85: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2905:9: warning: type ‘struct .omp_data_s.1076’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2752:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2604:20: note: the first difference of corresponding definitions is field ‘node_branch’ ./tree/phylokernelnew.h:2600:92: note: a field with different name is defined in another translation unit ./tree/phylokernelnew.h:2309:9: warning: type ‘struct .omp_data_s.378’ violates the C++ One Definition Rule [-Wodr] ./tree/phylokernelnew.h:2309:9: note: a different type is defined in another translation unit ./tree/phylokernelnew.h:2292:17: note: the first difference of corresponding definitions is field ‘all_lh’ ./tree/phylokernelnew.h:2292:17: note: a field of same name but different type is defined in another translation unit ./vectorclass/vectorf128.h:1507:7: note: type name ‘Vec2d’ should match type name ‘Vec4d’ ./vectorclass/vectorf256.h:1349:7: note: the incompatible type is defined here make[4]: Leaving directory '/<>/build.mpi' [100%] Built target iqtree2 make[3]: Leaving directory '/<>/build.mpi' /usr/bin/cmake -E cmake_progress_start /<>/build.mpi/CMakeFiles 0 make[2]: Leaving directory '/<>/build.mpi' # restore the old naming to avoid name space conflict with serial build if [ -x build.omp/iqtree2 ] ; then mv build.omp/iqtree2 build.omp/iqtree2-omp ; fi dh override_dh_auto_build make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' # 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.omp/iqtree2-omp -s example.phy -redo' >> example.short time sh example.short Executing tests using /<>/build.omp/iqtree2-omp ... + time /<>/build.omp/iqtree2-omp -s example.phy IQ-TREE multicore version 2.0.7 for Linux 64-bit built Jan 21 2022 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: lgw01-amd64-036 (AVX, 7 GB RAM) Command: /<>/build.omp/iqtree2-omp -s example.phy Seed: 494631 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Jun 22 20:04:09 2022 Kernel: AVX - 1 threads (4 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 4 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 Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) 1. Initial log-likelihood: -21149.241 Optimal log-likelihood: -21148.879 Rate parameters: A-C: 4.04634 A-G: 5.62615 A-T: 4.17804 C-G: 0.45965 C-T: 16.52262 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: 0.738 Parameters optimization took 1 rounds (0.086 sec) Time for fast ML tree search: 0.717 seconds NOTE: ModelFinder requires 6 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 1998) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 22701.485 39 45480.970 45482.563 45699.366 2 GTR+F+I 21615.548 40 43311.095 43312.771 43535.091 3 GTR+F+G4 21155.969 40 42391.938 42393.614 42615.934 4 GTR+F+I+G4 21148.850 41 42379.699 42381.460 42609.295 5 GTR+F+R2 21235.663 41 42553.326 42555.087 42782.922 6 GTR+F+R3 21147.207 43 42380.415 42382.351 42621.210 7 GTR+F+R4 21145.838 45 42381.675 42383.796 42633.671 16 SYM+G4 21317.781 37 42709.563 42710.998 42916.759 17 SYM+I+G4 21306.174 38 42688.347 42689.860 42901.144 29 TVM+F+G4 21300.237 39 42678.474 42680.067 42896.870 30 TVM+F+I+G4 21288.274 40 42656.549 42658.225 42880.545 42 TVMe+G4 21422.186 36 42916.373 42917.731 43117.969 43 TVMe+I+G4 21407.601 37 42889.203 42890.637 43096.399 55 TIM3+F+G4 21367.926 38 42811.853 42813.366 43024.649 56 TIM3+F+I+G4 21359.483 39 42796.966 42798.560 43015.362 68 TIM3e+G4 21717.462 35 43504.924 43506.209 43700.921 69 TIM3e+I+G4 21708.559 36 43489.119 43490.477 43690.715 81 TIM2+F+G4 21159.707 38 42395.414 42396.927 42608.211 82 TIM2+F+I+G4 21152.490 39 42382.981 42384.574 42601.377 94 TIM2e+G4 21320.880 35 42711.760 42713.045 42907.757 95 TIM2e+I+G4 21309.130 36 42690.259 42691.618 42891.856 107 TIM+F+G4 21368.780 38 42813.559 42815.073 43026.356 108 TIM+F+I+G4 21360.238 39 42798.476 42800.070 43016.872 120 TIMe+G4 21718.131 35 43506.262 43507.547 43702.259 121 TIMe+I+G4 21709.222 36 43490.443 43491.802 43692.040 133 TPM3u+F+G4 21488.892 37 43051.785 43053.219 43258.981 134 TPM3u+F+I+G4 21474.937 38 43025.874 43027.387 43238.670 146 TPM3+F+G4 21488.892 37 43051.785 43053.219 43258.981 147 TPM3+F+I+G4 21474.937 38 43025.874 43027.387 43238.670 159 TPM2u+F+G4 21303.797 37 42681.594 42683.029 42888.790 160 TPM2u+F+I+G4 21291.871 38 42659.741 42661.254 42872.538 172 TPM2+F+G4 21303.797 37 42681.594 42683.029 42888.790 173 TPM2+F+I+G4 21291.871 38 42659.741 42661.254 42872.538 185 K3Pu+F+G4 21489.348 37 43052.695 43054.130 43259.892 186 K3Pu+F+I+G4 21475.448 38 43026.895 43028.408 43239.691 198 K3P+G4 21847.490 34 43762.981 43764.193 43953.378 199 K3P+I+G4 21833.799 35 43737.597 43738.882 43933.594 211 TN+F+G4 21369.048 37 42812.095 42813.530 43019.292 212 TN+F+I+G4 21360.518 38 42797.036 42798.550 43009.833 224 TNe+G4 21718.201 34 43504.403 43505.615 43694.799 225 TNe+I+G4 21709.282 35 43488.563 43489.848 43684.560 237 HKY+F+G4 21489.737 36 43051.474 43052.832 43253.070 238 HKY+F+I+G4 21475.770 37 43025.540 43026.974 43232.736 250 K2P+G4 21847.675 33 43761.350 43762.492 43946.146 251 K2P+I+G4 21833.952 34 43735.903 43737.116 43926.300 263 F81+F+G4 22031.578 35 44133.155 44134.440 44329.152 264 F81+F+I+G4 22019.580 36 44111.159 44112.518 44312.756 276 JC+G4 22258.086 32 44580.172 44581.246 44759.368 277 JC+I+G4 22245.555 33 44557.111 44558.253 44741.908 Akaike Information Criterion: GTR+F+I+G4 Corrected Akaike Information Criterion: GTR+F+I+G4 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: 10.909 seconds (0h:0m:10s) Wall-clock time for ModelFinder: 10.997 seconds (0h:0m:10s) 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, 0.737 / Estimate: 0.000, 0.482 / LogL: -21159.748 Init pinv, alpha: 0.038, 0.737 / Estimate: 0.043, 0.532 / LogL: -21156.975 Init pinv, alpha: 0.076, 0.737 / Estimate: 0.085, 0.592 / LogL: -21154.640 Init pinv, alpha: 0.114, 0.737 / Estimate: 0.120, 0.654 / LogL: -21153.216 Init pinv, alpha: 0.153, 0.737 / Estimate: 0.153, 0.726 / LogL: -21152.514 Init pinv, alpha: 0.191, 0.737 / Estimate: 0.183, 0.804 / LogL: -21152.778 Init pinv, alpha: 0.229, 0.737 / Estimate: 0.187, 0.817 / LogL: -21152.912 Init pinv, alpha: 0.267, 0.737 / Estimate: 0.186, 0.813 / LogL: -21152.863 Init pinv, alpha: 0.305, 0.737 / Estimate: 0.186, 0.813 / LogL: -21152.873 Init pinv, alpha: 0.343, 0.737 / Estimate: 0.187, 0.816 / LogL: -21152.902 Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.514 Parameters optimization took 2.741 sec Computing ML distances based on estimated model parameters... 0.011 sec Computing BIONJ tree... 0.000 seconds Log-likelihood of BIONJ tree: -21157.741 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.550 second Computing log-likelihood of 98 initial trees ... 0.938 seconds Current best score: -21152.514 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -21152.511 Iteration 10 / LogL: -21157.879 / Time: 0h:0m:5s Iteration 20 / LogL: -21152.523 / Time: 0h:0m:6s Finish initializing candidate tree set (2) Current best tree score: -21152.511 / CPU time: 4.042 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -21152.551 / Time: 0h:0m:8s (0h:0m:20s left) Iteration 40 / LogL: -21152.549 / Time: 0h:0m:9s (0h:0m:14s left) Iteration 50 / LogL: -21152.722 / Time: 0h:0m:10s (0h:0m:11s left) Iteration 60 / LogL: -21152.646 / Time: 0h:0m:12s (0h:0m:8s left) Iteration 70 / LogL: -21154.457 / Time: 0h:0m:13s (0h:0m:6s left) Iteration 80 / LogL: -21152.718 / Time: 0h:0m:15s (0h:0m:4s left) Iteration 90 / LogL: -21152.516 / Time: 0h:0m:16s (0h:0m:2s left) Iteration 100 / LogL: -21153.802 / Time: 0h:0m:18s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:18s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -21152.511 Optimal log-likelihood: -21152.507 Rate parameters: A-C: 5.70370 A-G: 7.79572 A-T: 5.70370 C-G: 1.00000 C-T: 23.14180 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.154 Gamma shape alpha: 0.728 Parameters optimization took 1 rounds (0.033 sec) BEST SCORE FOUND : -21152.507 Total tree length: 4.226 Total number of iterations: 102 CPU time used for tree search: 15.331 sec (0h:0m:15s) Wall-clock time used for tree search: 15.525 sec (0h:0m:15s) Total CPU time used: 18.152 sec (0h:0m:18s) Total wall-clock time used: 18.379 sec (0h:0m:18s) 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 Jun 22 20:04:38 2022 29.07user 0.26system 0:29.42elapsed 99%CPU (0avgtext+0avgdata 15760maxresident)k 960inputs+120outputs (5major+3644minor)pagefaults 0swaps + time /<>/build.omp/iqtree2-omp -s example.phy -redo IQ-TREE multicore version 2.0.7 for Linux 64-bit built Jan 21 2022 Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. Host: lgw01-amd64-036 (AVX, 7 GB RAM) Command: /<>/build.omp/iqtree2-omp -s example.phy -redo Seed: 902258 (Using SPRNG - Scalable Parallel Random Number Generator) Time: Wed Jun 22 20:04:38 2022 Kernel: AVX - 1 threads (4 CPU cores detected) HINT: Use -nt option to specify number of threads because your CPU has 4 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 Perform fast likelihood tree search using GTR+I+G model... Estimate model parameters (epsilon = 5.000) Perform nearest neighbor interchange... Estimate model parameters (epsilon = 1.000) 1. Initial log-likelihood: -21149.241 Optimal log-likelihood: -21148.879 Rate parameters: A-C: 4.04634 A-G: 5.62615 A-T: 4.17804 C-G: 0.45965 C-T: 16.52262 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: 0.738 Parameters optimization took 1 rounds (0.080 sec) Time for fast ML tree search: 0.747 seconds NOTE: ModelFinder requires 6 MB RAM! ModelFinder will test up to 286 DNA models (sample size: 1998) ... No. Model -LnL df AIC AICc BIC 1 GTR+F 22701.485 39 45480.970 45482.563 45699.366 2 GTR+F+I 21615.548 40 43311.095 43312.771 43535.091 3 GTR+F+G4 21155.969 40 42391.938 42393.614 42615.934 4 GTR+F+I+G4 21148.850 41 42379.699 42381.460 42609.295 5 GTR+F+R2 21235.663 41 42553.326 42555.087 42782.922 6 GTR+F+R3 21147.207 43 42380.415 42382.351 42621.210 7 GTR+F+R4 21145.838 45 42381.675 42383.796 42633.671 16 SYM+G4 21317.781 37 42709.563 42710.998 42916.759 17 SYM+I+G4 21306.174 38 42688.347 42689.860 42901.144 29 TVM+F+G4 21300.237 39 42678.474 42680.067 42896.870 30 TVM+F+I+G4 21288.274 40 42656.549 42658.225 42880.545 42 TVMe+G4 21422.186 36 42916.373 42917.731 43117.969 43 TVMe+I+G4 21407.601 37 42889.203 42890.637 43096.399 55 TIM3+F+G4 21367.926 38 42811.853 42813.366 43024.649 56 TIM3+F+I+G4 21359.483 39 42796.966 42798.560 43015.362 68 TIM3e+G4 21717.462 35 43504.924 43506.209 43700.921 69 TIM3e+I+G4 21708.559 36 43489.119 43490.477 43690.715 81 TIM2+F+G4 21159.707 38 42395.414 42396.927 42608.211 82 TIM2+F+I+G4 21152.490 39 42382.981 42384.574 42601.377 94 TIM2e+G4 21320.880 35 42711.760 42713.045 42907.757 95 TIM2e+I+G4 21309.130 36 42690.259 42691.618 42891.856 107 TIM+F+G4 21368.780 38 42813.559 42815.073 43026.356 108 TIM+F+I+G4 21360.238 39 42798.476 42800.070 43016.872 120 TIMe+G4 21718.131 35 43506.262 43507.547 43702.259 121 TIMe+I+G4 21709.222 36 43490.443 43491.802 43692.040 133 TPM3u+F+G4 21488.892 37 43051.785 43053.219 43258.981 134 TPM3u+F+I+G4 21474.937 38 43025.874 43027.387 43238.670 146 TPM3+F+G4 21488.892 37 43051.785 43053.219 43258.981 147 TPM3+F+I+G4 21474.937 38 43025.874 43027.387 43238.670 159 TPM2u+F+G4 21303.797 37 42681.594 42683.029 42888.790 160 TPM2u+F+I+G4 21291.871 38 42659.741 42661.254 42872.538 172 TPM2+F+G4 21303.797 37 42681.594 42683.029 42888.790 173 TPM2+F+I+G4 21291.871 38 42659.741 42661.254 42872.538 185 K3Pu+F+G4 21489.348 37 43052.695 43054.130 43259.892 186 K3Pu+F+I+G4 21475.448 38 43026.895 43028.408 43239.691 198 K3P+G4 21847.490 34 43762.981 43764.193 43953.378 199 K3P+I+G4 21833.799 35 43737.597 43738.882 43933.594 211 TN+F+G4 21369.048 37 42812.095 42813.530 43019.292 212 TN+F+I+G4 21360.518 38 42797.036 42798.550 43009.833 224 TNe+G4 21718.201 34 43504.403 43505.615 43694.799 225 TNe+I+G4 21709.282 35 43488.563 43489.848 43684.560 237 HKY+F+G4 21489.737 36 43051.474 43052.832 43253.070 238 HKY+F+I+G4 21475.770 37 43025.540 43026.974 43232.736 250 K2P+G4 21847.675 33 43761.350 43762.492 43946.146 251 K2P+I+G4 21833.952 34 43735.903 43737.116 43926.300 263 F81+F+G4 22031.578 35 44133.155 44134.440 44329.152 264 F81+F+I+G4 22019.580 36 44111.159 44112.518 44312.756 276 JC+G4 22258.086 32 44580.172 44581.246 44759.368 277 JC+I+G4 22245.555 33 44557.111 44558.253 44741.908 Akaike Information Criterion: GTR+F+I+G4 Corrected Akaike Information Criterion: GTR+F+I+G4 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: 11.183 seconds (0h:0m:11s) Wall-clock time for ModelFinder: 11.316 seconds (0h:0m:11s) 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, 0.737 / Estimate: 0.000, 0.482 / LogL: -21159.748 Init pinv, alpha: 0.038, 0.737 / Estimate: 0.043, 0.532 / LogL: -21156.975 Init pinv, alpha: 0.076, 0.737 / Estimate: 0.085, 0.592 / LogL: -21154.640 Init pinv, alpha: 0.114, 0.737 / Estimate: 0.120, 0.654 / LogL: -21153.216 Init pinv, alpha: 0.153, 0.737 / Estimate: 0.153, 0.726 / LogL: -21152.514 Init pinv, alpha: 0.191, 0.737 / Estimate: 0.183, 0.804 / LogL: -21152.778 Init pinv, alpha: 0.229, 0.737 / Estimate: 0.187, 0.817 / LogL: -21152.912 Init pinv, alpha: 0.267, 0.737 / Estimate: 0.186, 0.813 / LogL: -21152.863 Init pinv, alpha: 0.305, 0.737 / Estimate: 0.186, 0.813 / LogL: -21152.873 Init pinv, alpha: 0.343, 0.737 / Estimate: 0.187, 0.816 / LogL: -21152.902 Optimal pinv,alpha: 0.153, 0.726 / LogL: -21152.514 Parameters optimization took 2.859 sec Computing ML distances based on estimated model parameters... 0.009 sec Computing BIONJ tree... 0.001 seconds Log-likelihood of BIONJ tree: -21157.741 -------------------------------------------------------------------- | INITIALIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Generating 98 parsimony trees... 0.319 second Computing log-likelihood of 98 initial trees ... 0.975 seconds Current best score: -21152.514 Do NNI search on 20 best initial trees Estimate model parameters (epsilon = 0.100) BETTER TREE FOUND at iteration 1: -21152.511 Iteration 10 / LogL: -21152.530 / Time: 0h:0m:5s Iteration 20 / LogL: -21158.007 / Time: 0h:0m:6s Finish initializing candidate tree set (2) Current best tree score: -21152.511 / CPU time: 3.558 Number of iterations: 20 -------------------------------------------------------------------- | OPTIMIZING CANDIDATE TREE SET | -------------------------------------------------------------------- Iteration 30 / LogL: -21152.645 / Time: 0h:0m:7s (0h:0m:19s left) Iteration 40 / LogL: -21152.640 / Time: 0h:0m:9s (0h:0m:14s left) Iteration 50 / LogL: -21158.525 / Time: 0h:0m:10s (0h:0m:10s left) Iteration 60 / LogL: -21152.591 / Time: 0h:0m:12s (0h:0m:8s left) Iteration 70 / LogL: -21152.660 / Time: 0h:0m:13s (0h:0m:6s left) Iteration 80 / LogL: -21152.526 / Time: 0h:0m:14s (0h:0m:3s left) Iteration 90 / LogL: -21152.547 / Time: 0h:0m:16s (0h:0m:2s left) Iteration 100 / LogL: -21152.631 / Time: 0h:0m:17s (0h:0m:0s left) TREE SEARCH COMPLETED AFTER 102 ITERATIONS / Time: 0h:0m:17s -------------------------------------------------------------------- | FINALIZING TREE SEARCH | -------------------------------------------------------------------- Performs final model parameters optimization Estimate model parameters (epsilon = 0.010) 1. Initial log-likelihood: -21152.511 Optimal log-likelihood: -21152.507 Rate parameters: A-C: 5.70370 A-G: 7.79572 A-T: 5.70370 C-G: 1.00000 C-T: 23.14180 G-T: 1.00000 Base frequencies: A: 0.355 C: 0.228 G: 0.192 T: 0.225 Proportion of invariable sites: 0.154 Gamma shape alpha: 0.728 Parameters optimization took 1 rounds (0.035 sec) BEST SCORE FOUND : -21152.507 Total tree length: 4.226 Total number of iterations: 102 CPU time used for tree search: 14.703 sec (0h:0m:14s) Wall-clock time used for tree search: 14.941 sec (0h:0m:14s) Total CPU time used: 17.634 sec (0h:0m:17s) Total wall-clock time used: 17.895 sec (0h:0m:17s) 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 Jun 22 20:05:08 2022 28.82user 0.35system 0:29.22elapsed 99%CPU (0avgtext+0avgdata 16240maxresident)k 0inputs+128outputs (0major+3723minor)pagefaults 0swaps + rm -rf /tmp/iqtree-test.Q7VJna 57.92user 0.75system 0:58.78elapsed 99%CPU (0avgtext+0avgdata 16240maxresident)k 1160inputs+328outputs (11major+8948minor)pagefaults 0swaps rm example.short make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_auto_install make[1]: Entering directory '/<>' if [ "omp" != "omp" ] ; then dh_auto_install -Bbuild.omp; fi if [ "serial" != "omp" ] ; then dh_auto_install -Bbuild.serial; fi cd build.serial && make -j4 install DESTDIR=/<>/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/build.serial' /usr/bin/cmake -S/<> -B/<>/build.serial --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/<>/build.serial' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/<>/build.serial' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/iqtree/usr/bin/iqtree2 -- Set runtime path of "/<>/debian/iqtree/usr/bin/iqtree2" to "" -- Installing: /<>/debian/iqtree/usr/./models.nex -- Installing: /<>/debian/iqtree/usr/./example.phy -- Installing: /<>/debian/iqtree/usr/./example.nex -- Installing: /<>/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/<>/build.serial' if [ "mpi" != "omp" ] ; then dh_auto_install -Bbuild.mpi; fi cd build.mpi && make -j4 install DESTDIR=/<>/iqtree-2.0.7\+dfsg/debian/iqtree AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/build.mpi' /usr/bin/cmake -S/<> -B/<>/build.mpi --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[3]: Entering directory '/<>/build.mpi' make[3]: Nothing to be done for 'preinstall'. make[3]: Leaving directory '/<>/build.mpi' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /<>/debian/iqtree/usr/bin/iqtree2-mpi -- Set runtime path of "/<>/debian/iqtree/usr/bin/iqtree2-mpi" to "" -- Up-to-date: /<>/debian/iqtree/usr/./models.nex -- Up-to-date: /<>/debian/iqtree/usr/./example.phy -- Up-to-date: /<>/debian/iqtree/usr/./example.nex -- Up-to-date: /<>/debian/iqtree/usr/./example.cf make[2]: Leaving directory '/<>/build.mpi' dh override_dh_auto_install make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' dh_install find debian -name iqtree2-mpi -exec chrpath --delete \{\} \; find debian -name iqtree2-omp -exec chrpath --delete \{\} \; make[1]: Leaving directory '/<>' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/<>' # 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 '/<>' debian/rules override_dh_installman make[1]: Entering directory '/<>' mkdir -p /<>/debian/iqtree/usr/share/man/man1/ help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood' \ --version-string="2.0.7+dfsg" /<>/debian/iqtree/usr/bin/iqtree2 > /<>/debian/iqtree/usr/share/man/man1//iqtree2.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="2.0.7+dfsg" /<>/debian/iqtree/usr/bin/iqtree2-omp > /<>/debian/iqtree/usr/share/man/man1//iqtree2-omp.1 help2man --no-info --no-discard-stderr --help-option="-h" \ --name='efficient phylogenetic software by maximum likelihood (multiprocessor version)' \ --version-string="2.0.7+dfsg" /<>/debian/iqtree/usr/bin/iqtree2-mpi > /<>/debian/iqtree/usr/share/man/man1//iqtree2-mpi.1 make[1]: Leaving directory '/<>' dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a debugedit: debian/iqtree/usr/bin/iqtree2-mpi: Unknown DWARF DW_FORM_0x1f21 49fd1cb91af2c511c8cc3dd0fccb26b06fa84703 debugedit: debian/iqtree/usr/bin/iqtree2-omp: Unknown DWARF DW_FORM_0x1f21 0e23effd855232ccfe59b7ba567f5ed51a955b1e debugedit: debian/iqtree/usr/bin/iqtree2: Unknown DWARF DW_FORM_0x1f21 a7d92e25ab4eaa1234db5012ae9dac30d13930b6 dh_makeshlibs -a dh_shlibdeps -a dh_installdeb dh_gencontrol dh_md5sums dh_builddeb INFO: pkgstriptranslations version 149 pkgstriptranslations: processing iqtree (in debian/iqtree); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/iqtree/DEBIAN/control, package iqtree, directory debian/iqtree pkgstripfiles: Truncating usr/share/doc/iqtree/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package iqtree ... pkgstripfiles: No PNG files. dpkg-deb: building package 'iqtree' in '../iqtree_2.0.7+dfsg-1_amd64.deb'. dpkg-genbuildinfo --build=binary -O../iqtree_2.0.7+dfsg-1_amd64.buildinfo dpkg-genchanges --build=binary -mLaunchpad Build Daemon -O../iqtree_2.0.7+dfsg-1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-06-22T20:07:19Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ iqtree_2.0.7+dfsg-1_amd64.changes: ---------------------------------- Format: 1.8 Date: Fri, 21 Jan 2022 12:05:21 +0100 Source: iqtree Binary: iqtree Built-For-Profiles: noudeb Architecture: amd64 Version: 2.0.7+dfsg-1 Distribution: kinetic Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Andreas Tille Description: iqtree - efficient phylogenetic software by maximum likelihood Changes: iqtree (2.0.7+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * New upstream version * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Build-Depends: libboost-dev * Executables are now named iqtree2 * Drop invalid option `-omp` from build time test . [ Steffen Moeller ] * Fix watchfile to detect new versions on github (routine-update) * Standards-Version: 4.6.0 Checksums-Sha1: 580e42ce4ecb3891abb40da7d0ebbbbfae1df3b0 8931 iqtree_2.0.7+dfsg-1_amd64.buildinfo 294e1c1162729be6aaae64f1df8402c16907ac75 3716500 iqtree_2.0.7+dfsg-1_amd64.deb Checksums-Sha256: cc5174990d6f83714d28f2b0a354cca55fd65eecd6817179b7a9f8057b2d3716 8931 iqtree_2.0.7+dfsg-1_amd64.buildinfo 3f6186da19cafaf5c644ec8cc95b865d2a4b54f4074fd79f92559890900947ac 3716500 iqtree_2.0.7+dfsg-1_amd64.deb Files: 092e60312707399b7c4c28093fcc345b 8931 science optional iqtree_2.0.7+dfsg-1_amd64.buildinfo 635cba9b4c601c7667ff11a7a6183fe3 3716500 science optional iqtree_2.0.7+dfsg-1_amd64.deb /<>/iqtree_2.0.7+dfsg-1_amd64.changes.new could not be renamed to /<>/iqtree_2.0.7+dfsg-1_amd64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: iqtree Binary: iqtree Architecture: amd64 Version: 2.0.7+dfsg-1 Checksums-Md5: 635cba9b4c601c7667ff11a7a6183fe3 3716500 iqtree_2.0.7+dfsg-1_amd64.deb Checksums-Sha1: 294e1c1162729be6aaae64f1df8402c16907ac75 3716500 iqtree_2.0.7+dfsg-1_amd64.deb Checksums-Sha256: 3f6186da19cafaf5c644ec8cc95b865d2a4b54f4074fd79f92559890900947ac 3716500 iqtree_2.0.7+dfsg-1_amd64.deb Build-Origin: Ubuntu Build-Architecture: amd64 Build-Date: Wed, 22 Jun 2022 20:07:18 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: adduser (= 3.121ubuntu1), autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-6), autotools-dev (= 20220109.1), base-files (= 12.2ubuntu1), base-passwd (= 3.5.52build1), bash (= 5.1-6ubuntu1), binutils (= 2.38.50.20220615-4ubuntu1), binutils-common (= 2.38.50.20220615-4ubuntu1), binutils-x86-64-linux-gnu (= 2.38.50.20220615-4ubuntu1), bsdextrautils (= 2.38-4ubuntu1), bsdutils (= 1:2.38-4ubuntu1), build-essential (= 12.9ubuntu3), bzip2 (= 1.0.8-5build1), chrpath (= 0.16-2), cmake (= 3.23.2-1ubuntu1), cmake-data (= 3.23.2-1ubuntu1), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.3.0-3ubuntu1), cpp-12 (= 12.1.0-2ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-3build1), debconf (= 1.5.79ubuntu1), debhelper (= 13.7.1ubuntu1), debianutils (= 5.7-0.2), debugedit (= 1:5.0-4build1), dh-autoreconf (= 20), dh-elpa-helper (= 2.0.9ubuntu1), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu2), dpkg (= 1.21.8ubuntu1), dpkg-dev (= 1.21.8ubuntu1), dwz (= 0.14-1build2), emacsen-common (= 3.0.4), file (= 1:5.41-4), findutils (= 4.8.0-1ubuntu3), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.3.0-3ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.3.0-3ubuntu1), gcc-11-base (= 11.3.0-3ubuntu1), gcc-12 (= 12.1.0-2ubuntu1), gcc-12-base (= 12.1.0-2ubuntu1), gettext (= 0.21-6), gettext-base (= 0.21-6), gfortran-12 (= 12.1.0-2ubuntu1), grep (= 3.7-1build1), groff-base (= 1.22.4-8build1), gzip (= 1.10-4ubuntu4), help2man (= 1.49.2), hostname (= 3.23ubuntu2), ibverbs-providers (= 40.0-1), init-system-helpers (= 1.63), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libarchive13 (= 3.6.0-1ubuntu1), libasan6 (= 11.3.0-3ubuntu1), libasan8 (= 12.1.0-2ubuntu1), libatomic1 (= 12.1.0-2ubuntu1), libattr1 (= 1:2.5.1-1build1), libaudit-common (= 1:3.0.7-1build1), libaudit1 (= 1:3.0.7-1build1), libbinutils (= 2.38.50.20220615-4ubuntu1), libblkid1 (= 2.38-4ubuntu1), libboost-dev (= 1.74.0.3ubuntu7), libboost1.74-dev (= 1.74.0-14ubuntu4), libbrotli1 (= 1.0.9-2build6), libbsd0 (= 0.11.6-1), libbz2-1.0 (= 1.0.8-5build1), libc-bin (= 2.35-0ubuntu3), libc-dev-bin (= 2.35-0ubuntu3), libc6 (= 2.35-0ubuntu3), libc6-dev (= 2.35-0ubuntu3), libcap-ng0 (= 0.7.9-4), libcap2 (= 1:2.44-1build3), libcbor0.8 (= 0.8.0-2ubuntu1), libcc1-0 (= 12.1.0-2ubuntu1), libcom-err2 (= 1.46.5-2ubuntu2), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libctf-nobfd0 (= 2.38.50.20220615-4ubuntu1), libctf0 (= 2.38.50.20220615-4ubuntu1), libcurl3-gnutls (= 7.83.1-2), libcurl4 (= 7.83.1-2), libdb5.3 (= 5.3.28+dfsg1-0.9), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.7.1ubuntu1), libdpkg-perl (= 1.21.8ubuntu1), libdw1 (= 0.187-1), libedit2 (= 3.1-20210910-1build1), libeigen3-dev (= 3.4.0-2ubuntu2), libelf1 (= 0.187-1), libevent-2.1-7 (= 2.1.12-stable-5), libevent-core-2.1-7 (= 2.1.12-stable-5), libevent-dev (= 2.1.12-stable-5), libevent-extra-2.1-7 (= 2.1.12-stable-5), libevent-openssl-2.1-7 (= 2.1.12-stable-5), libevent-pthreads-2.1-7 (= 2.1.12-stable-5), libexpat1 (= 2.4.8-1), libfabric1 (= 1.11.0-3), libffi8 (= 3.4.2-4), libfido2-1 (= 1.11.0-1), libfile-stripnondeterminism-perl (= 1.13.0-1), libgcc-11-dev (= 11.3.0-3ubuntu1), libgcc-12-dev (= 12.1.0-2ubuntu1), libgcc-s1 (= 12.1.0-2ubuntu1), libgcrypt20 (= 1.10.1-2ubuntu1), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgfortran-12-dev (= 12.1.0-2ubuntu1), libgfortran5 (= 12.1.0-2ubuntu1), libglib2.0-0 (= 2.72.2-2), libgmp-dev (= 2:6.2.1+dfsg-3ubuntu1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgmpxx4ldbl (= 2:6.2.1+dfsg-3ubuntu1), libgnutls30 (= 3.7.6-2ubuntu1), libgomp1 (= 12.1.0-2ubuntu1), libgpg-error0 (= 1.45-2), libgprofng0 (= 2.38.50.20220615-4ubuntu1), libgssapi-krb5-2 (= 1.19.2-2), libhogweed6 (= 3.7.3-1build2), libhwloc-dev (= 2.7.1-1), libhwloc-plugins (= 2.7.1-1), libhwloc15 (= 2.7.1-1), libibverbs-dev (= 40.0-1), libibverbs1 (= 40.0-1), libicu71 (= 71.1-3), libidn2-0 (= 2.3.2-2build1), libisl23 (= 0.24-2build1), libitm1 (= 12.1.0-2ubuntu1), libjs-jquery (= 3.6.0+dfsg+~3.5.13-1), libjs-jquery-ui (= 1.13.1+dfsg-1), libjsoncpp25 (= 1.9.5-4), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-3ubuntu1), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), libldap-2.5-0 (= 2.5.12+dfsg-2ubuntu1), liblocale-gettext-perl (= 1.07-4build3), liblsan0 (= 12.1.0-2ubuntu1), libltdl-dev (= 2.4.7-4), libltdl7 (= 2.4.7-4), liblz4-1 (= 1.9.3-2build2), liblzma5 (= 5.2.5-2.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-1build1), libmount1 (= 2.38-4ubuntu1), libmpc3 (= 1.2.1-2build1), libmpfr6 (= 4.1.0-3build3), libncurses6 (= 6.3+20220423-2), libncursesw6 (= 6.3+20220423-2), libnettle8 (= 3.7.3-1build2), libnghttp2-14 (= 1.47.0-1), libnl-3-200 (= 3.5.0-0.1), libnl-3-dev (= 3.5.0-0.1), libnl-route-3-200 (= 3.5.0-0.1), libnl-route-3-dev (= 3.5.0-0.1), libnsl-dev (= 1.3.0-2build2), libnsl2 (= 1.3.0-2build2), libnuma-dev (= 2.0.14-3ubuntu2), libnuma1 (= 2.0.14-3ubuntu2), libopenmpi-dev (= 4.1.4-1ubuntu1), libopenmpi3 (= 4.1.4-1ubuntu1), libp11-kit0 (= 0.24.1-1), libpam-modules (= 1.4.0-13ubuntu1), libpam-modules-bin (= 1.4.0-13ubuntu1), libpam-runtime (= 1.4.0-13ubuntu1), libpam0g (= 1.4.0-13ubuntu1), libpciaccess0 (= 0.16-3), libpcre2-8-0 (= 10.40-1), libpcre3 (= 2:8.39-14), libperl5.34 (= 5.34.0-3ubuntu1), libpipeline1 (= 1.5.6-1), libpmix-dev (= 4.1.2-2ubuntu1), libpmix2 (= 4.1.2-2ubuntu1), libprocps8 (= 2:3.3.17-6ubuntu2), libpsl5 (= 0.21.0-1.2build2), libpsm-infinipath1 (= 3.3+20.604758e7-6.1), libpsm2-2 (= 11.2.185-1), libquadmath0 (= 12.1.0-2ubuntu1), librdmacm1 (= 40.0-1), librhash0 (= 1.4.2-1ubuntu1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build4), libsasl2-2 (= 2.1.28+dfsg-6ubuntu1), libsasl2-modules-db (= 2.1.28+dfsg-6ubuntu1), libseccomp2 (= 2.5.4-1ubuntu1), libselinux1 (= 3.4-1), libsemanage-common (= 3.4-1), libsemanage2 (= 3.4-1), libsepol2 (= 3.4-2), libsigsegv2 (= 2.13-1ubuntu3), libsmartcols1 (= 2.38-4ubuntu1), libsprng2 (= 2.0a-13), libsprng2-dev (= 2.0a-13), libssh-4 (= 0.9.6-2build1), libssl3 (= 3.0.3-5ubuntu3), libstdc++-11-dev (= 11.3.0-3ubuntu1), libstdc++6 (= 12.1.0-2ubuntu1), libsub-override-perl (= 0.09-3), libsystemd0 (= 249.11-0ubuntu4), libtasn1-6 (= 4.18.0-4build1), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.2-2build1), libtirpc-dev (= 1.3.2-2build1), libtirpc3 (= 1.3.2-2build1), libtool (= 2.4.7-4), libtsan0 (= 11.3.0-3ubuntu1), libtsan2 (= 12.1.0-2ubuntu1), libubsan1 (= 12.1.0-2ubuntu1), libuchardet0 (= 0.0.7-1build2), libucx0 (= 1.13.0~rc1-1), libudev1 (= 249.11-0ubuntu4), libunistring2 (= 1.0-1), libuuid1 (= 2.38-4ubuntu1), libuv1 (= 1.44.1-2), libx11-6 (= 2:1.7.5-1), libx11-data (= 2:1.7.5-1), libxau6 (= 1:1.0.9-1build5), libxcb1 (= 1.14-3ubuntu3), libxdmcp6 (= 1:1.1.3-0ubuntu5), libxext6 (= 2:1.3.4-1build1), libxml2 (= 2.9.14+dfsg-1), libxnvctrl0 (= 510.47.03-0ubuntu1), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 5.15.0-27.28), login (= 1:4.11.1+dfsg1-2ubuntu1), lsb-base (= 11.1.0ubuntu4), lto-disabled-list (= 27), m4 (= 1.4.18-5ubuntu2), make (= 4.3-4.1build1), man-db (= 2.10.2-1), mawk (= 1.3.4.20200120-3.1), mpi-default-dev (= 1.14), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), ocl-icd-libopencl1 (= 2.2.14-3), openmpi-bin (= 4.1.4-1ubuntu1), openmpi-common (= 4.1.4-1ubuntu1), openssh-client (= 1:9.0p1-1), passwd (= 1:4.11.1+dfsg1-2ubuntu1), patch (= 2.7.6-7build2), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), pkg-config (= 0.29.2-1ubuntu3), po-debconf (= 1.0.21+nmu1), procps (= 2:3.3.17-6ubuntu2), rpcsvc-proto (= 1.4.2-0ubuntu6), sed (= 4.8-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build3), time (= 1.9-0.1build2), util-linux (= 2.38-4ubuntu1), util-linux-extra (= 2.38-4ubuntu1), xz-utils (= 5.2.5-2.1), zlib1g (= 1:1.2.11.dfsg-2ubuntu9), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu9) Environment: DEB_BUILD_OPTIONS="noautodbgsym parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1642763121" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ iqtree_2.0.7+dfsg-1_amd64.deb ----------------------------- new Debian package, version 2.0. size 3716500 bytes: control archive=1416 bytes. 1500 bytes, 30 lines control 942 bytes, 14 lines md5sums Package: iqtree Version: 2.0.7+dfsg-1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 23244 Depends: libc6 (>= 2.34), libgcc-s1 (>= 4.0), libgomp1 (>= 6), libopenmpi3 (>= 4.1.4), libstdc++6 (>= 11), zlib1g (>= 1:1.1.4) Section: science Priority: optional Homepage: http://www.cibiv.at/software/iqtree/ Description: efficient phylogenetic software by maximum likelihood IQ-TREE is a very efficient maximum likelihood phylogenetic software with following key features among others: . * A novel fast and effective stochastic algorithm to estimate maximum likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (see Nguyen et al., 2015) * An ultrafast bootstrap approximation to assess branch supports (see Minh et al., 2013). * A wide range of substitution models for binary, DNA, protein, codon, and morphological alignments. * Ultrafast model selection for all data types, 10 to 100 times faster than jModelTest and ProtTest. * Finding best partition scheme like PartitionFinder. * Partitioned models with mixed data types for phylogenomic (multi- gene) alignments, allowing for separate, proportional, or joint branch lengths among genes. * Supporting the phylogenetic likelihod library (PLL) (see Flouri et al., 2014) drwxr-xr-x root/root 0 2022-01-21 11:05 ./ drwxr-xr-x root/root 0 2022-01-21 11:05 ./usr/ drwxr-xr-x root/root 0 2022-01-21 11:05 ./usr/bin/ -rwxr-xr-x root/root 7095480 2022-01-21 11:05 ./usr/bin/iqtree2 -rwxr-xr-x root/root 7173304 2022-01-21 11:05 ./usr/bin/iqtree2-mpi -rwxr-xr-x root/root 7095480 2022-01-21 11:05 ./usr/bin/iqtree2-omp drwxr-xr-x root/root 0 2022-01-21 11:05 ./usr/share/ drwxr-xr-x root/root 0 2022-01-21 11:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-01-21 11:05 ./usr/share/doc/iqtree/ -rw-r--r-- root/root 278 2022-01-21 11:05 ./usr/share/doc/iqtree/README.test -rw-r--r-- root/root 955 2022-01-21 11:05 ./usr/share/doc/iqtree/changelog.Debian.gz -rw-r--r-- root/root 7971 2022-01-21 11:05 ./usr/share/doc/iqtree/copyright drwxr-xr-x root/root 0 2022-01-21 11:05 ./usr/share/doc/iqtree/examples/ -rw-r--r-- root/root 2237314 2020-06-17 07:05 ./usr/share/doc/iqtree/examples/example.cf -rw-r--r-- root/root 174 2020-06-17 07:05 ./usr/share/doc/iqtree/examples/example.nex -rw-r--r-- root/root 34178 2020-06-17 07:05 ./usr/share/doc/iqtree/examples/example.phy -rw-r--r-- root/root 121669 2020-06-17 07:05 ./usr/share/doc/iqtree/examples/models.nex -rw-r--r-- root/root 2188 2022-01-21 11:05 ./usr/share/doc/iqtree/run-unit-test drwxr-xr-x root/root 0 2022-01-21 11:05 ./usr/share/man/ drwxr-xr-x root/root 0 2022-01-21 11:05 ./usr/share/man/man1/ -rw-r--r-- root/root 5095 2022-01-21 11:05 ./usr/share/man/man1/iqtree2-mpi.1.gz -rw-r--r-- root/root 5093 2022-01-21 11:05 ./usr/share/man/man1/iqtree2-omp.1.gz -rw-r--r-- root/root 5072 2022-01-21 11:05 ./usr/share/man/man1/iqtree2.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 3843352 Build-Time: 3186 Distribution: kinetic Host Architecture: amd64 Install-Time: 58 Job: iqtree_2.0.7+dfsg-1.dsc Machine Architecture: amd64 Package: iqtree Package-Time: 3246 Source-Version: 2.0.7+dfsg-1 Space: 3843352 Status: successful Version: 2.0.7+dfsg-1 -------------------------------------------------------------------------------- Finished at 2022-06-22T20:07:19Z Build needed 00:54:06, 3843352k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=kinetic --arch=amd64 PACKAGEBUILD-24013293 Scanning for processes to kill in build PACKAGEBUILD-24013293